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
Aditi Sengupta, Julia Indivero, Cailene Gunn, Malak M. Tfaily, Rosalie K. Chu, Jason Toyoda, Vanessa L. Bailey, Nicholas D. Ward, and James C. Stegen
Biogeosciences, 16, 3911–3928, https://doi.org/10.5194/bg-16-3911-2019, https://doi.org/10.5194/bg-16-3911-2019, 2019
Short summary
Short summary
Coastal terrestrial–aquatic interfaces represent dynamic yet poorly understood zones of biogeochemical cycles. We evaluated associations between the soil salinity gradient, molecular-level soil-C chemistry, and microbial community assembly processes in a coastal watershed on the Olympic Peninsula in Washington, USA. Results revealed salinity-driven gradients in molecular-level C chemistry, with little evidence of an association between C chemistry and microbial community assembly processes.
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.
James Stegen, Amy Burgin, Michelle Busch, Joshua Fisher, Joshua Ladau, Jenna Abrahamson, Lauren Kinsman-Costello, Li Li, Xingyuan Chen, Thibault Datry, Nate McDowell, Corianne Tatariw, Anna Braswell, Jillian Deines, Julia Guimond, Peter Regier, Kenton Rod, Edward Bam, Etienne Fluet-Chouinard, Inke Forbrich, Kristin Jaeger, Teri O'Meara, Tim Scheibe, Erin Seybold, Jon Sweetman, Jianqiu Zheng, Daniel Allen, Elizabeth Herndon, Beth Middleton, Scott Painter, Kevin Roche, Julianne Scamardo, Ross Vander Vorste, Kristin Boye, Ellen Wohl, Margaret Zimmer, Kelly Hondula, Maggi Laan, Anna Marshall, and Kaizad Patel
EGUsphere, https://doi.org/10.5194/egusphere-2024-98, https://doi.org/10.5194/egusphere-2024-98, 2024
Short summary
Short summary
The loss and gain of surface water (variable inundation) is a common process across Earth. Global change shifts variable inundation dynamics, highlighting a need for unified understanding that transcends individual variably inundated ecosystems (VIEs). We review 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.
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.
Yilin Fang, Xingyuan Chen, Jesus Gomez Velez, Xuesong Zhang, Zhuoran Duan, Glenn E. Hammond, Amy E. Goldman, Vanessa A. Garayburu-Caruso, and Emily B. Graham
Geosci. Model Dev., 13, 3553–3569, https://doi.org/10.5194/gmd-13-3553-2020, https://doi.org/10.5194/gmd-13-3553-2020, 2020
Short summary
Short summary
Surface water quality along river corridors can be improved by the area of the stream bed and stream bank in which stream water mixes with shallow groundwater or hyporheic zones (HZs). These zones are ubiquitous and dominated by microorganisms that can process the dissolved nutrients exchanged at this interface of these zones. The modulation of surface water quality can be simulated by connecting the channel water and HZs through hyporheic exchanges using multirate mass transfer representation.
Stephanie C. Pennington, Nate G. McDowell, J. Patrick Megonigal, James C. Stegen, and Ben Bond-Lamberty
Biogeosciences, 17, 771–780, https://doi.org/10.5194/bg-17-771-2020, https://doi.org/10.5194/bg-17-771-2020, 2020
Short summary
Short summary
Soil respiration (Rs) is the flow of CO2 from the soil surface to the atmosphere and is one of the largest carbon fluxes on land. This study examined the effect of local basal area (tree area) on Rs in a coastal forest in eastern Maryland, USA. Rs measurements were taken as well as distance from soil collar, diameter, and species of each tree within a 15 m radius. We found that trees within 5 m of our sampling points had a positive effect on how sensitive soil respiration was to temperature.
Adam S. Ward, Steven M. Wondzell, Noah M. Schmadel, Skuyler Herzog, Jay P. Zarnetske, Viktor Baranov, Phillip J. Blaen, Nicolai Brekenfeld, Rosalie Chu, Romain Derelle, Jennifer Drummond, Jan H. Fleckenstein, Vanessa Garayburu-Caruso, Emily Graham, David Hannah, Ciaran J. Harman, Jase Hixson, Julia L. A. Knapp, Stefan Krause, Marie J. Kurz, Jörg Lewandowski, Angang Li, Eugènia Martí, Melinda Miller, Alexander M. Milner, Kerry Neil, Luisa Orsini, Aaron I. Packman, Stephen Plont, Lupita Renteria, Kevin Roche, Todd Royer, Catalina Segura, James Stegen, Jason Toyoda, Jacqueline Hager, and Nathan I. Wisnoski
Hydrol. Earth Syst. Sci., 23, 5199–5225, https://doi.org/10.5194/hess-23-5199-2019, https://doi.org/10.5194/hess-23-5199-2019, 2019
Short summary
Short summary
The movement of water and solutes between streams and their shallow, connected subsurface is important to many ecosystem functions. These exchanges are widely expected to vary with stream flow across space and time, but these assumptions are seldom tested across basin scales. We completed more than 60 experiments across a 5th-order river basin to document these changes, finding patterns in space but not time. We conclude space-for-time and time-for-space substitutions are not good assumptions.
Adam S. Ward, Jay P. Zarnetske, Viktor Baranov, Phillip J. Blaen, Nicolai Brekenfeld, Rosalie Chu, Romain Derelle, Jennifer Drummond, Jan H. Fleckenstein, Vanessa Garayburu-Caruso, Emily Graham, David Hannah, Ciaran J. Harman, Skuyler Herzog, Jase Hixson, Julia L. A. Knapp, Stefan Krause, Marie J. Kurz, Jörg Lewandowski, Angang Li, Eugènia Martí, Melinda Miller, Alexander M. Milner, Kerry Neil, Luisa Orsini, Aaron I. Packman, Stephen Plont, Lupita Renteria, Kevin Roche, Todd Royer, Noah M. Schmadel, Catalina Segura, James Stegen, Jason Toyoda, Jacqueline Hager, Nathan I. Wisnoski, and Steven M. Wondzell
Earth Syst. Sci. Data, 11, 1567–1581, https://doi.org/10.5194/essd-11-1567-2019, https://doi.org/10.5194/essd-11-1567-2019, 2019
Short summary
Short summary
Studies of river corridor exchange commonly focus on characterization of the physical, chemical, or biological system. As a result, complimentary systems and context are often lacking, which may limit interpretation. Here, we present a characterization of all three systems at 62 sites in a 5th-order river basin, including samples of surface water, hyporheic water, and sediment. These data will allow assessment of interacting processes in the river corridor.
Aditi Sengupta, Julia Indivero, Cailene Gunn, Malak M. Tfaily, Rosalie K. Chu, Jason Toyoda, Vanessa L. Bailey, Nicholas D. Ward, and James C. Stegen
Biogeosciences, 16, 3911–3928, https://doi.org/10.5194/bg-16-3911-2019, https://doi.org/10.5194/bg-16-3911-2019, 2019
Short summary
Short summary
Coastal terrestrial–aquatic interfaces represent dynamic yet poorly understood zones of biogeochemical cycles. We evaluated associations between the soil salinity gradient, molecular-level soil-C chemistry, and microbial community assembly processes in a coastal watershed on the Olympic Peninsula in Washington, USA. Results revealed salinity-driven gradients in molecular-level C chemistry, with little evidence of an association between C chemistry and microbial community assembly processes.
Ryan D. Cook, Ying-Hsuan Lin, Zhuoyu Peng, Eric Boone, Rosalie K. Chu, James E. Dukett, Matthew J. Gunsch, Wuliang Zhang, Nikola Tolic, Alexander Laskin, and Kerri A. Pratt
Atmos. Chem. Phys., 17, 15167–15180, https://doi.org/10.5194/acp-17-15167-2017, https://doi.org/10.5194/acp-17-15167-2017, 2017
Short summary
Short summary
Reactions occur within water in both atmospheric particles and cloud droplets, yet little is known about the organic compounds in cloud water. In this work, cloud water samples were collected at Whiteface Mountain, New York, and analyzed using ultra-high-resolution mass spectrometry to investigate the molecular composition of the dissolved organic compounds. The results focus on changes in cloud water composition with air mass origin – influences of forest, urban, and wildfire emissions.
James C. Stegen, Carolyn G. Anderson, Ben Bond-Lamberty, Alex R. Crump, Xingyuan Chen, and Nancy Hess
Biogeosciences, 14, 4341–4354, https://doi.org/10.5194/bg-14-4341-2017, https://doi.org/10.5194/bg-14-4341-2017, 2017
Short summary
Short summary
CO2 loss from soil to the atmosphere (
soil respiration) is a key ecosystem function, especially in systems with permafrost. We find that soil respiration shows a non-linear threshold at permafrost depths > 140 cm and that the number of large trees governs soil respiration. This suggests that remote sensing could be used to estimate spatial variation in soil respiration and (with knowledge of key thresholds) empirically constrain models that predict ecosystem responses to permafrost thaw.
Amy E. Goldman, Emily B. Graham, Alex R. Crump, David W. Kennedy, Elvira B. Romero, Carolyn G. Anderson, Karl L. Dana, Charles T. Resch, Jim K. Fredrickson, and James C. Stegen
Biogeosciences, 14, 4229–4241, https://doi.org/10.5194/bg-14-4229-2017, https://doi.org/10.5194/bg-14-4229-2017, 2017
Short summary
Short summary
The history of river inundation influences shoreline sediment biogeochemical cycling and microbial dynamics. Sediment exhibited a binary respiration response to rewetting, in which respiration from less recently saturated sediment was suppressed relative to more recently saturated sediment, likely due to inhibition of fungal metabolic activity. River shorelines should likely be integrated as a distinct environment into hydrobiogeochemical models to predict watershed biogeochemical function.
Related subject area
Biogeochemistry: Environmental Microbiology
Effects of surface water interactions with karst groundwater on microbial biomass, metabolism, and production
Overview: Global change effects on terrestrial biogeochemistry at the plant–soil interface
Ideas and perspectives: Microorganisms in the air through the lenses of atmospheric chemistry and microphysics
Grazing mortality as a controlling factor in the uncultured non-cyanobacterial diazotroph (Gamma A) around the Kuroshio region
Changes in diazotrophic community structure associated with Kuroshio succession in the northern South China Sea
Technical note: A comparison of methods for estimating coccolith mass
Fractionation of stable carbon isotopes during formate consumption in anoxic rice paddy soils and lake sediments
Characteristics of bacterial and fungal communities and their associations with sugar compounds in atmospheric aerosols at a rural site in northern China
Responses of globally important phytoplankton species to olivine dissolution products and implications for carbon dioxide removal via ocean alkalinity enhancement
Differentiation of cognate bacterial communities in thermokarst landscapes: implications for ecological consequences of permafrost degradation
A multi-phase biogeochemical model for mitigating earthquake-induced liquefaction via microbially induced desaturation and calcium carbonate precipitation
Phosphorus regulates ectomycorrhizal fungi biomass production in a Norway spruce forest
Reallocation of elemental content and macromolecules in the coccolithophore Emiliania huxleyi to acclimate to climate change
Abrasion of sedimentary rocks as a source of hydrogen peroxide and nutrients to subglacial ecosystems
Nitrous oxide (N2O) synthesis by the freshwater cyanobacterium Microcystis aeruginosa
Interdisciplinary strategy to assess the impact of meteorological variables on the biochemical composition of the rain and the dynamics of a small eutrophic lake under rain forcing
Depth-related patterns in microbial community responses to complex organic matter in the western North Atlantic Ocean
Assessing the influence of ocean alkalinity enhancement on a coastal phytoplankton community
Eddy-enhanced primary production sustains heterotrophic microbial activities in the Eastern Tropical North Atlantic
Composition and niche-specific characteristics of microbial consortia colonizing Marsberg copper mine in the Rhenish Massif
Diversity and assembly processes of microbial eukaryotic communities in Fildes Peninsula Lakes (West Antarctica)
Nitrophobic ectomycorrhizal fungi are associated with enhanced hydrophobicity of soil organic matter in a Norway spruce forest
Physiological control on carbon isotope fractionation in marine phytoplankton
Implementation of mycorrhizal mechanisms into soil carbon model improves the prediction of long-term processes of plant litter decomposition
Impact of dust addition on the microbial food web under present and future conditions of pH and temperature
Fractionation of stable carbon isotopes during acetate consumption by methanogenic and sulfidogenic microbial communities in rice paddy soils and lake sediments
Hydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific Ocean
Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin
Hydrographic fronts shape productivity, nitrogen fixation, and microbial community composition in the southern Indian Ocean and the Southern Ocean
Microbial and geo-archaeological records reveal the growth rate, origin and composition of desert rock surface communities
Metagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret iron-rich methanic sediments
Spatiotemporal patterns of N2 fixation in coastal waters derived from rate measurements and remote sensing
Biotic and abiotic transformation of amino acids in cloud water: experimental studies and atmospheric implications
Potential bioavailability of organic matter from atmospheric particles to marine heterotrophic bacteria
Microbial functional signature in the atmospheric boundary layer
New insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystem
Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics
Reviews and syntheses: Bacterial bioluminescence – ecology and impact in the biological carbon pump
Salinity-dependent algae uptake and subsequent carbon and nitrogen metabolisms of two intertidal foraminifera (Ammonia tepida and Haynesina germanica)
On giant shoulders: how a seamount affects the microbial community composition of seawater and sponges
Spatial variations in sedimentary N-transformation rates in the North Sea (German Bight)
Patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge
Co-occurrence of Fe and P stress in natural populations of the marine diazotroph Trichodesmium
Senescence as the main driver of iodide release from a diverse range of marine phytoplankton
Reviews and syntheses: Biological weathering and its consequences at different spatial levels – from nanoscale to global scale
Deep-sea sponge grounds as nutrient sinks: denitrification is common in boreo-Arctic sponges
Inducing the attachment of cable bacteria on oxidizing electrodes
Bacterial degradation activity in the eastern tropical South Pacific oxygen minimum zone
Macromolecular fungal ice nuclei in Fusarium: effects of physical and chemical processing
Effects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime Antarctica
Adrian Barry-Sosa, Madison K. Flint, Justin C. Ellena, Jonathan B. Martin, and Brent C. Christner
Biogeosciences, 21, 3965–3984, https://doi.org/10.5194/bg-21-3965-2024, https://doi.org/10.5194/bg-21-3965-2024, 2024
Short summary
Short summary
This study examined springs in north central Florida focusing on how interactions between the surface and subsurface affected the properties of groundwater microbes. We found that microbes reproduced at rates that greatly exceed those documented for any other aquifer. Although the groundwater discharged to spring runs contains low concentrations of nutrients, our results indicate that microbes have access to sources of energy and produce new cells at rates similar to surface waterbodies.
Lucia Fuchslueger, Emily Francesca Solly, Alberto Canarini, and Albert Carles Brangarí
Biogeosciences, 21, 3959–3964, https://doi.org/10.5194/bg-21-3959-2024, https://doi.org/10.5194/bg-21-3959-2024, 2024
Short summary
Short summary
This overview of the special issue “Global change effects on terrestrial biogeochemistry at the plant–soil interface” features empirical, conceptual and modelling-based studies and outlines key findings on plant responses to elevated CO2; soil organism responses to warming; impacts on soil organic carbon, nitrogen and mineral nutrient cycling; and water level changes affecting greenhouse gas emissions, from the Arctic to the tropics, which are crucial for deciphering feedbacks to global change.
Barbara Ervens, Pierre Amato, Kifle Aregahegn, Muriel Joly, Amina Khaled, Tiphaine Labed-Veydert, Frédéric Mathonat, Leslie Nuñez López, Raphaëlle Péguilhan, and Minghui Zhang
EGUsphere, https://doi.org/10.5194/egusphere-2024-2377, https://doi.org/10.5194/egusphere-2024-2377, 2024
Short summary
Short summary
Atmospheric microorganisms are a small fraction of Earth's microbiome, with bacteria being a significant part. Aerosolized bacteria are airborne for a few days encountering unique chemical and physical conditions affecting stress levels and survival. We explore chemical and microphysical conditions bacteria encounter, highlighting potential nutrient and oxidant limitations and diverse effects by pollutants, which may ultimately impact the microbiome's role in global ecosystems and biodiversity.
Takuya Sato, Tamaha Yamaguchi, Kiyotaka Hidataka, Sayaka Sogawa, Takashi Setou, Taketoshi Kodama, Takuhei Shiozaki, and Kazutaka Takahashi
EGUsphere, https://doi.org/10.5194/egusphere-2024-1294, https://doi.org/10.5194/egusphere-2024-1294, 2024
Short summary
Short summary
Gamma A is a widespread non-cyanobacterial diazotroph and plays a crucial role for marine ecosystems, but its controlling factors are still largely unknown. This study, for the first time, quantified microzooplankton grazing on Gamma A and revealed significance of grazing pressure on Gamma A distribution around the Kuroshio region. It highlights the importance of top-down controls on Gamma A abundance and the associated nitrogen cycle.
Han Zhang, Guangming Mai, Weicheng Luo, Meng Chen, Ran Duan, and Tuo Shi
Biogeosciences, 21, 2529–2546, https://doi.org/10.5194/bg-21-2529-2024, https://doi.org/10.5194/bg-21-2529-2024, 2024
Short summary
Short summary
We report taxon-specific biogeography of N2-fixing microbes (diazotrophs) driven by Kuroshio intrusion (Kl) into the South China Sea. We show that the composition and distribution of distinct diazotrophic taxa shift with Kl-induced variations in physicochemical parameters of seawater and that Kl shapes diazotrophic community primarily as a stochastic process. This study thus has implications for the distribution of diazotrophs in a future warming ocean, as Kls are projected to intensify.
Celina Rebeca Valença, Luc Beaufort, Gustaaf Marinus Hallegraeff, and Marius Nils Müller
Biogeosciences, 21, 1601–1611, https://doi.org/10.5194/bg-21-1601-2024, https://doi.org/10.5194/bg-21-1601-2024, 2024
Short summary
Short summary
Coccolithophores contribute to the global carbon cycle and their calcite structures (coccoliths) are used as a palaeoproxy to understand past oceanographic conditions. Here, we compared three frequently used methods to estimate coccolith mass from the model species Emiliania huxleyi and the results allow for a high level of comparability between the methods, facilitating future comparisons and consolidation of mass changes observed from ecophysiological and biogeochemical studies.
Ralf Conrad and Peter Claus
Biogeosciences, 21, 1161–1172, https://doi.org/10.5194/bg-21-1161-2024, https://doi.org/10.5194/bg-21-1161-2024, 2024
Short summary
Short summary
Knowledge of carbon isotope fractionation is important for the assessment of the pathways involved in the degradation of organic matter. Formate is an important intermediate during this process. It was mainly converted to carbon dioxide and acetate both in the presence and absence of sulfate. Methane was only a minor product and was mainly formed from the acetate. The acetate was depleted in the heavy carbon atom relative to formate, while the carbon dioxide was enriched.
Mutong Niu, Shu Huang, Wei Hu, Yajie Wang, Wanyun Xu, Wan Wei, Qiang Zhang, Zihan Wang, Donghuan Zhang, Rui Jin, Libin Wu, Junjun Deng, Fangxia Shen, and Pingqing Fu
Biogeosciences, 20, 4915–4930, https://doi.org/10.5194/bg-20-4915-2023, https://doi.org/10.5194/bg-20-4915-2023, 2023
Short summary
Short summary
Sugar compounds in air can trace the source of bioaerosols that affect public health and climate. In rural north China, we observed increased fungal activity at night and less variable bacterial community diversity. Certain night-increasing sugar compounds were more closely related to fungi than bacteria. The fungal community greatly influenced sugar compounds, while bacteria played a limited role. Caution is advised when using sugar compounds to trace airborne microbes, particularly bacteria.
David A. Hutchins, Fei-Xue Fu, Shun-Chung Yang, Seth G. John, Stephen J. Romaniello, M. Grace Andrews, and Nathan G. Walworth
Biogeosciences, 20, 4669–4682, https://doi.org/10.5194/bg-20-4669-2023, https://doi.org/10.5194/bg-20-4669-2023, 2023
Short summary
Short summary
Applications of the mineral olivine are a promising means to capture carbon dioxide via coastal enhanced weathering, but little is known about the impacts on important marine phytoplankton. We examined the effects of olivine dissolution products on species from three major phytoplankton groups: diatoms, coccolithophores, and cyanobacteria. Growth and productivity were generally either unaffected or stimulated, suggesting the effects of olivine on key phytoplankton are negligible or positive.
Ze Ren, Shudan Ye, Hongxuan Li, Xilei Huang, and Luyao Chen
Biogeosciences, 20, 4241–4258, https://doi.org/10.5194/bg-20-4241-2023, https://doi.org/10.5194/bg-20-4241-2023, 2023
Short summary
Short summary
Permafrost thaw initiates thermokarst landscape formation, resulting in distinct new habitats, including degraded permafrost soil, thermokarst lake sediments, and lake water. These distinct habitats harbored differentiated bacterial communities that originated from the same source, differing in diversity, assembly mechanisms, and environmental influences. The results imply ecological consequences of permafrost degradation in the face of further climate change.
Caitlyn A. Hall, Andre van Turnhout, Edward Kavazanjian Jr., Leon A. van Paassen, and Bruce Rittmann
Biogeosciences, 20, 2903–2917, https://doi.org/10.5194/bg-20-2903-2023, https://doi.org/10.5194/bg-20-2903-2023, 2023
Short summary
Short summary
Earthquake-induced soil liquefaction poses a significant global threat. Microbially induced desaturation and precipitation (MIDP) via denitrification is a potentially sustainable, non-disruptive bacteria-driven ground improvement technique under existing structures. We developed a next-generation biogeochemical model to understand and predict the behavior of MIDP in the natural environment to design field-based hazard mitigation treatments.
Juan Pablo Almeida, Lorenzo Menichetti, Alf Ekblad, Nicholas P. Rosenstock, and Håkan Wallander
Biogeosciences, 20, 1443–1458, https://doi.org/10.5194/bg-20-1443-2023, https://doi.org/10.5194/bg-20-1443-2023, 2023
Short summary
Short summary
In forests, trees allocate a significant amount of carbon belowground to support mycorrhizal symbiosis. In northern forests nitrogen normally regulates this allocation and consequently mycorrhizal fungi growth. In this study we demonstrate that in a conifer forest from Sweden, fungal growth is regulated by phosphorus instead of nitrogen. This is probably due to an increase in nitrogen deposition to soils caused by decades of human pollution that has altered the ecosystem nutrient regime.
Yong Zhang, Yong Zhang, Shuai Ma, Hanbing Chen, Jiabing Li, Zhengke Li, Kui Xu, Ruiping Huang, Hong Zhang, Yonghe Han, and Jun Sun
Biogeosciences, 20, 1299–1312, https://doi.org/10.5194/bg-20-1299-2023, https://doi.org/10.5194/bg-20-1299-2023, 2023
Short summary
Short summary
We found that increasing light intensity compensates for the negative effects of low phosphorus (P) availability on cellular protein and nitrogen contents. Reduced P availability, increasing light intensity, and ocean acidification act synergistically to increase cellular contents of carbohydrate and POC and the allocation of POC to carbohydrate. These regulation mechanisms in Emiliania huxleyi could provide vital information for evaluating carbon cycle in marine ecosystems under global change.
Beatriz Gill-Olivas, Jon Telling, Mark Skidmore, and Martyn Tranter
Biogeosciences, 20, 929–943, https://doi.org/10.5194/bg-20-929-2023, https://doi.org/10.5194/bg-20-929-2023, 2023
Short summary
Short summary
Microbial ecosystems have been found in all subglacial environments sampled to date. Yet, little is known of the sources of energy and nutrients that sustain these microbial populations. This study shows that crushing of sedimentary rocks, which contain organic carbon, carbonate and sulfide minerals, along with previously weathered silicate minerals, produces a range of compounds and nutrients which can be utilised by the diverse suite of microbes that inhabit glacier beds.
Federico Fabisik, Benoit Guieysse, Jonathan Procter, and Maxence Plouviez
Biogeosciences, 20, 687–693, https://doi.org/10.5194/bg-20-687-2023, https://doi.org/10.5194/bg-20-687-2023, 2023
Short summary
Short summary
We show, for the first time, that pure cultures of the cyanobacterium Microcystis aeruginosa can synthesize the potent greenhouse gas N2O using nitrite as substrate. Our findings have broad environmental implications because M. aeruginosa is globally found in freshwater ecosystems and is often the dominant species found in algae blooms. Further research is now needed to determine the occurrence and significance of N2O emissions from ecosystems rich with M. aeruginosa.
Fanny Noirmain, Jean-Luc Baray, Frédéric Tridon, Philippe Cacault, Hermine Billard, Guillaume Voyard, Joël Van Baelen, and Delphine Latour
Biogeosciences, 19, 5729–5749, https://doi.org/10.5194/bg-19-5729-2022, https://doi.org/10.5194/bg-19-5729-2022, 2022
Short summary
Short summary
We present a study linking rain, meteorology, and mountain lake phytoplankton dynamics on the basis of a case study at Aydat (France) in September 2020. The air mass origin mainly influences the rain chemical composition, which depends on the type of rain, convective or stratiform. Our results also highlighted a non-negligible presence of photosynthetic cells in rainwater. The impact of the atmospheric forcing on the lake could play a key role in phytoplankton dynamics in the temperate zone.
Sarah A. Brown, John Paul Balmonte, Adrienne Hoarfrost, Sherif Ghobrial, and Carol Arnosti
Biogeosciences, 19, 5617–5631, https://doi.org/10.5194/bg-19-5617-2022, https://doi.org/10.5194/bg-19-5617-2022, 2022
Short summary
Short summary
Bacteria use extracellular enzymes to cut large organic matter to sizes small enough for uptake. We compared the enzymatic response of surface, mid-water, and deep-ocean bacteria to complex natural substrates. Bacteria in surface and mid-depth waters produced a much wider range of enzymes than those in the deep ocean and may therefore consume a broader range of organic matter. The extent to which organic matter is recycled by bacteria depends in part on its residence time at different depths.
Aaron Ferderer, Zanna Chase, Fraser Kennedy, Kai G. Schulz, and Lennart T. Bach
Biogeosciences, 19, 5375–5399, https://doi.org/10.5194/bg-19-5375-2022, https://doi.org/10.5194/bg-19-5375-2022, 2022
Short summary
Short summary
Ocean alkalinity enhancement has the capacity to remove vast quantities of carbon from the atmosphere, but its effect on marine ecosystems is largely unknown. We assessed the effect of increased alkalinity on a coastal phytoplankton community when seawater was equilibrated and not equilibrated with atmospheric CO2. We found that the phytoplankton community was moderately affected by increased alkalinity and equilibration with atmospheric CO2 had little influence on this effect.
Quentin Devresse, Kevin W. Becker, Arne Bendinger, Johannes Hahn, and Anja Engel
Biogeosciences, 19, 5199–5219, https://doi.org/10.5194/bg-19-5199-2022, https://doi.org/10.5194/bg-19-5199-2022, 2022
Short summary
Short summary
Eddies are ubiquitous in the ocean and alter physical, chemical, and biological processes. However, how they affect organic carbon production and consumption is largely unknown. Here we show how an eddy triggers a cascade effect on biomass production and metabolic activities of phyto- and bacterioplankton. Our results may contribute to the improvement of biogeochemical models used to estimate carbon fluxes in the ocean.
Sania Arif, Heiko Nacke, Elias Schliekmann, Andreas Reimer, Gernot Arp, and Michael Hoppert
Biogeosciences, 19, 4883–4902, https://doi.org/10.5194/bg-19-4883-2022, https://doi.org/10.5194/bg-19-4883-2022, 2022
Short summary
Short summary
The natural enrichment of Chloroflexi (Ktedonobacteria) at the Kilianstollen Marsberg copper mine rocks being exposed to the acidic sulfate-rich leachate led to an investigation of eight metagenomically assembled genomes (MAGs) involved in copper and other transition heavy metal resistance in addition to low pH resistance and aromatic compounds degradation. The present study offers functional insights about a novel cold-adapted Ktedonobacteria MAG extremophily along with other phyla MAGs.
Chunmei Zhang, Huirong Li, Yinxin Zeng, Haitao Ding, Bin Wang, Yangjie Li, Zhongqiang Ji, Yonghong Bi, and Wei Luo
Biogeosciences, 19, 4639–4654, https://doi.org/10.5194/bg-19-4639-2022, https://doi.org/10.5194/bg-19-4639-2022, 2022
Short summary
Short summary
The unique microbial eukaryotic community structure and lower diversity have been demonstrated in five freshwater lakes of the Fildes Peninsula, Antarctica. Stochastic processes and biotic co-occurrence patterns were shown to be important in shaping microbial eukaryotic communities in the area. Our study provides a better understanding of the dynamic patterns and ecological assembly processes of microbial eukaryotic communities in Antarctic oligotrophic lakes (Fildes Peninsula).
Juan Pablo Almeida, Nicholas P. Rosenstock, Susanne K. Woche, Georg Guggenberger, and Håkan Wallander
Biogeosciences, 19, 3713–3726, https://doi.org/10.5194/bg-19-3713-2022, https://doi.org/10.5194/bg-19-3713-2022, 2022
Short summary
Short summary
Fungi living in symbiosis with tree roots can accumulate belowground, forming special tissues than can repel water. We measured the water repellency of organic material incubated belowground and correlated it with fungal growth. We found a positive association between water repellency and root symbiotic fungi. These results are important because an increase in soil water repellency can reduce the release of CO2 from soils into the atmosphere and mitigate the effects of greenhouse gasses.
Karen M. Brandenburg, Björn Rost, Dedmer B. Van de Waal, Mirja Hoins, and Appy Sluijs
Biogeosciences, 19, 3305–3315, https://doi.org/10.5194/bg-19-3305-2022, https://doi.org/10.5194/bg-19-3305-2022, 2022
Short summary
Short summary
Reconstructions of past CO2 concentrations rely on proxy estimates, with one line of proxies relying on the CO2-dependence of stable carbon isotope fractionation in marine phytoplankton. Culturing experiments provide insights into which processes may impact this. We found, however, that the methods with which these culturing experiments are performed also influence 13C fractionation. Caution should therefore be taken when extrapolating results from these experiments to proxy applications.
Weilin Huang, Peter M. van Bodegom, Toni Viskari, Jari Liski, and Nadejda A. Soudzilovskaia
Biogeosciences, 19, 1469–1490, https://doi.org/10.5194/bg-19-1469-2022, https://doi.org/10.5194/bg-19-1469-2022, 2022
Short summary
Short summary
This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the mediation of plant litter decomposition. We present a model based on litter chemical quality which precludes a conclusive examination of mycorrhizal impacts on soil C. It improves long-term decomposition predictions and advances our understanding of litter decomposition dynamics. It creates a benchmark in quantitatively examining the impacts of plant–microbe interactions on soil C dynamics.
Julie Dinasquet, Estelle Bigeard, Frédéric Gazeau, Farooq Azam, Cécile Guieu, Emilio Marañón, Céline Ridame, France Van Wambeke, Ingrid Obernosterer, and Anne-Claire Baudoux
Biogeosciences, 19, 1303–1319, https://doi.org/10.5194/bg-19-1303-2022, https://doi.org/10.5194/bg-19-1303-2022, 2022
Short summary
Short summary
Saharan dust deposition of nutrients and trace metals is crucial to microbes in the Mediterranean Sea. Here, we tested the response of microbial and viral communities to simulated dust deposition under present and future conditions of temperature and pH. Overall, the effect of the deposition was dependent on the initial microbial assemblage, and future conditions will intensify microbial responses. We observed effects on trophic interactions, cascading all the way down to viral processes.
Ralf Conrad, Pengfei Liu, and Peter Claus
Biogeosciences, 18, 6533–6546, https://doi.org/10.5194/bg-18-6533-2021, https://doi.org/10.5194/bg-18-6533-2021, 2021
Short summary
Short summary
Acetate is an important intermediate during the anaerobic degradation of organic matter. It is consumed by methanogenic and sulfidogenic microorganisms accompanied by stable carbon isotope fractionation. We determined isotope fractionation under different conditions in two paddy soils and two lake sediments and also determined the composition of the microbial communities. Despite a relatively wide range of experimental conditions, the range of fractionation factors was quite moderate.
Natalie R. Cohen, Abigail E. Noble, Dawn M. Moran, Matthew R. McIlvin, Tyler J. Goepfert, Nicholas J. Hawco, Christopher R. German, Tristan J. Horner, Carl H. Lamborg, John P. McCrow, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 18, 5397–5422, https://doi.org/10.5194/bg-18-5397-2021, https://doi.org/10.5194/bg-18-5397-2021, 2021
Short summary
Short summary
A previous study documented an intense hydrothermal plume in the South Pacific Ocean; however, the iron release associated with this plume and the impact on microbiology were unclear. We describe metal concentrations associated with multiple hydrothermal plumes in this region and protein signatures of plume-influenced microbes. Our findings demonstrate that resources released from these systems can be transported away from their source and may alter the physiology of surrounding microbes.
Sabyasachi Bhattacharya, Tarunendu Mapder, Svetlana Fernandes, Chayan Roy, Jagannath Sarkar, Moidu Jameela Rameez, Subhrangshu Mandal, Abhijit Sar, Amit Kumar Chakraborty, Nibendu Mondal, Sumit Chatterjee, Bomba Dam, Aditya Peketi, Ranadhir Chakraborty, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 18, 5203–5222, https://doi.org/10.5194/bg-18-5203-2021, https://doi.org/10.5194/bg-18-5203-2021, 2021
Short summary
Short summary
Physicochemical determinants of microbiome architecture across continental shelves–slopes are unknown, so we explored the geomicrobiology along 3 m sediment horizons of seasonal (shallow coastal) and perennial (deep sea) hypoxic zones of the Arabian Sea. Nature, concentration, and fate of the organic matter delivered to the sea floor were found to shape the microbiome across the western Indian margin, under direct–indirect influence of sedimentation rate and water column O2 level.
Cora Hörstmann, Eric J. Raes, Pier Luigi Buttigieg, Claire Lo Monaco, Uwe John, and Anya M. Waite
Biogeosciences, 18, 3733–3749, https://doi.org/10.5194/bg-18-3733-2021, https://doi.org/10.5194/bg-18-3733-2021, 2021
Short summary
Short summary
Microbes are the main drivers of productivity and nutrient cycling in the ocean. We present a combined approach assessing C and N uptake and microbial community diversity across ecological provinces in the Southern Ocean and southern Indian Ocean. Provinces showed distinct genetic fingerprints, but microbial activity varied gradually across regions, correlating with nutrient concentrations. Our study advances the biogeographic understanding of microbial diversity across C and N uptake regimes.
Nimrod Wieler, Tali Erickson Gini, Osnat Gillor, and Roey Angel
Biogeosciences, 18, 3331–3342, https://doi.org/10.5194/bg-18-3331-2021, https://doi.org/10.5194/bg-18-3331-2021, 2021
Short summary
Short summary
Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands. BRCs play a crucial role in arid environments because of the limited activity of plants and soil. Nevertheless, BRC development rates have never been dated. Here we integrated archaeological, microbiological and geological methods to provide a first estimation of the growth rate of BRCs under natural conditions. This can serve as an affordable dating tool in archaeological sites in arid regions.
Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, and Orit Sivan
Biogeosciences, 18, 2091–2106, https://doi.org/10.5194/bg-18-2091-2021, https://doi.org/10.5194/bg-18-2091-2021, 2021
Mindaugas Zilius, Irma Vybernaite-Lubiene, Diana Vaiciute, Donata Overlingė, Evelina Grinienė, Anastasija Zaiko, Stefano Bonaglia, Iris Liskow, Maren Voss, Agneta Andersson, Sonia Brugel, Tobia Politi, and Paul A. Bukaveckas
Biogeosciences, 18, 1857–1871, https://doi.org/10.5194/bg-18-1857-2021, https://doi.org/10.5194/bg-18-1857-2021, 2021
Short summary
Short summary
In fresh and brackish waters, algal blooms are often dominated by cyanobacteria, which have the ability to utilize atmospheric nitrogen. Cyanobacteria are also unusual in that they float to the surface and are dispersed by wind-driven currents. Their patchy and dynamic distribution makes it difficult to track their abundance and quantify their effects on nutrient cycling. We used remote sensing to map the distribution of cyanobacteria in a large Baltic lagoon and quantify their contributions.
Saly Jaber, Muriel Joly, Maxence Brissy, Martin Leremboure, Amina Khaled, Barbara Ervens, and Anne-Marie Delort
Biogeosciences, 18, 1067–1080, https://doi.org/10.5194/bg-18-1067-2021, https://doi.org/10.5194/bg-18-1067-2021, 2021
Short summary
Short summary
Our study is of interest to atmospheric scientists and environmental microbiologists, as we show that clouds can be considered a medium where bacteria efficiently degrade and transform amino acids, in competition with chemical processes. As current atmospheric multiphase models are restricted to chemical degradation of organic compounds, our conclusions motivate further model development.
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285, https://doi.org/10.5194/bg-17-6271-2020, https://doi.org/10.5194/bg-17-6271-2020, 2020
Romie Tignat-Perrier, Aurélien Dommergue, Alban Thollot, Olivier Magand, Timothy M. Vogel, and Catherine Larose
Biogeosciences, 17, 6081–6095, https://doi.org/10.5194/bg-17-6081-2020, https://doi.org/10.5194/bg-17-6081-2020, 2020
Short summary
Short summary
The adverse atmospheric environmental conditions do not appear suited for microbial life. We conducted the first global comparative metagenomic analysis to find out if airborne microbial communities might be selected by their ability to resist these adverse conditions. The relatively higher concentration of fungi led to the observation of higher proportions of stress-related functions in air. Fungi might likely resist and survive atmospheric physical stress better than bacteria.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032, https://doi.org/10.5194/bg-17-6017-2020, https://doi.org/10.5194/bg-17-6017-2020, 2020
Short summary
Short summary
Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Anna-Neva Visser, Scott D. Wankel, Pascal A. Niklaus, James M. Byrne, Andreas A. Kappler, and Moritz F. Lehmann
Biogeosciences, 17, 4355–4374, https://doi.org/10.5194/bg-17-4355-2020, https://doi.org/10.5194/bg-17-4355-2020, 2020
Short summary
Short summary
This study focuses on the chemical reaction between Fe(II) and nitrite, which has been reported to produce high levels of the greenhouse gas N2O. We investigated the extent to which dead biomass and Fe(II) minerals might enhance this reaction. Here, nitrite reduction was highest when both additives were present but less pronounced if only Fe(II) minerals were added. Both reaction systems show distinct differences, rather low N2O levels, and indicated the abiotic production of N2.
Lisa Tanet, Séverine Martini, Laurie Casalot, and Christian Tamburini
Biogeosciences, 17, 3757–3778, https://doi.org/10.5194/bg-17-3757-2020, https://doi.org/10.5194/bg-17-3757-2020, 2020
Short summary
Short summary
Bioluminescent bacteria, the most abundant light-emitting organisms in the ocean, can be free-living, be symbiotic or colonize organic particles. This review suggests that they act as a visual target and may indirectly influence the sequestration of biogenic carbon in oceans by increasing the attraction rate for consumers. We summarize the instrumentation available to quantify this impact in future studies and propose synthetic figures integrating these ecological and biogeochemical concepts.
Michael Lintner, Bianca Biedrawa, Julia Wukovits, Wolfgang Wanek, and Petra Heinz
Biogeosciences, 17, 3723–3732, https://doi.org/10.5194/bg-17-3723-2020, https://doi.org/10.5194/bg-17-3723-2020, 2020
Short summary
Short summary
Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changing salinity in the German Wadden Sea immediately influences the foraminiferal community. It seems that A. tepida is better adapted to salinity fluctuations than H. germanica.
Kathrin Busch, Ulrike Hanz, Furu Mienis, Benjamin Mueller, Andre Franke, Emyr Martyn Roberts, Hans Tore Rapp, and Ute Hentschel
Biogeosciences, 17, 3471–3486, https://doi.org/10.5194/bg-17-3471-2020, https://doi.org/10.5194/bg-17-3471-2020, 2020
Short summary
Short summary
Seamounts are globally abundant submarine structures that offer great potential to study the impacts and interactions of environmental gradients at a single geographic location. In an exemplary way, we describe potential mechanisms by which a seamount can affect the structure of pelagic and benthic (sponge-)associated microbial communities. We conclude that the geology, physical oceanography, biogeochemistry, and microbiology of seamounts are even more closely linked than currently appreciated.
Alexander Bratek, Justus E. E. van
Beusekom, Andreas Neumann, Tina Sanders, Jana Friedrich, Kay-Christian Emeis, and Kirstin Dähnke
Biogeosciences, 17, 2839–2851, https://doi.org/10.5194/bg-17-2839-2020, https://doi.org/10.5194/bg-17-2839-2020, 2020
Short summary
Short summary
The following paper highlights the importance of benthic N-transformation rates in different sediment types in the southern North Sea as a source of fixed nitrogen for primary producers and also as a sink of fixed nitrogen. Sedimentary fluxes of dissolved inorganic nitrogen support ∼7 to 59 % of the average annual primary production. Semi-permeable and permeable sediments contribute ∼68 % of the total benthic N2 production rates, counteracting eutrophication in the southern North Sea.
Sabine Haalboom, David M. Price, Furu Mienis, Judith D. L. van Bleijswijk, Henko C. de Stigter, Harry J. Witte, Gert-Jan Reichart, and Gerard C. A. Duineveld
Biogeosciences, 17, 2499–2519, https://doi.org/10.5194/bg-17-2499-2020, https://doi.org/10.5194/bg-17-2499-2020, 2020
Short summary
Short summary
Mineral mining in deep-sea hydrothermal settings will lead to the formation of plumes of fine-grained, chemically reactive, suspended matter. Understanding how natural hydrothermal plumes evolve as they disperse from their source, and how they affect their surrounding environment, may help in characterising the behaviour of the diluted part of mining plumes. The natural plume provided a heterogeneous, geochemically enriched habitat conducive to the development of a distinct microbial ecology.
Noelle A. Held, Eric A. Webb, Matthew M. McIlvin, David A. Hutchins, Natalie R. Cohen, Dawn M. Moran, Korinna Kunde, Maeve C. Lohan, Claire Mahaffey, E. Malcolm S. Woodward, and Mak A. Saito
Biogeosciences, 17, 2537–2551, https://doi.org/10.5194/bg-17-2537-2020, https://doi.org/10.5194/bg-17-2537-2020, 2020
Short summary
Short summary
Trichodesmium is a globally important marine nitrogen fixer that stimulates primary production in the surface ocean. We surveyed metaproteomes of Trichodesmium populations across the North Atlantic and other oceans, and we found that they experience simultaneous phosphate and iron stress because of the biophysical limits of nutrient uptake. Importantly, nitrogenase was most abundant during co-stress, indicating the potential importance of this phenotype to global nitrogen and carbon cycling.
Helmke Hepach, Claire Hughes, Karen Hogg, Susannah Collings, and Rosie Chance
Biogeosciences, 17, 2453–2471, https://doi.org/10.5194/bg-17-2453-2020, https://doi.org/10.5194/bg-17-2453-2020, 2020
Short summary
Short summary
Tropospheric iodine takes part in numerous atmospheric chemical cycles, including tropospheric ozone destruction and aerosol formation. Due to its significance for atmospheric processes, it is crucial to constrain its sources and sinks. This paper aims at investigating and understanding features of biogenic iodate-to-iodide reduction in microalgal monocultures. We find that phytoplankton senescence may play a crucial role in the release of iodide to the marine environment.
Roger D. Finlay, Shahid Mahmood, Nicholas Rosenstock, Emile B. Bolou-Bi, Stephan J. Köhler, Zaenab Fahad, Anna Rosling, Håkan Wallander, Salim Belyazid, Kevin Bishop, and Bin Lian
Biogeosciences, 17, 1507–1533, https://doi.org/10.5194/bg-17-1507-2020, https://doi.org/10.5194/bg-17-1507-2020, 2020
Short summary
Short summary
Effects of biological activity on mineral weathering operate at scales ranging from short-term, microscopic interactions to global, evolutionary timescale processes. Microorganisms have had well-documented effects at large spatio-temporal scales, but to establish the quantitative significance of microscopic measurements for field-scale processes, higher-resolution studies of liquid chemistry at local weathering sites and improved upscaling to soil-scale dissolution rates are still required.
Christine Rooks, James Kar-Hei Fang, Pål Tore Mørkved, Rui Zhao, Hans Tore Rapp, Joana R. Xavier, and Friederike Hoffmann
Biogeosciences, 17, 1231–1245, https://doi.org/10.5194/bg-17-1231-2020, https://doi.org/10.5194/bg-17-1231-2020, 2020
Short summary
Short summary
Sponge grounds are known as nutrient sources, providing nitrate and ammonium to the ocean. We found that they also can do the opposite: in six species from Arctic and North Atlantic sponge grounds, we measured high rates of denitrification, which remove these nutrients from the sea. Rates were highest when the sponge tissue got low in oxygen, which happens when sponges stop pumping because of stress. Sponge grounds may become nutrient sinks when exposed to stress.
Cheng Li, Clare E. Reimers, and Yvan Alleau
Biogeosciences, 17, 597–607, https://doi.org/10.5194/bg-17-597-2020, https://doi.org/10.5194/bg-17-597-2020, 2020
Short summary
Short summary
Novel filamentous cable bacteria that grow in the top layer of intertidal mudflat sediment were attracted to electrodes poised at a positive electrical potential. Several diverse morphologies of Desulfobulbaceae filaments, cells, and colonies were observed on the electrode surface. These observations provide information to suggest conditions that will induce cable bacteria to perform electron donation to an electrode, informing future experiments that culture cable bacteria outside of sediment.
Marie Maßmig, Jan Lüdke, Gerd Krahmann, and Anja Engel
Biogeosciences, 17, 215–230, https://doi.org/10.5194/bg-17-215-2020, https://doi.org/10.5194/bg-17-215-2020, 2020
Short summary
Short summary
Little is known about the rates of bacterial element cycling in oxygen minimum zones (OMZs). We measured bacterial production and rates of extracellular hydrolytic enzymes at various in situ oxygen concentrations in the OMZ off Peru. Our field data show unhampered bacterial activity at low oxygen concentrations. Meanwhile bacterial degradation of organic matter substantially contributed to the formation of the OMZ.
Anna T. Kunert, Mira L. Pöhlker, Kai Tang, Carola S. Krevert, Carsten Wieder, Kai R. Speth, Linda E. Hanson, Cindy E. Morris, David G. Schmale III, Ulrich Pöschl, and Janine Fröhlich-Nowoisky
Biogeosciences, 16, 4647–4659, https://doi.org/10.5194/bg-16-4647-2019, https://doi.org/10.5194/bg-16-4647-2019, 2019
Short summary
Short summary
A screening of more than 100 strains from 65 different species revealed that the ice nucleation activity within the fungal genus Fusarium is more widespread than previously assumed. Filtration experiments suggest that the single cell-free Fusarium IN is smaller than 100 kDa (~ 6 nm) and that aggregates can be formed in solution. Exposure experiments, freeze–thaw cycles, and long-term storage tests demonstrate a high stability of Fusarium IN under atmospherically relevant conditions.
Qing Wang, Renbin Zhu, Yanling Zheng, Tao Bao, and Lijun Hou
Biogeosciences, 16, 4113–4128, https://doi.org/10.5194/bg-16-4113-2019, https://doi.org/10.5194/bg-16-4113-2019, 2019
Short summary
Short summary
We investigated abundance, potential activity, and diversity of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) in five Antarctic tundra patches, including penguin colony, seal colony, and tundra marsh. We have found (1) sea animal colonization increased AOB population size.; (2) AOB contributed to ammonia oxidation rates more than AOA in sea animal colonies; (3) community structures of AOB and AOA were closely related to soil biogeochemical processes associated with animal activities.
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