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Chevillon C, de Thoisy B, Rakestraw AW, Fast KM, Pechal JL, Picq S, Epelboin L, Le Turnier P, Dogbe M, Jordan HR, Sandel MW, Benbow ME, Guégan JF. Ecological and evolutionary perspectives advance understanding of mycobacterial diseases. THE LANCET. MICROBE 2024:100906. [PMID: 39116907 DOI: 10.1016/s2666-5247(24)00138-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 08/10/2024]
Abstract
Predicting the outbreak of infectious diseases and designing appropriate preventive health actions require interdisciplinary research into the processes that drive exposure to and transmission of disease agents. In the case of mycobacterial diseases, the epidemiological understanding of the scientific community hitherto was based on the clinical studies of infections in vertebrates. To evaluate the information gained by comprehensively accounting for the ecological and evolutionary constraints, we conducted literature searches assessing the role of mycobacteria interactions with non-vertebrate species in the origin of their pathogenicity and variations in disease risk. The reviewed literature challenges the current theory of person-to-person transmission for several mycobacterial infections. Furthermore, the findings suggest that diverse non-vertebrate organisms influence virulence, mediate transmission, and contribute to pathogen abundance in relation to vertebrate exposure. We advocate that an ecological and evolutionary framework provides novel insights to support a more comprehensive understanding of the prevention and management of diseases in vertebrates.
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Affiliation(s)
- Christine Chevillon
- MIVEGEC, Université de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Institut National de Recherches pour l'Agriculture, l'Alimentation et l'Environnement, Montpellier, France.
| | - Benoît de Thoisy
- Laboratoire des Interactions Virus Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana, France
| | - Alex W Rakestraw
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Kayla M Fast
- Department of Wildlife, Fisheries, and Aquaculture, Mississippi State University, MS, USA
| | - Jennifer L Pechal
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Sophie Picq
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Loïc Epelboin
- Unité des Maladies Infectieuses et Tropicales, Centre Hospitalier de Cayenne, Cayenne, French Guiana, France; Centre d'Investigation Clinique Antilles-Guyane, Inserm 1424, Centre Hospitalier de Cayenne, Cayenne, French Guiana, France
| | - Paul Le Turnier
- Unité des Maladies Infectieuses et Tropicales, Centre Hospitalier de Cayenne, Cayenne, French Guiana, France; Centre d'Investigation Clinique Antilles-Guyane, Inserm 1424, Centre Hospitalier de Cayenne, Cayenne, French Guiana, France
| | - Magdalene Dogbe
- Department of Biological Sciences, Mississippi State University, MS, USA
| | - Heather R Jordan
- Department of Biological Sciences, Mississippi State University, MS, USA
| | - Michael W Sandel
- Department of Wildlife, Fisheries, and Aquaculture, Mississippi State University, MS, USA; Forest and Wildlife Research Center, Mississippi State University, MS, USA
| | - Mark Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, USA; Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, USA; Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA; Agbioresearch, Michigan State University, East Lansing, MI, USA
| | - Jean-François Guégan
- MIVEGEC, Université de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Institut National de Recherches pour l'Agriculture, l'Alimentation et l'Environnement, Montpellier, France; Epidémiologie des maladies animales et zoonotiques, Université Clermont Auvergne, INRAE, VetAgro Sup, Saint-Genès-Champanelle, France; Epidémiologie des maladies animales et zoonotiques, Université de Lyon, INRAE, VetAgro Sup, Marcy l'Etoile, France
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Li C, Liu C, Li H, Liao H, Xu L, Yao M, Li X. The microgeo: an R package rapidly displays the biogeography of soil microbial community traits on maps. FEMS Microbiol Ecol 2024; 100:fiae087. [PMID: 38866720 PMCID: PMC11212663 DOI: 10.1093/femsec/fiae087] [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: 01/15/2024] [Revised: 04/26/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024] Open
Abstract
Many R packages provide statistical approaches for elucidating the diversity of soil microbes, yet they still struggle to visualize microbial traits on a geographical map. This creates challenges in interpreting microbial biogeography on a regional scale, especially when the spatial scale is large or the distribution of sampling sites is uneven. Here, we developed a lightweight, flexible, and user-friendly R package called microgeo. This package integrates many functions involved in reading, manipulating, and visualizing geographical boundary data; downloading spatial datasets; and calculating microbial traits and rendering them onto a geographical map using grid-based visualization, spatial interpolation, or machine learning. Using this R package, users can visualize any trait calculated by microgeo or other tools on a map and can analyze microbiome data in conjunction with metadata derived from a geographical map. In contrast to other R packages that statistically analyze microbiome data, microgeo provides more-intuitive approaches in illustrating the biogeography of soil microbes on a large geographical scale, serving as an important supplement to statistically driven comparisons and facilitating the biogeographic analysis of publicly accessible microbiome data at a large spatial scale in a more convenient and efficient manner. The microgeo R package can be installed from the Gitee (https://gitee.com/bioape/microgeo) and GitHub (https://github.com/ChaonanLi/microgeo) repositories. Detailed tutorials for the microgeo R package are available at https://chaonanli.github.io/microgeo.
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Affiliation(s)
- Chaonan Li
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
| | - Chi Liu
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hankang Li
- Department of Electrical Engineering and Computer Science, University of California, Irvine, CA 92697, United States
| | - Haijun Liao
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Normal University of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
| | - Lin Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Minjie Yao
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiangzhen Li
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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3
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Shi YC, Zheng YJ, Lin YC, Huang CH, Shen TL, Hsu YC, Lee BH. Investigation of the Microbial Diversity in the Oryza sativa Cultivation Environment and Artificial Transplantation of Microorganisms to Improve Sustainable Mycobiota. J Fungi (Basel) 2024; 10:412. [PMID: 38921398 PMCID: PMC11205129 DOI: 10.3390/jof10060412] [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: 05/07/2024] [Revised: 05/31/2024] [Accepted: 06/02/2024] [Indexed: 06/27/2024] Open
Abstract
Rice straw is not easy to decompose, it takes a long time to compost, and the anaerobic bacteria involved in the decomposition process produce a large amount of carbon dioxide (CO2), indicating that applications for rice straw need to be developed. Recycling rice straw in agricultural crops is an opportunity to increase the sustainability of grain production. Several studies have shown that the probiotic population gradually decreases in the soil, leading to an increased risk of plant diseases and decreased biomass yield. Because the microorganisms in the soil are related to the growth of plants, when the soil microbial community is imbalanced it seriously affects plant growth. We investigated the feasibility of using composted rice stalks to artificially cultivate microorganisms obtained from the Oryza sativa-planted environment for analyzing the mycobiota and evaluating applications for sustainable agriculture. Microbes obtained from the water-submerged part (group-A) and soil part (group-B) of O. sativa were cultured in an artificial medium, and the microbial diversity was analyzed with internal transcribed spacer sequencing. Paddy field soil was mixed with fermented paddy straw compost, and the microbes obtained from the soil used for O. sativa planting were designated as group-C. The paddy fields transplanted with artificially cultured microbes from group-A were designated as group-D and those from group-B were designated as group-E. We found that fungi and yeasts can be cultured in groups-A and -B. These microbes altered the soil mycobiota in the paddy fields after transplantation in groups-D and -E compared to groups-A and -B. Development in O. sativa post treatment with microbial transplantation was observed in the groups-D and -E compared to group-C. These results showed that artificially cultured microorganisms could be efficiently transplanted into the soil and improve the mycobiota. Phytohormones were involved in improving O. sativa growth and rice yield via the submerged part-derived microbial medium (group-D) or the soil part-derived microbial medium (group-E) treatments. Collectively, these fungi and yeasts may be applied in microbial transplantation via rice straw fermentation to repair soil mycobiota imbalances, facilitating plant growth and sustainable agriculture. These fungi and yeasts may be applied in microbial transplantation to repair soil mycobiota imbalances and sustainable agriculture.
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Affiliation(s)
- Yeu-Ching Shi
- Department of Food Sciences, National Chiayi University, Chiayi 60004, Taiwan;
| | - Yu-Juan Zheng
- Department of Horticultural Sciences, National Chiayi University, Chiayi 60004, Taiwan; (Y.-J.Z.); (Y.-C.L.)
| | - Yi-Ching Lin
- Department of Horticultural Sciences, National Chiayi University, Chiayi 60004, Taiwan; (Y.-J.Z.); (Y.-C.L.)
| | - Cheng-Hao Huang
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701401, Taiwan;
| | - Tang-Long Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan;
| | - Yu-Chia Hsu
- Department of Agronomy, National Chiayi University, Chiayi 60004, Taiwan;
| | - Bao-Hong Lee
- Department of Horticultural Sciences, National Chiayi University, Chiayi 60004, Taiwan; (Y.-J.Z.); (Y.-C.L.)
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Yue C, Jian J, Ciais P, Ren X, Jiao J, An S, Li Y, Wu J, Zhang P, Bond-Lamberty B. Field experiments show no consistent reductions in soil microbial carbon in response to warming. Nat Commun 2024; 15:1731. [PMID: 38413557 PMCID: PMC10899254 DOI: 10.1038/s41467-024-45508-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Affiliation(s)
- Chao Yue
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A & F University, Yangling, China
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, China
| | - Jinshi Jian
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A & F University, Yangling, China.
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, China.
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Yangling, Shaanxi, China.
| | - Philippe Ciais
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Xiaohua Ren
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A & F University, Yangling, China
| | - Juying Jiao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A & F University, Yangling, China.
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Yangling, Shaanxi, China.
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A & F University, Yangling, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Yangling, Shaanxi, China
| | - Yu Li
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, China
| | - Jie Wu
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, China
| | - Pengyi Zhang
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, China
| | - Ben Bond-Lamberty
- Pacific Northwest National Laboratory, Joint Global Change Research Institute at the University of Maryland-College Park, College Park, MD, USA
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5
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Patoine G, Eisenhauer N, Cesarz S, Phillips HRP, Xu X, Zhang L, Guerra CA. Reply to: Field experiments show no consistent reductions in soil microbial carbon in response to warming. Nat Commun 2024; 15:1732. [PMID: 38413571 PMCID: PMC10899587 DOI: 10.1038/s41467-024-45509-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Affiliation(s)
- Guillaume Patoine
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
- Institute of Biology, Leipzig University, Puschstraße 4, 04103, Leipzig, Germany.
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103, Leipzig, Germany
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103, Leipzig, Germany
| | - Helen R P Phillips
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103, Leipzig, Germany
- Department of Environmental Science, Saint Mary's University, Halifax, NS, Canada
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 AB, Wageningen, The Netherlands
| | - Xiaofeng Xu
- Biology Department, San Diego State University, San Diego, CA, 92182, USA
| | - Lihua Zhang
- College of Life and Environmental Sciences, Minzu University of China, 100081, Beijing, China
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Institute of Biology, Martin Luther University Halle Wittenberg, Halle (Saale), Germany
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6
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Jurdzinski KT, Mehrshad M, Delgado LF, Deng Z, Bertilsson S, Andersson AF. Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity. SCIENCE ADVANCES 2023; 9:eadg2059. [PMID: 37235649 PMCID: PMC10219603 DOI: 10.1126/sciadv.adg2059] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome transitions, resulting in species-level separation between aquatic biomes.
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Affiliation(s)
- Krzysztof T. Jurdzinski
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Luis Fernando Delgado
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Ziling Deng
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F. Andersson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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Casamayor EO, Cáliz J, Triadó-Margarit X, Pointing SB. Understanding atmospheric intercontinental dispersal of harmful microorganisms. Curr Opin Biotechnol 2023; 81:102945. [PMID: 37087840 DOI: 10.1016/j.copbio.2023.102945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
Abstract
The atmosphere is a major route for microbial intercontinental dispersal, including harmful microorganisms, antibiotic resistance genes, and allergens, with strong implications in ecosystem functioning and global health. Long-distance dispersal is facilitated by air movement at higher altitudes in the free troposphere and is affected by anthropogenic forcing, climate change, and by the general atmospheric circulation, mainly in the intertropical convergence zone. The survival of microorganisms during atmospheric transport and their remote invasive potential are fundamental questions, but data are scarce. Extreme atmospheric conditions represent a challenge to survival that requires specific adaptive strategies, and recovery of air samples from the high altitudes relevant to study harmful microorganisms can be challenging. In this paper, we highlight the scope of the problem, identify challenges and knowledge gaps, and offer a roadmap for improved understanding of intercontinental microbial dispersal and their outcomes. Greater understanding of long-distance dispersal requires research focus on local factors that affect emissions, coupled with conditions influencing transport and survival at high altitudes, and eventual deposition at sink locations.
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Affiliation(s)
- Emilio O Casamayor
- Ecology of the Global Microbiome, Center for Advanced Studies of Blanes-CSIC, E-17300 Blanes, Spain.
| | - Joan Cáliz
- Ecology of the Global Microbiome, Center for Advanced Studies of Blanes-CSIC, E-17300 Blanes, Spain
| | - Xavier Triadó-Margarit
- Ecology of the Global Microbiome, Center for Advanced Studies of Blanes-CSIC, E-17300 Blanes, Spain
| | - Stephen B Pointing
- Yale-NUS College & Department of Biological Sciences, National University of Singapore, Singapore
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Baldrian P, López-Mondéjar R, Kohout P. Forest microbiome and global change. Nat Rev Microbiol 2023:10.1038/s41579-023-00876-4. [PMID: 36941408 DOI: 10.1038/s41579-023-00876-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/23/2023]
Abstract
Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
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Zhang J, Yu D, Wang Y, Shi L, Wang T, Simayijiang H, Yan J. Tracing recent outdoor geolocation by analyzing microbiota from shoe soles and shoeprints even after indoor walking. Forensic Sci Int Genet 2023; 65:102869. [PMID: 37054666 DOI: 10.1016/j.fsigen.2023.102869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
The microbial communities on shoe soles and shoeprints could carry microbial information about where someone walked. This is possible evidence to link a suspect in a crime case to a geographic location. A previous study had shown that the microbiota found on shoe soles depend on the microbiota of the soil on which people walk. However, there is a turnover of microbial communities on shoe soles during walking. The impact of microbial community turnover on tracing recent geolocation from shoe soles has not been adequately studied. In addition, it is still unclear whether the microbiota of shoeprints can be used to determine recent geolocation. In this preliminary study, we investigated whether the microbial characteristics of shoe soles and shoeprints can be used to trace geolocation and whether this information can be destroyed by walking on indoor floors. In this study, participants were asked to walk outdoors on exposed soil, then walk indoors on a hard wood floor. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial communities of shoe soles, shoeprints, indoor dust, and outdoor soil. Samples of shoe soles and shoeprints were collected at steps 5, 20, and 50 while walking indoors. The PCoA result showed that the samples were clustered by geographic origin. The shoeprint showed a more rapid turnover of microbial community than the shoe sole during indoor walking. The result of FEAST showed that the microbial communities of shoe sole and shoeprint were mainly (shoe sole, 86.21∼92.34 %; shoeprint, 61.66∼90.41 %) from the soil of the outdoor ground where the individual recently walked, and a small portion (shoe sole, 0.68∼3.33 %; shoeprint, 1.43∼27.14 %) from the indoor dust. Based on the matching of microbial communities between geolocation and shoe sole or shoeprint, we were able to infer the recent geolocation of the individual with relatively high accuracy using the random forest prediction model (shoe sole: 100.00 %, shoeprint: 93.33∼100.00 %). Overall, we are able to accurately infer the geolocation of an individual's most recent outdoor walk based on the microbiota of shoe sole and shoeprint, even though these microbiotas show a turnover when walking indoor floor. The pilot study was expected to provide a potential method for tracing recent geolocation of suspects.
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10
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Marasco R, Fusi M, Coscolín C, Barozzi A, Almendral D, Bargiela R, Nutschel CGN, Pfleger C, Dittrich J, Gohlke H, Matesanz R, Sanchez-Carrillo S, Mapelli F, Chernikova TN, Golyshin PN, Ferrer M, Daffonchio D. Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes. Nat Commun 2023; 14:1045. [PMID: 36828822 PMCID: PMC9958047 DOI: 10.1038/s41467-023-36610-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/08/2023] [Indexed: 02/26/2023] Open
Abstract
Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme response in all cases. Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility confirms the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response.
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Affiliation(s)
- Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre for Conservation and Restoration Science, Edinburgh Napier University Sighthill Campus, Edinburgh, UK
| | | | - Alan Barozzi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Almendral
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain
| | - Rafael Bargiela
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | | | - Christopher Pfleger
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jonas Dittrich
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC) and Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ruth Matesanz
- Spectroscopy Laboratory, Centro de Investigaciones Biologicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Sergio Sanchez-Carrillo
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, Madrid, Spain
| | - Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Tatyana N Chernikova
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain.
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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11
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Mishra A, Singh L, Singh D. Unboxing the black box-one step forward to understand the soil microbiome: A systematic review. MICROBIAL ECOLOGY 2023; 85:669-683. [PMID: 35112151 PMCID: PMC9957845 DOI: 10.1007/s00248-022-01962-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.
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Affiliation(s)
- Apurva Mishra
- Academy of Scientific and Innovative Research [AcSIR], Ghaziabad, 201002, India
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Lal Singh
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Dharmesh Singh
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstrasse 30, 81675, Munich, Bavaria, Germany.
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12
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Berg G, Schweitzer M, Abdelfattah A, Cernava T, Wassermann B. Missing symbionts – emerging pathogens? Microbiome management for sustainable agriculture. Symbiosis 2023. [DOI: 10.1007/s13199-023-00903-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractPlant diversification and co-evolution shaped the plant microbiome and vice versa. This resulted in a specific composition of the plant microbiome and a strong connection with the host in terms of functional interplay. Symbionts are part of the microbiota, and important for the plant’s germination and growth, nutrition, as well as stress protection. However, human activities in the Anthropocene are linked to a significant shift of diversity, evenness and specificity of the plant microbiota. In addition, and very importantly, many plant symbionts are missing or no longer functional. It will require targeted microbiome management to support and reintroduce them. In future agriculture, we should aim at replacing harmful chemicals in the field, as well as post-harvest, by using precision microbiome engineering. This is because the plant microbiome is connected across systems and crucial for human and planetary health. This commentary aims to inspire holistic studies for the development of solutions for sustainable agriculture in framework of the One Health and the Planetary Health concepts.
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13
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Vuong P, Chong S, Kaur P. The little things that matter: how bioprospecting microbial biodiversity can build towards the realization of United Nations Sustainable Development Goals. NPJ BIODIVERSITY 2022; 1:4. [PMID: 39242677 PMCID: PMC11290601 DOI: 10.1038/s44185-022-00006-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/03/2022] [Indexed: 09/09/2024]
Affiliation(s)
- Paton Vuong
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Sandy Chong
- Faculty of Science & Engineering, Curtin University, Perth, Australia
- United Nations Association of Australia (WA Division), Perth, Australia
| | - Parwinder Kaur
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia.
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14
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Maestre FT, Le Bagousse-Pinguet Y, Delgado-Baquerizo M, Eldridge DJ, Saiz H, Berdugo M, Gozalo B, Ochoa V, Guirado E, García-Gómez M, Valencia E, Gaitán JJ, Asensio S, Mendoza BJ, Plaza C, Díaz-Martínez P, Rey A, Hu HW, He JZ, Wang JT, Lehmann A, Rillig MC, Cesarz S, Eisenhauer N, Martínez-Valderrama J, Moreno-Jiménez E, Sala O, Abedi M, Ahmadian N, Alados CL, Aramayo V, Amghar F, Arredondo T, Ahumada RJ, Bahalkeh K, Ben Salem F, Blaum N, Boldgiv B, Bowker MA, Bran D, Bu C, Canessa R, Castillo-Monroy AP, Castro H, Castro I, Castro-Quezada P, Chibani R, Conceição AA, Currier CM, Darrouzet-Nardi A, Deák B, Donoso DA, Dougill AJ, Durán J, Erdenetsetseg B, Espinosa CI, Fajardo A, Farzam M, Ferrante D, Frank ASK, Fraser LH, Gherardi LA, Greenville AC, Guerra CA, Gusmán-Montalvan E, Hernández-Hernández RM, Hölzel N, Huber-Sannwald E, Hughes FM, Jadán-Maza O, Jeltsch F, Jentsch A, Kaseke KF, Köbel M, Koopman JE, Leder CV, Linstädter A, le Roux PC, Li X, Liancourt P, Liu J, Louw MA, Maggs-Kölling G, Makhalanyane TP, Issa OM, Manzaneda AJ, Marais E, Mora JP, Moreno G, Munson SM, Nunes A, Oliva G, Oñatibia GR, Peter G, Pivari MOD, Pueyo Y, Quiroga RE, Rahmanian S, Reed SC, Rey PJ, Richard B, Rodríguez A, Rolo V, Rubalcaba JG, Ruppert JC, Salah A, Schuchardt MA, Spann S, Stavi I, Stephens CRA, Swemmer AM, Teixido AL, Thomas AD, Throop HL, Tielbörger K, Travers S, Val J, Valkó O, van den Brink L, Ayuso SV, Velbert F, Wamiti W, Wang D, Wang L, Wardle GM, Yahdjian L, Zaady E, Zhang Y, Zhou X, Singh BK, Gross N. Grazing and ecosystem service delivery in global drylands. Science 2022; 378:915-920. [DOI: 10.1126/science.abq4062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Grazing represents the most extensive use of land worldwide. Yet its impacts on ecosystem services remain uncertain because pervasive interactions between grazing pressure, climate, soil properties, and biodiversity may occur but have never been addressed simultaneously. Using a standardized survey at 98 sites across six continents, we show that interactions between grazing pressure, climate, soil, and biodiversity are critical to explain the delivery of fundamental ecosystem services across drylands worldwide. Increasing grazing pressure reduced ecosystem service delivery in warmer and species-poor drylands, whereas positive effects of grazing were observed in colder and species-rich areas. Considering interactions between grazing and local abiotic and biotic factors is key for understanding the fate of dryland ecosystems under climate change and increasing human pressure.
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Affiliation(s)
- Fernando T. Maestre
- Instituto Multidisciplinar para el Estudio del Medio “Ramón Margalef,” Universidad de Alicante, Alicante, Spain
- Departamento de Ecología, Universidad de Alicante, Alicante, Spain
| | | | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - David J. Eldridge
- Department of Planning and Environment, c/o Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Hugo Saiz
- Departamento de Ciencias Agrarias y Medio Natural, Escuela Politécnica Superior, Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA), Universidad de Zaragoza, Huesca, Spain
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Miguel Berdugo
- Institut de Biología Evolutiva (UPF-CSIC), Barcelona, Spain
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Beatriz Gozalo
- Instituto Multidisciplinar para el Estudio del Medio “Ramón Margalef,” Universidad de Alicante, Alicante, Spain
| | - Victoria Ochoa
- Instituto Multidisciplinar para el Estudio del Medio “Ramón Margalef,” Universidad de Alicante, Alicante, Spain
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Emilio Guirado
- Instituto Multidisciplinar para el Estudio del Medio “Ramón Margalef,” Universidad de Alicante, Alicante, Spain
| | - Miguel García-Gómez
- Departamento de Ingeniería y Morfología del Terreno, Escuela Técnica Superior de Ingenieros de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Enrique Valencia
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan J. Gaitán
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Suelos-CNIA, Buenos Aires, Argentina
- Universidad Nacional de Luján, Departamento de Tecnología, Luján, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET), Buenos Aires, Argentina
| | - Sergio Asensio
- Instituto Multidisciplinar para el Estudio del Medio “Ramón Margalef,” Universidad de Alicante, Alicante, Spain
| | - Betty J. Mendoza
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
| | - César Plaza
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Paloma Díaz-Martínez
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ana Rey
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Hang-Wei Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Science, Fujian Normal University, Fuzhou, China
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ji-Zheng He
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Science, Fujian Normal University, Fuzhou, China
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jun-Tao Wang
- Global Centre for Land-Based Innovation, Western Sydney University, Sydney, New South Wales, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, New South Wales, Australia
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Anika Lehmann
- Freie Universität Berlin, Institute of Biology, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Matthias C. Rillig
- Freie Universität Berlin, Institute of Biology, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leipzig University, Institute of Biology, Leipzig, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leipzig University, Institute of Biology, Leipzig, Germany
| | - Jaime Martínez-Valderrama
- Instituto Multidisciplinar para el Estudio del Medio “Ramón Margalef,” Universidad de Alicante, Alicante, Spain
| | - Eduardo Moreno-Jiménez
- Department of Agricultural and Food Chemistry, Faculty of Sciences, Universidad Autónoma de Madrid, Madrid, Spain
| | - Osvaldo Sala
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- School of Sustainability, Arizona State University, Tempe, AZ, USA
- Global Drylands Center, Arizona State University, Tempe, AZ, USA
| | - Mehdi Abedi
- Department of Range Management, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran Province, Iran
| | - Negar Ahmadian
- Department of Range Management, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran Province, Iran
| | | | - Valeria Aramayo
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Bariloche, Bariloche, Río Negro, Argentina
| | - Fateh Amghar
- Laboratoire de Recherche: Biodiversité, Biotechnologie, Environnement et Développement Durable (BioDev), Faculté des Sciences, Université M’hamed Bougara de Boumerdès, Boumerdès, Algérie
| | - Tulio Arredondo
- Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico
| | - Rodrigo J. Ahumada
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Catamarca, Catamarca, Argentina
| | - Khadijeh Bahalkeh
- Department of Range Management, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran Province, Iran
| | - Farah Ben Salem
- Laboratory of Range Ecology, Institut des Régions Arides (IRA), Médenine, Tunisia
| | - Niels Blaum
- University of Potsdam, Plant Ecology and Conservation Biology, Potsdam, Germany
| | - Bazartseren Boldgiv
- Laboratory of Ecological and Evolutionary Synthesis, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Matthew A. Bowker
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Donaldo Bran
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Bariloche, Bariloche, Río Negro, Argentina
| | - Chongfeng Bu
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
| | - Rafaella Canessa
- Ecological Plant Geography, Faculty of Geography, University of Marburg, Marburg, Germany
- Plant Ecology Group, University of Tübingen, Tübingen, Germany
| | | | - Helena Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ignacio Castro
- Universidad Nacional Experimental Simón Rodríguez (UNESR), Instituto de Estudios Científicos y Tecnológicos (IDECYT), Centro de Estudios de Agroecología Tropical (CEDAT), Miranda, Venezuela
| | - Patricio Castro-Quezada
- Universidad de Cuenca, Facultad de Ciencias Agropecuarias, Carrera de Ingeniería Agronómica, Grupo de Agroforestería, Manejo y Conservación del paisaje, Cuenca, Ecuador
| | - Roukaya Chibani
- Laboratory of Range Ecology, Institut des Régions Arides (IRA), Médenine, Tunisia
| | - Abel A. Conceição
- Universidade Estadual de Feira de Santana (UEFS), Departamento de Ciências Biológicas, Bahia, Brazil
| | - Courtney M. Currier
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Global Drylands Center, Arizona State University, Tempe, AZ, USA
| | | | - Balázs Deák
- Lendület Seed Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | - David A. Donoso
- Departamento de Biología, Escuela Politécnica Nacional, Quito, Ecuador
- Centro de Investigación de la Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Andrew J. Dougill
- Department of Environment and Geography, University of York, York, UK
| | - Jorge Durán
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Misión Biolóxica de Galicia, CSIC, Pontevedra, Spain
| | - Batdelger Erdenetsetseg
- Laboratory of Ecological and Evolutionary Synthesis, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Carlos I. Espinosa
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Alex Fajardo
- Instituto de Investigación Interdisciplinaria (I3), Vicerrectoría Académica, Universidad de Talca, Talca, Chile
| | - Mohammad Farzam
- Department of Range and Watershed Management, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Daniela Ferrante
- Instituto Nacional de Tecnología Agropecuaria EEA Santa Cruz, Río Gallegos, Santa Cruz, Argentina
- Universidad Nacional de la Patagonia Austral, Río Gallegos, Santa Cruz, Argentina
| | - Anke S. K. Frank
- School of Agriculture, Environmental and Veterinary Sciences, Charles Sturt University, Port Macquarie, New South Wales, Australia
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Lauchlan H. Fraser
- Department of Natural Resource Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Laureano A. Gherardi
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Aaron C. Greenville
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Carlos A. Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Martin-Luther University Halle Wittenberg, Halle (Saale), Germany
| | | | - Rosa M. Hernández-Hernández
- Universidad Nacional Experimental Simón Rodríguez (UNESR), Instituto de Estudios Científicos y Tecnológicos (IDECYT), Centro de Estudios de Agroecología Tropical (CEDAT), Miranda, Venezuela
| | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | | | - Frederic M. Hughes
- Universidade Estadual de Feira de Santana (UEFS), Departamento de Ciências Biológicas, Bahia, Brazil
- Instituto Nacional da Mata Atlântica (INMA), Espírito Santo, Brazil
| | - Oswaldo Jadán-Maza
- Universidad de Cuenca, Facultad de Ciencias Agropecuarias, Carrera de Ingeniería Agronómica, Grupo de Agroforestería, Manejo y Conservación del paisaje, Cuenca, Ecuador
| | - Florian Jeltsch
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
- University of Potsdam, Plant Ecology and Conservation Biology, Potsdam, Germany
| | - Anke Jentsch
- Department of Disturbance Ecology, Bayreuth Center of Ecology and Environmental Research BayCEER, University of Bayreuth, Bayreuth, Germany
| | - Kudzai F. Kaseke
- Earth Research Institute, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Melanie Köbel
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Jessica E. Koopman
- Microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Cintia V. Leder
- Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET), Buenos Aires, Argentina
- Universidad Nacional de Río Negro, Sede Atlántica, CEANPa, Río Negro, Argentina
| | - Anja Linstädter
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
- Biodiversity Research/Systematic Botany Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Peter C. le Roux
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Xinkai Li
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, China
| | - Pierre Liancourt
- Plant Ecology Group, University of Tübingen, Tübingen, Germany
- Institute of Botany, Czech Academy of Sciences, Pruhonice, Czech Republic
- Botany Department, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Jushan Liu
- Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Michelle A. Louw
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Thulani P. Makhalanyane
- Microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Oumarou Malam Issa
- Institut d’Écologie et des Sciences de l’Environnement de Paris (iEES-Paris), Sorbonne Université, IRD, CNRS, INRAE, Université Paris Est Creteil, Université de Paris, Centre IRD de France Nord, Bondy, France
| | - Antonio J. Manzaneda
- Instituto Interuniversitario de Investigación del Sistema Tierra en Andalucía, Universidad de Jaén, Jaén, Spain
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Eugene Marais
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | - Juan P. Mora
- Instituto de Investigación Interdisciplinaria (I3), Vicerrectoría Académica, Universidad de Talca, Talca, Chile
| | - Gerardo Moreno
- Forestry School, INDEHESA, Universidad de Extremadura, Plasencia, Spain
| | - Seth M. Munson
- US Geological Survey, Southwest Biological Science Center, Flagstaff, AZ, USA
| | - Alice Nunes
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Gabriel Oliva
- Instituto Nacional de Tecnología Agropecuaria EEA Santa Cruz, Río Gallegos, Santa Cruz, Argentina
- Universidad Nacional de la Patagonia Austral, Río Gallegos, Santa Cruz, Argentina
| | - Gastón R. Oñatibia
- Cátedra de Ecología, Facultad de Agronomía, Universidad de Buenos Aires, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Guadalupe Peter
- Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET), Buenos Aires, Argentina
- Universidad Nacional de Río Negro, Sede Atlántica, CEANPa, Río Negro, Argentina
| | - Marco O. D. Pivari
- Departamento de Botânica, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Yolanda Pueyo
- Instituto Pirenaico de Ecología (IPE, CSIC), Zaragoza, Spain
| | - R. Emiliano Quiroga
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Catamarca, Catamarca, Argentina
- Cátedra de Manejo de Pastizales Naturales, Facultad de Ciencias Agrarias, Universidad Nacional de Catamarca, Catamarca, Argentina
| | - Soroor Rahmanian
- Department of Range and Watershed Management, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Forest Engineering, Forest Management Planning and Terrestrial Measurements, Faculty of Silviculture and Forest Engineering, Transilvania University of Brasov, Brasov, Romania
| | - Sasha C. Reed
- US Geological Survey, Southwest Biological Science Center, Moab, UT, USA
| | - Pedro J. Rey
- Instituto Interuniversitario de Investigación del Sistema Tierra en Andalucía, Universidad de Jaén, Jaén, Spain
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | | | - Alexandra Rodríguez
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Víctor Rolo
- Forestry School, INDEHESA, Universidad de Extremadura, Plasencia, Spain
| | | | - Jan C. Ruppert
- Plant Ecology Group, University of Tübingen, Tübingen, Germany
| | | | - Max A. Schuchardt
- Department of Disturbance Ecology, Bayreuth Center of Ecology and Environmental Research BayCEER, University of Bayreuth, Bayreuth, Germany
| | - Sedona Spann
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Ilan Stavi
- Dead Sea and Arava Science Center, Yotvata, Israel
| | - Colton R. A. Stephens
- Department of Natural Resource Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Anthony M. Swemmer
- South African Environmental Observation Network (SAEON), Phalaborwa, Kruger National Park, South Africa
| | - Alberto L. Teixido
- Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Mato Grosso, Brazil
| | - Andrew D. Thomas
- Department of Geography and Earth Sciences, Aberystwyth University, Wales, UK
| | - Heather L. Throop
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | | | - Samantha Travers
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - James Val
- Science Division, Department of Planning, Industry and Environment, New South Wales Government, Buronga, New South Wales, Australia
| | - Orsolya Valkó
- Lendület Seed Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | | | - Sergio Velasco Ayuso
- Cátedra de Ecología, Facultad de Agronomía, Universidad de Buenos Aires, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Frederike Velbert
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Wanyoike Wamiti
- Zoology Department, National Museums of Kenya, Nairobi, Kenya
| | - Deli Wang
- Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Lixin Wang
- Department of Earth Sciences, Indiana University–Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Glenda M. Wardle
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Laura Yahdjian
- Cátedra de Ecología, Facultad de Agronomía, Universidad de Buenos Aires, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Mobile Post Negev, Israel
| | - Yuanming Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Brajesh K. Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Sydney, New South Wales, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, New South Wales, Australia
| | - Nicolas Gross
- Université Clermont Auvergne, INRAE, VetAgro Sup, Unité Mixte de Recherche Ecosystème Prairial, Clermont-Ferrand, France
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15
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Tedersoo L, Mikryukov V, Zizka A, Bahram M, Hagh‐Doust N, Anslan S, Prylutskyi O, Delgado‐Baquerizo M, Maestre FT, Pärn J, Öpik M, Moora M, Zobel M, Espenberg M, Mander Ü, Khalid AN, Corrales A, Agan A, Vasco‐Palacios A, Saitta A, Rinaldi AC, Verbeken A, Sulistyo BP, Tamgnoue B, Furneaux B, Ritter CD, Nyamukondiwa C, Sharp C, Marín C, Gohar D, Klavina D, Sharmah D, Dai DQ, Nouhra E, Biersma EM, Rähn E, Cameron E, De Crop E, Otsing E, Davydov EA, Albornoz F, Brearley FQ, Buegger F, Zahn G, Bonito G, Hiiesalu I, Barrio IC, Heilmann‐Clausen J, Ankuda J, Kupagme JY, Maciá‐Vicente JG, Fovo JD, Geml J, Alatalo JM, Alvarez‐Manjarrez J, Põldmaa K, Runnel K, Adamson K, Bråthen KA, Pritsch K, Tchan KI, Armolaitis K, Hyde KD, Newsham K, Panksep K, Lateef AA, Tiirmann L, Hansson L, Lamit LJ, Saba M, Tuomi M, Gryzenhout M, Bauters M, Piepenbring M, Wijayawardene N, Yorou NS, Kurina O, Mortimer PE, Meidl P, Kohout P, Nilsson RH, Puusepp R, Drenkhan R, Garibay‐Orijel R, Godoy R, Alkahtani S, Rahimlou S, Dudov SV, Põlme S, Ghosh S, Mundra S, Ahmed T, Netherway T, Henkel TW, Roslin T, Nteziryayo V, Fedosov VE, Onipchenko V, Yasanthika WAE, Lim YW, Soudzilovskaia NA, Antonelli A, Kõljalg U, Abarenkov K. Global patterns in endemicity and vulnerability of soil fungi. GLOBAL CHANGE BIOLOGY 2022; 28:6696-6710. [PMID: 36056462 PMCID: PMC9826061 DOI: 10.1111/gcb.16398] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/09/2022] [Indexed: 05/29/2023]
Abstract
Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | | | | | - Mohammad Bahram
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Sten Anslan
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Oleh Prylutskyi
- Department of Mycology and Plant Resistance, School of BiologyV.N. Karazin Kharkiv National UniversityKharkivUkraine
| | - Manuel Delgado‐Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, and Unidad Asociada CSIC‐UPO (BioFun)Universidad Pablo de OlavideSevillaSpain
| | - Fernando T. Maestre
- Departamento de Ecología, Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’Universidad de AlicanteAlicanteSpain
| | - Jaan Pärn
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Maarja Öpik
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mari Moora
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Martin Zobel
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mikk Espenberg
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Ülo Mander
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | | | - Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología‐UR (CIMBIUR)Universidad del RosarioBogotáColombia
| | - Ahto Agan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Aída‐M. Vasco‐Palacios
- BioMicro, Escuela de MicrobiologíaUniversidad de Antioquia UdeAMedellinAntioquiaColombia
| | - Alessandro Saitta
- Department of Agricultural, Food and Forest SciencesUniversity of PalermoPalermoItaly
| | - Andrea C. Rinaldi
- Department of Biomedical SciencesUniversity of CagliariCagliariItaly
| | | | - Bobby P. Sulistyo
- Department of BiomedicineIndonesia International Institute for Life SciencesJakartaIndonesia
| | - Boris Tamgnoue
- Department of Crop ScienceUniversity of DschangDschangCameroon
| | - Brendan Furneaux
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | | | - Casper Nyamukondiwa
- Department of Biological Sciences and BiotechnologyBotswana International University of Science and TechnologyPalapyeBotswana
| | - Cathy Sharp
- Natural History Museum of ZimbabweBulawayoZimbabwe
| | - César Marín
- Centro de Investigación e Innovación para el Cambio Climático (CiiCC)Universidad SantoTomásSantiagoChile
| | - Daniyal Gohar
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Darta Klavina
- Latvian State Forest Research Insitute SilavaSalaspilsLatvia
| | - Dipon Sharmah
- Department of Botany, Jawaharlal Nehru Rajkeeya MahavidyalayaPondicherry UniversityPort BlairIndia
| | - Dong Qin Dai
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingChina
| | - Eduardo Nouhra
- Instituto Multidisciplinario de Biología Vegetal (CONICET)Universidad Nacional de CórdobaCordobaArgentina
| | | | - Elisabeth Rähn
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Erin K. Cameron
- Department of Environmental ScienceSaint Mary's UniversityHalifaxCanada
| | | | - Eveli Otsing
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | | | | | - Francis Q. Brearley
- Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
| | | | | | - Gregory Bonito
- Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Inga Hiiesalu
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Isabel C. Barrio
- Faculty of Natural and Environmental SciencesAgricultural University of IcelandHvanneyriIceland
| | | | - Jelena Ankuda
- Department of Silviculture and EcologyInstitute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC)GirionysLithuania
| | - John Y. Kupagme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Jose G. Maciá‐Vicente
- Plant Ecology and Nature ConservationWageningen University & ResearchWageningenThe Netherlands
| | | | - József Geml
- ELKH‐EKKE Lendület Environmental Microbiome Research GroupEszterházy Károly Catholic UniversityEgerHungary
| | | | | | - Kadri Põldmaa
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Kadri Runnel
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Kalev Adamson
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Kari Anne Bråthen
- Department of Arctic and Marine BiologyThe Arctic University of NorwayTromsøNorway
| | | | - Kassim I. Tchan
- Research Unit Tropical Mycology and Plants‐Soil Fungi InteractionsUniversity of ParakouParakouBenin
| | - Kęstutis Armolaitis
- Department of Silviculture and EcologyInstitute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC)GirionysLithuania
| | - Kevin D. Hyde
- Center of Excellence in Fungal ResearchMae Fah Luang UniversityChiang RaiThailand
| | | | - Kristel Panksep
- Chair of Hydrobiology and FisheryEstonian University of Life SciencesTartuEstonia
| | | | - Liis Tiirmann
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Linda Hansson
- Gothenburg Centre for Sustainable DevelopmentGothenburgSweden
| | - Louis J. Lamit
- Department of BiologySyracuse UniversitySyracuseNew YorkUSA
- Department of Environmental and Forest BiologyState University of New York College of Environmental Science and ForestrySyracuseNew YorkUSA
| | - Malka Saba
- Department of Plant SciencesQuaid‐i‐Azam UniversityIslamabadPakistan
| | - Maria Tuomi
- Department of Arctic and Marine BiologyThe Arctic University of NorwayTromsøNorway
| | - Marieka Gryzenhout
- Department of GeneticsUniversity of the Free StateBloemfonteinSouth Africa
| | | | - Meike Piepenbring
- Mycology Working GroupGoethe University Frankfurt am MainFrankfurt am MainGermany
| | - Nalin Wijayawardene
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingChina
| | - Nourou S. Yorou
- Research Unit Tropical Mycology and Plants‐Soil Fungi InteractionsUniversity of ParakouParakouBenin
| | - Olavi Kurina
- Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartuEstonia
| | - Peter E. Mortimer
- Center For Mountain Futures, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Peter Meidl
- Institut für BiologieFreie Universität BerlinBerlinGermany
| | - Petr Kohout
- Institute of MicrobiologyCzech Academy of SciencesPragueCzech Republic
| | - Rolf Henrik Nilsson
- Gothenburg Global Biodiversity CentreUniversity of GothenburgGothenburgSweden
| | - Rasmus Puusepp
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Rein Drenkhan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | | | - Roberto Godoy
- Instituto Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | - Saad Alkahtani
- College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Saleh Rahimlou
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Sergey V. Dudov
- Department of Ecology and Plant GeographyMoscow Lomonosov State UniversityMoscowRussia
| | - Sergei Põlme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Soumya Ghosh
- Department of GeneticsUniversity of the Free StateBloemfonteinSouth Africa
| | - Sunil Mundra
- Department of Biology, College of ScienceUnited Arab Emirates UniversityAbu DhabiUAE
| | - Talaat Ahmed
- Environmental Science CenterQatar UniversityDohaQatar
| | - Tarquin Netherway
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Terry W. Henkel
- Department of Biological SciencesCalifornia State Polytechnic UniversityArcataCaliforniaUSA
| | - Tomas Roslin
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Vincent Nteziryayo
- Department of Food Science and TechnologyUniversity of BurundiBujumburaBurundi
| | - Vladimir E. Fedosov
- Department of Ecology and Plant GeographyMoscow Lomonosov State UniversityMoscowRussia
| | | | | | - Young Woon Lim
- School of Biological Sciences and Institute of MicrobiologySeoul National UniversitySeoulSouth Korea
| | | | | | - Urmas Kõljalg
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
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16
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Guerra CA, Berdugo M, Eldridge DJ, Eisenhauer N, Singh BK, Cui H, Abades S, Alfaro FD, Bamigboye AR, Bastida F, Blanco-Pastor JL, de Los Ríos A, Durán J, Grebenc T, Illán JG, Liu YR, Makhalanyane TP, Mamet S, Molina-Montenegro MA, Moreno JL, Mukherjee A, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Picó S, Verma JP, Rey A, Rodríguez A, Tedersoo L, Teixido AL, Torres-Díaz C, Trivedi P, Wang J, Wang L, Wang J, Zaady E, Zhou X, Zhou XQ, Delgado-Baquerizo M. Global hotspots for soil nature conservation. Nature 2022; 610:693-698. [PMID: 36224389 DOI: 10.1038/s41586-022-05292-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/30/2022] [Indexed: 11/09/2022]
Abstract
Soils are the foundation of all terrestrial ecosystems1. However, unlike for plants and animals, a global assessment of hotspots for soil nature conservation is still lacking2. This hampers our ability to establish nature conservation priorities for the multiple dimensions that support the soil system: from soil biodiversity to ecosystem services. Here, to identify global hotspots for soil nature conservation, we performed a global field survey that includes observations of biodiversity (archaea, bacteria, fungi, protists and invertebrates) and functions (critical for six ecosystem services) in 615 composite samples of topsoil from a standardized survey in all continents. We found that each of the different ecological dimensions of soils-that is, species richness (alpha diversity, measured as amplicon sequence variants), community dissimilarity and ecosystem services-peaked in contrasting regions of the planet, and were associated with different environmental factors. Temperate ecosystems showed the highest species richness, whereas community dissimilarity peaked in the tropics, and colder high-latitudinal ecosystems were identified as hotspots of ecosystem services. These findings highlight the complexities that are involved in simultaneously protecting multiple ecological dimensions of soil. We further show that most of these hotspots are not adequately covered by protected areas (more than 70%), and are vulnerable in the context of several scenarios of global change. Our global estimation of priorities for soil nature conservation highlights the importance of accounting for the multidimensionality of soil biodiversity and ecosystem services to conserve soils for future generations.
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Affiliation(s)
- Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany. .,Institute of Biology, Martin Luther University Halle Wittenberg, Halle(Saale), Germany. .,Institute of Biology, Leipzig University, Leipzig, Germany.
| | - Miguel Berdugo
- Institute of Integrative Biology, Department of Environment Systems Science, ETH Zürich, Zürich, Switzerland
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Haiying Cui
- Institute of Grassland Science, School of Life Science, Northeast Normal University, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, China.,Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
| | - Sebastian Abades
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, Huechuraba, Chile
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, Huechuraba, Chile.,Instituto de Ecología & Biodiversidad (IEB), Santiago, Chile
| | | | - Felipe Bastida
- CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | | | - Asunción de Los Ríos
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jorge Durán
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,Misión Biolóxica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
| | - Tine Grebenc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Javier G Illán
- Department of Entomology, College of Agricultural, Human, and Natural Resource Sciences, Washington State University, Pullman, WA, USA
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Steven Mamet
- Department of Soil Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Marco A Molina-Montenegro
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.,CEAZA, Universidad Católica del Norte, Coquimbo, Chile
| | - José L Moreno
- CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Arpan Mukherjee
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | | | | | - César Plaza
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Sergio Picó
- Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - Jay Prakash Verma
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Ana Rey
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Alexandra Rodríguez
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Alberto L Teixido
- Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Brazil
| | - Cristian Torres-Díaz
- Grupo de Investigación en Biodiversidad y Cambio Global (GI BCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Ling Wang
- Institute of Grassland Science, School of Life Science, Northeast Normal University, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, China
| | - Jianyong Wang
- Institute of Grassland Science, School of Life Science, Northeast Normal University, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, China
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Negev, Israel
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xin-Quan Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain. .,Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Seville, Spain.
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17
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Defending Earth's terrestrial microbiome. Nat Microbiol 2022; 7:1717-1725. [PMID: 36192539 DOI: 10.1038/s41564-022-01228-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/17/2022] [Indexed: 11/08/2022]
Abstract
Microbial life represents the majority of Earth's biodiversity. Across disparate disciplines from medicine to forestry, scientists continue to discover how the microbiome drives essential, macro-scale processes in plants, animals and entire ecosystems. Yet, there is an emerging realization that Earth's microbial biodiversity is under threat. Here we advocate for the conservation and restoration of soil microbial life, as well as active incorporation of microbial biodiversity into managed food and forest landscapes, with an emphasis on soil fungi. We analyse 80 experiments to show that native soil microbiome restoration can accelerate plant biomass production by 64% on average, across ecosystems. Enormous potential also exists within managed landscapes, as agriculture and forestry are the dominant uses of land on Earth. Along with improving and stabilizing yields, enhancing microbial biodiversity in managed landscapes is a critical and underappreciated opportunity to build reservoirs, rather than deserts, of microbial life across our planet. As markets emerge to engineer the ecosystem microbiome, we can avert the mistakes of aboveground ecosystem management and avoid microbial monocultures of single high-performing microbial strains, which can exacerbate ecosystem vulnerability to pathogens and extreme events. Harnessing the planet's breadth of microbial life has the potential to transform ecosystem management, but it requires that we understand how to monitor and conserve the Earth's microbiome.
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18
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Peixoto RS, Voolstra CR, Sweet M, Duarte CM, Carvalho S, Villela H, Lunshof JE, Gram L, Woodhams DC, Walter J, Roik A, Hentschel U, Thurber RV, Daisley B, Ushijima B, Daffonchio D, Costa R, Keller-Costa T, Bowman JS, Rosado AS, Reid G, Mason CE, Walke JB, Thomas T, Berg G. Harnessing the microbiome to prevent global biodiversity loss. Nat Microbiol 2022; 7:1726-1735. [PMID: 35864220 DOI: 10.1038/s41564-022-01173-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/14/2022] [Indexed: 01/21/2023]
Abstract
Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges.
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Affiliation(s)
- Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Christian R Voolstra
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jeantine E Lunshof
- Department of Global Health and Social Medicine, Center for Bioethics, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jens Walter
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Brendan Daisley
- Lawson Health Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Jeff S Bowman
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
| | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gregor Reid
- Lawson Health Research Institute, University of Western Ontario, London, Ontario, Canada
| | | | - Jenifer B Walke
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Torsten Thomas
- Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.,University of Postdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
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19
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Patoine G, Eisenhauer N, Cesarz S, Phillips HRP, Xu X, Zhang L, Guerra CA. Drivers and trends of global soil microbial carbon over two decades. Nat Commun 2022; 13:4195. [PMID: 35858886 PMCID: PMC9300697 DOI: 10.1038/s41467-022-31833-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 07/04/2022] [Indexed: 12/21/2022] Open
Abstract
Soil microorganisms are central to sustain soil functions and services, like carbon and nutrient cycling. Currently, we only have a limited understanding of the spatial-temporal dynamics of soil microorganisms, restricting our ability to assess long-term effects of climate and land-cover change on microbial roles in soil biogeochemistry. This study assesses the temporal trends in soil microbial biomass carbon and identifies the main drivers of biomass change regionally and globally to detect the areas sensitive to these environmental factors. Here, we combined a global soil microbial biomass carbon data set, random forest modelling, and environmental layers to predict spatial-temporal dynamics of microbial biomass carbon stocks from 1992 to 2013. Soil microbial biomass carbon stocks decreased globally by 3.4 ± 3.0% (mean ± 95% CI) between 1992 and 2013 for the predictable regions, equivalent to 149 Mt being lost over the period, or ~1‰ of soil C. Northern areas with high soil microbial carbon stocks experienced the strongest decrease, mostly driven by increasing temperatures. In contrast, land-cover change was a weaker global driver of change in microbial carbon, but had, in some cases, important regional effects.
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Affiliation(s)
- Guillaume Patoine
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
- Institute of Biology, Leipzig University, Puschstraße 4, 04103, Leipzig, Germany.
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103, Leipzig, Germany
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103, Leipzig, Germany
| | - Helen R P Phillips
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103, Leipzig, Germany
- Department of Environmental Science, Saint Mary's University, Halifax, Nova Scotia, Canada
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 AB, Wageningen, Netherlands
| | - Xiaofeng Xu
- Biology Department, San Diego State University, San Diego, CA, 92182, USA
| | - Lihua Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103, Leipzig, Germany
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20
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Choudoir MJ, Eggleston EM. Reciprocal Inclusion of Microbiomes and Environmental Justice Contributes Solutions to Global Environmental Health Challenges. mSystems 2022; 7:e0146221. [PMID: 35642845 PMCID: PMC9239259 DOI: 10.1128/msystems.01462-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Generations of colonialism, industrialization, intensive agriculture, and anthropogenic climate change have radically altered global ecosystems and by extension, their environmental microbiomes. The environmental consequences of global change disproportionately burden racialized communities, those with lower socioeconomic status, and other systematically underserved populations. Environmental justice seeks to balance the relationships between environmental burden, beneficial ecosystem functions, and local communities. Given their direct links to human and ecosystem health, microbes are embedded within social and environmental justice. Considering scientific and technological advances is becoming an important step in developing actionable solutions to global equity challenges. Here we identify areas where inclusion of microbial knowledge and research can support planetary health goals. We offer guidelines for strengthening a reciprocal integration of environmental justice into environmental microbiology research. Microbes form intimate relationships with the environment and society, thus microbiologists have numerous and unique opportunities to incorporate equity into their research, teaching, and community engagement.
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Affiliation(s)
- Mallory J. Choudoir
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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21
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Legeay J, Hijri M. A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02060-2. [PMID: 35739325 DOI: 10.1007/s00248-022-02060-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
In the last decade, various large-scale projects describing soil microbial diversity across large geographical gradients have been undertaken. However, many questions remain unanswered about the best ways to conduct these studies. In this review, we present an overview of the experience gathered during these projects, and of the challenges that future projects will face, such as standardization of protocols and results, considering the temporal variation of microbiomes, and the legal constraints limiting such studies. We also present the arguments for and against the exhaustive description of soil microbiomes. Finally, we look at future developments of soil microbiome studies, notably emphasizing the important role of cultivation techniques.
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Affiliation(s)
- Jean Legeay
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
| | - Mohamed Hijri
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Institut de La Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montreal, QE, H1X 2B2, Canada
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22
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Berg G, Cernava T. The plant microbiota signature of the Anthropocene as a challenge for microbiome research. MICROBIOME 2022; 10:54. [PMID: 35346369 PMCID: PMC8959079 DOI: 10.1186/s40168-021-01224-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/23/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene. RESULTS Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies. CONCLUSIONS Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health. Video abstract.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria.
- Leibniz-Institute for Agricultural Engineering Potsdam, Max-Eyth-Allee 100, 14469, Potsdam, Germany.
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476, Potsdam, Germany.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
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23
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Perreault R, Laforest-Lapointe I. Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene. THE ISME JOURNAL 2022; 16:339-345. [PMID: 34522008 PMCID: PMC8776876 DOI: 10.1038/s41396-021-01109-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 02/08/2023]
Abstract
Global change is a defining feature of the Anthropocene, the current human-dominated epoch, and poses imminent threats to ecosystem dynamics and services such as plant productivity, biodiversity, and environmental regulation. In this era, terrestrial ecosystems are experiencing perturbations linked to direct habitat modifications as well as indirect effects of global change on species distribution and extreme abiotic conditions. Microorganisms represent an important reservoir of biodiversity that can influence macro-organisms as they face habitat loss, rising atmospheric CO2 concentration, pollution, global warming, and increased frequency of drought. Plant-microbe interactions in the phyllosphere have been shown to support plant growth and increase host resistance to biotic and abiotic stresses. Here, we review how plant-microbe interactions in the phyllosphere can influence host survival and fitness in the context of global change. We highlight evidence that plant-microbe interactions (1) improve urban pollution remediation through the degradation of pollutants such as ultrafine particulate matter, black carbon, and atmospheric hydrocarbons, (2) have contrasting impacts on plant species range shifts through the loss of symbionts or pathogens, and (3) drive plant host adaptation to drought and warming. Finally, we discuss how key community ecology processes could drive plant-microbe interactions facing challenges of the Anthropocene.
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Affiliation(s)
- Rosaëlle Perreault
- grid.86715.3d0000 0000 9064 6198Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1 Canada
| | - Isabelle Laforest-Lapointe
- grid.86715.3d0000 0000 9064 6198Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1 Canada ,grid.86715.3d0000 0000 9064 6198Centre Sève, Université de Sherbrooke, Sherbrooke, QC J1K 2R1 Canada
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24
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Meyer-Wolfarth F, Oldenburg E, Meiners T, Muñoz K, Schrader S. Effects of temperature and soil fauna on the reduction and leaching of deoxynivalenol and zearalenone from Fusarium graminearum-infected maize stubbles. Mycotoxin Res 2021; 37:249-263. [PMID: 34173210 PMCID: PMC8318931 DOI: 10.1007/s12550-021-00434-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/30/2022]
Abstract
A microcosm study was conducted at two different temperatures under laboratory conditions to investigate the regulatory capacity and the interactive performance of two soil fauna species (Aporrectodea caliginosa, earthworms, and Proisotoma minuta, collembolans) on the reduction of Fusarium toxins in contaminated maize stubbles. Single and mixed species treatments were exposed to artificially infected maize stubbles highly contaminated with the mycotoxins deoxynivalenol (DON) (10,462 µg kg−1) and zearalenone (ZEN) (2,780 µg kg−1) at 17 °C and 25 °C for time periods of 3 and 6 weeks. Immediately after the respective end of incubation, the microcosms were heavily watered to determine the leaching potential of DON and ZEN from contaminated maize stubbles. Maize residues, soil, and eluted water (percolate) samples were analysed for mycotoxin content using liquid chromatography coupled to mass spectrometry. The biomass of introduced earthworms and number of collembolans were monitored to get information about their adaptability to the experimental conditions. While the decline of ZEN was temperature-dependent, but not influenced by faunal activities, a reduction of DON due to faunal impact was observed by trend. In the leaching experiment, 67–82% of the DON content in the residual maize stubbles leached from the plant material by irrigation and was detected in the soil (1.9–3.4 µg kg−1) and in the percolate (12–295 µg L−1). In the case of ZEN, 27–50% of the mycotoxin leached from the residual maize stubbles due to watering but was only occasionally detected in traces in the soil and not found in the percolate. The results clearly reveal a leaching potential of both DON and ZEN, respectively, but a mobilisation with water was only observed for DON. Temperature confirmed to be a key factor, affecting the fate of the mycotoxins in the soil by driving the interaction between different soil fauna members as well as functional and trophic levels within the soil food web.
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Affiliation(s)
- Friederike Meyer-Wolfarth
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Field Crops and Grassland, Messeweg 11/12, 38104, Braunschweig, Germany. .,Johann Heinrich von Thünen Institute (TI) - Federal Research Institute for Rural Areas, Forestry and Fisheries, Institute of Biodiversity , Bundesallee 65, 38116, Braunschweig, Germany.
| | - Elisabeth Oldenburg
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Field Crops and Grassland, Messeweg 11/12, 38104, Braunschweig, Germany
| | - Torsten Meiners
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Königin-Luise-Straße 19, 14195, Berlin, Germany
| | - Katherine Muñoz
- University Koblenz-Landau, Institute for Environmental Sciences, Fortstr. 7, 76829, Landau, Germany
| | - Stefan Schrader
- Johann Heinrich von Thünen Institute (TI) - Federal Research Institute for Rural Areas, Forestry and Fisheries, Institute of Biodiversity , Bundesallee 65, 38116, Braunschweig, Germany
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