the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 05 Aug 2026
Monsoon-influenced terrestrial forcing shapes inter-reef carbonate production (Spermonde Archipelago, Indonesia)
Abstract. Monsoon-driven fluvial discharge exerts strong environmental control on water quality and carbonate sediment composition in tropical shelf systems, yet the capacity of photosymbiont-bearing calcifiers to sustain carbonate production under monsoon-amplified turbidity and nutrient loading across semi-enclosed platforms remains poorly understood. We here investigate inter-reef facies patterns and benthic foraminiferal assemblages across the Spermonde Archipelago (southwest Sulawesi, Indonesia), a land-attached tropical carbonate shelf subject to seasonal monsoon runoff and intensifying coastal development, using geochemical, sedimentological, and foraminiferal analyses of 51 inter-reef seafloor samples. Nearshore sediments are enriched in mud and organic matter, and dominated by heterozoan and stress-tolerant assemblages, yielding low values for the FoRAM Index (FI; an index that increases with the relative abundance of photosymbiont-bearing foraminifera), indicating conditions unfavourable for photosymbiont-bearing carbonate producers. Statistical separation of nearshore facies from all mid- and outer-shelf assemblages supports a threshold rather than gradual cross-shelf transition. This threshold is spatially asymmetrical, extending further offshore in the northern sector, likely reflecting enhanced retention of fluvially derived material within the more enclosed northern shelf geometry, with the southward Makassar Strait circulation limiting offshore dispersal. Mid- and outer-shelf deposits (~80% of the investigated area) are characterised by foramol facies dominated by benthic foraminifers, bivalves and gastropods, with Amphistegina and Operculina as the dominant symbiont-bearing foraminifera; FI values increase progressively offshore, reflecting improving photic conditions as terrestrially driven seasonal turbidity decreases with distance from the coast. Strong spatial correspondence between foraminiferal assemblages and independently derived sedimentary facies, including convergence of the foraminiferal community transition zone with foramol mud-supported carbonate sediment facies, validates the FI as an ecological proxy beyond shallow reef settings and demonstrates its utility in differentiating carbonate production modes in mesotrophic equatorial systems. These findings support a carbonate production continuum in which photozoan and heterozoan components are organised non-linearly along environmental gradients, with threshold responses emerging from the interaction of platform geometry and catchment-scale terrestrial forcing under seasonal monsoon modulation. We therefore interpret the Spermonde shelf as spatially structured by shifting autotrophic-heterotrophic balances, rather than discrete facies categories.
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Status: final response (author comments only)
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RC1: 'Comment on egusphere-2026-3460', Anonymous Referee #1, 02 Sep 2026
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AC1: 'Reply on RC1', Marleen Stuhr, 07 Sep 2026
Dear Referee #1,
Thank you very much for your kind assessment of our study! We are grateful for the thoughtful mechanistic hypotheses you raise regarding the seasonal ecology of Amphistegina and Operculina, and the potential roles of dormancy/senescence in sustaining these taxa across the monsoon cycle. I find these suggestions very interesting and will follow you reading suggestions, potentially among others, to take them into account for a dedicated treatment of possible mechanisms or future directions.
As the interactive discussion remains open for some more weeks, we will provide a full, point-by-point response and incorporate all corresponding revisions once the comments from all referees are complete.
With thanks and kind regards,
Marleen StuhrCitation: https://doi.org/10.5194/egusphere-2026-3460-AC1 -
AC3: 'Reply on RC3', Marleen Stuhr, 28 Sep 2026
Dear Referee 3,
We thank you for the assessment. Most of the points raised overlap with those of Referees 1 and 2, to which we have already responded in detail; we refer to those responses and comment briefly here.
- Authigenic gypsum: We agree, and addressed this in our response to Referee 2 (point 9). The gypsum will be reported separately from the biogenic and terrigenous components and excluded from compositional interpretation. We have verified that the classification does not depend on it: excluding the gypsum and renormalising the remaining components leaves the nearshore/offshore division unchanged (11 versus 40 samples, no reassignments) and the facies scheme essentially unaltered.
- Facies VI as a single sample: This point was not raised by the other Referees and we consider it well taken. Treating S04 as an anomalous sample outside the classification rather than as a facies would also resolve the concern raised by Referee 2 (point 6), since the linkage criterion would then apply without exception. As this affects the facies scheme throughout the manuscript, we will settle it with our co-authors in preparing a revised version.
- Taphonomic and transport biases: Addressed in our response to Referee 2 (points 1 and 3); the revised Discussion will treat these constraints explicitly, including post-mortem transport. On selective test destruction, we find no dissolution signature: agglutinated taxa are depleted alongside porcelaneous taxa in the nearshore samples (0.5% against 7.7-6% offshore) rather than enriched relative to them, as dissolution would predict.
- Bili-Bili Dam: Addressed in our response to Referee 2 (point 7); the attribution will be presented as a hypothesis rather than an explanation.
- Seasonal sampling versus satellite record: Addressed in our response to Referee 2 (point 8). The grab samples are kilogram-scale, penetrate several centimetres and were homogenised, so the assemblages are time-integrated rather than representative of the sampling date; we will state this explicitly in the revised Methods.
With thanks and kind regards,
Marleen StuhrCitation: https://doi.org/10.5194/egusphere-2026-3460-AC3 -
AC2: 'Comment on egusphere-2026-3460', Marleen Stuhr, 23 Sep 2026
Response to RC1:
Dear Referee 1,
We thank you for the careful reading of our manuscript and for the generous assessment. We are particularly grateful for the mechanistic hypotheses raised regarding the persistence of Amphistegina and Operculina on the mid- and outer shelf, which we find compelling and will address briefly in the revised manuscript. Our responses to the individual points follow.
We are very grateful for your suggestions, which we believe will strengthen the ecological interpretation of the manuscript.
- We agree that darkness-induced dormancy offers a plausible explanation for the maintenance of symbiont-bearing assemblages under seasonally reduced water transparency, and we were not previously aware of the extent of the supporting evidence. The experimental record is encouraging in this respect: reticulopodial activity resumed in more than 95% of A. gibbosa specimens following twelve months of aphotic conditions, with symbiont colour returning within days, whereas recovery became slower and less complete beyond fifteen months (Ross and Hallock, 2019). The authors of that study interpret this inflection as potentially reflecting dormancy mechanisms tuned to seasonal light limitation, and explicitly identify mid- and outer-shelf settings subject to monsoon-driven turbidity as an environment where such a strategy would be advantageous. The approximately six-month duration of the northwest monsoon on the Spermonde shelf falls well within the interval over which recovery appears essentially complete.
Two qualifications apply. First, the high recovery rates reported by Ross and Hallock (2019) were obtained under deliberately gradual re-illumination, and the authors note that abrupt return to full light may be stressful for dark-adapted individuals. Post-monsoon clearing on the Spermonde shelf is gradual and depth-attenuated, so this condition is plausibly satisfied, but the correspondence should be stated rather than assumed. Second, the experimental evidence derives from A. gibbosa, which belongs to the Atlantic lineage of the genus, phylogenetically separated from the Indo-Pacific A. lessonii–A. lobifera lineage (Larsen, 1978; Stuhr et al., 2022); as our counts are resolved to genus level, we cannot specify which species contribute to the assemblages reported here. Shorter survival was reported for A. lobifera by Lee et al., (1991), although those authors scored viability by pseudopodial activity and attachment (criteria that a dormant individual would not meet) and record that prolonged-darkness experiments on the same species yielded recovery within days of return to light (P. Hallock, personal communication in Lee et al., 1991). Together with the observation that repeated removal and observation may itself reduce the efficacy of dormancy (Ross and Hallock, 2019), this suggests the apparent contrast between congeners may be partly methodological. We note further that the Indo-Pacific lineage is characterised by more diverse and flexible photosymbiont associations (Prazeres et al., 2021; Stuhr et al., 2022), which may favour rather than constrain low-light tolerance.
We will further note that the relevance of dormancy may extend to the opposite end of the cross-shelf gradient. Quiescence in response to anoxia and reducing conditions has been documented for Nonion, Ammonia and Elphidium among other taxa (Ross and Hallock, 2016, and references therein), which are precisely the stress-tolerant genera that dominate our organic-rich nearshore facies. Dormancy may therefore contribute to assemblage persistence across the full gradient rather than only offshore, which we consider a useful addition to the interpretation.
- We also agree that propagule-mediated recruitment provides an equally plausible mechanism, and that the two are not mutually exclusive: cryptobiotic propagules are now recognised as a widespread feature of foraminiferal life cycles and allow assemblages to respond rapidly to changing conditions (Alve and Goldstein, 2003, 2010; Ross and Hallock, 2016; etc.). A dry season of roughly six months would plausibly permit recruits to approach adult size, and the relatively short life spans of these taxa are consistent with such a cycle.
For Operculina, where dormancy has not been tested, we would add a third possibility supported by direct experimental evidence. In a transplant experiment in the Gulf of Aqaba-Eilat, O. ammonoides constructed thinner chambers following relocation to low light, added more weight per unit area under high light, and adjusted chlorophyll content across a range of light conditions (Oron et al., 2018). Notably, evolute specimens acclimatised to very low light did not survive relocation to high light, apparently as a result of photo-oxidative stress. This suggests that Operculina may accommodate seasonal variation in irradiance through morphological and physiological acclimatisation rather than through dormancy, and generates a testable prediction: the cost of low-light acclimatisation is vulnerability to rapid re-illumination, which is consistent with a gradually clearing shelf but would not be sustainable under episodic flushing. We will refer to these briefly in the Discussion as alternative, non-exclusive mechanisms, together with a recommendation that the capacity for dormancy in Operculina be examined directly.
We thank the referee for this suggestion and want to express we have been contemplating it for a while. We do not question that dimorph ratios could represent the most direct available test of whether these assemblages are sustained by seasonal recruitment via propagules or by the persistence of individuals. Yet, a design consideration worth recording for whoever undertakes it: microspheric and megalospheric generations differ systematically in adult size, so ratios determined from a size-truncated death assemblage (as in our study, where our counts derive from the fraction >125 µm) would carry a size-selection bias that requires independent control. Scanning for growth hiatuses, as suggested, would provide valuable complementary evidence and is less exposed to this problem. Even though archive halves of all samples have of course been retained and remain available for this purpose, we unfortunately do not have the capacity to undertake this analysis within the present revision. But we will recommend this explicitly for future work.
Finally, we thank the Referee for the detailed editorial annotations provided in the supplementary file. We will accept all of these and incorporate them in the revised manuscript. We have additionally identified an internal inconsistency in the naming of facies II, which appears as "Bivalve-dominated terrigenous-bearing mud-supported carbonate sediment" in Section 3.5 but without the "-bearing" modifier in Table 3 and Fig. 8; we will thus standardise this to "Bivalve-dominated terrigenous mud-supported carbonate sediment" throughout.
With thanks and kind regards,
Marleen Stuhr, on behalf of all co-authors
References:
Alve, E. and Goldstein, S. T.: Propagule transport as a key method of dispersal in benthic foraminifera (Protista), Limnology and Oceanography, 48, 2163–2170, https://doi.org/10.4319/lo.2003.48.6.2163, 2003.
Alve, E. and Goldstein, S. T.: Dispersal, survival and delayed growth of benthic foraminiferal propagules, Journal of Sea Research, 63, 36–51, https://doi.org/10.1016/j.seares.2009.09.003, 2010.
Larsen, A. R.: Phylogenetic and paleobiogeographical trends in the foraminiferal genus Amphistegina, Revista Española de Micropaleontología, X, 217–243, 1978.
Lee, J. J., Sang, K., ter Kuile, B., Strauss, E., Lee, P. J., and Faber, W. W.: Nutritional and related experiments on laboratory maintenance of three species of symbiont-bearing, large foraminifera, Marine Biology, 109, 417–425, https://doi.org/10.1007/BF01313507, 1991.
Oron, S., Abramovich, S., Almogi-Labin, A., Woeger, J., and Erez, J.: Depth related adaptations in symbiont bearing benthic foraminifera: New insights from a field experiment on Operculina ammonoides, Scientific Reports, 8, 1–11, https://doi.org/10.1038/s41598-018-29216-w, 2018.
Prazeres, M., Roberts, T. E., Ramadhani, S. F., Doo, S. S., Schmidt, C., Stuhr, M., and Renema, W.: Diversity and flexibility of algal symbiont community in globally distributed larger benthic foraminifera of the genus Amphistegina, BMC Microbiology, 21, 1–16, https://doi.org/10.1186/s12866-021-02299-8, 2021.
Ross, B. J. and Hallock, P.: Dormancy in the foraminifera: A review, Journal of Foraminiferal Research, 46, 358–368, 2016.
Ross, B. J. and Hallock, P.: Survival and recovery of the foraminifer Amphistegina gibbosa and associated diatom endosymbionts following up to 20 months in aphotic conditions, Marine Micropaleontology, 149, 35–43, https://doi.org/10.1016/j.marmicro.2019.03.013, 2019.
Stuhr, M., Blank-Landeshammer, B., Meyer, A., Baumeister, V., Rahnenführer, J., Sickmann, A., and Westphal, H.: Proteome-based clustering approaches reveal phylogenetic insights into Amphistegina, Journal of Earth Science, https://doi.org/10.1007/s12583-022-1609-1, 2022.
Response to RC2:
Dear Referee 2,
We thank you for the constructive and detailed assessment, and for the methodological points raised, which we consider well founded. We have grouped and ordered our responses considering how the points are related. Since comments 1 and 3 concern the inferences that our sampling design supports, we address them together.
- 1. & 3.: We agree with your comment that the manuscript currently lacks an explicit treatment of the constraints imposed by the sampling design, and we agree this is a shortcoming. We will address these constraints explicitly in the revised Discussion: the use of total rather than living assemblages, the absence of station-level replication, the absence of direct nutrient and turbidity measurements, and possible post-mortem transport.
We accept the principle that contemporary ecological relationships are most securely established from living assemblages (Murray, 2006), and will revise any wording implying inference about living populations or contemporary ecological interactions. We also acknowledge post-mortem transport as an additional source of uncertainty. Tidal, wave-induced and density-driven bottom currents act across the shelf, and in the absence of hydrodynamic measurements we cannot exclude that tests have been displaced from their environment of origin.
- On point 3, we generally agree to your criticism. Our data establish that foraminiferal composition covaries with mud content, organic carbon and distance from land, and that this covariance is spatially organised in a manner consistent with terrestrial influence. They do not demonstrate that monsoon-driven fluvial nutrient and turbidity input is the mechanism producing the transition. We will revise the text throughout to maintain this distinction, including the title to "Terrestrial forcing and inter-reef carbonate production across a monsoon-influenced tropical shelf (Spermonde Archipelago, Indonesia)" so that it claims association rather than causation. Terrestrial influence will be presented as an association supported by our data; the monsoon-driven mechanism as an interpretation consistent with the spatial pattern and with independently documented seasonal hydrography, but not as a demonstrated causal link.
- We appreciate point 8 and would like to clarify our sampling design, which we recognise is not described with sufficient precision in the current Methods. Sediments were collected with a van Veen grab retrieving kilogram-scale bulk samples penetrating several cm into the seabed, and each sample was homogenised prior to analysis. The resulting assemblages are thus time-integrated rather than representative of conditions at the time of collection, and re-sampling the same stations in a different season would not be expected to yield a materially different assemblage. The July 2021 campaign should therefore not be read as a seasonal snapshot, and we will state this explicitly in the revised Methods.
This bears directly on the interpretation. Because the assemblages integrate conditions over time rather than sampling them at a single moment, they record persistent environmental structure, which is the basis on which we interpret the cross-shelf pattern as a stable feature of the shelf. In this respect the dataset is closer to a sedimentary record than to an ecological survey. What our data cannot do is resolve seasonal variability, and we will ensure the text does not imply otherwise: the proposition that monsoon forcing amplifies rather than creates the cross-shelf gradient rests on independently documented seasonal hydrography, and we will make that dependence explicit rather than leaving it implicit. Yet we appreciate that testing the seasonal hypothesis directly would be interesting indeed, but require a different design, targeting living assemblages in the uppermost few millimetres of sediment at seasonal intervals alongside in situ measurement of turbidity and dissolved nutrients. Such a design would simultaneously address the hypotheses raised by Referee 1 regarding dormancy and propagule-mediated recruitment, and we identify it as a priority for future work.
- We agree with point 5. The published biplot combined spatial, geochemical and biotic variables in a single unconstrained ordination, with no a priori separation of explanatory environmental parameters from biological response variables, and we accept that this is not the ideal way of presenting data for answering the question being asked. We have therefore carried out the suggested alternative and consider it an improvement; the resulting ordination (Fig. S1) will replace the current Fig. 9.
Detrended correspondence analysis gives a gradient length of 2.68 SD units on the first axis, below the threshold at which a unimodal response model becomes preferable, and we therefore use redundancy analysis (RDA) rather than CCA, with Hellinger-transformed genus composition as the response matrix and standardised environmental parameters as constraints (Legendre and Gallagher, 2001). Full model output is given in Table S1.
On the specifics: (i) no abundance-based filtering was applied previously and all 42 genera are likewise retained here, as the Hellinger transformation downweights rare taxa without requiring their removal; (ii) the previous biplot used a correlation matrix, which standardises variables but does not address the compositional nature of assemblage data, whereas the revised analysis uses relative abundances with Hellinger transformation for the response and standardisation for the constraints; (iii) gravel, sand and mud were previously retained together, but as proportions of a closed array summing to 100 wt% they are linearly dependent and variance inflation factors are undefined for the set. We therefore retain mud as a single textural descriptor and exclude gravel, sand and distance to the Strait of Makassar, the last being largely redundant with distance from the mainland; VIFs for the five retained constraints are all below 10. The FI and functional-group proportions were also previously included alongside the genus data from which they are derived; since FI is a deterministic function of those proportions, their inclusion is circular and may inflate apparent structure, and they are excluded here. FI is now used only as an independently derived variable for comparison. These decisions will be documented in the revised Methods 2.5, which we agree was previously insufficiently specific.
For the revised results section this will mean the following: The ordination separates nearshore facies I and II, associated with high mud and TOC, from mid- and outer-shelf facies associated with greater water depth, higher carbonate content and greater distance from the mainland. Ammonia, Nonion and Elphidium align with the nearshore end of the gradient and Amphistegina and Operculina with the offshore end, while Quinqueloculina, Cibicidoides, Cibicides and Spiroloculina occupy intermediate positions. Facies III to V overlap along the second axis, consistent with the gradational character of the mid- and outer-shelf transition described in the manuscript.
The revised analysis therefore reproduces the cross-shelf structure described in the original manuscript, but with explanatory and response variables properly separated and with explained variance attributable to identified environmental constraints. The constrained fraction is lower than the variance reported for the published unconstrained ordination, which we consider a more accurate reflection of the explanatory power of the measured environmental variables.
We agree that relating the main ordination axis to the spatial structure of the shelf is informative. Site scores on the first constrained axis have been extracted and are included in the supplementary data tables. As this axis essentially reproduces the cross-shelf gradient already shown by the FI, TOC, CaCO₃ and grain-size profiles in Fig. 10, we do not consider an additional map or profile necessary for the present paper.
- We agree with point 2 that the threshold interpretation required formal statistical support and have carried out the suggested analyses. The PERMANOVA and segmented regression results will be summarised briefly in the Results; the full outputs, including the TITAN, are provided in the supplementary material. PERMANOVA on Bray-Curtis dissimilarities of genus composition confirms the separation of nearshore from mid- and outer-shelf assemblages (pseudo-F = 28.77, R² = 0.37, p = 0.0002, 4999 permutations). A test of multivariate dispersion homogeneity is non-significant (PERMDISP, p = 0.77), indicating that this reflects genuine differences in assemblage composition rather than differing within-group variability. Across all six facies the model explains 54% of compositional variation (pseudo-F = 10.67, p = 0.0002).
Segmented regression identifies a change in the response of the FI to organic enrichment at TOC = 0.56% (SE 0.10; R² increasing from 0.63 to 0.71; Davies test p = 0.009). Community composition, summarised as the first principal coordinate of the Bray-Curtis dissimilarity matrix, shows significant breakpoints against mud content (72 wt%, p = 5.6 × 10⁻⁵), water depth (38.5 m, p = 0.004) and distance from the mainland (21.1 km, p = 0.015), but varies approximately linearly with TOC (p = 0.81). The estimated location of the mud breakpoint carries substantial uncertainty (SE 27.7 wt%), so we will report it as evidence for a change in slope rather than as a precisely located threshold. Full breakpoint estimates are given in Table S3.
This contrast is informative rather than contradictory. The FI responds non-linearly to organic enrichment, whereas total assemblage turnover tracks the physical gradients of substrate, depth and distance from land. We interpret this as indicating that the threshold behaviour we describe operates principally on the functional composition of the assemblage rather than on species turnover as a whole, and we will state it in these terms.
Threshold Indicator Taxa Analysis (TITAN, Fig. S2) along the TOC gradient identifies a community change point for increasing taxa at TOC = 0.345% (bootstrap 5-95% limits 0.305-0.610). Change points for individual pure and reliable taxa are concentrated within a narrow interval of the gradient rather than distributed across it: Elphidium at 0.345, Nonion and Ammonia at 0.450, Cornuspira at 0.320, Parasorites and Calcarina at 0.380, and Amphistegina at 0.450, with purity and reliability of 1.00 for several of these. This concentration is consistent with compositional reorganisation over a limited range of organic enrichment rather than with gradual replacement along the gradient.
We note that the three taxa identified as increasing along the gradient (Nonion, Ammonia and Elphidium) correspond exactly to the stress-tolerant functional group of the FI, although no information on functional assignment was supplied to the analysis. We regard this as supporting the applicability of the FI functional categories in this setting (see response to point 4), while recognising that it is consistent with, rather than independent of, the assemblage patterns already described in Section 3.4. Yet, two limitations should be recorded. The change point for declining taxa as a group is poorly constrained (5-95% limits 0.390-1.010), and the proportion of pure and reliable taxa is moderate (0.43). We will hence report bootstrap limits alongside all point estimates rather than the estimates alone.
- Point 6: The basis for distinguishing six facies was not made sufficiently explicit, so we will describe it in more detail in the revised Methods. We accept the specific concern raised: a single similarity threshold does not yield exactly the six units as published, and we will state this explicitly in the revised Methods.
The facies were defined by cutting the dendrogram at a linkage distance of ~82, which yields five groups, and then retaining facies VI as a separate unit on sedimentological grounds. Facies VI (sample S04) contains 33.5 wt% siliciclastic material distributed across multiple grain-size fractions and has a CaCO₃ content of 43.3%, whereas siliciclastic contributions are near-absent elsewhere on the shelf. We interpret this sample as relict, potentially reflecting late Pleistocene to early Holocene deposits emplaced prior to full shelf flooding, and discuss it as such in Section 4.1. Merging it with facies V (as suggested by the five-group cutoff, see Fig. S3 in attached PDF) would group a compositionally and genetically distinct deposit with the foramol mud-supported carbonate sediments of the mid shelf. Applying a lower threshold, such that facies VI separates automatically, would instead subdivide facies II, which we do not consider meaningful either. The separation of facies VI is therefore an interpretive decision informed by composition rather than one following directly from the linkage distance, and we will state this explicitly.
We noted above, a lower threshold would separate two nearshore samples from the central shelf (S25, S32) from facies II. These both lie in the central sector at comparable distance from the mainland (5-7 km), and we do not mean to exclude that they represent a distinguishable nearshore sub-environment. We have however, decided to retain the coarser subdivision here, as this distinction does not affect the cross-shelf structure that is the subject of the study, and note it as a possible refinement. Interestingly, we noticed upon this inspection that the first and highest split in the dendrogram separates facies I and II from all mid- and outer-shelf samples without exception (11 versus 40 samples). This division is better resolved than any subsequent split, whereas the subdivision of the mid and outer shelf into facies III, IV and V occurs at much lower linkage distances and separates units that grade into one another. This structure corresponds directly to the interpretation presented in the manuscript, in which a sharp nearshore threshold gives way to a continuum of mixed carbonate production modes across the mid and outer shelf, and we will use the opportunity of a revised manuscript to present the classification in these terms rather than as six equally discrete units.
Ultimately, the facies scheme is corroborated by data deliberately excluded from its construction. Cluster analysis was performed exclusively on grain-size, carbonate and skeletal-component data, with foraminiferal assemblage composition withheld. PERMANOVA on Bray-Curtis dissimilarities of genus composition shows that the six sediment-based facies explain 54% of variation in foraminiferal composition (pseudo-F = 10.67, p = 0.0002, 4999 permutations), and indicator species analysis identifies sixteen genera significantly associated with particular facies or facies combinations, including Cibicidoides, Operculina and Amphistegina with facies III–VI (IndVal ≥ 0.97, p = 0.001) and Nonion with facies I, II, V and VI (IndVal = 0.98, p = 0.001). Facies defined solely on sedimentological criteria therefore predict assemblage composition strongly. We regard this as more informative for judging whether the units are meaningful than internal cluster validation indices, and report it in the attached PDF here (Table S2).
- 4. Yes, the transferability of the FI beyond the shallow reef settings for which it was developed requires explicit discussion, and we will consider expanding the discussion accordingly. The FI is applied here as a relative proxy for spatial variation in foraminiferal functional composition rather than as an absolute predictor of reef development potential, and the published threshold values (>4, 4-2, <2) are interpreted in that light. We will state this more prominently, as we recognise the current text does not sufficiently separate the two uses. We would also like to note that the FI is routinely calculated from total rather than exclusively living assemblages, including in the studies cited in this context. Fajemila et al., (2025), for example, stained their samples with Rose Bengal but counted both living and dead specimens for the FI, reporting that a large proportion of the symbiont-bearing taxa were dead and that living individuals were scarce at all stations. Barbosa et al., (2025) likewise used combined living and dead counts, consistent with earlier local reef studies. Fajemila et al. (2025) further demonstrate the application of the index in a turbid, nutrient-enriched and taxonomically diverse coastal setting (61 genera), which is closer to the conditions considered here than the oligotrophic reef environments for which the index was originally developed.
On the transferability of the functional groups themselves, our threshold analysis provides relevant evidence. TITAN, applied to genus composition along the TOC gradient without any information on functional assignment (Fig. S2), identifies three taxa as increasing with organic enrichment: Nonion, Ammonia and Elphidium, which correspond exactly to the stress-tolerant group of the FI. The remaining pure and reliable indicator taxa, including Amphistegina, Operculina, Parasorites and Calcarina, all decline along the same gradient. The functional assignments therefore behave as expected in this setting, which we regard as support for applying the index here, while noting that this is consistent with rather than fully independent of the assemblage patterns already described.
We also accept the point regarding taxa that may tolerate more degraded conditions than their functional assignment implies. In our dataset Calcarina and Neorotalia together account for 0.82% of 8,304 counted tests, and neither genus occurs in any of the eleven nearshore samples comprising facies I and II. Calcarinids are restricted to mid- and outer-shelf samples, where they reach a maximum of 7.8% relative abundance in a single sample and average below 1%. The bias identified by the Referee, whereby calcarinid abundance under moderate nutrient enrichment may cause the FI to overestimate conditions favourable to photozoan production, therefore cannot act on the low-FI nearshore samples where it would be consequential. We will state this more explicitly, together with the caveat that the index requires greater caution in settings where calcarinids are abundant, referring to Girard et al., (2022) on the application of foraminiferal indices in highly diverse assemblages and to Prazeres et al., (2020).
- 7. We agree that in the absence of pre- and post-construction data, the reduction of fine-grained fluvial input to the southern shelf following impoundment of the Jene Berang River cannot be demonstrated directly from our data, and we will present this as a hypothesis consistent with the observed contrast between the northern and southern sectors rather than as a confirmed explanation. We will also make clear that alternative contributions to this contrast (e.g., differences in catchment size and discharge, and in shelf geometry and retention between the sectors) cannot be separated from the effect of impoundment on the basis of the present dataset.
- 9. We thank the Referee for this point, which has led us to identify an inconsistency in the manuscript. Section 3.3.2 notes that the gypsum crystals may have formed during laboratory drying, whereas Section 4.1 interprets them as indicating reducing conditions in organic-rich substrates. These statements are not compatible, and we will resolve them in favour of the former: gypsum precipitated during drying cannot be used as a proxy for reducing conditions in situ, and the interpretation in Section 4.1 will be removed. We will retain the observation itself, on the grounds that the distribution of the crystals remains informative. Gypsum occurs only in the mud-rich nearshore samples (>95 wt% mud), which are also those with the highest TOC contents; its restriction to these samples reflects the abundance of sulphate-bearing interstitial porewater retained in fine-grained, organic-rich sediment rather than conditions at the seafloor. We will present it on that basis as a feature consistent with the depositional character of the nearshore facies rather than as evidence of pore-water chemistry. We note further that the gypsum contributes substantially to the component composition of the nearshore samples, reaching 49.2 wt% of the analysed fractions in facies I, and that these components were among the variables used in the cluster analysis defining the facies. Because the crystals are a precipitate formed during drying rather than a seafloor constituent, we have verified that the facies classification does not depend on them: excluding the gypsum and renormalising the remaining components leaves the primary division between nearshore facies I and II and all mid- and outer-shelf samples unchanged (11 versus 40 samples, no reassignments), and the six-facies scheme essentially unaltered. We will report the gypsum separately from the biogenic and terrigenous components in the revised Table 3 and Fig. 6, and state explicitly that it is excluded from compositional interpretation.
Again, we want to thank the Referee for the detailed and constructive assessment. The points raised have led us to re-examine several analyses, and the manuscript will be improved as a result: the constrained ordination provides a more defensible treatment of the assemblage-environment relationship, the threshold analyses give quantitative support to an interpretation previously argued qualitatively, and the classification criterion is now set out explicitly.
We are also conscious that incorporating all of the above in full would considerably lengthen the manuscript without proportionate benefit to the reader. Additions to the main text will therefore be kept brief and will largely replace existing text, while the TITAN and indicator species analyses and the full breakpoint estimates will be reported in the supplementary material. The addition of ordination scores to the cross-shelf profiles, their spatial interpolation, and the determination of microspheric to megalospheric ratios lie beyond the scope of the present paper and are better addressed in a follow-up study. We will be glad to implement these revisions should the Editor invite a revised version.
With thanks and kind regards,
Marleen Stuhr, on behalf of all co-authors
References:
Barbosa, C. F., François do Nascimento Silva, D., Bellot, A. C. F., Hallock, P., Araujo, S. L. de, Arantes, R. C. M., and Seoane, J. C. S.: An integrated approach to environmental health assessment of a coral reef ecosystem based upon Foraminifera, Journal of Foraminiferal Research, 55, 60–77, https://doi.org/10.61551/gsjfr.55.1.60, 2025.
Fajemila, O. T., Martínez-Colón, M., Olajide-Kayode, J. O., and Olayiwola, M. A.: The FORAM Index (FI) as an indicator of environmental perturbations in coral ecosystems of Hong Kong, China, Revue de Micropaléontologie, 89, 100860, https://doi.org/10.1016/j.revmic.2025.100860, 2025.
Girard, E. B., Estradivari, Ferse, S., Ambo-Rappe, R., Jompa, J., and Renema, W.: Dynamics of large benthic foraminiferal assemblages: A tool to foreshadow reef degradation?, Science of the Total Environment, 811, 151396, https://doi.org/10.1016/j.scitotenv.2021.151396, 2022.
Legendre, P. and Gallagher, E. D.: Ecologically meaningful transformations for ordination of species data, Oecologia, 129, 271–280, https://doi.org/10.1007/s004420100716, 2001.
Murray, J.: Ecology and applications of benthic foraminifera, School of Ocean and Earth Science, University of Southampton, 440 pp., 2006.
Prazeres, M., Martínez-Colón, M., and Hallock, P.: Foraminifera as bioindicators of water quality: The FoRAM Index revisited, Environmental Pollution, 257, https://doi.org/10.1016/j.envpol.2019.113612, 2020.
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AC1: 'Reply on RC1', Marleen Stuhr, 07 Sep 2026
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RC2: 'Comment on egusphere-2026-3460', Anonymous Referee #2, 16 Sep 2026
The subject of the Ms falls perfectly within the general scope of Biogeosciences. It represents a very interesting contribution to the identification and characterization of facies within a sensitive but environmentally valuable inter-reef carbonate area in the Spermonde Archipelago (Indonesia). This is achieved by geochemical, sedimentological, and foraminiferal (i.e., LBF) analyses. The Ms is very clear and well structured. As an overall assessment, the Ms is grounded on a strong dataset and an interesting sedimentological–foraminiferal relationship. However, there are a few relevant weaknesses, particularly concerning the methodological approach and the extent to which some ecological and environmental interpretations are supported by the available data, which should be carefully considered.
1. the choices of not using living foraminiferal specimens, the lack of replicates and the collection of sediment with a grab represent important limitations of the sampling strategy. The potential ecological inferences in species and assemblages distribution might have been affected by the sampling strategy. As suggested by Murray (2006) “ecological relationships can satisfactorily be based only on the distribution of live organisms”. Although dead assemblages can provide valuable information on sedimentary and environmental patterns, the absence of living assemblages makes direct inference on contemporary ecological relationships more difficult. Given this limitation, the authors might consider toning down some of the ecological interpretations and explicitly discussing these limitations in a dedicated paragraph;
2. the relevance of a threshold over which a significant turnover (i.e., β diversity) of benthic foraminiferal assemblages occurs is reported along the Ms, but the definition of this threshold and its quantitative assessment are not sufficiently documented. The authors might consider providing a formal statistical assessment of the proposed turnover threshold for FI. Depending on the structure of the dataset, approaches such as TITAN, segmented regression, GAMs, random forest modeling or other suitable threshold/community-response methods could be considered to identify environmental variables associated with assemblage turnover and to estimate potential thresholds along environmental gradients. This would provide stronger quantitative support for the proposed ecological shift along environmental gradients;
3. data suggest spatial associations, but they do not directly evidence that monsoon-driven fluvial nutrient input induces the observed foraminiferal/facies transition. This is mainly ascribed to the sampling strategy that has not been seasonally organized and the lack of direct measurements (e.g., dissolved nutrients, turbidity, etc). The authors should therefore clearly distinguish between spatial covariance and the proposed causal mechanism. In particular, the observed relationships among mud, TOC, distance from land, and foraminiferal functional composition can support an association with terrestrial influence, but they do not by themselves demonstrate that nutrient and turbidity inputs are the mechanism driving the observed transition:
4. FI has been specifically developed for shallow-water reef environments and used in biomonitoring studies. It would be applied on living assemblages (e.g., Gonzales et al., 2022 as a reference cited in the Ms; Fajemila et al., 2025), authors should therefore discuss the applicability and limitations of the FI in inter-reef sediments and in highly diversified area (see, Girard et al., 2022). The authors should also clarify the extent to which the ecological tolerances assigned to the functional groups underlying the FI can be transferred to the present environmental setting. In particular, it would be useful to discuss that the FI is based on function groups and some taxa (e.g., Neorotalia gaimardi or Calcarina mayori) might have a higher tolerance for more degraded conditions than previously thought and considered in this index;
5. The PCA is apparently based on geographic (e.g., distance from the coast), environmental (e.g., TOC) and biotic (i.e., relative abundance of genus) variables without an a priori distinction between explanatory environmental variables and biological response variables. The former (i.e., environmental parameters) can be seen as those contributing to the distribution of the latter (i.e., LBF genera). To my knowledge, if both kind of variables are to be concurrently used, better to consider a CCA/RDA/DCA by also checking multicollinearity among them. Again, authors would explain i) if some variables were filtered out (e.g., removing genus with a lower abundance); ii) if data were transformed/normalized; iii) why highly correlated variables (i.e., mud vs. sand or FI vs. functional groups) were retained inflating the explained variances. The authors might also consider extracting the scores of PCA1 and plotting them spatially on the map. This could provide a useful visualization of the main environmental/assemblage gradient identified by the PCA and facilitate comparison with the groups identified by the cluster analysis.
6. Six groups (i.e., sub-clusters) have been identified but the rationale for selecting six groups should be made more explicit in order to avoid an apparently arbitrary choice of the clustering threshold. A straight line corresponding to the selected similarity (i.e., distance) threshold could be drawn on the dendrogram. The authors should explain the objective criterion used to select this threshold and the resulting number of groups. For example, if group VI is separated from V according to a given similarity threshold, the same criterion should be consistently applied to the remaining clusters (i.e., II);
7. The southern dam explanation is really interesting but given the absence of pre- and post-construction, I suggest that this interpretation should be presented as a hypothesis or possible explanation;
8. The influence of monsoon cannot be directly explored as sediment were collected during only one season, in addition to the absence of living assemblages and direct measurements of seasonal environmental variables. The authors should therefore be more cautious in the interpretation;
9. According to the authors, gypsum might have been formed in laboratory during the drying procedure, so its occurrence cannot be directly used as a proxy of reducing conditions and it requires to be fully discussed.Citation: https://doi.org/10.5194/egusphere-2026-3460-RC2 -
AC3: 'Reply on RC3', Marleen Stuhr, 28 Sep 2026
Dear Referee 3,
We thank you for the assessment. Most of the points raised overlap with those of Referees 1 and 2, to which we have already responded in detail; we refer to those responses and comment briefly here.
- Authigenic gypsum: We agree, and addressed this in our response to Referee 2 (point 9). The gypsum will be reported separately from the biogenic and terrigenous components and excluded from compositional interpretation. We have verified that the classification does not depend on it: excluding the gypsum and renormalising the remaining components leaves the nearshore/offshore division unchanged (11 versus 40 samples, no reassignments) and the facies scheme essentially unaltered.
- Facies VI as a single sample: This point was not raised by the other Referees and we consider it well taken. Treating S04 as an anomalous sample outside the classification rather than as a facies would also resolve the concern raised by Referee 2 (point 6), since the linkage criterion would then apply without exception. As this affects the facies scheme throughout the manuscript, we will settle it with our co-authors in preparing a revised version.
- Taphonomic and transport biases: Addressed in our response to Referee 2 (points 1 and 3); the revised Discussion will treat these constraints explicitly, including post-mortem transport. On selective test destruction, we find no dissolution signature: agglutinated taxa are depleted alongside porcelaneous taxa in the nearshore samples (0.5% against 7.7-6% offshore) rather than enriched relative to them, as dissolution would predict.
- Bili-Bili Dam: Addressed in our response to Referee 2 (point 7); the attribution will be presented as a hypothesis rather than an explanation.
- Seasonal sampling versus satellite record: Addressed in our response to Referee 2 (point 8). The grab samples are kilogram-scale, penetrate several centimetres and were homogenised, so the assemblages are time-integrated rather than representative of the sampling date; we will state this explicitly in the revised Methods.
With thanks and kind regards,
Marleen StuhrCitation: https://doi.org/10.5194/egusphere-2026-3460-AC3 -
AC2: 'Comment on egusphere-2026-3460', Marleen Stuhr, 23 Sep 2026
Response to RC1:
Dear Referee 1,
We thank you for the careful reading of our manuscript and for the generous assessment. We are particularly grateful for the mechanistic hypotheses raised regarding the persistence of Amphistegina and Operculina on the mid- and outer shelf, which we find compelling and will address briefly in the revised manuscript. Our responses to the individual points follow.
We are very grateful for your suggestions, which we believe will strengthen the ecological interpretation of the manuscript.
- We agree that darkness-induced dormancy offers a plausible explanation for the maintenance of symbiont-bearing assemblages under seasonally reduced water transparency, and we were not previously aware of the extent of the supporting evidence. The experimental record is encouraging in this respect: reticulopodial activity resumed in more than 95% of A. gibbosa specimens following twelve months of aphotic conditions, with symbiont colour returning within days, whereas recovery became slower and less complete beyond fifteen months (Ross and Hallock, 2019). The authors of that study interpret this inflection as potentially reflecting dormancy mechanisms tuned to seasonal light limitation, and explicitly identify mid- and outer-shelf settings subject to monsoon-driven turbidity as an environment where such a strategy would be advantageous. The approximately six-month duration of the northwest monsoon on the Spermonde shelf falls well within the interval over which recovery appears essentially complete.
Two qualifications apply. First, the high recovery rates reported by Ross and Hallock (2019) were obtained under deliberately gradual re-illumination, and the authors note that abrupt return to full light may be stressful for dark-adapted individuals. Post-monsoon clearing on the Spermonde shelf is gradual and depth-attenuated, so this condition is plausibly satisfied, but the correspondence should be stated rather than assumed. Second, the experimental evidence derives from A. gibbosa, which belongs to the Atlantic lineage of the genus, phylogenetically separated from the Indo-Pacific A. lessonii–A. lobifera lineage (Larsen, 1978; Stuhr et al., 2022); as our counts are resolved to genus level, we cannot specify which species contribute to the assemblages reported here. Shorter survival was reported for A. lobifera by Lee et al., (1991), although those authors scored viability by pseudopodial activity and attachment (criteria that a dormant individual would not meet) and record that prolonged-darkness experiments on the same species yielded recovery within days of return to light (P. Hallock, personal communication in Lee et al., 1991). Together with the observation that repeated removal and observation may itself reduce the efficacy of dormancy (Ross and Hallock, 2019), this suggests the apparent contrast between congeners may be partly methodological. We note further that the Indo-Pacific lineage is characterised by more diverse and flexible photosymbiont associations (Prazeres et al., 2021; Stuhr et al., 2022), which may favour rather than constrain low-light tolerance.
We will further note that the relevance of dormancy may extend to the opposite end of the cross-shelf gradient. Quiescence in response to anoxia and reducing conditions has been documented for Nonion, Ammonia and Elphidium among other taxa (Ross and Hallock, 2016, and references therein), which are precisely the stress-tolerant genera that dominate our organic-rich nearshore facies. Dormancy may therefore contribute to assemblage persistence across the full gradient rather than only offshore, which we consider a useful addition to the interpretation.
- We also agree that propagule-mediated recruitment provides an equally plausible mechanism, and that the two are not mutually exclusive: cryptobiotic propagules are now recognised as a widespread feature of foraminiferal life cycles and allow assemblages to respond rapidly to changing conditions (Alve and Goldstein, 2003, 2010; Ross and Hallock, 2016; etc.). A dry season of roughly six months would plausibly permit recruits to approach adult size, and the relatively short life spans of these taxa are consistent with such a cycle.
For Operculina, where dormancy has not been tested, we would add a third possibility supported by direct experimental evidence. In a transplant experiment in the Gulf of Aqaba-Eilat, O. ammonoides constructed thinner chambers following relocation to low light, added more weight per unit area under high light, and adjusted chlorophyll content across a range of light conditions (Oron et al., 2018). Notably, evolute specimens acclimatised to very low light did not survive relocation to high light, apparently as a result of photo-oxidative stress. This suggests that Operculina may accommodate seasonal variation in irradiance through morphological and physiological acclimatisation rather than through dormancy, and generates a testable prediction: the cost of low-light acclimatisation is vulnerability to rapid re-illumination, which is consistent with a gradually clearing shelf but would not be sustainable under episodic flushing. We will refer to these briefly in the Discussion as alternative, non-exclusive mechanisms, together with a recommendation that the capacity for dormancy in Operculina be examined directly.
We thank the referee for this suggestion and want to express we have been contemplating it for a while. We do not question that dimorph ratios could represent the most direct available test of whether these assemblages are sustained by seasonal recruitment via propagules or by the persistence of individuals. Yet, a design consideration worth recording for whoever undertakes it: microspheric and megalospheric generations differ systematically in adult size, so ratios determined from a size-truncated death assemblage (as in our study, where our counts derive from the fraction >125 µm) would carry a size-selection bias that requires independent control. Scanning for growth hiatuses, as suggested, would provide valuable complementary evidence and is less exposed to this problem. Even though archive halves of all samples have of course been retained and remain available for this purpose, we unfortunately do not have the capacity to undertake this analysis within the present revision. But we will recommend this explicitly for future work.
Finally, we thank the Referee for the detailed editorial annotations provided in the supplementary file. We will accept all of these and incorporate them in the revised manuscript. We have additionally identified an internal inconsistency in the naming of facies II, which appears as "Bivalve-dominated terrigenous-bearing mud-supported carbonate sediment" in Section 3.5 but without the "-bearing" modifier in Table 3 and Fig. 8; we will thus standardise this to "Bivalve-dominated terrigenous mud-supported carbonate sediment" throughout.
With thanks and kind regards,
Marleen Stuhr, on behalf of all co-authors
References:
Alve, E. and Goldstein, S. T.: Propagule transport as a key method of dispersal in benthic foraminifera (Protista), Limnology and Oceanography, 48, 2163–2170, https://doi.org/10.4319/lo.2003.48.6.2163, 2003.
Alve, E. and Goldstein, S. T.: Dispersal, survival and delayed growth of benthic foraminiferal propagules, Journal of Sea Research, 63, 36–51, https://doi.org/10.1016/j.seares.2009.09.003, 2010.
Larsen, A. R.: Phylogenetic and paleobiogeographical trends in the foraminiferal genus Amphistegina, Revista Española de Micropaleontología, X, 217–243, 1978.
Lee, J. J., Sang, K., ter Kuile, B., Strauss, E., Lee, P. J., and Faber, W. W.: Nutritional and related experiments on laboratory maintenance of three species of symbiont-bearing, large foraminifera, Marine Biology, 109, 417–425, https://doi.org/10.1007/BF01313507, 1991.
Oron, S., Abramovich, S., Almogi-Labin, A., Woeger, J., and Erez, J.: Depth related adaptations in symbiont bearing benthic foraminifera: New insights from a field experiment on Operculina ammonoides, Scientific Reports, 8, 1–11, https://doi.org/10.1038/s41598-018-29216-w, 2018.
Prazeres, M., Roberts, T. E., Ramadhani, S. F., Doo, S. S., Schmidt, C., Stuhr, M., and Renema, W.: Diversity and flexibility of algal symbiont community in globally distributed larger benthic foraminifera of the genus Amphistegina, BMC Microbiology, 21, 1–16, https://doi.org/10.1186/s12866-021-02299-8, 2021.
Ross, B. J. and Hallock, P.: Dormancy in the foraminifera: A review, Journal of Foraminiferal Research, 46, 358–368, 2016.
Ross, B. J. and Hallock, P.: Survival and recovery of the foraminifer Amphistegina gibbosa and associated diatom endosymbionts following up to 20 months in aphotic conditions, Marine Micropaleontology, 149, 35–43, https://doi.org/10.1016/j.marmicro.2019.03.013, 2019.
Stuhr, M., Blank-Landeshammer, B., Meyer, A., Baumeister, V., Rahnenführer, J., Sickmann, A., and Westphal, H.: Proteome-based clustering approaches reveal phylogenetic insights into Amphistegina, Journal of Earth Science, https://doi.org/10.1007/s12583-022-1609-1, 2022.
Response to RC2:
Dear Referee 2,
We thank you for the constructive and detailed assessment, and for the methodological points raised, which we consider well founded. We have grouped and ordered our responses considering how the points are related. Since comments 1 and 3 concern the inferences that our sampling design supports, we address them together.
- 1. & 3.: We agree with your comment that the manuscript currently lacks an explicit treatment of the constraints imposed by the sampling design, and we agree this is a shortcoming. We will address these constraints explicitly in the revised Discussion: the use of total rather than living assemblages, the absence of station-level replication, the absence of direct nutrient and turbidity measurements, and possible post-mortem transport.
We accept the principle that contemporary ecological relationships are most securely established from living assemblages (Murray, 2006), and will revise any wording implying inference about living populations or contemporary ecological interactions. We also acknowledge post-mortem transport as an additional source of uncertainty. Tidal, wave-induced and density-driven bottom currents act across the shelf, and in the absence of hydrodynamic measurements we cannot exclude that tests have been displaced from their environment of origin.
- On point 3, we generally agree to your criticism. Our data establish that foraminiferal composition covaries with mud content, organic carbon and distance from land, and that this covariance is spatially organised in a manner consistent with terrestrial influence. They do not demonstrate that monsoon-driven fluvial nutrient and turbidity input is the mechanism producing the transition. We will revise the text throughout to maintain this distinction, including the title to "Terrestrial forcing and inter-reef carbonate production across a monsoon-influenced tropical shelf (Spermonde Archipelago, Indonesia)" so that it claims association rather than causation. Terrestrial influence will be presented as an association supported by our data; the monsoon-driven mechanism as an interpretation consistent with the spatial pattern and with independently documented seasonal hydrography, but not as a demonstrated causal link.
- We appreciate point 8 and would like to clarify our sampling design, which we recognise is not described with sufficient precision in the current Methods. Sediments were collected with a van Veen grab retrieving kilogram-scale bulk samples penetrating several cm into the seabed, and each sample was homogenised prior to analysis. The resulting assemblages are thus time-integrated rather than representative of conditions at the time of collection, and re-sampling the same stations in a different season would not be expected to yield a materially different assemblage. The July 2021 campaign should therefore not be read as a seasonal snapshot, and we will state this explicitly in the revised Methods.
This bears directly on the interpretation. Because the assemblages integrate conditions over time rather than sampling them at a single moment, they record persistent environmental structure, which is the basis on which we interpret the cross-shelf pattern as a stable feature of the shelf. In this respect the dataset is closer to a sedimentary record than to an ecological survey. What our data cannot do is resolve seasonal variability, and we will ensure the text does not imply otherwise: the proposition that monsoon forcing amplifies rather than creates the cross-shelf gradient rests on independently documented seasonal hydrography, and we will make that dependence explicit rather than leaving it implicit. Yet we appreciate that testing the seasonal hypothesis directly would be interesting indeed, but require a different design, targeting living assemblages in the uppermost few millimetres of sediment at seasonal intervals alongside in situ measurement of turbidity and dissolved nutrients. Such a design would simultaneously address the hypotheses raised by Referee 1 regarding dormancy and propagule-mediated recruitment, and we identify it as a priority for future work.
- We agree with point 5. The published biplot combined spatial, geochemical and biotic variables in a single unconstrained ordination, with no a priori separation of explanatory environmental parameters from biological response variables, and we accept that this is not the ideal way of presenting data for answering the question being asked. We have therefore carried out the suggested alternative and consider it an improvement; the resulting ordination (Fig. S1) will replace the current Fig. 9.
Detrended correspondence analysis gives a gradient length of 2.68 SD units on the first axis, below the threshold at which a unimodal response model becomes preferable, and we therefore use redundancy analysis (RDA) rather than CCA, with Hellinger-transformed genus composition as the response matrix and standardised environmental parameters as constraints (Legendre and Gallagher, 2001). Full model output is given in Table S1.
On the specifics: (i) no abundance-based filtering was applied previously and all 42 genera are likewise retained here, as the Hellinger transformation downweights rare taxa without requiring their removal; (ii) the previous biplot used a correlation matrix, which standardises variables but does not address the compositional nature of assemblage data, whereas the revised analysis uses relative abundances with Hellinger transformation for the response and standardisation for the constraints; (iii) gravel, sand and mud were previously retained together, but as proportions of a closed array summing to 100 wt% they are linearly dependent and variance inflation factors are undefined for the set. We therefore retain mud as a single textural descriptor and exclude gravel, sand and distance to the Strait of Makassar, the last being largely redundant with distance from the mainland; VIFs for the five retained constraints are all below 10. The FI and functional-group proportions were also previously included alongside the genus data from which they are derived; since FI is a deterministic function of those proportions, their inclusion is circular and may inflate apparent structure, and they are excluded here. FI is now used only as an independently derived variable for comparison. These decisions will be documented in the revised Methods 2.5, which we agree was previously insufficiently specific.
For the revised results section this will mean the following: The ordination separates nearshore facies I and II, associated with high mud and TOC, from mid- and outer-shelf facies associated with greater water depth, higher carbonate content and greater distance from the mainland. Ammonia, Nonion and Elphidium align with the nearshore end of the gradient and Amphistegina and Operculina with the offshore end, while Quinqueloculina, Cibicidoides, Cibicides and Spiroloculina occupy intermediate positions. Facies III to V overlap along the second axis, consistent with the gradational character of the mid- and outer-shelf transition described in the manuscript.
The revised analysis therefore reproduces the cross-shelf structure described in the original manuscript, but with explanatory and response variables properly separated and with explained variance attributable to identified environmental constraints. The constrained fraction is lower than the variance reported for the published unconstrained ordination, which we consider a more accurate reflection of the explanatory power of the measured environmental variables.
We agree that relating the main ordination axis to the spatial structure of the shelf is informative. Site scores on the first constrained axis have been extracted and are included in the supplementary data tables. As this axis essentially reproduces the cross-shelf gradient already shown by the FI, TOC, CaCO₃ and grain-size profiles in Fig. 10, we do not consider an additional map or profile necessary for the present paper.
- We agree with point 2 that the threshold interpretation required formal statistical support and have carried out the suggested analyses. The PERMANOVA and segmented regression results will be summarised briefly in the Results; the full outputs, including the TITAN, are provided in the supplementary material. PERMANOVA on Bray-Curtis dissimilarities of genus composition confirms the separation of nearshore from mid- and outer-shelf assemblages (pseudo-F = 28.77, R² = 0.37, p = 0.0002, 4999 permutations). A test of multivariate dispersion homogeneity is non-significant (PERMDISP, p = 0.77), indicating that this reflects genuine differences in assemblage composition rather than differing within-group variability. Across all six facies the model explains 54% of compositional variation (pseudo-F = 10.67, p = 0.0002).
Segmented regression identifies a change in the response of the FI to organic enrichment at TOC = 0.56% (SE 0.10; R² increasing from 0.63 to 0.71; Davies test p = 0.009). Community composition, summarised as the first principal coordinate of the Bray-Curtis dissimilarity matrix, shows significant breakpoints against mud content (72 wt%, p = 5.6 × 10⁻⁵), water depth (38.5 m, p = 0.004) and distance from the mainland (21.1 km, p = 0.015), but varies approximately linearly with TOC (p = 0.81). The estimated location of the mud breakpoint carries substantial uncertainty (SE 27.7 wt%), so we will report it as evidence for a change in slope rather than as a precisely located threshold. Full breakpoint estimates are given in Table S3.
This contrast is informative rather than contradictory. The FI responds non-linearly to organic enrichment, whereas total assemblage turnover tracks the physical gradients of substrate, depth and distance from land. We interpret this as indicating that the threshold behaviour we describe operates principally on the functional composition of the assemblage rather than on species turnover as a whole, and we will state it in these terms.
Threshold Indicator Taxa Analysis (TITAN, Fig. S2) along the TOC gradient identifies a community change point for increasing taxa at TOC = 0.345% (bootstrap 5-95% limits 0.305-0.610). Change points for individual pure and reliable taxa are concentrated within a narrow interval of the gradient rather than distributed across it: Elphidium at 0.345, Nonion and Ammonia at 0.450, Cornuspira at 0.320, Parasorites and Calcarina at 0.380, and Amphistegina at 0.450, with purity and reliability of 1.00 for several of these. This concentration is consistent with compositional reorganisation over a limited range of organic enrichment rather than with gradual replacement along the gradient.
We note that the three taxa identified as increasing along the gradient (Nonion, Ammonia and Elphidium) correspond exactly to the stress-tolerant functional group of the FI, although no information on functional assignment was supplied to the analysis. We regard this as supporting the applicability of the FI functional categories in this setting (see response to point 4), while recognising that it is consistent with, rather than independent of, the assemblage patterns already described in Section 3.4. Yet, two limitations should be recorded. The change point for declining taxa as a group is poorly constrained (5-95% limits 0.390-1.010), and the proportion of pure and reliable taxa is moderate (0.43). We will hence report bootstrap limits alongside all point estimates rather than the estimates alone.
- Point 6: The basis for distinguishing six facies was not made sufficiently explicit, so we will describe it in more detail in the revised Methods. We accept the specific concern raised: a single similarity threshold does not yield exactly the six units as published, and we will state this explicitly in the revised Methods.
The facies were defined by cutting the dendrogram at a linkage distance of ~82, which yields five groups, and then retaining facies VI as a separate unit on sedimentological grounds. Facies VI (sample S04) contains 33.5 wt% siliciclastic material distributed across multiple grain-size fractions and has a CaCO₃ content of 43.3%, whereas siliciclastic contributions are near-absent elsewhere on the shelf. We interpret this sample as relict, potentially reflecting late Pleistocene to early Holocene deposits emplaced prior to full shelf flooding, and discuss it as such in Section 4.1. Merging it with facies V (as suggested by the five-group cutoff, see Fig. S3 in attached PDF) would group a compositionally and genetically distinct deposit with the foramol mud-supported carbonate sediments of the mid shelf. Applying a lower threshold, such that facies VI separates automatically, would instead subdivide facies II, which we do not consider meaningful either. The separation of facies VI is therefore an interpretive decision informed by composition rather than one following directly from the linkage distance, and we will state this explicitly.
We noted above, a lower threshold would separate two nearshore samples from the central shelf (S25, S32) from facies II. These both lie in the central sector at comparable distance from the mainland (5-7 km), and we do not mean to exclude that they represent a distinguishable nearshore sub-environment. We have however, decided to retain the coarser subdivision here, as this distinction does not affect the cross-shelf structure that is the subject of the study, and note it as a possible refinement. Interestingly, we noticed upon this inspection that the first and highest split in the dendrogram separates facies I and II from all mid- and outer-shelf samples without exception (11 versus 40 samples). This division is better resolved than any subsequent split, whereas the subdivision of the mid and outer shelf into facies III, IV and V occurs at much lower linkage distances and separates units that grade into one another. This structure corresponds directly to the interpretation presented in the manuscript, in which a sharp nearshore threshold gives way to a continuum of mixed carbonate production modes across the mid and outer shelf, and we will use the opportunity of a revised manuscript to present the classification in these terms rather than as six equally discrete units.
Ultimately, the facies scheme is corroborated by data deliberately excluded from its construction. Cluster analysis was performed exclusively on grain-size, carbonate and skeletal-component data, with foraminiferal assemblage composition withheld. PERMANOVA on Bray-Curtis dissimilarities of genus composition shows that the six sediment-based facies explain 54% of variation in foraminiferal composition (pseudo-F = 10.67, p = 0.0002, 4999 permutations), and indicator species analysis identifies sixteen genera significantly associated with particular facies or facies combinations, including Cibicidoides, Operculina and Amphistegina with facies III–VI (IndVal ≥ 0.97, p = 0.001) and Nonion with facies I, II, V and VI (IndVal = 0.98, p = 0.001). Facies defined solely on sedimentological criteria therefore predict assemblage composition strongly. We regard this as more informative for judging whether the units are meaningful than internal cluster validation indices, and report it in the attached PDF here (Table S2).
- 4. Yes, the transferability of the FI beyond the shallow reef settings for which it was developed requires explicit discussion, and we will consider expanding the discussion accordingly. The FI is applied here as a relative proxy for spatial variation in foraminiferal functional composition rather than as an absolute predictor of reef development potential, and the published threshold values (>4, 4-2, <2) are interpreted in that light. We will state this more prominently, as we recognise the current text does not sufficiently separate the two uses. We would also like to note that the FI is routinely calculated from total rather than exclusively living assemblages, including in the studies cited in this context. Fajemila et al., (2025), for example, stained their samples with Rose Bengal but counted both living and dead specimens for the FI, reporting that a large proportion of the symbiont-bearing taxa were dead and that living individuals were scarce at all stations. Barbosa et al., (2025) likewise used combined living and dead counts, consistent with earlier local reef studies. Fajemila et al. (2025) further demonstrate the application of the index in a turbid, nutrient-enriched and taxonomically diverse coastal setting (61 genera), which is closer to the conditions considered here than the oligotrophic reef environments for which the index was originally developed.
On the transferability of the functional groups themselves, our threshold analysis provides relevant evidence. TITAN, applied to genus composition along the TOC gradient without any information on functional assignment (Fig. S2), identifies three taxa as increasing with organic enrichment: Nonion, Ammonia and Elphidium, which correspond exactly to the stress-tolerant group of the FI. The remaining pure and reliable indicator taxa, including Amphistegina, Operculina, Parasorites and Calcarina, all decline along the same gradient. The functional assignments therefore behave as expected in this setting, which we regard as support for applying the index here, while noting that this is consistent with rather than fully independent of the assemblage patterns already described.
We also accept the point regarding taxa that may tolerate more degraded conditions than their functional assignment implies. In our dataset Calcarina and Neorotalia together account for 0.82% of 8,304 counted tests, and neither genus occurs in any of the eleven nearshore samples comprising facies I and II. Calcarinids are restricted to mid- and outer-shelf samples, where they reach a maximum of 7.8% relative abundance in a single sample and average below 1%. The bias identified by the Referee, whereby calcarinid abundance under moderate nutrient enrichment may cause the FI to overestimate conditions favourable to photozoan production, therefore cannot act on the low-FI nearshore samples where it would be consequential. We will state this more explicitly, together with the caveat that the index requires greater caution in settings where calcarinids are abundant, referring to Girard et al., (2022) on the application of foraminiferal indices in highly diverse assemblages and to Prazeres et al., (2020).
- 7. We agree that in the absence of pre- and post-construction data, the reduction of fine-grained fluvial input to the southern shelf following impoundment of the Jene Berang River cannot be demonstrated directly from our data, and we will present this as a hypothesis consistent with the observed contrast between the northern and southern sectors rather than as a confirmed explanation. We will also make clear that alternative contributions to this contrast (e.g., differences in catchment size and discharge, and in shelf geometry and retention between the sectors) cannot be separated from the effect of impoundment on the basis of the present dataset.
- 9. We thank the Referee for this point, which has led us to identify an inconsistency in the manuscript. Section 3.3.2 notes that the gypsum crystals may have formed during laboratory drying, whereas Section 4.1 interprets them as indicating reducing conditions in organic-rich substrates. These statements are not compatible, and we will resolve them in favour of the former: gypsum precipitated during drying cannot be used as a proxy for reducing conditions in situ, and the interpretation in Section 4.1 will be removed. We will retain the observation itself, on the grounds that the distribution of the crystals remains informative. Gypsum occurs only in the mud-rich nearshore samples (>95 wt% mud), which are also those with the highest TOC contents; its restriction to these samples reflects the abundance of sulphate-bearing interstitial porewater retained in fine-grained, organic-rich sediment rather than conditions at the seafloor. We will present it on that basis as a feature consistent with the depositional character of the nearshore facies rather than as evidence of pore-water chemistry. We note further that the gypsum contributes substantially to the component composition of the nearshore samples, reaching 49.2 wt% of the analysed fractions in facies I, and that these components were among the variables used in the cluster analysis defining the facies. Because the crystals are a precipitate formed during drying rather than a seafloor constituent, we have verified that the facies classification does not depend on them: excluding the gypsum and renormalising the remaining components leaves the primary division between nearshore facies I and II and all mid- and outer-shelf samples unchanged (11 versus 40 samples, no reassignments), and the six-facies scheme essentially unaltered. We will report the gypsum separately from the biogenic and terrigenous components in the revised Table 3 and Fig. 6, and state explicitly that it is excluded from compositional interpretation.
Again, we want to thank the Referee for the detailed and constructive assessment. The points raised have led us to re-examine several analyses, and the manuscript will be improved as a result: the constrained ordination provides a more defensible treatment of the assemblage-environment relationship, the threshold analyses give quantitative support to an interpretation previously argued qualitatively, and the classification criterion is now set out explicitly.
We are also conscious that incorporating all of the above in full would considerably lengthen the manuscript without proportionate benefit to the reader. Additions to the main text will therefore be kept brief and will largely replace existing text, while the TITAN and indicator species analyses and the full breakpoint estimates will be reported in the supplementary material. The addition of ordination scores to the cross-shelf profiles, their spatial interpolation, and the determination of microspheric to megalospheric ratios lie beyond the scope of the present paper and are better addressed in a follow-up study. We will be glad to implement these revisions should the Editor invite a revised version.
With thanks and kind regards,
Marleen Stuhr, on behalf of all co-authors
References:
Barbosa, C. F., François do Nascimento Silva, D., Bellot, A. C. F., Hallock, P., Araujo, S. L. de, Arantes, R. C. M., and Seoane, J. C. S.: An integrated approach to environmental health assessment of a coral reef ecosystem based upon Foraminifera, Journal of Foraminiferal Research, 55, 60–77, https://doi.org/10.61551/gsjfr.55.1.60, 2025.
Fajemila, O. T., Martínez-Colón, M., Olajide-Kayode, J. O., and Olayiwola, M. A.: The FORAM Index (FI) as an indicator of environmental perturbations in coral ecosystems of Hong Kong, China, Revue de Micropaléontologie, 89, 100860, https://doi.org/10.1016/j.revmic.2025.100860, 2025.
Girard, E. B., Estradivari, Ferse, S., Ambo-Rappe, R., Jompa, J., and Renema, W.: Dynamics of large benthic foraminiferal assemblages: A tool to foreshadow reef degradation?, Science of the Total Environment, 811, 151396, https://doi.org/10.1016/j.scitotenv.2021.151396, 2022.
Legendre, P. and Gallagher, E. D.: Ecologically meaningful transformations for ordination of species data, Oecologia, 129, 271–280, https://doi.org/10.1007/s004420100716, 2001.
Murray, J.: Ecology and applications of benthic foraminifera, School of Ocean and Earth Science, University of Southampton, 440 pp., 2006.
Prazeres, M., Martínez-Colón, M., and Hallock, P.: Foraminifera as bioindicators of water quality: The FoRAM Index revisited, Environmental Pollution, 257, https://doi.org/10.1016/j.envpol.2019.113612, 2020.
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AC3: 'Reply on RC3', Marleen Stuhr, 28 Sep 2026
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AC2: 'Comment on egusphere-2026-3460', Marleen Stuhr, 23 Sep 2026
Response to RC1:
Dear Referee 1,
We thank you for the careful reading of our manuscript and for the generous assessment. We are particularly grateful for the mechanistic hypotheses raised regarding the persistence of Amphistegina and Operculina on the mid- and outer shelf, which we find compelling and will address briefly in the revised manuscript. Our responses to the individual points follow.
We are very grateful for your suggestions, which we believe will strengthen the ecological interpretation of the manuscript.
- We agree that darkness-induced dormancy offers a plausible explanation for the maintenance of symbiont-bearing assemblages under seasonally reduced water transparency, and we were not previously aware of the extent of the supporting evidence. The experimental record is encouraging in this respect: reticulopodial activity resumed in more than 95% of A. gibbosa specimens following twelve months of aphotic conditions, with symbiont colour returning within days, whereas recovery became slower and less complete beyond fifteen months (Ross and Hallock, 2019). The authors of that study interpret this inflection as potentially reflecting dormancy mechanisms tuned to seasonal light limitation, and explicitly identify mid- and outer-shelf settings subject to monsoon-driven turbidity as an environment where such a strategy would be advantageous. The approximately six-month duration of the northwest monsoon on the Spermonde shelf falls well within the interval over which recovery appears essentially complete.
Two qualifications apply. First, the high recovery rates reported by Ross and Hallock (2019) were obtained under deliberately gradual re-illumination, and the authors note that abrupt return to full light may be stressful for dark-adapted individuals. Post-monsoon clearing on the Spermonde shelf is gradual and depth-attenuated, so this condition is plausibly satisfied, but the correspondence should be stated rather than assumed. Second, the experimental evidence derives from A. gibbosa, which belongs to the Atlantic lineage of the genus, phylogenetically separated from the Indo-Pacific A. lessonii–A. lobifera lineage (Larsen, 1978; Stuhr et al., 2022); as our counts are resolved to genus level, we cannot specify which species contribute to the assemblages reported here. Shorter survival was reported for A. lobifera by Lee et al., (1991), although those authors scored viability by pseudopodial activity and attachment (criteria that a dormant individual would not meet) and record that prolonged-darkness experiments on the same species yielded recovery within days of return to light (P. Hallock, personal communication in Lee et al., 1991). Together with the observation that repeated removal and observation may itself reduce the efficacy of dormancy (Ross and Hallock, 2019), this suggests the apparent contrast between congeners may be partly methodological. We note further that the Indo-Pacific lineage is characterised by more diverse and flexible photosymbiont associations (Prazeres et al., 2021; Stuhr et al., 2022), which may favour rather than constrain low-light tolerance.
We will further note that the relevance of dormancy may extend to the opposite end of the cross-shelf gradient. Quiescence in response to anoxia and reducing conditions has been documented for Nonion, Ammonia and Elphidium among other taxa (Ross and Hallock, 2016, and references therein), which are precisely the stress-tolerant genera that dominate our organic-rich nearshore facies. Dormancy may therefore contribute to assemblage persistence across the full gradient rather than only offshore, which we consider a useful addition to the interpretation.
- We also agree that propagule-mediated recruitment provides an equally plausible mechanism, and that the two are not mutually exclusive: cryptobiotic propagules are now recognised as a widespread feature of foraminiferal life cycles and allow assemblages to respond rapidly to changing conditions (Alve and Goldstein, 2003, 2010; Ross and Hallock, 2016; etc.). A dry season of roughly six months would plausibly permit recruits to approach adult size, and the relatively short life spans of these taxa are consistent with such a cycle.
For Operculina, where dormancy has not been tested, we would add a third possibility supported by direct experimental evidence. In a transplant experiment in the Gulf of Aqaba-Eilat, O. ammonoides constructed thinner chambers following relocation to low light, added more weight per unit area under high light, and adjusted chlorophyll content across a range of light conditions (Oron et al., 2018). Notably, evolute specimens acclimatised to very low light did not survive relocation to high light, apparently as a result of photo-oxidative stress. This suggests that Operculina may accommodate seasonal variation in irradiance through morphological and physiological acclimatisation rather than through dormancy, and generates a testable prediction: the cost of low-light acclimatisation is vulnerability to rapid re-illumination, which is consistent with a gradually clearing shelf but would not be sustainable under episodic flushing. We will refer to these briefly in the Discussion as alternative, non-exclusive mechanisms, together with a recommendation that the capacity for dormancy in Operculina be examined directly.
We thank the referee for this suggestion and want to express we have been contemplating it for a while. We do not question that dimorph ratios could represent the most direct available test of whether these assemblages are sustained by seasonal recruitment via propagules or by the persistence of individuals. Yet, a design consideration worth recording for whoever undertakes it: microspheric and megalospheric generations differ systematically in adult size, so ratios determined from a size-truncated death assemblage (as in our study, where our counts derive from the fraction >125 µm) would carry a size-selection bias that requires independent control. Scanning for growth hiatuses, as suggested, would provide valuable complementary evidence and is less exposed to this problem. Even though archive halves of all samples have of course been retained and remain available for this purpose, we unfortunately do not have the capacity to undertake this analysis within the present revision. But we will recommend this explicitly for future work.
Finally, we thank the Referee for the detailed editorial annotations provided in the supplementary file. We will accept all of these and incorporate them in the revised manuscript. We have additionally identified an internal inconsistency in the naming of facies II, which appears as "Bivalve-dominated terrigenous-bearing mud-supported carbonate sediment" in Section 3.5 but without the "-bearing" modifier in Table 3 and Fig. 8; we will thus standardise this to "Bivalve-dominated terrigenous mud-supported carbonate sediment" throughout.
With thanks and kind regards,
Marleen Stuhr, on behalf of all co-authors
References:
Alve, E. and Goldstein, S. T.: Propagule transport as a key method of dispersal in benthic foraminifera (Protista), Limnology and Oceanography, 48, 2163–2170, https://doi.org/10.4319/lo.2003.48.6.2163, 2003.
Alve, E. and Goldstein, S. T.: Dispersal, survival and delayed growth of benthic foraminiferal propagules, Journal of Sea Research, 63, 36–51, https://doi.org/10.1016/j.seares.2009.09.003, 2010.
Larsen, A. R.: Phylogenetic and paleobiogeographical trends in the foraminiferal genus Amphistegina, Revista Española de Micropaleontología, X, 217–243, 1978.
Lee, J. J., Sang, K., ter Kuile, B., Strauss, E., Lee, P. J., and Faber, W. W.: Nutritional and related experiments on laboratory maintenance of three species of symbiont-bearing, large foraminifera, Marine Biology, 109, 417–425, https://doi.org/10.1007/BF01313507, 1991.
Oron, S., Abramovich, S., Almogi-Labin, A., Woeger, J., and Erez, J.: Depth related adaptations in symbiont bearing benthic foraminifera: New insights from a field experiment on Operculina ammonoides, Scientific Reports, 8, 1–11, https://doi.org/10.1038/s41598-018-29216-w, 2018.
Prazeres, M., Roberts, T. E., Ramadhani, S. F., Doo, S. S., Schmidt, C., Stuhr, M., and Renema, W.: Diversity and flexibility of algal symbiont community in globally distributed larger benthic foraminifera of the genus Amphistegina, BMC Microbiology, 21, 1–16, https://doi.org/10.1186/s12866-021-02299-8, 2021.
Ross, B. J. and Hallock, P.: Dormancy in the foraminifera: A review, Journal of Foraminiferal Research, 46, 358–368, 2016.
Ross, B. J. and Hallock, P.: Survival and recovery of the foraminifer Amphistegina gibbosa and associated diatom endosymbionts following up to 20 months in aphotic conditions, Marine Micropaleontology, 149, 35–43, https://doi.org/10.1016/j.marmicro.2019.03.013, 2019.
Stuhr, M., Blank-Landeshammer, B., Meyer, A., Baumeister, V., Rahnenführer, J., Sickmann, A., and Westphal, H.: Proteome-based clustering approaches reveal phylogenetic insights into Amphistegina, Journal of Earth Science, https://doi.org/10.1007/s12583-022-1609-1, 2022.
Response to RC2:
Dear Referee 2,
We thank you for the constructive and detailed assessment, and for the methodological points raised, which we consider well founded. We have grouped and ordered our responses considering how the points are related. Since comments 1 and 3 concern the inferences that our sampling design supports, we address them together.
- 1. & 3.: We agree with your comment that the manuscript currently lacks an explicit treatment of the constraints imposed by the sampling design, and we agree this is a shortcoming. We will address these constraints explicitly in the revised Discussion: the use of total rather than living assemblages, the absence of station-level replication, the absence of direct nutrient and turbidity measurements, and possible post-mortem transport.
We accept the principle that contemporary ecological relationships are most securely established from living assemblages (Murray, 2006), and will revise any wording implying inference about living populations or contemporary ecological interactions. We also acknowledge post-mortem transport as an additional source of uncertainty. Tidal, wave-induced and density-driven bottom currents act across the shelf, and in the absence of hydrodynamic measurements we cannot exclude that tests have been displaced from their environment of origin.
- On point 3, we generally agree to your criticism. Our data establish that foraminiferal composition covaries with mud content, organic carbon and distance from land, and that this covariance is spatially organised in a manner consistent with terrestrial influence. They do not demonstrate that monsoon-driven fluvial nutrient and turbidity input is the mechanism producing the transition. We will revise the text throughout to maintain this distinction, including the title to "Terrestrial forcing and inter-reef carbonate production across a monsoon-influenced tropical shelf (Spermonde Archipelago, Indonesia)" so that it claims association rather than causation. Terrestrial influence will be presented as an association supported by our data; the monsoon-driven mechanism as an interpretation consistent with the spatial pattern and with independently documented seasonal hydrography, but not as a demonstrated causal link.
- We appreciate point 8 and would like to clarify our sampling design, which we recognise is not described with sufficient precision in the current Methods. Sediments were collected with a van Veen grab retrieving kilogram-scale bulk samples penetrating several cm into the seabed, and each sample was homogenised prior to analysis. The resulting assemblages are thus time-integrated rather than representative of conditions at the time of collection, and re-sampling the same stations in a different season would not be expected to yield a materially different assemblage. The July 2021 campaign should therefore not be read as a seasonal snapshot, and we will state this explicitly in the revised Methods.
This bears directly on the interpretation. Because the assemblages integrate conditions over time rather than sampling them at a single moment, they record persistent environmental structure, which is the basis on which we interpret the cross-shelf pattern as a stable feature of the shelf. In this respect the dataset is closer to a sedimentary record than to an ecological survey. What our data cannot do is resolve seasonal variability, and we will ensure the text does not imply otherwise: the proposition that monsoon forcing amplifies rather than creates the cross-shelf gradient rests on independently documented seasonal hydrography, and we will make that dependence explicit rather than leaving it implicit. Yet we appreciate that testing the seasonal hypothesis directly would be interesting indeed, but require a different design, targeting living assemblages in the uppermost few millimetres of sediment at seasonal intervals alongside in situ measurement of turbidity and dissolved nutrients. Such a design would simultaneously address the hypotheses raised by Referee 1 regarding dormancy and propagule-mediated recruitment, and we identify it as a priority for future work.
- We agree with point 5. The published biplot combined spatial, geochemical and biotic variables in a single unconstrained ordination, with no a priori separation of explanatory environmental parameters from biological response variables, and we accept that this is not the ideal way of presenting data for answering the question being asked. We have therefore carried out the suggested alternative and consider it an improvement; the resulting ordination (Fig. S1) will replace the current Fig. 9.
Detrended correspondence analysis gives a gradient length of 2.68 SD units on the first axis, below the threshold at which a unimodal response model becomes preferable, and we therefore use redundancy analysis (RDA) rather than CCA, with Hellinger-transformed genus composition as the response matrix and standardised environmental parameters as constraints (Legendre and Gallagher, 2001). Full model output is given in Table S1.
On the specifics: (i) no abundance-based filtering was applied previously and all 42 genera are likewise retained here, as the Hellinger transformation downweights rare taxa without requiring their removal; (ii) the previous biplot used a correlation matrix, which standardises variables but does not address the compositional nature of assemblage data, whereas the revised analysis uses relative abundances with Hellinger transformation for the response and standardisation for the constraints; (iii) gravel, sand and mud were previously retained together, but as proportions of a closed array summing to 100 wt% they are linearly dependent and variance inflation factors are undefined for the set. We therefore retain mud as a single textural descriptor and exclude gravel, sand and distance to the Strait of Makassar, the last being largely redundant with distance from the mainland; VIFs for the five retained constraints are all below 10. The FI and functional-group proportions were also previously included alongside the genus data from which they are derived; since FI is a deterministic function of those proportions, their inclusion is circular and may inflate apparent structure, and they are excluded here. FI is now used only as an independently derived variable for comparison. These decisions will be documented in the revised Methods 2.5, which we agree was previously insufficiently specific.
For the revised results section this will mean the following: The ordination separates nearshore facies I and II, associated with high mud and TOC, from mid- and outer-shelf facies associated with greater water depth, higher carbonate content and greater distance from the mainland. Ammonia, Nonion and Elphidium align with the nearshore end of the gradient and Amphistegina and Operculina with the offshore end, while Quinqueloculina, Cibicidoides, Cibicides and Spiroloculina occupy intermediate positions. Facies III to V overlap along the second axis, consistent with the gradational character of the mid- and outer-shelf transition described in the manuscript.
The revised analysis therefore reproduces the cross-shelf structure described in the original manuscript, but with explanatory and response variables properly separated and with explained variance attributable to identified environmental constraints. The constrained fraction is lower than the variance reported for the published unconstrained ordination, which we consider a more accurate reflection of the explanatory power of the measured environmental variables.
We agree that relating the main ordination axis to the spatial structure of the shelf is informative. Site scores on the first constrained axis have been extracted and are included in the supplementary data tables. As this axis essentially reproduces the cross-shelf gradient already shown by the FI, TOC, CaCO₃ and grain-size profiles in Fig. 10, we do not consider an additional map or profile necessary for the present paper.
- We agree with point 2 that the threshold interpretation required formal statistical support and have carried out the suggested analyses. The PERMANOVA and segmented regression results will be summarised briefly in the Results; the full outputs, including the TITAN, are provided in the supplementary material. PERMANOVA on Bray-Curtis dissimilarities of genus composition confirms the separation of nearshore from mid- and outer-shelf assemblages (pseudo-F = 28.77, R² = 0.37, p = 0.0002, 4999 permutations). A test of multivariate dispersion homogeneity is non-significant (PERMDISP, p = 0.77), indicating that this reflects genuine differences in assemblage composition rather than differing within-group variability. Across all six facies the model explains 54% of compositional variation (pseudo-F = 10.67, p = 0.0002).
Segmented regression identifies a change in the response of the FI to organic enrichment at TOC = 0.56% (SE 0.10; R² increasing from 0.63 to 0.71; Davies test p = 0.009). Community composition, summarised as the first principal coordinate of the Bray-Curtis dissimilarity matrix, shows significant breakpoints against mud content (72 wt%, p = 5.6 × 10⁻⁵), water depth (38.5 m, p = 0.004) and distance from the mainland (21.1 km, p = 0.015), but varies approximately linearly with TOC (p = 0.81). The estimated location of the mud breakpoint carries substantial uncertainty (SE 27.7 wt%), so we will report it as evidence for a change in slope rather than as a precisely located threshold. Full breakpoint estimates are given in Table S3.
This contrast is informative rather than contradictory. The FI responds non-linearly to organic enrichment, whereas total assemblage turnover tracks the physical gradients of substrate, depth and distance from land. We interpret this as indicating that the threshold behaviour we describe operates principally on the functional composition of the assemblage rather than on species turnover as a whole, and we will state it in these terms.
Threshold Indicator Taxa Analysis (TITAN, Fig. S2) along the TOC gradient identifies a community change point for increasing taxa at TOC = 0.345% (bootstrap 5-95% limits 0.305-0.610). Change points for individual pure and reliable taxa are concentrated within a narrow interval of the gradient rather than distributed across it: Elphidium at 0.345, Nonion and Ammonia at 0.450, Cornuspira at 0.320, Parasorites and Calcarina at 0.380, and Amphistegina at 0.450, with purity and reliability of 1.00 for several of these. This concentration is consistent with compositional reorganisation over a limited range of organic enrichment rather than with gradual replacement along the gradient.
We note that the three taxa identified as increasing along the gradient (Nonion, Ammonia and Elphidium) correspond exactly to the stress-tolerant functional group of the FI, although no information on functional assignment was supplied to the analysis. We regard this as supporting the applicability of the FI functional categories in this setting (see response to point 4), while recognising that it is consistent with, rather than independent of, the assemblage patterns already described in Section 3.4. Yet, two limitations should be recorded. The change point for declining taxa as a group is poorly constrained (5-95% limits 0.390-1.010), and the proportion of pure and reliable taxa is moderate (0.43). We will hence report bootstrap limits alongside all point estimates rather than the estimates alone.
- Point 6: The basis for distinguishing six facies was not made sufficiently explicit, so we will describe it in more detail in the revised Methods. We accept the specific concern raised: a single similarity threshold does not yield exactly the six units as published, and we will state this explicitly in the revised Methods.
The facies were defined by cutting the dendrogram at a linkage distance of ~82, which yields five groups, and then retaining facies VI as a separate unit on sedimentological grounds. Facies VI (sample S04) contains 33.5 wt% siliciclastic material distributed across multiple grain-size fractions and has a CaCO₃ content of 43.3%, whereas siliciclastic contributions are near-absent elsewhere on the shelf. We interpret this sample as relict, potentially reflecting late Pleistocene to early Holocene deposits emplaced prior to full shelf flooding, and discuss it as such in Section 4.1. Merging it with facies V (as suggested by the five-group cutoff, see Fig. S3 in attached PDF) would group a compositionally and genetically distinct deposit with the foramol mud-supported carbonate sediments of the mid shelf. Applying a lower threshold, such that facies VI separates automatically, would instead subdivide facies II, which we do not consider meaningful either. The separation of facies VI is therefore an interpretive decision informed by composition rather than one following directly from the linkage distance, and we will state this explicitly.
We noted above, a lower threshold would separate two nearshore samples from the central shelf (S25, S32) from facies II. These both lie in the central sector at comparable distance from the mainland (5-7 km), and we do not mean to exclude that they represent a distinguishable nearshore sub-environment. We have however, decided to retain the coarser subdivision here, as this distinction does not affect the cross-shelf structure that is the subject of the study, and note it as a possible refinement. Interestingly, we noticed upon this inspection that the first and highest split in the dendrogram separates facies I and II from all mid- and outer-shelf samples without exception (11 versus 40 samples). This division is better resolved than any subsequent split, whereas the subdivision of the mid and outer shelf into facies III, IV and V occurs at much lower linkage distances and separates units that grade into one another. This structure corresponds directly to the interpretation presented in the manuscript, in which a sharp nearshore threshold gives way to a continuum of mixed carbonate production modes across the mid and outer shelf, and we will use the opportunity of a revised manuscript to present the classification in these terms rather than as six equally discrete units.
Ultimately, the facies scheme is corroborated by data deliberately excluded from its construction. Cluster analysis was performed exclusively on grain-size, carbonate and skeletal-component data, with foraminiferal assemblage composition withheld. PERMANOVA on Bray-Curtis dissimilarities of genus composition shows that the six sediment-based facies explain 54% of variation in foraminiferal composition (pseudo-F = 10.67, p = 0.0002, 4999 permutations), and indicator species analysis identifies sixteen genera significantly associated with particular facies or facies combinations, including Cibicidoides, Operculina and Amphistegina with facies III–VI (IndVal ≥ 0.97, p = 0.001) and Nonion with facies I, II, V and VI (IndVal = 0.98, p = 0.001). Facies defined solely on sedimentological criteria therefore predict assemblage composition strongly. We regard this as more informative for judging whether the units are meaningful than internal cluster validation indices, and report it in the attached PDF here (Table S2).
- 4. Yes, the transferability of the FI beyond the shallow reef settings for which it was developed requires explicit discussion, and we will consider expanding the discussion accordingly. The FI is applied here as a relative proxy for spatial variation in foraminiferal functional composition rather than as an absolute predictor of reef development potential, and the published threshold values (>4, 4-2, <2) are interpreted in that light. We will state this more prominently, as we recognise the current text does not sufficiently separate the two uses. We would also like to note that the FI is routinely calculated from total rather than exclusively living assemblages, including in the studies cited in this context. Fajemila et al., (2025), for example, stained their samples with Rose Bengal but counted both living and dead specimens for the FI, reporting that a large proportion of the symbiont-bearing taxa were dead and that living individuals were scarce at all stations. Barbosa et al., (2025) likewise used combined living and dead counts, consistent with earlier local reef studies. Fajemila et al. (2025) further demonstrate the application of the index in a turbid, nutrient-enriched and taxonomically diverse coastal setting (61 genera), which is closer to the conditions considered here than the oligotrophic reef environments for which the index was originally developed.
On the transferability of the functional groups themselves, our threshold analysis provides relevant evidence. TITAN, applied to genus composition along the TOC gradient without any information on functional assignment (Fig. S2), identifies three taxa as increasing with organic enrichment: Nonion, Ammonia and Elphidium, which correspond exactly to the stress-tolerant group of the FI. The remaining pure and reliable indicator taxa, including Amphistegina, Operculina, Parasorites and Calcarina, all decline along the same gradient. The functional assignments therefore behave as expected in this setting, which we regard as support for applying the index here, while noting that this is consistent with rather than fully independent of the assemblage patterns already described.
We also accept the point regarding taxa that may tolerate more degraded conditions than their functional assignment implies. In our dataset Calcarina and Neorotalia together account for 0.82% of 8,304 counted tests, and neither genus occurs in any of the eleven nearshore samples comprising facies I and II. Calcarinids are restricted to mid- and outer-shelf samples, where they reach a maximum of 7.8% relative abundance in a single sample and average below 1%. The bias identified by the Referee, whereby calcarinid abundance under moderate nutrient enrichment may cause the FI to overestimate conditions favourable to photozoan production, therefore cannot act on the low-FI nearshore samples where it would be consequential. We will state this more explicitly, together with the caveat that the index requires greater caution in settings where calcarinids are abundant, referring to Girard et al., (2022) on the application of foraminiferal indices in highly diverse assemblages and to Prazeres et al., (2020).
- 7. We agree that in the absence of pre- and post-construction data, the reduction of fine-grained fluvial input to the southern shelf following impoundment of the Jene Berang River cannot be demonstrated directly from our data, and we will present this as a hypothesis consistent with the observed contrast between the northern and southern sectors rather than as a confirmed explanation. We will also make clear that alternative contributions to this contrast (e.g., differences in catchment size and discharge, and in shelf geometry and retention between the sectors) cannot be separated from the effect of impoundment on the basis of the present dataset.
- 9. We thank the Referee for this point, which has led us to identify an inconsistency in the manuscript. Section 3.3.2 notes that the gypsum crystals may have formed during laboratory drying, whereas Section 4.1 interprets them as indicating reducing conditions in organic-rich substrates. These statements are not compatible, and we will resolve them in favour of the former: gypsum precipitated during drying cannot be used as a proxy for reducing conditions in situ, and the interpretation in Section 4.1 will be removed. We will retain the observation itself, on the grounds that the distribution of the crystals remains informative. Gypsum occurs only in the mud-rich nearshore samples (>95 wt% mud), which are also those with the highest TOC contents; its restriction to these samples reflects the abundance of sulphate-bearing interstitial porewater retained in fine-grained, organic-rich sediment rather than conditions at the seafloor. We will present it on that basis as a feature consistent with the depositional character of the nearshore facies rather than as evidence of pore-water chemistry. We note further that the gypsum contributes substantially to the component composition of the nearshore samples, reaching 49.2 wt% of the analysed fractions in facies I, and that these components were among the variables used in the cluster analysis defining the facies. Because the crystals are a precipitate formed during drying rather than a seafloor constituent, we have verified that the facies classification does not depend on them: excluding the gypsum and renormalising the remaining components leaves the primary division between nearshore facies I and II and all mid- and outer-shelf samples unchanged (11 versus 40 samples, no reassignments), and the six-facies scheme essentially unaltered. We will report the gypsum separately from the biogenic and terrigenous components in the revised Table 3 and Fig. 6, and state explicitly that it is excluded from compositional interpretation.
Again, we want to thank the Referee for the detailed and constructive assessment. The points raised have led us to re-examine several analyses, and the manuscript will be improved as a result: the constrained ordination provides a more defensible treatment of the assemblage-environment relationship, the threshold analyses give quantitative support to an interpretation previously argued qualitatively, and the classification criterion is now set out explicitly.
We are also conscious that incorporating all of the above in full would considerably lengthen the manuscript without proportionate benefit to the reader. Additions to the main text will therefore be kept brief and will largely replace existing text, while the TITAN and indicator species analyses and the full breakpoint estimates will be reported in the supplementary material. The addition of ordination scores to the cross-shelf profiles, their spatial interpolation, and the determination of microspheric to megalospheric ratios lie beyond the scope of the present paper and are better addressed in a follow-up study. We will be glad to implement these revisions should the Editor invite a revised version.
With thanks and kind regards,
Marleen Stuhr, on behalf of all co-authors
References:
Barbosa, C. F., François do Nascimento Silva, D., Bellot, A. C. F., Hallock, P., Araujo, S. L. de, Arantes, R. C. M., and Seoane, J. C. S.: An integrated approach to environmental health assessment of a coral reef ecosystem based upon Foraminifera, Journal of Foraminiferal Research, 55, 60–77, https://doi.org/10.61551/gsjfr.55.1.60, 2025.
Fajemila, O. T., Martínez-Colón, M., Olajide-Kayode, J. O., and Olayiwola, M. A.: The FORAM Index (FI) as an indicator of environmental perturbations in coral ecosystems of Hong Kong, China, Revue de Micropaléontologie, 89, 100860, https://doi.org/10.1016/j.revmic.2025.100860, 2025.
Girard, E. B., Estradivari, Ferse, S., Ambo-Rappe, R., Jompa, J., and Renema, W.: Dynamics of large benthic foraminiferal assemblages: A tool to foreshadow reef degradation?, Science of the Total Environment, 811, 151396, https://doi.org/10.1016/j.scitotenv.2021.151396, 2022.
Legendre, P. and Gallagher, E. D.: Ecologically meaningful transformations for ordination of species data, Oecologia, 129, 271–280, https://doi.org/10.1007/s004420100716, 2001.
Murray, J.: Ecology and applications of benthic foraminifera, School of Ocean and Earth Science, University of Southampton, 440 pp., 2006.
Prazeres, M., Martínez-Colón, M., and Hallock, P.: Foraminifera as bioindicators of water quality: The FoRAM Index revisited, Environmental Pollution, 257, https://doi.org/10.1016/j.envpol.2019.113612, 2020.
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RC3: 'Comment on egusphere-2026-3460', Anonymous Referee #3, 25 Sep 2026
Overview and General Assessment
The manuscript presents a detailed investigation of shelf sedimentary dynamics, focusing on nearshore-to-offshore threshold responses, foramol facies distributions, and the application of the FORAM Index (FI) in mesotrophic inter-reef settings. The study highlights a non-linear nearshore threshold response and spatial asymmetry driven by fluvial nutrient input, demonstrates that mid- and outer-shelf settings are dominated by foramol facies with larger benthic foraminifera as primary carbonate producers (Amphistegina and Operculina), and validates the FI as a reliable ecological proxy in deeper inter-reef zones. While the integration of multi-annual satellite data strengthens the environmental context, several critical methodological and interpretive issues must be addressed before publication.
- Laboratory Artifacts in Sedimentary Facies: The authors explicitly note that authigenic gypsum crystals found in nearshore samples may have formed during the laboratory drying procedure. Quantifying these lab-grown crystals and utilizing them as variables within multivariate cluster analysis to define natural sedimentary facies (specifically Facies I) introduces a major methodological artifact that undermines the validity of that facies. These crystals should be excluded from statistical facies definitions.
The problem with the authigenic gypsum crystals is that they are artificial rather than natural ocean features; the authors explicitly note that these crystals "may have formed during the drying procedure in the laboratory". From this, the authors infer that these crystals are a genuine feature of the environment and use them as variables in a computer-based grouping analysis to define a natural sediment category called Facies I. They should not be interpreted this way because treating a laboratory side-effect as if it were a natural part of the ocean ecosystem introduces an error. Using man-made crystals to classify natural sediment groups distorts the data, rendering the resulting environmental classification scientifically unreliable.
2. Statistical Robustness of Facies Classification: Facies VI (mixed carbonate-siliciclastic sand) is established based on a single sample (S04). A single data point does not constitute a statistical facies; this sample should either be reclassified as an anomaly/outlier or integrated into a broader facies category.
3. Taphonomic and Transport Biases: The manuscript relies on dead foraminiferal assemblages to map modern environmental conditions without deeply evaluating potential taphonomic biases. Processes such as post-mortem cross-shelf transport, selective test destruction, and hydrodynamic winnowing can significantly decouple dead assemblages from living environments, and these factors require explicit discussion.
4. Unsupported Historical Attributions: The assertion that improved conditions in the southern shelf sector are linked to the 1990s construction of the Bili-Bili Dam on the Jene Berang River remains entirely speculative. Because the surface sediment dataset lacks down-core chronological control or sedimentation rate analyses, this historical shift cannot be proven from the current data and should be toned down or supported by direct sedimentary evidence.
Suggestions for Improvement:
- Refine Statistical Analyses: Re-run the multivariate cluster analysis for sedimentary facies after removing laboratory-induced artifacts (such as authigenic gypsum crystals) and re-evaluate singleton samples like S04 to ensure robust statistical groupings.
- Expand the Taphonomic Discussion: Incorporate a dedicated subsection addressing taphonomic limitations, explicitly considering how hydrodynamic transport and differential preservation might influence the dead foraminiferal assemblages.
- Moderate Historical Claims: Revise the discussion surrounding the Bili-Bili Dam to frame it as a plausible hypothesis rather than an established conclusion, unless supplementary historical core data can be introduced to substantiate the timeline.
- Clarify Seasonal vs. Long-term Integration: Ensure the text clearly distinguishes between the single-season field sampling (July 2021) and the long-term satellite forcing data (2000–2023), explicitly clarifying how taphonomic time-averaging bridges this temporal gap.
While the study presents valuable data regarding nearshore-to-shore threshold responses, foramol facies distributions, and the validation of the FORAM Index in deeper mesotrophic zones, the manuscript requires some corrections before it can be considered for publication. These necessary revisions include removing laboratory-induced artifacts from statistical facies models, eliminating single-sample facies classifications, addressing taphonomic transport biases, and moderating speculative historical claims regarding dam construction.
Citation: https://doi.org/10.5194/egusphere-2026-3460-RC3 -
AC3: 'Reply on RC3', Marleen Stuhr, 28 Sep 2026
Dear Referee 3,
We thank you for the assessment. Most of the points raised overlap with those of Referees 1 and 2, to which we have already responded in detail; we refer to those responses and comment briefly here.
- Authigenic gypsum: We agree, and addressed this in our response to Referee 2 (point 9). The gypsum will be reported separately from the biogenic and terrigenous components and excluded from compositional interpretation. We have verified that the classification does not depend on it: excluding the gypsum and renormalising the remaining components leaves the nearshore/offshore division unchanged (11 versus 40 samples, no reassignments) and the facies scheme essentially unaltered.
- Facies VI as a single sample: This point was not raised by the other Referees and we consider it well taken. Treating S04 as an anomalous sample outside the classification rather than as a facies would also resolve the concern raised by Referee 2 (point 6), since the linkage criterion would then apply without exception. As this affects the facies scheme throughout the manuscript, we will settle it with our co-authors in preparing a revised version.
- Taphonomic and transport biases: Addressed in our response to Referee 2 (points 1 and 3); the revised Discussion will treat these constraints explicitly, including post-mortem transport. On selective test destruction, we find no dissolution signature: agglutinated taxa are depleted alongside porcelaneous taxa in the nearshore samples (0.5% against 7.7-6% offshore) rather than enriched relative to them, as dissolution would predict.
- Bili-Bili Dam: Addressed in our response to Referee 2 (point 7); the attribution will be presented as a hypothesis rather than an explanation.
- Seasonal sampling versus satellite record: Addressed in our response to Referee 2 (point 8). The grab samples are kilogram-scale, penetrate several centimetres and were homogenised, so the assemblages are time-integrated rather than representative of the sampling date; we will state this explicitly in the revised Methods.
With thanks and kind regards,
Marleen StuhrCitation: https://doi.org/10.5194/egusphere-2026-3460-AC3 -
AC2: 'Comment on egusphere-2026-3460', Marleen Stuhr, 23 Sep 2026
Response to RC1:
Dear Referee 1,
We thank you for the careful reading of our manuscript and for the generous assessment. We are particularly grateful for the mechanistic hypotheses raised regarding the persistence of Amphistegina and Operculina on the mid- and outer shelf, which we find compelling and will address briefly in the revised manuscript. Our responses to the individual points follow.
We are very grateful for your suggestions, which we believe will strengthen the ecological interpretation of the manuscript.
- We agree that darkness-induced dormancy offers a plausible explanation for the maintenance of symbiont-bearing assemblages under seasonally reduced water transparency, and we were not previously aware of the extent of the supporting evidence. The experimental record is encouraging in this respect: reticulopodial activity resumed in more than 95% of A. gibbosa specimens following twelve months of aphotic conditions, with symbiont colour returning within days, whereas recovery became slower and less complete beyond fifteen months (Ross and Hallock, 2019). The authors of that study interpret this inflection as potentially reflecting dormancy mechanisms tuned to seasonal light limitation, and explicitly identify mid- and outer-shelf settings subject to monsoon-driven turbidity as an environment where such a strategy would be advantageous. The approximately six-month duration of the northwest monsoon on the Spermonde shelf falls well within the interval over which recovery appears essentially complete.
Two qualifications apply. First, the high recovery rates reported by Ross and Hallock (2019) were obtained under deliberately gradual re-illumination, and the authors note that abrupt return to full light may be stressful for dark-adapted individuals. Post-monsoon clearing on the Spermonde shelf is gradual and depth-attenuated, so this condition is plausibly satisfied, but the correspondence should be stated rather than assumed. Second, the experimental evidence derives from A. gibbosa, which belongs to the Atlantic lineage of the genus, phylogenetically separated from the Indo-Pacific A. lessonii–A. lobifera lineage (Larsen, 1978; Stuhr et al., 2022); as our counts are resolved to genus level, we cannot specify which species contribute to the assemblages reported here. Shorter survival was reported for A. lobifera by Lee et al., (1991), although those authors scored viability by pseudopodial activity and attachment (criteria that a dormant individual would not meet) and record that prolonged-darkness experiments on the same species yielded recovery within days of return to light (P. Hallock, personal communication in Lee et al., 1991). Together with the observation that repeated removal and observation may itself reduce the efficacy of dormancy (Ross and Hallock, 2019), this suggests the apparent contrast between congeners may be partly methodological. We note further that the Indo-Pacific lineage is characterised by more diverse and flexible photosymbiont associations (Prazeres et al., 2021; Stuhr et al., 2022), which may favour rather than constrain low-light tolerance.
We will further note that the relevance of dormancy may extend to the opposite end of the cross-shelf gradient. Quiescence in response to anoxia and reducing conditions has been documented for Nonion, Ammonia and Elphidium among other taxa (Ross and Hallock, 2016, and references therein), which are precisely the stress-tolerant genera that dominate our organic-rich nearshore facies. Dormancy may therefore contribute to assemblage persistence across the full gradient rather than only offshore, which we consider a useful addition to the interpretation.
- We also agree that propagule-mediated recruitment provides an equally plausible mechanism, and that the two are not mutually exclusive: cryptobiotic propagules are now recognised as a widespread feature of foraminiferal life cycles and allow assemblages to respond rapidly to changing conditions (Alve and Goldstein, 2003, 2010; Ross and Hallock, 2016; etc.). A dry season of roughly six months would plausibly permit recruits to approach adult size, and the relatively short life spans of these taxa are consistent with such a cycle.
For Operculina, where dormancy has not been tested, we would add a third possibility supported by direct experimental evidence. In a transplant experiment in the Gulf of Aqaba-Eilat, O. ammonoides constructed thinner chambers following relocation to low light, added more weight per unit area under high light, and adjusted chlorophyll content across a range of light conditions (Oron et al., 2018). Notably, evolute specimens acclimatised to very low light did not survive relocation to high light, apparently as a result of photo-oxidative stress. This suggests that Operculina may accommodate seasonal variation in irradiance through morphological and physiological acclimatisation rather than through dormancy, and generates a testable prediction: the cost of low-light acclimatisation is vulnerability to rapid re-illumination, which is consistent with a gradually clearing shelf but would not be sustainable under episodic flushing. We will refer to these briefly in the Discussion as alternative, non-exclusive mechanisms, together with a recommendation that the capacity for dormancy in Operculina be examined directly.
We thank the referee for this suggestion and want to express we have been contemplating it for a while. We do not question that dimorph ratios could represent the most direct available test of whether these assemblages are sustained by seasonal recruitment via propagules or by the persistence of individuals. Yet, a design consideration worth recording for whoever undertakes it: microspheric and megalospheric generations differ systematically in adult size, so ratios determined from a size-truncated death assemblage (as in our study, where our counts derive from the fraction >125 µm) would carry a size-selection bias that requires independent control. Scanning for growth hiatuses, as suggested, would provide valuable complementary evidence and is less exposed to this problem. Even though archive halves of all samples have of course been retained and remain available for this purpose, we unfortunately do not have the capacity to undertake this analysis within the present revision. But we will recommend this explicitly for future work.
Finally, we thank the Referee for the detailed editorial annotations provided in the supplementary file. We will accept all of these and incorporate them in the revised manuscript. We have additionally identified an internal inconsistency in the naming of facies II, which appears as "Bivalve-dominated terrigenous-bearing mud-supported carbonate sediment" in Section 3.5 but without the "-bearing" modifier in Table 3 and Fig. 8; we will thus standardise this to "Bivalve-dominated terrigenous mud-supported carbonate sediment" throughout.
With thanks and kind regards,
Marleen Stuhr, on behalf of all co-authors
References:
Alve, E. and Goldstein, S. T.: Propagule transport as a key method of dispersal in benthic foraminifera (Protista), Limnology and Oceanography, 48, 2163–2170, https://doi.org/10.4319/lo.2003.48.6.2163, 2003.
Alve, E. and Goldstein, S. T.: Dispersal, survival and delayed growth of benthic foraminiferal propagules, Journal of Sea Research, 63, 36–51, https://doi.org/10.1016/j.seares.2009.09.003, 2010.
Larsen, A. R.: Phylogenetic and paleobiogeographical trends in the foraminiferal genus Amphistegina, Revista Española de Micropaleontología, X, 217–243, 1978.
Lee, J. J., Sang, K., ter Kuile, B., Strauss, E., Lee, P. J., and Faber, W. W.: Nutritional and related experiments on laboratory maintenance of three species of symbiont-bearing, large foraminifera, Marine Biology, 109, 417–425, https://doi.org/10.1007/BF01313507, 1991.
Oron, S., Abramovich, S., Almogi-Labin, A., Woeger, J., and Erez, J.: Depth related adaptations in symbiont bearing benthic foraminifera: New insights from a field experiment on Operculina ammonoides, Scientific Reports, 8, 1–11, https://doi.org/10.1038/s41598-018-29216-w, 2018.
Prazeres, M., Roberts, T. E., Ramadhani, S. F., Doo, S. S., Schmidt, C., Stuhr, M., and Renema, W.: Diversity and flexibility of algal symbiont community in globally distributed larger benthic foraminifera of the genus Amphistegina, BMC Microbiology, 21, 1–16, https://doi.org/10.1186/s12866-021-02299-8, 2021.
Ross, B. J. and Hallock, P.: Dormancy in the foraminifera: A review, Journal of Foraminiferal Research, 46, 358–368, 2016.
Ross, B. J. and Hallock, P.: Survival and recovery of the foraminifer Amphistegina gibbosa and associated diatom endosymbionts following up to 20 months in aphotic conditions, Marine Micropaleontology, 149, 35–43, https://doi.org/10.1016/j.marmicro.2019.03.013, 2019.
Stuhr, M., Blank-Landeshammer, B., Meyer, A., Baumeister, V., Rahnenführer, J., Sickmann, A., and Westphal, H.: Proteome-based clustering approaches reveal phylogenetic insights into Amphistegina, Journal of Earth Science, https://doi.org/10.1007/s12583-022-1609-1, 2022.
Response to RC2:
Dear Referee 2,
We thank you for the constructive and detailed assessment, and for the methodological points raised, which we consider well founded. We have grouped and ordered our responses considering how the points are related. Since comments 1 and 3 concern the inferences that our sampling design supports, we address them together.
- 1. & 3.: We agree with your comment that the manuscript currently lacks an explicit treatment of the constraints imposed by the sampling design, and we agree this is a shortcoming. We will address these constraints explicitly in the revised Discussion: the use of total rather than living assemblages, the absence of station-level replication, the absence of direct nutrient and turbidity measurements, and possible post-mortem transport.
We accept the principle that contemporary ecological relationships are most securely established from living assemblages (Murray, 2006), and will revise any wording implying inference about living populations or contemporary ecological interactions. We also acknowledge post-mortem transport as an additional source of uncertainty. Tidal, wave-induced and density-driven bottom currents act across the shelf, and in the absence of hydrodynamic measurements we cannot exclude that tests have been displaced from their environment of origin.
- On point 3, we generally agree to your criticism. Our data establish that foraminiferal composition covaries with mud content, organic carbon and distance from land, and that this covariance is spatially organised in a manner consistent with terrestrial influence. They do not demonstrate that monsoon-driven fluvial nutrient and turbidity input is the mechanism producing the transition. We will revise the text throughout to maintain this distinction, including the title to "Terrestrial forcing and inter-reef carbonate production across a monsoon-influenced tropical shelf (Spermonde Archipelago, Indonesia)" so that it claims association rather than causation. Terrestrial influence will be presented as an association supported by our data; the monsoon-driven mechanism as an interpretation consistent with the spatial pattern and with independently documented seasonal hydrography, but not as a demonstrated causal link.
- We appreciate point 8 and would like to clarify our sampling design, which we recognise is not described with sufficient precision in the current Methods. Sediments were collected with a van Veen grab retrieving kilogram-scale bulk samples penetrating several cm into the seabed, and each sample was homogenised prior to analysis. The resulting assemblages are thus time-integrated rather than representative of conditions at the time of collection, and re-sampling the same stations in a different season would not be expected to yield a materially different assemblage. The July 2021 campaign should therefore not be read as a seasonal snapshot, and we will state this explicitly in the revised Methods.
This bears directly on the interpretation. Because the assemblages integrate conditions over time rather than sampling them at a single moment, they record persistent environmental structure, which is the basis on which we interpret the cross-shelf pattern as a stable feature of the shelf. In this respect the dataset is closer to a sedimentary record than to an ecological survey. What our data cannot do is resolve seasonal variability, and we will ensure the text does not imply otherwise: the proposition that monsoon forcing amplifies rather than creates the cross-shelf gradient rests on independently documented seasonal hydrography, and we will make that dependence explicit rather than leaving it implicit. Yet we appreciate that testing the seasonal hypothesis directly would be interesting indeed, but require a different design, targeting living assemblages in the uppermost few millimetres of sediment at seasonal intervals alongside in situ measurement of turbidity and dissolved nutrients. Such a design would simultaneously address the hypotheses raised by Referee 1 regarding dormancy and propagule-mediated recruitment, and we identify it as a priority for future work.
- We agree with point 5. The published biplot combined spatial, geochemical and biotic variables in a single unconstrained ordination, with no a priori separation of explanatory environmental parameters from biological response variables, and we accept that this is not the ideal way of presenting data for answering the question being asked. We have therefore carried out the suggested alternative and consider it an improvement; the resulting ordination (Fig. S1) will replace the current Fig. 9.
Detrended correspondence analysis gives a gradient length of 2.68 SD units on the first axis, below the threshold at which a unimodal response model becomes preferable, and we therefore use redundancy analysis (RDA) rather than CCA, with Hellinger-transformed genus composition as the response matrix and standardised environmental parameters as constraints (Legendre and Gallagher, 2001). Full model output is given in Table S1.
On the specifics: (i) no abundance-based filtering was applied previously and all 42 genera are likewise retained here, as the Hellinger transformation downweights rare taxa without requiring their removal; (ii) the previous biplot used a correlation matrix, which standardises variables but does not address the compositional nature of assemblage data, whereas the revised analysis uses relative abundances with Hellinger transformation for the response and standardisation for the constraints; (iii) gravel, sand and mud were previously retained together, but as proportions of a closed array summing to 100 wt% they are linearly dependent and variance inflation factors are undefined for the set. We therefore retain mud as a single textural descriptor and exclude gravel, sand and distance to the Strait of Makassar, the last being largely redundant with distance from the mainland; VIFs for the five retained constraints are all below 10. The FI and functional-group proportions were also previously included alongside the genus data from which they are derived; since FI is a deterministic function of those proportions, their inclusion is circular and may inflate apparent structure, and they are excluded here. FI is now used only as an independently derived variable for comparison. These decisions will be documented in the revised Methods 2.5, which we agree was previously insufficiently specific.
For the revised results section this will mean the following: The ordination separates nearshore facies I and II, associated with high mud and TOC, from mid- and outer-shelf facies associated with greater water depth, higher carbonate content and greater distance from the mainland. Ammonia, Nonion and Elphidium align with the nearshore end of the gradient and Amphistegina and Operculina with the offshore end, while Quinqueloculina, Cibicidoides, Cibicides and Spiroloculina occupy intermediate positions. Facies III to V overlap along the second axis, consistent with the gradational character of the mid- and outer-shelf transition described in the manuscript.
The revised analysis therefore reproduces the cross-shelf structure described in the original manuscript, but with explanatory and response variables properly separated and with explained variance attributable to identified environmental constraints. The constrained fraction is lower than the variance reported for the published unconstrained ordination, which we consider a more accurate reflection of the explanatory power of the measured environmental variables.
We agree that relating the main ordination axis to the spatial structure of the shelf is informative. Site scores on the first constrained axis have been extracted and are included in the supplementary data tables. As this axis essentially reproduces the cross-shelf gradient already shown by the FI, TOC, CaCO₃ and grain-size profiles in Fig. 10, we do not consider an additional map or profile necessary for the present paper.
- We agree with point 2 that the threshold interpretation required formal statistical support and have carried out the suggested analyses. The PERMANOVA and segmented regression results will be summarised briefly in the Results; the full outputs, including the TITAN, are provided in the supplementary material. PERMANOVA on Bray-Curtis dissimilarities of genus composition confirms the separation of nearshore from mid- and outer-shelf assemblages (pseudo-F = 28.77, R² = 0.37, p = 0.0002, 4999 permutations). A test of multivariate dispersion homogeneity is non-significant (PERMDISP, p = 0.77), indicating that this reflects genuine differences in assemblage composition rather than differing within-group variability. Across all six facies the model explains 54% of compositional variation (pseudo-F = 10.67, p = 0.0002).
Segmented regression identifies a change in the response of the FI to organic enrichment at TOC = 0.56% (SE 0.10; R² increasing from 0.63 to 0.71; Davies test p = 0.009). Community composition, summarised as the first principal coordinate of the Bray-Curtis dissimilarity matrix, shows significant breakpoints against mud content (72 wt%, p = 5.6 × 10⁻⁵), water depth (38.5 m, p = 0.004) and distance from the mainland (21.1 km, p = 0.015), but varies approximately linearly with TOC (p = 0.81). The estimated location of the mud breakpoint carries substantial uncertainty (SE 27.7 wt%), so we will report it as evidence for a change in slope rather than as a precisely located threshold. Full breakpoint estimates are given in Table S3.
This contrast is informative rather than contradictory. The FI responds non-linearly to organic enrichment, whereas total assemblage turnover tracks the physical gradients of substrate, depth and distance from land. We interpret this as indicating that the threshold behaviour we describe operates principally on the functional composition of the assemblage rather than on species turnover as a whole, and we will state it in these terms.
Threshold Indicator Taxa Analysis (TITAN, Fig. S2) along the TOC gradient identifies a community change point for increasing taxa at TOC = 0.345% (bootstrap 5-95% limits 0.305-0.610). Change points for individual pure and reliable taxa are concentrated within a narrow interval of the gradient rather than distributed across it: Elphidium at 0.345, Nonion and Ammonia at 0.450, Cornuspira at 0.320, Parasorites and Calcarina at 0.380, and Amphistegina at 0.450, with purity and reliability of 1.00 for several of these. This concentration is consistent with compositional reorganisation over a limited range of organic enrichment rather than with gradual replacement along the gradient.
We note that the three taxa identified as increasing along the gradient (Nonion, Ammonia and Elphidium) correspond exactly to the stress-tolerant functional group of the FI, although no information on functional assignment was supplied to the analysis. We regard this as supporting the applicability of the FI functional categories in this setting (see response to point 4), while recognising that it is consistent with, rather than independent of, the assemblage patterns already described in Section 3.4. Yet, two limitations should be recorded. The change point for declining taxa as a group is poorly constrained (5-95% limits 0.390-1.010), and the proportion of pure and reliable taxa is moderate (0.43). We will hence report bootstrap limits alongside all point estimates rather than the estimates alone.
- Point 6: The basis for distinguishing six facies was not made sufficiently explicit, so we will describe it in more detail in the revised Methods. We accept the specific concern raised: a single similarity threshold does not yield exactly the six units as published, and we will state this explicitly in the revised Methods.
The facies were defined by cutting the dendrogram at a linkage distance of ~82, which yields five groups, and then retaining facies VI as a separate unit on sedimentological grounds. Facies VI (sample S04) contains 33.5 wt% siliciclastic material distributed across multiple grain-size fractions and has a CaCO₃ content of 43.3%, whereas siliciclastic contributions are near-absent elsewhere on the shelf. We interpret this sample as relict, potentially reflecting late Pleistocene to early Holocene deposits emplaced prior to full shelf flooding, and discuss it as such in Section 4.1. Merging it with facies V (as suggested by the five-group cutoff, see Fig. S3 in attached PDF) would group a compositionally and genetically distinct deposit with the foramol mud-supported carbonate sediments of the mid shelf. Applying a lower threshold, such that facies VI separates automatically, would instead subdivide facies II, which we do not consider meaningful either. The separation of facies VI is therefore an interpretive decision informed by composition rather than one following directly from the linkage distance, and we will state this explicitly.
We noted above, a lower threshold would separate two nearshore samples from the central shelf (S25, S32) from facies II. These both lie in the central sector at comparable distance from the mainland (5-7 km), and we do not mean to exclude that they represent a distinguishable nearshore sub-environment. We have however, decided to retain the coarser subdivision here, as this distinction does not affect the cross-shelf structure that is the subject of the study, and note it as a possible refinement. Interestingly, we noticed upon this inspection that the first and highest split in the dendrogram separates facies I and II from all mid- and outer-shelf samples without exception (11 versus 40 samples). This division is better resolved than any subsequent split, whereas the subdivision of the mid and outer shelf into facies III, IV and V occurs at much lower linkage distances and separates units that grade into one another. This structure corresponds directly to the interpretation presented in the manuscript, in which a sharp nearshore threshold gives way to a continuum of mixed carbonate production modes across the mid and outer shelf, and we will use the opportunity of a revised manuscript to present the classification in these terms rather than as six equally discrete units.
Ultimately, the facies scheme is corroborated by data deliberately excluded from its construction. Cluster analysis was performed exclusively on grain-size, carbonate and skeletal-component data, with foraminiferal assemblage composition withheld. PERMANOVA on Bray-Curtis dissimilarities of genus composition shows that the six sediment-based facies explain 54% of variation in foraminiferal composition (pseudo-F = 10.67, p = 0.0002, 4999 permutations), and indicator species analysis identifies sixteen genera significantly associated with particular facies or facies combinations, including Cibicidoides, Operculina and Amphistegina with facies III–VI (IndVal ≥ 0.97, p = 0.001) and Nonion with facies I, II, V and VI (IndVal = 0.98, p = 0.001). Facies defined solely on sedimentological criteria therefore predict assemblage composition strongly. We regard this as more informative for judging whether the units are meaningful than internal cluster validation indices, and report it in the attached PDF here (Table S2).
- 4. Yes, the transferability of the FI beyond the shallow reef settings for which it was developed requires explicit discussion, and we will consider expanding the discussion accordingly. The FI is applied here as a relative proxy for spatial variation in foraminiferal functional composition rather than as an absolute predictor of reef development potential, and the published threshold values (>4, 4-2, <2) are interpreted in that light. We will state this more prominently, as we recognise the current text does not sufficiently separate the two uses. We would also like to note that the FI is routinely calculated from total rather than exclusively living assemblages, including in the studies cited in this context. Fajemila et al., (2025), for example, stained their samples with Rose Bengal but counted both living and dead specimens for the FI, reporting that a large proportion of the symbiont-bearing taxa were dead and that living individuals were scarce at all stations. Barbosa et al., (2025) likewise used combined living and dead counts, consistent with earlier local reef studies. Fajemila et al. (2025) further demonstrate the application of the index in a turbid, nutrient-enriched and taxonomically diverse coastal setting (61 genera), which is closer to the conditions considered here than the oligotrophic reef environments for which the index was originally developed.
On the transferability of the functional groups themselves, our threshold analysis provides relevant evidence. TITAN, applied to genus composition along the TOC gradient without any information on functional assignment (Fig. S2), identifies three taxa as increasing with organic enrichment: Nonion, Ammonia and Elphidium, which correspond exactly to the stress-tolerant group of the FI. The remaining pure and reliable indicator taxa, including Amphistegina, Operculina, Parasorites and Calcarina, all decline along the same gradient. The functional assignments therefore behave as expected in this setting, which we regard as support for applying the index here, while noting that this is consistent with rather than fully independent of the assemblage patterns already described.
We also accept the point regarding taxa that may tolerate more degraded conditions than their functional assignment implies. In our dataset Calcarina and Neorotalia together account for 0.82% of 8,304 counted tests, and neither genus occurs in any of the eleven nearshore samples comprising facies I and II. Calcarinids are restricted to mid- and outer-shelf samples, where they reach a maximum of 7.8% relative abundance in a single sample and average below 1%. The bias identified by the Referee, whereby calcarinid abundance under moderate nutrient enrichment may cause the FI to overestimate conditions favourable to photozoan production, therefore cannot act on the low-FI nearshore samples where it would be consequential. We will state this more explicitly, together with the caveat that the index requires greater caution in settings where calcarinids are abundant, referring to Girard et al., (2022) on the application of foraminiferal indices in highly diverse assemblages and to Prazeres et al., (2020).
- 7. We agree that in the absence of pre- and post-construction data, the reduction of fine-grained fluvial input to the southern shelf following impoundment of the Jene Berang River cannot be demonstrated directly from our data, and we will present this as a hypothesis consistent with the observed contrast between the northern and southern sectors rather than as a confirmed explanation. We will also make clear that alternative contributions to this contrast (e.g., differences in catchment size and discharge, and in shelf geometry and retention between the sectors) cannot be separated from the effect of impoundment on the basis of the present dataset.
- 9. We thank the Referee for this point, which has led us to identify an inconsistency in the manuscript. Section 3.3.2 notes that the gypsum crystals may have formed during laboratory drying, whereas Section 4.1 interprets them as indicating reducing conditions in organic-rich substrates. These statements are not compatible, and we will resolve them in favour of the former: gypsum precipitated during drying cannot be used as a proxy for reducing conditions in situ, and the interpretation in Section 4.1 will be removed. We will retain the observation itself, on the grounds that the distribution of the crystals remains informative. Gypsum occurs only in the mud-rich nearshore samples (>95 wt% mud), which are also those with the highest TOC contents; its restriction to these samples reflects the abundance of sulphate-bearing interstitial porewater retained in fine-grained, organic-rich sediment rather than conditions at the seafloor. We will present it on that basis as a feature consistent with the depositional character of the nearshore facies rather than as evidence of pore-water chemistry. We note further that the gypsum contributes substantially to the component composition of the nearshore samples, reaching 49.2 wt% of the analysed fractions in facies I, and that these components were among the variables used in the cluster analysis defining the facies. Because the crystals are a precipitate formed during drying rather than a seafloor constituent, we have verified that the facies classification does not depend on them: excluding the gypsum and renormalising the remaining components leaves the primary division between nearshore facies I and II and all mid- and outer-shelf samples unchanged (11 versus 40 samples, no reassignments), and the six-facies scheme essentially unaltered. We will report the gypsum separately from the biogenic and terrigenous components in the revised Table 3 and Fig. 6, and state explicitly that it is excluded from compositional interpretation.
Again, we want to thank the Referee for the detailed and constructive assessment. The points raised have led us to re-examine several analyses, and the manuscript will be improved as a result: the constrained ordination provides a more defensible treatment of the assemblage-environment relationship, the threshold analyses give quantitative support to an interpretation previously argued qualitatively, and the classification criterion is now set out explicitly.
We are also conscious that incorporating all of the above in full would considerably lengthen the manuscript without proportionate benefit to the reader. Additions to the main text will therefore be kept brief and will largely replace existing text, while the TITAN and indicator species analyses and the full breakpoint estimates will be reported in the supplementary material. The addition of ordination scores to the cross-shelf profiles, their spatial interpolation, and the determination of microspheric to megalospheric ratios lie beyond the scope of the present paper and are better addressed in a follow-up study. We will be glad to implement these revisions should the Editor invite a revised version.
With thanks and kind regards,
Marleen Stuhr, on behalf of all co-authors
References:
Barbosa, C. F., François do Nascimento Silva, D., Bellot, A. C. F., Hallock, P., Araujo, S. L. de, Arantes, R. C. M., and Seoane, J. C. S.: An integrated approach to environmental health assessment of a coral reef ecosystem based upon Foraminifera, Journal of Foraminiferal Research, 55, 60–77, https://doi.org/10.61551/gsjfr.55.1.60, 2025.
Fajemila, O. T., Martínez-Colón, M., Olajide-Kayode, J. O., and Olayiwola, M. A.: The FORAM Index (FI) as an indicator of environmental perturbations in coral ecosystems of Hong Kong, China, Revue de Micropaléontologie, 89, 100860, https://doi.org/10.1016/j.revmic.2025.100860, 2025.
Girard, E. B., Estradivari, Ferse, S., Ambo-Rappe, R., Jompa, J., and Renema, W.: Dynamics of large benthic foraminiferal assemblages: A tool to foreshadow reef degradation?, Science of the Total Environment, 811, 151396, https://doi.org/10.1016/j.scitotenv.2021.151396, 2022.
Legendre, P. and Gallagher, E. D.: Ecologically meaningful transformations for ordination of species data, Oecologia, 129, 271–280, https://doi.org/10.1007/s004420100716, 2001.
Murray, J.: Ecology and applications of benthic foraminifera, School of Ocean and Earth Science, University of Southampton, 440 pp., 2006.
Prazeres, M., Martínez-Colón, M., and Hallock, P.: Foraminifera as bioindicators of water quality: The FoRAM Index revisited, Environmental Pollution, 257, https://doi.org/10.1016/j.envpol.2019.113612, 2020.
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- 1
This is a beautifully written manuscript. A few minor editorial comments are provided. Thoughts on the work and results presented are as follows:
Are Amphistegina and Operculina particularly well adapted to taking advantage of warm-water middle- and outer-shelf benthic environments that alternate seasonally, especially with respect to water transparency? Here are two factors supporting such an hypothesis?
The authors are welcome to ignore these thoughts, or to suggest these hypotheses if they wish, along with recommendations for future studies of a) whether Operculina are capable of becoming dormant under unfavorable environmental conditions or b) investigation of microspheric to macrospheric ratios.
Ross & Hallock, 2016: Journal of Foraminiferal Research, v. 46, no. 4, p. 358–368
Ross & Hallock, 2019: https://doi.org/10.1016/j.marmicro.2019.03.013