1
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Wang X, Guo N, Zhang Y, Wang G, Shi K. Cross-protection and cross-feeding between Enterobacter and Comamonas promoting their coexistence and cadmium tolerance in Oryza sativa L. Microbiol Res 2024; 286:127806. [PMID: 38924817 DOI: 10.1016/j.micres.2024.127806] [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: 01/27/2024] [Revised: 04/13/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Metabolic cross-feeding is a pervasive interaction between bacteria to acquire novel phenotypes. However, our current understanding of the survival mechanism for cross-feeding in cocultured bacterial biofilms under heavy-metal conditions remains limited. Herein, we found that Comamonas sp. A23 produces L-phenylalanine to activate the L-phenylalanine degradation pathway in Enterobacter sp. A11, enhancing biofilm formation and cadmium [Cd(II)] immobilization in A11. The genes responsible for L-phenylalanine-degradation (paaK) and cell attachment and aggregation (csgAD) are essential for biofilm formation and Cd(II) immobilization in A11 induced by L-phenylalanine. The augmentation of A11 biofilms, in turn, protects A23 under Cd(II) and H2O2 stresses. The plant-based experiments demonstrate that the induction of two rice Cd(II) transporters, OsCOPT4 and OsBCP1, by A11 and A23 enhances rice resistance against Cd(II) and H2O2 stresses. Overall, our findings unveil the mutual dependence between bacteria and rice on L-phenylalanine cross-feeding for survival under abiotic stress.
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Affiliation(s)
- Xing Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Naijiang Guo
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yao Zhang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Gejiao Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Kaixiang Shi
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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2
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Pereira TJ, De Santiago A, Bik HM. Soil properties predict below-ground community structure, but not nematode microbiome patterns in semi-arid habitats. Mol Ecol 2024:e17501. [PMID: 39175265 DOI: 10.1111/mec.17501] [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: 01/02/2024] [Revised: 08/02/2024] [Accepted: 08/07/2024] [Indexed: 08/24/2024]
Abstract
Microbial and microeukaryotic communities are extremely abundant and diverse in soil habitats where they play critical roles in ecosystem functioning and services that are essential to soil health. Soil biodiversity is influenced by above-ground (vegetation) and below-ground factors (soil properties), which together create habitat-specific conditions. However, the compound effects of vegetation and soil properties on soil communities are less studied or often focused on one component of the soil biota. Here, we integrate metabarcoding (16S and 18S rRNA genes) and nematode morphology to assess the effects of habitat and soil properties shaping microbial and microeukaryotic communities as well as nematode-associated microbiomes. We show that both vegetation and soil properties (soil bulk density) were major factors structuring microbial and microeukaryotic communities in semi-arid soil habitats. Despite having lower nutrients and lower pH, denser soils displayed significantly higher alpha diversity than less dense soils across datasets. Nematode-associated microbiomes have lower microbial diversity, strongly differ from soil microbes and are more likely to respond to microscale variations among samples than to vegetation or soil bulk density. Consequently, different nematode lineages and trophic groups are likely to display similar associated microbiomes when sharing the same microhabitat. Different microbiome taxa were enriched within specific nematode lineages (e.g. Mycobacterium, Candidatus Cardinium) highlighting potentially new species-specific associations that may confer benefits to their soil nematode hosts. Our findings highlight the importance of exploring above- and below-ground effects to assess community structure in terrestrial habitats, and how fine-scale analyses are critical for understanding patterns of host-associated microbiomes.
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Affiliation(s)
- Tiago José Pereira
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Alejandro De Santiago
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Holly M Bik
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
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3
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Carreira C, Lønborg C, Acharya B, Aryal L, Buivydaite Z, Borim Corrêa F, Chen T, Lorenzen Elberg C, Emerson JB, Hillary L, Khadka RB, Langlois V, Mason-Jones K, Netherway T, Sutela S, Trubl G, Wa Kang'eri A, Wang R, White RA, Winding A, Zhao T, Sapkota R. Integrating viruses into soil food web biogeochemistry. Nat Microbiol 2024:10.1038/s41564-024-01767-x. [PMID: 39095499 DOI: 10.1038/s41564-024-01767-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/19/2024] [Indexed: 08/04/2024]
Abstract
The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. We highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.
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Affiliation(s)
- Cátia Carreira
- Department of Environmental Science, Aarhus University, Roskilde, Denmark.
- Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.
| | | | - Basistha Acharya
- Directorate of Agricultural Research, Nepal Agricultural Research Council, Khajura, Nepal
| | - Laxman Aryal
- Nepal Agricultural Research Council, National Wheat Research Program, Bhairahawa, Nepal
| | - Zivile Buivydaite
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Felipe Borim Corrêa
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Tingting Chen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
- Department of Ecology, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | | | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Luke Hillary
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Ram B Khadka
- National Plant Pathology Research Center, Nepal Agricultural Research Council, Lalitpur, Nepal
| | - Valérie Langlois
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec City, Québec, Canada
| | - Kyle Mason-Jones
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Suvi Sutela
- Natural Resources Institute Finland, Helsinki, Finland
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | - Ruiqi Wang
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, the Netherlands
| | - Richard Allen White
- Computational Intelligence to Predict Health and Environmental Risks, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
- North Carolina Research Campus, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Anne Winding
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Tianci Zhao
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Rumakanta Sapkota
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
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4
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Wang B, Wang S, Wu L, Wu Y, Wang S, Bai Y, Chen D. Temporal asynchrony of plant and soil biota determines ecosystem multifunctional stability. GLOBAL CHANGE BIOLOGY 2024; 30:e17483. [PMID: 39171768 DOI: 10.1111/gcb.17483] [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: 02/18/2024] [Revised: 07/17/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024]
Abstract
The role of plant biodiversity in stabilizing ecosystem multifunctionality has been extensively studied; however, the impact of soil biota biodiversity on ecosystem multifunctional stability, particularly under multiple environmental changes, remains unexplored. By conducting an experiment with environmental changes (adding water and nitrogen to a long-term grazing experiment) and an experiment without environmental changes (an undisturbed site) in semi-arid grasslands, our research revealed that environmental changes-induced changes in temporal stability of both above- and belowground multifunctionality were mainly impacted by plant and soil biota asynchrony, rather than by species diversity. Furthermore, changes in temporal stability of above- and belowground multifunctionality, under both experiments with and without environmental changes, were mainly associated with plant and soil biota asynchrony, respectively, suggesting that the temporal asynchrony of plant and soil biota has independent and non-substitutable effects on multifunctional stability. Our findings emphasize the importance of considering both above- and belowground biodiversity or functions when evaluating the stabilizing effects of biodiversity on ecosystem functions.
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Affiliation(s)
- Bing Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Shuaifei Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Liji Wu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Ying Wu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Shaopeng Wang
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Yongfei Bai
- 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
| | - Dima Chen
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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5
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Ficetola GF, Marta S, Guerrieri A, Cantera I, Bonin A, Cauvy-Fraunié S, Ambrosini R, Caccianiga M, Anthelme F, Azzoni RS, Almond P, Alviz Gazitúa P, Ceballos Lievano JL, Chand P, Chand Sharma M, Clague JJ, Cochachín Rapre JA, Compostella C, Encarnación RC, Dangles O, Deline P, Eger A, Erokhin S, Franzetti A, Gielly L, Gili F, Gobbi M, Hågvar S, Kaufmann R, Khedim N, Meneses RI, Morales-Martínez MA, Peyre G, Pittino F, Proietto A, Rabatel A, Sieron K, Tielidze L, Urseitova N, Yang Y, Zaginaev V, Zerboni A, Zimmer A, Diolaiuti GA, Taberlet P, Poulenard J, Fontaneto D, Thuiller W, Carteron A. The development of terrestrial ecosystems emerging after glacier retreat. Nature 2024; 632:336-342. [PMID: 39085613 DOI: 10.1038/s41586-024-07778-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/02/2024] [Indexed: 08/02/2024]
Abstract
The global retreat of glaciers is dramatically altering mountain and high-latitude landscapes, with new ecosystems developing from apparently barren substrates1-4. The study of these emerging ecosystems is critical to understanding how climate change interacts with microhabitat and biotic communities and determines the future of ice-free terrains1,5. Here, using a comprehensive characterization of ecosystems (soil properties, microclimate, productivity and biodiversity by environmental DNA metabarcoding6) across 46 proglacial landscapes worldwide, we found that all the environmental properties change with time since glaciers retreated, and that temperature modulates the accumulation of soil nutrients. The richness of bacteria, fungi, plants and animals increases with time since deglaciation, but their temporal patterns differ. Microorganisms colonized most rapidly in the first decades after glacier retreat, whereas most macroorganisms took longer. Increased habitat suitability, growing complexity of biotic interactions and temporal colonization all contribute to the increase in biodiversity over time. These processes also modify community composition for all the groups of organisms. Plant communities show positive links with all other biodiversity components and have a key role in ecosystem development. These unifying patterns provide new insights into the early dynamics of deglaciated terrains and highlight the need for integrated surveillance of their multiple environmental properties5.
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Affiliation(s)
- Gentile Francesco Ficetola
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milan, Italy.
- University of Grenoble Alpes, University of Savoie Mont Blanc, CNRS, LECA, Grenoble, France.
| | - Silvio Marta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milan, Italy.
- CNR - Institute of Geosciences and Earth Resources, Pisa, Italy.
| | - Alessia Guerrieri
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milan, Italy
- Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
| | - Isabel Cantera
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Aurélie Bonin
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milan, Italy
- Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
| | | | - Roberto Ambrosini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Marco Caccianiga
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Fabien Anthelme
- AMAP, University of Montpellier, IRD, CIRAD, CNRS, INRAE, Montpellier, France
| | - Roberto Sergio Azzoni
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milan, Italy
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milan, Italy
| | - Peter Almond
- Department of Soil and Physical Sciences, Lincoln University, Lincoln, New Zealand
| | - Pablo Alviz Gazitúa
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | | | - Pritam Chand
- Department of Geography, School of Environment and Earth Sciences, Central University of Punjab, VPO-Ghudda, Bathinda, India
| | - Milap Chand Sharma
- Centre for the Study of Regional Development, School of Social Sciences, Jawaharlal Nehru University, New Delhi, India
| | - John J Clague
- Department of Earth Sciences, Simon Fraser University, Burnaby, British Colombia, Canada
| | | | - Chiara Compostella
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milan, Italy
| | | | - Olivier Dangles
- CEFE, University of Montpellier, CNRS, EPHE, IRD, University of Paul Valéry Montpellier 3, Montpellier, France
| | - Philip Deline
- University of Savoie Mont Blanc, University of Grenoble Alpes, EDYTEM, Chambéry, France
| | - Andre Eger
- Mannaki Whenua - Landcare Research, Soils and Landscapes, Lincoln, New Zealand
| | - Sergey Erokhin
- Institute of Water Problems and Hydro-Energy, Kyrgyz National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milan, Italy
| | - Ludovic Gielly
- University of Grenoble Alpes, University of Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Fabrizio Gili
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milan, Italy
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Mauro Gobbi
- Research and Museum Collections Office, Climate and Ecology Unit, MUSE-Science Museum, Trento, Italy
| | - Sigmund Hågvar
- Faculty of Environmental Sciences and Natural Resource Management (INA), Norwegian University of Life Sciences, Ås, Norway
| | - Rüdiger Kaufmann
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Norine Khedim
- University of Savoie Mont Blanc, University of Grenoble Alpes, EDYTEM, Chambéry, France
| | - Rosa Isela Meneses
- Herbario Nacional de Bolivia: La Paz, La Paz, Bolivia
- Millenium Nucleus in Andean Peatlands, Arica, Chile
| | | | - Gwendolyn Peyre
- Department of Civil and Environmental Engineering, University of the Andes, Bogotá, Colombia
| | - Francesca Pittino
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milan, Italy
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Angela Proietto
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Antoine Rabatel
- University of Grenoble Alpes, CNRS, IRD, INRAE, Grenoble-INP, Institut des Géosciences de l'Environnement (IGE UMR 5001), Grenoble, France
| | - Katrin Sieron
- Universidad Veracruzana, Centro de Ciencias de la Tierra, Xalapa, Veracruz, Mexico
| | - Levan Tielidze
- Securing Antarctica's Environmental Future, School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria, Australia
- School of Natural Sciences and Medicine, Ilia State University, Tbilisi, Georgia
| | - Nurai Urseitova
- Institute of Water Problems and Hydro-Energy, Kyrgyz National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Yan Yang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Vitalii Zaginaev
- Institute of Water Problems and Hydro-Energy, Kyrgyz National Academy of Sciences, Bishkek, Kyrgyzstan
- Mountain Societies Research Institute, University of Central Asia, Bishkek, Kyrgyzstan
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra "Ardito Desio", Università degli Studi di Milano, Milan, Italy
| | - Anaïs Zimmer
- Department of Geography and the Environment, University of Texas at Austin, Austin, TX, USA
| | | | - Pierre Taberlet
- University of Grenoble Alpes, University of Savoie Mont Blanc, CNRS, LECA, Grenoble, France
- UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Jerome Poulenard
- University of Savoie Mont Blanc, University of Grenoble Alpes, EDYTEM, Chambéry, France
| | - Diego Fontaneto
- CNR - Water Research Institute, Verbania, Italy
- NBFC - National Biodiversity Future Center, Palermo, Italy
| | - Wilfried Thuiller
- University of Grenoble Alpes, University of Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Alexis Carteron
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milan, Italy.
- Université de Toulouse, École d'Ingénieurs de PURPAN, UMR INRAE-INPT DYNAFOR, Toulouse, France.
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6
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Peddle SD, Hodgson RJ, Borrett RJ, Brachmann S, Davies TC, Erickson TE, Liddicoat C, Muñoz-Rojas M, Robinson JM, Watson CD, Krauss SL, Breed MF. Practical applications of soil microbiota to improve ecosystem restoration: current knowledge and future directions. Biol Rev Camb Philos Soc 2024. [PMID: 39075839 DOI: 10.1111/brv.13124] [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: 03/16/2023] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 07/31/2024]
Abstract
Soil microbiota are important components of healthy ecosystems. Greater consideration of soil microbiota in the restoration of biodiverse, functional, and resilient ecosystems is required to address the twin global crises of biodiversity decline and climate change. In this review, we discuss available and emerging practical applications of soil microbiota into (i) restoration planning, (ii) direct interventions for shaping soil biodiversity, and (iii) strategies for monitoring and predicting restoration trajectories. We show how better planning of restoration activities to account for soil microbiota can help improve progress towards restoration targets. We show how planning to embed soil microbiota experiments into restoration projects will permit a more rigorous assessment of the effectiveness of different restoration methods, especially when complemented by statistical modelling approaches that capitalise on existing data sets to improve causal understandings and prioritise research strategies where appropriate. In addition to recovering belowground microbiota, restoration strategies that include soil microbiota can improve the resilience of whole ecosystems. Fundamentally, restoration planning should identify appropriate reference target ecosystem attributes and - from the perspective of soil microbiota - comprehensibly consider potential physical, chemical and biological influences on recovery. We identify that inoculating ecologically appropriate soil microbiota into degraded environments can support a range of restoration interventions (e.g. targeted, broad-spectrum and cultured inoculations) with promising results. Such inoculations however are currently underutilised and knowledge gaps persist surrounding successful establishment in light of community dynamics, including priority effects and community coalescence. We show how the ecological trajectories of restoration sites can be assessed by characterising microbial diversity, composition, and functions in the soil. Ultimately, we highlight practical ways to apply the soil microbiota toolbox across the planning, intervention, and monitoring stages of ecosystem restoration and address persistent open questions at each stage. With continued collaborations between researchers and practitioners to address knowledge gaps, these approaches can improve current restoration practices and ecological outcomes.
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Affiliation(s)
- Shawn D Peddle
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Riley J Hodgson
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Ryan J Borrett
- SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, Western Australia, 6150, Australia
| | - Stella Brachmann
- University of Waikato Te Whare Wananga o Waikato Gate 1, Knighton Road, Hamilton, 3240, New Zealand
| | - Tarryn C Davies
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Todd E Erickson
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, Kattidj Close, Kings Park, Western Australia, 6005, Australia
- Centre for Engineering Innovation, School of Agriculture and Environment, The University of Western Australia, Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Miriam Muñoz-Rojas
- Department of Plant Biology and Ecology, University of Seville, C. San Fernando, Sevilla, Spain
- School of Biological, Earth and Environmental Sciences, Centre for Ecosystem Science, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Jake M Robinson
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Carl D Watson
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Siegfried L Krauss
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, Kattidj Close, Kings Park, Western Australia, 6005, Australia
- School of Biological Sciences, The University of Western Australia, Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
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7
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Hale B, Watts C, Conatser M, Brown E, Wijeratne AJ. Fine-scale characterization of the soybean rhizosphere microbiome via synthetic long reads and avidity sequencing. ENVIRONMENTAL MICROBIOME 2024; 19:46. [PMID: 38997772 PMCID: PMC11241880 DOI: 10.1186/s40793-024-00590-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND The rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, and environmental factors. While such plasticity is a well-evidenced determinant of host health, individual and community-level microbial activity within the rhizosphere remain poorly understood, due in part to the insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) to derive ecological inferences with practical application. To this end, the present study coupled synthetic long-read technology with avidity sequencing to investigate eukaryotic and prokaryotic microbiome dynamics within the soybean (Glycine max) rhizosphere under field conditions. RESULTS Synthetic long-read sequencing permitted de novo reconstruction of the entire 18S-ITS1-ITS2 region of the eukaryotic rRNA operon as well as all nine hypervariable regions of the 16S rRNA gene. All full-length, mapped eukaryotic amplicon sequence variants displayed genus-level classification, and 44.77% achieved species-level classification. The resultant eukaryotic microbiome encompassed five kingdoms (19 genera) of protists in addition to fungi - a depth unattainable with conventional short-read methods. In the prokaryotic fraction, every full-length, mapped amplicon sequence variant was resolved at the species level, and 23.13% at the strain level. Thirteen species of Bradyrhizobium were thereby distinguished in the prokaryotic microbiome, with strain-level identification of the two Bradyrhizobium species most reported to nodulate soybean. Moreover, the applied methodology delineated structural and compositional dynamism in response to experimental parameters (i.e., growth stage, cultivar, and biostimulant application), unveiled a saprotroph-rich core microbiome, provided empirical evidence for host selection of mutualistic taxa, and identified key microbial co-occurrence network members likely associated with edaphic and agronomic properties. CONCLUSIONS This study is the first to combine synthetic long-read technology and avidity sequencing to profile both eukaryotic and prokaryotic fractions of a plant-associated microbiome. Findings herein provide an unparalleled taxonomic resolution of the soybean rhizosphere microbiota and represent significant biological and technological advancements in crop microbiome research.
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Affiliation(s)
- Brett Hale
- AgriGro Incorporated, Doniphan, MO, USA
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA
- College of Science and Mathematics, Arkansas State University, State University, AR, USA
| | - Caitlin Watts
- College of Agriculture, Arkansas State University, State University, AR, USA
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthew Conatser
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Edward Brown
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Asela J Wijeratne
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA.
- College of Science and Mathematics, Arkansas State University, State University, AR, USA.
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8
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Tang B, Man J, Lehmann A, Rillig MC. Arbuscular mycorrhizal fungi attenuate negative impact of drought on soil functions. GLOBAL CHANGE BIOLOGY 2024; 30:e17409. [PMID: 38978455 DOI: 10.1111/gcb.17409] [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: 02/21/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/10/2024]
Abstract
Although positive effects of arbuscular mycorrhizal (AM) fungi on plant performance under drought have been well documented, how AM fungi regulate soil functions and multifunctionality requires further investigation. In this study, we first performed a meta-analysis to test the potential role of AM fungi in maintaining soil functions under drought. Then, we conducted a greenhouse experiment, using a pair of hyphal ingrowth cores to spatially separate the growth of AM fungal hyphae and plant roots, to further investigate the effects of AM fungi on soil multifunctionality and its resistance against drought. Our meta-analysis showed that AM fungi promote multiple soil functions, including soil aggregation, microbial biomass and activities of soil enzymes related to nutrient cycling. The greenhouse experiment further demonstrated that AM fungi attenuate the negative impact of drought on these soil functions and thus multifunctionality, therefore, increasing their resistance against drought. Moreover, this buffering effect of AM fungi persists across different frequencies of water supply and plant species. These findings highlight the unique role of AM fungi in maintaining multiple soil functions by mitigating the negative impact of drought. Our study highlights the importance of AM fungi as a nature-based solution to sustaining multiple soil functions in a world where drought events are intensifying.
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Affiliation(s)
- Bo Tang
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Jing Man
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Anika Lehmann
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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9
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Li C, Chen X, Jia Z, Zhai L, Zhang B, Grüters U, Ma S, Qian J, Liu X, Zhang J, Müller C. Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities. Nat Ecol Evol 2024; 8:1270-1284. [PMID: 38849504 DOI: 10.1038/s41559-024-02437-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/13/2024] [Indexed: 06/09/2024]
Abstract
Microbial inoculation involves transplanting microorganisms from their natural habitat to new plants or soils to improve plant performance, and it is being increasingly used in agriculture and ecological restoration. However, microbial inoculants can invade and alter the composition of native microbial communities; thus, a comprehensive analysis is urgently needed to understand the overall impact of microbial inoculants on the biomass, diversity, structure and network complexity of native communities. Here we provide a meta-analysis of 335 studies revealing a positive effect of microbial inoculants on soil microbial biomass. This positive effect was weakened by environmental stress and enhanced by the use of fertilizers and native inoculants. Although microbial inoculants did not alter microbial diversity, they induced major changes in the structure and bacterial composition of soil microbial communities, reducing the complexity of bacterial networks and increasing network stability. Finally, higher initial levels of soil nutrients amplified the positive impact of microbial inoculants on fungal biomass, actinobacterial biomass, microbial biomass carbon and microbial biomass nitrogen. Together, our results highlight the positive effects of microbial inoculants on soil microbial biomass, emphasizing the benefits of native inoculants and the important regulatory roles of soil nutrient levels and environmental stress.
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Affiliation(s)
- Chong Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
| | - Xinli Chen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Zhaohui Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Lu Zhai
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK, USA
| | - Bo Zhang
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Uwe Grüters
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
| | - Shilin Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Jing Qian
- Yangzhou China Grand Canal Museum, Yangzhou, China
| | - Xin Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China.
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China.
| | - Christoph Müller
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Liebig Centre for Agroecology and Climate Impact Research, Justus-Liebig University, Giessen, Germany
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10
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Kayiranga A, Isabwe A, Yao H, Shangguan H, Coulibaly JLK, Breed M, Sun X. Distribution patterns of soil bacteria, fungi, and protists emerge from distinct assembly processes across subcommunities. Ecol Evol 2024; 14:e11672. [PMID: 38988351 PMCID: PMC11236429 DOI: 10.1002/ece3.11672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 07/12/2024] Open
Abstract
Environmental change exerts a profound effect on soil microbial domains-including bacteria, fungi, and protists-that each perform vital ecological processes. While these microbial domains are ubiquitous and extremely diverse, little is known about how they respond to environmental changes in urban soil ecosystems and what ecological processes shape them. Here we investigated the community assembly processes governing bacteria, fungi, and protists through the lens of four distinct subcommunities: abundant, conditionally rare, conditionally abundant, and rare taxa. We show that transient taxa, including the conditionally rare and conditionally rare or abundant taxa, were the predominant subcommunities. Deterministic processes (e.g., environmental filtering) had major roles in structuring all subcommunities of fungi, as well as conditionally rare and abundant protists. Stochastic processes had strong effects in structuring all subcommunities of bacteria (except rare taxa) and conditionally rare protists. Overall, our study underscores the importance of complementing the traditional taxonomy of microbial domains with the subcommunity approach when investigating microbial communities in urban soil ecosystems.
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Affiliation(s)
- Alexis Kayiranga
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Alain Isabwe
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
| | - Haifeng Yao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Huayuan Shangguan
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Justin Louis Kafana Coulibaly
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Martin Breed
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
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11
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Gao C, Bezemer TM, de Vries FT, van Bodegom PM. Trade-offs in soil microbial functions and soil health in agroecosystems. Trends Ecol Evol 2024:S0169-5347(24)00138-1. [PMID: 38910081 DOI: 10.1016/j.tree.2024.05.013] [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: 01/31/2024] [Revised: 04/24/2024] [Accepted: 05/31/2024] [Indexed: 06/25/2024]
Abstract
Soil microbial communities play pivotal roles in maintaining soil health in agroecosystems. However, how the delivery of multiple microbial functions in agroecosystems is maintained remains poorly understood. This may put us at risk of incurring unexpected trade-offs between soil functions. We elucidate how interactions between soil microbes can lead to trade-offs in the functioning of agricultural soils. Interactions within soil microbial communities can result in not only positive but also neutral and negative relationships among soil functions. Altering soil conditions through soil health-improving agricultural management can alleviate these functional trade-offs by promoting the diversity and interrelationships of soil microbes, which can help to achieve more productive and sustainable agroecosystems.
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Affiliation(s)
- Chenguang Gao
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands.
| | - Thiemo Martijn Bezemer
- Institute of Biology, Above-Belowground Interactions Group, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1090 GE Amsterdam, The Netherlands
| | - Peter M van Bodegom
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands
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12
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Angst G, Potapov A, Joly FX, Angst Š, Frouz J, Ganault P, Eisenhauer N. Conceptualizing soil fauna effects on labile and stabilized soil organic matter. Nat Commun 2024; 15:5005. [PMID: 38886372 PMCID: PMC11183196 DOI: 10.1038/s41467-024-49240-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024] Open
Abstract
Fauna is highly abundant and diverse in soils worldwide, but surprisingly little is known about how it affects soil organic matter stabilization. Here, we review how the ecological strategies of a multitude of soil faunal taxa can affect the formation and persistence of labile (particulate organic matter, POM) and stabilized soil organic matter (mineral-associated organic matter, MAOM). We propose three major mechanisms - transformation, translocation, and grazing on microorganisms - by which soil fauna alters factors deemed essential in the formation of POM and MAOM, including the quantity and decomposability of organic matter, soil mineralogy, and the abundance, location, and composition of the microbial community. Determining the relevance of these mechanisms to POM and MAOM formation in cross-disciplinary studies that cover individual taxa and more complex faunal communities, and employ physical fractionation, isotopic, and microbiological approaches is essential to advance concepts, models, and policies focused on soil organic matter and effectively manage soils as carbon sinks, nutrient stores, and providers of food.
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Affiliation(s)
- Gerrit Angst
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
- Institute of Biology, Leipzig University, Leipzig, Germany.
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & Biogeochemistry, Na Sádkách 7, 37005, České Budějovice, Czech Republic.
- Institute for Environmental Studies, Charles University, Benátská 2, Praha 2, Prague, Czech Republic.
| | - Anton Potapov
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Senckenberg Museum für Naturkunde Görlitz, Postfach 300 154, 02806, Görlitz, Germany
| | - François-Xavier Joly
- Eco&Sols, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Šárka Angst
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Jan Frouz
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & Biogeochemistry, Na Sádkách 7, 37005, České Budějovice, Czech Republic
- Institute for Environmental Studies, Charles University, Benátská 2, Praha 2, Prague, Czech Republic
| | - Pierre Ganault
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
- Laboratoire ECODIV USC INRAE 1499, Université de Rouen Normandie, FR CNRS 3730 SCALE, Rouen, France
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
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13
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Gao C, Bezemer TM, van Bodegom PM, Baldrian P, Kohout P, Mancinelli R, van der Hagen H, Soudzilovskaia NA. Fungal communities are passengers in community development of dune ecosystems, while bacteria are not. Ecology 2024; 105:e4312. [PMID: 38666421 DOI: 10.1002/ecy.4312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/14/2024] [Indexed: 06/04/2024]
Abstract
An increasing number of studies of above-belowground interactions provide a fundamental basis for our understanding of the coexistence between plant and soil communities. However, we lack empirical evidence to understand the directionality of drivers of plant and soil communities under natural conditions: 'Are soil microorganisms driving plant community functioning or do they adapt to the plant community?' In a field experiment in an early successional dune ecosystem, we manipulated soil communities by adding living (i.e., natural microbial communities) and sterile soil inocula, originating from natural ecosystems, and examined the annual responses of soil and plant communities. The experimental manipulations had a persistent effect on the soil microbial community with divergent impacts for living and sterile soil inocula. The plant community was also affected by soil inoculation, but there was no difference between the impacts of living and sterile inocula. We also observed an increasing convergence of plant and soil microbial composition over time. Our results show that alterations in soil abiotic and biotic conditions have long-term effects on the composition of both plant and soil microbial communities. Importantly, our study provides direct evidence that soil microorganisms are not "drivers" of plant community dynamics. We found that soil fungi and bacteria manifest different community assemblies in response to treatments. Soil fungi act as "passengers," that is, soil microorganisms reflect plant community dynamics but do not alter it, whereas soil bacteria are neither "drivers" nor "passengers" of plant community dynamics in early successional ecosystems. These results are critical for understanding the community assembly of plant and soil microbial communities under natural conditions and are directly relevant for ecosystem management and restoration.
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Affiliation(s)
- Chenguang Gao
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - T Martijn Bezemer
- Institute of Biology, Above-Belowground Interactions Group, Leiden University, Leiden, The Netherlands
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Peter M van Bodegom
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Riccardo Mancinelli
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | | | - Nadejda A Soudzilovskaia
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
- Center for Environmental Sciences, Hasselt University, Hasselt, Belgium
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14
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Berlinches de Gea A, Geisen S, Grootjans F, Wilschut RA, Schwelm A. Species-specific predation determines the feeding impacts of six soil protist species on bacterial and eukaryotic prey. Eur J Protistol 2024; 94:126090. [PMID: 38795654 DOI: 10.1016/j.ejop.2024.126090] [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: 12/15/2023] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/28/2024]
Abstract
Predatory protists play a central role in nutrient cycling and are involved in other ecosystem functions by predating the microbiome. While most soil predatory protist species arguably are bacterivorous, some protist species can prey on eukaryotes. However, studies about soil protist feeding mainly focused on bacteria as prey and rarely tested both bacteria and eukaryotes as potential prey. In this study, we aimed to decipher soil predator-prey interactions of three amoebozoan and three heterolobosean soil protists and potential bacterial (Escherichia coli; 0.5-1.5 µm), fungal (Saccharomyces cerevisiae; 5-7 µm) and protist (Plasmodiophora brassicae; 3-5 µm) prey, either as individual prey or in all their combinations. We related protist performance (relative abundance) and prey consumption (qPCR) to the protist phylogenetic group and volume. We showed that for the six soil protist predators, the most suitable prey was E. coli, but some species also grew on P. brassicae or S. cerevisiae. While protist relative abundances and growth rates depended on prey type in a protist species-specific manner, phylogenetic groups and volume affected prey consumption. Yet we conclude that protist feeding patterns are mainly species-specific and that some known bacterivores might be more generalist than expected, even preying on eukaryotic plant pathogens such as P. brassicae.
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Affiliation(s)
- Alejandro Berlinches de Gea
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Franka Grootjans
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Rutger A Wilschut
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Arne Schwelm
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands; TEAGASC - The Agriculture and Food Development Authority Department of Crops, Environment & Land Use, Wexford, Ireland.
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15
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Zhang R, Ye Z, Guo X, Yang Y, Li G. Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater. ENVIRONMENT INTERNATIONAL 2024; 188:108755. [PMID: 38772206 DOI: 10.1016/j.envint.2024.108755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
The rapid advance in shotgun metagenome sequencing has enabled us to identify uncultivated functional microorganisms in polluted environments. While aerobic petrochemical-degrading pathways have been extensively studied, the anaerobic mechanisms remain less explored. Here, we conducted a study at a petrochemical-polluted groundwater site in Henan Province, Central China. A total of twelve groundwater monitoring wells were installed to collect groundwater samples. Benzene appeared to be the predominant pollutant, detected in 10 out of 12 samples, with concentrations ranging from 1.4 μg/L to 5,280 μg/L. Due to the low aquifer permeability, pollutant migration occurred slowly, resulting in relatively low benzene concentrations downstream within the heavily polluted area. Deep metagenome sequencing revealed Proteobacteria as the dominant phylum, accounting for over 63 % of total abundances. Microbial α-diversity was low in heavily polluted samples, with community compositions substantially differing from those in lightly polluted samples. dmpK encoding the phenol/toluene 2-monooxygenase was detected across all samples, while the dioxygenase bedC1 was not detected, suggesting that aerobic benzene degradation might occur through monooxygenation. Sequence assembly and binning yielded 350 high-quality metagenome-assembled genomes (MAGs), with 30 MAGs harboring functional genes associated with aerobic or anaerobic benzene degradation. About 80 % of MAGs harboring functional genes associated with anaerobic benzene degradation remained taxonomically unclassified at the genus level, suggesting that our current database coverage of anaerobic benzene-degrading microorganisms is very limited. Furthermore, two genes integral to anaerobic benzene metabolism, i.e, benzoyl-CoA reductase (bamB) and glutaryl-CoA dehydrogenase (acd), were not annotated by metagenome functional analyses but were identified within the MAGs, signifying the importance of integrating both contig-based and MAG-based approaches. Together, our efforts of functional annotation and metagenome binning generate a robust blueprint of microbial functional potentials in petrochemical-polluted groundwater, which is crucial for designing proficient bioremediation strategies.
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Affiliation(s)
- Ruihuan Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhencheng Ye
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Guanghe Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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16
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Zhao Q, Bertolli S, Park YJ, Tan Y, Cutler KJ, Srinivas P, Asfahl KL, Fonesca-García C, Gallagher LA, Li Y, Wang Y, Coleman-Derr D, DiMaio F, Zhang D, Peterson SB, Veesler D, Mougous JD. Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 2024; 629:165-173. [PMID: 38632398 PMCID: PMC11062931 DOI: 10.1038/s41586-024-07298-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive1. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species1,2. Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein. A cryo-electron microscopy structure of these particles reveals an extended stalk topped by a ringed crown comprising the toxin repeats scaffolding five lectin-tipped spokes, which led us to name them umbrella particles. Streptomyces coelicolor encodes three umbrella particles with distinct toxin and lectin composition. Notably, supernatant containing these toxins specifically and potently inhibits the growth of select Streptomyces species from among a diverse collection of bacteria screened. For one target, Streptomyces griseus, inhibition relies on a single toxin and that intoxication manifests as rapid cessation of vegetative hyphal growth. Our data show that Streptomyces umbrella particles mediate competition among vegetative mycelia of related species, a function distinct from small-molecule antibiotics, which are produced at the onset of reproductive growth and act broadly3,4. Sequence analyses suggest that this role of umbrella particles extends beyond Streptomyces, as we identified umbrella loci in nearly 1,000 species across Actinobacteria.
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Affiliation(s)
- Qinqin Zhao
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Savannah Bertolli
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Yongjun Tan
- Department of Biology, St Louis University, St Louis, MO, USA
| | - Kevin J Cutler
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Pooja Srinivas
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kyle L Asfahl
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA
| | - Citlali Fonesca-García
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Larry A Gallagher
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaqiao Li
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Devin Coleman-Derr
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Dapeng Zhang
- Department of Biology, St Louis University, St Louis, MO, USA
- Program of Bioinformatic and Computational Biology, St Louis University, St Louis, MO, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - David Veesler
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA.
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17
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Loos D, Filho APDC, Dutilh BE, Barber AE, Panagiotou G. A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists. Cell Rep 2024; 43:114046. [PMID: 38581683 DOI: 10.1016/j.celrep.2024.114046] [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: 07/28/2023] [Revised: 12/22/2023] [Accepted: 03/19/2024] [Indexed: 04/08/2024] Open
Abstract
Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.
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Affiliation(s)
- Daniel Loos
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Ailton Pereira da Costa Filho
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Bas E Dutilh
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany; Institute of Biodiversity, Friedrich Schiller University, Jena, Germany; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Amelia E Barber
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany.
| | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
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18
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Dauphin B, Peter M. Tracking signatures of selection in natural populations of ectomycorrhizal fungi - progress, challenges, and prospects. THE NEW PHYTOLOGIST 2024; 242:384-388. [PMID: 38268341 DOI: 10.1111/nph.19553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/11/2024] [Indexed: 01/26/2024]
Affiliation(s)
- Benjamin Dauphin
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Martina Peter
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
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19
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Anthony MA, Tedersoo L, De Vos B, Croisé L, Meesenburg H, Wagner M, Andreae H, Jacob F, Lech P, Kowalska A, Greve M, Popova G, Frey B, Gessler A, Schaub M, Ferretti M, Waldner P, Calatayud V, Canullo R, Papitto G, Marinšek A, Ingerslev M, Vesterdal L, Rautio P, Meissner H, Timmermann V, Dettwiler M, Eickenscheidt N, Schmitz A, Van Tiel N, Crowther TW, Averill C. Fungal community composition predicts forest carbon storage at a continental scale. Nat Commun 2024; 15:2385. [PMID: 38493170 PMCID: PMC10944544 DOI: 10.1038/s41467-024-46792-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.
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Affiliation(s)
- Mark A Anthony
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland.
- Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Bruno De Vos
- Environment & Climate Unit, Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Luc Croisé
- French National Forest Office, Fontainebleau, France
| | | | - Markus Wagner
- Northwest German Forest Research Institute, Göttingen, Germany
| | | | - Frank Jacob
- Sachsenforst State Forest, Pirna OT Graupa, Germany
| | - Paweł Lech
- Forest Research Institute, Sękocin Stary, Poland
| | | | - Martin Greve
- Research Institute for Forest Ecology and Forestry, Trippstadt, Germany
| | - Genoveva Popova
- Executive Environmental Agency at the Ministry of Environment and Water, Sofia, Bulgaria
| | - Beat Frey
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland
| | - Arthur Gessler
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland
| | - Marcus Schaub
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland
| | - Marco Ferretti
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland
| | - Peter Waldner
- Swiss Federal Institute for Forests, Snow, and the Landscape Research (WSL), Birmensdorf, Switzerland
| | | | - Roberto Canullo
- Department of Plant Diversity and Ecosystem Management, University of Camerino, Camerino, Italy
| | - Giancarlo Papitto
- Arma dei Carabinieri Forestry Environmental and Agri-food protection Units, Rome, Italy
| | | | - Morten Ingerslev
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, Denmark
| | - Lars Vesterdal
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, Denmark
| | - Pasi Rautio
- Natural Resources Institute Finland, Rovaniemi, Finland
| | - Helge Meissner
- Division of Forest and Forest Resources, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Volkmar Timmermann
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Mike Dettwiler
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Nadine Eickenscheidt
- State Agency for Nature, Environment and Consumer Protection of North Rhine-Westphalia, Recklinghausen, Germany
| | - Andreas Schmitz
- State Agency for Nature, Environment and Consumer Protection of North Rhine-Westphalia, Recklinghausen, Germany
- Thuenen Institut of Forest Ecosystems, 16225, Eberswalde, Germany
| | - Nina Van Tiel
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Environmetnal Computational Science and Earth Observation Laboratory, EPFL, Lausanne, Switzerland
| | - Thomas W Crowther
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Colin Averill
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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20
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Lan Y, Luo X, Fan X, Wang G, Zheng S, Shi K. Arsenite Mediates Selenite Resistance and Reduction in Enterobacter sp. Z1, Thereby Enhancing Bacterial Survival in Selenium Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4204-4213. [PMID: 38373240 DOI: 10.1021/acs.est.3c08346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Arsenic (As) is widely present in the environment, and virtually all bacteria possess a conserved ars operon to resist As toxicity. High selenium (Se) concentrations tend to be cytotoxic. Se has an uneven regional distribution and is added to mitigate As contamination in Se-deficient areas. However, the bacterial response to exogenous Se remains poorly understood. Herein, we found that As(III) presence was crucial for Enterobacter sp. Z1 to develop resistance against Se(IV). Se(IV) reduction served as a detoxification mechanism in bacteria, and our results demonstrated an increase in the production of Se nanoparticles (SeNPs) in the presence of As(III). Tandem mass tag proteomics analysis revealed that the induction of As(III) activated the inositol phosphate, butanoyl-CoA/dodecanoyl-CoA, TCA cycle, and tyrosine metabolism pathways, thereby enhancing bacterial metabolism to resist Se(IV). Additionally, arsHRBC, sdr-mdr, purHD, and grxA were activated to participate in the reduction of Se(IV) into SeNPs. Our findings provide innovative perspectives for exploring As-induced Se biotransformation in prokaryotes.
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Affiliation(s)
- Yan Lan
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiong Luo
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xia Fan
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang 438000, Hubei, China
| | - Gejiao Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shixue Zheng
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kaixiang Shi
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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21
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Birnbaum C, Dearnaley J, Egidi E, Frew A, Hopkins A, Powell J, Aguilar-Trigueros C, Liddicoat C, Albornoz F, Heuck MK, Dadzie FA, Florence L, Singh P, Mansfield T, Rajapaksha K, Stewart J, Rallo P, Peddle SD, Chiarenza G. Integrating soil microbial communities into fundamental ecology, conservation, and restoration: examples from Australia: Ecological Society of Australia (ESA) and Society of Conservation Biology Oceania (SCBO) joint Conference, Wollongong, Australia, 28 November-2 December 2022. THE NEW PHYTOLOGIST 2024; 241:974-981. [PMID: 38098200 DOI: 10.1111/nph.19440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Affiliation(s)
- Christina Birnbaum
- School of Agriculture & Environmental Science, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
- Center for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4370, Australia
| | - John Dearnaley
- School of Agriculture & Environmental Science, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
- Center for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4370, Australia
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Adam Frew
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Anna Hopkins
- School of Science, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Jeff Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Carlos Aguilar-Trigueros
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Sturt Road Bedford Park, Adelaide, SA, 5042, Australia
- School of Public Health, The University of Adelaide, Adelaide, SA, 5005, Australia
| | | | - Meike K Heuck
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Frederick A Dadzie
- School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Luke Florence
- Department of Environment & Genetics, La Trobe University, Science Drive, Bundoora, VIC, 3086, Australia
| | - Pankaj Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6000, Australia
| | - Tomas Mansfield
- Harry Butler Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Kumari Rajapaksha
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Jana Stewart
- School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Paola Rallo
- Department of Terrestrial Ecology, Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
| | - Shawn D Peddle
- College of Science and Engineering, Flinders University, Sturt Road Bedford Park, Adelaide, SA, 5042, Australia
| | - Giancarlo Chiarenza
- Evolution and Ecology Research Center, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
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22
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Zhang C, de Pasquale S, Hartman K, Stanley CE, Berendsen RL, van der Heijden MGA. The microbial contribution to litter decomposition and plant growth. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13205. [PMID: 38018445 PMCID: PMC10866077 DOI: 10.1111/1758-2229.13205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/06/2023] [Indexed: 11/30/2023]
Abstract
Soil and plant roots are colonized by highly complex and diverse communities of microbes. It has been proposed that bacteria and fungi have synergistic effects on litter decomposition, but experimental evidence supporting this claim is weak. In this study, we manipulated the composition of two microbial kingdoms (Bacteria and Fungi) in experimental microcosms. In microcosms that were inoculated with fungi, litter loss was 47% higher than in microcosms that were not inoculated or only inoculated with bacteria. Combined inoculation with both bacteria and fungi did not significantly enhance decomposition compared with the fungi-only treatments, and, as such, we found no evidence for complementary effects using our experimental setup. Inoculation with fungi also had a positive impact on plant growth after 4 and 8 weeks (480% and 710% growth stimulation, respectively). After 16 weeks, plant biomass was highest in microcosms where both bacteria and fungi were present pointing to fungal-bacterial complementarity in stimulating plant growth. Overall, this study suggests that fungi are the main decomposers of plant litter and that the inoculated fungi contribute to plant growth in our experimental system.
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Affiliation(s)
- Changfeng Zhang
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Simone de Pasquale
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Kyle Hartman
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Claire E. Stanley
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Roeland L. Berendsen
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
| | - Marcel G. A. van der Heijden
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
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23
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Brown GG, Demetrio WC, Gabriac Q, Pasini A, Korasaki V, Oliveira LJ, dos Santos JC, Torres E, Galerani PR, Gazziero DLP, Benito NP, Nunes DH, Santos A, Ferreira T, Nadolny HS, Bartz MLC, Maschio W, Dudas RT, Zagatto MRG, Niva CC, Clasen LA, Sautter KD, Froufe LC, Seoane CES, de Moraes A, James S, Alberton O, Brandão Júnior O, Saraiva O, Garcia A, Oliveira E, César RM, Corrêa-Ferreira BS, Bruz LSM, da Silva E, Cardoso GBX, Lavelle P, Velásquez E, Cremonesi M, Parron LM, Baggio AJ, Neves E, Hungria M, Campos TA, da Silva VL, Reissmann CB, Conrado AC, Bouillet JPD, Gonçalves JLM, Brandani CB, Viani RAG, Paula RR, Laclau JP, Peña-Venegas CP, Peres C, Decaëns T, Pey B, Eisenhauer N, Cooper M, Mathieu J. Soil macrofauna communities in Brazilian land-use systems. Biodivers Data J 2024; 12:e115000. [PMID: 38314121 PMCID: PMC10837794 DOI: 10.3897/bdj.12.e115000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/07/2024] [Indexed: 02/06/2024] Open
Abstract
Background Soil animal communities include more than 40 higher-order taxa, representing over 23% of all described species. These animals have a wide range of feeding sources and contribute to several important soil functions and ecosystem services. Although many studies have assessed macroinvertebrate communities in Brazil, few of them have been published in journals and even fewer have made the data openly available for consultation and further use. As part of ongoing efforts to synthesise the global soil macrofauna communities and to increase the amount of openly-accessible data in GBIF and other repositories related to soil biodiversity, the present paper provides links to 29 soil macroinvertebrate datasets covering 42 soil fauna taxa, collected in various land-use systems in Brazil. A total of 83,085 georeferenced occurrences of these taxa are presented, based on quantitative estimates performed using a standardised sampling method commonly adopted worldwide to collect soil macrofauna populations, i.e. the TSBF (Tropical Soil Biology and Fertility Programme) protocol. This consists of digging soil monoliths of 25 x 25 cm area, with handsorting of the macroinvertebrates visible to the naked eye from the surface litter and from within the soil, typically in the upper 0-20 cm layer (but sometimes shallower, i.e. top 0-10 cm or deeper to 0-40 cm, depending on the site). The land-use systems included anthropogenic sites managed with agricultural systems (e.g. pastures, annual and perennial crops, agroforestry), as well as planted forests and native vegetation located mostly in the southern Brazilian State of Paraná (96 sites), with a few additional sites in the neighbouring states of São Paulo (21 sites) and Santa Catarina (five sites). Important metadata on soil properties, particularly soil chemical parameters (mainly pH, C, P, Ca, K, Mg, Al contents, exchangeable acidity, Cation Exchange Capacity, Base Saturation and, infrequently, total N), particle size distribution (mainly % sand, silt and clay) and, infrequently, soil moisture and bulk density, as well as on human management practices (land use and vegetation cover) are provided. These data will be particularly useful for those interested in estimating land-use change impacts on soil biodiversity and its implications for below-ground foodwebs, ecosystem functioning and ecosystem service delivery. New information Quantitative estimates are provided for 42 soil animal taxa, for two biodiversity hotspots: the Brazilian Atlantic Forest and Cerrado biomes. Data are provided at the individual monolith level, representing sampling events ranging from February 2001 up to September 2016 in 122 sampling sites and over 1800 samples, for a total of 83,085 ocurrences.
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Affiliation(s)
- George G. Brown
- Embrapa Florestas, Colombo, BrazilEmbrapa FlorestasColomboBrazil
- UFPR, Curitiba, BrazilUFPRCuritibaBrazil
| | | | | | - Amarildo Pasini
- Universidade Estadual de Londrina, Londrina, BrazilUniversidade Estadual de LondrinaLondrinaBrazil
| | - Vanesca Korasaki
- Universidade do Estado de Minas Gerais, Frutal, BrazilUniversidade do Estado de Minas GeraisFrutalBrazil
| | | | | | - Eleno Torres
- Embrapa Soja, Londrina, BrazilEmbrapa SojaLondrinaBrazil
| | | | | | - Norton P. Benito
- Embrapa Recursos Genéticos, Brasília, BrazilEmbrapa Recursos GenéticosBrasíliaBrazil
| | - Daiane H. Nunes
- Instituto Federal Catarinense, Camboriu, BrazilInstituto Federal CatarinenseCamboriuBrazil
| | - Alessandra Santos
- Universidade Federal do Paraná, Curitiba, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Talita Ferreira
- Universidade Federal do Paraná, Curitiba, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Herlon S. Nadolny
- Universidade Federal do Paraná, Curitiba, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | | | - Wagner Maschio
- Embrapa Florestas, Colombo, BrazilEmbrapa FlorestasColomboBrazil
| | - Rafaela T. Dudas
- Universidade Federal do Paraná, Curitiba, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Mauricio R. G. Zagatto
- DungTech Biofertilizantes Ltda, Piracicaba, BrazilDungTech Biofertilizantes LtdaPiracicabaBrazil
| | - Cintia C. Niva
- Embrapa Cerrados, Planaltina, BrazilEmbrapa CerradosPlanaltinaBrazil
| | - Lina A. Clasen
- University of Copenhagen, Copenhagen, DenmarkUniversity of CopenhagenCopenhagenDenmark
| | | | - Luis C.M. Froufe
- Embrapa Florestas, Colombo, BrazilEmbrapa FlorestasColomboBrazil
| | | | - Aníbal de Moraes
- Universidade Federal do Paraná, Curitiba, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Samuel James
- Maharishi University, Fairfield, United States of AmericaMaharishi UniversityFairfieldUnited States of America
| | - Odair Alberton
- Universidade Paranaense, Umuarama, BrazilUniversidade ParanaenseUmuaramaBrazil
| | | | - Odilon Saraiva
- Embrapa Soja, Londrina, BrazilEmbrapa SojaLondrinaBrazil
| | - Antonio Garcia
- Embrapa Soja, Londrina, BrazilEmbrapa SojaLondrinaBrazil
| | - Elma Oliveira
- Universidade Federal do Paraná, Curitiba, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Raul M. César
- Universidade Federal do Paraná, Curitiba, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | | | - Lilianne S. M. Bruz
- Universidade Federal do Paraná, Curitiba, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Elodie da Silva
- Embrapa Florestas, Colombo, BrazilEmbrapa FlorestasColomboBrazil
| | - Gilherme B. X. Cardoso
- Universidade Federal do Paraná, Curitiba, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Patrick Lavelle
- Université Pierre et Marie Curie (Paris 6), Paris, FranceUniversité Pierre et Marie Curie (Paris 6)ParisFrance
| | - Elena Velásquez
- Universidad Nacional de Colombia, Palmira, ColombiaUniversidad Nacional de ColombiaPalmiraColombia
| | - Marcus Cremonesi
- Federal University of Paraná (UFPR), Curitiba, BrazilFederal University of Paraná (UFPR)CuritibaBrazil
| | | | | | - Edinelson Neves
- Embrapa Florestas, Colombo, BrazilEmbrapa FlorestasColomboBrazil
| | | | - Thiago A. Campos
- Universidade Estadual de Londrina, Londrina, BrazilUniversidade Estadual de LondrinaLondrinaBrazil
| | - Vagner L. da Silva
- Universidad de la República, Montevidéo, UruguayUniversidad de la RepúblicaMontevidéoUruguay
| | - Carlos B. Reissmann
- Universidade Federal do Paraná, Curitiba, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Ana C. Conrado
- Universidade Federal do Paraná, Curitiba, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | | | | | - Carolina B. Brandani
- Texas A&M AgriLife, Amarillo, United States of AmericaTexas A&M AgriLifeAmarilloUnited States of America
| | - Ricardo A. G. Viani
- Universidade Federal de São Carlos, Araras, BrazilUniversidade Federal de São CarlosArarasBrazil
| | - Ranieri R. Paula
- Université du Québec, Chicoutimi, CanadaUniversité du QuébecChicoutimiCanada
| | | | | | - Carlos Peres
- University of East Anglia, Norwich, United KingdomUniversity of East AngliaNorwichUnited Kingdom
| | - Thibaud Decaëns
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, FranceCEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Benjamin Pey
- Université de Toulouse, Toulouse, FranceUniversité de ToulouseToulouseFrance
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, GermanyGerman Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzigGermany
- Leipzig University, Leipzig, GermanyLeipzig UniversityLeipzigGermany
| | - Miguel Cooper
- ESALQ-USP, Piracicaba, BrazilESALQ-USPPiracicabaBrazil
| | - Jérôme Mathieu
- Sorbonne Université, Paris, FranceSorbonne UniversitéParisFrance
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24
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Simon E, Guseva K, Darcy S, Alteio L, Pjevac P, Schmidt H, Jenab K, Ranits C, Kaiser C. Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates. THE ISME JOURNAL 2024; 18:wrae156. [PMID: 39105276 PMCID: PMC11325450 DOI: 10.1093/ismejo/wrae156] [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: 04/18/2024] [Revised: 06/29/2024] [Accepted: 08/05/2024] [Indexed: 08/07/2024]
Abstract
Soils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogeneous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre scale. In this study, we examined whether bacteria, archaea, and fungi organize into distinct communities in individual 2-mm-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate communities displayed exceptionally high beta-diversity, with 3-4 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20%-30% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils.
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Affiliation(s)
- Eva Simon
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Ksenia Guseva
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Sean Darcy
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Lauren Alteio
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, 3430 Tulln, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Kian Jenab
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Christian Ranits
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
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Banerjee S, Zhao C, Garland G, Edlinger A, García-Palacios P, Romdhane S, Degrune F, Pescador DS, Herzog C, Camuy-Velez LA, Bascompte J, Hallin S, Philippot L, Maestre FT, Rillig MC, van der Heijden MGA. Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe. Nat Commun 2024; 15:327. [PMID: 38184663 PMCID: PMC10771452 DOI: 10.1038/s41467-023-44073-6] [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: 03/01/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024] Open
Abstract
Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.
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Affiliation(s)
- Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA.
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
| | - Cheng Zhao
- ETH Zurich, Institute for Environmental Decisions, 8092, Zurich, Switzerland
| | - Gina Garland
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Anna Edlinger
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
- Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3, 6708 PB, Wageningen, The Netherlands
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland
| | - Sana Romdhane
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Florine Degrune
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
| | - David S Pescador
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28940, Madrid, Spain
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933, Móstoles, Spain
| | - Chantal Herzog
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Lennel A Camuy-Velez
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Jordi Bascompte
- University of Zurich, Department of Evolutionary Biology and Environmental Studies, 8057, Zurich, Switzerland
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 750 07, Uppsala, Sweden
| | - Laurent Philippot
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Fernando T Maestre
- Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente del Raspeig, Alicante, Spain
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente, del Raspeig, Alicante, Spain
| | - Matthias C Rillig
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland.
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Berrios L, Venturini AM, Ansell TB, Tok E, Johnson W, Willing CE, Peay KG. Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses. ISME COMMUNICATIONS 2024; 4:ycae104. [PMID: 39188310 PMCID: PMC11346365 DOI: 10.1093/ismeco/ycae104] [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: 04/16/2024] [Revised: 07/15/2024] [Accepted: 08/06/2024] [Indexed: 08/28/2024]
Abstract
Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, United States
| | - Andressa M Venturini
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, United States
| | - Tillson Bertie Ansell
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, United States
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, United States
| | - Esther Tok
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, United States
| | - William Johnson
- Oceans Department, Hopkins Marine Station of Stanford University, 120 Ocean View Blvd., Pacific Grove, CA 93950, United States
| | - Claire E Willing
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, United States
| | - Kabir G Peay
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, United States
- Department of Earth System Science, Stanford University, Stanford, CA 94305, United States
- Woods Institute for the Environment, Stanford University, Stanford, CA 94305, United States
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27
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Gepts P. Biocultural diversity and crop improvement. Emerg Top Life Sci 2023; 7:ETLS20230067. [PMID: 38084755 PMCID: PMC10754339 DOI: 10.1042/etls20230067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Biocultural diversity is the ever-evolving and irreplaceable sum total of all living organisms inhabiting the Earth. It plays a significant role in sustainable productivity and ecosystem services that benefit humanity and is closely allied with human cultural diversity. Despite its essentiality, biodiversity is seriously threatened by the insatiable and inequitable human exploitation of the Earth's resources. One of the benefits of biodiversity is its utilization in crop improvement, including cropping improvement (agronomic cultivation practices) and genetic improvement (plant breeding). Crop improvement has tended to decrease agricultural biodiversity since the origins of agriculture, but awareness of this situation can reverse this negative trend. Cropping improvement can strive to use more diverse cultivars and a broader complement of crops on farms and in landscapes. It can also focus on underutilized crops, including legumes. Genetic improvement can access a broader range of biodiversity sources and, with the assistance of modern breeding tools like genomics, can facilitate the introduction of additional characteristics that improve yield, mitigate environmental stresses, and restore, at least partially, lost crop biodiversity. The current legal framework covering biodiversity includes national intellectual property and international treaty instruments, which have tended to limit access and innovation to biodiversity. A global system of access and benefit sharing, encompassing digital sequence information, would benefit humanity but remains an elusive goal. The Kunming-Montréal Global Biodiversity Framework sets forth an ambitious set of targets and goals to be accomplished by 2030 and 2050, respectively, to protect and restore biocultural diversity, including agrobiodiversity.
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Affiliation(s)
- Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95616-8780, U.S.A
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Bardgett RD. The hidden majority in soil. Proc Natl Acad Sci U S A 2023; 120:e2312358120. [PMID: 37647365 PMCID: PMC10500176 DOI: 10.1073/pnas.2312358120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Affiliation(s)
- Richard D. Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, ManchesterM13 9PT, United Kingdom
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Youngblom MA, Imhoff MR, Smyth LM, Mohamed MA, Pepperell CS. Portrait of a generalist bacterium: pathoadaptation, metabolic specialization and extreme environments shape diversity of Staphylococcus saprophyticus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.18.553882. [PMID: 37645846 PMCID: PMC10462137 DOI: 10.1101/2023.08.18.553882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Staphylococcus saprophyticus is a Gram-positive, coagulase-negative staphylococcus found in diverse environments including soil and freshwater, meat, and dairy foods. S. saprophyticus is also an important cause of urinary tract infections (UTIs) in humans, and mastitis in cattle. However, the genetic determinants of virulence have not yet been identified, and it remains unclear whether there are distinct sub-populations adapted to human and animal hosts. Using a diverse sample of S. saprophyticus isolates from food, animals, environmental sources, and human infections, we characterized the population structure and diversity of global populations of S. saprophyticus . We found that divergence of the two major clades of S. saprophyticus is likely facilitated by barriers to horizontal gene transfer (HGT) and differences in metabolism. Using genome-wide association study (GWAS) tools we identified the first Type VII secretion system (T7SS) described in S. saprophyticus and its association with bovine mastitis. Finally, we found that in general, strains of S. saprophyticus from different niches are genetically similar with the exception of built environments, which function as a 'sink' for S. saprophyticus populations. This work increases our understanding of the ecology of S. saprophyticus and of the genomics of bacterial generalists. Data summary Raw sequencing data for newly sequenced S. saprophyticus isolates have been deposited to the NCBI SRA under the project accession PRJNA928770. A list of all genomes used in this work and their associated metadata are available in the supplementary material. Custom scripts used in the comparative genomics and GWAS analyses are available here: https://github.com/myoungblom/sapro_genomics . Impact statement It is not known whether human and cattle diseases caused by S. saprophyticus represent spillover events from a generalist adapted to survive in a range of environments, or whether the capacity to cause disease represents a specific adaptation. Seasonal cycles of S. saprophyticus UTIs and molecular epidemiological evidence suggest that these infections may be environmentally-acquired rather than via transmission from person to person. Using comparative genomics and genome wide association study tools, we found that S. saprophyticus appears adapted to inhabit a wide range of environments (generalist), with isolates from animals, food, natural environments and human infections being closely related. Bacteria that routinely switch environments, particularly between humans and animals, are of particular concern when it comes to the spread of antibiotic resistance from farm environments into human populations. This work provides a framework for comparative genomic analyses of bacterial generalists and furthers our understanding of how bacterial populations move between humans, animals, and the environment.
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