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Wang Y, Xiao B, Wang W, Saéz-Sandino T, Delgado-Baquerizo M. Cyanobacterial and moss biocrusts shape soil nematode community in dryland mountain ecosystems with increasing aridity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172750. [PMID: 38677426 DOI: 10.1016/j.scitotenv.2024.172750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024]
Abstract
Soil nematodes are the most abundant animals on Earth and play critical roles in regulating numerous ecosystem processes, from enhancing primary productivity to mineralizing multiple nutrients. In dryland soils, a rich community of microphyte organisms (biocrusts) provide critical habitats for soil nematodes, but their presence is being threatened by increasing aridity induced by global climate change. Despite its importance, how types of biocrusts and aridity index influence soil nematode community in dryland mountain ecosystems remains largely unknown. To fill these knowledge gaps, we conducted a field survey with contrasting aridity indexes (0.2, 0.4, and 0.6) and three types of biocrusts (cyanobacterial, cyanobacterial-moss mixed, and moss crusts) in the topsoil (0-5 cm) from the northern Chinese Loess Plateau. We found that the abundance (number of individuals per gram of soil), richness (number of Operational Taxonomic Units; OTUs), and diversity (number of different species) of soil nematodes were remarkably higher under biocrusts than in bare soils, regardless of aridity index and types of biocrusts. Our results also showed that the same variables had the highest values in moss crusts compared to cyanobacterial and cyanobacterial-moss mixed crusts. Structural equation modelling further revealed that biocrust types and traits (i.e., biocrust thickness, chlorophyll content, shear force, and penetration resistance) are the most important factors associated with both nematode abundance and richness. Together, our findings indicate that biocrusts, especially moss cover, and less stressful aridity conditions favor soil nematodes community in dryland mountain regions. Such knowledge is critical for anticipating the distribution of these animals under climate change scenarios and, ultimately, the numerous ecosystem services supported by soil nematodes.
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Affiliation(s)
- Yanfeng Wang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Xiao
- Key Laboratory of Arable Land Conservation in North China, Ministry of Agriculture and Rural Affairs/College of Land Science and Technology, China Agricultural University, Beijing 100193, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wanfu Wang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tadeo Saéz-Sandino
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla 41013, Spain
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville E-41012, Spain
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2
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Barbour KM, Martiny JBH. Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system. THE ISME JOURNAL 2024; 18:wrae043. [PMID: 38506671 PMCID: PMC11008689 DOI: 10.1093/ismejo/wrae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/13/2024] [Accepted: 03/19/2024] [Indexed: 03/21/2024]
Abstract
Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change.
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Affiliation(s)
- Kristin M Barbour
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
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3
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Heffner T, Brami SA, Mendes LW, Kaupper T, Hannula ES, Poehlein A, Horn MA, Ho A. Interkingdom interaction: the soil isopod Porcellio scaber stimulates the methane-driven bacterial and fungal interaction. ISME COMMUNICATIONS 2023; 3:62. [PMID: 37355679 PMCID: PMC10290665 DOI: 10.1038/s43705-023-00271-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/06/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
Porcellio scaber (woodlice) are (sub-)surface-dwelling isopods, widely recognized as "soil bioengineers", modifying the edaphic properties of their habitat, and affecting carbon and nitrogen mineralization that leads to greenhouse gas emissions. Yet, the impact of soil isopods on methane-cycling processes remains unknown. Using P. scaber as a model macroinvertebrate in a microcosm study, we determined how the isopod influences methane uptake and the associated interaction network in an agricultural soil. Stable isotope probing (SIP) with 13C-methane was combined to a co-occurrence network analysis to directly link activity to the methane-oxidizing community (bacteria and fungus) involved in the trophic interaction. Compared to microcosms without the isopod, P. scaber significantly induced methane uptake, associated to a more complex bacteria-bacteria and bacteria-fungi interaction, and modified the soil nutritional status. Interestingly, 13C was transferred via the methanotrophs into the fungi, concomitant to significantly higher fungal abundance in the P. scaber-impacted soil, indicating that the fungal community utilized methane-derived substrates in the food web along with bacteria. Taken together, results showed the relevance of P. scaber in modulating methanotrophic activity with implications for bacteria-fungus interaction.
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Affiliation(s)
- Tanja Heffner
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Semi A Brami
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Lucas W Mendes
- University of São Paulo CENA-USP, Center for Nuclear Energy in Agriculture, Avenida Centenario, 303, 13416-000, Piracicaba (SP), Brazil
| | - Thomas Kaupper
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Emilia S Hannula
- Leiden University, Department of Environmental Biology, Institute of Environmental Sciences, Einsteinweg 2, 2333CC, Leiden, the Netherlands
| | - Anja Poehlein
- Georg-August University Göttingen, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Marcus A Horn
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Adrian Ho
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany.
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4
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Perreault L, Forrester JA, Lindner DL, Jusino MA, Fraver S, Banik MT, Mladenoff DJ. Linking wood-decay fungal communities to decay rates: Using a long-term experimental manipulation of deadwood and canopy gaps. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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The neglected role of micronutrients in predicting soil microbial structure. NPJ Biofilms Microbiomes 2022; 8:103. [PMID: 36575178 PMCID: PMC9794713 DOI: 10.1038/s41522-022-00363-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/29/2022] [Indexed: 12/28/2022] Open
Abstract
Predicting the distribution patterns of soil microbial communities requires consideration of more environmental drivers. The effects of soil micronutrients on composition of microbial communities are largely unknown despite micronutrients closely relating to soil fertility and plant communities. Here we used data from 228 agricultural fields to identify the importance of micronutrients (iron, zinc, copper and manganese) in shaping structure of soil microbial communities (bacteria, fungi and protist) along latitudinal gradient over 3400 km, across diverse edaphic conditions and climatic gradients. We found that micronutrients explained more variations in the structure of microbial communities than macronutrients in maize soils. Moreover, micronutrients, particularly iron and copper, explained a unique percentage of the variation in structure of microbial communities in maize soils even after controlling for climate, soil physicochemical properties and macronutrients, but these effects were stronger for fungi and protist than for bacteria. The ability of micronutrients to predict the structure of soil microbial communities declined greatly in paddy soils. Machine learning approach showed that the addition of micronutrients substantially increased the predictive power by 9-17% in predicting the structure of soil microbial communities with up to 69-78% accuracy. These results highlighted the considerable contributions of soil micronutrients to microbial community structure, and advocated that soil micronutrients should be considered when predicting the structure of microbial communities in a changing world.
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Grazing Effects of Soil Fauna on White-Rot Fungi: Biomass, Enzyme Production and Litter Decomposition Ability. J Fungi (Basel) 2022; 8:jof8040348. [PMID: 35448579 PMCID: PMC9032049 DOI: 10.3390/jof8040348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 11/28/2022] Open
Abstract
Soil invertebrates and microorganisms are two major drivers of litter decomposition. Even though the importance of invertebrates and microorganisms in biogeochemical soil cycles and soil food webs has been studied, the effects of invertebrates on fungi are not well understood compared to other organisms. In this work, we investigated the effects of soil invertebrates on fungi as a factor that cannot be ignored in the study of nutrient cycling. The result showed the grazing of isopods on white-rot fungi was transitive and persistent. The grazed fungi appeared “compensatory” growing. The biomass of fungi increased after grazing. The activities of enzymes associated with nutrient cycling were increased under grazing. The zymography images showed the enzyme hotspots and activities also increased significantly in the grazing area. The results suggest that invertebrate grazing can significantly increase the fungal biomass and enzyme activity, accelerating litter decomposition in the unreached grazer area. The grazing effects of invertebrate plays an important role in promoting the nutrient cycling of the forest ecosystem. We believe that this study will be a good reference related to showing the relationship between soil invertebrates, fungi and soil biogeochemical cycles.
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Nishiya N, Yonezawa H. Domestication of chemicals attacking metazoan embryogenesis: identification of safe natural products modifying developmental signaling pathways in human. J Antibiot (Tokyo) 2021; 74:651-659. [PMID: 34381189 DOI: 10.1038/s41429-021-00461-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 02/06/2023]
Abstract
Soil microorganisms are rich sources of bioactive natural products. Interspecies interactions are the cues of their production and refine biological activities. These interactions in natural environments include the interplay between microorganisms and Metazoans (animals), such as nematodes, insects, and ticks. Chemical intercellular communication modulators could exert ideal Metazoan-selective toxicity for defending microorganisms. Developmental signaling pathways, such as the Notch, TGF-beta, and Wnt pathways, are intercellular communication networks that contribute to the reproducible formation of complex higher-order Metazoan body structures. Natural modifiers of the developmental signaling pathway are attractive therapeutic seeds for carcinoma and sarcoma treatment. However, these fundamental signaling pathways also play indispensable physiological roles and their perturbation could lead to toxicity, such as defects in stem cell physiology and tissue regeneration processes. In this review, we introduce a screening system that selects developmental signaling inhibitors with wide therapeutic windows using zebrafish embryonic phenotypes and provide examples of microorganism-derived Wnt pathway inhibitors. Moreover, we discuss safety prospects of the developmental signaling inhibitors.
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Affiliation(s)
- Naoyuki Nishiya
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Yahaba, Japan.
| | - Honami Yonezawa
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, Yahaba, Japan
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8
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Wang YM, Guan PT, Chen JW, Li ZX, Yang YR, Wang P. A comparison of soil nematode community structure and environmental factors along fen-bush-forest succession in a peatland, northeastern China. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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9
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Wu D, Pietsch KA, Staab M, Yu M. Wood species identity alters dominant factors driving fine wood decomposition along a tree diversity gradient in subtropical plantation forests. Biotropica 2021. [DOI: 10.1111/btp.12906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Donghao Wu
- College of Life Sciences Zhejiang University Hangzhou China
| | - Katherina A. Pietsch
- Institute of Systematic Botany and Functional Biodiversity University of Leipzig Leipzig Germany
| | - Michael Staab
- Department of Nature Conservation and Landscape Ecology Albert‐Ludwigs‐University Freiburg Freiburg Germany
| | - Mingjian Yu
- College of Life Sciences Zhejiang University Hangzhou China
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10
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Des Marteaux LE, Kullik SA, Habash M, Schmidt JM. Terrestrial Isopods Porcellio scaber and Oniscus asellus (Crustacea: Isopoda) Increase Bacterial Abundance and Modify Microbial Community Structure in Leaf Litter Microcosms: a Short-Term Decomposition Study. MICROBIAL ECOLOGY 2020; 80:690-702. [PMID: 32440700 DOI: 10.1007/s00248-020-01527-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Invasive terrestrial isopods are likely to have altered leaf litter decomposition processes in North American forests, but the mechanisms underlying these alterations and the degree to which they differ among isopod species are poorly characterized. Using mixed-deciduous leaf litter microcosms, we quantified the effects of two common, invasive isopods (Oniscus asellus and Porcellio scaber) on short-term leaf litter decomposition and microbial community structure and function. Microcosms containing ground litter and a microbial inoculant were exposed to one of the two isopod species or no isopods for 21 days. Mass loss was then quantified as the change in litter dry mass after leaching, and microbial respiration was quantified as the mass of CO2 absorbed by soda lime. Litter leachates were plated on agar to quantify culturable bacterial and fungal abundance, and denaturing gradient gel electrophoresis of amplified leachate microbial DNA was used to characterize shifts in microbial community structure. Isopod presence increased litter mass loss by a modest ~ 6%, but did not affect litter microbial respiration. Bacterial abundance increased significantly in the presence of isopods, while fungal abundance was either unchanged or reduced. Overall litter microbial species richness was reduced by isopods, with O. asellus specifically reducing fungal abundance and diversity. Isopods modified the microbial community structure by suppressing four bacterial and one fungal species, while promoting growth of four other bacterial species (two unique to each isopod species) and two fungal species (one which was unique to O. asellus).
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Affiliation(s)
- Lauren E Des Marteaux
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada.
- Graduate School of Science, Osaka City University, Osaka, Japan.
| | - Sigrun A Kullik
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Marc Habash
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Jonathan M Schmidt
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
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11
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Coq S, Nahmani J, Kazakou E, Fromin N, David JF. Do litter-feeding macroarthropods disrupt cascading effects of land use on microbial decomposer activity? Basic Appl Ecol 2020. [DOI: 10.1016/j.baae.2020.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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van den Hoogen J, Geisen S, Wall DH, Wardle DA, Traunspurger W, de Goede RGM, Adams BJ, Ahmad W, Ferris H, Bardgett RD, Bonkowski M, Campos-Herrera R, Cares JE, Caruso T, de Brito Caixeta L, Chen X, Costa SR, Creamer R, da Cunha E Castro JM, Dam M, Djigal D, Escuer M, Griffiths BS, Gutiérrez C, Hohberg K, Kalinkina D, Kardol P, Kergunteuil A, Korthals G, Krashevska V, Kudrin AA, Li Q, Liang W, Magilton M, Marais M, Martín JAR, Matveeva E, Mayad EH, Mzough E, Mulder C, Mullin P, Neilson R, Nguyen TAD, Nielsen UN, Okada H, Rius JEP, Pan K, Peneva V, Pellissier L, da Silva JCP, Pitteloud C, Powers TO, Powers K, Quist CW, Rasmann S, Moreno SS, Scheu S, Setälä H, Sushchuk A, Tiunov AV, Trap J, Vestergård M, Villenave C, Waeyenberge L, Wilschut RA, Wright DG, Keith AM, Yang JI, Schmidt O, Bouharroud R, Ferji Z, van der Putten WH, Routh D, Crowther TW. A global database of soil nematode abundance and functional group composition. Sci Data 2020; 7:103. [PMID: 32218461 PMCID: PMC7099023 DOI: 10.1038/s41597-020-0437-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/02/2020] [Indexed: 11/14/2022] Open
Abstract
As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.
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Affiliation(s)
- Johan van den Hoogen
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
| | - Diana H Wall
- Department of Biology and School of Global Environmental Sustainability, Colorado State University, Fort Collins, CO, USA
| | - David A Wardle
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | | | - Ron G M de Goede
- Soil Biology Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Byron J Adams
- Department of Biology, Evolutionary Ecology Laboratories, Monte L. Bean Museum, Brigham Young University, Provo, UT, USA
| | - Wasim Ahmad
- Nematode Biodiversity Research Laboratory, Department of Zoology, Aligarh Muslim University, Aligarh, India
| | - Howard Ferris
- Department of Entomology & Nematology, University of California, Davis, CA, USA
| | - Richard D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, University of Cologne and Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Raquel Campos-Herrera
- Instituto de Ciencias de la Vid y del Vino (Universidad de La Rioja, CSIC, Gobierno de La Rioja), Logroño, Spain
| | - Juvenil E Cares
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Tancredi Caruso
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Larissa de Brito Caixeta
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Xiaoyun Chen
- Soil Ecology Laboratory, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Sofia R Costa
- Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Rachel Creamer
- Soil Biology Group, Wageningen University & Research, Wageningen, The Netherlands
| | - José Mauro da Cunha E Castro
- Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Centro de Pesquisa Agropecuária do Trópico Semiárido, Petrolina, Brazil
| | - Marie Dam
- Zealand Institute of Business and Technology, Slagelse, Denmark
| | - Djibril Djigal
- Institut Sénégalais de Recherches Agricoles/CDH, Dakar, Senegal
| | | | | | | | - Karin Hohberg
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Daria Kalinkina
- Institute of Biology of Karelian Research Centre, Russian Academy of Sciences, Petrozavodsk, Russia
| | - Paul Kardol
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Alan Kergunteuil
- Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Gerard Korthals
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Valentyna Krashevska
- J. F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Alexey A Kudrin
- Institute of Biology of the Komi Scientific Centre, Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Qi Li
- Erguna Forest-Steppe Ecotone Research Station, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Wenju Liang
- Erguna Forest-Steppe Ecotone Research Station, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Matthew Magilton
- School of Biological Sciences, Institute for Global Food Security, Queen's University of Belfast, Belfast, UK
| | - Mariette Marais
- Nematology Unit, Agricultural Research Council, Plant Health and Protection, Pretoria, South Africa
| | | | - Elizaveta Matveeva
- Institute of Biology of Karelian Research Centre, Russian Academy of Sciences, Petrozavodsk, Russia
| | - El Hassan Mayad
- Laboratory of Biotechnology and Valorization of Natural Resources, Faculty of Science Agadir, Ibn Zohr University, Agadir, Morocco
| | - E Mzough
- Laboratory of Biotechnology and Valorization of Natural Resources, Faculty of Science Agadir, Ibn Zohr University, Agadir, Morocco
| | - Christian Mulder
- Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Peter Mullin
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, UK
| | - T A Duong Nguyen
- Institute of Zoology, Terrestrial Ecology, University of Cologne and Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Uffe N Nielsen
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Hiroaki Okada
- Nematode Management Group, Division of Applied Entomology and Zoology, Central Region Agricultural Research Center, NARO, Tsukuba, Japan
| | | | - Kaiwen Pan
- Ecological Processes and Biodiversity, Center for Ecological Studies, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Vlada Peneva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Camille Pitteloud
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Thomas O Powers
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Kirsten Powers
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Casper W Quist
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Sergio Rasmann
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Sara Sánchez Moreno
- Plant Protection Products Unit, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Stefan Scheu
- J. F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany
| | - Heikki Setälä
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Anna Sushchuk
- Institute of Biology of Karelian Research Centre, Russian Academy of Sciences, Petrozavodsk, Russia
| | - Alexei V Tiunov
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Jean Trap
- Eco&Sols, University of Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Mette Vestergård
- Department of Agroecology, AU-Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Cecile Villenave
- Eco&Sols, University of Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- ELISOL Environnement, Congénies, France
| | - Lieven Waeyenberge
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Merelbeke, Belgium
| | - Rutger A Wilschut
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Daniel G Wright
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, UK
| | - Aidan M Keith
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, UK
| | - Jiue-In Yang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Olaf Schmidt
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - R Bouharroud
- Research Unit of Integrated Crop Production, Centre Regional de la Recherche Agronomique d'Agadir, Agadir, Morocco
| | - Z Ferji
- Institut Agronomique et Vétérinaire Hassan II, Campus d'Agadir, Département de Protection des Plantes, Agadir, Morocco
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Devin Routh
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.
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De Gruyter J, Weedon JT, Bazot S, Dauwe S, Fernandez-Garberí PR, Geisen S, De La Motte LG, Heinesch B, Janssens IA, Leblans N, Manise T, Ogaya R, Löfvenius MO, Peñuelas J, Sigurdsson BD, Vincent G, Verbruggen E. Patterns of local, intercontinental and interseasonal variation of soil bacterial and eukaryotic microbial communities. FEMS Microbiol Ecol 2020; 96:5719567. [DOI: 10.1093/femsec/fiaa018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/29/2020] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Although ongoing research has revealed some of the main drivers behind global spatial patterns of microbial communities, spatio-temporal dynamics of these communities still remain largely unexplored. Here, we investigate spatio-temporal variability of both bacterial and eukaryotic soil microbial communities at local and intercontinental scales. We compare how temporal variation in community composition scales with spatial variation in community composition, and explore the extent to which bacteria, protists, fungi and metazoa have similar patterns of temporal community dynamics. All soil microbial groups displayed a strong correlation between spatial distance and community dissimilarity, which was related to the ratio of organism to sample size. Temporal changes were variable, ranging from equal to local between-sample variation, to as large as that between communities several thousand kilometers apart. Moreover, significant correlations were found between bacterial and protist communities, as well as between protist and fungal communities, indicating that these microbial groups change in tandem, potentially driven by interactions between them. We conclude that temporal variation can be considerable in soil microbial communities, and that future studies need to consider temporal variation in order to reliably capture all drivers of soil microbiome changes.
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Affiliation(s)
- Johan De Gruyter
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - James T Weedon
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
- Department of Ecological Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Stéphane Bazot
- Ecologie Systématique Evolution, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Steven Dauwe
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Pere-Roc Fernandez-Garberí
- CREAF, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands
| | - Louis Gourlez De La Motte
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, B-5030 Gembloux, Belgium
| | - Bernard Heinesch
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, B-5030 Gembloux, Belgium
| | - Ivan A Janssens
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Niki Leblans
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Tanguy Manise
- AGROBIOCHEM Research Unit, Gembloux Agro-Bio Tech, University of Liege, B-5030 Gembloux, Belgium
| | - Romà Ogaya
- CREAF, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain
| | - Mikaell Ottosson Löfvenius
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), SE-901 83 Umeå, Sweden
| | - Josep Peñuelas
- CREAF, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain
| | - Bjarni D Sigurdsson
- Faculty of Environmental Sciences, Agricultural University of Iceland, Hvanneyri, IS-311 Borgarnes, Iceland
| | - Gaëlle Vincent
- Ecologie Systématique Evolution, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Erik Verbruggen
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
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14
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc 2019; 94:1443-1476. [PMID: 31021528 PMCID: PMC6850671 DOI: 10.1111/brv.12510] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
Abstract
Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREA, Pg. Lluís Companys 2308010BarcelonaSpain
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15
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Soil nematode abundance and functional group composition at a global scale. Nature 2019; 572:194-198. [DOI: 10.1038/s41586-019-1418-6] [Citation(s) in RCA: 374] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 06/27/2019] [Indexed: 01/28/2023]
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16
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Čuchta P, Kaňa J, Pouska V. An important role of decomposing wood for soil environment with a reference to communities of springtails (Collembola). ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:222. [PMID: 30877494 DOI: 10.1007/s10661-019-7363-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/01/2019] [Indexed: 06/09/2023]
Abstract
Present study focused on how the presence of decaying wood affects soil environment including its biota. The study was carried out in the montane spruce forest, disturbed by wind and bark beetles in Trojmezná Mt. of the Bohemian Forest in the Czech Republic. According to the results, presence of decomposing wood influenced soil environment in terms of its chemical properties by increasing soil pH and total carbon content significantly in soil below the trunks compared with soil from further distance. Decomposing wood did not affect total density and species richness of Collembola, but it had a significant influence on species composition and some species were more abundant in soil right below the trunks whereas others preferred soil environment further from them. Finally, significant relations, both positive and negative, were recorded between some Collembola species and ammonium. Thus, this substance might play a role of a volatile attractant in soil environment.
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Affiliation(s)
- Peter Čuchta
- Biology Centre CAS, Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
| | - Jiří Kaňa
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31a, 370 05, České Budějovice, Czech Republic
| | - Václav Pouska
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praha 6 - Suchdol, Czech Republic
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17
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Consistent trade-offs in fungal trait expression across broad spatial scales. Nat Microbiol 2019; 4:846-853. [DOI: 10.1038/s41564-019-0361-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/06/2019] [Indexed: 12/27/2022]
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18
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Bray N, Kao-Kniffin J, Frey SD, Fahey T, Wickings K. Soil Macroinvertebrate Presence Alters Microbial Community Composition and Activity in the Rhizosphere. Front Microbiol 2019; 10:256. [PMID: 30853947 PMCID: PMC6395791 DOI: 10.3389/fmicb.2019.00256] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Despite decades of research, our understanding of the importance of invertebrates for soil biogeochemical processes remains incomplete. This is especially true when considering soil invertebrate effects mediated through their interactions with soil microbes. The aim of this study was to elucidate how soil macroinvertebrates affect soil microbial community composition and function within the root zone of a managed grass system. We conducted a 2-year field mesocosm study in which soil macroinvertebrate communities were manipulated through size-based exclusion and tracked changes in microbial community composition, diversity, biomass and activity to quantify macroinvertebrate-driven effects on microbial communities and their functions within the rhizosphere. The presence of soil macroinvertebrates created distinct microbial communities and altered both microbial biomass and function. Soil macroinvertebrates increased bacterial diversity and fungal biomass, as well as increased phenol oxidase and glucosidase activities, which are important in the degradation of organic matter. Macroinvertebrates also caused distinct shifts in the relative abundance of different bacterial phyla. Our findings indicate that within the rhizosphere, macroinvertebrates have a stimulatory effect on microbial communities and processes, possibly due to low-intensity microbial grazing or through the dispersal of microbial cells and spores by mobile invertebrates. Our results suggest that macroinvertebrate activity can be an important control on microbially-mediated processes in the rhizosphere such as nitrogen mineralization and soil organic matter formation.
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Affiliation(s)
- Natalie Bray
- Department of Entolomology, Cornell AgriTech, Cornell University, Geneva, NY, United States
| | - Jenny Kao-Kniffin
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Serita D. Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States
| | - Timothy Fahey
- Department of Natural Resources, Cornell University, Ithaca, NY, United States
| | - Kyle Wickings
- Department of Entolomology, Cornell AgriTech, Cornell University, Geneva, NY, United States
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19
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Ohlmann M, Mazel F, Chalmandrier L, Bec S, Coissac E, Gielly L, Pansu J, Schilling V, Taberlet P, Zinger L, Chave J, Thuiller W. Mapping the imprint of biotic interactions on β-diversity. Ecol Lett 2018; 21:1660-1669. [DOI: 10.1111/ele.13143] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/01/2018] [Accepted: 07/25/2018] [Indexed: 01/23/2023]
Affiliation(s)
- Marc Ohlmann
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Florent Mazel
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Loïc Chalmandrier
- Landscape Ecology; Institute of Terrestrial Ecosystems; ETH Zürich; Zürich Switzerland
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | - Stéphane Bec
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Eric Coissac
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Ludovic Gielly
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Johan Pansu
- Princeton University; 110 Morrison Hall Princeton NJ 08544 USA
| | - Vincent Schilling
- Université Toulouse 3 Paul Sabatier; CNRS; IRD; UMR 5174 Evolution et Diversité Biologique (EDB); F-31062 Toulouse France
| | - Pierre Taberlet
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Lucie Zinger
- Ecole Normale Supérieure; PSL Research University; CNRS; Inserm; Institut de Biologie de l'Ecole Normale Supérieure (IBENS); F-75005 Paris France
| | - Jérome Chave
- Université Toulouse 3 Paul Sabatier; CNRS; IRD; UMR 5174 Evolution et Diversité Biologique (EDB); F-31062 Toulouse France
| | - Wilfried Thuiller
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
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Abstract
Understanding the mechanisms underlying wood decay basidiomycete community dynamics is crucial for fully understanding decomposition processes, and for modelling ecosystem function and resilience to environmental change. Competition drives community development in decaying woody resources, with interactions occurring at a distance, following physical contact, and through specialised relationships such as mycoparasitism. Outcomes of combative interactions range from replacement, where one mycelium displaces another, to deadlock, where neither combatant captures territory from the other; and a spectrum of intermediate outcomes (i.e. partial or mutual replacement) lie between these extremes. Many wood decay basidiomycetes coexist within a resource, in a complex and dynamic community, and new research techniques are focussing on spatial orientation of interactions in 3 dimensions, as opposed to historical two-dimensional research. Not only do interactions drive changes in species composition and thus wood decomposition rate, they also may have industrial applications in biocontrol of pathogenic or nuisance fungi, enzyme production, and in the production of novel antifungals and antibiotics. Altogether, fungal interactions are a fascinating and important field of study.
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21
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Birkemoe T, Jacobsen RM, Sverdrup-Thygeson A, Biedermann PHW. Insect-Fungus Interactions in Dead Wood Systems. SAPROXYLIC INSECTS 2018. [DOI: 10.1007/978-3-319-75937-1_12] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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22
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Leopold DR, Wilkie JP, Dickie IA, Allen RB, Buchanan PK, Fukami T. Priority effects are interactively regulated by top‐down and bottom‐up forces: evidence from wood decomposer communities. Ecol Lett 2017; 20:1054-1063. [DOI: 10.1111/ele.12803] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/26/2017] [Accepted: 06/04/2017] [Indexed: 02/06/2023]
Affiliation(s)
| | | | - Ian A. Dickie
- BioProtection Research Centre Lincoln University Lincoln7647 New Zealand
- University of Canterbury School of Biological Sciences Christchurch8140 New Zealand
| | | | | | - Tadashi Fukami
- Department of Biology Stanford University Stanford CA94305 USA
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23
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Diversity begets diversity in competition for space. Nat Ecol Evol 2017; 1:156. [DOI: 10.1038/s41559-017-0156] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 04/04/2017] [Indexed: 11/09/2022]
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24
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25
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Thakur MP, Herrmann M, Steinauer K, Rennoch S, Cesarz S, Eisenhauer N. Cascading effects of belowground predators on plant communities are density-dependent. Ecol Evol 2015; 5:4300-14. [PMID: 26664680 PMCID: PMC4667818 DOI: 10.1002/ece3.1597] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/10/2015] [Accepted: 06/14/2015] [Indexed: 11/17/2022] Open
Abstract
Soil food webs comprise a multitude of trophic interactions that can affect the composition and productivity of plant communities. Belowground predators feeding on microbial grazers like Collembola could decelerate nutrient mineralization by reducing microbial turnover in the soil, which in turn could negatively influence plant growth. However, empirical evidences for the ecological significance of belowground predators on nutrient cycling and plant communities are scarce. Here, we manipulated predator density (Hypoaspis aculeifer: predatory mite) with equal densities of three Collembola species as a prey in four functionally dissimilar plant communities in experimental microcosms: grass monoculture (Poa pratensis), herb monoculture (Rumex acetosa), legume monoculture (Trifolium pratense), and all three species as a mixed plant community. Density manipulation of predators allowed us to test for density‐mediated effects of belowground predators on Collembola and lower trophic groups. We hypothesized that predator density will reduce Collembola population causing a decrease in nutrient mineralization and hence detrimentally affect plant growth. First, we found a density‐dependent population change in predators, that is, an increase in low‐density treatments, but a decrease in high‐density treatments. Second, prey suppression was lower at high predator density, which caused a shift in the soil microbial community by increasing the fungal: bacterial biomass ratio, and an increase of nitrification rates, particularly in legume monocultures. Despite the increase in nutrient mineralization, legume monocultures performed worse at high predator density. Further, individual grass shoot biomass decreased in monocultures, while it increased in mixed plant communities with increasing predator density, which coincided with elevated soil N uptake by grasses. As a consequence, high predator density significantly increased plant complementarity effects indicating a decrease in interspecific plant competition. These results highlight that belowground predators can relax interspecific plant competition by increasing nutrient mineralization through their density‐dependent cascading effects on detritivore and soil microbial communities.
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Affiliation(s)
- Madhav Prakash Thakur
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Deutscher Platz 5e 04103 Leipzig Germany ; Institute of Biology University of Leipzig Johannisallee 21 04103 Leipzig Germany
| | - Martina Herrmann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Deutscher Platz 5e 04103 Leipzig Germany ; Institute of Ecology Friedrich Schiller Jena University Dornburger Str. 159 07743 Jena Germany
| | - Katja Steinauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Deutscher Platz 5e 04103 Leipzig Germany ; Institute of Biology University of Leipzig Johannisallee 21 04103 Leipzig Germany
| | - Saskia Rennoch
- Institute of Ecology Friedrich Schiller Jena University Dornburger Str. 159 07743 Jena Germany
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Deutscher Platz 5e 04103 Leipzig Germany ; Institute of Biology University of Leipzig Johannisallee 21 04103 Leipzig Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Deutscher Platz 5e 04103 Leipzig Germany ; Institute of Biology University of Leipzig Johannisallee 21 04103 Leipzig Germany
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26
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Scheunemann N, Digel C, Scheu S, Butenschoen O. Roots rather than shoot residues drive soil arthropod communities of arable fields. Oecologia 2015; 179:1135-45. [DOI: 10.1007/s00442-015-3415-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/15/2015] [Indexed: 11/29/2022]
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27
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Home Field Advantage of Litter Decomposition in Pure and Mixed Plantations Under Boreal Climate. Ecosystems 2015. [DOI: 10.1007/s10021-015-9880-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Fungal Secondary Metabolism in the Light of Animal–Fungus Interactions: From Mechanism to Ecological Function. Fungal Biol 2015. [DOI: 10.1007/978-1-4939-2531-5_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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29
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30
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Walker DM, Lawrence BR, Esterline D, Graham SP, Edelbrock MA, Wooten JA. A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest. Ecol Evol 2014; 4:4106-16. [PMID: 25505537 PMCID: PMC4242563 DOI: 10.1002/ece3.1259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 08/26/2014] [Accepted: 09/03/2014] [Indexed: 11/17/2022] Open
Abstract
The flow of energy within an ecosystem can be considered either top-down, where predators influence consumers, or bottom-up, where producers influence consumers. Plethodon cinereus (Red-backed Salamander) is a terrestrial keystone predator who feeds on invertebrates within the ecosystem. We investigated the impact of the removal of P. cinereus on the detritivore food web in an upland deciduous forest in northwest Ohio, U.S.A. A total of eight aluminum enclosures, each containing a single P. cinereus under a small log, were constructed in the deciduous forest. On Day 1 of the experiment, four salamanders were evicted from four of the eight enclosures. Organic matter and soil were collected from the center of each enclosure at Day 1 and Day 21. From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU). Changes in overall fungal community composition or species diversity were not statistically significant between treatments. Statistically significant shifts in the most abundant taxonomic groups of fungi were documented in presence but not absence enclosures. We concluded that P. cinereus does not affect the overall composition or diversity of fungal communities, but does have an impact on specific groups of fungi. This study used a metagenomics-based approach to investigate a missing link among a keystone predator, P. cinereus, invertebrates, and fungal communities, all of which are critical in the detritivore food web.
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Affiliation(s)
- Donald M Walker
- Department of Natural Sciences, The University of Findlay Findlay, Ohio, 45840
| | | | - Dakota Esterline
- Department of Natural Sciences, The University of Findlay Findlay, Ohio, 45840
| | - Sean P Graham
- The Department of Agricultural and Natural Resource Sciences, Sul Ross State University Alpine, Texas, 79832
| | - Michael A Edelbrock
- Department of Natural Sciences, The University of Findlay Findlay, Ohio, 45840
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31
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A'Bear AD, Jones TH, Boddy L. Potential impacts of climate change on interactions among saprotrophic cord-forming fungal mycelia and grazing soil invertebrates. FUNGAL ECOL 2014. [DOI: 10.1016/j.funeco.2013.01.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Churchland C, Grayston SJ. Specificity of plant-microbe interactions in the tree mycorrhizosphere biome and consequences for soil C cycling. Front Microbiol 2014; 5:261. [PMID: 24917855 PMCID: PMC4042908 DOI: 10.3389/fmicb.2014.00261] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 05/13/2014] [Indexed: 01/22/2023] Open
Abstract
Mycorrhizal associations are ubiquitous and form a substantial component of the microbial biomass in forest ecosystems and fluxes of C to these belowground organisms account for a substantial portion of carbon assimilated by forest vegetation. Climate change has been predicted to alter belowground plant-allocated C which may cause compositional shifts in soil microbial communities, and it has been hypothesized that this community change will influence C mitigation in forest ecosystems. Some 10,000 species of ectomycorrhizal fungi are currently recognized, some of which are host specific and will only associate with a single tree species, for example, Suillus grevillei with larch. Mycorrhizae are a strong sink for plant C, differences in mycorrhizal anatomy, particularly the presence and extent of emanating hyphae, can affect the amount of plant C allocated to these assemblages. Mycorrhizal morphology affects not only spatial distribution of C in forests, but also differences in the longevity of these diverse structures may have important consequences for C sequestration in soil. Mycorrhizal growth form has been used to group fungi into distinctive functional groups that vary qualitatively and spatially in their foraging and nutrient acquiring potential. Through new genomic techniques we are beginning to understand the mechanisms involved in the specificity and selection of ectomycorrhizal associations though much less is known about arbuscular mycorrhizal associations. In this review we examine evidence for tree species- mycorrhizal specificity, and the mechanisms involved (e.g., signal compounds). We also explore what is known about the effects of these associations and interactions with other soil organisms on the quality and quantity of C flow into the mycorrhizosphere (the area under the influence of mycorrhizal root tips), including spatial and seasonal variations. The enormity of the mycorrhizosphere biome in forests and its potential to sequester substantial C belowground highlights the vital importance of increasing our knowledge of the dynamics of the different mycorrhizal functional groups in diverse forests.
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Affiliation(s)
| | - Sue J. Grayston
- Belowground Ecosystem Group, Department of Forest and Conservation Sciences, University of British ColumbiaVancouver, BC, Canada
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A′Bear AD, Murray W, Webb R, Boddy L, Jones TH. Contrasting effects of elevated temperature and invertebrate grazing regulate multispecies interactions between decomposer fungi. PLoS One 2013; 8:e77610. [PMID: 24194892 PMCID: PMC3806825 DOI: 10.1371/journal.pone.0077610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 09/08/2013] [Indexed: 12/01/2022] Open
Abstract
Predicting the influence of biotic and abiotic factors on species interactions and ecosystem processes is among the primary aims of community ecologists. The composition of saprotrophic fungal communities is a consequence of competitive mycelial interactions, and a major determinant of woodland decomposition and nutrient cycling rates. Elevation of atmospheric temperature is predicted to drive changes in fungal community development. Top-down regulation of mycelial growth is an important determinant of, and moderator of temperature-driven changes to, two-species interaction outcomes. This study explores the interactive effects of a 4 °C temperature increase and soil invertebrate (collembola or woodlice) grazing on multispecies interactions between cord-forming basidiomycete fungi emerging from colonised beech (Fagus sylvatica) wood blocks. The fungal dominance hierarchy at ambient temperature (16 °C; Phanerochaete velutina > Resinicium bicolor > Hypholoma fasciculare) was altered by elevated temperature (20 °C; R. bicolor > P. velutina > H. fasciculare) in ungrazed systems. Warming promoted the competitive ability of the fungal species (R. bicolor) that was preferentially grazed by all invertebrate species. As a consequence, grazing prevented the effect of temperature on fungal community development and maintained a multispecies assemblage. Decomposition of fungal-colonised wood was stimulated by warming, with implications for increased CO2 efflux from woodland soil. Analogous to aboveground plant communities, increasing complexity of biotic and abiotic interactions appears to be important in buffering climate change effects on soil decomposers.
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Affiliation(s)
- A. Donald A′Bear
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - William Murray
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Rachel Webb
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Lynne Boddy
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
- * E-mail:
| | - T. Hefin Jones
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
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Crowther TW, Stanton DWG, Thomas SM, A'Bear AD, Hiscox J, Jones TH, Voříšková J, Baldrian P, Boddy L. Top-down control of soil fungal community composition by a globally distributed keystone consumer. Ecology 2013; 94:2518-28. [DOI: 10.1890/13-0197.1] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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van der Wal A, Geydan TD, Kuyper TW, de Boer W. A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes. FEMS Microbiol Rev 2013; 37:477-94. [DOI: 10.1111/1574-6976.12001] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 08/02/2012] [Accepted: 08/21/2012] [Indexed: 12/24/2022] Open
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Crowther TW, Bradford MA. Thermal acclimation in widespread heterotrophic soil microbes. Ecol Lett 2013; 16:469-77. [PMID: 23331708 DOI: 10.1111/ele.12069] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/12/2012] [Accepted: 12/08/2012] [Indexed: 11/28/2022]
Abstract
Respiration by plants and microorganisms is primarily responsible for mediating carbon exchanges between the biosphere and atmosphere. Climate warming has the potential to influence the activity of these organisms, regulating exchanges between carbon pools. Physiological 'down-regulation' of warm-adapted species (acclimation) could ameliorate the predicted respiratory losses of soil carbon under climate change scenarios, but unlike plants and symbiotic microbes, the existence of this phenomenon in heterotrophic soil microbes remains controversial. Previous studies using complex soil microbial communities are unable to distinguish physiological acclimation from other community-scale adjustments. We explored the temperature-sensitivity of individual saprotrophic basidiomycete fungi growing in agar, showing definitively that these widespread heterotrophic fungi can acclimate to temperature. In almost all cases, the warm-acclimated individuals had lower growth and respiration rates at intermediate temperatures than cold-acclimated isolates. Inclusion of such microbial physiological responses to warming is essential to enhance the robustness of global climate-ecosystem carbon models.
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Affiliation(s)
- Thomas W Crowther
- Yale School of Forestry and Environmental Studies, Yale University, New Haven, CT, USA.
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Crowther TW, Boddy L, Hefin Jones T. Functional and ecological consequences of saprotrophic fungus-grazer interactions. ISME JOURNAL 2012; 6:1992-2001. [PMID: 22717883 DOI: 10.1038/ismej.2012.53] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Saprotrophic fungi are key regulators of nutrient cycling in terrestrial ecosystems. They are the primary agents of plant litter decomposition and their hyphal networks, which grow throughout the soil-litter interface, represent highly dynamic channels through which nutrients are readily distributed. By ingesting hyphae and dispersing spores, soil invertebrates, including Arthropoda, Oligochaetae and Nematoda, influence fungal-mediated nutrient distribution within soil. Fungal physiological responses to grazing include changes to hydrolytic enzyme production and respiration rates. These directly affect nutrient mineralisation and the flux of CO(2) between terrestrial and atmospheric pools. Preferential grazing may also exert selective pressures on saprotrophic communities, driving shifts in fungal succession and community composition. These functional and ecological consequences of grazing are intrinsically linked, and influenced by invertebrate grazing intensity. High-intensity grazing often reduces fungal growth and activity, whereas low-intensity grazing can have stimulatory effects. Grazing intensity is directly related to invertebrate abundance, and varies dramatically between species and functional groups. Invertebrate diversity and community composition, therefore, represent key factors determining the functioning of saprotrophic fungal communities and the services they provide.
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Affiliation(s)
- Thomas W Crowther
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, UK.
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Crowther TW, Littleboy A, Jones TH, Boddy L. Interactive effects of warming and invertebrate grazing on the outcomes of competitive fungal interactions. FEMS Microbiol Ecol 2012; 81:419-26. [PMID: 22432587 DOI: 10.1111/j.1574-6941.2012.01364.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/23/2012] [Accepted: 03/12/2012] [Indexed: 11/29/2022] Open
Abstract
Saprotrophic fungal community composition, determined by the outcomes of competitive mycelial interactions, represents a key determinant of woodland carbon and nutrient cycling. Atmospheric warming is predicted to drive changes in fungal community composition. Grazing by invertebrates can also exert selective pressures on fungal communities and alter the outcome of competitive fungal interactions; their potential to do so is determined by grazing intensity. Temperature regulates the abundance of soil collembola, but it remains unclear whether this will alter the top-down determination of fungal community composition. We use soil microcosms to explore the direct (via effects on interacting fungi) and indirect (by influencing top-down grazing pressures) effects of a 3 °C temperature increase on the outcomes of competitive interactions between cord-forming basidiomycete fungi. By differentially affecting the fungal growth rates, warming reversed the outcomes of specific competitive interactions. Collembola populations also increased at elevated temperature, and these larger, more active, populations exerted stronger grazing pressures. Consequently, grazing mitigated the effects of temperature on these interactions, restoring fungal communities to those recorded at ambient temperature. The interactive effects of biotic and abiotic factors are a key in determining the functional and ecological responses of microbial communities to climate change.
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Heaton L, Obara B, Grau V, Jones N, Nakagaki T, Boddy L, Fricker MD. Analysis of fungal networks. FUNGAL BIOL REV 2012. [DOI: 10.1016/j.fbr.2012.02.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Crowther TW, A’Bear AD. Impacts of grazing soil fauna on decomposer fungi are species-specific and density-dependent. FUNGAL ECOL 2012. [DOI: 10.1016/j.funeco.2011.07.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Crowther TW, Jones TH, Boddy L. Species-specific effects of grazing invertebrates on mycelial emergence and growth from woody resources into soil. FUNGAL ECOL 2011. [DOI: 10.1016/j.funeco.2011.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Crowther TW, Boddy L, Jones TH. Outcomes of fungal interactions are determined by soil invertebrate grazers. Ecol Lett 2011; 14:1134-42. [PMID: 21929699 DOI: 10.1111/j.1461-0248.2011.01682.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Saprotrophic fungal community composition, determined by the outcome of competitive mycelial interactions, is one of the many key factors affecting soil nutrient mineralisation and decomposition rates. Fungal communities are not generally predicted to be regulated by top-down factors, such as predation, but rather by bottom-up factors, including resource availability. We show that invertebrate grazers can exert selective pressures on fungal decomposer communities in soil, reversing the outcomes of competitive interactions. By feeding selectively on the cord-forming fungus Resinicium bicolor, isopods prevented the competitive exclusion of Hypholoma fasciculare and Phanerochaete velutina in soil and wood. Nematode populations also reversed the outcomes of competitive interactions by stimulating growth of less competitive fungi. These represent two opposing mechanisms by which soil fauna may influence fungal community composition and diversity. Factors affecting soil invertebrate communities will have direct consequences for fungal-mediated nutrient cycling in woodland soils.
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Affiliation(s)
- Thomas W Crowther
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
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