the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 17 Dec 2025
Basin-scale connections between reach-scale sediment respiration and point-scale organic-matter decomposition
Abstract. Stream and river ecosystems play a central role in the movement and decomposition of particulate organic matter, serving as a conduit between terrestrial hillslopes and coastal environments. Microbial-catalyzed decomposition generates simpler organic molecules that fuel respiration, often in the sediments of these ecosystems. However, the degree of connection between sediment-associated respiration (ERsed) and organic-matter decomposition remains poorly understood. How that relationship compares to decomposition’s relationship with whole ecosystem (ERtot) and water column (ERwc) respiration is also not clear. We examined the link between particulate organic matter decomposition—using cellulose-based cotton strips as a standardized substrate—and all three components of respiration across 48 sites in the environmentally diverse Yakima River Basin (Washington State, USA). We hypothesized that decomposition within sediments would be most strongly related to ERsed, but decomposition rates were more closely associated with ERtot, with little connection to ERsed or ERwc. This suggests that particulate organic matter decomposition within stream/river sediments reflects integrated system respiration rather than processes confined to sediments or the water column alone. Further, across the basin, decomposition rates nearly spanned the previously reported global range for streams and rivers and were best explained by total dissolved nitrogen (TDN), sediment grain size, and aridity of the upstream drainage area. These results highlight the strong influence of land cover and basin-scale biophysical variation on sediment-associated decomposition processes and indicate that mechanistic models of organic matter decomposition in streams/rivers should account for coupled sediment–water–land interactions.
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Status: open (until 17 Feb 2026)
- RC1: 'Comment on egusphere-2025-6084', Arturo Elosegi, 27 Jan 2026 reply
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RC2: 'Comment on egusphere-2025-6084', Anonymous Referee #2, 30 Jan 2026
reply
This MS describes the results of a comparison of cotton strip decomposition rates within the riverbed with whole ecosystem and water column respiration rates measured at the same set of sites across the Yakima River Basin. The authors found that cotton strip decomposition rates were more closely related with whole ecosystem respiration than they were with an estimate of sediment-associated respiration calculated as the difference between measured whole ecosystem and water column respiration rates. The MS is generally well-written and will make a useful contribution to the literature on the relative contribution of different elements to overall river ecosystem respiration.
My main concern with the MS relates to the use of the term sediment-associated respiration (ERsed). My initial perception was that this parameter represents respiration within the sediment beneath the riverbed, when in fact it represents respiration both within and on the riverbed. I think this needs to be emphasized early in the MS so readers are clear about what this parameter really represents. Importantly, a large component of ERsed may be attributed to autotrophic respiration from periphyton and aquatic plants growing on the riverbed and not associated with heterotrophic carbon decomposition. Therefore, there is less expectation that there should be a strong link between ERsed and cotton strip decomposition rates within the bed.
It would also be useful for the authors to emphasize what other elements might be included in the ERsed parameter, since it was not measured directly. For example, has the potential impact of low DO groundwater inputs on whole ecosystem respiration been accounted for? Could chemical oxygen demand contribute to some of the ERsed?
I’m also concerned about whether the overall weak relationships between point-scale cotton strip decomposition and reach scale measures of respiration primarily reflect differences in the scale of measurement rather than poor linkage between different components of the river ecosystem. I’d like to see some evidence in the MS that 4 replicate measures of cotton strip decomposition are sufficient to represent small-scale variability in decomposition at a reach scale. How did within-reach variability compare with between-reach variability in cotton strip decomposition? At the very least, this issue deserves some attention in the discussion.
I note that cotton strip decay rates were weakly correlated with both ERtot (R2 = 0.29) and ERsed (R2 = 0.22). Does the slightly stronger correlation with ERtot really justify the key conclusion of the MS that ‘decomposition is the result of integrated processes occurring across the sediment-water continuum’? Presumably there is a strong correlation between ERtot and ERsed – is this correlation presented in the MS?
Specific comments:
Lines 220-228: I agree with the comment made by Arturo Elosegi that this part of the MS is very speculative. A measure of algal biofilms on the cotton strips may or may not be related to the autotrophic respiration component of ERsed.
Line 402: remove ‘++’ from within the title of this reference
Line 570: ...shown WITH solid black lines….
Citation: https://doi.org/10.5194/egusphere-2025-6084-RC2
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General
As papers on river ecosystem functioning are booming, the exact meaning and the interrelation of different "ecosystem processes" are becoming a hot issue. The paper by Stegen et al. makes an interesting contribution to the field. They measured cotton-strip decomposition at 48 sites across the Yakima River Basin (YRB) and compared the results to a paper (Garayburu-Caruso et al., 2025), performed at the same sites, that measured whole-ecosystem and water-column respiration, and inferred sediment respiration. Stegen et al. found that cotton-strip decomposition is more tightly linked to total (whole-ecosystem) than to sediment respiration, an unexpected outcome. They also found, unsurprisingly, a very high variability in cotton decomposition across the YRB.
Overall, the paper makes a nice contribution to the field. The methods are sound, results interesting and the discussion mostly accurate. There are, however, some small issues that should be considered before publication.
Specific comments
The title is a bit misleading. The paper shows point-scale organic matter decomposition to be more tightly linked to total than to sediment respiration but does not clearly address (or not in sufficient detail) the basin-scale connection between both processes. The authors should find a title that better reflects their findings.
L15-16. Is "microbial-catalyzed" a correct expression? Better rewrite as "microbially-catalyzed" or as "microbe-catalyzed".
L24-26. It is hard to imagine a mechanism for this relationship between cotton decomposition and whole-ecosystem (but not sediment) respiration.
L51. The accumulation or release of carbon is not a measure of heterotrophicity. A heterotrophic ecosystem is one that produces more organic carbon than it mineralizes, which is not exactly the same thing. Please, rephrase.
L88-96. Please, give more details about the Garayburu-Caruso paper. Explain the estimated length of the reaches for which whole-ecosystem respiration was calculated and whether this length could create autocorrelation issues between neighboring sites.
L100-101. ERsed was calculated from the difference between ERtot and ERwc. This will, thus, include respiration in the hyporheos, on the sediment surface and by submerged plants, but also any non-respiratory process that consumes oxygen, such as oxydation of metals in upwelling groundwaters. The authors should be more cautious when linking oxygen consumption and respiration and specifically state that there can be multiple non-respiratory processes consuming oxygen across a basin. It would also be nice to see this issue in the discussion.
L106. Strips were deployed on the surface of the riverbed and covered with a brick. This makes them much more likely to correlate with processes occurring at the water column than if they had been deployed deeper into the sediments. Authors should at least discuss the effects of their methodological choice.
L113. 7th-order rivers can have very deep sections. The authors seem to have deployed all their strips on wadeable parts of the river. It would be good to at least give some caveats about this reflecting "true" decomposition across the river, and better to discuss how this could have affected results.
L116. The four replicated strips were deployed next to each other, which is very convenient to deploy and recover them, but not at all when we want to capture sediment decomposition rate of a reach that for whole-ecosystem respiration can be hundreds to thousends metres long. The literature has shown breakdown rates to differ markedly from consecutive riffles, even more so between riffles and pools, and even more between substrata deployed on the sediment, as is the case here, and in the sediment. This should be mentioned as a caveat on the methodology and discussed later on.
L139-146. It would be interesting to compute respiration in degree days also.
L14. "....rates, a..." replace point by comma.
L169. The variation in decomposition rate is surprising given that data come from a single basin? Not so much. Benthic processes are extremely patchy. But this also draws the question whether 4 strips are enough to characterize the decomposition of a reach whose metabolism has been characterized by the open-channel method, which typically has a spatial extent of hundreds to thousands of metres.
L173-174. Delete. Climatically diverse basins are interesting, but any other diversity factor (geologic, topographic, human...) can result in interesting information.
L178-181. High decomposition rates in summer have been often reported. Nevertheless, it is unclear whether these derive from high temperatures, as even when correcting by degree days the decomposition tends to be higher in summer. It is also unclear these high rates are a consequence of slow flows, as slow flows can also reduce the exchange of nutrients etc. between water and OM, thus slowing decomposition. In fact, comparison between mesohabitats systematically show decomposition to be faster on riffles than on runs or pools. Therefore, the high summer decomposition rate more probably is a consequence of the longer time of stability since the last disrupting floods, which allows developing the biological communities, or the less diluted waters, which enhance nutrient concentration. Please, discuss in greater detail.
L182-185. Not so surprising. This simply shows that in the YRB other factors (nutrients? sediment biota? fine sediment accumulation? toxics?) override the effects of temperature, what also has been reported in many papers.
L215-217. I cannot agree. From the description it seems the strips were located on top of the sediments, and below one brick. This is not exactly hyporheic. Other authors have measured decomposition within the sediments and found it to greatly differ from that on the surface.
L220-228. Very speculative and will depend ultimately on the contribution of epilithon to the total sediment respiration, which can be highly variable depending on the extent and activity of the hyporheic zone.
L256-259. That would affect Rsed, but not K values, as the surface for microbial attachment of cotton strips would be independent of the sediment. What about other factors? Aridity usually results in higher temporal variability in flows, lower nutrient concentration during baseflow, less fungal inoculum, higher deposition of fine sediments, which cloggs intestices...
L273-275. Not convincing. These authors show that a large fraction of respiration comes from the degradation of labile carbon produced by photosynthetic organisms, but this should have no effect on cotton decomposition, unless you are talking about the priming effect?