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Lennon JT, Abramoff RZ, Allison SD, Burckhardt RM, DeAngelis KM, Dunne JP, Frey SD, Friedlingstein P, Hawkes CV, Hungate BA, Khurana S, Kivlin SN, Levine NM, Manzoni S, Martiny AC, Martiny JBH, Nguyen NK, Rawat M, Talmy D, Todd-Brown K, Vogt M, Wieder WR, Zakem EJ. Priorities, opportunities, and challenges for integrating microorganisms into Earth system models for climate change prediction. mBio 2024:e0045524. [PMID: 38526088 DOI: 10.1128/mbio.00455-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a "top 10" list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy.
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Affiliation(s)
- J T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - R Z Abramoff
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Ronin Institute, Montclair, New Jersey, USA
| | - S D Allison
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
- Department of Earth System Science, University of California Irvine, Irvine, California, USA
| | | | - K M DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - J P Dunne
- NOAA/OAR Geophysical Fluid Dynamics Laboratory, Princeton, New Jersey, USA
| | - S D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - P Friedlingstein
- College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - C V Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - B A Hungate
- Department of Biological Sciences, Center for Ecosystem Science, Northern Arizona University, Flagstaff, Arizona, USA
| | - S Khurana
- Department of Physical Geography, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - S N Kivlin
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - N M Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - S Manzoni
- Department of Physical Geography, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - A C Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - J B H Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - N K Nguyen
- American Society for Microbiology, Washington, DC, USA
| | - M Rawat
- National Science Foundation, Washington, DC, USA
| | - D Talmy
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - K Todd-Brown
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - M Vogt
- Institute for Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - W R Wieder
- National Center for Atmospheric Research, Boulder, Colorado, USA
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
| | - E J Zakem
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
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2
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Tao F, Houlton BZ, Frey SD, Lehmann J, Manzoni S, Huang Y, Jiang L, Mishra U, Hungate BA, Schmidt MWI, Reichstein M, Carvalhais N, Ciais P, Wang YP, Ahrens B, Hugelius G, Hocking TD, Lu X, Shi Z, Viatkin K, Vargas R, Yigini Y, Omuto C, Malik AA, Peralta G, Cuevas-Corona R, Di Paolo LE, Luotto I, Liao C, Liang YS, Saynes VS, Huang X, Luo Y. Reply to: Model uncertainty obscures major driver of soil carbon. Nature 2024; 627:E4-E6. [PMID: 38448699 DOI: 10.1038/s41586-023-07000-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/19/2023] [Indexed: 03/08/2024]
Affiliation(s)
- Feng Tao
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Department of Earth System Science, Ministry of Education Key Laboratory for Earth System Modelling, Institute for Global Change Studies, Tsinghua University, Beijing, China
| | - Benjamin Z Houlton
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Department of Global Development, Cornell University, Ithaca, NY, USA
| | - Serita D Frey
- Center for Soil Biogeochemistry and Microbial Ecology, Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Johannes Lehmann
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Stefano Manzoni
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Yuanyuan Huang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Lifen Jiang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Umakant Mishra
- Computational Biology & Biophysics, Sandia National Laboratories, Livermore, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | | | | | - Nuno Carvalhais
- Max Planck Institute for Biogeochemistry, Jena, Germany
- Departamento de Ciências e Engenharia do Ambiente, DCEA, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, Caparica, Portugal
| | - Philippe Ciais
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | | | - Gustaf Hugelius
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Toby D Hocking
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Xingjie Lu
- School of Atmospheric Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zheng Shi
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Kostiantyn Viatkin
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Ronald Vargas
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Yusuf Yigini
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Christian Omuto
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Ashish A Malik
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Guillermo Peralta
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | | | | | - Isabel Luotto
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Cuijuan Liao
- Department of Earth System Science, Ministry of Education Key Laboratory for Earth System Modelling, Institute for Global Change Studies, Tsinghua University, Beijing, China
| | - Yi-Shuang Liang
- Department of Earth System Science, Ministry of Education Key Laboratory for Earth System Modelling, Institute for Global Change Studies, Tsinghua University, Beijing, China
| | - Vinisa S Saynes
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Xiaomeng Huang
- Department of Earth System Science, Ministry of Education Key Laboratory for Earth System Modelling, Institute for Global Change Studies, Tsinghua University, Beijing, China.
| | - Yiqi Luo
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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3
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Zhang Y, Cheng X, van Groenigen KJ, García-Palacios P, Cao J, Zheng X, Luo Y, Hungate BA, Terrer C, Butterbach-Bahl K, Olesen JE, Chen J. Shifts in soil ammonia-oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions. Glob Chang Biol 2024; 30:e16989. [PMID: 37888833 DOI: 10.1111/gcb.16989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 10/01/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023]
Abstract
Anthropogenic nitrogen (N) loading alters soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize 68 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N-stimulation of nitrification, but does so via climate-related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N-availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate-related shifts in soil ammonia-oxidizing community maintain the N-stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Xiaoli Cheng
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Kees Jan van Groenigen
- Department of Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, UK
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Junji Cao
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Xunhua Zheng
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Yiqi Luo
- School of Integrative Plant Science, Cornell University, New York, Ithaca, USA
| | - Bruce A Hungate
- Department of Biological Sciences, Northern Arizona University, Arizona, Flagstaff, USA
| | - Cesar Terrer
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Massachusetts, Cambridge, USA
| | - Klaus Butterbach-Bahl
- Institute for Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany
- Center for Landscape Research in Sustainable Agricultural Futures, Land-CRAFT, Department of Agroecology, Aarhus University, Aarhus, Denmark
| | - Jørgen Eivind Olesen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Agroecology, Aarhus University, Tjele, Denmark
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4
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Purcell AM, Dijkstra P, Hungate BA, McMillen K, Schwartz E, van Gestel N. Rapid growth rate responses of terrestrial bacteria to field warming on the Antarctic Peninsula. ISME J 2023; 17:2290-2302. [PMID: 37872274 PMCID: PMC10689830 DOI: 10.1038/s41396-023-01536-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023]
Abstract
Ice-free terrestrial environments of the western Antarctic Peninsula are expanding and subject to colonization by new microorganisms and plants, which control biogeochemical cycling. Measuring growth rates of microbial populations and ecosystem carbon flux is critical for understanding how terrestrial ecosystems in Antarctica will respond to future warming. We implemented a field warming experiment in early (bare soil; +2 °C) and late (peat moss-dominated; +1.2 °C) successional glacier forefield sites on the western Antarctica Peninsula. We used quantitative stable isotope probing with H218O using intact cores in situ to determine growth rate responses of bacterial taxa to short-term (1 month) warming. Warming increased the growth rates of bacterial communities at both sites, even doubling the number of taxa exhibiting significant growth at the early site. Growth responses varied among taxa. Despite that warming induced a similar response for bacterial relative growth rates overall, the warming effect on ecosystem carbon fluxes was stronger at the early successional site-likely driven by increased activity of autotrophs which switched the ecosystem from a carbon source to a carbon sink. At the late-successional site, warming caused a significant increase in growth rate of many Alphaproteobacteria, but a weaker and opposite gross ecosystem productivity response that decreased the carbon sink-indicating that the carbon flux rates were driven more strongly by the plant communities. Such changes to bacterial growth and ecosystem carbon cycling suggest that the terrestrial Antarctic Peninsula can respond fast to increases in temperature, which can have repercussions for long-term elemental cycling and carbon storage.
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Affiliation(s)
- Alicia M Purcell
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Kelly McMillen
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Natasja van Gestel
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
- TTU Climate Center, Texas Tech University, Lubbock, TX, USA
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5
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Lai D, Hedlund BP, Mau RL, Jiao JY, Li J, Hayer M, Dijkstra P, Schwartz E, Li WJ, Dong H, Palmer M, Dodsworth JA, Zhou EM, Hungate BA. Resource partitioning and amino acid assimilation in a terrestrial geothermal spring. ISME J 2023; 17:2112-2122. [PMID: 37741957 PMCID: PMC10579274 DOI: 10.1038/s41396-023-01517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]
Abstract
High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.
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Affiliation(s)
- Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
- Nevada Institute for Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China and Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- School of Resource Environment and Earth Science, Yunnan University, Kunming, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
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Nadimpalli ML, Stegger M, Viau R, Yith V, de Lauzanne A, Sem N, Borand L, Huynh BT, Brisse S, Passet V, Overballe-Petersen S, Aziz M, Gouali M, Jacobs J, Phe T, Hungate BA, Leshyk VO, Pickering AJ, Gravey F, Liu CM, Johnson TJ, Hello SL, Price LB. Plugging the leaks: antibiotic resistance at human-animal interfaces in low-resource settings. Front Ecol Environ 2023; 21:428-434. [PMID: 38464945 PMCID: PMC10923528 DOI: 10.1002/fee.2639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Antibiotic resistance is one of the greatest public health challenges of our time. International efforts to curb resistance have largely focused on drug development and limiting unnecessary antibiotic use. However, in areas where water, sanitation, and hygiene infrastructure is lacking, we propose that bacterial flow between humans and animals can exacerbate the emergence and spread of resistant pathogens. Here, we describe the consequences of poor environmental controls by comparing mobile resistance elements among Escherichia coli recovered from humans and meat in Cambodia, a middle-income country with substantial human-animal connectivity and unregulated antibiotic use. We identified identical mobile resistance elements and a conserved transposon region that were widely dispersed in both humans and animals, a phenomenon rarely observed in high-income settings. Our findings indicate that plugging leaks at human-animal interfaces should be a critical part of addressing antibiotic resistance in low- and especially middle-income countries.
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Affiliation(s)
- Maya L Nadimpalli
- Gangarosa Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, GA
- Stuart B Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, MA
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, DC
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia
| | - Roberto Viau
- Stuart B Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, MA
- Department of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA
| | - Vuthy Yith
- Laboratory of Environment and Food Safety, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Agathe de Lauzanne
- Epidemiology and Public Health Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Nita Sem
- Laboratory of Environment and Food Safety, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Laurence Borand
- Epidemiology and Public Health Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Bich-tram Huynh
- Université Paris-Saclay, UVSQ, Inserm, Anti-Infective Evasion and Pharmacoepidemiology Team, CESP, Montigny le Bretonneux, France
- UMR 1181, Inserm, University of Versailles Saint-Quentin-en-Yvelines, Saint-Quentin-en-Yvelines, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Virginie Passet
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | | | - Maliha Aziz
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, DC
| | - Malika Gouali
- Laboratory of Environment and Food Safety, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
- Enteric Bacterial Pathogens Unit, Institut Pasteur, Paris, France
| | - Jan Jacobs
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Thong Phe
- Sihanouk Hospital Center for Hope, Phnom Penh, Cambodia
| | - Bruce A Hungate
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ
| | - Victor O Leshyk
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ
| | - Amy J Pickering
- Stuart B Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, MA
- Department of Civil and Environmental Engineering, University of California–Berkeley, Berkeley, CA
| | - François Gravey
- Université de Caen Normandie, Université de Rouen Normandie, Inserm, DYNAMICURE UMR 1311, CHU Caen, Caen, France
- Department of Bacteriology, CHU Caen, Caen, France
| | - Cindy M Liu
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, DC
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St Paul, MN
| | - Simon Le Hello
- Enteric Bacterial Pathogens Unit, Institut Pasteur, Paris, France
- Université de Caen Normandie, Université de Rouen Normandie, Inserm, DYNAMICURE UMR 1311, CHU Caen, Caen, France
- Department of Bacteriology, CHU Caen, Caen, France
| | - Lance B Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, DC
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7
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Pappalardo P, Song C, Hungate BA, Osenberg CW. A meta-evaluation of the quality of reporting and execution in ecological meta-analyses. PLoS One 2023; 18:e0292606. [PMID: 37824448 PMCID: PMC10569516 DOI: 10.1371/journal.pone.0292606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/25/2023] [Indexed: 10/14/2023] Open
Abstract
Quantitatively summarizing results from a collection of primary studies with meta-analysis can help answer ecological questions and identify knowledge gaps. The accuracy of the answers depends on the quality of the meta-analysis. We reviewed the literature assessing the quality of ecological meta-analyses to evaluate current practices and highlight areas that need improvement. From each of the 18 review papers that evaluated the quality of meta-analyses, we calculated the percentage of meta-analyses that met criteria related to specific steps taken in the meta-analysis process (i.e., execution) and the clarity with which those steps were articulated (i.e., reporting). We also re-evaluated all the meta-analyses available from Pappalardo et al. [1] to extract new information on ten additional criteria and to assess how the meta-analyses recognized and addressed non-independence. In general, we observed better performance for criteria related to reporting than for criteria related to execution; however, there was a wide variation among criteria and meta-analyses. Meta-analyses had low compliance with regard to correcting for phylogenetic non-independence, exploring temporal trends in effect sizes, and conducting a multifactorial analysis of moderators (i.e., explanatory variables). In addition, although most meta-analyses included multiple effect sizes per study, only 66% acknowledged some type of non-independence. The types of non-independence reported were most often related to the design of the original experiment (e.g., the use of a shared control) than to other sources (e.g., phylogeny). We suggest that providing specific training and encouraging authors to follow the PRISMA EcoEvo checklist recently developed by O'Dea et al. [2] can improve the quality of ecological meta-analyses.
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Affiliation(s)
- Paula Pappalardo
- Smithsonian Environmental Research Center, Tiburon, California, United States of America
| | - Chao Song
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems and College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Bruce A. Hungate
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Craig W. Osenberg
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
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8
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Metze D, Schnecker J, Canarini A, Fuchslueger L, Koch BJ, Stone BW, Hungate BA, Hausmann B, Schmidt H, Schaumberger A, Bahn M, Kaiser C, Richter A. Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions. Nat Commun 2023; 14:5895. [PMID: 37736743 PMCID: PMC10516970 DOI: 10.1038/s41467-023-41524-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed 'vapor-qSIP') to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Benjamin J Koch
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Schaumberger
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria.
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9
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Wang M, Sun X, Cao B, Chiariello NR, Docherty KM, Field CB, Gao Q, Gutknecht JLM, Guo X, He G, Hungate BA, Lei J, Niboyet A, Le Roux X, Shi Z, Shu W, Yuan M, Zhou J, Yang Y. Long-term elevated precipitation induces grassland soil carbon loss via microbe-plant-soil interplay. Glob Chang Biol 2023; 29:5429-5444. [PMID: 37317051 DOI: 10.1111/gcb.16811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023]
Abstract
Global climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere-climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2 ), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2 . Collectively, we demonstrate that long-term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere-climate feedback in Mediterranean-type water-limited ecosystems, namely how eP induces soil C loss via microbe-plant-soil interplay.
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Affiliation(s)
- Mengmeng Wang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Xin Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Yale Institute for Biospheric Studies, Yale University, New Haven, Connecticut, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
| | - Baichuan Cao
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Nona R Chiariello
- Jasper Ridge Biological Preserve, Stanford University, Stanford, California, USA
| | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - Christopher B Field
- Stanford Woods Institute for the Environment, Stanford University, Stanford, California, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jessica L M Gutknecht
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Genhe He
- School of Life Sciences, Key Laboratory of Agricultural Environmental Pollution Prevention and Control in Red Soil Hilly Region of Jiangxi Province, Jinggangshan University, Ji'an, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Audrey Niboyet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, CNRS, INRAE, IRD, Sorbonne Université, Université Paris Cité, UPEC, Paris, France
- AgroParisTech, Palaiseau, France
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne, INRAE, CNRS, VetAgroSup, UMR INRAE 1418, UMR CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Zhou Shi
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Wensheng Shu
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Mengting Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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10
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Walkup J, Dang C, Mau RL, Hayer M, Schwartz E, Stone BW, Hofmockel KS, Koch BJ, Purcell AM, Pett-Ridge J, Wang C, Hungate BA, Morrissey EM. The predictive power of phylogeny on growth rates in soil bacterial communities. ISME Commun 2023; 3:73. [PMID: 37454187 PMCID: PMC10349831 DOI: 10.1038/s43705-023-00281-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement of taxon-specific traits within natural microbial communities. There is mounting evidence of a phylogenetic signal in these traits, which may support prediction and microbiome management frameworks. We investigated phylogeny-based trait prediction using bacterial growth rates from soil communities in Arctic, boreal, temperate, and tropical ecosystems. Here we show that phylogeny predicts growth rates of soil bacteria, explaining an average of 31%, and up to 58%, of the variation within ecosystems. Despite limited overlap in community composition across these ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Phylogenetic relationships could explain up to 38% (averaging 14%) of the variation in growth rates across the highly disparate ecosystems studied. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria in the wild, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems.
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Affiliation(s)
- Jeth Walkup
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Chansotheary Dang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA
- University of California Merced, Life & Environmental Sciences Department, Merced, CA, 95343, USA
| | - Chao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, LN, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA.
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11
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Tao F, Huang Y, Hungate BA, Manzoni S, Frey SD, Schmidt MWI, Reichstein M, Carvalhais N, Ciais P, Jiang L, Lehmann J, Wang YP, Houlton BZ, Ahrens B, Mishra U, Hugelius G, Hocking TD, Lu X, Shi Z, Viatkin K, Vargas R, Yigini Y, Omuto C, Malik AA, Peralta G, Cuevas-Corona R, Di Paolo LE, Luotto I, Liao C, Liang YS, Saynes VS, Huang X, Luo Y. Microbial carbon use efficiency promotes global soil carbon storage. Nature 2023; 618:981-985. [PMID: 37225998 PMCID: PMC10307633 DOI: 10.1038/s41586-023-06042-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 04/03/2023] [Indexed: 05/26/2023]
Abstract
Soils store more carbon than other terrestrial ecosystems1,2. How soil organic carbon (SOC) forms and persists remains uncertain1,3, which makes it challenging to understand how it will respond to climatic change3,4. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss5-7. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways4,6,8-11, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes12,13. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved7,14,15. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.
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Affiliation(s)
- Feng Tao
- Department of Earth System Science, Ministry of Education Key Laboratory for Earth System Modelling, Institute for Global Change Studies, Tsinghua University, Beijing, China
- Max Planck Institute for Biogeochemistry, Jena, Germany
- Food and Agricultural Organization of the United Nations, Rome, Italy
| | - Yuanyuan Huang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Stefano Manzoni
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Serita D Frey
- Center for Soil Biogeochemistry and Microbial Ecology, Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | | | | | - Nuno Carvalhais
- Max Planck Institute for Biogeochemistry, Jena, Germany
- Departamento de Ciências e Engenharia do Ambiente, DCEA, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, Caparica, Portugal
| | - Philippe Ciais
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Lifen Jiang
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Johannes Lehmann
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Benjamin Z Houlton
- Department of Ecology and Evolutionary Biology and Department of Global Development, Cornell University, Ithaca, NY, USA
| | | | - Umakant Mishra
- Computational Biology and Biophysics, Sandia National Laboratories, Livermore, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Gustaf Hugelius
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Toby D Hocking
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Xingjie Lu
- School of Atmospheric Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zheng Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Kostiantyn Viatkin
- Food and Agricultural Organization of the United Nations, Rome, Italy
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Ronald Vargas
- Food and Agricultural Organization of the United Nations, Rome, Italy
| | - Yusuf Yigini
- Food and Agricultural Organization of the United Nations, Rome, Italy
| | - Christian Omuto
- Food and Agricultural Organization of the United Nations, Rome, Italy
| | - Ashish A Malik
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Guillermo Peralta
- Food and Agricultural Organization of the United Nations, Rome, Italy
| | | | | | - Isabel Luotto
- Food and Agricultural Organization of the United Nations, Rome, Italy
| | - Cuijuan Liao
- Department of Earth System Science, Ministry of Education Key Laboratory for Earth System Modelling, Institute for Global Change Studies, Tsinghua University, Beijing, China
| | - Yi-Shuang Liang
- Department of Earth System Science, Ministry of Education Key Laboratory for Earth System Modelling, Institute for Global Change Studies, Tsinghua University, Beijing, China
| | - Vinisa S Saynes
- Food and Agricultural Organization of the United Nations, Rome, Italy
| | - Xiaomeng Huang
- Department of Earth System Science, Ministry of Education Key Laboratory for Earth System Modelling, Institute for Global Change Studies, Tsinghua University, Beijing, China.
| | - Yiqi Luo
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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12
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Liu CM, Aziz M, Park DE, Wu Z, Stegger M, Li M, Wang Y, Schmidlin K, Johnson TJ, Koch BJ, Hungate BA, Nordstrom L, Gauld L, Weaver B, Rolland D, Statham S, Hall B, Sariya S, Davis GS, Keim PS, Johnson JR, Price LB. Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections. One Health 2023; 16:100518. [PMID: 37363239 PMCID: PMC10288061 DOI: 10.1016/j.onehlt.2023.100518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
A one-health perspective may provide new and actionable information about Escherichia coli transmission. E. coli colonizes a broad range of vertebrates, including humans and food-production animals, and is a leading cause of bladder, kidney, and bloodstream infections in humans. Substantial evidence supports foodborne transmission of pathogenic E. coli strains from food animals to humans. However, the relative contribution of foodborne zoonotic E. coli (FZEC) to the human extraintestinal disease burden and the distinguishing characteristics of such strains remain undefined. Using a comparative genomic analysis of a large collection of contemporaneous, geographically-matched clinical and meat-source E. coli isolates (n = 3111), we identified 17 source-associated mobile genetic elements - predominantly plasmids and bacteriophages - and integrated them into a novel Bayesian latent class model to predict the origins of clinical E. coli isolates. We estimated that approximately 8 % of human extraintestinal E. coli infections (mostly urinary tract infections) in our study population were caused by FZEC. FZEC strains were equally likely to cause symptomatic disease as non-FZEC strains. Two FZEC lineages, ST131-H22 and ST58, appeared to have particularly high virulence potential. Our findings imply that FZEC strains collectively cause more urinary tract infections than does any single non-E. coli uropathogenic species (e.g., Klebsiella pneumoniae). Our novel approach can be applied in other settings to identify the highest-risk FZEC strains, determine their sources, and inform new one-health strategies to decrease the heavy public health burden imposed by extraintestinal E. coli infections.
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Affiliation(s)
- Cindy M. Liu
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
- The Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Room 210 Building 56, Applied Research & Development, 1395 S Knoles Drive, Flagstaff, AZ 86011, USA
| | - Maliha Aziz
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Daniel E. Park
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Zhenke Wu
- Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
- Michigan Institute for Data Science (MIDAS), University of Michigan, 500 Church Street, Suite 600, Ann Arbor, MI 48109, USA
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - Mengbing Li
- Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Yashan Wang
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Kara Schmidlin
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1365 Gortner Ave, St Paul, MN 55108, USA
| | - Benjamin J. Koch
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Lora Nordstrom
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Lori Gauld
- Flagstaff Medical Center, 1200 N. Beaver St. Flagstaff, AZ 86001, USA
| | - Brett Weaver
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Diana Rolland
- Flagstaff Medical Center, 1200 N. Beaver St. Flagstaff, AZ 86001, USA
| | - Sally Statham
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Brantley Hall
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sanjeev Sariya
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Gregg S. Davis
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Paul S. Keim
- The Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Room 210 Building 56, Applied Research & Development, 1395 S Knoles Drive, Flagstaff, AZ 86011, USA
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - James R. Johnson
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN 55417, USA
| | - Lance B. Price
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
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13
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Stone BWG, Dijkstra P, Finley BK, Fitzpatrick R, Foley MM, Hayer M, Hofmockel KS, Koch BJ, Li J, Liu XJA, Martinez A, Mau RL, Marks J, Monsaint-Queeney V, Morrissey EM, Propster J, Pett-Ridge J, Purcell AM, Schwartz E, Hungate BA. Life history strategies among soil bacteria-dichotomy for few, continuum for many. ISME J 2023; 17:611-619. [PMID: 36732614 PMCID: PMC10030646 DOI: 10.1038/s41396-022-01354-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 02/04/2023]
Abstract
Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both 18O-H2O and 13C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms' joint 18O-13C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.
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Affiliation(s)
- Bram W G Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA.
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Brianna K Finley
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Raina Fitzpatrick
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Megan M Foley
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Xiao Jun A Liu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Ayla Martinez
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jane Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Jeffrey Propster
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA
- Life and Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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14
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Stone BW, Blazewicz SJ, Koch BJ, Dijkstra P, Hayer M, Hofmockel KS, Liu XJA, Mau RL, Pett-Ridge J, Schwartz E, Hungate BA. Nutrients strengthen density dependence of per-capita growth and mortality rates in the soil bacterial community. Oecologia 2023; 201:771-782. [PMID: 36847885 DOI: 10.1007/s00442-023-05322-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/15/2023] [Indexed: 03/01/2023]
Abstract
Density dependence in an ecological community has been observed in many macro-organismal ecosystems and is hypothesized to maintain biodiversity but is poorly understood in microbial ecosystems. Here, we analyze data from an experiment using quantitative stable isotope probing (qSIP) to estimate per-capita growth and mortality rates of bacterial populations in soils from several ecosystems along an elevation gradient which were subject to nutrient addition of either carbon alone (glucose; C) or carbon with nitrogen (glucose + ammonium-sulfate; C + N). Across all ecosystems, we found that higher population densities, quantified by the abundance of genomes per gram of soil, had lower per-capita growth rates in C + N-amended soils. Similarly, bacterial mortality rates in C + N-amended soils increased at a significantly higher rate with increasing population size than mortality rates in control and C-amended soils. In contrast to the hypothesis that density dependence would promote or maintain diversity, we observed significantly lower bacterial diversity in soils with stronger negative density-dependent growth. Here, density dependence was significantly but weakly responsive to nutrients and was not associated with higher bacterial diversity.
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Affiliation(s)
- Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Xiao Jun Allen Liu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA
- Life and Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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15
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Zhou G, Terrer C, Huang A, Hungate BA, van Gestel N, Zhou X, van Groenigen KJ. Nitrogen and water availability control plant carbon storage with warming. Sci Total Environ 2022; 851:158243. [PMID: 36007637 DOI: 10.1016/j.scitotenv.2022.158243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Plants may slow global warming through enhanced growth, because increased levels of photosynthesis stimulate the land carbon (C) sink. However, how climate warming affects plant C storage globally and key drivers determining the response of plant C storage to climate warming remains unclear, causing uncertainty in climate projections. We performed a comprehensive meta-analysis, compiling 393 observations from 99 warming studies to examine the global patterns of plant C storage responses to climate warming and explore the key drivers. Warming significantly increased total biomass (+8.4 %), aboveground biomass (+12.6 %) and belowground biomass (+10.1 %). The effect of experimental warming on plant biomass was best explained by the availability of soil nitrogen (N) and water. Across the entire dataset, warming-induced changes in total, aboveground and belowground biomass all positively correlated with soil C:N ratio, an indicator of soil N availability. In addition, warming stimulated plant biomass more strongly in humid than in dry ecosystems, and warming tended to decrease root:shoot ratios at high soil C:N ratios. Together, these results suggest dual controls of warming effects on plant C storage; warming increases plant growth in ecosystems where N is limiting plant growth, but it reduces plant growth where water availability is limiting plant growth.
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Affiliation(s)
- Guiyao Zhou
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Center for Global Change and Ecological Forecasting, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Cesar Terrer
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Boston, MA, USA
| | - An Huang
- School of Public Administration, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Natasja van Gestel
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Xuhui Zhou
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Center for Global Change and Ecological Forecasting, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China.
| | - Kees Jan van Groenigen
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4 RJ, UK.
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16
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Wu W, Dijkstra P, Hungate BA, Shi L, Dippold MA. In situ diversity of metabolism and carbon use efficiency among soil bacteria. Sci Adv 2022; 8:eabq3958. [PMID: 36332015 PMCID: PMC9635821 DOI: 10.1126/sciadv.abq3958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
The central carbon (C) metabolic network harvests energy to power the cell and feed biosynthesis for growth. In pure cultures, bacteria use some but not all of the network's major pathways, such as glycolysis and pentose phosphate and Entner-Doudoroff pathways. However, how these pathways are used in microorganisms in intact soil communities is unknown. Here, we analyzed the incorporation of 13C from glucose isotopomers into phospholipid fatty acids. We showed that groups of Gram-positive and Gram-negative bacteria in an intact agricultural soil used different pathways to metabolize glucose. They also differed in C use efficiency (CUE), the efficiency with which a substrate is used for biosynthesis. Our results provide experimental evidence for diversity among microbes in the organization of their central carbon metabolic network and CUE under in situ conditions. These results have important implications for our understanding of how community composition affects soil C cycling and organic matter formation.
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Affiliation(s)
- Weichao Wu
- Biogeochemistry of Agroecosystem, University of Goettingen, Goettingen, Germany
- Department of Environmental Science, Stockholm University, Stockholm, Sweden
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai, China
| | - Paul Dijkstra
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Lingling Shi
- Key Laboratory of Economics Plants and Biotechnology, Institute of Botany, Chinese Academy of Sciences, Kunming, China
- World Agroforestry Centre, China and East-Asia Office, Kunming, China
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Michaela A. Dippold
- Biogeochemistry of Agroecosystem, University of Goettingen, Goettingen, Germany
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
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17
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Ma X, Wang T, Shi Z, Chiariello NR, Docherty K, Field CB, Gutknecht J, Gao Q, Gu Y, Guo X, Hungate BA, Lei J, Niboyet A, Le Roux X, Yuan M, Yuan T, Zhou J, Yang Y. Correction: Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity. Microbiome 2022; 10:144. [PMID: 36056428 PMCID: PMC9440569 DOI: 10.1186/s40168-022-01349-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
- China Urban Construction Design & Research Institute Co., Ltd, Beijing, 100120, China
| | - Tengxu Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
- North China Municipal Engineering Design & Research Institute Co., Ltd., the Beijing Branch, Beijing, 100081, China
| | - Zhou Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Nona R Chiariello
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kathryn Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, 49008, USA
| | - Christopher B Field
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, 06120, Halle, Germany
- Present Address: Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN, 55104, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yunfu Gu
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, and Department of Biological Sciences, Northern Arizona University, Flagstaf, AZ, 86011, USA
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Audrey Niboyet
- Sorbonne Université, Université Paris Cité, UPEC, CNRS, INRAE, IRD, Institut d'Ecologie et des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
- AgroParisTech, Paris, France
| | - Xavier Le Roux
- Microbial Ecology Centre LEM, INRAE, CNRS, University of Lyon, University Lyon 1, VetAgroSup, UMR INRAE 1418, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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18
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Ma X, Wang T, Shi Z, Chiariello NR, Docherty K, Field CB, Gutknecht J, Gao Q, Gu Y, Guo X, Hungate BA, Lei J, Niboyet A, Le Roux X, Yuan M, Yuan T, Zhou J, Yang Y. Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity. Microbiome 2022; 10:112. [PMID: 35902889 PMCID: PMC9330674 DOI: 10.1186/s40168-022-01309-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m-2 year-1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century. RESULTS Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition. CONCLUSIONS We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation. Video Abstract.
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Affiliation(s)
- Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
- China Urban Construction Design & Research Institute Co., Ltd, Beijing, 100120, China
| | - Tengxu Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
- North China Municipal Engineering Design & Research Institute Co., Ltd., the Beijing Branch, Beijing, 100081, China
| | - Zhou Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Nona R Chiariello
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kathryn Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, 49008, USA
| | - Christopher B Field
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, 06120, Halle, Germany
- Present address: Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN, 55104, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yunfu Gu
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Audrey Niboyet
- Sorbonne Université, Université Paris Cité, UPEC, CNRS, INRAE, IRD, Institut d'Ecologie et des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
- AgroParisTech, Paris, France
| | - Xavier Le Roux
- Microbial Ecology Centre LEM, INRAE, CNRS, University of Lyon, University Lyon 1, VetAgroSup, UMR INRAE 1418, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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19
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Finley BK, Mau RL, Hayer M, Stone BW, Morrissey EM, Koch BJ, Rasmussen C, Dijkstra P, Schwartz E, Hungate BA. Soil minerals affect taxon-specific bacterial growth. ISME J 2022; 16:1318-1326. [PMID: 34931028 PMCID: PMC9038713 DOI: 10.1038/s41396-021-01162-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 11/08/2021] [Accepted: 11/22/2021] [Indexed: 01/01/2023]
Abstract
Secondary minerals (clays and metal oxides) are important components of the soil matrix. Clay minerals affect soil carbon persistence and cycling, and they also select for distinct microbial communities. Here we show that soil mineral assemblages-particularly short-range order minerals-affect both bacterial community composition and taxon-specific growth. Three soils with different parent material and presence of short-range order minerals were collected from ecosystems with similar vegetation and climate. These three soils were provided with 18O-labeled water and incubated with or without artificial root exudates or pine needle litter. Quantitative stable isotope probing was used to determine taxon-specific growth. We found that the growth of bacteria varied among soils of different mineral assemblages but found the trend of growth suppression in the presence of short-range order minerals. Relative growth of bacteria declined with increasing concentration of short-range order minerals between 25-36% of taxa present in all soils. Carbon addition in the form of plant litter or root exudates weakly affected relative growth of taxa (p = 0.09) compared to the soil type (p < 0.01). However, both exudate and litter carbon stimulated growth for at least 34% of families in the soils with the most and least short-range order minerals. In the intermediate short-range order soil, fresh carbon reduced growth for more bacterial families than were stimulated. These results highlight how bacterial-mineral-substrate interactions are critical to soil organic carbon processing, and how growth variation in bacterial taxa in these interactions may contribute to soil carbon persistence and loss.
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Affiliation(s)
- Brianna K. Finley
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.266093.80000 0001 0668 7243Present Address: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 USA
| | - Rebecca L. Mau
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Michaela Hayer
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Bram W. Stone
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.451303.00000 0001 2218 3491Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Ember M. Morrissey
- grid.268154.c0000 0001 2156 6140Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506 USA
| | - Benjamin J. Koch
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Craig Rasmussen
- grid.134563.60000 0001 2168 186XDepartment of Environmental Science, University of Arizona, Tucson, AZ 85721 USA
| | - Paul Dijkstra
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Egbert Schwartz
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Bruce A. Hungate
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
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20
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Qian H, Zhang N, Chen J, Chen C, Hungate BA, Ruan J, Huang S, Cheng K, Song Z, Hou P, Zhang B, Zhang J, Wang Z, Zhang X, Li G, Liu Z, Wang S, Zhou G, Zhang W, Ding Y, van Groenigen KJ, Jiang Y. Unexpected Parabolic Temperature Dependency of CH 4 Emissions from Rice Paddies. Environ Sci Technol 2022; 56:4871-4881. [PMID: 35369697 DOI: 10.1021/acs.est.2c00738] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Global warming is expected to affect methane (CH4) emissions from rice paddies, one of the largest human-induced sources of this potent greenhouse gas. However, the large variability in warming impacts on CH4 emissions makes it difficult to extrapolate the experimental results over large regions. Here, we show, through meta-analysis and multi-site warming experiments using the free air temperature increase facility, that warming stimulates CH4 emissions most strongly at background air temperatures during the flooded stage of ∼26 °C, with smaller responses of CH4 emissions to warming at lower and higher temperatures. This pattern can be explained by divergent warming responses of plant growth, methanogens, and methanotrophs. The effects of warming on rice biomass decreased with the background air temperature. Warming increased the abundance of methanogens more strongly at the medium air temperature site than the low and high air temperature sites. In contrast, the effects of warming on the abundance of methanotrophs were similar across the three temperature sites. We estimate that 1 °C warming will increase CH4 emissions from paddies in China by 12.6%─substantially higher than the estimates obtained from leading ecosystem models. Our findings challenge model assumptions and suggest that the estimates of future paddy CH4 emissions need to consider both plant and microbial responses to warming.
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Affiliation(s)
- Haoyu Qian
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Nan Zhang
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Junjie Chen
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Changqing Chen
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona 86011, United States
| | - Junmei Ruan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shan Huang
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Kun Cheng
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenwei Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pengfu Hou
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Bin Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jun Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhen Wang
- International Institute for Earth System Science, Nanjing University, Nanjing 210023, China
| | - Xiuying Zhang
- International Institute for Earth System Science, Nanjing University, Nanjing 210023, China
| | - Ganghua Li
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenghui Liu
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Songhan Wang
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiyao Zhou
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Weijian Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanfeng Ding
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Kees Jan van Groenigen
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4RJ, U.K
| | - Yu Jiang
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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21
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Zhang Y, Zhang F, Abalos D, Luo Y, Hui D, Hungate BA, García-Palacios P, Kuzyakov Y, Olesen JE, Jørgensen U, Chen J. Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N 2 O emission. Glob Chang Biol 2022. [PMID: 34923712 DOI: 10.6084/m9.figshare.14370896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N2 O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N2 O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N2 O emission by 261%, whereas there was no clear relationship between changes in soil N2 O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N2 O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N2 O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N2 O emission.
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Affiliation(s)
- Yong Zhang
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Feng Zhang
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Diego Abalos
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Yiqi Luo
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, Tennessee, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Pablo García-Palacios
- Departamento de Biología y Geología, Física y Química Inorgánica y Analítica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, Spain
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany
- Agro-Technological Institute, RUDN University, Moscow, Russia
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
| | - Jørgen Eivind Olesen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
| | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
| | - Ji Chen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
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22
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Zhang Y, Zhang F, Abalos D, Luo Y, Hui D, Hungate BA, García‐Palacios P, Kuzyakov Y, Olesen JE, Jørgensen U, Chen J. Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N 2 O emission. Glob Chang Biol 2022; 28:2158-2168. [PMID: 34923712 PMCID: PMC9303726 DOI: 10.1111/gcb.16042] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/10/2021] [Indexed: 05/15/2023]
Abstract
Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N2 O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N2 O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N2 O emission by 261%, whereas there was no clear relationship between changes in soil N2 O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N2 O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N2 O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N2 O emission.
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Affiliation(s)
- Yong Zhang
- School of Resources and Environmental EngineeringAnhui UniversityHefeiChina
| | - Feng Zhang
- School of Resources and Environmental EngineeringAnhui UniversityHefeiChina
| | - Diego Abalos
- Department of AgroecologyAarhus UniversityTjeleDenmark
| | - Yiqi Luo
- Center for Ecosystem Science and Society and Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Dafeng Hui
- Department of Biological SciencesTennessee State UniversityNashvilleTennesseeUSA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society and Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Pablo García‐Palacios
- Departamento de Biología y GeologíaFísica y Química Inorgánica y AnalíticaEscuela Superior de Ciencias Experimentales y TecnologíaUniversidad Rey Juan CarlosMóstolesSpain
- Instituto de Ciencias AgrariasConsejo Superior de Investigaciones CientíficasMadridSpain
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate EcosystemsUniversity of GöttingenGöttingenGermany
- Agro‐Technological InstituteRUDN UniversityMoscowRussia
- Institute of Environmental SciencesKazan Federal UniversityKazanRussia
| | - Jørgen Eivind Olesen
- Department of AgroecologyAarhus UniversityTjeleDenmark
- iCLIMATE Interdisciplinary Centre for Climate ChangeAarhus UniversityRoskildeDenmark
- Aarhus University Centre for Circular BioeconomyAarhus UniversityTjeleDenmark
| | - Uffe Jørgensen
- Department of AgroecologyAarhus UniversityTjeleDenmark
- Aarhus University Centre for Circular BioeconomyAarhus UniversityTjeleDenmark
| | - Ji Chen
- Department of AgroecologyAarhus UniversityTjeleDenmark
- iCLIMATE Interdisciplinary Centre for Climate ChangeAarhus UniversityRoskildeDenmark
- Aarhus University Centre for Circular BioeconomyAarhus UniversityTjeleDenmark
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23
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Hayer M, Wymore AS, Hungate BA, Schwartz E, Koch BJ, Marks JC. Microbes on decomposing litter in streams: entering on the leaf or colonizing in the water? ISME J 2022; 16:717-725. [PMID: 34580429 PMCID: PMC8857200 DOI: 10.1038/s41396-021-01114-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 08/29/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023]
Abstract
When leaves fall in rivers, microbial decomposition commences within hours. Microbial assemblages comprising hundreds of species of fungi and bacteria can vary with stream conditions, leaf litter species, and decomposition stage. In terrestrial ecosystems, fungi and bacteria that enter soils with dead leaves often play prominent roles in decomposition, but their role in aquatic decomposition is less known. Here, we test whether fungi and bacteria that enter streams on senesced leaves are growing during decomposition and compare their abundances and growth to bacteria and fungi that colonize leaves in the water. We employ quantitative stable isotope probing to identify growing microbes across four leaf litter species and two decomposition times. We find that most of the growing fungal species on decomposing leaves enter the water with the leaf, whereas most growing bacteria colonize from the water column. Results indicate that the majority of bacteria found on litter are growing, whereas the majority of fungi are dormant. Both bacterial and fungal assemblages differed with leaf type on the dried leaves and throughout decomposition. This research demonstrates the importance of fungal species that enter with the leaf on aquatic decomposition and the prominence of bacteria that colonize decomposing leaves in the water.
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Affiliation(s)
- Michaela Hayer
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Adam S. Wymore
- grid.167436.10000 0001 2192 7145Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824 USA
| | - Bruce A. Hungate
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Egbert Schwartz
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Benjamin J. Koch
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Jane C. Marks
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA
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24
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Purcell AM, Hayer M, Koch BJ, Mau RL, Blazewicz SJ, Dijkstra P, Mack MC, Marks JC, Morrissey EM, Pett‐Ridge J, Rubin RL, Schwartz E, van Gestel NC, Hungate BA. Decreased growth of wild soil microbes after 15 years of transplant-induced warming in a montane meadow. Glob Chang Biol 2022; 28:128-139. [PMID: 34587352 PMCID: PMC9293287 DOI: 10.1111/gcb.15911] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 05/19/2023]
Abstract
The carbon stored in soil exceeds that of plant biomass and atmospheric carbon and its stability can impact global climate. Growth of decomposer microorganisms mediates both the accrual and loss of soil carbon. Growth is sensitive to temperature and given the vast biological diversity of soil microorganisms, the response of decomposer growth rates to warming may be strongly idiosyncratic, varying among taxa, making ecosystem predictions difficult. Here, we show that 15 years of warming by transplanting plant-soil mesocosms down in elevation, strongly reduced the growth rates of soil microorganisms, measured in the field using undisturbed soil. The magnitude of the response to warming varied among microbial taxa. However, the direction of the response-reduced growth-was universal and warming explained twofold more variation than did the sum of taxonomic identity and its interaction with warming. For this ecosystem, most of the growth responses to warming could be explained without taxon-specific information, suggesting that in some cases microbial responses measured in aggregate may be adequate for climate modeling. Long-term experimental warming also reduced soil carbon content, likely a consequence of a warming-induced increase in decomposition, as warming-induced changes in plant productivity were negligible. The loss of soil carbon and decreased microbial biomass with warming may explain the reduced growth of the microbial community, more than the direct effects of temperature on growth. These findings show that direct and indirect effects of long-term warming can reduce growth rates of soil microbes, which may have important feedbacks to global warming.
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Affiliation(s)
- Alicia M. Purcell
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Michaela Hayer
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Benjamin J. Koch
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Rebecca L. Mau
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Steven J. Blazewicz
- Physical and Life Sciences DirectorateLawrence Livermore National LabLivermoreCaliforniaUSA
| | - Paul Dijkstra
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Michelle C. Mack
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Jane C. Marks
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Ember M. Morrissey
- Division of Plant and Soil SciencesWest Virginia UniversityMorgantownWest VirginiaUSA
| | - Jennifer Pett‐Ridge
- Physical and Life Sciences DirectorateLawrence Livermore National LabLivermoreCaliforniaUSA
- Life & Environmental Sciences DepartmentUniversity of California MercedMercedCAUSA
| | - Rachel L. Rubin
- Department of Environmental SciencesMount Holyoke CollegeSouth HadleyMassachusettsUSA
| | - Egbert Schwartz
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Natasja C. van Gestel
- Department of Biological Sciences & TTU Climate CenterTexas Tech UniversityLubbockTexasUSA
| | - Bruce A. Hungate
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
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25
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Abstract
ABSTRACT
Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these traits to detect relationships between microbial communities and ecosystem-scale properties, few studies have assessed these traits on a community-scale. Here, we analysed these traits from publicly available metagenomes derived from marine, soil, host-associated and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, consistent with genomic streamlining, with GC content in thermophilic communities generally higher than in marine systems. In contrast, soil communities averaging smaller genomes featured higher GC content and were often from low-carbon environments, suggesting unique selection pressures in soil bacteria. The abundance of specific σ-factors varied with average genome size and ecosystem type. In oceans, abundance of fliA, a σ-factor controlling flagella biosynthesis, was positively correlated with community average genome size—reflecting known trade-offs between nutrient conservation and chemotaxis. In soils, a high abundance of the stress response σ-factor gene rpoS was associated with smaller average genome size and often located in harsh and/or carbon-limited environments—a result which tracks features observed in culture and indicates an increased capacity for stress response in nutrient-poor soils. This work shows how ecosystem-specific constraints are associated with trade-offs which are embedded in the genomic features of bacteria in microbial communities, and which can be detected at the community level, highlighting the importance of genomic features in microbial community analysis.
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Affiliation(s)
- Peter F Chuckran
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Bruce A Hungate
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Egbert Schwartz
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Dijkstra
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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26
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Dang C, Walkup JGV, Hungate BA, Franklin RB, Schwartz E, Morrissey EM. Phylogenetic organization in the assimilation of chemically distinct substrates by soil bacteria. Environ Microbiol 2021; 24:357-369. [PMID: 34811865 DOI: 10.1111/1462-2920.15843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 11/30/2022]
Abstract
Soils are among the most biodiverse habitats on earth and while the species composition of microbial communities can influence decomposition rates and pathways, the functional significance of many microbial species and phylogenetic groups remains unknown. If bacteria exhibit phylogenetic organization in their function, this could enable ecologically meaningful classification of bacterial clades. Here, we show non-random phylogenetic organization in the rates of relative carbon assimilation for both rapidly mineralized substrates (amino acids and glucose) assimilated by many microbial taxa and slowly mineralized substrates (lipids and cellulose) assimilated by relatively few microbial taxa. When mapped onto bacterial phylogeny using ancestral character estimation this phylogenetic organization enabled the identification of clades involved in the decomposition of specific soil organic matter substrates. Phylogenetic organization in substrate assimilation could provide a basis for predicting the functional attributes of uncharacterized microbial taxa and understanding the significance of microbial community composition for soil organic matter decomposition.
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Affiliation(s)
- Chansotheary Dang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Jeth G V Walkup
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Rima B Franklin
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA
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27
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Li J, Jia C, Lu Q, Hungate BA, Dijkstra P, Wang S, Wu C, Chen S, Li D, Shim H. Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures. J Hazard Mater 2021; 418:126384. [PMID: 34329005 DOI: 10.1016/j.jhazmat.2021.126384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/17/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.
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Affiliation(s)
- Junhui Li
- Vanderbilt Microbiome Initiative, Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA.
| | - Chongjian Jia
- Guangdong Eco-Engineering Polytechnic, Guangzhou 510520, China
| | - Qihong Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Shanquan Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Cuiyu Wu
- College of Natural Resources and Environmental Science, South China Agricultural University, Guangzhou 510642, China
| | - Shaohua Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Deqiang Li
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Hojae Shim
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR 999078, China.
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28
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Stone BW, Li J, Koch BJ, Blazewicz SJ, Dijkstra P, Hayer M, Hofmockel KS, Liu XJA, Mau RL, Morrissey EM, Pett-Ridge J, Schwartz E, Hungate BA. Author Correction: Nutrients cause consolidation of soil carbon flux to small proportion of bacterial community. Nat Commun 2021; 12:4052. [PMID: 34168161 PMCID: PMC8225670 DOI: 10.1038/s41467-021-24314-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA. .,Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.,Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Xiao-Jun Allen Liu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.,Life and Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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29
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Hungate BA, Marks JC, Power ME, Schwartz E, van Groenigen KJ, Blazewicz SJ, Chuckran P, Dijkstra P, Finley BK, Firestone MK, Foley M, Greenlon A, Hayer M, Hofmockel KS, Koch BJ, Mack MC, Mau RL, Miller SN, Morrissey EM, Propster JR, Purcell AM, Sieradzki E, Starr EP, Stone BWG, Terrer C, Pett-Ridge J. The Functional Significance of Bacterial Predators. mBio 2021; 12:e00466-21. [PMID: 33906922 PMCID: PMC8092244 DOI: 10.1128/mbio.00466-21] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in part because these are difficult to quantify. Here, we show that growth and carbon uptake were higher in predatory bacteria compared to nonpredatory bacteria, a finding across 15 sites, synthesizing 82 experiments and over 100,000 taxon-specific measurements of element flow into newly synthesized bacterial DNA. Obligate predatory bacteria grew 36% faster and assimilated carbon at rates 211% higher than nonpredatory bacteria. These differences were less pronounced for facultative predators (6% higher growth rates, 17% higher carbon assimilation rates), though high growth and carbon assimilation rates were observed for some facultative predators, such as members of the genera Lysobacter and Cytophaga, both capable of gliding motility and wolf-pack hunting behavior. Added carbon substrates disproportionately stimulated growth of obligate predators, with responses 63% higher than those of nonpredators for the Bdellovibrionales and 81% higher for the Vampirovibrionales, whereas responses of facultative predators to substrate addition were no different from those of nonpredators. This finding supports the ecological theory that higher productivity increases predator control of lower trophic levels. These findings also indicate that the functional significance of bacterial predators increases with energy flow and that predatory bacteria influence element flow through microbial food webs.IMPORTANCE The word "predator" may conjure images of leopards killing and eating impala on the African savannah or of great white sharks attacking elephant seals off the coast of California. But microorganisms are also predators, including bacteria that kill and eat other bacteria. While predatory bacteria have been found in many environments, it has been challenging to document their importance in nature. This study quantified the growth of predatory and nonpredatory bacteria in soils (and one stream) by tracking isotopically labeled substrates into newly synthesized DNA. Predatory bacteria were more active than nonpredators, and obligate predators, such as Bdellovibrionales and Vampirovibrionales, increased in growth rate in response to added substrates at the base of the food chain, strong evidence of trophic control. This work provides quantitative measures of predator activity and suggests that predatory bacteria-along with protists, nematodes, and phages-are active and important in microbial food webs.
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Affiliation(s)
- Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Mary E Power
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Kees Jan van Groenigen
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Peter Chuckran
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Brianna K Finley
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Megan Foley
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alex Greenlon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - Kirsten S Hofmockel
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Michelle C Mack
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Samantha N Miller
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Jeffrey R Propster
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Ella Sieradzki
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Evan P Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Bram W G Stone
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - César Terrer
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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30
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Wang C, Morrissey EM, Mau RL, Hayer M, Piñeiro J, Mack MC, Marks JC, Bell SL, Miller SN, Schwartz E, Dijkstra P, Koch BJ, Stone BW, Purcell AM, Blazewicz SJ, Hofmockel KS, Pett-Ridge J, Hungate BA. The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization. ISME J 2021; 15:2738-2747. [PMID: 33782569 DOI: 10.1038/s41396-021-00959-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/19/2021] [Accepted: 03/04/2021] [Indexed: 11/09/2022]
Abstract
Microorganisms drive soil carbon mineralization and changes in their activity with increased temperature could feedback to climate change. Variation in microbial biodiversity and the temperature sensitivities (Q10) of individual taxa may explain differences in the Q10 of soil respiration, a possibility not previously examined due to methodological limitations. Here, we show phylogenetic and taxonomic variation in the Q10 of growth (5-35 °C) among soil bacteria from four sites, one from each of Arctic, boreal, temperate, and tropical biomes. Differences in the temperature sensitivities of taxa and the taxonomic composition of communities determined community-assembled bacterial growth Q10, which was strongly predictive of soil respiration Q10 within and across biomes. Our results suggest community-assembled traits of microbial taxa may enable enhanced prediction of carbon cycling feedbacks to climate change in ecosystems across the globe.
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Affiliation(s)
- Chao Wang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA.,CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Juan Piñeiro
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Michelle C Mack
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Sheryl L Bell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Samantha N Miller
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Steven J Blazewicz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kirsten S Hofmockel
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA.,Ecology, Evolution and Organismal Biology Department, Iowa State University, Ames, IA, USA
| | - Jennifer Pett-Ridge
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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31
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Walker AP, De Kauwe MG, Bastos A, Belmecheri S, Georgiou K, Keeling RF, McMahon SM, Medlyn BE, Moore DJP, Norby RJ, Zaehle S, Anderson-Teixeira KJ, Battipaglia G, Brienen RJW, Cabugao KG, Cailleret M, Campbell E, Canadell JG, Ciais P, Craig ME, Ellsworth DS, Farquhar GD, Fatichi S, Fisher JB, Frank DC, Graven H, Gu L, Haverd V, Heilman K, Heimann M, Hungate BA, Iversen CM, Joos F, Jiang M, Keenan TF, Knauer J, Körner C, Leshyk VO, Leuzinger S, Liu Y, MacBean N, Malhi Y, McVicar TR, Penuelas J, Pongratz J, Powell AS, Riutta T, Sabot MEB, Schleucher J, Sitch S, Smith WK, Sulman B, Taylor B, Terrer C, Torn MS, Treseder KK, Trugman AT, Trumbore SE, van Mantgem PJ, Voelker SL, Whelan ME, Zuidema PA. Integrating the evidence for a terrestrial carbon sink caused by increasing atmospheric CO 2. New Phytol 2021; 229:2413-2445. [PMID: 32789857 DOI: 10.1111/nph.16866] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/06/2020] [Indexed: 05/22/2023]
Abstract
Atmospheric carbon dioxide concentration ([CO2 ]) is increasing, which increases leaf-scale photosynthesis and intrinsic water-use efficiency. These direct responses have the potential to increase plant growth, vegetation biomass, and soil organic matter; transferring carbon from the atmosphere into terrestrial ecosystems (a carbon sink). A substantial global terrestrial carbon sink would slow the rate of [CO2 ] increase and thus climate change. However, ecosystem CO2 responses are complex or confounded by concurrent changes in multiple agents of global change and evidence for a [CO2 ]-driven terrestrial carbon sink can appear contradictory. Here we synthesize theory and broad, multidisciplinary evidence for the effects of increasing [CO2 ] (iCO2 ) on the global terrestrial carbon sink. Evidence suggests a substantial increase in global photosynthesis since pre-industrial times. Established theory, supported by experiments, indicates that iCO2 is likely responsible for about half of the increase. Global carbon budgeting, atmospheric data, and forest inventories indicate a historical carbon sink, and these apparent iCO2 responses are high in comparison to experiments and predictions from theory. Plant mortality and soil carbon iCO2 responses are highly uncertain. In conclusion, a range of evidence supports a positive terrestrial carbon sink in response to iCO2 , albeit with uncertain magnitude and strong suggestion of a role for additional agents of global change.
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Affiliation(s)
- Anthony P Walker
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Martin G De Kauwe
- ARC Centre of Excellence for Climate Extremes, University of New South Wales, Sydney, NSW, 2052, Australia
- Climate Change Research Centre, University of New South Wales, Sydney, NSW, 2052, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ana Bastos
- Ludwig Maximilians University of Munich, Luisenstr. 37, Munich, 80333, Germany
| | - Soumaya Belmecheri
- Laboratory of Tree Ring Research, University of Arizona, 1215 E Lowell St, Tucson, AZ, 85721, USA
| | - Katerina Georgiou
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Ralph F Keeling
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92093, USA
| | - Sean M McMahon
- Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - Belinda E Medlyn
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - David J P Moore
- School of Natural Resources and the Environment, 1064 East Lowell Street, Tucson, AZ, 85721, USA
| | - Richard J Norby
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sönke Zaehle
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, Jena, 07745, Germany
| | - Kristina J Anderson-Teixeira
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, MRC 5535, Front Royal, VA, 22630, USA
- Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama City, Panama
| | - Giovanna Battipaglia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università della Campania, Caserta, 81100, Italy
| | | | - Kristine G Cabugao
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Maxime Cailleret
- INRAE, UMR RECOVER, Aix-Marseille Université, 3275 route de Cézanne, Aix-en-Provence Cedex 5, 13182, France
- Swiss Federal Institute for Forest Snow and Landscape Research (WSL), Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Elliott Campbell
- Department of Geography, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Josep G Canadell
- CSIRO Oceans and Atmosphere, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Philippe Ciais
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, F-91191, France
| | - Matthew E Craig
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - David S Ellsworth
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Graham D Farquhar
- Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Simone Fatichi
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore, 117576, Singapore
- Institute of Environmental Engineering, ETH Zurich, Stefano-Franscini Platz 5, Zurich, 8093, Switzerland
| | - Joshua B Fisher
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - David C Frank
- Laboratory of Tree Ring Research, University of Arizona, 1215 E Lowell St, Tucson, AZ, 85721, USA
| | - Heather Graven
- Department of Physics, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Lianhong Gu
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Vanessa Haverd
- CSIRO Oceans and Atmosphere, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Kelly Heilman
- Laboratory of Tree Ring Research, University of Arizona, 1215 E Lowell St, Tucson, AZ, 85721, USA
| | - Martin Heimann
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, Jena, 07745, Germany
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Colleen M Iversen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Fortunat Joos
- Climate and Environmental Physics, Physics Institute and Oeschger Centre for Climate Change Research, University of Bern, Sidlerstr. 5, Bern, CH-3012, Switzerland
| | - Mingkai Jiang
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Trevor F Keenan
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, CA, 94720, USA
- Earth and Environmental Sciences Area, Lawrence Berkeley National Lab., Berkeley, CA, 94720, USA
| | - Jürgen Knauer
- CSIRO Oceans and Atmosphere, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Christian Körner
- Department of Environmental Sciences, Botany, University of Basel, Basel, 4056, Switzerland
| | - Victor O Leshyk
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Sebastian Leuzinger
- School of Science, Auckland University of Technology, Auckland, 1142, New Zealand
| | - Yao Liu
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Natasha MacBean
- Department of Geography, Indiana University, Bloomington, IN, 47405, USA
| | - Yadvinder Malhi
- School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, UK
| | - Tim R McVicar
- CSIRO Land and Water, GPO Box 1700, Canberra, ACT, 2601, Australia
- Australian Research Council Centre of Excellence for Climate Extremes, 142 Mills Rd, Australian National University, Canberra, ACT, 2601, Australia
| | - Josep Penuelas
- CSIC, Global Ecology CREAF-CSIC-UAB, Bellaterra, Barcelona, Catalonia, 08193, Spain
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, 08193, Spain
| | - Julia Pongratz
- Ludwig Maximilians University of Munich, Luisenstr. 37, Munich, 80333, Germany
- Max Planck Institute for Meteorology, Bundesstr. 53, 20146 Hamburg, Germany
| | - A Shafer Powell
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Terhi Riutta
- School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, UK
| | - Manon E B Sabot
- ARC Centre of Excellence for Climate Extremes, University of New South Wales, Sydney, NSW, 2052, Australia
- Climate Change Research Centre, University of New South Wales, Sydney, NSW, 2052, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Juergen Schleucher
- Department of Medical Biochemistry & Biophysics, Umeå University, Umea, 901 87, Sweden
| | - Stephen Sitch
- College of Life and Environmental Sciences, University of Exeter, Exeter, Laver Building, EX4 4QF, UK
| | - William K Smith
- School of Natural Resources and the Environment, 1064 East Lowell Street, Tucson, AZ, 85721, USA
| | - Benjamin Sulman
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Benton Taylor
- Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - César Terrer
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Margaret S Torn
- Earth and Environmental Sciences Area, Lawrence Berkeley National Lab., Berkeley, CA, 94720, USA
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Anna T Trugman
- Department of Geography, 1832 Ellison Hall, Santa Barbara, CA, 93016, USA
| | - Susan E Trumbore
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, Jena, 07745, Germany
| | | | - Steve L Voelker
- Department of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, 13210, USA
| | - Mary E Whelan
- Department of Environmental Sciences, Rutgers University, 14 College Farm Road, New Brunswick, NJ, 08901, USA
| | - Pieter A Zuidema
- Forest Ecology and Forest Management group, Wageningen University, PO Box 47, Wageningen, 6700 AA, the Netherlands
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32
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Gao Y, Ding J, Yuan M, Chiariello N, Docherty K, Field C, Gao Q, Gu B, Gutknecht J, Hungate BA, Le Roux X, Niboyet A, Qi Q, Shi Z, Zhou J, Yang Y. Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition. NPJ Biofilms Microbiomes 2021; 7:17. [PMID: 33558544 PMCID: PMC7870951 DOI: 10.1038/s41522-021-00187-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Climate warming is known to impact ecosystem composition and functioning. However, it remains largely unclear how soil microbial communities respond to long-term, moderate warming. In this study, we used Illumina sequencing and microarrays (GeoChip 5.0) to analyze taxonomic and functional gene compositions of the soil microbial community after 14 years of warming (at 0.8–1.0 °C for 10 years and then 1.5–2.0 °C for 4 years) in a Californian grassland. Long-term warming had no detectable effect on the taxonomic composition of soil bacterial community, nor on any plant or abiotic soil variables. In contrast, functional gene compositions differed between warming and control for bacterial, archaeal, and fungal communities. Functional genes associated with labile carbon (C) degradation increased in relative abundance in the warming treatment, whereas those associated with recalcitrant C degradation decreased. A number of functional genes associated with nitrogen (N) cycling (e.g., denitrifying genes encoding nitrate-, nitrite-, and nitrous oxidereductases) decreased, whereas nifH gene encoding nitrogenase increased in the warming treatment. These results suggest that microbial functional potentials are more sensitive to long-term moderate warming than the taxonomic composition of microbial community.
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Affiliation(s)
- Ying Gao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Junjun Ding
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Key Laboratory of Dryland Agriculture, Ministry of Agriculture of the People's Republic of China, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Nona Chiariello
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Kathryn Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Chris Field
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Xavier Le Roux
- Mirobial Ecology Centre LEM, INRA, CNRS, University of Lyon, University Lyon 1, UMR INRA 1418, Villeurbanne, France
| | - Audrey Niboyet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (Sorbonne Université, CNRS, INRA, IRD, Université Paris Diderot, UPEC), Paris, France.,AgroParisTech, Paris, France
| | - Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Zhou Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
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33
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Rubin RL, Jones AN, Hayer M, Shuman-Goodier ME, Andrews LV, Hungate BA. Opposing effects of bacterial endophytes on biomass allocation of a wild donor and agricultural recipient. FEMS Microbiol Ecol 2020; 96:5710930. [PMID: 31960901 DOI: 10.1093/femsec/fiaa012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 01/17/2020] [Indexed: 11/12/2022] Open
Abstract
Root endophytes are a promising tool for increasing plant growth, but it is unclear whether they perform consistently across plant hosts. We characterized the blue grama (Bouteloua gracilis) root microbiome using two sequencing methods, quantified the effects of root endophytes in the original host (blue grama) and an agricultural recipient, corn (Zea mays), under drought and well-watered conditions and examined in vitro mechanisms for plant growth promotion. 16S rRNA amplicon sequencing revealed that the blue grama root microbiome was similar across an elevation gradient, with the exception of four genera. Culturing and Sanger sequencing revealed eight unique endophytes belonging to the genera Bacillus, Lysinibacillus and Pseudomonas. All eight endophytes colonized corn roots, but had opposing effects on aboveground and belowground biomass in each plant species: they increased blue grama shoot mass by 45% (19) (mean +/- SE) while decreasing corn shoot mass by 10% (19), and increased corn root:shoot by 44% (7), while decreasing blue grama root:shoot by 17% (7). Furthermore, contrary to our expectations, endophytes had stronger effects on plant growth under well-watered conditions rather than drought conditions. Collectively, these results suggest that ecological features, including host identity, bacterial traits, climate conditions and morphological outcomes, should be carefully considered in the design and implementation of agricultural inocula.
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Affiliation(s)
- Rachel L Rubin
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Environmental Studies, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Ashley N Jones
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Molly E Shuman-Goodier
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Lela V Andrews
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Environmental Genetics and Genomics Laboratory, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
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34
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Chen J, van Groenigen KJ, Hungate BA, Terrer C, van Groenigen JW, Maestre FT, Ying SC, Luo Y, Jørgensen U, Sinsabaugh RL, Olesen JE, Elsgaard L. Long-term nitrogen loading alleviates phosphorus limitation in terrestrial ecosystems. Glob Chang Biol 2020; 26:5077-5086. [PMID: 32529708 DOI: 10.1111/gcb.15218] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 05/21/2020] [Indexed: 05/02/2023]
Abstract
Increased human-derived nitrogen (N) deposition to terrestrial ecosystems has resulted in widespread phosphorus (P) limitation of net primary productivity. However, it remains unclear if and how N-induced P limitation varies over time. Soil extracellular phosphatases catalyze the hydrolysis of P from soil organic matter, an important adaptive mechanism for ecosystems to cope with N-induced P limitation. Here we show, using a meta-analysis of 140 studies and 668 observations worldwide, that N stimulation of soil phosphatase activity diminishes over time. Whereas short-term N loading (≤5 years) significantly increased soil phosphatase activity by 28%, long-term N loading had no significant effect. Nitrogen loading did not affect soil available P and total P content in either short- or long-term studies. Together, these results suggest that N-induced P limitation in ecosystems is alleviated in the long-term through the initial stimulation of soil phosphatase activity, thereby securing P supply to support plant growth. Our results suggest that increases in terrestrial carbon uptake due to ongoing anthropogenic N loading may be greater than previously thought.
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Affiliation(s)
- Ji Chen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- Aarhus University Center for Circular Bioeconomy, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
| | - Kees J van Groenigen
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - César Terrer
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory (LLNL), Livermore, CA, USA
| | | | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramon Margalef", Universidad de Alicante, Alicante, Spain
- Departamento de Ecología, Universidad de Alicante, Alicante, Spain
| | - Samantha C Ying
- Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Yiqi Luo
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- Aarhus University Center for Circular Bioeconomy, Aarhus University, Tjele, Denmark
| | | | - Jørgen E Olesen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
| | - Lars Elsgaard
- Department of Agroecology, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
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35
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Pappalardo P, Ogle K, Hamman EA, Bence JR, Hungate BA, Osenberg CW. Comparing traditional and Bayesian approaches to ecological meta‐analysis. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13445] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Kiona Ogle
- School of Informatics, Computing, and Cyber Systems Northern Arizona University Flagstaff AZ USA
- Center for Ecosystem Science and Society and Department of Biological Sciences Northern Arizona University Flagstaff AZ USA
| | | | - James R. Bence
- Quantitative Fisheries Center Department of Fisheries and Wildlife Michigan State University East Lansing MI USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences Northern Arizona University Flagstaff AZ USA
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36
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Sieradzki ET, Koch BJ, Greenlon A, Sachdeva R, Malmstrom RR, Mau RL, Blazewicz SJ, Firestone MK, Hofmockel KS, Schwartz E, Hungate BA, Pett-Ridge J. Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design. mSystems 2020; 5:e00151-20. [PMID: 32694124 PMCID: PMC7566279 DOI: 10.1128/msystems.00151-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of individual microbes and can link microbial biodiversity and biogeochemistry in complex communities. As with any quantitative estimation technique, qSIP involves measurement error, and a fuller understanding of error, precision, and statistical power benefits qSIP experimental design and data interpretation. We used several qSIP data sets-from soil and seawater microbiomes-to evaluate how variance in isotope incorporation estimates depends on organism abundance and resolution of the density fractionation scheme. We assessed statistical power for replicated qSIP studies, plus sensitivity and specificity for unreplicated designs. As a taxon's abundance increases, the variance of its weighted mean density declines. Nine fractions appear to be a reasonable trade-off between cost and precision for most qSIP applications. Increasing the number of density fractions beyond that reduces variance, although the magnitude of this benefit declines with additional fractions. Our analysis suggests that, if a taxon has an isotope enrichment of 10 atom% excess, there is a 60% chance that this will be detected as significantly different from zero (with alpha 0.1). With five replicates, isotope enrichment of 5 atom% could be detected with power (0.6) and alpha (0.1). Finally, we illustrate the importance of internal standards, which can help to calibrate per sample conversions of %GC to mean weighted density. These results should benefit researchers designing future SIP experiments and provide a useful reference for metagenomic SIP applications where both financial and computational limitations constrain experimental scope.IMPORTANCE One of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about their genomic content and potential functions but may not reflect an organism's activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of community interactions but often fail to link the two. Quantitative stable isotope probing (qSIP) is a method that can link the identity and functional activity of specific microbes within a naturally occurring community. Here, we explore how the resolution of density gradient fractionation affects the error and precision of qSIP results, how they may be improved via additional experimental replication, and discuss cost-benefit balanced scenarios for SIP experimental design.
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Affiliation(s)
- Ella T Sieradzki
- University of California Berkeley, Environmental Science and Policy Management, Berkeley, California, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alex Greenlon
- University of California Berkeley, Environmental Science and Policy Management, Berkeley, California, USA
| | - Rohan Sachdeva
- University of California Berkeley, Earth and Planetary Sciences, Berkeley, California, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Mary K Firestone
- University of California Berkeley, Environmental Science and Policy Management, Berkeley, California, USA
| | - Kirsten S Hofmockel
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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Blazewicz SJ, Hungate BA, Koch BJ, Nuccio EE, Morrissey E, Brodie EL, Schwartz E, Pett-Ridge J, Firestone MK. Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil. ISME J 2020; 14:1520-1532. [PMID: 32203117 PMCID: PMC7242442 DOI: 10.1038/s41396-020-0617-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 02/10/2020] [Accepted: 02/17/2020] [Indexed: 02/01/2023]
Abstract
Microbial activity increases after rewetting dry soil, resulting in a pulse of carbon mineralization and nutrient availability. The biogeochemical responses to wet-up are reasonably well understood and known to be microbially mediated. Yet, the population level dynamics, and the resulting changes in microbial community patterns, are not well understood as ecological phenomena. Here, we used sequencing of 16S rRNA genes coupled with heavy water (H218O) DNA quantitative stable isotope probing to estimate population-specific rates of growth and mortality in response to a simulated wet-up event in a California annual grassland soil. Bacterial growth and mortality responded rapidly to wet-up, within 3 h, and continued throughout the 168 h incubation, with patterns of sequential growth observed at the phylum level. Of the 37 phyla detected in the prewet community, growth was found in 18 phyla while mortality was measured in 26 phyla. Rapid growth and mortality rates were measurable within 3 h of wet-up but had contrasting characteristics; growth at 3 h was dominated by select taxa within the Proteobacteria and Firmicutes, whereas mortality was taxonomically widespread. Furthermore, across the community, mortality exhibited density-independence, consistent with the indiscriminate shock resulting from dry-down and wet-up, whereas growth was density-dependent, consistent with control by competition or predation. Total aggregated growth across the community was highly correlated with total soil CO2 production. Together, these results illustrate how previously "invisible" population responses can translate quantitatively to emergent observations of ecosystem-scale biogeochemistry.
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Affiliation(s)
- Steven J Blazewicz
- Department of Environmental Science, Policy, and Management, University of California, 137 Mulford Hall, Berkeley, CA, 94720, USA.
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA.
- Lawrence Livermore National Laboratory, 7000 East Ave L-231, Livermore, CA, 94550, USA.
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Ember Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26505, USA
| | - Eoin L Brodie
- Department of Environmental Science, Policy, and Management, University of California, 137 Mulford Hall, Berkeley, CA, 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd. MS70A-3317, Berkeley, CA, 94720, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, 137 Mulford Hall, Berkeley, CA, 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd. MS70A-3317, Berkeley, CA, 94720, USA
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38
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Chen J, Elsgaard L, van Groenigen KJ, Olesen JE, Liang Z, Jiang Y, Laerke PE, Zhang Y, Luo Y, Hungate BA, Sinsabaugh RL, Jørgensen U. Soil carbon loss with warming: New evidence from carbon-degrading enzymes. Glob Chang Biol 2020; 26:1944-1952. [PMID: 31909849 DOI: 10.1111/gcb.14986] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 12/16/2019] [Indexed: 06/10/2023]
Abstract
Climate warming affects soil carbon (C) dynamics, with possible serious consequences for soil C stocks and atmospheric CO2 concentrations. However, the mechanisms underlying changes in soil C storage are not well understood, hampering long-term predictions of climate C-feedbacks. The activity of the extracellular enzymes ligninase and cellulase can be used to track changes in the predominant C sources of soil microbes and can thus provide mechanistic insights into soil C loss pathways. Here we show, using meta-analysis, that reductions in soil C stocks with warming are associated with increased ratios of ligninase to cellulase activity. Furthermore, whereas long-term (≥5 years) warming reduced the soil recalcitrant C pool by 14%, short-term warming had no significant effect. Together, these results suggest that warming stimulates microbial utilization of recalcitrant C pools, possibly exacerbating long-term climate-C feedbacks.
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Affiliation(s)
- Ji Chen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- Center for Circular Bioeconomy, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
| | - Lars Elsgaard
- Department of Agroecology, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
| | - Kees Jan van Groenigen
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Jørgen E Olesen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
| | - Zhi Liang
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Yu Jiang
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Poul E Laerke
- Department of Agroecology, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
| | - Yuefang Zhang
- Jiangsu Academy of Agricultural Sciences, East China Scientific Observing and Experimental Station of Development and Utilization of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Yiqi Luo
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- Center for Circular Bioeconomy, Aarhus University, Tjele, Denmark
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39
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Qian H, Huang S, Chen J, Wang L, Hungate BA, van Kessel C, Zhang J, Deng A, Jiang Y, van Groenigen KJ, Zhang W. Lower-than-expected CH 4 emissions from rice paddies with rising CO 2 concentrations. Glob Chang Biol 2020; 26:2368-2376. [PMID: 32003939 DOI: 10.1111/gcb.14984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
Elevated atmospheric CO2 (eCO2 ) generally increases carbon input in rice paddy soils and stimulates the growth of methane-producing microorganisms. Therefore, eCO2 is widely expected to increase methane (CH4 ) emissions from rice agriculture, a major source of anthropogenic CH4 . Agricultural practices strongly affect CH4 emissions from rice paddies as well, but whether these practices modulate effects of eCO2 is unclear. Here we show, by combining a series of experiments and meta-analyses, that whereas eCO2 strongly increased CH4 emissions from paddies without straw incorporation, it tended to reduce CH4 emissions from paddy soils with straw incorporation. Our experiments also identified the microbial processes underlying these results: eCO2 increased methane-consuming microorganisms more strongly in soils with straw incorporation than in soils without straw, with the opposite pattern for methane-producing microorganisms. Accounting for the interaction between CO2 and straw management, we estimate that eCO2 increases global CH4 emissions from rice paddies by 3.7%, an order of magnitude lower than previous estimates. Our results suggest that the effect of eCO2 on CH4 emissions from rice paddies is smaller than previously thought and underline the need for judicious agricultural management to curb future CH4 emissions.
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Affiliation(s)
- Haoyu Qian
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Shan Huang
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, China
| | - Jin Chen
- Soil and Fertilizer & Resources and Environmental Institute, Jiangxi Academy of Agricultural Science, Nanchang, China
| | - Ling Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Chris van Kessel
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Jun Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Aixing Deng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yu Jiang
- Jiangsu Collaborative Innovation Center for Modern Crop Production/Key Laboratory of Crop Physiology and Ecology in Southern China, Nanjing Agricultural University, Nanjing, China
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Kees Jan van Groenigen
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Weijian Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing, China
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40
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Chen C, van Groenigen KJ, Yang H, Hungate BA, Yang B, Tian Y, Chen J, Dong W, Huang S, Deng A, Jiang Y, Zhang W. Global warming and shifts in cropping systems together reduce China's rice production. Global Food Security 2020. [DOI: 10.1016/j.gfs.2020.100359] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Yang S, Zheng Q, Yang Y, Yuan M, Ma X, Chiariello NR, Docherty KM, Field CB, Gutknecht JLM, Hungate BA, Niboyet A, Le Roux X, Zhou J. Fire affects the taxonomic and functional composition of soil microbial communities, with cascading effects on grassland ecosystem functioning. Glob Chang Biol 2020; 26:431-442. [PMID: 31562826 DOI: 10.1111/gcb.14852] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/18/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies have focused on how fire affects taxonomic and functional diversities of soil microbial communities, along with changes in plant communities and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects in a grassland ecosystem 9 months after an experimental fire at the Jasper Ridge Global Change Experiment site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis showing that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa was able to withstand the disturbance. In addition, fire decreased the relative abundances of most functional genes associated with C degradation and N cycling, implicating a slowdown of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated above- and belowground plant growth, likely enhancing plant-microbe competition for soil inorganic N, which was reduced by a factor of about 2. To synthesize those findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for significantly higher soil respiration rates in burned sites. Together, our results demonstrate that fire 'reboots' the grassland ecosystem by differentially regulating plant and soil microbial communities, leading to significant changes in soil C and N dynamics.
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Affiliation(s)
- Sihang Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Qiaoshu Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Nona R Chiariello
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Christopher B Field
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Jessica L M Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Audrey Niboyet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (Sorbonne Université, CNRS, INRA, IRD, Université Paris Diderot, UPEC), Paris, France
- AgroParisTech, Paris, France
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne, CNRS, INRA, Université de Lyon, Université Lyon 1, UMR INRA 1418, UMR CNRS 5557, Villeurbanne, France
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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42
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Adams EM, von Hippel FA, Hungate BA, Buck CL. Polychlorinated biphenyl (PCB) contamination of subsistence species on Unalaska Island in the Aleutian Archipelago. Heliyon 2019; 5:e02989. [PMID: 31890953 PMCID: PMC6926255 DOI: 10.1016/j.heliyon.2019.e02989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/17/2019] [Accepted: 12/03/2019] [Indexed: 11/16/2022] Open
Abstract
Polychlorinated biphenyls (PCBs) are a group of synthetic, lipophilic organochlorines that were banned due to their impacts on human and wildlife health and environmental persistence. Although banned, the continued release from pre-banned products allows them to persist at toxic levels in the environment. This is especially the case in lipid rich food webs of the Arctic, where PCBs accumulate due to both long-range atmospheric transport and locally contaminated sites such as formerly used defense (FUD) sites. At the request of the leadership of the Qawalangin Tribe of Unalaska Island in the Aleutian Archipelago, we analyzed PCB concentrations in samples of threespine stickleback (Gasterosteus aculeatus) and subsistence foods (i.e., salmonid species and blue mussels [Mytilus edulis]) collected at both FUD and non-FUD sites. PCBs were extracted from samples using a QuEChERS method. The mean PCB concentrations across all mussel samples was 6.1 ppb; mussels from FUD sites had nearly double the PCB concentrations (7.6 ppb) compared to non-military sites (3.9 ppb), and at two FUD sites the PCB concentrations exceeded safe consumption guidelines. The mean total PCB concentration for fish was 2.8 ppb; fish PCB concentrations were higher at FUD sites (3.2 ppb) compared to non-military sites (1.2 ppb). These results support the need to remediate the FUD sites of "Building 551/T Dock to Airport" and "Delta Western". More generally, these results provide further evidence of the continued problem of PCB contamination at FUD sites in the Arctic, many of which are co-located with indigenous communities.
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Affiliation(s)
- Elise M Adams
- Department of Biological Sciences, Northern Arizona University, USA
| | | | - Bruce A Hungate
- Department of Biological Sciences and Center for Ecosystem Science and Society, Northern Arizona University, USA
| | - C Loren Buck
- Department of Biological Sciences, Northern Arizona University, USA
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43
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Papp K, Hungate BA, Schwartz E. Glucose triggers strong taxon-specific responses in microbial growth and activity: insights from DNA and RNA qSIP. Ecology 2019; 101:e02887. [PMID: 31502670 DOI: 10.1002/ecy.2887] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/16/2019] [Accepted: 08/06/2019] [Indexed: 01/10/2023]
Abstract
Growth of soil microorganisms is often described as carbon limited, and adding labile carbon to soil often results in a transient and large increase in respiration. In contrast, soil microbial biomass changes little, suggesting that growth and respiration are decoupled in response to a carbon pulse. Alternatively, measuring bulk responses of the entire community (total respiration and biomass) could mask ecologically important variation among taxa in response to the added carbon. Here, we assessed taxon-specific variation in cellular growth (measured as DNA synthesis) and metabolic activity (measured as rRNA synthesis) following glucose addition to soil using quantitative stable isotope probing with H2 18 O. We found that glucose addition altered rates of DNA and rRNA synthesis, but the effects were strongly taxon specific: glucose stimulated growth and rRNA transcription for some taxa, and suppressed these for others. These contrasting taxon-specific responses could explain the small and transient changes in total soil microbial biomass. Responses to glucose were not well predicted by a priori assignments of taxa into copiotrophic or oligotrophic categories. Across all taxa, rates of DNA and rRNA synthesis changed in parallel, indicating that growth and activity were coupled, and the degree of coupling was unaffected by glucose addition. This pattern argues against the idea that labile carbon addition causes a large reduction in metabolic growth efficiency; rather, the large pulse of respiration observed with labile substrate addition is more likely to be the result of rapid turnover of microbial biomass, possibly due to trophic interactions. Our results support a strong connection between rRNA synthesis and bacterial growth, and indicate that taxon-specific responses among soil bacteria can buffer responses at the scale of the whole community.
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Affiliation(s)
- Katerina Papp
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
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44
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Li J, Mau RL, Dijkstra P, Koch BJ, Schwartz E, Liu XJA, Morrissey EM, Blazewicz SJ, Pett-Ridge J, Stone BW, Hayer M, Hungate BA. Predictive genomic traits for bacterial growth in culture versus actual growth in soil. ISME J 2019. [PMID: 31053828 DOI: 10.1038/s41396‐019‐0422‐z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Relationships between microbial genes and performance are often evaluated in the laboratory in pure cultures, with little validation in nature. Here, we show that genomic traits related to laboratory measurements of maximum growth potential failed to predict the growth rates of bacteria in unamended soil, but successfully predicted growth responses to resource pulses: growth increased with 16S rRNA gene copy number and declined with genome size after substrate addition to soils, responses that were repeated in four different ecosystems. Genome size best predicted growth rate in response to addition of glucose alone; adding ammonium with glucose weakened the relationship, and the relationship was absent in nutrient-replete pure cultures, consistent with the idea that reduced genome size is a mechanism of nutrient conservation. Our findings demonstrate that genomic traits of soil bacteria can map to their ecological performance in nature, but the mapping is poor under native soil conditions, where genomic traits related to stress tolerance may prove more predictive. These results remind that phenotype depends on environmental context, underscoring the importance of verifying proposed schemes of trait-based strategies through direct measurement of performance in nature, an important and currently missing foundation for translating microbial processes from genes to ecosystems.
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Affiliation(s)
- Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Xiao-Jun Allen Liu
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Ember M Morrissey
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Bram W Stone
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA. .,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
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45
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Yang S, Zheng Q, Yuan M, Shi Z, Chiariello NR, Docherty KM, Dong S, Field CB, Gu Y, Gutknecht J, Hungate BA, Le Roux X, Ma X, Niboyet A, Yuan T, Zhou J, Yang Y. Long-term elevated CO 2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials. Sci Total Environ 2019; 652:1474-1481. [PMID: 30586832 DOI: 10.1016/j.scitotenv.2018.10.353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/22/2018] [Accepted: 10/26/2018] [Indexed: 06/09/2023]
Abstract
The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3-) (-27.4%) and ammonium (NH4+) (-15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.
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Affiliation(s)
- Sihang Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Qiaoshu Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Mengting Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Zhou Shi
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | | | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Shikui Dong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing normal university, Beijing 100875, PR China
| | | | - Yunfu Gu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA; Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle 06120, Germany; Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN 55104, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Xavier Le Roux
- Microbial ecology Centre, INRA, CNRS, University of Lyon, University Lyon 1, UMR INRA 1418, UMR CNRS 5557, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Audrey Niboyet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (Sorbonne Université, CNRS, INRA, IRD, Université Paris Diderot, UPEC), 4 place Jussieu, 75005 Paris, France; AgroParisTech, 75005 Paris, France
| | - Tong Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
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Jiang Y, Qian H, Wang L, Feng J, Huang S, Hungate BA, van Kessel C, Horwath WR, Zhang X, Qin X, Li Y, Feng X, Zhang J, Deng A, Zheng C, Song Z, Hu S, van Groenigen KJ, Zhang W. Limited potential of harvest index improvement to reduce methane emissions from rice paddies. Glob Chang Biol 2019; 25:686-698. [PMID: 30449058 DOI: 10.1111/gcb.14529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/16/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Rice is a staple food for nearly half of the world's population, but rice paddies constitute a major source of anthropogenic CH4 emissions. Root exudates from growing rice plants are an important substrate for methane-producing microorganisms. Therefore, breeding efforts optimizing rice plant photosynthate allocation to grains, i.e., increasing harvest index (HI), are widely expected to reduce CH4 emissions with higher yield. Here we show, by combining a series of experiments, meta-analyses and an expert survey, that the potential of CH4 mitigation from rice paddies through HI improvement is in fact small. Whereas HI improvement reduced CH4 emissions under continuously flooded (CF) irrigation, it did not affect CH4 emissions in systems with intermittent irrigation (II). We estimate that future plant breeding efforts aimed at HI improvement to the theoretical maximum value will reduce CH4 emissions in CF systems by 4.4%. However, CF systems currently make up only a small fraction of the total rice growing area (i.e., 27% of the Chinese rice paddy area). Thus, to achieve substantial CH4 mitigation from rice agriculture, alternative plant breeding strategies may be needed, along with alternative management.
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Affiliation(s)
- Yu Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
- Institute of Applied Ecology, Nanjing Agricultural University, Nanjing, China
| | - Haoyu Qian
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Ling Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Jinfei Feng
- China National Rice Research Institute, Hangzhou, China
| | - Shan Huang
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona
| | - Chris van Kessel
- Department of Plant Sciences, University of California, Davis, California
| | - William R Horwath
- Department of Land, Air & Water Resources, University of California, Davis, California
| | - Xingyue Zhang
- Department of Land, Air & Water Resources, University of California, Davis, California
| | - Xiaobo Qin
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Yue Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Xiaomin Feng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Jun Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Aixing Deng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Chenyan Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Zhenwei Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Shuijin Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina
| | | | - Weijian Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
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Papp K, Mau RL, Hayer M, Koch BJ, Hungate BA, Schwartz E. Quantitative stable isotope probing with H 218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA. ISME J 2018; 12:3043-3045. [PMID: 30042501 PMCID: PMC6246559 DOI: 10.1038/s41396-018-0233-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 11/09/2022]
Abstract
Most soil bacterial taxa are thought to be dormant, or inactive, yet the extent to which they synthetize new rRNA is poorly understood. We analyzed 18O composition of RNA extracted from soil incubated with H218O and used quantitative stable isotope probing to characterize rRNA synthesis among microbial taxa. RNA was not fully labeled with 18O, peaking at a mean of 23.6 ± 6.8 atom percent excess (APE) 18O after eight days of incubation, suggesting some ribonucleotides in soil were more than eight days old. Microbial taxa varied in the degree they incorporated 18O into their rRNA over time and there was no correlation between the APE 18O of bacterial rRNA and their rRNA to DNA ratios, suggesting that the ratios were not appropriate to measure ribonucleotide synthesis. Our study indicates that, on average, 94% of soil taxa produced new rRNA and therefore were metabolically active.
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Affiliation(s)
- Katerina Papp
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
- Division of Hydrological Sciences, Desert Research Institute, Las Vegas, NV, USA.
- Department of Civil and Environmental Engineering and Construction, University of Las Vegas, Las Vegas, NV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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48
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Davis GS, Waits K, Nordstrom L, Grande H, Weaver B, Papp K, Horwinski J, Koch B, Hungate BA, Liu CM, Price LB. Antibiotic-resistant Escherichia coli from retail poultry meat with different antibiotic use claims. BMC Microbiol 2018; 18:174. [PMID: 30390618 PMCID: PMC6215666 DOI: 10.1186/s12866-018-1322-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 10/21/2018] [Indexed: 11/23/2022] Open
Abstract
Background We sought to determine if the prevalence of antibiotic-resistant Escherichia coli differed across retail poultry products and among major production categories, including organic, “raised without antibiotics”, and conventional. Results We collected all available brands of retail chicken and turkey—including conventional, “raised without antibiotic”, and organic products—every two weeks from January to December 2012. In total, E. coli was recovered from 91% of 546 turkey products tested and 88% of 1367 chicken products tested. The proportion of samples contaminated with E. coli was similar across all three production categories. Resistance prevalence varied by meat type and was highest among E. coli isolates from turkey for the majority of antibiotics tested. In general, production category had little effect on resistance prevalence among E. coli isolates from chicken, although resistance to gentamicin and multidrug resistance did vary. In contrast, resistance prevalence was significantly higher for 6 of the antibiotics tested—and multidrug resistance—among isolates from conventional turkey products when compared to those labelled organic or “raised without antibiotics”. E. coli isolates from chicken varied strongly in resistance prevalence among different brands within each production category. Conclusion The high prevalence of resistance among E. coli isolates from conventionally-raised turkey meat suggests greater antimicrobial use in conventional turkey production as compared to “raised without antibiotics” and organic systems. However, among E. coli from chicken meat, resistance prevalence was more strongly linked to brand than to production category, which could be caused by brand-level differences during production and/or processing, including variations in antimicrobial use. Electronic supplementary material The online version of this article (10.1186/s12866-018-1322-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregg S Davis
- George Washington University Milken Institute School of Public Health, Washington, DC, USA.
| | - Kara Waits
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA.,The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Lora Nordstrom
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Heidi Grande
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Brett Weaver
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Katerina Papp
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA.,Department of Civil and Environmental Engineering and Construction, University of Las Vegas, Las Vegas, NV, USA.,Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Joseph Horwinski
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Benjamin Koch
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Cindy M Liu
- George Washington University Milken Institute School of Public Health, Washington, DC, USA.,Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Lance B Price
- George Washington University Milken Institute School of Public Health, Washington, DC, USA.,Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
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49
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Rubin RL, Koch GW, Martinez A, Mau RL, Bowker MA, Hungate BA. Developing climate-smart restoration: Can plant microbiomes be hardened against heat waves? Ecol Appl 2018; 28:1594-1605. [PMID: 29989265 DOI: 10.1002/eap.1763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/24/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
Heat waves are increasing in frequency and intensity, presenting a challenge for the already difficult practice of ecological restoration. We investigated whether pre-heating locally sourced rhizosphere soil (inoculum) could acclimatize plants to a field-imposed heat wave in a restoration setting. Soil heating in the laboratory caused a marked shift in rhizosphere bacterial community composition, accompanied by an increase in species evenness. Furthermore, pre-heated rhizosphere soil reduced plant height, number of leaves, and shoot mass of the C4 grass, blue grama (Bouteloua gracilis), and it reduced the shoot mass of the C3 grass, Arizona fescue (Festuca arizonica) in the glasshouse. Following transplantation and the application of a field heat wave, pre-heated inoculum did not influence heat wave survival for either plant species. However, there were strong species-level responses to the field heat wave. For instance, heat wave survivorship was over four times higher in blue grama (92%) than in Arizona fescue (22%). These results suggest that the use of C4 seeds may be preferable for sites exhibiting high heat wave risk. Further research is needed to understand whether inocula are more effective in highly degraded soil in comparison with partially degraded soils.
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Affiliation(s)
- Rachel L Rubin
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - George W Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Ayla Martinez
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Rebecca L Mau
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
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50
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Carol Adair E, Hooper DU, Paquette A, Hungate BA. Ecosystem context illuminates conflicting roles of plant diversity in carbon storage. Ecol Lett 2018; 21:1604-1619. [DOI: 10.1111/ele.13145] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/08/2018] [Accepted: 07/24/2018] [Indexed: 01/31/2023]
Affiliation(s)
- E. Carol Adair
- Rubenstein School of Environment and Natural Resources University of Vermont Burlington VT05405 USA
| | - David U. Hooper
- Department of Biology Western Washington University Bellingham WA98225‐9160 USA
| | - Alain Paquette
- Centre for Forest Research Département des sciences biologiques Université du Québec à Montréal CP 8888, Succursale Centre‐ville Montréal QC Canada H3C 3P8
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences Northern Arizona University Flagstaff AZ86011 USA
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