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Liu Y, Delgado-Baquerizo M, Bing H, Wang Y, Wang J, Chen J, Qiu S, Zhu H, Wu Y, Fang L, Chang R. Warming-induced shifts in alpine soil microbiome: An ecosystem-scale study with environmental context-dependent insights. ENVIRONMENTAL RESEARCH 2024; 255:119206. [PMID: 38782346 DOI: 10.1016/j.envres.2024.119206] [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: 03/29/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Climate warming is a pressing global issue with substantial impacts on soil health and function. However, the influence of environmental context on the responses of soil microorganisms to warming remains largely elusive, particularly in alpine ecosystems. This study examined the responses of the soil microbiome to in situ experimental warming across three elevations (3850 m, 4100 m, and 4250 m) in the meadow of Gongga Mountain, eastern Tibetan Plateau. Our findings demonstrate that soil microbial diversity is highly resilient to warming, with significant impacts observed only at specific elevations. Furthermore, the influence of warming on the composition of the soil microbial community is also elevation-dependent, underscoring the importance of local environmental context in shaping microbial evolution in alpine soils under climate warming. Notably, we identified soil moisture at 3850 m and carbon-to-nitrogen ratio at 4250 m as indirect predictors regulating the responses of microbial diversity to warming at specific elevations. These findings underscore the paramount importance of considering pre-existing environmental conditions in predicting the response of alpine soil microbiomes to climate warming. Our study provides novel insights into the intricate interactions between climate warming, soil microbiome, and environmental context in alpine ecosystems, illuminating the complex mechanisms governing soil microbial ecology in these fragile and sensitive environments.
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Affiliation(s)
- Ye Liu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Institutode Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Haijian Bing
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China.
| | - Yuhan Wang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China; Key Laboratory of Green Utilization of Critical Non-Metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, 430070, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, 710061, China
| | - Shaojun Qiu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China
| | - He Zhu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China
| | - Yanhong Wu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China
| | - Linchuan Fang
- Key Laboratory of Green Utilization of Critical Non-Metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, 430070, China
| | - Ruiying Chang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610299, China
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Bielčik M, Schlägel UE, Schäfer M, Aguilar-Trigueros CA, Lakovic M, Sosa-Hernández MA, Hammer EC, Jeltsch F, Rillig MC. Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence. Biol Rev Camb Philos Soc 2024. [PMID: 39073180 DOI: 10.1111/brv.13119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024]
Abstract
Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.
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Affiliation(s)
- Miloš Bielčik
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research (ZALF), Eberswalder Str.84, Müncheberg, 15374, Germany
| | - Ulrike E Schlägel
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
| | - Merlin Schäfer
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
- Federal Agency for Nature Conservation, Alte Messe 6, Leipzig, 04103, Germany
| | - Carlos A Aguilar-Trigueros
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Building R2, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Seminaarinkatu 15, Jyväskylä, 40014, Finland
| | - Milica Lakovic
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
| | - Moisés A Sosa-Hernández
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
| | - Edith C Hammer
- Department of Biology, Microbial Ecology, Lund University, Ekologihuset, Sölvegatan 37, Lund, 22362, Sweden
| | - Florian Jeltsch
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
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Jing J, Garbeva P, Raaijmakers JM, Medema MH. Strategies for tailoring functional microbial synthetic communities. THE ISME JOURNAL 2024; 18:wrae049. [PMID: 38537571 PMCID: PMC11008692 DOI: 10.1093/ismejo/wrae049] [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: 01/08/2024] [Revised: 02/26/2024] [Indexed: 04/12/2024]
Abstract
Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.
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Affiliation(s)
- Jiayi Jing
- Bioinformatics Group, Department of Plant Science, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Department of Plant Science, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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Christel A, Chemidlin Prevost-Bouré N, Dequiedt S, Saby N, Mercier F, Tripied J, Comment G, Villerd J, Djemiel C, Hermant A, Blondon M, Bargeot L, Matagne E, Horrigue W, Maron PA, Ranjard L. Differential responses of soil microbial biomass, diversity and interactions to land use intensity at a territorial scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167454. [PMID: 37783435 DOI: 10.1016/j.scitotenv.2023.167454] [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: 07/20/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/04/2023]
Abstract
Impact of land use intensification on soil microbial communities across a territory remains poorly documented. Yet, it has to be deciphered to validate the results obtained at local and global scales by integrating the variations of environmental conditions and agricultural systems at a territorial scale. We investigated the impact of different land uses (from forest to agricultural systems) and associated soil management practices on soil molecular microbial biomass and diversity across a territory of 3300 km2 in Burgundy (France). Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA from 300 soils, respectively. Geostatistics were applied to map the soil macro-ecological patterns and variance partitioning analysis was used to rank the influence of soil physicochemical characteristics, land uses and associated practices on soil microbial communities. Geographical patterns differed between microbial biomass and diversity, emphasizing that distinct environmental drivers shaped these parameters. Soil microbial biomass was mainly driven by the soil organic carbon content and was significantly altered by agricultural land uses, with a loss of about 71 % from natural to agricultural ecosystems. The best predictors of bacterial and fungal richness were soil texture and pH, respectively. Microbial diversity was less sensitive than microbial biomass to land use intensification, and fungal richness appeared more impacted than bacteria. Co-occurrence network analysis of the interactions among microbial communities showed a decline of about 95 % of network complexity with land use intensification, which counterbalanced the weak response of microbial diversity. Grouping of the 147 cropland plots in four clusters according to their agricultural practices confirmed that microbial parameters exhibited different responses to soil management intensification, especially soil tillage and crop protection. Our results altogether allow evaluating the different levels of microbial parameters' vulnerability to land use intensity at a territorial scale.
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Affiliation(s)
- A Christel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France; AgroParisTech, 75732 Paris, France
| | | | - S Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - N Saby
- INRAE, US1106 Info&Sols, F-45075 Orleans, France
| | - F Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France; Dijon Céréales, Alliance BFC, 4 Boulevard de Beauregard, 21600 Longvic, France
| | - J Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - G Comment
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - J Villerd
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - C Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - A Hermant
- Chambre d'agriculture de Côte d'Or, 1 rue des Coulots, 21110 Bretenière, France
| | - M Blondon
- Dijon Céréales, Alliance BFC, 4 Boulevard de Beauregard, 21600 Longvic, France
| | - L Bargeot
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - E Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - W Horrigue
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - P A Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - L Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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Bergmann GE, Leveau JHJ. A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds. Front Microbiol 2022; 13:877519. [PMID: 35935241 PMCID: PMC9355165 DOI: 10.3389/fmicb.2022.877519] [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: 02/16/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.
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Affiliation(s)
| | - Johan H. J. Leveau
- Department of Plant Pathology, University of California-Davis, Davis, CA, United States
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Cai YJ, Liu ZA, Zhang S, Liu H, Nicol GW, Chen Z. Microbial community structure is stratified at the millimeter-scale across the soil-water interface. ISME COMMUNICATIONS 2022; 2:53. [PMID: 37938662 PMCID: PMC9723559 DOI: 10.1038/s43705-022-00138-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/25/2022] [Accepted: 06/14/2022] [Indexed: 08/09/2023]
Abstract
Soil-water interfaces (SWI) are biogeochemical hotspots characterized by millimeter-scale redox gradients, indicating that parallel changes are also present in microbial community structure and activity. However, soil-based analyses of microbial community structure typically examine bulk samples and seldom consider variation at a scale relevant to changes in environmental conditions. Here we presented a study that aimed to describe millimeter-scale variance in both microbial community structure and physicochemical properties in a lab flooded soil. At this fine-scale resolution, the stratification of biogeochemical properties (e.g., redox potential, nitrate concentration) was consistent with the structure of the active microbial community with clear shifts in the relative abundance of transcriptionally active populations associated with changing redox conditions. Our results demonstrate that spatial scale should be carefully considered when investigating ecological mechanisms that influence soil microbial community structures.
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Affiliation(s)
- Yu-Jia Cai
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu, 215123, China
- Department of Geography & Planning, School of Environmental Sciences, University of Liverpool, Brownlow Hill, Liverpool, L697ZX, UK
| | - Zi-Ao Liu
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu, 215123, China
| | - Sha Zhang
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu, 215123, China
- Department of Geography & Planning, School of Environmental Sciences, University of Liverpool, Brownlow Hill, Liverpool, L697ZX, UK
| | - Hao Liu
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu, 215123, China
- Department of Geography & Planning, School of Environmental Sciences, University of Liverpool, Brownlow Hill, Liverpool, L697ZX, UK
| | - Graeme W Nicol
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69134, Ecully cedex, France
| | - Zheng Chen
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu, 215123, China.
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Biogeographic Patterns and Elevational Differentiation of Sedimentary Bacterial Communities across River Systems in China. Appl Environ Microbiol 2022; 88:e0059722. [PMID: 35638840 DOI: 10.1128/aem.00597-22] [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: 11/20/2022] Open
Abstract
Bacterial biodiversity is tightly correlated with ecological functions of natural systems, and bacterial rare and abundant subcommunities make distinct contributions to ecosystem functioning. However, the biogeographic pattern and elevational differentiation of sedimentary bacterial diversity have rarely been studied in cross-river systems at a continental scale. This study analyzed the biogeographic patterns and elevational differentiations of the entire, abundant, and rare bacterial (sub)communities as well as the underlying mechanisms across nine rivers that span distinct geographic regions and large elevational gradients in China. We found that bacterial rare and abundant subcommunities shared similar biogeographic patterns and both demonstrated strong distance-decay relationships, despite their distinct community compositions. However, both null model and variation partitioning analysis results showed that while environmental selection governed rare subcommunity assemblies (contribution: 51.9%), dispersal limitation (62.7%) controlled the assembly of abundant subcommunities. The disparity was associated with the broader threshold width of abundant taxa to water temperature and pH variations than rare taxa. Elevation-induced bacterial composition variations were more evident than latitude-induced ones. Some specific operational taxonomic units (OTUs), representing 16.4% of the total sequences, much preferentially and even exclusively lived in high-elevation or low-elevation habitats and demonstrated some adaptations to local conditions. Greater positive: negative link ratios in bacterial co-occurrence networks of low elevations than high elevations (P < 0.05) partly resulted from their harboring higher organic carbon: nitrogen ratios. Together, this study draws a biogeographic picture of sedimentary bacterial communities in a continental-scale riverine system and highlights the importance of incorporating elevation-associated patterns of microbial diversity into riverine microbial ecology studies. IMPORTANCE Bacterial diversity is tightly correlated with the nutrient cycling of river systems. However, previous studies on bacterial diversity are mainly constrained to one single river system, although microbial biogeography and its drivers exhibit strong spatial scale dependence. Moreover, elevational differentiations of bacterial communities across river systems have also rarely been studied. Bacterial rare and abundant subcommunities make distinct contributions to ecosystem functioning, and they share similar biogeographic patterns in some environments but not in others. Therefore, we explored the biogeography of the entire, abundant, and rare (sub)communities in nine rivers that cover a wide space range and large elevational gradient in China. Our results revealed that bacterial rare and abundant subcommunities shared similar biogeographic patterns but their assembly mechanisms were much different in these rivers. Moreover, bacterial communities showed evident differentiations between high elevations and low elevations. These findings will facilitate a better understanding of bacterial diversity features in river systems.
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Abstract
A key challenge in microbiome science is the scale mismatch problem, which arises when the scale at which microbial communities are sampled, interrogated, and averaged is different from the scale at which individual microorganisms within those communities interact with each other and with their environment. Profiling the microbial communities in a teaspoon of soil, from a scoop of fecal matter, or along a plant leaf surface represents a scale mismatch of multiple orders of magnitude, which may limit our ability to interpret or predict species interactions and community assembly within such samples. In this Perspective, we explore how economists, who are historically and topically split along the lines of micro- and macroeconomics, deal with the scale mismatch problem, and how taking clues from (micro)economists could benefit the field of microbiomics.
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Contribution of single-cell omics to microbial ecology. Trends Ecol Evol 2021; 37:67-78. [PMID: 34602304 DOI: 10.1016/j.tree.2021.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022]
Abstract
Micro-organisms play key roles in various ecosystems, but many of their functions and interactions remain undefined. To investigate the ecological relevance of microbial communities, new molecular tools are being developed. Among them, single-cell omics assessing genetic diversity at the population and community levels and linking each individual cell to its functions is gaining interest in microbial ecology. By giving access to a wider range of ecological scales (from individual to community) than culture-based approaches and meta-omics, single-cell omics can contribute not only to micro-organisms' genomic and functional identification but also to the testing of concepts in ecology. Here, we discuss the contribution of single-cell omics to possible breakthroughs in concepts and knowledge on microbial ecosystems and ecoevolutionary processes.
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