1
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Guo Y, Cheng S, Fang H, Geng J, Li Y, Shi F, Wang H, Chen L, Zhou Y. Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135626. [PMID: 39197279 DOI: 10.1016/j.jhazmat.2024.135626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/27/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024]
Abstract
The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.
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Affiliation(s)
- Yifan Guo
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shulan Cheng
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huajun Fang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; The Zhongke-Ji'an Institute for Eco-Environmental Sciences, Ji'an 343000, China.
| | - Jing Geng
- School of Geospatial Engineering and Science, Sun Yat-sen University, Zhuhai 519082, China
| | - Yuna Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangying Shi
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long Chen
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zhou
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Dalcin Martins P, de Monlevad JPC, Echeveste Medrano MJ, Lenstra WK, Wallenius AJ, Hermans M, Slomp CP, Welte CU, Jetten MSM, van Helmond NAGM. Sulfide Toxicity as Key Control on Anaerobic Oxidation of Methane in Eutrophic Coastal Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11421-11435. [PMID: 38888209 PMCID: PMC11223495 DOI: 10.1021/acs.est.3c10418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
Coastal zones account for 75% of marine methane emissions, despite covering only 15% of the ocean surface area. In these ecosystems, the tight balance between methane production and oxidation in sediments prevents most methane from escaping into seawater. However, anthropogenic activities could disrupt this balance, leading to an increased methane escape from coastal sediments. To quantify and unravel potential mechanisms underlying this disruption, we used a suite of biogeochemical and microbiological analyses to investigate the impact of anthropogenically induced redox shifts on methane cycling in sediments from three sites with contrasting bottom water redox conditions (oxic-hypoxic-euxinic) in the eutrophic Stockholm Archipelago. Our results indicate that the methane production potential increased under hypoxia and euxinia, while anaerobic oxidation of methane was disrupted under euxinia. Experimental, genomic, and biogeochemical data suggest that the virtual disappearance of methane-oxidizing archaea at the euxinic site occurred due to sulfide toxicity. This could explain a near 7-fold increase in the extent of escape of benthic methane at the euxinic site relative to the hypoxic one. In conclusion, these insights reveal how the development of euxinia could disrupt the coastal methane biofilter, potentially leading to increased methane emissions from coastal zones.
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Affiliation(s)
- Paula Dalcin Martins
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
- Department
of Ecosystem and Landscape Dynamics, Institute for Biodiversity and
Ecosystem Dynamics (IBED), University of
Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - João P.
R. C. de Monlevad
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Maider J. Echeveste Medrano
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Wytze Klaas Lenstra
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
- Department
of Earth Sciences—Geochemistry, Utrecht
University, Utrecht 3584 CB, The Netherlands
| | - Anna Julia Wallenius
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Martijn Hermans
- Department
of Earth Sciences—Geochemistry, Utrecht
University, Utrecht 3584 CB, The Netherlands
- Baltic
Sea Centre, Stockholm University, Stockholm 114 18, Sweden
| | - Caroline P. Slomp
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
- Department
of Earth Sciences—Geochemistry, Utrecht
University, Utrecht 3584 CB, The Netherlands
| | - Cornelia Ulrike Welte
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Mike S. M. Jetten
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Niels A. G. M. van Helmond
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
- Department
of Earth Sciences—Geochemistry, Utrecht
University, Utrecht 3584 CB, The Netherlands
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3
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Soued C, Bogard MJ, Finlay K, Bortolotti LE, Leavitt PR, Badiou P, Knox SH, Jensen S, Mueller P, Lee SC, Ng D, Wissel B, Chan CN, Page B, Kowal P. Salinity causes widespread restriction of methane emissions from small inland waters. Nat Commun 2024; 15:717. [PMID: 38267478 PMCID: PMC10808391 DOI: 10.1038/s41467-024-44715-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024] Open
Abstract
Inland waters are one of the largest natural sources of methane (CH4), a potent greenhouse gas, but emissions models and estimates were developed for solute-poor ecosystems and may not apply to salt-rich inland waters. Here we combine field surveys and eddy covariance measurements to show that salinity constrains microbial CH4 cycling through complex mechanisms, restricting aquatic emissions from one of the largest global hardwater regions (the Canadian Prairies). Existing models overestimated CH4 emissions from ponds and wetlands by up to several orders of magnitude, with discrepancies linked to salinity. While not significant for rivers and larger lakes, salinity interacted with organic matter availability to shape CH4 patterns in small lentic habitats. We estimate that excluding salinity leads to overestimation of emissions from small Canadian Prairie waterbodies by at least 81% ( ~ 1 Tg yr-1 CO2 equivalent), a quantity comparable to other major national emissions sources. Our findings are consistent with patterns in other hardwater landscapes, likely leading to an overestimation of global lentic CH4 emissions. Widespread salinization of inland waters may impact CH4 cycling and should be considered in future projections of aquatic emissions.
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Affiliation(s)
- Cynthia Soued
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Matthew J Bogard
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada.
| | - Kerri Finlay
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Institute of Environmental Change and Society, University of Regina, S4S 0A2, Regina, SK, Canada
| | - Lauren E Bortolotti
- Institute for Wetland & Waterfowl Research, Ducks Unlimited Canada, PO Box 1160, R0C 2Z0, Stonewall, MB, Canada
| | - Peter R Leavitt
- Institute of Environmental Change and Society, University of Regina, S4S 0A2, Regina, SK, Canada
- Limnology Laboratory, Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Pascal Badiou
- Institute for Wetland & Waterfowl Research, Ducks Unlimited Canada, PO Box 1160, R0C 2Z0, Stonewall, MB, Canada
| | - Sara H Knox
- Department of Geography, The University of British Columbia, Vancouver, BC, Canada
- Department of Geography, McGill University, Montreal, QC, Canada
| | - Sydney Jensen
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Peka Mueller
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Sung Ching Lee
- Department of Geography, The University of British Columbia, Vancouver, BC, Canada
- Department of Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Darian Ng
- Department of Geography, The University of British Columbia, Vancouver, BC, Canada
| | - Björn Wissel
- Institute of Environmental Change and Society, University of Regina, S4S 0A2, Regina, SK, Canada
- LEHNA, Université Claude Bernard Lyon 1, 69622, Villeurbanne, Cedex, France
| | - Chun Ngai Chan
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Bryan Page
- Institute for Wetland & Waterfowl Research, Ducks Unlimited Canada, PO Box 1160, R0C 2Z0, Stonewall, MB, Canada
| | - Paige Kowal
- Institute for Wetland & Waterfowl Research, Ducks Unlimited Canada, PO Box 1160, R0C 2Z0, Stonewall, MB, Canada
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4
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Bansal S, Creed IF, Tangen BA, Bridgham SD, Desai AR, Krauss KW, Neubauer SC, Noe GB, Rosenberry DO, Trettin C, Wickland KP, Allen ST, Arias-Ortiz A, Armitage AR, Baldocchi D, Banerjee K, Bastviken D, Berg P, Bogard MJ, Chow AT, Conner WH, Craft C, Creamer C, DelSontro T, Duberstein JA, Eagle M, Fennessy MS, Finkelstein SA, Göckede M, Grunwald S, Halabisky M, Herbert E, Jahangir MMR, Johnson OF, Jones MC, Kelleway JJ, Knox S, Kroeger KD, Kuehn KA, Lobb D, Loder AL, Ma S, Maher DT, McNicol G, Meier J, Middleton BA, Mills C, Mistry P, Mitra A, Mobilian C, Nahlik AM, Newman S, O’Connell JL, Oikawa P, van der Burg MP, Schutte CA, Song C, Stagg CL, Turner J, Vargas R, Waldrop MP, Wallin MB, Wang ZA, Ward EJ, Willard DA, Yarwood S, Zhu X. Practical Guide to Measuring Wetland Carbon Pools and Fluxes. WETLANDS (WILMINGTON, N.C.) 2023; 43:105. [PMID: 38037553 PMCID: PMC10684704 DOI: 10.1007/s13157-023-01722-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/24/2023] [Indexed: 12/02/2023]
Abstract
Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades of research, many observational, experimental, and analytical approaches have been developed to understand and quantify pools and fluxes of wetland C. Sampling approaches range in their representation of wetland C from short to long timeframes and local to landscape spatial scales. This review summarizes common and cutting-edge methodological approaches for quantifying wetland C pools and fluxes. We first define each of the major C pools and fluxes and provide rationale for their importance to wetland C dynamics. For each approach, we clarify what component of wetland C is measured and its spatial and temporal representativeness and constraints. We describe practical considerations for each approach, such as where and when an approach is typically used, who can conduct the measurements (expertise, training requirements), and how approaches are conducted, including considerations on equipment complexity and costs. Finally, we review key covariates and ancillary measurements that enhance the interpretation of findings and facilitate model development. The protocols that we describe to measure soil, water, vegetation, and gases are also relevant for related disciplines such as ecology. Improved quality and consistency of data collection and reporting across studies will help reduce global uncertainties and develop management strategies to use wetlands as nature-based climate solutions. Supplementary Information The online version contains supplementary material available at 10.1007/s13157-023-01722-2.
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Affiliation(s)
- Sheel Bansal
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND USA
| | - Irena F. Creed
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON Canada
| | - Brian A. Tangen
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND USA
| | - Scott D. Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR USA
| | - Ankur R. Desai
- Department of Atmospheric and Oceanic Sciences, University of Wisconsin-Madison, Madison, WI USA
| | - Ken W. Krauss
- U.S. Geological Survey, Wetland and Aquatic Research Center, Lafayette, LA USA
| | - Scott C. Neubauer
- Department of Biology, Virginia Commonwealth University, Richmond, VA USA
| | - Gregory B. Noe
- U.S. Geological Survey, Florence Bascom Geoscience Center, Reston, VA USA
| | | | - Carl Trettin
- U.S. Forest Service, Pacific Southwest Research Station, Davis, CA USA
| | - Kimberly P. Wickland
- U.S. Geological Survey, Geosciences and Environmental Change Science Center, Denver, CO USA
| | - Scott T. Allen
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, Reno, NV USA
| | - Ariane Arias-Ortiz
- Ecosystem Science Division, Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
| | - Anna R. Armitage
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX USA
| | - Dennis Baldocchi
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
| | - Kakoli Banerjee
- Department of Biodiversity and Conservation of Natural Resources, Central University of Odisha, Koraput, Odisha India
| | - David Bastviken
- Department of Thematic Studies – Environmental Change, Linköping University, Linköping, Sweden
| | - Peter Berg
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA USA
| | - Matthew J. Bogard
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
| | - Alex T. Chow
- Earth and Environmental Sciences Programme, The Chinese University of Hong Kong, Shatin, Hong Kong SAR China
| | - William H. Conner
- Baruch Institute of Coastal Ecology and Forest Science, Clemson University, Georgetown, SC USA
| | - Christopher Craft
- O’Neill School of Public and Environmental Affairs, Indiana University, Bloomington, IN USA
| | - Courtney Creamer
- U.S. Geological Survey, Geology, Minerals, Energy and Geophysics Science Center, Menlo Park, CA USA
| | - Tonya DelSontro
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, ON Canada
| | - Jamie A. Duberstein
- Baruch Institute of Coastal Ecology and Forest Science, Clemson University, Georgetown, SC USA
| | - Meagan Eagle
- U.S. Geological Survey, Woods Hole Coastal & Marine Science Center, Woods Hole, MA USA
| | | | | | - Mathias Göckede
- Department for Biogeochemical Signals, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Sabine Grunwald
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL USA
| | - Meghan Halabisky
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA USA
| | | | | | - Olivia F. Johnson
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND USA
- Departments of Biology and Environmental Studies, Kent State University, Kent, OH USA
| | - Miriam C. Jones
- U.S. Geological Survey, Florence Bascom Geoscience Center, Reston, VA USA
| | - Jeffrey J. Kelleway
- School of Earth, Atmospheric and Life Sciences and Environmental Futures Research Centre, University of Wollongong, Wollongong, NSW Australia
| | - Sara Knox
- Department of Geography, McGill University, Montreal, Canada
| | - Kevin D. Kroeger
- U.S. Geological Survey, Woods Hole Coastal & Marine Science Center, Woods Hole, MA USA
| | - Kevin A. Kuehn
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS USA
| | - David Lobb
- Department of Soil Science, University of Manitoba, Winnipeg, MB Canada
| | - Amanda L. Loder
- Department of Geography, University of Toronto, Toronto, ON Canada
| | - Shizhou Ma
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK Canada
| | - Damien T. Maher
- Faculty of Science and Engineering, Southern Cross University, Lismore, NSW Australia
| | - Gavin McNicol
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, IL USA
| | - Jacob Meier
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND USA
| | - Beth A. Middleton
- U.S. Geological Survey, Wetland and Aquatic Research Center, Lafayette, LA USA
| | - Christopher Mills
- U.S. Geological Survey, Geology, Geophysics, and Geochemistry Science Center, Denver, CO USA
| | - Purbasha Mistry
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK Canada
| | - Abhijit Mitra
- Department of Marine Science, University of Calcutta, Kolkata, West Bengal India
| | - Courtney Mobilian
- O’Neill School of Public and Environmental Affairs, Indiana University, Bloomington, IN USA
| | - Amanda M. Nahlik
- Office of Research and Development, Center for Public Health and Environmental Assessments, Pacific Ecological Systems Division, U.S. Environmental Protection Agency, Corvallis, OR USA
| | - Sue Newman
- South Florida Water Management District, Everglades Systems Assessment Section, West Palm Beach, FL USA
| | - Jessica L. O’Connell
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, CO USA
| | - Patty Oikawa
- Department of Earth and Environmental Sciences, California State University, East Bay, Hayward, CA USA
| | - Max Post van der Burg
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND USA
| | - Charles A. Schutte
- Department of Environmental Science, Rowan University, Glassboro, NJ USA
| | - Changchun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Camille L. Stagg
- U.S. Geological Survey, Wetland and Aquatic Research Center, Lafayette, LA USA
| | - Jessica Turner
- Freshwater and Marine Science, University of Wisconsin-Madison, Madison, WI USA
| | - Rodrigo Vargas
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE USA
| | - Mark P. Waldrop
- U.S. Geological Survey, Geology, Minerals, Energy and Geophysics Science Center, Menlo Park, CA USA
| | - Marcus B. Wallin
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Zhaohui Aleck Wang
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Eric J. Ward
- U.S. Geological Survey, Wetland and Aquatic Research Center, Lafayette, LA USA
| | - Debra A. Willard
- U.S. Geological Survey, Florence Bascom Geoscience Center, Reston, VA USA
| | - Stephanie Yarwood
- Environmental Science and Technology, University of Maryland, College Park, MD USA
| | - Xiaoyan Zhu
- Key Laboratory of Songliao Aquatic Environment, Ministry of Education, Jilin Jianzhu University, Changchun, China
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5
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Cornish CM, Bergholz P, Schmidt K, Sweetman J. How Benthic Sediment Microbial Communities Respond to Glyphosate and Its Metabolite: a Microcosm Experiment. MICROBIAL ECOLOGY 2023; 86:2949-2958. [PMID: 37674014 DOI: 10.1007/s00248-023-02296-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023]
Abstract
Glyphosate is the most commonly used agricultural herbicide in the world. In aquatic ecosystems, glyphosate often adsorbs to benthic substrates or is metabolized and degraded by microorganisms. The effects of glyphosate on microbial communities vary widely as microorganisms respond differently to exposure. To help understand the impacts of glyphosate on the sediment microbiome, we conducted a microcosm experiment examining the responses of benthic sediment microbial communities to herbicide treatments. Sediments from a prairie pothole wetland were collected, and 16S rRNA gene sequencing was used to analyze community composition 2-h and 14-days after a single treatment of low (0.07 ppm), medium (0.7 ppm), or high (7 ppm) glyphosate, aminomethylphosphonic acid (glyphosate metabolite), or a glyphosate-based commercial formula. We found no significant differences in microbial community composition across treatments, concentration levels, or day of sampling. These findings suggest that microbial species in the Prairie Pothole Region of North America may be tolerant to glyphosate exposure.
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Affiliation(s)
- Christine M Cornish
- Department of Biological Sciences, North Dakota State University, Fargo, ND, 58105, USA.
| | - Peter Bergholz
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58105, USA
- Institute for Quantitative Health Sciences & Engineering, Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48823, USA
| | - Kaycie Schmidt
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58105, USA
| | - Jon Sweetman
- Department of Biological Sciences, North Dakota State University, Fargo, ND, 58105, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
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6
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Sheng M, Chen S, Liu CQ, Fu Q, Zhang D, Hu W, Deng J, Wu L, Li P, Yan Z, Zhu YG, Fu P. Spatial and molecular variations in forest topsoil dissolved organic matter as revealed by FT-ICR mass spectrometry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165099. [PMID: 37379928 DOI: 10.1016/j.scitotenv.2023.165099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/01/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023]
Abstract
Forest soils cover about 30 % of the Earth's land surface and play a fundamental role in the global cycle of organic matter. Dissolved organic matter (DOM), the largest active pool of terrestrial carbon, is essential for soil development, microbial metabolism and nutrient cycling. However, forest soil DOM is a highly complex mixture of tens of thousands of individual compounds, which is largely composed of organic matter from primary producers, residues from microbial process and the corresponding chemical reactions. Therefore, we need a detailed picture of molecular composition in forest soil, especially the pattern of large-scale spatial distribution, which can help us understand the role of DOM in the carbon cycle. To explore the spatial and molecular variations of DOM in forest soil, we choose six major forest reserves located in different latitudes ranging in China, which were investigated by Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). Results show that aromatic-like molecules are preferentially enriched in DOM at high latitude forest soils, while aliphatic/peptide-like, carbohydrate-like, and unsaturated hydrocarbon molecules are preferentially enriched in DOM at low latitude forest soils, besides, lignin-like compounds account for the highest proportion in all forest soil DOM. High latitude forest soils have higher aromatic equivalents and aromatic indices than low latitude forest soils, which suggest that organic matter at higher latitude forest soils preferentially contain plant-derived ingredients and are refractory to degradation while microbially derived carbon is dominant in organic matter at low latitudes. Besides, we found that CHO and CHON compounds make up the majority in all forest soil samples. Finally, we visualized the complexity and diversity of soil organic matter molecules through network analysis. Our study provides a molecular-level understanding of forest soil organic matter at large scales, which may contribute to the conservation and utilization of forest resources.
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Affiliation(s)
- Ming Sheng
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Shuang Chen
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.
| | - Qinglong Fu
- School of Environment Studies, China University of Geosciences, Wuhan 430074, China
| | - Donghuan Zhang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Wei Hu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Junjun Deng
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Libin Wu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Ping Li
- LAPC, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China
| | - Zhifeng Yan
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Pingqing Fu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.
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7
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Lacroix EM, Aeppli M, Boye K, Brodie E, Fendorf S, Keiluweit M, Naughton HR, Noël V, Sihi D. Consider the Anoxic Microsite: Acknowledging and Appreciating Spatiotemporal Redox Heterogeneity in Soils and Sediments. ACS EARTH & SPACE CHEMISTRY 2023; 7:1592-1609. [PMID: 37753209 PMCID: PMC10519444 DOI: 10.1021/acsearthspacechem.3c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/07/2023] [Accepted: 07/21/2023] [Indexed: 09/28/2023]
Abstract
Reduction-oxidation (redox) reactions underlie essentially all biogeochemical cycles. Like most soil properties and processes, redox is spatiotemporally heterogeneous. However, unlike other soil features, redox heterogeneity has yet to be incorporated into mainstream conceptualizations of soil biogeochemistry. Anoxic microsites, the defining feature of redox heterogeneity in bulk oxic soils and sediments, are zones of oxygen depletion in otherwise oxic environments. In this review, we suggest that anoxic microsites represent a critical component of soil function and that appreciating anoxic microsites promises to advance our understanding of soil and sediment biogeochemistry. In sections 1 and 2, we define anoxic microsites and highlight their dynamic properties, specifically anoxic microsite distribution, redox gradient magnitude, and temporality. In section 3, we describe the influence of anoxic microsites on several key elemental cycles, organic carbon, nitrogen, iron, manganese, and sulfur. In section 4, we evaluate methods for identifying and characterizing anoxic microsites, and in section 5, we highlight past and current approaches to modeling anoxic microsites. Finally, in section 6, we suggest steps for incorporating anoxic microsites and redox heterogeneities more broadly into our understanding of soils and sediments.
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Affiliation(s)
- Emily M. Lacroix
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Meret Aeppli
- Institut
d’ingénierie de l’environnement (IIE), École Polytechnique Fédérale
de Lausanne, 1015 Lausanne, Switzerland
| | - Kristin Boye
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Eoin Brodie
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Scott Fendorf
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Marco Keiluweit
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
| | - Hannah R. Naughton
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Vincent Noël
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Debjani Sihi
- Department
of Environmental Sciences, Emory University, Atlanta, Georgia 30322, United States
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8
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Qian L, Yu X, Gu H, Liu F, Fan Y, Wang C, He Q, Tian Y, Peng Y, Shu L, Wang S, Huang Z, Yan Q, He J, Liu G, Tu Q, He Z. Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes. MICROBIOME 2023; 11:71. [PMID: 37020239 PMCID: PMC10074775 DOI: 10.1186/s40168-023-01501-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH4), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches. RESULTS Our results showed that the metabolic pathways involved in CH4, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N2O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments. CONCLUSIONS In addition to offering a perspective on the vertical distribution of microbially driven CH4, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N2O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.
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Affiliation(s)
- Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yijun Fan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qiang He
- Department of Civil and Environmental Engineering, the University of Tennessee, Knoxville, TN 37996 USA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhijian Huang
- School of Marine Science, Sun Yat-Sen University, Zhuhai, 519080 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Jianguo He
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Guangli Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
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9
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Bansal S, Post van der Burg M, Fern RR, Jones JW, Lo R, McKenna OP, Tangen BA, Zhang Z, Gleason RA. Large increases in methane emissions expected from North America's largest wetland complex. SCIENCE ADVANCES 2023; 9:eade1112. [PMID: 36857447 PMCID: PMC9977182 DOI: 10.1126/sciadv.ade1112] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Natural methane (CH4) emissions from aquatic ecosystems may rise because of human-induced climate warming, although the magnitude of increase is highly uncertain. Using an exceptionally large CH4 flux dataset (~19,000 chamber measurements) and remotely sensed information, we modeled plot- and landscape-scale wetland CH4 emissions from the Prairie Pothole Region (PPR), North America's largest wetland complex. Plot-scale CH4 emissions were driven by hydrology, temperature, vegetation, and wetland size. Historically, landscape-scale PPR wetland CH4 emissions were largely dependent on total wetland extent. However, regardless of future wetland extent, PPR CH4 emissions are predicted to increase by two- or threefold by 2100 under moderate or severe warming scenarios, respectively. Our findings suggest that international efforts to decrease atmospheric CH4 concentrations should jointly account for anthropogenic and natural emissions to maintain climate mitigation targets to the end of the century.
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Affiliation(s)
- Sheel Bansal
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND, USA
| | - Max Post van der Burg
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND, USA
| | - Rachel R. Fern
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND, USA
- Texas Parks and Wildlife Department, San Marcos, TX, USA
| | - John W. Jones
- U.S. Geological Survey, Hydrologic Remote Sensing Branch, Kearneysville, WV, USA
| | - Rachel Lo
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND, USA
| | - Owen P. McKenna
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND, USA
| | - Brian A. Tangen
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND, USA
| | - Zhen Zhang
- Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD, USA
| | - Robert A. Gleason
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Jamestown, ND, USA
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10
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Torgeson JM, Rosenfeld CE, Dunshee AJ, Duhn K, Schmitter R, O'Hara PA, Ng GHC, Santelli CM. Hydrobiogechemical interactions in the hyporheic zone of a sulfate-impacted, freshwater stream and riparian wetland ecosystem. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1360-1382. [PMID: 35661843 DOI: 10.1039/d2em00024e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Coupled abiotic and biotic processes in the hyporheic zone, where surface water and groundwater mix, play a critical role in the biogeochemical cycling of carbon, nutrients, and trace elements in streams and wetlands. Dynamic hydrologic conditions and anthropogenic pollution can impact redox gradients and biogeochemical response, although few studies examine the resulting hydrobiogeochemical interactions generated within the hyporheic zone. This study examines the effect of hyporheic flux dynamics and anthropogenic sulfate loading on the biogeochemistry of a riparian wetland and stream system. The hydrologic gradient as well as sediment, surface water, and porewater geochemistry chemistry was characterized at multiple points throughout the 2017 spring-summer-fall season at a sulfate-impacted stream flanked by wetlands in northern Minnesota. Results show that organic-rich sediments largely buffer the geochemical responses to brief or low magnitude changes in hydrologic gradient, but sustained or higher magnitude fluxes may variably alter the redox regime and, ultimately, the environmental geochemistry. This has implications for a changing climate that is expected to dramatically alter the hydrological cycle. Further, increased sulfate loading and dissolved or adsorbed ferric iron complexes in the hyporheic zone may induce a cryptic sulfur cycle linked to iron and carbon cycling, as indicated by the abundance of intermediate valence sulfur compounds (e.g., polysulfide, elemental sulfur, thiosulfate) throughout the anoxic wetland and stream-channel sediment column. The observed deviation from a classical redox tower coupled with potential changes in hydraulic gradient in these organic-rich wetland and stream hyporheic zones has implications for nutrient, trace element, and greenhouse gas fluxes into surface water and groundwater, ultimately influencing water quality and global climate.
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Affiliation(s)
- Joshua M Torgeson
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Carla E Rosenfeld
- Section of Minerals and Earth Sciences, Carnegie Museum of Natural History, USA.
| | - Aubrey J Dunshee
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Kelly Duhn
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
| | - Riley Schmitter
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Patrick A O'Hara
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - G H Crystal Ng
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
- St. Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cara M Santelli
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
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11
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Gilmour K, Hoggarth C, Williams C, Baulch HM. Cold spots and cold moments: The potential for sediment freezing to depress denitrification in wetland sediments. JOURNAL OF ENVIRONMENTAL QUALITY 2022; 51:990-1002. [PMID: 35819079 DOI: 10.1002/jeq2.20384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Within the north-temperate zone, winters can be long and are associated with conditions of low temperature and potential for sediment freezing. There are critical gaps in our knowledge of biogeochemical cycling during winter and inadequate knowledge of how warming winters and changing snowpack might affect biogeochemistry. Here, we assessed the impacts of sediment freeze-thaw cycling and nitrate amendment on denitrification rates in the littoral fringe of four urban wetlands. We demonstrate the potential for experimental sediment freezing to suppress denitrification, although freezing effects were not observed at all sites. Multiple freeze-thaw cycles were assessed, and, although subsequent cycles may affect denitrification, the first instance of our experimental freezing seems the most critical. Although this work demonstrates potential sensitivity of wetland denitrification rates to changing winter conditions, we note nitrate availability has a larger impact upon denitrification rates. This suggests nitrification rates and changing nitrate loads may be more important determinants of nitrate retention than sediment freeze-thaw history. Although there has been great interest in hot spots and moments for biogeochemical cycling, we suggest there is similar need to understand cold spots and moments, as evidenced here. This is particularly important where cold moments may correspond with critical periods of nitrate transport, such as snowmelt.
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Affiliation(s)
- Kimberly Gilmour
- Dep. of Biology, Univ. of Saskatchewan, 112 Science Place, Saskatoon, SK, S7N 5E2, Canada
- Global Institute for Water Security National Hydrology Research Centre, 11 Innovation Blvd, Saskatoon, SK, S7N 3H5, Canada
| | - Cameron Hoggarth
- Global Institute for Water Security National Hydrology Research Centre, 11 Innovation Blvd, Saskatoon, SK, S7N 3H5, Canada
| | - Clayton Williams
- Dep. of Environmental Studies and Science, Saint Michael's College, One Winooski Park, Colchester, VT 05439, USA
| | - Helen M Baulch
- Global Institute for Water Security National Hydrology Research Centre, 11 Innovation Blvd, Saskatoon, SK, S7N 3H5, Canada
- School of Environment and Sustainability, Univ. of Saskatchewan, 117 Science Place, Saskatoon, SK, S7N 5C8, Canada
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12
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Yang M, Liu CQ, Li XD, Ding S, Cui G, Teng HH, Lv H, Wang Y, Zhang X, Guan T. Carbon‑sulfur coupling in a seasonally hypoxic, high-sulfate reservoir in SW China: Evidence from stable CS isotopes and sulfate-reducing bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154537. [PMID: 35292324 DOI: 10.1016/j.scitotenv.2022.154537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/08/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Anthropogenic input of sulfate (SO42-) in reservoirs may enhance bacterial sulfate reduction (BSR) under seasonally hypoxic conditions in the water column. However, factors that control BSR and its coupling to organic carbon (OC) mineralization in seasonally hypoxic reservoirs remain unclear. The present study elucidates the coupling processes by analyzing the concentrations and isotopic composition of dissolved inorganic carbon (DIC) and sulfur (SO42-, sulfide) species, and the microbial community in water of the Aha reservoir, SW China, which has high SO42- concentration due to the inputs from acid mine drainage about twenty years ago. The water column at two sites in July and October revealed significant thermal stratification. In the hypoxic bottom water, the δ13C-DIC decreased while the δ34S-SO42- increased, implying organic carbon mineralization due to BSR. The magnitude of S isotope fractionation (Δ34S, obtained from δ34Ssulfate-δ34Ssulfide) during the process of BSR fell in the range of 3.4‰ to 27.0‰ in July and 21.6‰ to 31.8‰ in October, suggesting a change in the community of sulfate-reducing bacteria (SRB). The relatively low water column stability in October compared to that in July weakened the difference of water chemistry and ultimately affected the SRB diversity. The production of DIC (ΔDIC) scaled a strong positive relationship with the Δ34S in July (p < 0.01), indicating that high OC availability favored the survival of incomplete oxidizers of SRB. However, in October, Δ13C-DIC was correlated with the Δ34S in the bottom hypoxic water (p < 0.01), implying that newly degraded OC depleted in 13C could favor the dominance of complete oxidizers of SRB which caused greater S isotope fractionation. Moreover, the sulfide supplied by BSR might stimulate the reductive dissolution of Fe and Mn oxides (Fe(O)OH and MnO2). The present study helps to understand the coupling of C and S in seasonally hypoxic reservoirs characterized by high SO42- concentration.
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Affiliation(s)
- Mengdi Yang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Earth's Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China
| | - Xiao-Dong Li
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Earth's Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China.
| | - Shiyuan Ding
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; State Key Laboratory of Environmental Geochemistry, Guiyang 550081, China
| | - Gaoyang Cui
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Environment and Planning, Henan University, Kaifeng 475004, China
| | - Hui Henry Teng
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Hong Lv
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Yiyao Wang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Xuecheng Zhang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Tianhao Guan
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
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13
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Baron AAP, Dyck LT, Amjad H, Bragg J, Kroft E, Newson J, Oleson K, Casson NJ, North RL, Venkiteswaran JJ, Whitfield CJ. Differences in ebullitive methane release from small, shallow ponds present challenges for scaling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149685. [PMID: 34464805 DOI: 10.1016/j.scitotenv.2021.149685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/16/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Small, shallow waterbodies are potentially important sites of greenhouse gas release to the atmosphere. The role of ebullition may be enhanced here relative to larger and deeper systems, due to their shallow water, but these features remain relatively infrequently studied in comparison to larger systems. Herein, we quantify ebullitive release of methane (CH4) in small shallow ponds in three regions of North America and investigate the role of potential drivers. Shallow ponds exhibited open-water season ebullitive CH4 release rates as high as 40 mmol m-2 d-1, higher than previously reported for similar systems. Ebullitive release of CH4 varied by four orders of magnitude across our 15 study sites, with differences in flux rates both within and between regions. What is less clear are the drivers responsible for these differences. There were few relationships between open water-season ebullitive flux and physicochemical characteristics, including organic matter, temperature, and sulphate. Temperature was only weakly related to ebullitive CH4 release across the study when considering all observation intervals. Only four individual sites exhibited significant relationships between temperature and ebullitive CH4 release. Other sites were unresponsive to temperature, and region-specific factors may play a role. There is some evidence that where surface water sulphate concentrations are high, CH4 production and release may be suppressed. Missouri sites (n = 5) had characteristically low ebullitive CH4 release; here bioturbation could be important. While this work greatly expands the number of open-water season ebullition rates for small and shallow ponds, more research is needed to disentangle the role of different drivers. Further investigation of the potential thresholding behaviour of sulphate as a control on ebullitive CH4 release in lentic systems is one such opportunity. What is clear, however, is that efforts to scale emissions (e.g., as a function of temperature) must be undertaken with caution.
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Affiliation(s)
- A A P Baron
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK S7N 3H5, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK S7N 3H5, Canada
| | - L T Dyck
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK S7N 3H5, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK S7N 3H5, Canada
| | - H Amjad
- Department of Geography, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
| | - J Bragg
- School of Natural Resources, University of Missouri, Columbia, MO 65211, United States of America
| | - E Kroft
- Department of Geography, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
| | - J Newson
- School of Natural Resources, University of Missouri, Columbia, MO 65211, United States of America
| | - K Oleson
- Department of Geography, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
| | - N J Casson
- Department of Geography, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
| | - R L North
- School of Natural Resources, University of Missouri, Columbia, MO 65211, United States of America
| | - J J Venkiteswaran
- Department of Geography and Environmental Studies, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
| | - C J Whitfield
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK S7N 3H5, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK S7N 3H5, Canada.
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14
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Davidson SJ, Smith M, Prystupa E, Murray K, Nwaishi FC, Petrone RM, Strack M. High sulfate concentrations maintain low methane emissions at a constructed fen over the first seven years of ecosystem development. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:148014. [PMID: 34323820 DOI: 10.1016/j.scitotenv.2021.148014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/14/2021] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
Wetlands comprise a large expanse of the pre-disturbance landscape in the Athabasca Oil Sands Region (AOSR) and have become a focus of reclamation in recent years. An important aspect of wetland reclamation is understanding the biogeochemical functioning and carbon exchange, including methane (CH4) emissions, in the developing ecosystem. This study investigates the drivers of CH4 emissions over the first seven years of ecosystem development at a constructed fen in the AOSR and looks towards future CH4 emissions from this site. Specifically, the objectives were to: 1) investigate the environmental controls on CH4 emissions measured using manual static chambers between 2013 and 2019 and 2) investigate the relationship between water table depth, sulfate (SO42-) concentrations and CH4 emissions during the 2019 growing season. Methane emissions remained low throughout the majority of the measurement period; however, in later years, a small but significant increase became apparent. High levels of SO42- are likely the cause of the low CH4 emissions, despite the high-water tables and dominance of vegetation with aerenchyma such as Carex aquatilis and Typha latifolia in later years. Although low CH4 emissions may be beneficial from a climate warming perspective, the results also suggest that this constructed peatland is not functioning similarly to regional reference fens. Future climate scenarios across Western Boreal Canada could lead to higher air temperatures and changing precipitation patterns, influencing the direction of future CH4 emissions from this site. However, given the likelihood of this site maintaining extremely high SO42- concentrations over the next decade, it is expected that CH4 emissions will remain low.
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Affiliation(s)
- Scott J Davidson
- Department of Geography and Environmental Management, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
| | - Mariah Smith
- Department of Geography and Environmental Management, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Emily Prystupa
- Department of Geography and Environmental Management, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Kimberley Murray
- Department of Geography and Environmental Management, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Felix C Nwaishi
- Department of Earth and Environmental Sciences, Mount Royal University, 4825 Mt Royal Gate SW, Calgary, AB T3E 6K6, Canada
| | - Richard M Petrone
- Department of Geography and Environmental Management, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Maria Strack
- Department of Geography and Environmental Management, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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15
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Abstract
Interactions between soils and climate impact wider environmental sustainability. Soil heterogeneity intricately regulates these interactions over short spatiotemporal scales and therefore needs to be more finely examined. This paper examines how redox heterogeneity at the level of minerals, microbial cells, organic matter, and the rhizosphere entangles biogeochemical cycles in soil with climate change. Redox heterogeneity is used to develop a conceptual framework that encompasses soil microsites (anaerobic and aerobic) and cryptic biogeochemical cycling, helping to explain poorly understood processes such as methanogenesis in oxygenated soils. This framework is further shown to disentangle global carbon (C) and nitrogen (N) pathways that include CO2, CH4, and N2O. Climate-driven redox perturbations are discussed using wetlands and tropical forests as model systems. Powerful analytical methods are proposed to be combined and used more extensively to study coupled abiotic and biotic reactions that are affected by redox heterogeneity. A core view is that emerging and future research will benefit substantially from developing multifaceted analyses of redox heterogeneity over short spatiotemporal scales in soil. Taking a leap in our understanding of soil and climate interactions and their evolving influence on environmental sustainability then depends on greater collaborative efforts to comprehensively investigate redox heterogeneity spanning the domain of microscopic soil interfaces.
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Block KR, O'Brien JM, Edwards WJ, Marnocha CL. Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake. Microbiologyopen 2021; 10:e1228. [PMID: 34459548 PMCID: PMC8330806 DOI: 10.1002/mbo3.1228] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 11/08/2022] Open
Abstract
The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.
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Affiliation(s)
| | - Joy M. O'Brien
- Department of BiologyNiagara UniversityLewistonNew YorkUSA
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17
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Bahureksa W, Tfaily MM, Boiteau RM, Young RB, Logan MN, McKenna AM, Borch T. Soil Organic Matter Characterization by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR MS): A Critical Review of Sample Preparation, Analysis, and Data Interpretation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9637-9656. [PMID: 34232025 DOI: 10.1021/acs.est.1c01135] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The biogeochemical cycling of soil organic matter (SOM) plays a central role in regulating soil health, water quality, carbon storage, and greenhouse gas emissions. Thus, many studies have been conducted to reveal how anthropogenic and climate variables affect carbon sequestration and nutrient cycling. Among the analytical techniques used to better understand the speciation and transformation of SOM, Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) is the only technique that has sufficient mass resolving power to separate and accurately assign elemental compositions to individual SOM molecules. The global increase in the application of FTICR MS to address SOM complexity has highlighted the many challenges and opportunities associated with SOM sample preparation, FTICR MS analysis, and mass spectral interpretation. Here, we provide a critical review of recent strategies for SOM characterization by FTICR MS with emphasis on SOM sample collection, preparation, analysis, and data interpretation. Data processing and visualization methods are presented with suggested workflows that detail the considerations needed for the application of molecular information derived from FTICR MS. Finally, we highlight current research gaps, biases, and future directions needed to improve our understanding of organic matter chemistry and cycling within terrestrial ecosystems.
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Affiliation(s)
- William Bahureksa
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, Tucson, Arizona 85721, United States
| | - Rene M Boiteau
- College of Earth, Ocean, Atmospheric Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Robert B Young
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170, United States
| | - Merritt N Logan
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310-4005, United States
| | - Thomas Borch
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170, United States
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18
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Influence of Temperature and Sulfate Concentration on the Sulfate/Sulfite Reduction Prokaryotic Communities in the Tibetan Hot Springs. Microorganisms 2021; 9:microorganisms9030583. [PMID: 33809110 PMCID: PMC8002027 DOI: 10.3390/microorganisms9030583] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 11/18/2022] Open
Abstract
The distribution and diversity of sulfate/sulfite reduction prokaryotic (SRP) communities in hot springs from the Quzhuomu and Daggyai Geothermal Zone of Tibetan, China, was reported for the first time. In hot springs that are naturally hyperthermal and anoxic, the sulfur cycle is one of the most active cycles of the elements. The distribution of SRP in response to temperature is of great importance to the understanding of biogeochemical cycling of sulfur in geothermal features. Little is known about the SRP in geothermal zone. In this study, the diversity of SRP was investigated in the sediments from the Daggyai and Quzhuomu geothermal zone using PCR amplification, cloning and sequencing of the dissimilatory sulfite reductase beta subunit gene (dsrB). The abundance of dsrB and 16S rRNA genes, were determined by quantitative polymerase chain reactions. In addition, correlations of the SRP assemblages with environmental factors were analyzed by the aggregated boosted tree (ABT) statistical analysis. The results showed that SRP populations were diverse, but were mainly composed of Desulfobacterales, Desulfovibrionales, Syntrophobacterales, Clostridia and Nitrospirales, and large fraction (25%) of novel sequences have branched groups in the dsrB phylogenetic tree. In Quzhuomu geothermal zone, sulfate-rich hot springs are characterized by thick bacterial mats that are green or red and the SRP populations mainly appear at mid-temperature (50 °C to 70 °C). In low-sulfate hot springs in the Daggyai geothermal zone, although gray or pink streamers are widely formed at 60 °C to 80 °C, they prefer to inhabit in green mat at lower temperature (30 °C to 50 °C). With increasing temperature, the diversity of the dsrB gene at the OTU level (cutoff 97%) decreased, while its relative abundance increased. This result suggests that temperature played an important role in affecting dsrB gene distribution.
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Using metacommunity ecology to understand environmental metabolomes. Nat Commun 2020; 11:6369. [PMID: 33311510 PMCID: PMC7732844 DOI: 10.1038/s41467-020-19989-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/29/2020] [Indexed: 12/26/2022] Open
Abstract
Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics ‘meta-metabolome ecology’ and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail. Despite growing interest in environmental metabolomics, we lack conceptual frameworks for considering how metabolites vary across space and time in ecological systems. Here, the authors apply (species) community assembly concepts to metabolomics data, offering a way forward in understanding the assembly of metabolite assemblages.
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20
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Lv X, Ma B, Lee K, Ulrich A. Potential syntrophic associations in anaerobic naphthenic acids biodegrading consortia inferred with microbial interactome networks. JOURNAL OF HAZARDOUS MATERIALS 2020; 397:122678. [PMID: 32497975 DOI: 10.1016/j.jhazmat.2020.122678] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 03/18/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Naphthenic acids (NAs) can be syntrophically metabolized by indigenous microbial communities in pristine sediments beneath oil sands tailings ponds. Syntrophy is an essential determinant of the microbial interactome, however, the interactome network in anaerobic NAs-degrading consortia has not been previously addressed due to complexity and resistance of NAs. To evaluate the impact of electron acceptors on topology of interactome networks, we inferred two microbial interactome networks for anaerobic NAs-degrading consortia under nitrate- and sulfate-reducing conditions. The complexity of the network was higher under sulfate-reducing conditions than nitrate-reducing conditions. Differences in the taxonomic composition between the two modules implies that different potential syntrophic interactions exist in each network. We inferred the presence of the same syntrophic microorganisms, from genera Bellilinea, Longilinea, and Litorilinea, initiating the metabolism in both networks, but within each network, we predicted unique syntrophic associations that have not been reported. Electron acceptor has a large effect on the interactome networks for anaerobic NAs-degrading consortia, offers insight into an unrecognized dimension of these consortia. These results provide a novel approach for exploring potential syntrophic relationships in biodegrading processes to help cost-effectively remove NAs in oil sands tailings ponds.
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Affiliation(s)
- Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, 310018, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Korris Lee
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada
| | - Ania Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada
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21
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Donato M, Johnson O, Steven B, Lawrence BA. Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses. PLoS One 2020; 15:e0235225. [PMID: 32649660 PMCID: PMC7351200 DOI: 10.1371/journal.pone.0235225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/10/2020] [Indexed: 11/30/2022] Open
Abstract
Freshwater wetlands of the temperate north are exposed to a range of pollutants that may alter their function, including nitrogen (N)-rich agricultural and urban runoff, seawater intrusion, and road salt contamination, though it is largely unknown how these drivers of change interact with the vegetation to affect wetland carbon (C) fluxes and microbial communities. We implemented a full factorial mesocosm (378.5 L tanks) experiment investigating C-related responses to three common wetland plants of eastern North America (Phragmites australis, Spartina pectinata, Typha latifolia), and four water quality treatments (fresh water control, N, road salt, sea salt). During the 2017 growing season, we quantified carbon dioxide (CO2) and methane (CH4) fluxes, above- and below-ground biomass, root porosity, light penetration, pore water chemistry (NH4+, NO3-, SO4-2, Cl-, DOC), soil C mineralization, as well as sediment microbial communities via 16S rRNA gene sequencing. Relative to freshwater controls, N enrichment stimulated plant biomass, which in turn increased CO2 uptake and reduced light penetration, especially in Spartina stands. Root porosity was not affected by water quality, but was positively correlated with CH4 emissions, suggesting that plants can be important conduits for CH4 from anoxic sediment to the atmosphere. Sediment microbial composition was largely unaffected by N addition, whereas salt amendments induced structural shifts, reduced sediment community diversity, and reduced C mineralization rates, presumably due to osmotic stress. Methane emissions were suppressed by sea salt, but not road salt, providing evidence for the additional chemical control (SO4-2 availability) on this microbial-mediated process. Thus, N may have stimulated plant activity while salting treatments preferentially enriched specific microbial populations. Together our findings underpin the utility of combining plant and microbial responses, and highlight the need for more integrative studies to predict the consequences of a changing environment on freshwater wetlands.
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Affiliation(s)
- Mary Donato
- Department of Natural Resources, University of Connecticut, Storrs, Connecticut, United States of America
| | - Olivia Johnson
- Department of Natural Resources, University of Connecticut, Storrs, Connecticut, United States of America
| | - Blaire Steven
- Department of Natural Resources, University of Connecticut, Storrs, Connecticut, United States of America
- Department of Environmental Sciences, Connecticut Agricultural Experiment Station, New Haven, Connecticut, United States of America
| | - Beth A. Lawrence
- Department of Natural Resources, University of Connecticut, Storrs, Connecticut, United States of America
- Center for Environmental Sciences and Engineering, University of Connecticut, Storrs, Connecticut, United States of America
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22
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Scott B, Baldwin AH, Ballantine K, Palmer M, Yarwood S. The role of organic amendments in wetland restorations. Restor Ecol 2020. [DOI: 10.1111/rec.13179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Brian Scott
- Department of Environmental Science and Technology University of Maryland Agricultural Engineering Building 142 College Park MD 20742 U.S.A
| | - Andrew H. Baldwin
- Department of Environmental Science and Technology University of Maryland Agricultural Engineering Building 142 College Park MD 20742 U.S.A
| | - Kate Ballantine
- Department of Environmental Studies Mount Holyoke College 50 College Street South Hadley MA 01075 U.S.A
| | - Margaret Palmer
- National Socio‐Environmental Synthesis Center, University of Maryland Plant Sciences Building 4112 College Park MD 20742 U.S.A
| | - Stephanie Yarwood
- Department of Environmental Science and Technology University of Maryland Agricultural Engineering Building 142 College Park MD 20742 U.S.A
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23
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Fudyma JD, Lyon J, AminiTabrizi R, Gieschen H, Chu RK, Hoyt DW, Kyle JE, Toyoda J, Tolic N, Heyman HM, Hess NJ, Metz TO, Tfaily MM. Untargeted metabolomic profiling of Sphagnum fallax reveals novel antimicrobial metabolites. PLANT DIRECT 2019; 3:e00179. [PMID: 31742243 PMCID: PMC6848953 DOI: 10.1002/pld3.179] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 05/06/2023]
Abstract
Sphagnum mosses dominate peatlands by employing harsh ecosystem tactics to prevent vascular plant growth and microbial degradation of these large carbon stores. Knowledge about Sphagnum-produced metabolites, their structure and their function, is important to better understand the mechanisms, underlying this carbon sequestration phenomenon in the face of climate variability. It is currently unclear which compounds are responsible for inhibition of organic matter decomposition and the mechanisms by which this inhibition occurs. Metabolite profiling of Sphagnum fallax was performed using two types of mass spectrometry (MS) systems and 1H nuclear magnetic resonance spectroscopy (1H NMR). Lipidome profiling was performed using LC-MS/MS. A total of 655 metabolites, including one hundred fifty-two lipids, were detected by NMR and LC-MS/MS-329 of which were novel metabolites (31 unknown lipids). Sphagum fallax metabolite profile was composed mainly of acid-like and flavonoid glycoside compounds, that could be acting as potent antimicrobial compounds, allowing Sphagnum to control its environment. Sphagnum fallax metabolite composition comparison against previously known antimicrobial plant metabolites confirmed this trend, with seventeen antimicrobial compounds discovered to be present in Sphagnum fallax, the majority of which were acids and glycosides. Biological activity of these compounds needs to be further tested to confirm antimicrobial qualities. Three fungal metabolites were identified providing insights into fungal colonization that may benefit Sphagnum. Characterizing the metabolite profile of Sphagnum fallax provided a baseline to understand the mechanisms in which Sphagnum fallax acts on its environment, its relation to carbon sequestration in peatlands, and provide key biomarkers to predict peatland C store changes (sequestration, emissions) as climate shifts.
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Affiliation(s)
- Jane D. Fudyma
- Department of Environmental ScienceUniversity of ArizonaTucsonAZUSA
| | - Jamee Lyon
- Department of Environmental ScienceUniversity of ArizonaTucsonAZUSA
| | | | - Hans Gieschen
- Department of Environmental ScienceUniversity of ArizonaTucsonAZUSA
| | - Rosalie K. Chu
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
| | - David W. Hoyt
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
| | - Jennifer E. Kyle
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Jason Toyoda
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
| | - Nikola Tolic
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
| | | | - Nancy J. Hess
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
| | - Thomas O. Metz
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Malak M. Tfaily
- Department of Environmental ScienceUniversity of ArizonaTucsonAZUSA
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
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24
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Wetland Sediments Host Diverse Microbial Taxa Capable of Cycling Alcohols. Appl Environ Microbiol 2019; 85:AEM.00189-19. [PMID: 30979841 PMCID: PMC6544822 DOI: 10.1128/aem.00189-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/07/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding patterns of organic matter degradation in wetlands is essential for identifying the substrates and mechanisms supporting greenhouse gas production and emissions from wetlands, the main natural source of methane in the atmosphere. Alcohols are common fermentation products but are poorly studied as key intermediates in organic matter degradation in wetlands. By investigating genes, pathways, and microorganisms potentially accounting for the high concentrations of ethanol and isopropanol measured in Prairie Pothole wetland sediments, this work advanced our understanding of alcohol fermentations in wetlands linked to extremely high greenhouse gas emissions. Moreover, the novel alcohol dehydrogenases and microbial taxa potentially involved in alcohol metabolism may serve biotechnological efforts in bioengineering commercially valuable alcohol production and in the discovery of novel isopropanol producers or isopropanol fermentation pathways. Alcohols are commonly derived from the degradation of organic matter and yet are rarely measured in environmental samples. Wetlands in the Prairie Pothole Region (PPR) support extremely high methane emissions and the highest sulfate reduction rates reported to date, likely contributing to a significant proportion of organic matter mineralization in this system. While ethanol and isopropanol concentrations up to 4 to 5 mM in PPR wetland pore fluids have been implicated in sustaining these high rates of microbial activity, the mechanisms that support alcohol cycling in this ecosystem are poorly understood. We leveraged metagenomic and transcriptomic tools to identify genes, pathways, and microorganisms potentially accounting for alcohol cycling in PPR wetlands. Phylogenetic analyses revealed diverse alcohol dehydrogenases and putative substrates. Alcohol dehydrogenase and aldehyde dehydrogenase genes were included in 62 metagenome-assembled genomes (MAGs) affiliated with 16 phyla. The most frequently encoded pathway (in 30 MAGs) potentially accounting for alcohol production was a Pyrococcus furiosus-like fermentation which can involve pyruvate:ferredoxin oxidoreductase (PFOR). Transcripts for 93 of 137 PFOR genes in these MAGs were detected, as well as for 158 of 243 alcohol dehydrogenase genes retrieved from these same MAGs. Mixed acid fermentation and heterofermentative lactate fermentation were also frequently encoded. Finally, we identified 19 novel putative isopropanol dehydrogenases in 15 MAGs affiliated with Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Ignavibacteriae, Thaumarchaeota, and the candidate divisions KSB1 and Rokubacteria. We conclude that diverse microorganisms may use uncommon and potentially novel pathways to produce ethanol and isopropanol in PPR wetland sediments. IMPORTANCE Understanding patterns of organic matter degradation in wetlands is essential for identifying the substrates and mechanisms supporting greenhouse gas production and emissions from wetlands, the main natural source of methane in the atmosphere. Alcohols are common fermentation products but are poorly studied as key intermediates in organic matter degradation in wetlands. By investigating genes, pathways, and microorganisms potentially accounting for the high concentrations of ethanol and isopropanol measured in Prairie Pothole wetland sediments, this work advanced our understanding of alcohol fermentations in wetlands linked to extremely high greenhouse gas emissions. Moreover, the novel alcohol dehydrogenases and microbial taxa potentially involved in alcohol metabolism may serve biotechnological efforts in bioengineering commercially valuable alcohol production and in the discovery of novel isopropanol producers or isopropanol fermentation pathways.
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25
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Abstract
Hydrologic margins of wetlands are narrow, transient zones between inundated and dry areas. As water levels fluctuate, the dynamic hydrology at margins may impact wetland greenhouse gas (GHG) fluxes that are sensitive to soil saturation. The Prairie Pothole Region of North America consists of millions of seasonally-ponded wetlands that are ideal for studying hydrologic transition states. Using a long-term GHG database with biweekly flux measurements from 88 seasonal wetlands, we categorized each sample event into wet to wet (W→W), dry to wet (D→W), dry to dry (D→D), or wet to dry (W→D) hydrologic states based on the presence or absence of ponded water from the previous and current event. Fluxes of methane were 5-times lower in the D→W compared to W→W states, indicating a lag ‘ramp-up’ period following ponding. Nitrous oxide fluxes were highest in the W→D state and accounted for 20% of total emissions despite accounting for only 5.2% of wetland surface area during the growing season. Fluxes of carbon dioxide were unaffected by transitions, indicating a rapid acclimation to current conditions by respiring organisms. Results of this study highlight how seasonal drying and re-wetting impact GHGs and demonstrate the importance of hydrologic transitions on total wetland GHG balance.
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26
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Smith GJ, Angle JC, Solden LM, Borton MA, Morin TH, Daly RA, Johnston MD, Stefanik KC, Wolfe R, Gil B, Wrighton KC. Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland. mBio 2018; 9:e00815-18. [PMID: 30401770 PMCID: PMC6222125 DOI: 10.1128/mbio.00815-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
Microbial carbon degradation and methanogenesis in wetland soils generate a large proportion of atmospheric methane, a highly potent greenhouse gas. Despite their potential to mitigate greenhouse gas emissions, knowledge about methane-consuming methanotrophs is often limited to lower-resolution single-gene surveys that fail to capture the taxonomic and metabolic diversity of these microorganisms in soils. Here our objective was to use genome-enabled approaches to investigate methanotroph membership, distribution, and in situ activity across spatial and seasonal gradients in a freshwater wetland near Lake Erie. 16S rRNA gene analyses demonstrated that members of the methanotrophic Methylococcales were dominant, with the dominance largely driven by the relative abundance of four taxa, and enriched in oxic surface soils. Three methanotroph genomes from assembled soil metagenomes were assigned to the genus Methylobacter and represented the most abundant methanotrophs across the wetland. Paired metatranscriptomes confirmed that these Old Woman Creek (OWC) Methylobacter members accounted for nearly all the aerobic methanotrophic activity across two seasons. In addition to having the capacity to couple methane oxidation to aerobic respiration, these new genomes encoded denitrification potential that may sustain energy generation in soils with lower dissolved oxygen concentrations. We further show that Methylobacter members that were closely related to the OWC members were present in many other high-methane-emitting freshwater and soil sites, suggesting that this lineage could participate in methane consumption in analogous ecosystems. This work contributes to the growing body of research suggesting that Methylobacter may represent critical mediators of methane fluxes in freshwater saturated sediments and soils worldwide.IMPORTANCE Here we used soil metagenomics and metatranscriptomics to uncover novel members within the genus Methylobacter We denote these closely related genomes as members of the lineage OWC Methylobacter Despite the incredibly high microbial diversity in soils, here we present findings that unexpectedly showed that methane cycling was primarily mediated by a single genus for both methane production ("Candidatus Methanothrix paradoxum") and methane consumption (OWC Methylobacter). Metatranscriptomic analyses revealed that decreased methanotrophic activity rather than increased methanogenic activity possibly contributed to the greater methane emissions that we had previously observed in summer months, findings important for biogeochemical methane models. Although members of this Methylococcales order have been cultivated for decades, multi-omic approaches continue to illuminate the methanotroph phylogenetic and metabolic diversity harbored in terrestrial and marine ecosystems.
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Affiliation(s)
- Garrett J Smith
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Jordan C Angle
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Lindsey M Solden
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Mikayla A Borton
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
- Environmental Science Graduate Program, The Ohio State University, Columbus, Ohio, USA
| | - Timothy H Morin
- Department of Environmental Resources Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, New York, USA
| | - Rebecca A Daly
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michael D Johnston
- National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Kay C Stefanik
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Civil and Environmental Engineering and Geodetic Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Richard Wolfe
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Bohrer Gil
- Environmental Science Graduate Program, The Ohio State University, Columbus, Ohio, USA
- Department of Civil and Environmental Engineering and Geodetic Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
- Environmental Science Graduate Program, The Ohio State University, Columbus, Ohio, USA
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27
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Dalcin Martins P, Danczak RE, Roux S, Frank J, Borton MA, Wolfe RA, Burris MN, Wilkins MJ. Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems. MICROBIOME 2018; 6:138. [PMID: 30086797 PMCID: PMC6081815 DOI: 10.1186/s40168-018-0522-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/25/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Microorganisms drive high rates of methanogenesis and carbon mineralization in wetland ecosystems. These signals are especially pronounced in the Prairie Pothole Region of North America, the tenth largest wetland ecosystem in the world. Sulfate reduction rates up to 22 μmol cm-3 day-1 have been measured in these wetland sediments, as well as methane fluxes up to 160 mg m-2 h-1-some of the highest emissions ever measured in North American wetlands. While pore waters from PPR wetlands are characterized by high concentrations of sulfur species and dissolved organic carbon, the constraints on microbial activity are poorly understood. Here, we utilized metagenomics to investigate candidate sulfate reducers and methanogens in this ecosystem and identify metabolic and viral controls on microbial activity. RESULTS We recovered 162 dsrA and 206 dsrD sequences from 18 sediment metagenomes and reconstructed 24 candidate sulfate reducer genomes assigned to seven phyla. These genomes encoded the potential for utilizing a wide variety of electron donors, such as methanol and other alcohols, methylamines, and glycine betaine. We also identified 37 mcrA sequences spanning five orders and recovered two putative methanogen genomes representing the most abundant taxa-Methanosaeta and Methanoregulaceae. However, given the abundance of Methanofollis-affiliated mcrA sequences, the detection of F420-dependent alcohol dehydrogenases, and millimolar concentrations of ethanol and 2-propanol in sediment pore fluids, we hypothesize that these alcohols may drive a significant fraction of methanogenesis in this ecosystem. Finally, extensive viral novelty was detected, with approximately 80% of viral populations being unclassified at any known taxonomic levels and absent from publicly available databases. Many of these viral populations were predicted to target dominant sulfate reducers and methanogens. CONCLUSIONS Our results indicate that diversity is likely key to extremely high rates of methanogenesis and sulfate reduction observed in these wetlands. The inferred genomic diversity and metabolic versatility could result from dynamic environmental conditions, viral infections, and niche differentiation in the heterogeneous sediment matrix. These processes likely play an important role in modulating carbon and sulfur cycling in this ecosystem.
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Affiliation(s)
| | - Robert E. Danczak
- Department of Microbiology, The Ohio State University, Columbus, OH USA
| | - Simon Roux
- Department of Energy, Joint Genome Institute, Walnut Creek, CA USA
| | - Jeroen Frank
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Mikayla A. Borton
- Department of Microbiology, The Ohio State University, Columbus, OH USA
| | - Richard A. Wolfe
- Department of Microbiology, The Ohio State University, Columbus, OH USA
| | - Marie N. Burris
- Department of Microbiology, The Ohio State University, Columbus, OH USA
| | - Michael J. Wilkins
- Department of Microbiology, The Ohio State University, Columbus, OH USA
- School of Earth Sciences, The Ohio State University, Columbus, OH USA
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Flynn TM, Koval JC, Greenwald SM, Owens SM, Kemner KM, Antonopoulos DA. Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities. Front Microbiol 2017; 8:2321. [PMID: 29234312 PMCID: PMC5712364 DOI: 10.3389/fmicb.2017.02321] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022] Open
Abstract
Microbial communities that inhabit environments such as soil can contain thousands of distinct taxa, yet little is known about how this diversity is maintained in response to environmental perturbations such as changes in the availability of carbon. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment. Dilute subsamples from each environment were used to inoculate 96-well microtiter plates containing triplicate wells amended with one of 31 carbon sources from six different classes of organic compounds (phenols, polymers, carbohydrates, carboxylic acids, amines, amino acids). After incubating each well aerobically in the dark for 72 h, we analyzed the composition of the microbial communities on the substrate arrays as well as the initial inocula by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Comparisons of alpha and beta diversity in these systems showed that, while the composition of the communities that grow to inhabit the wells in each substrate array diverges sharply from that of the original community in the inoculum, these enrichment communities are still strongly affected by the inoculum source. We found most enrichments were dominated by one or several OTUs most closely related to aerobes or facultative anaerobes from the Proteobacteria (e.g., Pseudomonas, Burkholderia, and Ralstonia) or Bacteroidetes (e.g., Chryseobacterium). Comparisons within each substrate array based on the class of carbon source further show that the communities inhabiting wells amended with a carbohydrate differ significantly from those enriched with a phenolic compound. Selection therefore seems to play a role in shaping the communities in the substrate arrays, although some stochasticity is also seen whereby several replicate wells within a single substrate array display strongly divergent community compositions. Overall, the use of highly parallel substrate arrays offers a promising path forward to study the response of microbial communities to perturbations in a changing environment.
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Affiliation(s)
- Theodore M Flynn
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | - Jason C Koval
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | | | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
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