1
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Lin C, Li WJ, Li LJ, Neilson R, An XL, Zhu YG. Movement of protistan trophic groups in soil-plant continuums. Environ Microbiol 2023; 25:2641-2652. [PMID: 37547979 DOI: 10.1111/1462-2920.16477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Protists, functionally divided into consumers, phototrophs, and parasites act as integral components and vital regulators of microbiomes in soil-plant continuums. However, the drivers of community structure, assembly mechanisms, co-occurrence patterns, and the associations with human pathogens and different protistan trophic groups remain unknown. Here, we characterized the phyllosphere and soil protistan communities associated with three vegetables under different fertilization treatments (none and organic fertilization) at five growth stages. In this study, consumers were the most diverse soil protist group, had the role of inter-kingdom connector, and were the primary biomarker for rhizosphere soils which were subjected to decreasing deterministic processes during plant growth. In contrast, phototrophs had the greatest niche breadth and formed soil protistan hubs, and were the primary biomarkers for both bulk soils and the phyllosphere. Parasites had minimal input to microbial co-occurrence networks. Organic fertilization increased the relative abundance (RA) of pathogenic protists and the number of pathogen-consumer connections in rhizosphere soils but decreased protistan richness and the number of internal protistan links. This study advances our understanding of the ecological roles and potential links between human pathogens and protistan trophic groups associated with soil-plant continuums, which is fundamental to the regulation of soil-plant microbiomes and maintenance of environmental and human health.
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Affiliation(s)
- Chenshuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Jing Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Juan Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, Scotland, UK
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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2
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Zhu L, Chen Y, Sun R, Zhang J, Hale L, Dumack K, Geisen S, Deng Y, Duan Y, Zhu B, Li Y, Liu W, Wang X, Griffiths BS, Bonkowski M, Zhou J, Sun B. Resource-dependent biodiversity and potential multi-trophic interactions determine belowground functional trait stability. MICROBIOME 2023; 11:95. [PMID: 37127665 PMCID: PMC10150482 DOI: 10.1186/s40168-023-01539-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND For achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organism interactions that ultimately lead to the stabilization or collapse of terrestrial ecosystem functions, but evidence to support this belief is still limited. Here, we leveraged field experiments from the Chinese National Ecosystem Research Network (CERN) and two microcosm experiments mimicking high and low resource conditions to explore how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability. RESULTS We found that agricultural practice-induced higher resource availability increased potential cross-trophic interactions over 316% in fields, which in turn had a greater effect on functional trait stability, while low resource availability made the stability more dependent on the potential within trophic interactions and soil biodiversity. This large-scale pattern was confirmed by fine-scale microcosm systems, showing that microcosms with sufficient nutrient supply increase the proportion of potential cross-trophic interactions, which were positively associated with functional stability. Resource-driven belowground biodiversity and multi-trophic interactions ultimately feedback to the stability of plant biomass. CONCLUSIONS Our results indicated the importance of potential multi-trophic interactions in supporting belowground functional trait stability, especially when nutrients are sufficient, and also suggested the ecological benefits of fertilization programs in modern agricultural intensification. Video Abstract.
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Affiliation(s)
- Lingyue Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Nanjing, 210008, China.
| | - Ruibo Sun
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Nanjing, 210008, China.
| | - Lauren Hale
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- United States Department of Agriculture, Agricultural Research Service (ARS), Washington, DC, 20250, USA
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, 50674, Cologne, Germany
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6700AB, The Netherlands
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100081, China
| | - Yinghua Duan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bo Zhu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yan Li
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Wenzhao Liu
- Institute of Soil and Water Conservation, Chine, Academy of Sciences and Ministry of Water Resources , Yangling, 712100, China
| | - Xiaoyue Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Nanjing, 210008, China
| | - Bryan S Griffiths
- SRUC, Crop and Soil System Research Group, West Mains Road, Edinburgh, EH93JG, UK
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, 50674, Cologne, Germany
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Nanjing, 210008, China.
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3
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Kulaš A, Žutinić P, Gulin Beljak V, Kepčija RM, Perić MS, Orlić S, Petrić IS, Marković T, Gligora Udovič M. Diversity of protist genera in periphyton of tufa-depositing karstic river. ANN MICROBIOL 2023. [DOI: 10.1186/s13213-023-01712-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023] Open
Abstract
Abstract
Purpose
In aquatic ecosystems, protists play a crucial role and cover numerous ecological functions. The karstic Krka River (Croatia) is a unique hotspot for high diversity of aquatic organisms, especially protists. The main objective of the present study was to obtain a detailed overview of the protist community structure in the periphyton of the Krka River and to determine the differences in protist diversity along the river.
Methods
Protist diversity was detected by amplicon sequencing of the hypervariable region V9 of the 18S rRNA gene, using the universal eukaryotic primer pair.
Results
The three main groups of protists were as follows: Ciliophora, Cercozoa, and Bacillariophyta. In terms of abundance of protist OTUs, the shade plot revealed an evident difference from the upstream to downstream river section, which increased between locations from Krka spring to Skradinski buk. Diversity was explored using measures of alpha and beta diversity. Alpha diversity showed an increasing trend in the downstream direction of the river. The location effect, or clustering/grouping of samples by location, was confirmed by the PERMANOVA permutation test of beta diversity.
Conclusion
The combination of alpha and beta diversity can help provide deeper insight into the study of diversity patterns, but also point out to decline in species diversity and allow for effective ways to protect aquatic karst habitats in future management.
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4
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Wang L, Zhao M, Du X, Feng K, Gu S, Zhou Y, Yang X, Zhang Z, Wang Y, Zhang Z, Zhang Q, Xie B, Han G, Deng Y. Fungi and cercozoa regulate methane-associated prokaryotes in wetland methane emissions. Front Microbiol 2023; 13:1076610. [PMID: 36687630 PMCID: PMC9853292 DOI: 10.3389/fmicb.2022.1076610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023] Open
Abstract
Wetlands are natural sources of methane (CH4) emissions, providing the largest contribution to the atmospheric CH4 pool. Changes in the ecohydrological environment of coastal salt marshes, especially the surface inundation level, cause instability in the CH4 emission levels of coastal ecosystems. Although soil methane-associated microorganisms play key roles in both CH4 generation and metabolism, how other microorganisms regulate methane emission and their responses to inundation has not been investigated. Here, we studied the responses of prokaryotic, fungal and cercozoan communities following 5 years of inundation treatments in a wetland experimental site, and molecular ecological networks analysis (MENs) was constructed to characterize the interdomain relationship. The result showed that the degree of inundation significantly altered the CH4 emissions, and the abundance of the pmoA gene for methanotrophs shifted more significantly than the mcrA gene for methanogens, and they both showed significant positive correlations to methane flux. Additionally, we found inundation significantly altered the diversity of the prokaryotic and fungal communities, as well as the composition of key species in interactions within prokaryotic, fungal, and cercozoan communities. Mantel tests indicated that the structure of the three communities showed significant correlations to methane emissions (p < 0.05), suggesting that all three microbial communities directly or indirectly contributed to the methane emissions of this ecosystem. Correspondingly, the interdomain networks among microbial communities revealed that methane-associated prokaryotic and cercozoan OTUs were all keystone taxa. Methane-associated OTUs were more likely to interact in pairs and correlated negatively with the fungal and cercozoan communities. In addition, the modules significantly positively correlated with methane flux were affected by environmental stress (i.e., pH) and soil nutrients (i.e., total nitrogen, total phosphorus and organic matter), suggesting that these factors tend to positively regulate methane flux by regulating microbial relationships under inundation. Our findings demonstrated that the inundation altered microbial communities in coastal wetlands, and the fungal and cercozoan communities played vital roles in regulating methane emission through microbial interactions with the methane-associated community.
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Affiliation(s)
- Linlin Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mingliang Zhao
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yuqi Zhou
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yingcheng Wang
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Zheng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qi Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Baohua Xie
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China,Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Guangxuan Han
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China,Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Ye Deng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China,CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Ye Deng,
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5
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Hess S, Suthaus A. The Vampyrellid Amoebae (Vampyrellida, Rhizaria). Protist 2022; 173:125854. [DOI: 10.1016/j.protis.2021.125854] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/25/2021] [Accepted: 12/13/2021] [Indexed: 11/29/2022]
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6
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Dumack K, Ferlian O, Morselli Gysi D, Degrune F, Jauss RT, Walden S, Öztoprak H, Wubet T, Bonkowski M, Eisenhauer N. Contrasting protist communities (Cercozoa: Rhizaria) in pristine and earthworm-invaded North American deciduous forests. Biol Invasions 2022. [DOI: 10.1007/s10530-021-02726-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractEarthworms are considered ecosystem engineers due to their fundamental impact on soil structure, soil processes and on other soil biota. An invasion of non-native earthworm species has altered soils of North America since European settlement, a process currently expanding into still earthworm-free forest ecosystems due to continuous spread and increasing soil temperatures owing to climate change. Although earthworms are known to modify soil microbial diversity and activity, it is as yet unclear how eukaryote consumers in soil microbial food webs will be affected. Here, we investigated how earthworm invasion affects the diversity of Cercozoa, one of the most dominant protist taxa in soils. Although the composition of the native cercozoan community clearly shifted in response to earthworm invasion, the communities of the different forests showed distinct responses. We identified 39 operational taxonomic units (OTUs) exclusively indicating earthworm invasion, hinting at an earthworm-associated community of Cercozoa. In particular, Woronina pythii, a hyper-parasite of plant-parasitic Oomycota in American forests, increased strongly in the presence of invasive earthworms, indicating an influence of invasive earthworms on oomycete communities and potentially on forest health, which requires further research.
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7
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Mazel F, Malard L, Niculita-Hirzel H, Yashiro E, Mod HK, Mitchell EAD, Singer D, Buri A, Pinto E, Guex N, Lara E, Guisan A. Soil protist function varies with elevation in the Swiss Alps. Environ Microbiol 2021; 24:1689-1702. [PMID: 34347350 PMCID: PMC9290697 DOI: 10.1111/1462-2920.15686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/06/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600 m of elevation in the Swiss Alps (from 400 to 3000 m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400–1000 m), this ratio increases to 12 at high elevation (2000–3000 m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Lucie Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Hélène Niculita-Hirzel
- Department of Occupational Health and Environment, Center for Primary Care and Public Health (Unisanté), University of Lausanne, Epalinges, CH-1066, Switzerland
| | - Erika Yashiro
- Center for Microbial Communities, Section of Biotechnology, Aalborg University, Aalborg, Denmark
| | - Heidi K Mod
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel, CH-2000, Switzerland
| | - David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,UMR CNRS 6112 LPG-BIAF, Université d'Angers, Angers Cedex 1, France
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Eric Pinto
- Terrabiom Association, Dörflistrasse 32, Oberrieden, Zürich, 8942, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Enrique Lara
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.,Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
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8
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Le Provost G, Thiele J, Westphal C, Penone C, Allan E, Neyret M, van der Plas F, Ayasse M, Bardgett RD, Birkhofer K, Boch S, Bonkowski M, Buscot F, Feldhaar H, Gaulton R, Goldmann K, Gossner MM, Klaus VH, Kleinebecker T, Krauss J, Renner S, Scherreiks P, Sikorski J, Baulechner D, Blüthgen N, Bolliger R, Börschig C, Busch V, Chisté M, Fiore-Donno AM, Fischer M, Arndt H, Hoelzel N, John K, Jung K, Lange M, Marzini C, Overmann J, Paŝalić E, Perović DJ, Prati D, Schäfer D, Schöning I, Schrumpf M, Sonnemann I, Steffan-Dewenter I, Tschapka M, Türke M, Vogt J, Wehner K, Weiner C, Weisser W, Wells K, Werner M, Wolters V, Wubet T, Wurst S, Zaitsev AS, Manning P. Contrasting responses of above- and belowground diversity to multiple components of land-use intensity. Nat Commun 2021; 12:3918. [PMID: 34168127 PMCID: PMC8225671 DOI: 10.1038/s41467-021-23931-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/21/2021] [Indexed: 11/08/2022] Open
Abstract
Land-use intensification is a major driver of biodiversity loss. However, understanding how different components of land use drive biodiversity loss requires the investigation of multiple trophic levels across spatial scales. Using data from 150 agricultural grasslands in central Europe, we assess the influence of multiple components of local- and landscape-level land use on more than 4,000 above- and belowground taxa, spanning 20 trophic groups. Plot-level land-use intensity is strongly and negatively associated with aboveground trophic groups, but positively or not associated with belowground trophic groups. Meanwhile, both above- and belowground trophic groups respond to landscape-level land use, but to different drivers: aboveground diversity of grasslands is promoted by diverse surrounding land-cover, while belowground diversity is positively related to a high permanent forest cover in the surrounding landscape. These results highlight a role of landscape-level land use in shaping belowground communities, and suggest that revised agroecosystem management strategies are needed to conserve whole-ecosystem biodiversity.
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Affiliation(s)
- Gaëtane Le Provost
- Senckenberg Biodiversity and Climate Research Centre (SBIK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany.
| | - Jan Thiele
- Thünen Institute of Biodiversity, Braunschweig, Germany
| | - Catrin Westphal
- Functional Agrobiodiversity, Department of Crop Sciences, University of Göttingen, Göttingen, Germany
| | - Caterina Penone
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Eric Allan
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Margot Neyret
- Senckenberg Biodiversity and Climate Research Centre (SBIK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
| | - Fons van der Plas
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, Leipzig, Germany
- Plant Ecology and Nature Conservation Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Manfred Ayasse
- Institute of Evolutionary Ecology and Conservations Genomics, University of Ulm, Ulm, Germany
| | - Richard D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Klaus Birkhofer
- Department of Ecology, Brandenburg University of Technology, Cottbus, Germany
| | - Steffen Boch
- Biodiversity and Conservation Biology, WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Köln, Germany
| | - Francois Buscot
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Heike Feldhaar
- Animal Ecology I, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Rachel Gaulton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Kezia Goldmann
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
| | - Martin M Gossner
- Forest Entomology, WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Universitätstr. 16, Zürich, Switzerland
| | - Valentin H Klaus
- Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zürich, Universitätstr. 2, Zürich, Switzerland
| | - Till Kleinebecker
- Department of Landscape Ecology and Resources Management, Justus Liebig University Giessen, Gießen, Germany
| | - Jochen Krauss
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Swen Renner
- Institute of Evolutionary Ecology and Conservations Genomics, University of Ulm, Ulm, Germany
- Ornithology, Natural History Museum Vienna, Vienna, Austria
| | | | - Johannes Sikorski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dennis Baulechner
- Department of Animal Ecology, Justus Liebig University Giessen, Giessen, Germany
| | - Nico Blüthgen
- Ecological Networks, Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Ralph Bolliger
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Carmen Börschig
- Agroecology, Department of Crop Sciences, Georg-August University of Göttingen, Göttingen, Germany
| | - Verena Busch
- Department of Landscape Ecology and Resources Management, Justus Liebig University Giessen, Gießen, Germany
| | - Melanie Chisté
- Ecological Networks, Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | | | - Markus Fischer
- Senckenberg Biodiversity and Climate Research Centre (SBIK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Hartmut Arndt
- Institute of Zoology, General Ecology, University of Cologne, Köln (Cologne), Germany
| | - Norbert Hoelzel
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Katharina John
- Ecological Networks, Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Kirsten Jung
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Markus Lange
- Max Planck Institute for Biogeochemistry, Jena, Germany
- Institute of Ecology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Carlo Marzini
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Esther Paŝalić
- Institute of Ecology, Friedrich-Schiller-University Jena, Jena, Germany
| | - David J Perović
- DPI Agriculture, NSW Department of Primary Industries, Australian Cotton Research Institute, Narrabri, NSW, Australia
| | - Daniel Prati
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Deborah Schäfer
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Ingo Schöning
- Max Planck Institute for Biogeochemistry, Jena, Germany
| | | | - Ilja Sonnemann
- Institute of Biology, Functional Biodiversity, Freie Universität Berlin, Berlin, Germany
| | - Ingolf Steffan-Dewenter
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Marco Tschapka
- Institute of Evolutionary Ecology and Conservations Genomics, University of Ulm, Ulm, Germany
| | - Manfred Türke
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Juliane Vogt
- Terrestrial Ecology Research Group, Department of Ecology and Ecosystem Management, Technical University of Munich, Freising, Germany
| | - Katja Wehner
- Ecological Networks, Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Christiane Weiner
- Ecological Networks, Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Wolfgang Weisser
- Terrestrial Ecology Research Group, Department of Ecology and Ecosystem Management, Technical University of Munich, Freising, Germany
| | - Konstans Wells
- Department of Biosciences, Swansea University, Swansea, UK
| | - Michael Werner
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Volkmar Wolters
- Department of Animal Ecology, Justus Liebig University Giessen, Giessen, Germany
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Susanne Wurst
- Institute of Biology, Functional Biodiversity, Freie Universität Berlin, Berlin, Germany
| | - Andrey S Zaitsev
- Department of Animal Ecology, Justus Liebig University Giessen, Giessen, Germany
- Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Peter Manning
- Senckenberg Biodiversity and Climate Research Centre (SBIK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
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9
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Walden S, Jauss RT, Feng K, Fiore-Donno AM, Dumack K, Schaffer S, Wolf R, Schlegel M, Bonkowski M. On the phenology of protists: recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa and Endomyxa) communities in tree canopies. FEMS Microbiol Ecol 2021; 97:fiab081. [PMID: 34117748 PMCID: PMC8213970 DOI: 10.1093/femsec/fiab081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/10/2021] [Indexed: 11/23/2022] Open
Abstract
Tree canopies are colonized by billions of highly specialized microorganisms that are well adapted to the highly variable microclimatic conditions, caused by diurnal fluctuations and seasonal changes. In this study, we investigated seasonality patterns of protists in the tree canopies of a temperate floodplain forest via high-throughput sequencing with group-specific primers for the phyla Cercozoa and Endomyxa. We observed consistent seasonality, and identified divergent spring and autumn taxa. Tree crowns were characterized by a dominance of bacterivores and omnivores, while eukaryvores gained a distinctly larger share in litter and soil communities on the ground. In the canopy seasonality was largest among communities detected on the foliar surface: In spring, higher variance within alpha diversity of foliar samples indicated greater heterogeneity during initial colonization. However, communities underwent compositional changes during the aging of leaves in autumn, highly reflecting recurring phenological changes during protistan colonization. Surprisingly, endomyxan root pathogens appeared to be exceptionally abundant across tree canopies during autumn, demonstrating a potential role of the canopy surface as a physical filter for air-dispersed propagules. Overall, about 80% of detected OTUs could not be assigned to known species-representing dozens of microeukaryotic taxa whose canopy inhabitants are waiting to be discovered.
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Affiliation(s)
- Susanne Walden
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Robin-Tobias Jauss
- Institute of Biology, Biodiversity and Evolution, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, No. 18 Shuangqing Road, 100085 Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, 100049 Beijing, China
| | - Anna Maria Fiore-Donno
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Kenneth Dumack
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Stefan Schaffer
- Institute of Biology, Molecular Evolution and Animal Systematics, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ronny Wolf
- Institute of Biology, Molecular Evolution and Animal Systematics, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Martin Schlegel
- Institute of Biology, Biodiversity and Evolution, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
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10
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Jauss RT, Nowack A, Walden S, Wolf R, Schaffer S, Schellbach B, Bonkowski M, Schlegel M. To the canopy and beyond: Air dispersal as a mechanism of ubiquitous protistan pathogen assembly in tree canopies. Eur J Protistol 2021; 80:125805. [PMID: 34090087 DOI: 10.1016/j.ejop.2021.125805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 01/19/2023]
Abstract
Cercozoa and Oomycota contain a huge biodiversity and important pathogens of forest trees and other vegetation. We analyzed air dispersal of these protistan phyla with an air sampler near-ground (~2 m) and in tree crowns (~25 m) of three tree species (oak, linden and ash) in a temperate floodplain forest in March (before leafing) and May (after leaf unfolding) 2019 with a cultivation-independent high-throughput metabarcoding approach. We found a high diversity of Cercozoa and Oomycota in air samples with 122 and 81 OTUs, respectively. Especially oomycetes showed a significant difference in community composition between both sampling dates. Differences in community composition between air samples in tree canopies and close to the ground were however negligible, and also tree species identity did not affect communities in air samples, indicating that the distribution of protistan propagules through the air was not spatially restricted in the forest ecosystem. OTUs of plant pathogens, whose host species did not occur in the forest, demonstrate dispersal of propagules from outside the forest biome. Overall, our results lead to a better understanding of the stochastic processes of air dispersal of protists and protistan pathogens, a prerequisite to understand the mechanisms of their community assembly in forest ecosystems.
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Affiliation(s)
- Robin-Tobias Jauss
- University of Leipzig, Institute of Biology, Biodiversity and Evolution, Talstraße 33, 04103 Leipzig, Germany.
| | - Anne Nowack
- University of Leipzig, Institute of Biology, Biodiversity and Evolution, Talstraße 33, 04103 Leipzig, Germany
| | - Susanne Walden
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Ronny Wolf
- University of Leipzig, Institute of Biology, Molecular Evolution & Animal Systematics, Talstraße 33, 04103 Leipzig, Germany
| | - Stefan Schaffer
- University of Leipzig, Institute of Biology, Molecular Evolution & Animal Systematics, Talstraße 33, 04103 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Barbara Schellbach
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Michael Bonkowski
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Martin Schlegel
- University of Leipzig, Institute of Biology, Biodiversity and Evolution, Talstraße 33, 04103 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
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11
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Rüger L, Feng K, Dumack K, Freudenthal J, Chen Y, Sun R, Wilson M, Yu P, Sun B, Deng Y, Hochholdinger F, Vetterlein D, Bonkowski M. Assembly Patterns of the Rhizosphere Microbiome Along the Longitudinal Root Axis of Maize ( Zea mays L.). Front Microbiol 2021; 12:614501. [PMID: 33643242 PMCID: PMC7906986 DOI: 10.3389/fmicb.2021.614501] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/25/2021] [Indexed: 02/02/2023] Open
Abstract
It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil - their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly of communities of prokaryotes (archaea and bacteria) and their protistan predators (Cercozoa, Rhizaria) along the longitudinal root axis of maize (Zea mays L.). We grew maize plants in an agricultural loamy soil and sampled rhizosphere soil at distinct locations along maize roots. We applied high-throughput sequencing, followed by diversity and network analyses in order to track changes in relative abundances, diversity and co-occurrence of rhizosphere microbiota along the root axis. Apart from a reduction of operational taxonomic unit (OTU) richness and a strong shift in community composition between bulk soil and root tips, patterns of microbial community assembly along maize-roots were more complex than expected. High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Root hair zone communities were characterized by massive co-occurrence of microbial taxa, likely fueled by abundant resource supply from rhizodeposition. Further up the root where lateral roots emerged processes of community assembly appeared to be more deterministic (e.g., through competition and predation). This shift toward significance of deterministic processes was revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their potential protistan predators. Such patterns were strongest in regions with fully developed laterals, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is crucially important.
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Affiliation(s)
- Lioba Rüger
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Jule Freudenthal
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Yan Chen
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ruibo Sun
- Microbial Ecology Lab, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Monica Wilson
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Peng Yu
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Bo Sun
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
- Soil Science, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
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12
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Khanipour Roshan S, Dumack K, Bonkowski M, Leinweber P, Karsten U, Glaser K. Taxonomic and Functional Diversity of Heterotrophic Protists (Cercozoa and Endomyxa) from Biological Soil Crusts. Microorganisms 2021; 9:205. [PMID: 33498223 PMCID: PMC7908994 DOI: 10.3390/microorganisms9020205] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/25/2022] Open
Abstract
Biological soil crusts (biocrusts) accommodate diverse communities of phototrophic and heterotrophic microorganisms. Heterotrophic protists have critical roles in the microbial food webs of soils, with Cercozoa and Endomyxa often being dominant groups. Still, the diversity, community composition, and functions of Cercozoa and Endomyxa in biocrusts have been little explored. In this study, using a high-throughput sequencing method with taxon-specific barcoded primers, we studied cercozoan and endomyxan communities in biocrusts from two unique habitats (subarctic grassland and temperate dunes). The communities differed strongly, with the grassland and dunes being dominated by Sarcomonadea (69%) and Thecofilosea (43%), respectively. Endomyxa and Phytomyxea were the minor components in dunes. Sandonidae, Allapsidae, and Rhogostomidae were the most abundant taxa in both habitats. In terms of functionality, up to 69% of the grassland community was constituted by bacterivorous Cercozoa. In contrast, cercozoan and endomyxan communities in dunes consisted of 31% bacterivores, 25% omnivores, and 20% eukaryvores. Facultative and obligate eukaryvores mostly belonged to the families Rhogostomidae, Fiscullidae, Euglyphidae, Leptophryidae, and Cercomonadidae, most of which are known to feed mainly on algae. Biocrust edaphic parameters such as pH, total organic carbon, nitrogen, and phosphorus did not have any significant influence on shaping cercozoan communities within each habitat, which confirms previous results from dunes.
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Affiliation(s)
- Samira Khanipour Roshan
- Institute for Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (U.K.); (K.G.)
| | - Kenneth Dumack
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany; (K.D.); (M.B.)
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany; (K.D.); (M.B.)
| | - Peter Leinweber
- Faculty of Agriculture and Environmental Sciences, Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany;
| | - Ulf Karsten
- Institute for Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (U.K.); (K.G.)
| | - Karin Glaser
- Institute for Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (U.K.); (K.G.)
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13
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Jauss RT, Walden S, Fiore-Donno AM, Dumack K, Schaffer S, Wolf R, Schlegel M, Bonkowski M. From Forest Soil to the Canopy: Increased Habitat Diversity Does Not Increase Species Richness of Cercozoa and Oomycota in Tree Canopies. Front Microbiol 2020; 11:592189. [PMID: 33414768 PMCID: PMC7782269 DOI: 10.3389/fmicb.2020.592189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/07/2020] [Indexed: 02/02/2023] Open
Abstract
Tree canopies provide habitats for diverse and until now, still poorly characterized communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa (Rhizaria) and Oomycota (Stramenopiles), was performed. Group specific primers were used to comprehensively analyze their diversity in various microhabitats of a floodplain forest from the forest floor to the canopy region. Beta diversity indicated highly dissimilar protistan communities in the investigated microhabitats. However, the majority of operational taxonomic units (OTUs) was present in all samples, and therefore differences in beta diversity were mainly related to species performance (i.e., relative abundance). Accordingly, habitat diversity strongly favored distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible.
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Affiliation(s)
- Robin-Tobias Jauss
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Susanne Walden
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | | | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Stefan Schaffer
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Ronny Wolf
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Martin Schlegel
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Leipzig, Germany
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
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