1
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Metze D, Schnecker J, de Carlan CLN, Bhattarai B, Verbruggen E, Ostonen I, Janssens IA, Sigurdsson BD, Hausmann B, Kaiser C, Richter A. Soil warming increases the number of growing bacterial taxa but not their growth rates. SCIENCE ADVANCES 2024; 10:eadk6295. [PMID: 38394199 PMCID: PMC10889357 DOI: 10.1126/sciadv.adk6295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.
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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
| | | | - Biplabi Bhattarai
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Erik Verbruggen
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Ivika Ostonen
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ivan A. Janssens
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Bjarni D. Sigurdsson
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Hvanneyri, Borgarnes, Iceland
| | - 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
| | - 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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2
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Tian J, Dungait JAJ, Hou R, Deng Y, Hartley IP, Yang Y, Kuzyakov Y, Zhang F, Cotrufo MF, Zhou J. Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming. Nat Commun 2024; 15:377. [PMID: 38191568 PMCID: PMC10774409 DOI: 10.1038/s41467-023-44647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024] Open
Abstract
Increasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.
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Affiliation(s)
- Jing Tian
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, PR China.
| | - Jennifer A J Dungait
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Rennes Drive, Exeter, EX4 4RJ, UK
- Carbon Management Centre, SRUC-Scotland's Rural College, Edinburgh, EH9 3JG, UK
| | - Ruixing Hou
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), 100101, Beijing, PR China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, PR China
| | - Iain P Hartley
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Rennes Drive, Exeter, EX4 4RJ, UK
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, PR China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, 37077, Göttingen, Germany
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, PR China.
| | - M Francesca Cotrufo
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA.
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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3
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Söllinger A, Ahlers LS, Dahl MB, Sigurðsson P, Le Noir de Carlan C, Bhattarai B, Gall C, Martin VS, Rottensteiner C, Motleleng LL, Breines EM, Verbruggen E, Ostonen I, Sigurdsson BD, Richter A, Tveit AT. Microorganisms in subarctic soils are depleted of ribosomes under short-, medium-, and long-term warming. THE ISME JOURNAL 2024; 18:wrae081. [PMID: 38722823 PMCID: PMC11126301 DOI: 10.1093/ismejo/wrae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/26/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]
Abstract
Physiological responses of soil microorganisms to global warming are important for soil ecosystem function and the terrestrial carbon cycle. Here, we investigate the effects of weeks, years, and decades of soil warming across seasons and time on the microbial protein biosynthesis machineries (i.e. ribosomes), the most abundant cellular macromolecular complexes, using RNA:DNA and RNA:MBC (microbial biomass carbon) ratios as proxies for cellular ribosome contents. We compared warmed soils and non-warmed controls of 15 replicated subarctic grassland and forest soil temperature gradients subject to natural geothermal warming. RNA:DNA ratios tended to be lower in the warmed soils during summer and autumn, independent of warming duration (6 weeks, 8-14 years, and > 50 years), warming intensity (+3°C, +6°C, and +9°C), and ecosystem type. With increasing temperatures, RNA:MBC ratios were also decreasing. Additionally, seasonal RNA:DNA ratios of the consecutively sampled forest showed the same temperature-driven pattern. This suggests that subarctic soil microorganisms are depleted of ribosomes under warm conditions and the lack of consistent relationships with other physicochemical parameters besides temperature further suggests temperature as key driver. Furthermore, in incubation experiments, we measured significantly higher CO2 emission rates per unit of RNA from short- and long-term warmed soils compared to non-warmed controls. In conclusion, ribosome reduction may represent a widespread microbial physiological response to warming that offers a selective advantage at higher temperatures, as energy and matter can be reallocated from ribosome synthesis to other processes including substrate uptake and turnover. This way, ribosome reduction could have a substantial effect on soil carbon dynamics.
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Affiliation(s)
- Andrea Söllinger
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Laureen S Ahlers
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Mathilde Borg Dahl
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489 Greifswald, Germany
| | - Páll Sigurðsson
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Árleynir 22, 112 Reykjavík, Iceland
- Present address: Icelandic Forest Service, Austurvegi 3, 800 Selfoss, Iceland
| | - Coline Le Noir de Carlan
- Research Group Plants and Ecosystems (PLECO), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Biplabi Bhattarai
- Department of Geography, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Christoph Gall
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Victoria S Martin
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Cornelia Rottensteiner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Liabo L Motleleng
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Eva Marie Breines
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Erik Verbruggen
- Research Group Plants and Ecosystems (PLECO), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Ivika Ostonen
- Department of Geography, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Bjarni D Sigurdsson
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Árleynir 22, 112 Reykjavík, Iceland
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
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4
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Xiong W, Ye Y, He D, He S, Xiang Y, Xiao J, Feng W, Wu M, Yang Z, Wang D. Deregulation of Ribosome Biogenesis in Nitrite-Oxidizing Bacteria Leads to Nitrite Accumulation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16673-16684. [PMID: 37862695 DOI: 10.1021/acs.est.3c06002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Nitrite (NO2-) accumulation caused by nitrite-oxidizing bacteria (NOB) inhibition in nitrification is a double-edged sword, i.e., a disaster in aquatic environments but a hope for innovating nitrogen removal technology in wastewater treatment. However, little information is available regarding the molecular mechanism of NOB inhibition at the cellular level. Herein, we investigate the response of NOB inhibition on NO2- accumulation established by a side-stream free ammonia treatment unit in a nitrifying reactor using integrated metagenomics and metaproteomics. Results showed that compared with the baseline, the relative abundance and activity of NOB in the experimental stage decreased by 91.64 and 68.66%, respectively, directly resulting in a NO2- accumulation rate of 88%. Moreover, RNA polymerase, translation factors, and aa-tRNA ligase were significantly downregulated, indicating that protein synthesis in NOB was interfered during NO2- accumulation. Further investigations showed that ribosomal proteins and GTPases, responsible for bindings between either ribosomal proteins and rRNA or ribosome subunits, were remarkably downregulated. This suggests that ribosome biogenesis was severely disrupted, which might be the key reason for the inhibited protein synthesis. Our findings fill a knowledge gap regarding the underlying mechanisms of NO2- accumulation, which would be beneficial for regulating the accumulation of NO2- in aquatic environments and engineered systems.
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Affiliation(s)
- Weiping Xiong
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Yuhang Ye
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Dandan He
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Siying He
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Yinping Xiang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Jun Xiao
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Wenyi Feng
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Mengru Wu
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Zhaohui Yang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Dongbo Wang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
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5
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Meng D, Ai S, Spanos M, Shi X, Li G, Cretoiu D, Zhou Q, Xiao J. Exercise and microbiome: From big data to therapy. Comput Struct Biotechnol J 2023; 21:5434-5445. [PMID: 38022690 PMCID: PMC10665598 DOI: 10.1016/j.csbj.2023.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Exercise is a vital component in maintaining optimal health and serves as a prospective therapeutic intervention for various diseases. The human microbiome, comprised of trillions of microorganisms, plays a crucial role in overall health. Given the advancements in microbiome research, substantial databases have been created to decipher the functionality and mechanisms of the microbiome in health and disease contexts. This review presents an initial overview of microbiomics development and related databases, followed by an in-depth description of the multi-omics technologies for microbiome. It subsequently synthesizes the research pertaining to exercise-induced modifications of the microbiome and diseases that impact the microbiome. Finally, it highlights the potential therapeutic implications of an exercise-modulated microbiome in intestinal disease, obesity and diabetes, cardiovascular disease, and immune/inflammation-related diseases.
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Affiliation(s)
- Danni Meng
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Songwei Ai
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Michail Spanos
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Xiaohui Shi
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Dragos Cretoiu
- Department of Medical Genetics, Carol Davila University of Medicine and Pharmacy, Bucharest 020031, Romania
- Materno-Fetal Assistance Excellence Unit, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest 011062, Romania
| | - Qiulian Zhou
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
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6
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Li C, Miao L, Adyel TM, Wu J, Hou J. Transformation of Biofilm to Carbon Sinks after Prolonged Droughts Linked with Algal Biodiversity Change. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:15487-15498. [PMID: 37807898 DOI: 10.1021/acs.est.3c04631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Global climate change significantly increased the duration of droughts in intermittent rivers, impacting benthic microbial-mediated biogeochemical processes. However, the impact of prolonged droughts on the carbon contribution of intermittent rivers remains poorly understood. In this study, we investigated the potential effects of varying drought gradients (ranging from 20 to 130 days) on benthic biofilms community structure (algae, bacteria, and fungi) and their carbon metabolism functions (ecosystem metabolism and carbon dioxide (CO2) emission fluxes) using mesocosm experiments. Our findings indicate that longer drought durations lead to reduced alpha diversity and community heterogeneity, tighter interdomain networks, and an increased role of stochastic processes in community assembly, with a discernible threshold at around 60 days. Concurrently, the biofilm transforms into a carbon sink following a drought period of 60 days, as evidenced by the transformation of CO2 emission fluxes from 633.25 ± 194.69 to -349.61 ± 277.79 mg m-2 h-1. Additionally, the partial least-squares path model revealed that the resilience of algal communities and network stability may drive biofilm's transformation into a carbon sink, primarily through the heightened resilience of autotrophic metabolism. This study underscores the significance of the carbon contribution from intermittent rivers, as the shift in carbon metabolism functions with increasing droughts could lead to skewed estimations of current riverine carbon fluxes.
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Affiliation(s)
- Chaoran Li
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Tanveer M Adyel
- STEM, University of South Australia, Mawson Lakes 5095, SA, Australia
| | - Jun Wu
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
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7
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Wang J, Chen S, Sun R, Liu B, Waghmode T, Hu C. Spatial and temporal dynamics of the bacterial community under experimental warming in field-grown wheat. PeerJ 2023; 11:e15428. [PMID: 37334112 PMCID: PMC10276554 DOI: 10.7717/peerj.15428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/25/2023] [Indexed: 06/20/2023] Open
Abstract
Climate change may lead to adverse effects on agricultural crops, plant microbiomes have the potential to help hosts counteract these effects. While plant-microbe interactions are known to be sensitive to temperature, how warming affects the community composition and functioning of plant microbiomes in most agricultural crops is still unclear. Here, we utilized a 10-year field experiment to investigate the effects of warming on root zone carbon availability, microbial activity and community composition at spatial (root, rhizosphere and bulk soil) and temporal (tillering, jointing and ripening stages of plants) scales in field-grown wheat (Triticum aestivum L.). The dissolved organic carbon and microbial activity in the rhizosphere were increased by soil warming and varied considerably across wheat growth stages. Warming exerted stronger effects on the microbial community composition in the root and rhizosphere samples than in the bulk soil. Microbial community composition, particularly the phyla Actinobacteria and Firmicutes, shifted considerably in response to warming. Interestingly, the abundance of a number of known copiotrophic taxa, such as Pseudomonas and Bacillus, and genera in Actinomycetales increased in the roots and rhizosphere under warming and the increase in these taxa implies that they may play a role in increasing the resilience of plants to warming. Taken together, we demonstrated that soil warming along with root proximity and plant growth status drives changes in the microbial community composition and function in the wheat root zone.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuaimin Chen
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Ruibo Sun
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- Xiong’an Institute of Innovation, Chinese Academy of Sciences, Xiong’an New Area, China
| | - Tatoba Waghmode
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- Xiong’an Institute of Innovation, Chinese Academy of Sciences, Xiong’an New Area, China
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8
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Abreu CI, Dal Bello M, Bunse C, Pinhassi J, Gore J. Warmer temperatures favor slower-growing bacteria in natural marine communities. SCIENCE ADVANCES 2023; 9:eade8352. [PMID: 37163596 PMCID: PMC10171810 DOI: 10.1126/sciadv.ade8352] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Earth's life-sustaining oceans harbor diverse bacterial communities that display varying composition across time and space. While particular patterns of variation have been linked to a range of factors, unifying rules are lacking, preventing the prediction of future changes. Here, analyzing the distribution of fast- and slow-growing bacteria in ocean datasets spanning seasons, latitude, and depth, we show that higher seawater temperatures universally favor slower-growing taxa, in agreement with theoretical predictions of how temperature-dependent growth rates differentially modulate the impact of mortality on species abundances. Changes in bacterial community structure promoted by temperature are independent of variations in nutrients along spatial and temporal gradients. Our results help explain why slow growers dominate at the ocean surface, during summer, and near the tropics and provide a framework to understand how bacterial communities will change in a warmer world.
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Affiliation(s)
- Clare I Abreu
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Martina Dal Bello
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carina Bunse
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution of Microbial Model Systems, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
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9
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Pande PM, Azarbad H, Tremblay J, St-Arnaud M, Yergeau E. Metatranscriptomic response of the wheat holobiont to decreasing soil water content. ISME COMMUNICATIONS 2023; 3:30. [PMID: 37061589 PMCID: PMC10105728 DOI: 10.1038/s43705-023-00235-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/17/2023]
Abstract
Crops associate with microorganisms that help their resistance to biotic stress. However, it is not clear how the different partners of this association react during exposure to stress. This knowledge is needed to target the right partners when trying to adapt crops to climate change. Here, we grew wheat in the field under rainout shelters that let through 100%, 75%, 50% and 25% of the precipitation. At the peak of the growing season, we sampled plant roots and rhizosphere, and extracted and sequenced their RNA. We compared the 100% and the 25% treatments using differential abundance analysis. In the roots, most of the differentially abundant (DA) transcripts belonged to the fungi, and most were more abundant in the 25% precipitation treatment. About 10% of the DA transcripts belonged to the plant and most were less abundant in the 25% precipitation treatment. In the rhizosphere, most of the DA transcripts belonged to the bacteria and were generally more abundant in the 25% precipitation treatment. Taken together, our results show that the transcriptomic response of the wheat holobiont to decreasing precipitation levels is stronger for the fungal and bacterial partners than for the plant.
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Affiliation(s)
- Pranav M Pande
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | - Hamed Azarbad
- Department of Biology, Evolutionary Ecology of Plants, Philipps-University Marburg, Marburg, Germany
| | - Julien Tremblay
- National Research Council of Canada, Energy Mining and Environment, Montréal, Québec, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Université de Montréal et Jardin Botanique de Montréal, Montréal, Québec, Canada
| | - Etienne Yergeau
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada.
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10
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Tveit AT, Söllinger A, Rainer EM, Didriksen A, Hestnes AG, Motleleng L, Hellinger HJ, Rattei T, Svenning MM. Thermal acclimation of methanotrophs from the genus Methylobacter. THE ISME JOURNAL 2023; 17:502-513. [PMID: 36650275 PMCID: PMC10030640 DOI: 10.1038/s41396-023-01363-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Methanotrophs oxidize most of the methane (CH4) produced in natural and anthropogenic ecosystems. Often living close to soil surfaces, these microorganisms must frequently adjust to temperature change. While many environmental studies have addressed temperature effects on CH4 oxidation and methanotrophic communities, there is little knowledge about the physiological adjustments that underlie these effects. We have studied thermal acclimation in Methylobacter, a widespread, abundant, and environmentally important methanotrophic genus. Comparisons of growth and CH4 oxidation kinetics at different temperatures in three members of the genus demonstrate that temperature has a strong influence on how much CH4 is consumed to support growth at different CH4 concentrations. However, the temperature effect varies considerably between species, suggesting that how a methanotrophic community is composed influences the temperature effect on CH4 uptake. To understand thermal acclimation mechanisms widely we carried out a transcriptomics experiment with Methylobacter tundripaludum SV96T. We observed, at different temperatures, how varying abundances of transcripts for glycogen and protein biosynthesis relate to cellular glycogen and ribosome concentrations. Our data also demonstrated transcriptional adjustment of CH4 oxidation, oxidative phosphorylation, membrane fatty acid saturation, cell wall composition, and exopolysaccharides between temperatures. In addition, we observed differences in M. tundripaludum SV96T cell sizes at different temperatures. We conclude that thermal acclimation in Methylobacter results from transcriptional adjustment of central metabolism, protein biosynthesis, cell walls and storage. Acclimation leads to large shifts in CH4 consumption and growth efficiency, but with major differences between species. Thus, our study demonstrates that physiological adjustments to temperature change can substantially influence environmental CH4 uptake rates and that consideration of methanotroph physiology might be vital for accurate predictions of warming effects on CH4 emissions.
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Affiliation(s)
- Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Andrea Söllinger
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Edda Marie Rainer
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alena Didriksen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anne Grethe Hestnes
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Liabo Motleleng
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Hans-Jörg Hellinger
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Thomas Rattei
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
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11
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Domeignoz-Horta LA, Pold G, Erb H, Sebag D, Verrecchia E, Northen T, Louie K, Eloe-Fadrosh E, Pennacchio C, Knorr MA, Frey SD, Melillo JM, DeAngelis KM. Substrate availability and not thermal acclimation controls microbial temperature sensitivity response to long-term warming. GLOBAL CHANGE BIOLOGY 2023; 29:1574-1590. [PMID: 36448874 DOI: 10.1111/gcb.16544] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/18/2022] [Indexed: 05/28/2023]
Abstract
Microbes are responsible for cycling carbon (C) through soils, and predicted changes in soil C stocks under climate change are highly sensitive to shifts in the mechanisms assumed to control the microbial physiological response to warming. Two mechanisms have been suggested to explain the long-term warming impact on microbial physiology: microbial thermal acclimation and changes in the quantity and quality of substrates available for microbial metabolism. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-term warming, we sampled soils from 13- and 28-year-old soil warming experiments in different seasons. We performed short-term laboratory incubations across a range of temperatures to measure the relationships between temperature sensitivity of physiology (growth, respiration, carbon use efficiency, and extracellular enzyme activity) and the chemical composition of soil organic matter. We observed apparent thermal acclimation of microbial respiration, but only in summer, when warming had exacerbated the seasonally-induced, already small dissolved organic matter pools. Irrespective of warming, greater quantity and quality of soil carbon increased the extracellular enzymatic pool and its temperature sensitivity. We propose that fresh litter input into the system seasonally cancels apparent thermal acclimation of C-cycling processes to decadal warming. Our findings reveal that long-term warming has indirectly affected microbial physiology via reduced C availability in this system, implying that earth system models including these negative feedbacks may be best suited to describe long-term warming effects on these soils.
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Affiliation(s)
- Luiz A Domeignoz-Horta
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Grace Pold
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hailey Erb
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - David Sebag
- IFP Energies Nouvelles, Rueil-Malmaison, France
- Faculty of Geosciences and the Environment, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Eric Verrecchia
- Faculty of Geosciences and the Environment, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Trent Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Katherine Louie
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Emiley Eloe-Fadrosh
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christa Pennacchio
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Melissa A Knorr
- School of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Serita D Frey
- School of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Jerry M Melillo
- The Ecosystems Center, Marine Biological Laboratories, Woods Hole, Massachusetts, USA
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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12
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Täumer J, Marhan S, Groß V, Jensen C, Kuss AW, Kolb S, Urich T. Linking transcriptional dynamics of CH 4-cycling grassland soil microbiomes to seasonal gas fluxes. THE ISME JOURNAL 2022; 16:1788-1797. [PMID: 35388141 PMCID: PMC9213473 DOI: 10.1038/s41396-022-01229-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/07/2022] [Accepted: 03/21/2022] [Indexed: 11/09/2022]
Abstract
Soil CH4 fluxes are driven by CH4-producing and -consuming microorganisms that determine whether soils are sources or sinks of this potent greenhouse gas. To date, a comprehensive understanding of underlying microbiome dynamics has rarely been obtained in situ. Using quantitative metatranscriptomics, we aimed to link CH4-cycling microbiomes to net surface CH4 fluxes throughout a year in two grassland soils. CH4 fluxes were highly dynamic: both soils were net CH4 sources in autumn and winter and sinks in spring and summer, respectively. Correspondingly, methanogen mRNA abundances per gram soil correlated well with CH4 fluxes. Methanotroph to methanogen mRNA ratios were higher in spring and summer, when the soils acted as net CH4 sinks. CH4 uptake was associated with an increased proportion of USCα and γ pmoA and pmoA2 transcripts. We assume that methanogen transcript abundance may be useful to approximate changes in net surface CH4 emissions from grassland soils. High methanotroph to methanogen ratios would indicate CH4 sink properties. Our study links for the first time the seasonal transcriptional dynamics of CH4-cycling soil microbiomes to gas fluxes in situ. It suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes.
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Affiliation(s)
- Jana Täumer
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Verena Groß
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Corinna Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Andreas W Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Steffen Kolb
- RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Tim Urich
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany.
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