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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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Buezo J, Medina NG, Hereş AM, Petritan IC, Cornelissen JHC, Petritan AM, Esteban R, Ilinca E, Stoian R, Curiel Yuste J. Downed woody debris carbon emissions in a European temperate virgin forest as driven by species, decay classes, diameter and microclimate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169133. [PMID: 38070551 DOI: 10.1016/j.scitotenv.2023.169133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/17/2023] [Accepted: 12/03/2023] [Indexed: 01/18/2024]
Abstract
Downed woody debris (DWD) plays an important role as regulator of nutrient and carbon (C) cycling in forests, accounting for up to the 20 % of the total C stocks in primary forests. DWD persistence is highly influenced by microbial decomposition, which is determined by various environmental factors, including fluctuations in temperature and moisture, as well as in intrinsic DWD properties determined by species, diameter, or decay classes (DCs). The relative importance of these different drivers, as well as their interactions, remains largely unknown. Moreover, the importance of DWD for C cycling in virgin forests remains poorly understood, due to their scarcity and poor accessibility. To address this research gap, we conducted a study on DWD respiration (RDWD), in a temperate virgin forest dominated by European beech and silver fir. Our investigation analysed the correlation between RDWD of these two dominant tree species and the seasonal changes in climate (temperature and moisture), considering other intrinsic DWD traits such as DCs (1, 2 and 4) and diameters (1, 10 and 25 cm). As anticipated, RDWD (normalized per gram of dry DWD) increased with air temperature. Surprisingly, DWD diameter also had a strong positive correlation with RDWD. Nonetheless, the sensitivity to both variables and other intrinsic traits (DC and density) was greatly modulated by the species. On the contrary, water content, which exhibited a considerable spatial variation, had an overall negative effect on RDWD. Virgin forests are generally seen as ineffective C sinks due to their lack of net productivity and high respiration and nutrient turnover. However, the rates of RDWD in this virgin forest were significantly lower than those previously estimated for managed forests. This suggests that DWD in virgin forests may be buffering forest CO2 emissions to the atmosphere more than previously thought.
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Affiliation(s)
- J Buezo
- Department of Forest Engineering, Forest Management Planning and Terrestrial Measurements, Faculty of Silviculture and Forest Engineering, Transilvania University of Braşov, Braşov, Romania; Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, E-31192 Mutilva, Navarre, Spain
| | - N G Medina
- Departamento de Biología (Botánica), Universidad Autónoma de Madrid, Madrid, Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Madrid, Madrid, Spain
| | - A-M Hereş
- Department of Forest Engineering, Forest Management Planning and Terrestrial Measurements, Faculty of Silviculture and Forest Engineering, Transilvania University of Braşov, Braşov, Romania; BC3 - Basque Centre for Climate Change, Scientific Campus of the University of the Basque Country, 48940 Leioa, Spain
| | - I C Petritan
- Department of Forest Engineering, Forest Management Planning and Terrestrial Measurements, Faculty of Silviculture and Forest Engineering, Transilvania University of Braşov, Braşov, Romania.
| | - J H C Cornelissen
- Systems Ecology, Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit, Amsterdam, the Netherlands
| | - A-M Petritan
- National Institute for Research and Development in Forestry "Marin Dracea", Eroilor 128, 077190 Voluntari, Romania
| | - R Esteban
- Department of Plant Biology and Ecology, University of Basque Country (UPV/EHU), Leioa Bizkaia, Spain
| | - E Ilinca
- Environmental Management and Engineering, AgroParisTech, Paris, France
| | - R Stoian
- Department of Forest Engineering, Forest Management Planning and Terrestrial Measurements, Faculty of Silviculture and Forest Engineering, Transilvania University of Braşov, Braşov, Romania
| | - J Curiel Yuste
- BC3 - Basque Centre for Climate Change, Scientific Campus of the University of the Basque Country, 48940 Leioa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
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3
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Wu H, Cui H, Fu C, Li R, Qi F, Liu Z, Yang G, Xiao K, Qiao M. Unveiling the crucial role of soil microorganisms in carbon cycling: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168627. [PMID: 37977383 DOI: 10.1016/j.scitotenv.2023.168627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.
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Affiliation(s)
- Haowei Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Huiling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Chenxi Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ran Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Fengyuan Qi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhelun Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Keqing Xiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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Lei J, Su Y, Jian S, Guo X, Yuan M, Bates CT, Shi ZJ, Li J, Su Y, Ning D, Wu L, Zhou J, Yang Y. Warming effects on grassland soil microbial communities are amplified in cool months. THE ISME JOURNAL 2024; 18:wrae088. [PMID: 38747385 PMCID: PMC11170927 DOI: 10.1093/ismejo/wrae088] [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: 01/10/2024] [Revised: 03/25/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024]
Abstract
Global warming modulates soil respiration (RS) via microbial decomposition, which is seasonally dependent. Yet, the magnitude and direction of this modulation remain unclear, partly owing to the lack of knowledge on how microorganisms respond to seasonal changes. Here, we investigated the temporal dynamics of soil microbial communities over 12 consecutive months under experimental warming in a tallgrass prairie ecosystem. The interplay between warming and time altered (P < 0.05) the taxonomic and functional compositions of microbial communities. During the cool months (January to February and October to December), warming induced a soil microbiome with a higher genomic potential for carbon decomposition, community-level ribosomal RNA operon (rrn) copy numbers, and microbial metabolic quotients, suggesting that warming stimulated fast-growing microorganisms that enhanced carbon decomposition. Modeling analyses further showed that warming reduced the temperature sensitivity of microbial carbon use efficiency (CUE) by 28.7% when monthly average temperature was low, resulting in lower microbial CUE and higher heterotrophic respiration (Rh) potentials. Structural equation modeling showed that warming modulated both Rh and RS directly by altering soil temperature and indirectly by influencing microbial community traits, soil moisture, nitrate content, soil pH, and gross primary productivity. The modulation of Rh by warming was more pronounced in cooler months compared to warmer ones. Together, our findings reveal distinct warming-induced effects on microbial functional traits in cool months, challenging the norm of soil sampling only in the peak growing season, and advancing our mechanistic understanding of the seasonal pattern of RS and Rh sensitivity to warming.
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Affiliation(s)
- Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yuanlong Su
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Siyang Jian
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94704, United States
| | - Colin T Bates
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Zhou Jason Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences and Environmental Microbiology & Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Yifan Su
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Daliang Ning
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Liyou Wu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019, United States
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
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5
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Qu L, Wang C, Manzoni S, Dacal M, Maestre FT, Bai E. Stronger compensatory thermal adaptation of soil microbial respiration with higher substrate availability. THE ISME JOURNAL 2024; 18:wrae025. [PMID: 38366058 PMCID: PMC10945366 DOI: 10.1093/ismejo/wrae025] [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: 01/22/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024]
Abstract
Ongoing global warming is expected to augment soil respiration by increasing the microbial activity, driving self-reinforcing feedback to climate change. However, the compensatory thermal adaptation of soil microorganisms and substrate depletion may weaken the effects of rising temperature on soil respiration. To test this hypothesis, we collected soils along a large-scale forest transect in eastern China spanning a natural temperature gradient, and we incubated the soils at different temperatures with or without substrate addition. We combined the exponential thermal response function and a data-driven model to study the interaction effect of thermal adaptation and substrate availability on microbial respiration and compared our results to those from two additional continental and global independent datasets. Modeled results suggested that the effect of thermal adaptation on microbial respiration was greater in areas with higher mean annual temperatures, which is consistent with the compensatory response to warming. In addition, the effect of thermal adaptation on microbial respiration was greater under substrate addition than under substrate depletion, which was also true for the independent datasets reanalyzed using our approach. Our results indicate that thermal adaptation in warmer regions could exert a more pronounced negative impact on microbial respiration when the substrate availability is abundant. These findings improve the body of knowledge on how substrate availability influences the soil microbial community-temperature interactions, which could improve estimates of projected soil carbon losses to the atmosphere through respiration.
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Affiliation(s)
- Lingrui Qu
- CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China
| | - Chao Wang
- CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China
- Key Laboratory of Terrestrial Ecosystem Carbon Neutrality, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, 110016, China
| | - Stefano Manzoni
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, Stockholm, 10691, Sweden
| | - Marina Dacal
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’, Universidad de Alicante, Alicante, 03690, Spain
- Freie Universität Berlin, Institute of Biology, Berlin, 14195, Germany
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’, Universidad de Alicante, Alicante, 03690, Spain
- Departamento de Ecología, Universidad de Alicante, Alicante, 03690, Spain
| | - Edith Bai
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, Northeast Normal University, Changchun, Jilin, 130024, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, Jilin, 130024, China
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6
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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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7
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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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8
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Liu XJA, Han S, Frey SD, Melillo JM, Zhou J, DeAngelis KM. Microbial responses to long-term warming differ across soil microenvironments. ISME COMMUNICATIONS 2024; 4:ycae051. [PMID: 38699060 PMCID: PMC11065356 DOI: 10.1093/ismeco/ycae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024]
Abstract
Soil carbon loss is likely to increase due to climate warming, but microbiomes and microenvironments may dampen this effect. In a 30-year warming experiment, physical protection within soil aggregates affected the thermal responses of soil microbiomes and carbon dynamics. In this study, we combined metagenomic analysis with physical characterization of soil aggregates to explore mechanisms by which microbial communities respond to climate warming across different soil microenvironments. Long-term warming decreased the relative abundances of genes involved in degrading labile compounds (e.g. cellulose), but increased those genes involved in degrading recalcitrant compounds (e.g. lignin) across aggregate sizes. These changes were observed in most phyla of bacteria, especially for Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes. Microbial community composition was considerably altered by warming, leading to declined diversity for bacteria and fungi but not for archaea. Microbial functional genes, diversity, and community composition differed between macroaggregates and microaggregates, indicating the essential role of physical protection in controlling microbial community dynamics. Our findings suggest that microbes have the capacity to employ various strategies to acclimate or adapt to climate change (e.g. warming, heat stress) by shifting functional gene abundances and community structures in varying microenvironments, as regulated by soil physical protection.
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Affiliation(s)
- Xiao Jun A Liu
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, United States
- Institute for Environmental Genomics and School of Biological Sciences, University of Oklahoma , Norman, OK 73019, United States
| | - Shun Han
- Institute for Environmental Genomics and School of Biological Sciences, University of Oklahoma , Norman, OK 73019, United States
| | - Serita D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, United States
| | - Jerry M Melillo
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA 02543, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics and School of Biological Sciences, University of Oklahoma , Norman, OK 73019, United States
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- School of Civil Engineering and Environmental Sciences and School of Computer Science, University of Oklahoma, Norman, OK 73019, United States
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, United States
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Chen Y, Han M, Qin W, Hou Y, Zhang Z, Zhu B. Effects of whole-soil warming on CH 4 and N 2 O fluxes in an alpine grassland. GLOBAL CHANGE BIOLOGY 2024; 30:e17033. [PMID: 38273530 DOI: 10.1111/gcb.17033] [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: 07/10/2023] [Accepted: 10/23/2023] [Indexed: 01/27/2024]
Abstract
Global climate warming could affect the methane (CH4 ) and nitrous oxide (N2 O) fluxes between soils and the atmosphere, but how CH4 and N2 O fluxes respond to whole-soil warming is unclear. Here, we for the first time investigated the effects of whole-soil warming on CH4 and N2 O fluxes in an alpine grassland ecosystem on the Tibetan Plateau, and also studied the effects of experimental warming on CH4 and N2 O fluxes across terrestrial ecosystems through a global-scale meta-analysis. The whole-soil warming (0-100 cm, +4°C) significantly elevated soil N2 O emission by 101%, but had a minor effect on soil CH4 uptake. However, the meta-analysis revealed that experimental warming did not significantly alter CH4 and N2 O fluxes, and it may be that most field warming experiments could only heat the surface soils. Moreover, the warming-induced higher plant litter and available N in soils may be the main reason for the higher N2 O emission under whole-soil warming in the alpine grassland. We need to pay more attention to the long-term response of greenhouse gases (including CH4 and N2 O fluxes) from different soil depths to whole-soil warming over year-round, which could help us more accurately assess and predict the ecosystem-climate feedback under realistic warming scenarios in the future.
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Affiliation(s)
- Ying Chen
- College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Institute of Ecology, Peking University, Beijing, China
| | - Mengguang Han
- College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Institute of Ecology, Peking University, Beijing, China
| | - Wenkuan Qin
- College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Institute of Ecology, Peking University, Beijing, China
| | - Yanhui Hou
- College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Institute of Ecology, Peking University, Beijing, China
| | - Zhenhua Zhang
- Qinghai Haibei National Field Research Station of Alpine Grassland Ecosystem, and Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Biao Zhu
- College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Institute of Ecology, Peking University, Beijing, China
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Han H, Li C, Liu R, Jian J, Abulimiti M, Yuan P. Warming promotes accumulation of microbial- and plant-derived carbon in terrestrial ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166977. [PMID: 37716687 DOI: 10.1016/j.scitotenv.2023.166977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 09/18/2023]
Abstract
The impact of global warming on soil carbon pools has been extensively investigated, however, there is still a lack of understanding regarding the specific response of microbial- and plant-derived carbon to warming. To address this knowledge gap, we conducted a comprehensive meta-analysis of 142 studies and evaluated 986 observations comparisons of different carbon source responses to warming. Our results revealed several key insights. Firstly, climate warming resulted in an average increase of 5.46 % in the terrestrial soil carbon pool. Specifically, microbial-derived carbon showed an average increase of 6.32 %, while plant-derived carbon exhibited an average increase of 3.70 %. Secondly, while warming duration and magnitude do not significantly affect the response of microbial-derived carbon to warming, they did impact the response of plant-derived carbon. Lastly, we observed that the response of different carbon sources to warming was affected by the specific environmental backgrounds:ecosystem and climatic zone types affect the response of warming to microbial-derived carbon, while differences in climatic region affect response of warming to plant-derived carbon. The variations in the response of different soil carbon sources to warming can be attributed to the nature of the carbon source themselves, as well as the complex transformations that occur between them through microbial metabolic processes and their interactions with soil mineral particles. We suggest that interactions at the soil-plant-microbe interface should be considered more carefully, and the response of ecosystems to warming should be observed from the perspective of soil organic carbon sources, so as to better understand the response of terrestrial ecosystems carbon cycle to global warming.
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Affiliation(s)
- Huan Han
- National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congjuan Li
- National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China.
| | - Ran Liu
- State Key Lab of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Fukang National Station of Observation and Research for Desert Ecosystem, Fukang 831505, Xinjiang, China
| | - Jinshi Jian
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, Shaanxi, China; Institute of Soil and Water Conservation, CAS & MWR, 26 Xinong Road, Yangling, Shaanxi Province 712100, PR China
| | - Madinai Abulimiti
- National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Yuan
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
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Romanowicz KJ, Crump BC, Kling GW. Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost. ISME COMMUNICATIONS 2023; 3:124. [PMID: 37996661 PMCID: PMC10667234 DOI: 10.1038/s43705-023-00326-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023]
Abstract
Microorganisms drive many aspects of organic carbon cycling in thawing permafrost soils, but the compositional trajectory of the post-thaw microbiome and its metabolic activity remain uncertain, which limits our ability to predict permafrost-climate feedbacks in a warming world. Using quantitative metabarcoding and metagenomic sequencing, we determined relative and absolute changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA. Organic soils from the tundra active-layer (0-50 cm), transition-zone (50-70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration. Following extended thaw, we found that iron (Fe)-cycling Gammaproteobacteria, specifically the heterotrophic Fe(III)-reducing Rhodoferax sp. and chemoautotrophic Fe(II)-oxidizing Gallionella sp., increased by 3-5 orders of magnitude in absolute abundance within the transition-zone and permafrost microbiomes, accounting for 65% of community abundance. We also found that the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) oxidation (e.g., Cyc1) increased concurrently with genes for benzoate degradation and pyruvate metabolism, in which pyruvate is used to generate acetate that can be oxidized, along with benzoate, to CO2 when coupled with Fe(III) reduction. Gene abundance for CH4 metabolism decreased following extended thaw, suggesting dissimilatory Fe(III) reduction suppresses acetoclastic methanogenesis under reducing conditions. Our genomic evidence indicates that microbial carbon degradation is dominated by iron redox metabolism via an increase in gene abundance associated with Fe(III) reduction and Fe(II) oxidation during initial permafrost thaw, likely increasing microbial respiration while suppressing methanogenesis in wet sedge tundra.
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Affiliation(s)
- Karl J Romanowicz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - George W Kling
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
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12
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Meeran K, Verbrigghe N, Ingrisch J, Fuchslueger L, Müller L, Sigurðsson P, Sigurdsson BD, Wachter H, Watzka M, Soong JL, Vicca S, Janssens IA, Bahn M. Individual and interactive effects of warming and nitrogen supply on CO 2 fluxes and carbon allocation in subarctic grassland. GLOBAL CHANGE BIOLOGY 2023; 29:5276-5291. [PMID: 37427494 PMCID: PMC10962691 DOI: 10.1111/gcb.16851] [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: 07/29/2022] [Accepted: 05/21/2023] [Indexed: 07/11/2023]
Abstract
Climate warming has been suggested to impact high latitude grasslands severely, potentially causing considerable carbon (C) losses from soil. Warming can also stimulate nitrogen (N) turnover, but it is largely unclear whether and how altered N availability impacts belowground C dynamics. Even less is known about the individual and interactive effects of warming and N availability on the fate of recently photosynthesized C in soil. On a 10-year geothermal warming gradient in Iceland, we studied the effects of soil warming and N addition on CO2 fluxes and the fate of recently photosynthesized C through CO2 flux measurements and a 13 CO2 pulse-labeling experiment. Under warming, ecosystem respiration exceeded maximum gross primary productivity, causing increased net CO2 emissions. N addition treatments revealed that, surprisingly, the plants in the warmed soil were N limited, which constrained primary productivity and decreased recently assimilated C in shoots and roots. In soil, microbes were increasingly C limited under warming and increased microbial uptake of recent C. Soil respiration was increased by warming and was fueled by increased belowground inputs and turnover of recently photosynthesized C. Our findings suggest that a decade of warming seemed to have induced a N limitation in plants and a C limitation by soil microbes. This caused a decrease in net ecosystem CO2 uptake and accelerated the respiratory release of photosynthesized C, which decreased the C sequestration potential of the grassland. Our study highlights the importance of belowground C allocation and C-N interactions in the C dynamics of subarctic ecosystems in a warmer world.
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Affiliation(s)
| | - Niel Verbrigghe
- Research Group Plants and EcosystemsUniversity of AntwerpAntwerpBelgium
| | | | - Lucia Fuchslueger
- Research Group Plants and EcosystemsUniversity of AntwerpAntwerpBelgium
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
| | - Lena Müller
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | | | | | - Herbert Wachter
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
| | - Jennifer L. Soong
- Research Group Plants and EcosystemsUniversity of AntwerpAntwerpBelgium
- Soil and Crop Sciences DepartmentColorado State UniversityFort CollinsColoradoUSA
| | - Sara Vicca
- Research Group Plants and EcosystemsUniversity of AntwerpAntwerpBelgium
| | - Ivan A. Janssens
- Research Group Plants and EcosystemsUniversity of AntwerpAntwerpBelgium
| | - Michael Bahn
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
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