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Wang X, Wang Z, Chen F, Zhang Z, Fang J, Xing L, Zeng J, Zhang Q, Liu H, Liu W, Ren C, Yang G, Zhong Z, Zhang W, Han X. Deterministic assembly of grassland soil microbial communities driven by climate warming amplifies soil carbon loss. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171418. [PMID: 38460701 DOI: 10.1016/j.scitotenv.2024.171418] [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: 11/25/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
Perturbations in soil microbial communities caused by climate warming are expected to have a strong impact on biodiversity and future climate-carbon (C) feedback, especially in vulnerable habitats that are highly sensitive to environmental change. Here, we investigate the impact of four-year experimental warming on soil microbes and C cycling in the Loess Hilly Region of China. The results showed that warming led to soil C loss, mainly from labile C, and this C loss is associated with microbial response. Warming significantly decreased soil bacterial diversity and altered its community structure, especially increasing the abundance of heat-tolerant microorganisms, but had no effect on fungi. Warming also significantly increased the relative importance of homogeneous selection and decreased "drift" of bacterial and fungal communities. Moreover, warming decreased bacterial network stability but increased fungal network stability. Notably, the magnitude of soil C loss was significantly and positively correlated with differences in bacterial community characteristics under ambient and warming conditions, including diversity, composition, network stability, and community assembly. This result suggests that microbial responses to warming may amplify soil C loss. Combined, these results provide insights into soil microbial responses and C feedback in vulnerable ecosystems under climate warming scenarios.
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Affiliation(s)
- Xing Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Zhengchen Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Fang Chen
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Zhenjiao Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Jingbo Fang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Liheng Xing
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Jia Zeng
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Qi Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Hanyu Liu
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Weichao Liu
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Chengjie Ren
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Gaihe Yang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Zekun Zhong
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Wei Zhang
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
| | - Xinhui Han
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China.
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Zhao J, Xie X, Jiang Y, Li J, Fu Q, Qiu Y, Fu X, Yao Z, Dai Z, Qiu Y, Chen H. Effects of simulated warming on soil microbial community diversity and composition across diverse ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168793. [PMID: 37996030 DOI: 10.1016/j.scitotenv.2023.168793] [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: 09/27/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
Soil warming can directly affect the microbial community, or indirectly affect the microbial community by affecting soil moisture, nutrient availability, vegetation growth, etc. However, the response of microorganisms to soil warming is complex, and there is no uniform conclusion on the impact and mechanism of warming on microbial diversity. As the global climate gradually warms, a comprehensive assessment of warming on soil microbial community changes is essential to understand and predict the response of microbial geochemical processes to soil warming. Here, we perform a meta-analysis of studies to investigate changes in soil microbial communities along soil warming gradients and the response of soil microbes to elevated temperature in different ecosystems. We found that the α diversity index of soil microorganisms decreased significantly with the increase in temperature, and the β diversity altered with the increase in soil temperature and the shifts in ecosystem. Most bacteria only alter when the temperature rises higher. Compared to the non-warming condition, the relative abundance of Acidobacteria, Proteobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia decreased by 19 %, 11 %, 19 %, 8 % and 6 %, respectively, and the relative abundance of Firmicutes increased by 34 %. Compared to farmland, forest, grassland and tundra ecosystems, soil microorganisms in wetland ecosystems were more sensitive to temperature increase, and the changes in bacteria were consistent with the overall alterations. This meta-analysis revealed significant changes in the composition of microbial communities on soil warming. With the decrease in biodiversity under increasing temperature conditions, these dominant microbiomes, which can grow well under high-temperature conditions, will play a stronger role in regulating nutrient and energy flow. Our analysis adds a global perspective to the temperature response of soil microbes, which is critical to improving our understanding of the mechanisms of how soil microbes change in response to climate warming.
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Affiliation(s)
- Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xuan Xie
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yuying Jiang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiaxin Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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3
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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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Simister RL, Iulianella Phillips BP, Wickham AP, Cayer EM, Hart CJR, Winterburn PA, Crowe SA. DNA sequencing, microbial indicators, and the discovery of buried kimberlites. COMMUNICATIONS EARTH & ENVIRONMENT 2023; 4:387. [PMID: 38665197 PMCID: PMC11041713 DOI: 10.1038/s43247-023-01020-z] [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: 02/19/2023] [Accepted: 09/19/2023] [Indexed: 04/28/2024]
Abstract
Population growth and technological advancements are placing growing demand on mineral resources. New and innovative exploration technologies that improve detection of deeply buried mineralization and host rocks are required to meet these demands. Here we used diamondiferous kimberlite ore bodies as a test case and show that DNA amplicon sequencing of soil microbial communities resolves anomalies in microbial community composition and structure that reflect the surface expression of kimberlites buried under 10 s of meters of overburden. Indicator species derived from laboratory amendment experiments were employed in an exploration survey in which the species distributions effectively delineated the surface expression of buried kimberlites. Additional indicator species derived directly from field observations improved the blind discovery of kimberlites buried beneath similar overburden types. Application of DNA sequence-based analyses of soil microbial communities to mineral deposit exploration provides a powerful illustration of how genomics technologies can be leveraged in the discovery of critical new resources.
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Affiliation(s)
- Rachel L. Simister
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Bianca P. Iulianella Phillips
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Andrew P. Wickham
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Erika M. Cayer
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Craig J. R. Hart
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Peter A. Winterburn
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Sean A. Crowe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
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5
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Yu X, Tu Q, Liu J, Peng Y, Wang C, Xiao F, Lian Y, Yang X, Hu R, Yu H, Qian L, Wu D, He Z, Shu L, He Q, Tian Y, Wang F, Wang S, Wu B, Huang Z, He J, Yan Q, He Z. Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes. MLIFE 2023; 2:253-266. [PMID: 38817818 PMCID: PMC10989796 DOI: 10.1002/mlf2.12077] [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: 01/22/2023] [Revised: 05/21/2023] [Accepted: 06/29/2023] [Indexed: 06/01/2024]
Abstract
Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning. However, how such activities affect microbially driven methane (CH4), nitrogen (N), and sulfur (S) cycling of rhizosphere microbiomes remains unclear. To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres, we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies. Compared with the native mangrove (Kandelia obovata, KO), the introduced mangrove (Sonneratia apetala, SA) rhizosphere microbiome had significantly (p < 0.05) higher average genome size (AGS) (5.8 vs. 5.5 Mb), average 16S ribosomal RNA gene copy number (3.5 vs. 3.1), relative abundances of mobile genetic elements, and functional diversity in terms of the Shannon index (7.88 vs. 7.84) but lower functional potentials involved in CH4 cycling (e.g., mcrABCDG and pmoABC), N2 fixation (nifHDK), and inorganic S cycling (dsrAB, dsrC, dsrMKJOP, soxB, sqr, and fccAB). Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere. Additionally, salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes. This study advances our understanding of microbially mediated biogeochemical cycling of CH4, N, and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions, which has important implications for future mangrove reforestation.
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Affiliation(s)
- Xiaoli Yu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Qichao Tu
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
| | - Jihua Liu
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
| | - Yisheng Peng
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Cheng Wang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Fanshu Xiao
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Yingli Lian
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Xueqin Yang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Ruiwen Hu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Huang Yu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Lu Qian
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Daoming Wu
- College of Forestry & Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Ziying He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine ScienceSun Yat‐sen UniversityGuangzhouChina
| | - Longfei Shu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Qiang He
- Department of Civil and Environmental EngineeringThe University of TennesseeKnoxvilleTennesseeUSA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life SciencesXiamen UniversityXiamenChina
| | - Faming Wang
- Xiaoliang Research Station for Tropical Coastal Ecosystems and Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Shanquan Wang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Bo Wu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Zhijian Huang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine ScienceSun Yat‐sen UniversityGuangzhouChina
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine ScienceSun Yat‐sen UniversityGuangzhouChina
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Qingyun Yan
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
| | - Zhili He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering, Environmental Microbiomics Research CenterSun Yat‐sen UniversityGuangzhouChina
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6
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Winder JC, Braga LPP, Kuhn MA, Thompson LM, Olefeldt D, Tanentzap AJ. Climate warming has direct and indirect effects on microbes associated with carbon cycling in northern lakes. GLOBAL CHANGE BIOLOGY 2023; 29:3039-3053. [PMID: 36843502 DOI: 10.1111/gcb.16655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 05/03/2023]
Abstract
Northern lakes disproportionately influence the global carbon cycle, and may do so more in the future depending on how their microbial communities respond to climate warming. Microbial communities can change because of the direct effects of climate warming on their metabolism and the indirect effects of climate warming on groundwater connectivity from thawing of surrounding permafrost, especially at lower landscape positions. Here we used shotgun metagenomics to compare the taxonomic and functional gene composition of sediment microbes in 19 peatland lakes across a 1600-km permafrost transect in boreal western Canada. We found microbes responded differently to the loss of regional permafrost cover than to increases in local groundwater connectivity. These results suggest that both the direct and indirect effects of climate warming, which were respectively associated with loss of permafrost and subsequent changes in groundwater connectivity interact to change microbial composition and function. Archaeal methanogens and genes involved in all major methanogenesis pathways were more abundant in warmer regions with less permafrost, but higher groundwater connectivity partly offset these effects. Bacterial community composition and methanotrophy genes did not vary with regional permafrost cover, and the latter changed similarly to methanogenesis with groundwater connectivity. Finally, we found an increase in sugar utilization genes in regions with less permafrost, which may further fuel methanogenesis. These results provide the microbial mechanism for observed increases in methane emissions associated with loss of permafrost cover in this region and suggest that future emissions will primarily be controlled by archaeal methanogens over methanotrophic bacteria as northern lakes warm. Our study more generally suggests that future predictions of aquatic carbon cycling will be improved by considering how climate warming exerts both direct effects associated with regional-scale permafrost thaw and indirect effects associated with local hydrology.
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Affiliation(s)
- Johanna C Winder
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Lucas P P Braga
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - McKenzie A Kuhn
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Lauren M Thompson
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - David Olefeldt
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
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7
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Qian L, Yu X, Gu H, Liu F, Fan Y, Wang C, He Q, Tian Y, Peng Y, Shu L, Wang S, Huang Z, Yan Q, He J, Liu G, Tu Q, He Z. Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes. MICROBIOME 2023; 11:71. [PMID: 37020239 PMCID: PMC10074775 DOI: 10.1186/s40168-023-01501-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH4), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches. RESULTS Our results showed that the metabolic pathways involved in CH4, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N2O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments. CONCLUSIONS In addition to offering a perspective on the vertical distribution of microbially driven CH4, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N2O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.
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Affiliation(s)
- Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yijun Fan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qiang He
- Department of Civil and Environmental Engineering, the University of Tennessee, Knoxville, TN 37996 USA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhijian Huang
- School of Marine Science, Sun Yat-Sen University, Zhuhai, 519080 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Jianguo He
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Guangli Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
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8
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Distinct Growth Responses of Tundra Soil Bacteria to Short-Term and Long-Term Warming. Appl Environ Microbiol 2023; 89:e0154322. [PMID: 36847530 PMCID: PMC10056963 DOI: 10.1128/aem.01543-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Increases in Arctic temperatures have thawed permafrost and accelerated tundra soil microbial activity, releasing greenhouse gases that amplify climate warming. Warming over time has also accelerated shrub encroachment in the tundra, altering plant input abundance and quality, and causing further changes to soil microbial processes. To better understand the effects of increased temperature and the accumulated effects of climate change on soil bacterial activity, we quantified the growth responses of individual bacterial taxa to short-term warming (3 months) and long-term warming (29 years) in moist acidic tussock tundra. Intact soil was assayed in the field for 30 days using 18O-labeled water, from which taxon-specific rates of 18O incorporation into DNA were estimated as a proxy for growth. Experimental treatments warmed the soil by approximately 1.5°C. Short-term warming increased average relative growth rates across the assemblage by 36%, and this increase was attributable to emergent growing taxa not detected in other treatments that doubled the diversity of growing bacteria. However, long-term warming increased average relative growth rates by 151%, and this was largely attributable to taxa that co-occurred in the ambient temperature controls. There was also coherence in relative growth rates within broad taxonomic levels with orders tending to have similar growth rates in all treatments. Growth responses tended to be neutral in short-term warming and positive in long-term warming for most taxa and phylogenetic groups co-occurring across treatments regardless of phylogeny. Taken together, growing bacteria responded distinctly to short-term and long-term warming, and taxa growing in each treatment exhibited deep phylogenetic organization. IMPORTANCE Soil carbon stocks in the tundra and underlying permafrost have become increasingly vulnerable to microbial decomposition due to climate change. The microbial responses to Arctic warming must be understood in order to predict the effects of future microbial activity on carbon balance in a warming Arctic. In response to our warming treatments, tundra soil bacteria grew faster, consistent with increased rates of decomposition and carbon flux to the atmosphere. Our findings suggest that bacterial growth rates may continue to increase in the coming decades as faster growth is driven by the accumulated effects of long-term warming. Observed phylogenetic organization of bacterial growth rates may also permit taxonomy-based predictions of bacterial responses to climate change and inclusion into ecosystem models.
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9
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Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming. mBio 2023; 14:e0300922. [PMID: 36786571 PMCID: PMC10127799 DOI: 10.1128/mbio.03009-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research.
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10
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Zhou J, Song W, Tu Q. To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities. Brief Bioinform 2023; 24:6961613. [PMID: 36575570 DOI: 10.1093/bib/bbac594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/22/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022] Open
Abstract
High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.
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Affiliation(s)
- Jiayin Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China.,Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China
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11
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Qi Q, Zhao J, Tian R, Zeng Y, Xie C, Gao Q, Dai T, Wang H, He JS, Konstantinidis KT, Yang Y, Zhou J, Guo X. Microbially enhanced methane uptake under warming enlarges ecosystem carbon sink in a Tibetan alpine grassland. GLOBAL CHANGE BIOLOGY 2022; 28:6906-6920. [PMID: 36191158 DOI: 10.1111/gcb.16444] [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: 04/12/2022] [Revised: 08/10/2022] [Accepted: 09/02/2022] [Indexed: 05/25/2023]
Abstract
The alpine grasslands of the Tibetan Plateau store 23.2 Pg soil organic carbon, which becomes susceptible to microbial degradation with climate warming. However, accurate prediction of how the soil carbon stock changes under future climate warming is hampered by our limited understanding of belowground complex microbial communities. Here, we show that 4 years of warming strongly stimulated methane (CH4 ) uptake by 93.8% and aerobic respiration (CO2 ) by 11.3% in the soils of alpine grassland ecosystem. Due to no significant effects of warming on net ecosystem CO2 exchange (NEE), the warming-stimulated CH4 uptake enlarged the carbon sink capacity of whole ecosystem. Furthermore, precipitation alternation did not alter such warming effects, despite the significant effects of precipitation on NEE and soil CH4 fluxes were observed. Metagenomic sequencing revealed that warming led to significant shifts in the overall microbial community structure and the abundances of functional genes, which contrasted to no detectable changes after 2 years of warming. Carbohydrate utilization genes were significantly increased by warming, corresponding with significant increases in soil aerobic respiration. Increased methanotrophic genes and decreased methanogenic genes were observed under warming, which significantly (R2 = .59, p < .001) correlated with warming-enhanced CH4 uptakes. Furthermore, 212 metagenome-assembled genomes were recovered, including many populations involved in the degradation of various organic matter and a highly abundant methylotrophic population of the Methyloceanibacter genus. Collectively, our results provide compelling evidence that specific microbial functional traits for CH4 and CO2 cycling processes respond to climate warming with differential effects on soil greenhouse gas emissions. Alpine grasslands may play huge roles in mitigating climate warming through such microbially enhanced CH4 uptake.
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Affiliation(s)
- Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jianshu Zhao
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Yufei Zeng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Changyi Xie
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Tianjiao Dai
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Hao Wang
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, China
| | - Jin-Sheng He
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- 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
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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12
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Kim D, Chae N, Kim M, Nam S, Kim TK, Park KT, Lee BY, Kim E, Lee H. Microbial metabolic responses and CO 2 emissions differentiated by soil water content variation in subarctic tundra soils. J Microbiol 2022; 60:1130-1138. [PMID: 36422843 DOI: 10.1007/s12275-022-2378-3] [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: 08/18/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Recent rapid air temperature increases across the northern-latitude tundra have prolonged permafrost thawing and snow melting periods, resulting in increased soil temperature (Ts) and volumetric soil water content (SWC). Under prolonged soil warming at 8°C, Alaskan tundra soils were incubated in a microcosm system and examined for the SWC differential influence on the microbial decomposition activity of large molecular weight (MW) humic substances (HS). When one microcosm soil (AKC1-1) was incubated at a constant SWC of 41% for 90 days (T = 90) and then SWC was gradually decreased from 41% to 29% for another T = 90, the initial HS was partly depolymerized. In contrast, in AKC1-2 incubated at a gradually decreasing SWC from the initial 32% to 10% for T = 90 and then increasing to 27% for another T = 90, HS depolymerization was undetected. Overall, the microbial communities in AKC1-1 could maintain metabolic activity at sufficient and constant SWC during the initial T = 90 incubation. In contrast, AKC1-2 microbes may have been damaged by drought stress during the drying SWC regimen, possibly resulting in the loss of HS decomposition activity, which did not recover even after re-wetting to an optimal SWC range (20-40%). After T = 90, the CO2 production in both treatments was attributed to the increased decomposition of small-MW organic compounds (including aerobic HS-degradative products) within an optimal SWC range. We expect this study to provide new insights into the early effects of warming- and topography-induced SWC variations on the microbial contribution to CO2 emissions via HS decomposition in northern-latitude tundra soil.
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Affiliation(s)
- Dockyu Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
| | - Namyi Chae
- Institutes of Life Sciences and Natural Resources, Korea University, Seoul, 02841, Republic of Korea
| | - Mincheol Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sungjin Nam
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Tai Kyoung Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Ki-Tea Park
- Division of Atmospheric Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Bang Yong Lee
- Division of Atmospheric Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Eungbin Kim
- Department of Systems Biology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hyoungseok Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
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13
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Parada-Pozo G, Bravo LA, Sáez PL, Cavieres LA, Reyes-Díaz M, Abades S, Alfaro FD, De la Iglesia R, Trefault N. Vegetation drives the response of the active fraction of the rhizosphere microbial communities to soil warming in Antarctic vascular plants. FEMS Microbiol Ecol 2022; 98:6679102. [PMID: 36040342 DOI: 10.1093/femsec/fiac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/11/2022] [Accepted: 08/27/2022] [Indexed: 01/21/2023] Open
Abstract
In the Antarctic Peninsula, increases in mean annual temperature are associated with the coverage and population density of the two Antarctic vascular plant species-Deschampsia antarctica and Colobanthus quitensis-potentially modifying critical soil processes. In this study, we characterized the diversity and community composition of active microorganisms inhabiting the vascular plant rhizosphere in two sites with contrasting vegetation cover in King George Island, Western Antarctic Peninsula. We assessed the interplay between soil physicochemical properties and microbial diversity and composition, evaluating the effect of an in situ experimental warming on the microbial communities of the rhizosphere from D. antarctica and C. quitensis. Bacteria and Eukarya showed different responses to warming in both sites, and the effect was more noticeable in microbial eukaryotes from the low vegetation site. Furthermore, important changes were found in the relative abundance of Tepidisphaerales (Bacteria) and Ciliophora (Eukarya) between warming and control treatments. Our results showed that rhizosphere eukaryal communities are more sensitive to in situ warming than bacterial communities. Overall, our results indicate that vegetation drives the response of the active fraction of the microbial communities from the rhizosphere of Antarctic vascular plants to soil warming.
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Affiliation(s)
- Génesis Parada-Pozo
- Centro GEMA-Genómica, Ecología & Medio Ambiente, Facultad de Ciencias, Universidad Mayor, 8580745, Santiago, Chile
| | - León A Bravo
- Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera. 4811230, Temuco, Chile
| | - Patricia L Sáez
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, 4070386, Chile.,Instituto de Ecología y Biodiversidad (IEB), 775000, Santiago, Chile
| | - Lohengrin A Cavieres
- Instituto de Ecología y Biodiversidad (IEB), 775000, Santiago, Chile.,Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, 4070386, Chile
| | - Marjorie Reyes-Díaz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, 4811230, Chile.,Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, 4811230, Chile
| | - Sebastián Abades
- Centro GEMA-Genómica, Ecología & Medio Ambiente, Facultad de Ciencias, Universidad Mayor, 8580745, Santiago, Chile
| | - Fernando D Alfaro
- Centro GEMA-Genómica, Ecología & Medio Ambiente, Facultad de Ciencias, Universidad Mayor, 8580745, Santiago, Chile
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8320000, Chile
| | - Nicole Trefault
- Centro GEMA-Genómica, Ecología & Medio Ambiente, Facultad de Ciencias, Universidad Mayor, 8580745, Santiago, Chile
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14
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Ernakovich JG, Barbato RA, Rich VI, Schädel C, Hewitt RE, Doherty SJ, Whalen E, Abbott BW, Barta J, Biasi C, Chabot CL, Hultman J, Knoblauch C, Vetter M, Leewis M, Liebner S, Mackelprang R, Onstott TC, Richter A, Schütte U, Siljanen HMP, Taş N, Timling I, Vishnivetskaya TA, Waldrop MP, Winkel M. Microbiome assembly in thawing permafrost and its feedbacks to climate. GLOBAL CHANGE BIOLOGY 2022; 28:5007-5026. [PMID: 35722720 PMCID: PMC9541943 DOI: 10.1111/gcb.16231] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/24/2022] [Indexed: 05/15/2023]
Abstract
The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost-climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well-suited to thrive in changing environmental conditions. We predict that on a short timescale and following high-disturbance thaw (e.g., thermokarst), stochasticity dominates post-thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower-intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post-thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.
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Affiliation(s)
- Jessica G. Ernakovich
- Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
- Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
- EMergent Ecosystem Response to ChanGE (EMERGE) Biology Integration Institute
| | - Robyn A. Barbato
- U.S. Army Cold Regions Research and Engineering LaboratoryHanoverNew HampshireUSA
| | - Virginia I. Rich
- EMergent Ecosystem Response to ChanGE (EMERGE) Biology Integration Institute
- Microbiology DepartmentOhio State UniversityColumbusOhioUSA
- Byrd Polar and Climate Research CenterOhio State UniversityColombusOhioUSA
- Center of Microbiome ScienceOhio State UniversityColombusOhioUSA
| | - Christina Schädel
- Center for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Rebecca E. Hewitt
- Center for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
- Department of Environmental StudiesAmherst CollegeAmherstMassachusettsUSA
| | - Stacey J. Doherty
- Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
- U.S. Army Cold Regions Research and Engineering LaboratoryHanoverNew HampshireUSA
| | - Emily D. Whalen
- Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
| | - Benjamin W. Abbott
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUtahUSA
| | - Jiri Barta
- Centre for Polar EcologyUniversity of South BohemiaCeske BudejoviceCzech Republic
| | - Christina Biasi
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandKuopioFinland
| | - Chris L. Chabot
- California State University NorthridgeNorthridgeCaliforniaUSA
| | | | - Christian Knoblauch
- Institute of Soil ScienceUniversität HamburgHamburgGermany
- Center for Earth System Research and SustainabilityUniversität HamburgHamburgGermany
| | - Maggie C. Y. Lau Vetter
- Department of GeosciencesPrinceton UniversityPrincetonNew JerseyUSA
- Laboratory of Extraterrestrial Ocean Systems (LEOS)Institute of Deep‐sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Mary‐Cathrine Leewis
- U.S. Geological Survey, GeologyMinerals, Energy and Geophysics Science CenterMenlo ParkCaliforniaUSA
- Agriculture and Agri‐Food CanadaQuebec Research and Development CentreQuebecQuebecCanada
| | - Susanne Liebner
- GFZ German Research Centre for GeosciencesSection GeomicrobiologyPotsdamGermany
| | | | | | - Andreas Richter
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
- Austrian Polar Research InstituteViennaAustria
| | | | - Henri M. P. Siljanen
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandKuopioFinland
| | - Neslihan Taş
- Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | | | - Tatiana A. Vishnivetskaya
- University of TennesseeKnoxvilleTennesseeUSA
- Institute of Physicochemical and Biological Problems of Soil SciencePushchinoRussia
| | - Mark P. Waldrop
- U.S. Geological Survey, GeologyMinerals, Energy and Geophysics Science CenterMenlo ParkCaliforniaUSA
| | - Matthias Winkel
- GFZ German Research Centre for GeosciencesInterface GeochemistryPotsdamGermany
- BfR Federal Institute for Risk AssessmentBerlinGermany
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15
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Viitamäki S, Pessi IS, Virkkala AM, Niittynen P, Kemppinen J, Eronen-Rasimus E, Luoto M, Hultman J. The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types. FEMS Microbiol Ecol 2022; 98:6626023. [PMID: 35776963 PMCID: PMC9341781 DOI: 10.1093/femsec/fiac079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/14/2022] Open
Abstract
Due to climate change, increased microbial activity in high-latitude soils may lead to higher greenhouse gas (GHG) emissions. However, microbial GHG production and consumption mechanisms in tundra soils are not thoroughly understood. To investigate how the diversity and functional potential of bacterial and archaeal communities vary across vegetation types and soil layers, we analyzed 116 soil metatranscriptomes from 73 sites in the Finnish sub-Arctic. Meadow soils were characterized by higher pH and lower soil organic matter (SOM) and carbon/nitrogen ratio. By contrast, dwarf shrub-dominated ecosystems had higher SOM and lower pH. Although Actinobacteria, Acidobacteria, Alphaproteobacteria and Planctomycetes were dominant in all communities, there were significant differences at the genus level between vegetation types; plant polymer-degrading groups were more active in shrub-dominated soils than in meadows. Given that climate-change scenarios predict the expansion of shrubs at high latitudes, our results indicate that tundra soil microbial communities harbor potential decomposers of increased plant litter, which may affect the rate of carbon turnover in tundra soils. Additionally, transcripts of methanotrophs were detected in the mineral layer of all soils, which may moderate methane fluxes. This study provides new insights into possible shifts in tundra microbial diversity and activity due to climate change.
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Affiliation(s)
| | - Igor S Pessi
- Department of Microbiology, University of Helsinki, Finland.,Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
| | - Anna-Maria Virkkala
- Department of Geosciences and Geography, University of Helsinki, Finland.,Woodwell Climate Research Center, Falmouth, MA, USA
| | - Pekka Niittynen
- Department of Geosciences and Geography, University of Helsinki, Finland
| | | | - Eeva Eronen-Rasimus
- Department of Microbiology, University of Helsinki, Finland.,Finnish Environment Institute, Marine Research Centre, Helsinki, Finland
| | - Miska Luoto
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland.,Department of Geosciences and Geography, University of Helsinki, Finland
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Finland.,Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland.,Natural Resources Institute Finland, Helsinki, Finland
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16
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Seitz TJ, Schütte UME, Drown DM. Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient. Front Microbiol 2022; 13:781051. [PMID: 35685929 PMCID: PMC9171198 DOI: 10.3389/fmicb.2022.781051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Permafrost, an important source of soil disturbance, is particularly vulnerable to climate change in Alaska where 85% of the land is underlained with discontinuous permafrost. Boreal forests, home to plants integral to subsistence diets of many Alaska Native communities, are not immune to the effects of climate change. Soil disturbance events, such as permafrost thaw, wildfires, and land use change can influence abiotic conditions, which can then affect active layer soil microbial communities. In a previous study, we found negative effects on boreal plants inoculated with microbes impacted by soil disturbance compared to plants inoculated with microbes from undisturbed soils. Here, we identify key shifts in microbial communities altered by soil disturbance using 16S rRNA gene sequencing and make connections between microbial community changes and previously observed plant growth. Additionally, we identify further community shifts in potential functional mechanisms using long read metagenomics. Across a soil disturbance gradient, microbial communities differ significantly based on the level of soil disturbance. Consistent with the earlier study, the family Acidobacteriaceae, which consists of known plant growth promoters, was abundant in undisturbed soil, but practically absent in most disturbed soil. In contrast, Comamonadaceae, a family with known agricultural pathogens, was overrepresented in most disturbed soil communities compared to undisturbed. Within our metagenomic data, we found that soil disturbance level is associated with differences in microbial community function, including mechanisms potentially involved in plant pathogenicity. These results indicate that a decrease in plant growth can be linked to changes in the microbial community and functional composition driven by soil disturbance and climate change. Together, these results build a genomic understanding of how shifting soil microbiomes may affect plant productivity and ecosystem health as the Arctic warms.
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Affiliation(s)
- Taylor J. Seitz
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Ursel M. E. Schütte
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Devin M. Drown
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, United States
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, United States
- *Correspondence: Devin M. Drown,
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17
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Li Y, Ma J, Yu Y, Li Y, Shen X, Huo S, Xia X. Effects of multiple global change factors on soil microbial richness, diversity and functional gene abundances: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152737. [PMID: 34998753 DOI: 10.1016/j.scitotenv.2021.152737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Soil microbial richness, diversity, and functional gene abundance are crucial factors affecting belowground ecosystem functions; however, there is still a lack of systematic understanding of their responses to global change. Here, we conducted a worldwide meta-analysis using 1071 observation data concerning the effects of global change factors (GCFs), including warming (W), increased precipitation (PPT+), decreased precipitation (PPT-), elevated CO2 concentration (eCO2), and nitrogen deposition (N), to evaluate their individual, combined, and interactive effects on soil microbial properties across different groups and ecosystems. Across the dataset, eCO2 increased microbial richness and diversity by 40.5% and 4.6%, respectively; warming and N addition decreased the abundance of denitrification functional genes (nirS, nirK, and nozS); N addition had a greater impact on soil C-cycling functional genes than on N-cycling ones. Long-term precipitation change was conducive to the increase in soil microbial richness, and fungal richness change was more sensitive than bacterial richness, but the sensitivity of bacteria richness to N addition was positively correlated with experimental duration. Soil microbial richness, diversity, and functional gene abundances could be significantly affected by individual or multiple GCF changes, and their interactions are mainly additive. W×eCO2 on microbial diversity, and N×PPT+ and W×N on N-cycling functional gene abundance showed synergistic interactions. Based on the limitations of the collected data and the findings, we suggest designing experiments with multiple GCFs and long experimental durations and incorporating the effects and interactions of multiple drivers into ecosystem models to accurately predict future soil microbial properties and functions under future global changes.
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Affiliation(s)
- Yuqian Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing 100875, PR China.
| | - Junwei Ma
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing 100875, PR China.
| | - Yi Yu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing 100875, PR China
| | - Yijia Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing 100875, PR China.
| | - Xinyi Shen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing 100875, PR China
| | - Shouliang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Xinghui Xia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing 100875, PR China.
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18
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Naylor D, McClure R, Jansson J. Trends in Microbial Community Composition and Function by Soil Depth. Microorganisms 2022; 10:microorganisms10030540. [PMID: 35336115 PMCID: PMC8954175 DOI: 10.3390/microorganisms10030540] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.
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19
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Dove NC, Barnes ME, Moreland K, Graham RC, Berhe AA, Hart SC. Depth dependence of climatic controls on soil microbial community activity and composition. ISME COMMUNICATIONS 2021; 1:78. [PMID: 37938290 PMCID: PMC9723684 DOI: 10.1038/s43705-021-00081-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 05/11/2023]
Abstract
Subsoil microbiomes play important roles in soil carbon and nutrient cycling, yet our understanding of the controls on subsoil microbial communities is limited. Here, we investigated the direct (mean annual temperature and precipitation) and indirect (soil chemistry) effects of climate on microbiome composition and extracellular enzyme activity throughout the soil profile across two elevation-bioclimatic gradients in central California, USA. We found that microbiome composition changes and activity decreases with depth. Across these sites, the direct influence of climate on microbiome composition and activity was relatively lower at depth. Furthermore, we found that certain microbial taxa change in relative abundance over large temperature and precipitation gradients only in specific soil horizons, highlighting the depth dependence of the climatic controls on microbiome composition. Our finding that the direct impacts of climate are muted at depth suggests that deep soil microbiomes may lag in their acclimation to new temperatures with a changing climate.
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Affiliation(s)
- Nicholas C Dove
- Environmental Systems Graduate Group, University of California, Merced, CA, 95343, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
| | - Morgan E Barnes
- Environmental Systems Graduate Group, University of California, Merced, CA, 95343, USA
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kimber Moreland
- Environmental Systems Graduate Group, University of California, Merced, CA, 95343, USA
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Robert C Graham
- Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Asmeret Asefaw Berhe
- Department of Life & Environmental Sciences, University of California, Merced, CA, 95343, USA
- Sierra Nevada Research Institute, Merced, CA, 95343, USA
| | - Stephen C Hart
- Department of Life & Environmental Sciences, University of California, Merced, CA, 95343, USA
- Sierra Nevada Research Institute, Merced, CA, 95343, USA
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20
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Wu L, Yang F, Feng J, Tao X, Qi Q, Wang C, Schuur EAG, Bracho R, Huang Y, Cole JR, Tiedje JM, Zhou J. Permafrost thaw with warming reduces microbial metabolic capacities in subsurface soils. Mol Ecol 2021; 31:1403-1415. [PMID: 34878672 DOI: 10.1111/mec.16319] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/04/2021] [Accepted: 12/01/2021] [Indexed: 01/27/2023]
Abstract
Microorganisms are major constituents of the total biomass in permafrost regions, whose underlain soils are frozen for at least two consecutive years. To understand potential microbial responses to climate change, here we examined microbial community compositions and functional capacities across four soil depths in an Alaska tundra site. We showed that a 5-year warming treatment increased soil thaw depth by 25.7% (p = .011) within the deep organic layer (15-25 cm). Concurrently, warming reduced 37% of bacterial abundance and 64% of fungal abundances in the deep organic layer, while it did not affect microbial abundance in other soil layers (i.e., 0-5, 5-15, and 45-55 cm). Warming treatment altered fungal community composition and microbial functional structure (p < .050), but not bacterial community composition. Using a functional gene array, we found that the relative abundances of a variety of carbon (C)-decomposing, iron-reducing, and sulphate-reducing genes in the deep organic layer were decreased, which was not observed by the shotgun sequencing-based metagenomics analysis of those samples. To explain the reduced metabolic capacities, we found that warming treatment elicited higher deterministic environmental filtering, which could be linked to water-saturated time, soil moisture, and soil thaw duration. In contrast, plant factors showed little influence on microbial communities in subsurface soils below 15 cm, despite a 25.2% higher (p < .05) aboveground plant biomass by warming treatment. Collectively, we demonstrate that microbial metabolic capacities in subsurface soils are reduced, probably arising from enhanced thaw by warming.
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Affiliation(s)
- Linwei Wu
- Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Felix Yang
- Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Jiajie Feng
- Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Xuanyu Tao
- Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Qi Qi
- School of Environment, State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing, China
| | - Cong Wang
- Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Edward A G Schuur
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - Rosvel Bracho
- Department of Biology, School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, USA
| | - Yi Huang
- College of Environmental Science and Engineering, State Key Joint Laboratory of Environmental Simulation and Pollution Control, Peking University, Beijing, China
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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21
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ter Horst AM, Santos-Medellín C, Sorensen JW, Zinke LA, Wilson RM, Johnston ER, Trubl G, Pett-Ridge J, Blazewicz SJ, Hanson PJ, Chanton JP, Schadt CW, Kostka JE, Emerson JB. Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. MICROBIOME 2021; 9:233. [PMID: 34836550 PMCID: PMC8626947 DOI: 10.1186/s40168-021-01156-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/02/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. RESULTS Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. CONCLUSIONS Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.
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Affiliation(s)
| | | | - Jackson W. Sorensen
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
| | - Laura A. Zinke
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
| | - Rachel M. Wilson
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | - Eric R. Johnston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Paul J. Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jeffrey P. Chanton
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | | | - Joel E. Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Joanne B. Emerson
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
- Genome Center, University of California, Davis, Davis, CA USA
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22
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Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils. Proc Natl Acad Sci U S A 2021; 118:2025322118. [PMID: 34732568 DOI: 10.1073/pnas.2025322118] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.
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23
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Pold G, Baillargeon N, Lepe A, Rastetter EB, Sistla SA. Warming effects on arctic tundra biogeochemistry are limited but habitat‐dependent: a meta‐analysis. Ecosphere 2021. [DOI: 10.1002/ecs2.3777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Grace Pold
- Natural Resources Management & Environmental Sciences College of Agriculture, Food & Environmental Sciences California Polytechnic State University San Luis Obispo California USA
| | - Natalie Baillargeon
- Smith College Northampton Massachusetts USA
- Woodwell Climate Research Center Woods Hole Massachusetts USA
| | - Adan Lepe
- Amherst College Amherst Massachusetts USA
| | - Edward B. Rastetter
- Marine Biological Laboratories The Ecosystems Center Woods Hole Massachusetts USA
| | - Seeta A. Sistla
- Natural Resources Management & Environmental Sciences College of Agriculture, Food & Environmental Sciences California Polytechnic State University San Luis Obispo California USA
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24
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Yuan X, Chen Y, Qin W, Xu T, Mao Y, Wang Q, Chen K, Zhu B. Plant and microbial regulations of soil carbon dynamics under warming in two alpine swamp meadow ecosystems on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148072. [PMID: 34098273 DOI: 10.1016/j.scitotenv.2021.148072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/19/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
Increasing temperature plays important roles in affecting plant and soil microbial communities as well as ecological processes and functions in terrestrial ecosystems. However, mechanisms of warming influencing soil carbon dynamics associated with plant-microbe interactions remain unclear. In this study, open-top chambers (OTCs) experiments were carried out to detect the responses of plants, soil microbes, and SOC contents, physical fractions (by particle-size fractionation) and chemical composition (by solid-state 13C NMR spectroscopy) to warming in two alpine swamp meadows (Kobresia humilis vs K. tibetica) on the Tibetan Plateau. Our results showed that four years of warming had significant influences on plant belowground biomass, microbial community and SOC contents in the K. humilis swamp meadow, but had much weaker or minor effects in the K. tibetica swamp meadow with water-logged status and lower level of warming. In the K. humilis swamp meadow, warming increased microbial biomass, C-hydrolysis gene abundance and N-acetylglucosaminidase enzyme activity. These positive effects of warming on microbial biomass and functions further increased soil dissolved inorganic nitrogen and alleviated the nitrogen limitation for plant growth, potentially leading to higher plant biomass. Therefore, increases in SOC and particulate organic carbon (POC) under warming were likely attributed to the higher C input with promoted plant biomass overweighting the simultaneous higher C degradation and release in the K. humilis swamp meadow. Conversely, warming marginally reduced soil alkyl C, which was likely associated with enhanced decomposition by fungi and gram-positive bacteria. Overall, the increases in unprotected POC and decreases in recalcitrant alkyl C demonstrate the sensitivity of SOC physical fractions as well as chemical composition to climate warming in the K. humilis alpine swamp meadow, and suggest that the overall stability of SOC might be lower despite the gain in the content of SOC after climate warming in this alpine swamp meadow.
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Affiliation(s)
- Xia Yuan
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Ying Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Wenkuan Qin
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Tianle Xu
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Yahui Mao
- College of Geographic Sciences, Qinghai Normal University, Xining 810008, China
| | - Qi Wang
- College of Geographic Sciences, Qinghai Normal University, Xining 810008, China
| | - Kelong Chen
- College of Geographic Sciences, Qinghai Normal University, Xining 810008, China
| | - Biao Zhu
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China.
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25
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Emerson JB, Varner RK, Wik M, Parks DH, Neumann RB, Johnson JE, Singleton CM, Woodcroft BJ, Tollerson R, Owusu-Dommey A, Binder M, Freitas NL, Crill PM, Saleska SR, Tyson GW, Rich VI. Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes. Nat Commun 2021; 12:5815. [PMID: 34611153 PMCID: PMC8492752 DOI: 10.1038/s41467-021-25983-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/07/2021] [Indexed: 11/23/2022] Open
Abstract
Northern post-glacial lakes are significant, increasing sources of atmospheric carbon through ebullition (bubbling) of microbially-produced methane (CH4) from sediments. Ebullitive CH4 flux correlates strongly with temperature, reflecting that solar radiation drives emissions. However, here we show that the slope of the temperature-CH4 flux relationship differs spatially across two post-glacial lakes in Sweden. We compared these CH4 emission patterns with sediment microbial (metagenomic and amplicon), isotopic, and geochemical data. The temperature-associated increase in CH4 emissions was greater in lake middles—where methanogens were more abundant—than edges, and sediment communities were distinct between edges and middles. Microbial abundances, including those of CH4-cycling microorganisms and syntrophs, were predictive of porewater CH4 concentrations. Results suggest that deeper lake regions, which currently emit less CH4 than shallower edges, could add substantially to CH4 emissions in a warmer Arctic and that CH4 emission predictions may be improved by accounting for spatial variations in sediment microbiota. Arctic lakes are strong and increasing sources of atmospheric methane, but extreme conditions and limited observations hinder robust understanding. Here the authors show that microbes in the middle of Arctic lakes have elevated methane producing potential, and are poised to release even more in the future.
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Affiliation(s)
- Joanne B Emerson
- Department of Microbiology, The Ohio State University, 496W 12th Ave, Columbus, OH, 43210, USA. .,Department of Plant Pathology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
| | - Ruth K Varner
- Department of Earth Sciences, University of New Hampshire, 56 College Road, Durham, NH, 03824, USA. .,Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space, University of New Hampshire, 8 College Road, Durham, NH, 03824, USA.
| | - Martin Wik
- Department of Geological Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Rebecca B Neumann
- Civil & Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - Joel E Johnson
- Department of Earth Sciences, University of New Hampshire, 56 College Road, Durham, NH, 03824, USA
| | - Caitlin M Singleton
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, 9220, Denmark
| | - Ben J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Rodney Tollerson
- Department of Microbiology, The Ohio State University, 496W 12th Ave, Columbus, OH, 43210, USA.,Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91106, USA
| | - Akosua Owusu-Dommey
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA.,Parkland Hospital, 5200 Harry Hines Blvd., Dallas, TX, 75235, USA
| | - Morgan Binder
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA.,John C. Lincoln Health Network, 34975N North Valley Pkwy Ste 100, Phoenix, AZ, 85086, USA
| | - Nancy L Freitas
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA.,Energy and Resources Group, University of California, Berkeley, USA
| | - Patrick M Crill
- Department of Geological Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Scott R Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia.,Centre for Microbiome Research, Queensland University of Technology, 37 Kent St, Woolloongabba, QLD, 4102, Australia
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, 496W 12th Ave, Columbus, OH, 43210, USA.
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26
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Cha G, Meinhardt KA, Orellana LH, Hatt JK, Pannu MW, Stahl DA, Konstantinidis KT. The influence of alfalfa-switchgrass intercropping on microbial community structure and function. Environ Microbiol 2021; 23:6828-6843. [PMID: 34554631 DOI: 10.1111/1462-2920.15785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 09/17/2021] [Indexed: 11/30/2022]
Abstract
The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching and emissions of N2 O, a potent greenhouse gas. Intercropping with nitrogen-fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. We analysed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared with the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, ammonia-oxidizing archaea and bacteria increased in abundance with intercropping and fertilization. However, only betaproteobacterial ammonia-oxidizing bacteria abundance in fertilized plots significantly correlated to N2 O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization.
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Affiliation(s)
- Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Kelley A Meinhardt
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Manmeet W Pannu
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
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27
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Impact of river channel lateral migration on microbial communities across a discontinuous permafrost floodplain. Appl Environ Microbiol 2021; 87:e0133921. [PMID: 34347514 DOI: 10.1128/aem.01339-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Permafrost soils store approximately twice the amount of carbon currently present in Earth's atmosphere and are acutely impacted by climate change due to the polar amplification of increasing global temperature. Many organic-rich permafrost sediments are located on large river floodplains, where river channel migration periodically erodes and re-deposits the upper tens of meters of sediment. Channel migration exerts a first-order control on the geographic distribution of permafrost and floodplain stratigraphy and thus may affect microbial habitats. To examine how river channel migration in discontinuous permafrost environments affects microbial community composition, we used amplicon sequencing of the 16S rRNA gene on sediment samples from floodplain cores and exposed riverbanks along the Koyukuk River, a large tributary of the Yukon River in west-central Alaska. Microbial communities are sensitive to permafrost thaw: communities found in deep samples thawed by the river closely resembled near-surface active layer communities in non-metric multidimensional scaling analyses but did not resemble floodplain permafrost communities at the same depth. Microbial communities also displayed lower diversity and evenness in permafrost than in both the active layer and permafrost-free point bars recently deposited by river channel migration. Taxonomic assignments based on 16S and quantitative PCR for the methyl-coenzyme M reductase functional gene demonstrated that methanogens and methanotrophs are abundant in older permafrost-bearing deposits, but not in younger, non-permafrost point bar deposits. The results suggested that river migration, which regulates the distribution of permafrost, also modulates the distribution of microbes potentially capable of producing and consuming methane on the Koyukuk River floodplain. Importance Arctic lowlands contain large quantities of soil organic carbon that is currently sequestered in permafrost. With rising temperatures, permafrost thaw may allow this carbon to be consumed by microbial communities and released to the atmosphere as carbon dioxide or methane. We used gene sequencing to determine the microbial communities present in the floodplain of a river running through discontinuous permafrost. We found the river's lateral movement across its floodplain influences the occurrence of certain microbial communities-in particular, methane-cycling microbes were present on the older, permafrost-bearing eroding riverbank but absent on the newly deposited river bars. Riverbank sediment had microbial communities more similar to the floodplain active layer than permafrost samples from the same depth. Therefore, spatial patterns of river migration influence the distribution of microbial taxa relevant to the warming Arctic climate.
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Song Y, Chen L, Kang L, Yang G, Qin S, Zhang Q, Mao C, Kou D, Fang K, Feng X, Yang Y. Methanogenic Community, CH 4 Production Potential and Its Determinants in the Active Layer and Permafrost Deposits on the Tibetan Plateau. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:11412-11423. [PMID: 34310124 DOI: 10.1021/acs.est.0c07267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Permafrost thaw could increase methane (CH4) emissions, which largely depends on CH4 production driven by methanogenic archaea. However, large-scale evidence regarding key methanogenic taxa and their relative importance to abiotic factors in mediating methanogenesis remains limited. Here, we explored the methanogenic community, potential CH4 production and its determinants in the active layer and permafrost deposits based on soil samples acquired from 12 swamp meadow sites along a ∼1000 km permafrost transect on the Tibetan Plateau. Our results revealed lower CH4 production potential, mcrA gene abundance, and richness in the permafrost layer than those in the active layer. CH4 production potential in both soil layers was regulated by microbial and abiotic factors. Of the microbial properties, marker OTUs, rather than the abundance and diversity of methanogens, stimulated CH4 production potential. Marker OTUs differed between the two soil layers with hydrogenotrophic Methanocellales and facultative acetoclastic Methanosarcina predominant in regulating CH4 production potential in the permafrost and active layer, respectively. Besides microbial drivers, CH4 production potential increased with the carbon/nitrogen (C/N) ratio in both soil layers and was also stimulated by soil moisture in the permafrost layer. These results provide empirical evidence for model improvements to better predict permafrost carbon feedback to climate warming.
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Affiliation(s)
- Yutong Song
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leiyi Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Luyao Kang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guibiao Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shuqi Qin
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiwen Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chao Mao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan Kou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Kai Fang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuehui Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Chen Y, Liu F, Kang L, Zhang D, Kou D, Mao C, Qin S, Zhang Q, Yang Y. Large-scale evidence for microbial response and associated carbon release after permafrost thaw. GLOBAL CHANGE BIOLOGY 2021; 27:3218-3229. [PMID: 33336478 DOI: 10.1111/gcb.15487] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Permafrost thaw could trigger the release of greenhouse gases through microbial decomposition of the large quantities of carbon (C) stored within frozen soils. However, accurate evaluation of soil C emissions from thawing permafrost is still a big challenge, partly due to our inadequate understanding about the response of microbial communities and their linkage with soil C release upon permafrost thaw. Based on a large-scale permafrost sampling across 24 sites on the Tibetan Plateau, we employed meta-genomic technologies (GeoChip and Illumina MiSeq sequencing) to explore the impacts of permafrost thaw (permafrost samples were incubated for 11 days at 5°C) on microbial taxonomic and functional communities, and then conducted a laboratory incubation to investigate the linkage of microbial taxonomic and functional diversity with soil C release after permafrost thaw. We found that bacterial and fungal α diversity decreased, but functional gene diversity and the normalized relative abundance of C degradation genes increased after permafrost thaw, reflecting the rapid microbial response to permafrost thaw. Moreover, both the microbial taxonomic and functional community structures differed between the thawed permafrost and formerly frozen soils. Furthermore, soil C release rate over five month incubation was associated with microbial functional diversity and C degradation gene abundances. By contrast, neither microbial taxonomic diversity nor community structure exhibited any significant effects on soil C release over the incubation period. These findings demonstrate that permafrost thaw could accelerate C emissions by altering the function potentials of microbial communities rather than taxonomic diversity, highlighting the crucial role of microbial functional genes in mediating the responses of permafrost C cycle to climate warming.
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Affiliation(s)
- Yongliang Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Futing Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Luyao Kang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dianye Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Dan Kou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chao Mao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuqi Qin
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiwen Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Coutinho FH, Zaragoza-Solas A, López-Pérez M, Barylski J, Zielezinski A, Dutilh BE, Edwards R, Rodriguez-Valera F. RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content. PATTERNS 2021; 2:100274. [PMID: 34286299 PMCID: PMC8276007 DOI: 10.1016/j.patter.2021.100274] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/23/2020] [Accepted: 05/07/2021] [Indexed: 02/06/2023]
Abstract
Culture-independent approaches have recently shed light on the genomic diversity of viruses of prokaryotes. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), that uses scores to 43,644 protein clusters to assign hosts to complete or fragmented genomes of viruses of Archaea and Bacteria. RaFAH displayed performance comparable with that of other methods for virus-host prediction in three different benchmarks encompassing viruses from RefSeq, single amplified genomes, and metagenomes. RaFAH was applied to assembled metagenomic datasets of uncultured viruses from eight different biomes of medical, biotechnological, and environmental relevance. Our analyses led to the identification of 537 sequences of archaeal viruses representing unknown lineages, whose genomes encode novel auxiliary metabolic genes, shedding light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/. RaFAH was developed to predict the hosts of viruses of Bacteria and Archaea RaFAH displayed comparable or superior performance to other host-prediction tools RaFAH performed well across viromes from eight different ecosystems RaFAH identified hundreds of genomic sequences as derived from viruses of Archaea
Viruses that infect Bacteria and Archaea are ubiquitous and extremely abundant. Recent advances have led to the discovery of many thousands of complete and partial genomes of these biological entities. Understanding the biology of these viruses and how they influence their ecosystems depends on knowing which hosts they infect. We developed a tool that uses data from complete or fragmented genomes to predict the hosts of viruses using a machine-learning approach. Our tool, RaFAH, displayed performance comparable with or superior to that of other host-prediction tools. In addition, it identified hundreds of sequences as derived from the genomes of viruses of Archaea, which are one of the least characterized fractions of the global virosphere.
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Affiliation(s)
- Felipe Hernandes Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550 Alicante, Spain
| | - Asier Zaragoza-Solas
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550 Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550 Alicante, Spain
| | - Jakub Barylski
- Molecular Virology Research Unit, Faculty of Biology, Adam Mickiewicz University Poznan, 61-614 Poznan, Poland
| | - Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University Poznan, 61-614 Poznan, Poland
| | - Bas E Dutilh
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre/Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, the Netherlands.,Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), 3584 CH Utrecht, the Netherlands
| | - Robert Edwards
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550 Alicante, Spain.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
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Soil metabolome response to whole-ecosystem warming at the Spruce and Peatland Responses under Changing Environments experiment. Proc Natl Acad Sci U S A 2021; 118:2004192118. [PMID: 34161254 DOI: 10.1073/pnas.2004192118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In this study, a suite of complementary environmental geochemical analyses, including NMR and gas chromatography-mass spectrometry (GC-MS) analyses of central metabolites, Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) of secondary metabolites, and lipidomics, was used to investigate the influence of organic matter (OM) quality on the heterotrophic microbial mechanisms controlling peatland CO2, CH4, and CO2:CH4 porewater production ratios in response to climate warming. Our investigations leverage the Spruce and Peatland Responses under Changing Environments (SPRUCE) experiment, where air and peat warming were combined in a whole-ecosystem warming treatment. We hypothesized that warming would enhance the production of plant-derived metabolites, resulting in increased labile OM inputs to the surface peat, thereby enhancing microbial activity and greenhouse gas production. Because shallow peat is most susceptible to enhanced warming, increases in labile OM inputs to the surface, in particular, are likely to result in significant changes to CO2 and CH4 dynamics and methanogenic pathways. In support of this hypothesis, significant correlations were observed between metabolites and temperature consistent with increased availability of labile substrates, which may stimulate more rapid turnover of microbial proteins. An increase in the abundance of methanogenic genes in response to the increase in the abundance of labile substrates was accompanied by a shift toward acetoclastic and methylotrophic methanogenesis. Our results suggest that as peatland vegetation trends toward increasing vascular plant cover with warming, we can expect a concomitant shift toward increasingly methanogenic conditions and amplified climate-peatland feedbacks.
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Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile. Nat Commun 2021; 12:2089. [PMID: 33828081 PMCID: PMC8027381 DOI: 10.1038/s41467-021-22408-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/10/2021] [Indexed: 02/01/2023] Open
Abstract
Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile-but to a greater extent in the subsoil-physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.
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Perez-Mon C, Qi W, Vikram S, Frossard A, Makhalanyane T, Cowan D, Frey B. Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps). Microb Genom 2021; 7:000558. [PMID: 33848236 PMCID: PMC8208683 DOI: 10.1099/mgen.0.000558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.
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Affiliation(s)
- Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Carla Perez-Mon,
| | - Weihong Qi
- Functional Genomics Center of the University of Zurich and the ETH Zurich, Zurich, Switzerland
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Thulani Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Beat Frey,
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Zhuang W, Yu X, Hu R, Luo Z, Liu X, Zheng X, Xiao F, Peng Y, He Q, Tian Y, Yang T, Wang S, Shu L, Yan Q, Wang C, He Z. Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale. NPJ Biofilms Microbiomes 2020; 6:52. [PMID: 33184266 PMCID: PMC7665043 DOI: 10.1038/s41522-020-00164-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Mangrove roots harbor a repertoire of microbial taxa that contribute to important ecological functions in mangrove ecosystems. However, the diversity, function, and assembly of mangrove root-associated microbial communities along a continuous fine-scale niche remain elusive. Here, we applied amplicon and metagenome sequencing to investigate the bacterial and fungal communities among four compartments (nonrhizosphere, rhizosphere, episphere, and endosphere) of mangrove roots. We found different distribution patterns for both bacterial and fungal communities in all four root compartments, which could be largely due to niche differentiation along the root compartments and exudation effects of mangrove roots. The functional pattern for bacterial and fungal communities was also divergent within the compartments. The endosphere harbored more genes involved in carbohydrate metabolism, lipid transport, and methane production, and fewer genes were found to be involved in sulfur reduction compared to other compartments. The dynamics of root-associated microbial communities revealed that 56-74% of endosphere bacterial taxa were derived from nonrhizosphere, whereas no fungal OTUs of nonrhizosphere were detected in the endosphere. This indicates that roots may play a more strictly selective role in the assembly of the fungal community compared to the endosphere bacterial community, which is consistent with the projections established in an amplification-selection model. This study reveals the divergence in the diversity and function of root-associated microbial communities along a continuous fine-scale niche, thereby highlighting a strictly selective role of soil-root interfaces in shaping the fungal community structure in the mangrove root systems.
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Affiliation(s)
- Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Tony Yang
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3×2, Canada
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China.
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China.
- College of Agronomy, Hunan Agricultural University, 410128, Changsha, China.
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Islam W, Noman A, Naveed H, Huang Z, Chen HYH. Role of environmental factors in shaping the soil microbiome. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:41225-41247. [PMID: 32829437 DOI: 10.1007/s11356-020-10471-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/10/2020] [Indexed: 05/09/2023]
Abstract
The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.
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Affiliation(s)
- Waqar Islam
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
| | - Hassan Naveed
- College of Life Science, Leshan Normal University, Leshan, 614004, Sichuan, China
| | - Zhiqun Huang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
| | - Han Y H Chen
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
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Tienda S, Vida C, Lagendijk E, de Weert S, Linares I, González-Fernández J, Guirado E, de Vicente A, Cazorla FM. Soil Application of a Formulated Biocontrol Rhizobacterium, Pseudomonas chlororaphis PCL1606, Induces Soil Suppressiveness by Impacting Specific Microbial Communities. Front Microbiol 2020; 11:1874. [PMID: 32849458 PMCID: PMC7426498 DOI: 10.3389/fmicb.2020.01874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
Biocontrol bacteria can be used for plant protection against some plant diseases. Pseudomonas chlororaphis PCL1606 (PcPCL1606) is a model bacterium isolated from the avocado rhizosphere with strong antifungal antagonism mediated by the production of 2-hexyl, 5-propil resorcinol (HPR). Additionally, PcPCL1606 has biological control against different soil-borne fungal pathogens, including the causal agent of the white root rot of many woody crops and avocado in the Mediterranean area, Rosellinia necatrix. The objective of this study was to assess whether the semicommercial application of PcPCL1606 to soil can potentially affect avocado soil and rhizosphere microbial communities and their activities in natural conditions and under R. necatrix infection. To test the putative effects of PcPCL1606 on soil eukaryotic and prokaryotic communities, a formulated PcPCL1606 was prepared and applied to the soil of avocado plants growing in mesocosm experiments, and the communities were analyzed by using 16S/ITS metagenomics. PcPCL1606 survived until the end of the experiments. The effect of PcPCL1606 application on prokaryotic communities in soil and rhizosphere samples from natural soil was not detectable, and very minor changes were observed in eukaryotic communities. In the infested soils, the presence of R. necatrix strongly impacted the soil and rhizosphere microbial communities. However, after PcPCL1606 was applied to soil infested with R. necatrix, the prokaryotic community reacted by increasing the relative abundance of few families with protective features against fungal soilborne pathogens and organic matter decomposition (Chitinophagaceae, Cytophagaceae), but no new prokaryotic families were detected. The treatment of PcPCL1606 impacted the fungal profile, which strongly reduced the presence of R. necatrix in avocado soil and rhizosphere, minimizing its effect on the rest of the microbial communities. The bacterial treatment of formulated PcPCL1606 on avocado soils infested with R. necatrix resulted in biological control of the pathogen. This suppressiveness phenotype was analyzed, and PcPCL1606 has a key role in suppressiveness induction; in addition, this phenotype was strongly dependent on the production of HPR.
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Affiliation(s)
- Sandra Tienda
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Carmen Vida
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Ellen Lagendijk
- Koppert Biological Systems, Berkel en Rodenrijs, Netherlands
| | - Sandra de Weert
- Koppert Biological Systems, Berkel en Rodenrijs, Netherlands
| | - Irene Linares
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Jorge González-Fernández
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Estación Experimental “La Mayora”, Algarrobo, Spain
| | - Emilio Guirado
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Estación Experimental “La Mayora”, Algarrobo, Spain
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Francisco M. Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
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Luo Y, Schuur EAG. Model parameterization to represent processes at unresolved scales and changing properties of evolving systems. GLOBAL CHANGE BIOLOGY 2020; 26:1109-1117. [PMID: 31782216 DOI: 10.1111/gcb.14939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Modeling has become an indispensable tool for scientific research. However, models generate great uncertainty when they are used to predict or forecast ecosystem responses to global change. This uncertainty is partly due to parameterization, which is an essential procedure for model specification via defining parameter values for a model. The classic doctrine of parameterization is that a parameter is constant. However, it is commonly known from modeling practice that a model that is well calibrated for its parameters at one site may not simulate well at another site unless its parameters are tuned again. This common practice implies that parameter values have to vary with sites. Indeed, parameter values that are estimated using a statistically rigorous approach, that is, data assimilation, vary with time, space, and treatments in global change experiments. This paper illustrates that varying parameters is to account for both processes at unresolved scales and changing properties of evolving systems. A model, no matter how complex it is, could not represent all the processes of one system at resolved scales. Interactions of processes at unresolved scales with those at resolved scales should be reflected in model parameters. Meanwhile, it is pervasively observed that properties of ecosystems change over time, space, and environmental conditions. Parameters, which represent properties of a system under study, should change as well. Tuning has been practiced for many decades to change parameter values. Yet this activity, unfortunately, did not contribute to our knowledge on model parameterization at all. Data assimilation makes it possible to rigorously estimate parameter values and, consequently, offers an approach to understand which, how, how much, and why parameters vary. To fully understand those issues, extensive research is required. Nonetheless, it is clear that changes in parameter values lead to different model predictions even if the model structure is the same.
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Affiliation(s)
- Yiqi Luo
- Department of Biological Sciences, Center for Ecosystem Sciences and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Edward A G Schuur
- Department of Biological Sciences, Center for Ecosystem Sciences and Society, Northern Arizona University, Flagstaff, AZ, USA
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Kluber LA, Johnston ER, Allen SA, Hendershot JN, Hanson PJ, Schadt CW. Constraints on microbial communities, decomposition and methane production in deep peat deposits. PLoS One 2020; 15:e0223744. [PMID: 32027653 PMCID: PMC7004313 DOI: 10.1371/journal.pone.0223744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/20/2020] [Indexed: 11/19/2022] Open
Abstract
Peatlands play outsized roles in the global carbon cycle. Despite occupying a rather small fraction of the terrestrial biosphere (~3%), these ecosystems account for roughly one third of the global soil carbon pool. This carbon is largely comprised of undecomposed deposits of plant material (peat) that may be meters thick. The fate of this deep carbon stockpile with ongoing and future climate change is thus of great interest and has large potential to induce positive feedback to climate warming. Recent in situ warming of an ombrotrophic peatland indicated that the deep peat microbial communities and decomposition rates were resistant to elevated temperatures. In this experiment, we sought to understand how nutrient and pH limitations may interact with temperature to limit microbial activity and community composition. Anaerobic microcosms of peat collected from 1.5 to 2 meters in depth were incubated at 6°C and 15°C with elevated pH, nitrogen (NH4Cl), and/or phosphorus (KH2PO4) in a full factorial design. The production of CO2 and CH4 was significantly greater in microcosms incubated at 15°C, although the structure of the microbial community did not differ between the two temperatures. Increasing the pH from ~3.5 to ~5.5 altered microbial community structure, however increases in CH4 production were non-significant. Contrary to expectations, N and P additions did not increase CO2 and CH4 production, indicating that nutrient availability was not a primary constraint in microbial decomposition of deep peat. Our findings indicate that temperature is a key factor limiting the decomposition of deep peat, however other factors such as the availability of O2 or alternative electron donors and high concentrations of phenolic compounds, may also exert constraints. Continued experimental peat warming studies will be necessary to assess if the deep peat carbon bank is susceptible to increased temperatures over the longer time scales.
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Affiliation(s)
- Laurel A. Kluber
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- Climate Change Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - Eric R. Johnston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- Climate Change Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - Samantha A. Allen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- Climate Change Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - J. Nicholas Hendershot
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- Climate Change Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - Paul J. Hanson
- Climate Change Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - Christopher W. Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- Climate Change Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States of America
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Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths. Proc Natl Acad Sci U S A 2019; 116:15096-15105. [PMID: 31285347 DOI: 10.1073/pnas.1901307116] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Northern-latitude tundra soils harbor substantial carbon (C) stocks that are highly susceptible to microbial degradation with rising global temperatures. Understanding the magnitude and direction (e.g., C release or sequestration) of the microbial responses to warming is necessary to accurately model climate change. In this study, Alaskan tundra soils were subjected to experimental in situ warming by ∼1.1 °C above ambient temperature, and the microbial communities were evaluated using metagenomics after 4.5 years, at 2 depths: 15 to 25 cm (active layer at outset of the experiment) and 45 to 55 cm (transition zone at the permafrost/active layer boundary at the outset of the experiment). In contrast to small or insignificant shifts after 1.5 years of warming, 4.5 years of warming resulted in significant changes to the abundances of functional traits and the corresponding taxa relative to control plots (no warming), and microbial shifts differed qualitatively between the two soil depths. At 15 to 25 cm, increased abundances of carbohydrate utilization genes were observed that correlated with (increased) measured ecosystem carbon respiration. At the 45- to 55-cm layer, increased methanogenesis potential was observed, which corresponded with a 3-fold increase in abundance of a single archaeal clade of the Methanosarcinales order, increased annual thaw duration (45.3 vs. 79.3 days), and increased CH4 emissions. Collectively, these data demonstrate that the microbial responses to warming in tundra soil are rapid and markedly different between the 2 critical soil layers evaluated, and identify potential biomarkers for the corresponding microbial processes that could be important in modeling.
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