Articles | Volume 18, issue 16
https://doi.org/10.5194/bg-18-4773-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-18-4773-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
24 Aug 2021
Research article |
| 24 Aug 2021
| 24 Aug 2021
Disturbance triggers non-linear microbe–environment feedbacks
California Lutheran University, Biology Department, Thousand Oaks, CA, USA
Sarah J. Fansler
Pacific Northwest National Laboratory, Ecosystem Science Team, Richland, WA, USA
Rosalie K. Chu
Environmental Molecular Sciences Laboratory, Richland, WA, USA
Robert E. Danczak
Pacific Northwest National Laboratory, Ecosystem Science Team, Richland, WA, USA
Vanessa A. Garayburu-Caruso
Pacific Northwest National Laboratory, Ecosystem Science Team, Richland, WA, USA
Lupita Renteria
Pacific Northwest National Laboratory, Ecosystem Science Team, Richland, WA, USA
Hyun-Seob Song
University of Nebraska-Lincoln, Biological Systems Engineering, Lincoln, NE, USA
Jason Toyoda
Environmental Molecular Sciences Laboratory, Richland, WA, USA
Jacqueline Hager
Oregon State University, Chemical, Biological & Environmental Engineering, Corvallis, OR, USA
James C. Stegen
Pacific Northwest National Laboratory, Ecosystem Science Team, Richland, WA, USA
Related authors
No articles found.
Morgan E. Barnes, J. Alan Roebuck Jr., Samantha Grieger, Paul J. Aronstein, Vanessa A. Garayburu-Caruso, Kathleen Munson, Robert P. Young, Kevin D. Bladon, John D. Bailey, Emily B. Graham, Lupita Renteria, Peggy A. O'Day, Timothy D. Scheibe, and Allison N. Myers-Pigg
Biogeosciences, 22, 4491–4505, https://doi.org/10.5194/bg-22-4491-2025, https://doi.org/10.5194/bg-22-4491-2025, 2025
Short summary
Short summary
Wildfires impact nutrient cycles on land and in water. We used burning experiments to understand the types of phosphorous (P), an essential nutrient, that might be released to the environment after different types of fires. We found the amount of P moving through the environment post-fire is dependent on the type of vegetation and degree of burning, which may influence when and where this material is processed or stored.
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
EGUsphere, https://doi.org/10.5194/egusphere-2025-1109, https://doi.org/10.5194/egusphere-2025-1109, 2025
Short summary
Short summary
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.
James Stegen, Amy J. Burgin, Michelle H. Busch, Joshua B. Fisher, Joshua Ladau, Jenna Abrahamson, Lauren Kinsman-Costello, Li Li, Xingyuan Chen, Thibault Datry, Nate McDowell, Corianne Tatariw, Anna Braswell, Jillian M. Deines, Julia A. Guimond, Peter Regier, Kenton Rod, Edward K. P. Bam, Etienne Fluet-Chouinard, Inke Forbrich, Kristin L. Jaeger, Teri O'Meara, Tim Scheibe, Erin Seybold, Jon N. Sweetman, Jianqiu Zheng, Daniel C. Allen, Elizabeth Herndon, Beth A. Middleton, Scott Painter, Kevin Roche, Julianne Scamardo, Ross Vander Vorste, Kristin Boye, Ellen Wohl, Margaret Zimmer, Kelly Hondula, Maggi Laan, Anna Marshall, and Kaizad F. Patel
Biogeosciences, 22, 995–1034, https://doi.org/10.5194/bg-22-995-2025, https://doi.org/10.5194/bg-22-995-2025, 2025
Short summary
Short summary
The loss and gain of surface water (variable inundation) are common processes across Earth. Global change shifts variable inundation dynamics, highlighting a need for unified understanding that transcends individual variably inundated ecosystems (VIEs). We review the literature, highlight challenges, and emphasize opportunities to generate transferable knowledge by viewing VIEs through a common lens. We aim to inspire the emergence of a cross-VIE community based on a proposed continuum approach.
Robert E. Danczak, Amy E. Goldman, Mikayla A. Borton, Rosalie K. Chu, Jason G. Toyoda, Vanessa A. Garayburu-Caruso, Emily B. Graham, Joseph W. Morad, Lupita Renteria, Jacqueline R. Hager, Shai Arnon, Scott Brooks, Edo Bar-Zeev, Michael Jones, Nikki Jones, Jorg Lewandowski, Christof Meile, Birgit M. Muller, John Schalles, Hanna Schulz, Adam Ward, and James C. Stegen
EGUsphere, https://doi.org/10.1101/2024.01.10.575030, https://doi.org/10.1101/2024.01.10.575030, 2025
Preprint archived
Short summary
Short summary
As dissolved organic matter (DOM) is transported from land to the ocean through rivers, it interacts with the environment and some is converted to CO2. We used high-resolution carbon analysis to show that DOM from seven rivers exhibited ecological patterns particular to the corresponding river. These results indicate that local processes play an outsized role in shaping DOM. By understanding these interactions across environments, we can predict DOM across spatial scales or under perturbations.
Katherine A. Muller, Peishi Jiang, Glenn Hammond, Tasneem Ahmadullah, Hyun-Seob Song, Ravi Kukkadapu, Nicholas Ward, Madison Bowe, Rosalie K. Chu, Qian Zhao, Vanessa A. Garayburu-Caruso, Alan Roebuck, and Xingyuan Chen
Geosci. Model Dev., 17, 8955–8968, https://doi.org/10.5194/gmd-17-8955-2024, https://doi.org/10.5194/gmd-17-8955-2024, 2024
Short summary
Short summary
The new Lambda-PFLOTRAN workflow incorporates organic matter chemistry into reaction networks to simulate aerobic respiration and biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow in a Jupyter notebook interface that digests raw organic matter chemistry data via Fourier transform ion cyclotron resonance mass spectrometry, develops a representative reaction network, and completes a biogeochemical simulation with the open-source, parallel-reactive-flow, and transport code PFLOTRAN.
William Kew, Allison Myers-Pigg, Christine H. Chang, Sean M. Colby, Josie Eder, Malak M. Tfaily, Jeffrey Hawkes, Rosalie K. Chu, and James C. Stegen
Biogeosciences, 21, 4665–4679, https://doi.org/10.5194/bg-21-4665-2024, https://doi.org/10.5194/bg-21-4665-2024, 2024
Short summary
Short summary
Natural organic matter (NOM) is often studied via Fourier transform mass spectrometry (FTMS), which identifies organic molecules as mass spectra peaks. The intensity of peaks is data that is often discarded due to technical concerns. We review the theory behind these concerns and show they are supported empirically. However, simulations show that ecological analyses of NOM data that include FTMS peak intensities are often valid. This opens a path for robust use of FTMS peak intensities for NOM.
Stephanie G. Fulton, Morgan Barnes, Mikayla A. Borton, Xingyuan Chen, Yuliya Farris, Brieanne Forbes, Vanessa A. Garayburu-Caruso, Amy E. Goldman, Samantha Grieger, Robert Hall Jr., Matthew H. Kaufman, Xinming Lin, Erin McCann, Sophia A. McKever, Allison Myers-Pigg, Opal C. Otenburg, Aaron C. Pelly, Huiying Ren, Lupita Renteria, Timothy D. Scheibe, Kyongho Son, Jerry Tagestad, Joshua M. Torgeson, and James C. Stegen
EGUsphere, https://doi.org/10.5194/egusphere-2023-3038, https://doi.org/10.5194/egusphere-2023-3038, 2024
Preprint archived
Short summary
Short summary
This research examines oxygen use in rivers, which is central to the carbon cycle and water quality. The study focused on an environmentally diverse river basin in the western United States and found that oxygen use in river water was very slow and influenced by factors like water temperature and concentrations of nutrients and carbon in the water. Results suggest that in the study system, most of the oxygen use occurs via mechanisms directly or indirectly associated with riverbed sediments.
Emily B. Graham, Hyun-Seob Song, Samantha Grieger, Vanessa A. Garayburu-Caruso, James C. Stegen, Kevin D. Bladon, and Allison N. Myers-Pigg
Biogeosciences, 20, 3449–3457, https://doi.org/10.5194/bg-20-3449-2023, https://doi.org/10.5194/bg-20-3449-2023, 2023
Short summary
Short summary
Intensifying wildfires are increasing pyrogenic organic matter (PyOM) production and its impact on water quality. Recent work indicates that PyOM may have a greater impact on aquatic biogeochemistry than previously assumed, driven by higher bioavailability. We provide a full assessment of the potential bioavailability of PyOM across its chemical spectrum. We indicate that PyOM can be actively transformed within the river corridor and, therefore, may be a growing source of riverine C emissions.
James C. Stegen, Vanessa A. Garayburu-Caruso, Robert E. Danczak, Amy E. Goldman, Lupita Renteria, Joshua M. Torgeson, and Jacqueline Hager
Biogeosciences, 20, 2857–2867, https://doi.org/10.5194/bg-20-2857-2023, https://doi.org/10.5194/bg-20-2857-2023, 2023
Short summary
Short summary
Chemical reactions in river sediments influence how clean the water is and how much greenhouse gas comes out of a river. Our study investigates why some sediments have higher rates of chemical reactions than others. We find that to achieve high rates, sediments need to have two things: only a few different kinds of molecules, but a lot of them. This result spans about 80 rivers such that it could be a general rule, helpful for predicting the future of rivers and our planet.
Heewon Jung, Hyun-Seob Song, and Christof Meile
Geosci. Model Dev., 16, 1683–1696, https://doi.org/10.5194/gmd-16-1683-2023, https://doi.org/10.5194/gmd-16-1683-2023, 2023
Short summary
Short summary
Microbial activity responsible for many chemical transformations depends on environmental conditions. These can vary locally, e.g., between poorly connected pores in porous media. We present a modeling framework that resolves such small spatial scales explicitly, accounts for feedback between transport and biogeochemical conditions, and can integrate state-of-the-art representations of microbes in a computationally efficient way, making it broadly applicable in science and engineering use cases.
James C. Stegen, Sarah J. Fansler, Malak M. Tfaily, Vanessa A. Garayburu-Caruso, Amy E. Goldman, Robert E. Danczak, Rosalie K. Chu, Lupita Renteria, Jerry Tagestad, and Jason Toyoda
Biogeosciences, 19, 3099–3110, https://doi.org/10.5194/bg-19-3099-2022, https://doi.org/10.5194/bg-19-3099-2022, 2022
Short summary
Short summary
Rivers are vital to Earth, and in rivers, organic matter (OM) is an energy source for microbes that make greenhouse gas and remove contaminants. Predicting Earth’s future requires understanding how and why river OM is transformed. Our results help meet this need. We found that the processes influencing OM transformations diverge between river water and riverbed sediments. This can be used to build new models for predicting the future of rivers and, in turn, the Earth system.
Cited articles
Arntzen, E.: Effects of fluctuating river flow on groundwater/surface water mixing in the hyporheic zone of a regulated, large cobble bed river – River Research and Applications – Wiley Online Library, https://doi.org/10.1002/rra.947, 2006.
Arora, B., Briggs, M. A., Zarnetske, J., Stegen, J. C.,
Gomez-Velez, J., Dwivedi, D., and Steefel, C. I.: Hot Spots and Hot
Moments in the Critical Zone: Identification of and Incorporation
into Reactive Transport Models, in: Biogeochemistry of the Critical
Zone, Wymore, A., Yang, W., Silver, W., McDowell, B., and Chorover, J.
(Eds.), Springer-Nature, in press, 2020.
Baldwin, D. S. and Mitchell, A. M.: The effects of drying and re-flooding on the sediment and soil nutrient dynamics of lowland river–floodplain systems: a synthesis, Regul. River., 16, 457–467, https://doi.org/10.1002/1099-1646(200009/10)16:5<457::AID-RRR597>3.0.CO;2-B, 2000.
Barnard, R. L., Osborne, C. A., and Firestone, M. K.: Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate, ISME J., 9, 946–957, https://doi.org/10.1038/ismej.2014.192, 2015.
Bartelme, R. P., Custer, J. M., Dupont, C. L., Espinoza, J. L., Torralba, M., Khalili, B., and Carini, P.: Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation, mSphere, 5, e00024-20, https://doi.org/10.1128/mSphere.00024-20, 2020.
Behrens, S., Kappler, A., and Obst, M.: Linking environmental processes to the in situ functioning of microorganisms by high-resolution secondary ion mass spectrometry (NanoSIMS), and scanning transmission X-ray microscopy (STXM), Environ. Microbiol., 14, 2851–2869, https://doi.org/10.1111/j.1462-2920.2012.02724.x, 2012.
Bernhardt, E. S., Blaszczak, J. R., Ficken, C. D., Fork, M. L., Kaiser, K. E., and Seybold, E. C.: Control Points in Ecosystems: Moving Beyond the Hot Spot Hot Moment Concept, Ecosystems, 20, 665–682, https://doi.org/10.1007/s10021-016-0103-y, 2017.
Bier, R. L., Bernhardt, E. S., Boot, C. M., Graham, E. B., Hall, E. K., Lennon, J. T., Nemergut, D. R., Osborne, B. B., Ruiz-González, C., Schimel, J. P., Waldrop, M. P., and Wallenstein, M. D.: Linking microbial community structure and microbial processes: an empirical and conceptual overview, FEMS Microbiol. Ecol., 91, fiv113, https://doi.org/10.1093/femsec/fiv113, 2015.
Birch, H. F.: Mineralisation of plant nitrogen following alternate wet and dry conditions, Plant Soil, 20, 43–49, https://doi.org/10.1007/BF01378096, 1964.
Birch, H. F. and Friend, M. T.: Humus Decomposition in East African Soils, Nature, 178, 500–501, https://doi.org/10.1038/178500a0, 1956.
Blazewicz, S. J., Barnard, R. L., Daly, R. A., and Firestone, M. K.: Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses, ISME J., 7, 2061–2068, https://doi.org/10.1038/ismej.2013.102, 2013.
Boano, F., Harvey, J. W., Marion, A., Packman, A. I., Revelli, R., Ridolfi, L., and Wörman, A.: Hyporheic flow and transport processes: Mechanisms, models, and biogeochemical implications, Rev. Geophys., 52, 603–679, https://doi.org/10.1002/2012RG000417, 2014.
Bottos, E. M., Kennedy, D. W., Romero, E. B., Fansler, S. J., Brown, J. M., Bramer, L. M., Chu, R. K., Tfaily, M. M., Jansson, J. K., and Stegen, J. C.: Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities, FEMS Microbiol. Ecol., 94, fiy110, https://doi.org/10.1093/femsec/fiy110, 2018.
Boyd, E. S., Cummings, D. E., and Geesey, G. G.: Mineralogy Influences Structure and Diversity of Bacterial Communities Associated with Geological Substrata in a Pristine Aquifer, Microb. Ecol., 54, 170–182, https://doi.org/10.1007/s00248-006-9187-9, 2007.
Boye, K., Noël, V., Tfaily, M. M., Bone, S. E., Williams, K. H., Bargar, J. R., and Fendorf, S.: Thermodynamically controlled preservation of organic carbon in floodplains, Nat. Geosci., 10, 415–419, https://doi.org/10.1038/ngeo2940, 2017.
Brown, J., Zavoshy, N., Brislawn, C. J., and McCue,
L. A.: Hundo: a Snakemake workflow for microbial community sequence
data, PeerJ Inc., 2018.
Burrows, R. M., Rutlidge, H., Bond, N. R., Eberhard, S. M., Auhl, A., Andersen, M. S., Valdez, D. G., and Kennard, M. J.: High rates of organic carbon processing in the hyporheic zone of intermittent streams, Sci. Rep., 7, 1–11, https://doi.org/10.1038/s41598-017-12957-5, 2017.
Caporaso, J. G.: EMP 16S Illumina Amplicon Protocol, https://doi.org/10.17504/protocols.io.nuudeww, 2018.
Cardoso, D. C., Sandionigi, A., Cretoiu, M. S., Casiraghi, M., Stal, L., and Bolhuis, H.: Comparison of the active and resident community of a coastal microbial mat, Sci. Rep., 7, 1–10, https://doi.org/10.1038/s41598-017-03095-z, 2017.
Carson, J. K., Campbell, L., Rooney, D., Clipson, N., and Gleeson, D. B.: Minerals in soil select distinct bacterial communities in their microhabitats, FEMS Microbiol. Ecol., 67, 381–388, https://doi.org/10.1111/j.1574-6941.2008.00645.x, 2009.
Chase, J. M.: Drought mediates the importance of
stochastic community assembly, P. Natl. Acad. Sci. USA, 104, 17430–17434, https://doi.org/10.1073/pnas.0704350104, 2007.
Chen, W., Ren, K., Isabwe, A., Chen, H., Liu, M., and Yang, J.: Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons, Microbiome, 7, 138, https://doi.org/10.1186/s40168-019-0749-8, 2019.
Daly, R. A., Borton, M. A., Wilkins, M. J., Hoyt, D. W., Kountz, D. J., Wolfe, R. A., Welch, S. A., Marcus, D. N., Trexler, R. V., MacRae, J. D., Krzycki, J. A., Cole, D. R., Mouser, P. J., and Wrighton, K. C.: Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales, Nat. Microbiol., 1, 1–9, https://doi.org/10.1038/nmicrobiol.2016.146, 2016.
Danczak, R. E., Goldman, A. E., Chu, R. K., Toyoda, J. G., Garayburu-Caruso, V. A., Tolić, N., Graham, E. B., Morad, J. W., Renteria, L., Wells, J. R., Herzog, S. P., Ward, A. S., and Stegen, J. C.: Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties, bioRxiv, 2020.02.12.946459, https://doi.org/10.1101/2020.02.12.946459, 2020.
Demars, B. O. L.: Hydrological pulses and burning of dissolved organic carbon by stream respiration, Limnol. Oceanogr., 64, 406–421, https://doi.org/10.1002/lno.11048, 2019.
Dini-Andreote, F., Stegen, J. C., Elsas, J. D. van, and
Salles, J. F.: Disentangling mechanisms that mediate the balance
between stochastic and deterministic processes in microbial
succession, Proc. Natl. Acad. Sci. USA, 112, E1326–E1332, https://doi.org/10.1073/pnas.1414261112, 2015.
Doetterl, S., Berhe, A. A., Arnold, C., Bodé, S., Fiener, P., Finke, P., Fuchslueger, L., Griepentrog, M., Harden, J. W., Nadeu, E., Schnecker, J., Six, J., Trumbore, S., Van Oost, K., Vogel, C., and Boeckx, P.: Links among warming, carbon and microbial dynamics mediated by soil mineral weathering, Nat. Geosci., 11, 589–593, https://doi.org/10.1038/s41561-018-0168-7, 2018.
Fatichi, S., Manzoni, S., Or, D., and Paschalis, A.: A Mechanistic Model of Microbially Mediated Soil Biogeochemical Processes: A Reality Check, Global Biogeochem. Cy., 33, 620–648, https://doi.org/10.1029/2018GB006077, 2019.
Fauvel, B., Cauchie, H.-M., Gantzer, C., and Ogorzaly, L.: Influence of physico-chemical characteristics of sediment on the in situ spatial distribution of F-specific RNA phages in the riverbed, FEMS Microbiol. Ecol., 95, fiy240, https://doi.org/10.1093/femsec/fiy240, 2019.
Feng, Y., Chen, R., Stegen, J. C., Guo, Z., Zhang, J., Li, Z., and Lin, X.: Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions, Mol. Ecol., 27, 5238–5251, https://doi.org/10.1111/mec.14914, 2018.
Fierer, N., Allen, A. S., Schimel, J. P., and Holden, P. A.: Controls on microbial CO2 production: a comparison of surface and subsurface soil horizons, Glob. Change Biol., 9, 1322–1332, https://doi.org/10.1046/j.1365-2486.2003.00663.x, 2003.
Fillinger, L., Zhou, Y., Kellermann, C., and Griebler, C.: Non-random processes determine the colonization of groundwater sediments by microbial communities in a pristine porous aquifer, Environ. Microbiol., 21, 327–342, https://doi.org/10.1111/1462-2920.14463, 2019.
Fischer, H., Kloep, F., Wilzcek, S., and Pusch, M. T.: A River's Liver – Microbial Processes within the Hyporheic Zone of a Large Lowland River, Biogeochemistry, 76, 349–371, https://doi.org/10.1007/s10533-005-6896-y, 2005.
Freedman, Z. B., Romanowicz, K. J., Upchurch, R. A., and Zak, D. R.: Differential responses of total and active soil microbial communities to long-term experimental N deposition, Soil Biol. Biochem., 90, 275–282, https://doi.org/10.1016/j.soilbio.2015.08.014, 2015.
Fu, X., Li, Y., Meng, Y., Yuan, Q., Zhang, Z., Norbäck, D., Deng, Y., Zhang, X., and Sun, Y.: Derived ecological niches of indoor microbes are crucial for asthma symptoms in university dormitories, bioRxiv, 2020.01.05.893529, https://doi.org/10.1101/2020.01.05.893529, 2020.
Garayburu-Caruso, V. A., Stegen, J. C., Song, H.-S.,
Renteria, L., Wells, J., Garcia, W., Resch, C. T., Goldman, A. E.,
Chu, R. K., Toyoda, J., and Graham, E. B.: Carbon Limitation Leads
to Thermodynamic Regulation of Aerobic Metabolism,
Environ. Sci. Technol. Let., 7, 517–524, https://doi.org/10.1021/acs.estlett.0c00258, 2020.
Gilbert, J. A., Jansson, J. K., and Knight, R.: Earth Microbiome Project and Global Systems Biology, mSystems, 3, e00217-17, https://doi.org/10.1128/mSystems.00217-17, 2018.
Gionchetta, G., Oliva, F., Romani, A. M., and Baneras, L.: Hydrological variations shape diversity and functional responses of streambed microbes, Sci. Total Environ., 714, 136838, https://doi.org/10.1016/j.scitotenv.2020.136838, 2020.
Goldman, A. E., Graham, E. B., Crump, A. R., Kennedy, D. W., Romero, E. B., Anderson, C. G., Dana, K. L., Resch, C. T., Fredrickson, J. K., and Stegen, J. C.: Biogeochemical cycling at the aquatic–terrestrial interface is linked to parafluvial hyporheic zone inundation history, Biogeosciences, 14, 4229–4241, https://doi.org/10.5194/bg-14-4229-2017, 2017.
Graham, E. B. and Stegen, J. C.: Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function, Processes, 5, 65, https://doi.org/10.3390/pr5040065, 2017.
Graham, E. B., Crump, A. R., Resch, C. T., Fansler, S., Arntzen, E., Kennedy, D. W., Fredrickson, J. K., and Stegen, J. C.: Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism, Front. Microbiol., 7, 1949, https://doi.org/10.3389/fmicb.2016.01949, 2016.
Graham, E. B., Tfaily, M. M., Crump, A. R., Goldman, A. E., Bramer, L. M., Arntzen, E., Romero, E., Resch, C. T., Kennedy, D. W., and Stegen, J. C.: Carbon Inputs From Riparian Vegetation Limit Oxidation of Physically Bound Organic Carbon Via Biochemical and Thermodynamic Processes, J. Geophys. Res.-Biogeo., 122, 3188–3205, https://doi.org/10.1002/2017JG003967, 2017a.
Graham, E. B., Crump, A. R., Resch, C. T., Fansler, S., Arntzen, E., Kennedy, D. W., Fredrickson, J. K., and Stegen, J. C.: Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes, Environ. Microbiol., 19, 1552–1567, https://doi.org/10.1111/1462-2920.13720, 2017b.
Graham, E. B., Crump, A. R., Kennedy, D. W., Arntzen, E., Fansler, S., Purvine, S. O., Nicora, C. D., Nelson, W., Tfaily, M. M., and Stegen, J. C.: Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone, Sci. Total Environ., 642, 742–753, https://doi.org/10.1016/j.scitotenv.2018.05.256, 2018.
Grilli, J., Barabás, G., Michalska-Smith, M. J., and Allesina, S.: Higher-order interactions stabilize dynamics in competitive network models, Nature, 548, 210–213, https://doi.org/10.1038/nature23273, 2017.
Hall, E. K., Bernhardt, E. S., Bier, R. L., Bradford, M. A., Boot, C. M., Cotner, J. B., del Giorgio, P. A., Evans, S. E., Graham, E. B., Jones, S. E., Lennon, J. T., Locey, K. J., Nemergut, D., Osborne, B. B., Rocca, J. D., Schimel, J. P., Waldrop, M. P., and Wallenstein, M. D.: Understanding how microbiomes influence the systems they inhabit, Nat. Microbiol., 3, 977–982, https://doi.org/10.1038/s41564-018-0201-z, 2018.
Homyak, P. M., Blankinship, J. C., Slessarev, E. W., Schaeffer, S. M., Manzoni, S., and Schimel, J. P.: Effects of altered dry season length and plant inputs on soluble soil carbon, Ecology, 99, 2348–2362, https://doi.org/10.1002/ecy.2473, 2018.
Jia, X., Dini-Andreote, F., and Falcão Salles, J.: Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data, Microorganisms, 8, 798, https://doi.org/10.3390/microorganisms8060798, 2020.
Jurburg, S. D., Nunes, I., Stegen, J. C., Le Roux, X., Priemé, A., Sørensen, S. J., and Salles, J. F.: Autogenic succession and deterministic recovery following disturbance in soil bacterial communities, Sci. Rep., 7, 1–11, https://doi.org/10.1038/srep45691, 2017.
Kaufman, M. H., Cardenas, M. B., Buttles, J., Kessler, A. J., and Cook, P. L. M.: Hyporheic hot moments: Dissolved oxygen dynamics in the hyporheic zone in response to surface flow perturbations, Water Resour. Res., 53, 6642–6662, https://doi.org/10.1002/2016WR020296, 2017.
Kearns, P. J., Angell, J. H., Howard, E. M., Deegan, L. A., Stanley, R. H. R., and Bowen, J. L.: Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments, Nat. Commun., 7, 12881, https://doi.org/10.1038/ncomms12881, 2016.
König, S., Worrich, A., Banitz, T., Centler, F., Harms, H., Kästner, M., Miltner, A., Wick, L. Y., Thullner, M., and Frank, K.: Spatiotemporal disturbance characteristics determine functional stability and collapse risk of simulated microbial ecosystems, Sci. Rep., 8, 1–13, https://doi.org/10.1038/s41598-018-27785-4, 2018.
Larned, S. T., Datry, T., Arscott, D. B., and Tockner, K.: Emerging concepts in temporary-river ecology, Freshwater Biol., 55, 717–738, https://doi.org/10.1111/j.1365-2427.2009.02322.x, 2010.
LaRowe, D. E. and Van Cappellen, P.: Degradation of natural organic matter: A thermodynamic analysis, Geochim. Cosmochim. Ac., 75, 2030–2042, https://doi.org/10.1016/j.gca.2011.01.020, 2011.
Leventhal, G. E., Ackermann, M., and Schiessl, K. T.: Why microbes secrete molecules to modify their environment: the case of iron-chelating siderophores, J. R. Soc. Interface, 16, 20180674, https://doi.org/10.1098/rsif.2018.0674, 2019.
Levy-Booth, D. J., Giesbrecht, I. J. W., Kellogg, C. T. E., Heger, T. J., D'Amore, D. V., Keeling, P. J., Hallam, S. J., and Mohn, W. W.: Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil, ISME J., 13, 950–963, https://doi.org/10.1038/s41396-018-0334-3, 2019.
Li, Y., Gao, Y., Zhang, W., Wang, C., Wang, P., Niu, L., and Wu, H.: Homogeneous selection dominates the microbial community assembly in the sediment of the Three Gorges Reservoir, Sci. Total Environ., 690, 50–60, https://doi.org/10.1016/j.scitotenv.2019.07.014, 2019.
Lloyd-Price, J., Arze, C., Ananthakrishnan, A. N., Schirmer, M., Avila-Pacheco, J., Poon, T. W., Andrews, E., Ajami, N. J., Bonham, K. S., Brislawn, C. J., Casero, D., Courtney, H., Gonzalez, A., Graeber, T. G., Hall, A. B., Lake, K., Landers, C. J., Mallick, H., Plichta, D. R., Prasad, M., Rahnavard, G., Sauk, J., Shungin, D., Vázquez-Baeza, Y., White, R. A., Braun, J., Denson, L. A., Jansson, J. K., Knight, R., Kugathasan, S., McGovern, D. P. B., Petrosino, J. F., Stappenbeck, T. S., Winter, H. S., Clish, C. B., Franzosa, E. A., Vlamakis, H., Xavier, R. J., and Huttenhower, C.: Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases, Nature, 569, 655–662, https://doi.org/10.1038/s41586-019-1237-9, 2019.
Louca, S., Polz, M. F., Mazel, F., Albright, M. B. N., Huber, J. A., O'Connor, M. I., Ackermann, M., Hahn, A. S., Srivastava, D. S., Crowe, S. A., Doebeli, M., and Parfrey, L. W.: Function and functional redundancy in microbial systems, Nat. Ecol. Evol., 2, 936–943, https://doi.org/10.1038/s41559-018-0519-1, 2018.
Malik, A. A., Martiny, J. B. H., Brodie, E. L., Martiny, A. C., Treseder, K. K., and Allison, S. D.: Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change, ISME J., 14, 1–9, https://doi.org/10.1038/s41396-019-0510-0, 2020.
Manzella, M., Geiss, R., and Hall, E. K.: Evaluating the stoichiometric trait distributions of cultured bacterial populations and uncultured microbial communities, Environ. Microbiol., 21, 3613–3626, https://doi.org/10.1111/1462-2920.14684, 2019.
Manzoni, S., Schimel, J. P., and Porporato, A.: Responses of soil microbial communities to water stress: results from a meta-analysis, Ecology, 93, 930–938, https://doi.org/10.1890/11-0026.1, 2012.
Martínez, I., Stegen, J. C., Maldonado-Gómez, M. X., Eren, A. M., Siba, P. M., Greenhill, A. R., and Walter, J.: The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes, Cell Rep., 11, 527–538, https://doi.org/10.1016/j.celrep.2015.03.049, 2015.
Mauck, B. S. and Roberts, J. A.: Mineralogic Control on Abundance and Diversity of Surface-Adherent Microbial Communities, Geomicrobiol. J., 24, 167–177, https://doi.org/10.1080/01490450701457162, 2007.
McClain, M. E., Boyer, E. W., Dent, C. L., Gergel, S. E., Grimm, N. B., Groffman, P. M., Hart, S. C., Harvey, J. W., Johnston, C. A., Mayorga, E., McDowell, W. H., and Pinay, G.: Biogeochemical Hot Spots and Hot Moments at the Interface of Terrestrial and Aquatic Ecosystems, Ecosystems, 6, 301–312, https://doi.org/10.1007/s10021-003-0161-9, 2003.
Norland, S., Fagerbakke, K. M., and Heldal, M.: Light element analysis of individual bacteria by x-ray microanalysis, Appl. Environ. Microbiol., 61, 1357–1362, https://doi.org/10.1128/AEM.61.4.1357-1362.1995, 1995.
Ofiţeru, I. D., Lunn, M., Curtis, T. P., Wells,
G. F., Criddle, C. S., Francis, C. A., and Sloan, W. T.: Combined
niche and neutral effects in a microbial wastewater treatment
community, Proc. Natl. Acad. Sci. USA, 107, 15345–15350, https://doi.org/10.1073/pnas.1000604107, 2010.
Pérez Castro, S., Cleland, E. E., Wagner, R., Sawad, R. A., and Lipson, D. A.: Soil microbial responses to drought and exotic plants shift carbon metabolism, ISME J., 13, 1776–1787, https://doi.org/10.1038/s41396-019-0389-9, 2019.
Prosser, J. I. and Martiny, J. B. H.: Conceptual challenges in microbial community ecology, Philos. T. R. Soc. B, 375, 20190241, https://doi.org/10.1098/rstb.2019.0241, 2020.
Ratzke, C., Denk, J., and Gore, J.: Ecological suicide in microbes, Nat. Ecol. Evol., 2, 867–872, https://doi.org/10.1038/s41559-018-0535-1, 2018.
Romaní, A. M., Vázquez, E., and Butturini, A.: Microbial Availability and Size Fractionation of Dissolved Organic Carbon After Drought in an Intermittent Stream: Biogeochemical Link Across the Stream–Riparian Interface, Microb. Ecol., 52, 501–512, https://doi.org/10.1007/s00248-006-9112-2, 2006.
Sengupta, A., Stegen, J. C., Neto, A. A. M., Wang, Y., Neilson, J. W., Tatarin, T., Hunt, E., Dontsova, K., Chorover, J., Troch, P. A., and Maier, R. M.: Assessing Microbial Community Patterns During Incipient Soil Formation From Basalt, J. Geophys. Res.-Biogeo., 124, 941–958, https://doi.org/10.1029/2017JG004315, 2019a.
Sengupta, A., Indivero, J., Gunn, C., Tfaily, M. M., Chu, R. K., Toyoda, J., Bailey, V. L., Ward, N. D., and Stegen, J. C.: Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities, Biogeosciences, 16, 3911–3928, https://doi.org/10.5194/bg-16-3911-2019, 2019b.
Shu, D., Guo, J., Zhang, B., He, Y., and Wei, G.: rDNA- and rRNA-derived communities present divergent assemblage patterns and functional traits throughout full-scale landfill leachate treatment process trains, Sci. Total Environ., 646, 1069–1079, https://doi.org/10.1016/j.scitotenv.2018.07.388, 2019.
Slater, L. D., Ntarlagiannis, D., Day-Lewis, F. D., Mwakanyamale, K., Versteeg, R. J., Ward, A., Strickland, C., Johnson, C. D., and Lane, J. W.: Use of electrical imaging and distributed temperature sensing methods to characterize surface water–groundwater exchange regulating uranium transport at the Hanford 300 Area, Washington, Water Resour. Res., 46, W10533, https://doi.org/10.1029/2010WR009110, 2010.
Song, H.-S., Stegen, J. C., Graham, E. B., Lee, J.-Y., Garayburu-Caruso, V. A., Nelson, W. C., Chen, X., Moulton, J. D., and Scheibe, T. D.: Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling, bioRxiv, 2020.02.27.968669, https://doi.org/10.1101/2020.02.27.968669, 2020.
Starnawski, P., Bataillon, T., Ettema, T. J. G., Jochum,
L. M., Schreiber, L., Chen, X., Lever, M. A., Polz, M. F.,
Jørgensen, B. B., Schramm, A., and Kjeldsen, K. U.: Microbial
community assembly and evolution in subseafloor sediment,
Proc. Natl. Acad. Sci. USA, 114, 2940–2945, https://doi.org/10.1073/pnas.1614190114, 2017.
Stegen, J. C., Lin, X., Konopka, A. E., and Fredrickson, J. K.: Stochastic and deterministic assembly processes in subsurface microbial communities, ISME J., 6, 1653–1664, https://doi.org/10.1038/ismej.2012.22, 2012.
Stegen, J. C., Lin, X., Fredrickson, J. K., Chen, X., Kennedy, D. W., Murray, C. J., Rockhold, M. L., and Konopka, A.: Quantifying community assembly processes and identifying features that impose them, ISME J., 7, 2069–2079, https://doi.org/10.1038/ismej.2013.93, 2013.
Stegen, J. C., Lin, X., Fredrickson, J. K., and Konopka, A. E.: Estimating and mapping ecological processes influencing microbial community assembly, Front. Microbiol., 6, 370, https://doi.org/10.3389/fmicb.2015.00370, 2015.
Stegen, J. C., Konopka, A., McKinley, J. P., Murray, C., Lin, X., Miller, M. D., Kennedy, D. W., Miller, E. A., Resch, C. T., and Fredrickson, J. K.: Coupling among Microbial Communities, Biogeochemistry and Mineralogy across Biogeochemical Facies, Sci. Rep., 6, 1–14, https://doi.org/10.1038/srep30553, 2016.
Stegen, J. C., Bottos, E. M., and Jansson, J. K.: A
unified conceptual framework for prediction and control of
microbiomes, Curr. Opin. Microbiol., 44, 20–27, https://doi.org/10.1016/j.mib.2018.06.002, 2018a.
Stegen, J. C., Johnson, T., Fredrickson, J. K., Wilkins, M. J., Konopka, A. E., Nelson, W. C., Arntzen, E. V., Chrisler, W. B., Chu, R. K., Fansler, S. J., Graham, E. B., Kennedy, D. W., Resch, C. T., Tfaily, M., and Zachara, J.: Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology, Nat. Commun., 9, 1–11, https://doi.org/10.1038/s41467-018-02922-9, 2018b.
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J. T., Mirarab, S., Zech Xu, Z., Jiang, L., Haroon, M. F., Kanbar, J., Zhu, Q., Jin Song, S., Kosciolek, T., Bokulich, N. A., Lefler, J., Brislawn, C. J., Humphrey, G., Owens, S. M., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J. A., Clauset, A., Stevens, R. L., Shade, A., Pollard, K. S., Goodwin, K. D., Jansson, J. K., Gilbert, J. A., and Knight, R.: A communal catalogue reveals Earth's multiscale microbial diversity, Nature, 551, 457–463, https://doi.org/10.1038/nature24621, 2017.
Tripathi, B. M., Stegen, J. C., Kim, M., Dong, K., Adams, J. M., and Lee, Y. K.: Soil pH mediates the balance between stochastic and deterministic assembly of bacteria, ISME J., 12, 1072–1083, https://doi.org/10.1038/s41396-018-0082-4, 2018.
Wagner, M.: Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging, Annu. Rev. Microbiol., 63, 411–429, https://doi.org/10.1146/annurev.micro.091208.073233, 2009.
Wallenstein, M. D. and Hall, E. K.: A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning, Biogeochemistry, 109, 35–47, https://doi.org/10.1007/s10533-011-9641-8, 2012.
Wang, J., Shen, J., Wu, Y., Tu, C., Soininen, J., Stegen, J. C., He, J., Liu, X., Zhang, L., and Zhang, E.: Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes, ISME J., 7, 1310–1321, https://doi.org/10.1038/ismej.2013.30, 2013.
Whitman, T., Neurath, R., Perera, A., Chu-Jacoby, I., Ning, D., Zhou, J., Nico, P., Pett-Ridge, J., and Firestone, M.: Microbial community assembly differs across minerals in a rhizosphere microcosm, Environ. Microbiol., 20, 4444–4460, https://doi.org/10.1111/1462-2920.14366, 2018.
Wieder, W. R., Allison, S. D., Davidson, E. A., Georgiou, K., Hararuk, O., He, Y., Hopkins, F., Luo, Y., Smith, M. J., Sulman, B., Todd-Brown, K., Wang, Y.-P., Xia, J., and Xu, X.: Explicitly representing soil microbial processes in Earth system models, Global Biogeochem. Cy., 29, 1782–1800, https://doi.org/10.1002/2015GB005188, 2015.
Wisnoski, N. I., Muscarella, M. E., Larsen, M. L., Peralta, A. L., and Lennon, J. T.: Metabolic insight into bacterial community assembly across ecosystem boundaries, Ecology, 101, e02968, https://doi.org/10.1002/ecy.2968, 2020.
Wu, W., Lu, H.-P., Sastri, A., Yeh, Y.-C., Gong, G.-C., Chou, W.-C., and Hsieh, C.-H.: Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities, ISME J., 12, 485–494, https://doi.org/10.1038/ismej.2017.183, 2018.
Zachara, J. M., Long, P. E., Bargar, J., Davis, J. A., Fox, P., Fredrickson, J. K., Freshley, M. D., Konopka, A. E., Liu, C., McKinley, J. P., Rockhold, M. L., Williams, K. H., and Yabusaki, S. B.: Persistence of uranium groundwater plumes: Contrasting mechanisms at two DOE sites in the groundwater–river interaction zone, J. Contam. Hydrol., 147, 45–72, https://doi.org/10.1016/j.jconhyd.2013.02.001, 2013.
Zhou, J. and Ning, D.: Stochastic Community Assembly: Does It Matter in Microbial Ecology?, Microbiol. Mol. Biol. R., 81, e00002-17, https://doi.org/10.1128/MMBR.00002-17, 2017.
Zhou, J., Liu, W., Deng, Y., Jiang, Y.-H., Xue, K., He, Z., Nostrand, J. D. V., Wu, L., Yang, Y., and Wang, A.: Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community, mBio, 4, e00584-12, https://doi.org/10.1128/mBio.00584-12, 2013.
Short summary
Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
Conceptual models link microbes with the environment but are untested. We test a recent model...
Altmetrics
Final-revised paper
Preprint