Water Column Respiration in the Yakima River Basin is Explained by Temperature, Nutrients and Suspended Solids

Laan, Maggi M.; Fulton, Stephanie G.; Garayburu-Caruso, Vanessa A.; Barnes, Morgan E.; Borton, Mikayla A.; Chen, Xingyuan; Farris, Yuliya; Forbes, Brieanne; Goldman, Amy E.; Grieger, Samantha; Hall Jr., Robert O.; Kaufman, Matthew H.; Lin, Xinming; Zionce, Erin L. M.; McKever, Sophia A.; Myers-Pigg, Allison; Otenburg, Opal; Pelly, Aaron C.; Ren, Huiying; Renteria, Lupita; Scheibe, Timothy D.; Son, Kyongho; Tagestad, Jerry; Torgeson, Joshua M.; Stegen, James C.

doi:https://doi.org/10.5194/egusphere-2025-1109

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https://doi.org/10.5194/egusphere-2025-1109

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21 Mar 2025

| 21 Mar 2025

Water Column Respiration in the Yakima River Basin is Explained by Temperature, Nutrients and Suspended Solids

Maggi M. Laan, Stephanie G. Fulton, Vanessa A. Garayburu-Caruso, Morgan E. Barnes, Mikayla A. Borton, Xingyuan Chen, Yuliya Farris, Brieanne Forbes, Amy E. Goldman, Samantha Grieger, Robert O. Hall Jr., Matthew H. Kaufman, Xinming Lin, Erin L. M. Zionce, Sophia A. McKever, Allison Myers-Pigg, Opal Otenburg, Aaron C. Pelly, Huiying Ren, Lupita Renteria, Timothy D. Scheibe, Kyongho Son, Jerry Tagestad, Joshua M. Torgeson, and James C. Stegen

Abstract. Understanding aquatic ecosystem metabolism involves the study of two key processes: carbon fixation via primary production and organic C mineralization as total ecosystem respiration (ER_tot). In streams and rivers, ER_tot includes respiration in the water column (ER_wc) and in the sediments (ER_sed). While literature surveys suggest that ER_sed is often a dominant contributor to ER_tot, recent studies indicate that the relative influence of sediment-associated processes versus water column processes can fluctuate along the river continuum. Still, a comprehensive understanding of the factors contributing to these shifts within basins and across stream orders is needed. Here we contribute to this need by measuring ER_wc and aqueous chemistry across 47 sites in the Yakima River basin, Washington, USA. We found that ER_wc rates varied throughout the basin during baseflow conditions, ranging from –7.38 to 0.36 g O₂ m⁻³ d⁻¹, and encompassed the entire range of ER_wc rates from previous work. Additionally, by comparing to ER_tot estimates for rivers across the contiguous United States, we suggest that the contribution of ER_wc rates to reach-scale ER_tot rates across the Yakima River basin are likely highly variable, but we did not test this directly. We did not observe clear increases in ER_wc moving down the stream network, and instead observed that ER_wc is locally controlled by temperature, dissolved organic carbon, total dissolved nitrogen, and total suspended solids, which explained 40 % of ER_wc variability across the basin. Our findings highlight the potential relevance of water column processes in aquatic ecosystem metabolism across the entire stream network and that these influences are likely not predictable simply via position in the stream network. Our results are generally congruent with previous work in terms of locally-influential variables, suggesting that the observed variability and suite of associated environmental factors influencing ER_wc are potentially transferable across basins.

How to cite. Laan, M. M., Fulton, S. G., Garayburu-Caruso, V. A., Barnes, M. E., Borton, M. A., Chen, X., Farris, Y., Forbes, B., Goldman, A. E., Grieger, S., Hall Jr., R. O., Kaufman, M. H., Lin, X., Zionce, E. L. M., McKever, S. A., Myers-Pigg, A., Otenburg, O., Pelly, A. C., Ren, H., Renteria, L., Scheibe, T. D., Son, K., Tagestad, J., Torgeson, J. M., and Stegen, J. C.: Water Column Respiration in the Yakima River Basin is Explained by Temperature, Nutrients and Suspended Solids, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2025-1109, 2025.

Received: 07 Mar 2025 – Discussion started: 21 Mar 2025

Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims made in the text, published maps, institutional affiliations, or any other geographical representation in this paper. While Copernicus Publications makes every effort to include appropriate place names, the final responsibility lies with the authors. Views expressed in the text are those of the authors and do not necessarily reflect the views of the publisher.

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Journal article(s) based on this preprint

28 Oct 2025

Water column respiration in the Yakima River basin is explained by temperature, nutrients, and suspended solids

Biogeosciences, 22, 6137–6152, https://doi.org/10.5194/bg-22-6137-2025,https://doi.org/10.5194/bg-22-6137-2025, 2025

Short summary

Interactive discussion

Status: closed

RC1:
'Comment on egusphere-2025-1109', Anonymous Referee #1, 09 Apr 2025

The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2025/egusphere-2025-1109/egusphere-2025-1109-RC1-supplement.pdf

Citation: https://doi.org/10.5194/egusphere-2025-1109-RC1
- AC1: 'Reply on RC1', James Stegen, 09 May 2025
  
  Please see attached file.
  
  Citation: https://doi.org/10.5194/egusphere-2025-1109-AC1
RC2:
'Comment on egusphere-2025-1109', Anonymous Referee #2, 18 Apr 2025

Laan et al. evaluated water column respiration (ERwc) and water quality parameters at 47 sites in the Yakima River Basin. The goal of the study was to identify factors driving changes in ERwc throughout the river network using LASSO regressions. In addition, the authors collected total and ERwc values from other studies in the continental US and the Amazon River basin. In general, the authors found no clear increase in ERwc over the course of the river network, and ERwc rates were influenced by local factors such as temperature, dissolved organic carbon, total dissolved nitrogen, and suspended sediment, rather than position in the stream network. In addition, the range of ERwc in the Yakima River Basin encompassed the entire range of ERwc that the authors found in the other studies, and ERwc contributed differentially to ERtot from the other studies.
This study is well-focused and addresses a question regarding the processes occurring in the water column of river networks. The research is thorough and directed, leaving little room for criticism from my perspective. I'll leave two comments here that I would have liked the authors to address in a little more detail to see if/how relevant this might be to their study.
One point I am thinking about is the discussion of the importance of water column and sediment processes to overall metabolism. In line 22 of the abstract and several times throughout the manuscript, the authors state that “the relative influence of sediment-associated processes versus water column processes can fluctuate along the river continuum.” In my opinion, an important factor in this statement is the greater influence of water column processes due to higher water levels when going downstream, which increases the areal influence of the water column. However, the authors compare volumetric rates, which do not consider the influence of water column height. Why did the authors decide to compare volumetric values? I'm not criticizing the approach, but I think the theory they are testing is largely based on this relationship. This could be a point that could (or should?) be included in the discussion.
The authors state in line 395 that “Nitrogen is a key nutrient for microbial growth and is often a limiting nutrient in freshwater rivers (Carroll, 2022).” Another common limiting factor is phosphorus. The authors use a variety of water and catchment parameters to perform the regression. However, phosphorus was not examined. Is there a reason for this? Is this not a potential important factor for ecosystem metabolism in the Yakima River Basin? Including this factor could improve the significance of the regression and significantly influence the conclusion that 40% can be predicted.

Minor comments:
Line 30: „…which explained 40% of ERwc variability across the basin.” You could add here the method you used to come to this number as you use LASSO regression, which has certain assumptions.
Line 216: Reference missing
Line 390: Could not find Ochs et al. 2010 in the reference list

Citation: https://doi.org/10.5194/egusphere-2025-1109-RC2
- AC2: 'Reply on RC2', James Stegen, 09 May 2025
  
  Please see attached file.
  
  Citation: https://doi.org/10.5194/egusphere-2025-1109-AC2

Interactive discussion

Status: closed

RC1:
'Comment on egusphere-2025-1109', Anonymous Referee #1, 09 Apr 2025

The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2025/egusphere-2025-1109/egusphere-2025-1109-RC1-supplement.pdf

Citation: https://doi.org/10.5194/egusphere-2025-1109-RC1
- AC1: 'Reply on RC1', James Stegen, 09 May 2025
  
  Please see attached file.
  
  Citation: https://doi.org/10.5194/egusphere-2025-1109-AC1
RC2:
'Comment on egusphere-2025-1109', Anonymous Referee #2, 18 Apr 2025

Laan et al. evaluated water column respiration (ERwc) and water quality parameters at 47 sites in the Yakima River Basin. The goal of the study was to identify factors driving changes in ERwc throughout the river network using LASSO regressions. In addition, the authors collected total and ERwc values from other studies in the continental US and the Amazon River basin. In general, the authors found no clear increase in ERwc over the course of the river network, and ERwc rates were influenced by local factors such as temperature, dissolved organic carbon, total dissolved nitrogen, and suspended sediment, rather than position in the stream network. In addition, the range of ERwc in the Yakima River Basin encompassed the entire range of ERwc that the authors found in the other studies, and ERwc contributed differentially to ERtot from the other studies.
This study is well-focused and addresses a question regarding the processes occurring in the water column of river networks. The research is thorough and directed, leaving little room for criticism from my perspective. I'll leave two comments here that I would have liked the authors to address in a little more detail to see if/how relevant this might be to their study.
One point I am thinking about is the discussion of the importance of water column and sediment processes to overall metabolism. In line 22 of the abstract and several times throughout the manuscript, the authors state that “the relative influence of sediment-associated processes versus water column processes can fluctuate along the river continuum.” In my opinion, an important factor in this statement is the greater influence of water column processes due to higher water levels when going downstream, which increases the areal influence of the water column. However, the authors compare volumetric rates, which do not consider the influence of water column height. Why did the authors decide to compare volumetric values? I'm not criticizing the approach, but I think the theory they are testing is largely based on this relationship. This could be a point that could (or should?) be included in the discussion.
The authors state in line 395 that “Nitrogen is a key nutrient for microbial growth and is often a limiting nutrient in freshwater rivers (Carroll, 2022).” Another common limiting factor is phosphorus. The authors use a variety of water and catchment parameters to perform the regression. However, phosphorus was not examined. Is there a reason for this? Is this not a potential important factor for ecosystem metabolism in the Yakima River Basin? Including this factor could improve the significance of the regression and significantly influence the conclusion that 40% can be predicted.

Minor comments:
Line 30: „…which explained 40% of ERwc variability across the basin.” You could add here the method you used to come to this number as you use LASSO regression, which has certain assumptions.
Line 216: Reference missing
Line 390: Could not find Ochs et al. 2010 in the reference list

Citation: https://doi.org/10.5194/egusphere-2025-1109-RC2
- AC2: 'Reply on RC2', James Stegen, 09 May 2025
  
  Please see attached file.
  
  Citation: https://doi.org/10.5194/egusphere-2025-1109-AC2

Peer review completion

AR: Author's response | RR: Referee report | ED: Editor decision | EF: Editorial file upload

ED: Reconsider after major revisions (12 May 2025) by Gabriel Singer

Dear authors,

Thank you for your insightful answers to the reviewer comments. Please proceed with your outlined actions and submit a revision of your manuscript. I regard this as a request for major revision, mostly motivated by my wish to reconsult the more critical one of the two reviews.

Please make sure that you adequately address the issue of water column ER to show different signs in its relationship with catchment area. This requires at least appropriate text, likely in the Discussion. If needed to actually make a compelling argument, partial regression plots or your analysis on potential collinearity effects could find their way into the Supplement, but I do not think that they deserve a more prominent place. I see no particular need to report on collinearity issues in a detailed manner per se, but I do find it disturbing to see signs of relationships change without further explanation.

I agree with the reviewer´s suggestion to consider not using positive ER data or setting those values to zero. Yes, these are data, but unless you have a compelling ecological reason for the observed oxygen increases, I would rather think of these as faulty measurements. I can see that data considered as "faulty" now may become useful in the future, however. A compromise approach could be to report these data in overview tables and data tables, but for plots and data analysis you might want to set them to zero as - at the moment - you simply lack the framework to explain them. Anyways, please provide good reasoning for your final decision in the response letter, and also report about these values and how you dealt with them in the revised manuscript.

Regards, Gabriel

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AR by James Stegen on behalf of the Authors (28 May 2025) Author's response Author's tracked changes

EF by Mario Ebel (05 Jun 2025) Manuscript

ED: Referee Nomination & Report Request started (05 Jun 2025) by Gabriel Singer

RR by Anonymous Referee #2 (17 Jun 2025)

RR by Anonymous Referee #1 (18 Jun 2025)

Suggestions for revision or reasons for rejection

Second review of “Water Column Respiration in the Yakima River Basin is Explained by Temperature, Nutrients and Suspended Solids” by Laan et al.

The revision addresses the main points that I raised in my review of the first submission of this paper and I appreciate the work the authors have put in to clarify and improve the manuscript. I have only one more concern:
I do not agree with line 374 and 376 where the authors state that the correlation between ERWC and total drainage area is too weak to confirm their hypothesis, i.e. ERWC fastens downstream. Because I actually see a descent relationship of ERWC with total drainage area (Figure 3b). This is underlined by a Pearson correlation coefficient of -0.39 and a p-value below 0.05 (Figure S5). In fact, the relationship seems to be curvilinear saturating and therefore the Pearson correlation coefficient, which specifically measures linear correlation and does not capture non-linear relationships such as those represented in Figure 3b, might even underestimate the strength of the relationship. Such non-linear relationships are also visible in Figure 4d and to some extent in Figure 4a. A log transformation of the predictors instead of a cube root transformation might “linearize” those relationships. I apologize for not pointing this out already in the first review. Having said that, I agree with the authors’ general conclusion “that localized factors, not upstream conditions or drainage area, provide primary controls over ERWC”, as well as I appreciate the added more detailed discussion starting in line 414, still, I think in general ERWC seems to accelerate towards downstream locations, despite strong local controls.

Referee Report: PDF

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ED: Publish subject to minor revisions (review by editor) (20 Jun 2025) by Gabriel Singer

AR by James Stegen on behalf of the Authors (27 Jun 2025) Author's response Author's tracked changes Manuscript

ED: Publish as is (10 Jul 2025) by Gabriel Singer

AR by James Stegen on behalf of the Authors (17 Jul 2025) Manuscript

Journal article(s) based on this preprint

28 Oct 2025

Water column respiration in the Yakima River basin is explained by temperature, nutrients, and suspended solids

Biogeosciences, 22, 6137–6152, https://doi.org/10.5194/bg-22-6137-2025,https://doi.org/10.5194/bg-22-6137-2025, 2025

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Respiration is a process that combines carbon and oxygen to generate energy for living organisms. Within a river, respiration in sediments and water have variable contributions to respiration of the whole river system. Contrary to conventional wisdom, we found that water column respiration did not increase systematically moving from small streams to big rivers. Instead, it was locally influenced by temperature, nutrients and suspended solids.


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