the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 04 Dec 2025
Microbial role in CO2 fluxes along the river-estuary continuum in a rapidly uplifting catchment of eastern Taiwan
Abstract. The contribution of river metabolisms to carbon cycling is an essential issue, but not well examined in the catchment susceptible to the modulation of active tectonics. This study aims to quantify the rates of autotrophy and heterotrophy, and to identify the community compositions and potential members involved in these microbial processes in the Beinan River in eastern Taiwan. To address this, river water samples were collected in both the wet and dry seasons for incubations amended with 13C-labeled dissolved carbon dioxide and amino acids. The analyses revealed a general pattern pointing to the higher rates in the wet season than in the dry season, and for heterotrophy than for autotrophy. The obtained rates were further scaled up, resulting in the catchment-scale CO2 evasion of ~ 107 mole yr-1, a range constituting several percent of the CO2 flux derived from pyrite-induced weathering, oxidation of petrogenic carbon, and the river-air exchange. The community compositions generally varied with season for most upstream sites and with more abundant sulfur or nitrogen metabolizers in the wet season, as opposed to more abundant phototrophs or heterotrophs in the dry season. This study highlights the complex and dynamic nature of river metabolisms that contribute to carbon evasion in oligotrophic mountainous systems prone to the impacts of rapid uplift and erosion.
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Status: final response (author comments only)
- RC1: 'Comment on egusphere-2025-5904', Anonymous Referee #1, 20 Feb 2026
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RC2: 'Comment on egusphere-2025-5904', Anonymous Referee #2, 16 Mar 2026
The manuscript describes the role of microbial C assimilation and respiration along a Taiwanese river continuum.
The experimental work was conducted at seven timepoints for five locations. For four of them, phototrophy and autotrophy were determined using 13-DIC and two of these also quantified heterotrophy using two 13C-labelled amino acids (1 x summer, 1 x winter). These detailed 13C studies are complemented by environmental parameters and geochemical analyses at all campaigns and 16S rRNA analyses at five. The combination of 13C-labelling and genomic analyses represents highly complementary methodology that can bring new insight into the contribution of the riverine microbial community to CO2 flux from such a system.
Major concerns
The manuscript lacks hypotheses and the introduction and later discussion would benefit from, especially to interlink the different datasets.
The labelling design for the DIC aims to enrich to ~5% of the DIC pool, which is consistent with wider stable isotope probing approaches to provide sufficient enrichment while minimising perturbation of the system by excess increase of the pool. However, the extent of addition for the amino acids does not follow this. A final concentration of 50 µM when the DOC concentration (which is made up of much more than just free amino acids) is between 20-80 µM represents a significant increase in the pool size. While it is acknowledged that rates determined may be stimulated as a result (line 139-140) and I appreciate that rates were still often below detection limits, this very important caveat is lost later in the manuscript. This is especially important to consider when these values are then scaled up to the catchment level but could hugely overestimate actual metabolic fluxes from organic pools. These limitations need to be made much clearer both in the methodology and when you upscale these values to a catchment level.
Furthermore, there is no consideration of co-added N for the amino acids (C:N 2:1 glycine; 6:1 leucine) which may also influence the diverging processing of the two amino acids (i.e. if being utilised for N and C is largely being respired, glycine is a much more efficient resource to use than leucine). How the underlying biochemistry may control the observed rates is severely lacking, but important rationale given you select leucine to represent a conservative estimate of heterotrophic activity without any rationale other than it is lower (line 221-222). At points (e.g. Line 444-447), it is implied there is direct uptake but there is no evidence to support this. Finally have the authors considered that only one C position was labelled for both amino acid forms?
Minor comments:
The abstract needs to expand briefly on the rationale behind this work.
Line 11: “issue” is vague – is problem or unknown more precise?
Line 15: higher rates of what? Both hetero and autotrophy? Add some values / relative differences of these rates into the abstract.
Line 72: states that the Beinan River has some of the highest sediment exports and weathering rates in Taiwan. It would be beneficial to put this on a larger context beyond country-specific for an international journal.
Line 74: why were leucine and glycine selected?
Line 154: Should be ICP-MS
Line 178: Formatting of equation is strange
Line 183-184: Why was the instream δ13C not measured? This is an important end member.
Line 250: TSM should be defined at first time of use in main text (only defined in footnote of subsequent table).
Line 254: “smaller” to indicate more negative delta values should be replaced by terminology like “more depleted” as is used in other areas of the MS.
Line 255-256: This states that ammonium was higher in the wet season than the dry season however this was not significant based on Table 2 – please clarify. If it is the case it is as some sites, they could be bold in the table rather than just the heading to provide these site-specific differences.
Figure 3: due to some very high values, it is very difficult to see the low values in panel b and c; in caption state replication level and what the error bars represent (standard error of the mean? Standard deviation?). Also need to state limit of detection.
The statistical analyses need to be improved as only applied to river chemistry data.
Line 356: You call this organic matter degradation – but you have only looked at final mineralisation step of these processes. Depolymerisation is generally considered the rate limiting step, so the fluxes quantified only reflect one, generally very rapid, stage of organic matter degradation.
Line 359-370: There are a lot of assumptions or suggestions here just for ammonium concentrations which are point measurements only that is limited to determine in situ production especially when high additions of organic nitrogen may influence ammonification rates. The production rates are more potential rather than true so this caveat must be extended to residence times.
Line 401-410: were there any links with the community observed i.e. riverine vs. soil? More primary producers downstream where input from surrounding catchment is relatively less and more processed/recalcitrant therefore rely more on primary producers? Currently only consider the nutrients as a control here but community may also reflect this and provide additional support to this suggestion.
Citation: https://doi.org/10.5194/egusphere-2025-5904-RC2
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- 1
Review Biogeosciences 2025-5904
Microbial role in CO2 fluxes along the river-estuary continuum in a rapidly uplifting catchment of eastern Taiwan.
Chen et al.
This manuscript describes the role of microbial CO2 fluxes along a river-estuary continuum in Taiwan. The specific situation with an uplifting catchment because of active tectonics is identified as a unique feature of this catchment study.
This study can reduce the bias towards river continuum studies in low altitude; temperate catchment as opposed to mountainous catchments. However, apart from better data coverage of CO2 exchange from mountainous catchments it is important to stress that insights this study, performed in a unique tectonic situation and related dynamic turbid river systems can bring new insights to the current field of river metabolism studies.
The study aims to disentangle assimilation rates and respiration rates of different metabolisms with 13C labelling techniques using DIC and amino acids. Furthermore, microbial community compositions were determined based on 16S rRNA gene tags. Sampling took place at different sampling sites in the Beinan river system. Specific metabolic rates were measured during four of seven field campaigns.
The results of this study give an indication of the size of the yearly CO2 evasion of the whole catchment and show seasonal shifts in the dominant metabolism in upstream systems waters between the wet and dry season.
General comments
This is a nice and thorough study on metabolic rates in dynamic turbid river systems in a tectonic active area. The use of isotopic labelling of DIC and amino acids in combination with environmental parameter measured in field campaigns and characterisation of the microbial community composition is an impressive achievement. Although at some point it is questionable if all this information in one paper is contributing to the communication of the main message and findings (e.g. are alpha diversity, Shannon index beta diversity needed?). The storyline can be strengthened in the intro and discussion if more focussed hypothesis are formulated.
The objective of this study was to get insights in the role of microbial CO2 fluxes at catchment scale and disentangling the metabolic processes of autotrophic and heterotrophic CO2 exchange in these understudied dynamic mountainous river systems in contrast to the more stable low-land catchments. The sampling strategy and major findings reported (seasonal shifts in metabolic wet-vs dry), although nice, do not seem to fully comply with my view of a study major strength to determine the effect of event-based flushes of groundwater and sediments on CO2 fluxes.
Furthermore, while Wang et al 2024 identified the effects of hot springs on the enrichment of waters with bicarbonate in the same sample locations in the tectonic active Beinan catchment this is not mentioned in this study. Is this not relevant in the total CO2 flux or is it included?
What about redox situation in the streams influenced by tectonics? Is CH4 exchange not relevant?
Specific comments
Abstract line 18 “several percent” please be more specific here. 107mol yr-1 from microbial origin vs annual total emission across the catchment 2,6 .109 ? (Line 295)
Line 38 landscape controlled or is it more topographically controlled?
Line 68 term “individual metabolisms” needs more clarification.
Lines 59-61 The information in this sentence is essential why this study in a rapid uplifting area is so different from the dominant body of literature in this field which is performed on the cratonic continent. While this relation between tectonics and torrential precipitation is a probably obvious for the authors this is not evident for everyone. It would help the storyline if this is relation between tectonics and dynamic, turbid high energy river systems is more explicit.
The expected deviations from the general bentic and hyporheic processes due to the turbid and dynamic river systems can be formulated more explicitely in hypothesis which will give ther reader more guidelines for interpretation in the result section.
Line 107-108, The selection of the 5 sample locations along the Beinan rver and tributaries is not explained. Which criteria were used to determine these sample sites? Likewise no argumentation is provided for the selection of sample moments/ timing. As the dynamic nature of the Beinan river is a part of the research objective the regular bi-monthly sampling scheme is surprising. One would expect a focus on events ( hot moments) and baseline moments.
Line 115. The use of cellulose membranes is not common practice and strongly discouraged in research on carbon dynamics due to the risks of contamination. Especially for DOC determination. The same is true for the use of polypropylene sample containers (risk of DOC contamination).
Line 386: is this influenced or correlation based?
Technical corrections
Figure 3 needs a more elaborate figure caption.