1
|
Ochoa-Hueso R, Eldridge DJ, Berdugo M, Trivedi P, Sokoya B, Cano-Díaz C, Abades S, Alfaro F, Bamigboye AR, Bastida F, Blanco-Pastor JL, de Los Rios A, Durán J, Geisen S, Grebenc T, Illán JG, Liu YR, Makhalanyane TP, Mamet S, Molina-Montenegro MA, Moreno JL, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Rey A, Rodríguez A, Siebe C, Singh BK, Teixido AL, Torres-Díaz C, Wang L, Wang J, Wang J, Zaady E, Zhou X, Zhou XQ, Tedersoo L, Delgado-Baquerizo M. Unearthing the soil-borne microbiome of land plants. GLOBAL CHANGE BIOLOGY 2024; 30:e17295. [PMID: 38804108 DOI: 10.1111/gcb.17295] [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: 09/04/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 05/29/2024]
Abstract
Plant-soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change.
Collapse
Affiliation(s)
- Raúl Ochoa-Hueso
- Department of Biology, Botany Area, University of Cádiz, Vitivinicultural and Agri-Food Research Institute (IVAGRO), Cádiz, Spain
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of NSW, Sydney, New South Wales, Australia
| | - Miguel Berdugo
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Pankaj Trivedi
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Blessing Sokoya
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Concha Cano-Díaz
- CISAS - Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial Nun'Álvares, Viana do Castelo, Portugal
| | | | - Fernando Alfaro
- GEMA Center for Genomics, Ecology & Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, Santiago, Chile
| | - Adebola R Bamigboye
- Natural History Museum (Botany Unit), Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Felipe Bastida
- CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - José L Blanco-Pastor
- Department of Biology, Botany Area, University of Cádiz, Vitivinicultural and Agri-Food Research Institute (IVAGRO), Cádiz, Spain
| | - Asunción de Los Rios
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jorge Durán
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Tine Grebenc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Javier G Illán
- Department of Entomology, Washington State University, Pullman, Washington, USA
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Steven Mamet
- College of Agriculture and Bioresources, Department of Soil Science, University of Saskatchewan, Saskatoon, Canada
| | | | - José L Moreno
- CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | | | - Gabriel F Peñaloza-Bojacá
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - César Plaza
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ana Rey
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Alexandra Rodríguez
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith South, New South Wales, Australia
| | - Alberto L Teixido
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Cristian Torres-Díaz
- Grupo de Biodiversidad y Cambio Global (BCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Ling Wang
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, China
| | - Jianyong Wang
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, China
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Negev, Israel
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Xinjiang, China
| | - Xin-Quan Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| |
Collapse
|
2
|
Guo J, Ning H, Li Y, Xu Q, Shen Q, Ling N, Guo S. Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice. mBio 2024; 15:e0273323. [PMID: 38319112 PMCID: PMC10936437 DOI: 10.1128/mbio.02733-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits. IMPORTANCE The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.
Collapse
Affiliation(s)
- Junjie Guo
- State Key Lab of Biocontrol, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, China
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Huiling Ning
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yong Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qicheng Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
3
|
Aaronson JK, Kulmatiski A, Forero LE, Grenzer J, Norton JM. Are Plant-Soil Feedbacks Caused by Many Weak Microbial Interactions? BIOLOGY 2023; 12:1374. [PMID: 37997973 PMCID: PMC10669423 DOI: 10.3390/biology12111374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
We used high-throughput sequencing and multivariate analyses to describe soil microbial community composition in two four-year field plant-soil feedback (PSF) experiments in Minnesota, USA and Jena, Germany. In descending order of variation explained, microbial community composition differed between the two study sites, among years, between bulk and rhizosphere soils, and among rhizosphere soils cultivated by different plant species. To try to identify soil organisms or communities that may cause PSF, we correlated plant growth responses with the microbial community composition associated with different plants. We found that plant biomass was correlated with values on two multivariate axes. These multivariate axes weighted dozens of soil organisms, suggesting that PSF was not caused by individual pathogens or symbionts but instead was caused by 'many weak' plant-microbe interactions. Taken together, the results suggest that PSFs result from complex interactions that occur within the context of a much larger soil microbial community whose composition is determined by factors associated with 'site' or year, such as soil pH, soil type, and weather. The results suggest that PSFs may be highly variable and difficult to reproduce because they result from complex interactions that occur in the context of a larger soil microbial community.
Collapse
Affiliation(s)
- Julia K. Aaronson
- Wildland Resources and the Ecology Center, Utah State University, Logan, UT 84322, USA; (J.K.A.); (L.E.F.); (J.G.)
| | - Andrew Kulmatiski
- Wildland Resources and the Ecology Center, Utah State University, Logan, UT 84322, USA; (J.K.A.); (L.E.F.); (J.G.)
| | - Leslie E. Forero
- Wildland Resources and the Ecology Center, Utah State University, Logan, UT 84322, USA; (J.K.A.); (L.E.F.); (J.G.)
| | - Josephine Grenzer
- Wildland Resources and the Ecology Center, Utah State University, Logan, UT 84322, USA; (J.K.A.); (L.E.F.); (J.G.)
| | - Jeanette M. Norton
- Plants, Soils and Climate Department and the Ecology Center, Utah State University, Logan, UT 84322, USA;
| |
Collapse
|
4
|
Roy J, Reichel R, Brüggemann N, Rillig MC. Functional, not Taxonomic, Composition of Soil Fungi Reestablishes to Pre-mining Initial State After 52 Years of Recultivation. MICROBIAL ECOLOGY 2023; 86:213-223. [PMID: 35821127 PMCID: PMC10293406 DOI: 10.1007/s00248-022-02058-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Open-cast mining leads to the loss of naturally developed soils and their ecosystem functions and services. Soil restoration after mining aims to restore the agricultural productivity in which the functions of the fungal community play a crucial role. Whether fungi reach a comparable functional state as in the soil before mining within half a century of recultivation is still unanswered. Here, we characterised the soil fungal community using ITS amplicon Illumina sequencing across a 52-year chronosequence of agricultural recultivation after open-cast mining in northern Europe. Both taxonomic and functional community composition showed profound shifts over time, which could be attributed to the changes in nutrient status, especially phosphorus availability. However, taxonomic composition did not reach the pre-mining state, whereas functional composition did. Importantly, we identified a positive development of arbuscular mycorrhizal root fungal symbionts after the initial three years of alfalfa cultivation, followed by a decline after conversion to conventional farming, with arbuscular mycorrhizal fungi being replaced by soil saprobes. We conclude that appropriate agricultural management can steer the fungal community to its functional pre-mining state despite stochasticity in the reestablishment of soil fungal communities. Nonetheless, conventional agricultural management results in the loss of plant symbionts, favouring non-symbiotic fungi.
Collapse
Affiliation(s)
- Julien Roy
- Institut Für Biologie, Ökologie Der Pflanzen, Freie Universität Berlin, 14195, Berlin, Germany.
- Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany.
| | - Rüdiger Reichel
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Agrosphere (IBG-3), 52425, Jülich, Germany
| | - Nicolas Brüggemann
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Agrosphere (IBG-3), 52425, Jülich, Germany
| | - Matthias C Rillig
- Institut Für Biologie, Ökologie Der Pflanzen, Freie Universität Berlin, 14195, Berlin, Germany
- Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany
| |
Collapse
|
5
|
Niego AGT, Rapior S, Thongklang N, Raspé O, Hyde KD, Mortimer P. Reviewing the contributions of macrofungi to forest ecosystem processes and services. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
6
|
Chen S, Cao P, Li T, Wang Y, Liu X. Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau. PeerJ 2023; 11:e15361. [PMID: 37250704 PMCID: PMC10224674 DOI: 10.7717/peerj.15361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/16/2023] [Indexed: 05/31/2023] Open
Abstract
In the extreme alpine climate of the Qinghai-Tibet Plateau (QTP), plant growth and reproduction are limited by extremely cold temperatures, low soil moisture, and scarce nutrient availability. The root-associated microbiome indirectly promotes plant growth and plays a role in the fitness of plants on the QTP, particularly in Tibetan medicinal plants. Despite the importance of the root-associated microbiome, little is known about the root zone. This study used high-throughput sequencing to investigate two medicinal Meconopsis plants, M. horridula and M. integrifolia, to determine whether habitat or plant identity had a more significant impact on the microbial composition of the roots. The fungal sequences were obtained using ITS-1 and ITS-2, and bacterial sequences were obtained using 16S rRNA. Different microbial patterns were observed in the microbial compositions of fungi and bacteria in the root zones of two Meconopsis plants. In contrast to bacteria, which were not significantly impacted by plant identity or habitat, the fungi in the root zone were significantly impacted by plant identity, but not habitat. In addition, the synergistic effect was more significant than the antagonistic effect in the correlation between fungi and bacteria in the root zone soil. The fungal structure was influenced by total nitrogen and pH, whereas the structure of bacterial communities was influenced by soil moisture and organic matter. Plant identity had a greater influence on fungal structure than habitat in two Meconopsis plants. The dissimilarity of fungal communities suggests that more attention should be paid to fungi-plant interactions.
Collapse
Affiliation(s)
- Shuting Chen
- Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Pengxi Cao
- Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Ting Li
- Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Yuyan Wang
- Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Xing Liu
- Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, School of Ecology and Environment, Tibet University, Lhasa, China
- State Key Laboratory of Hybrid Rice, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau, Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
| |
Collapse
|
7
|
Faticov M, Abdelfattah A, Hambäck P, Roslin T, Tack AJM. Different spatial structure of plant-associated fungal communities above- and belowground. Ecol Evol 2023; 13:e10065. [PMID: 37223309 PMCID: PMC10200691 DOI: 10.1002/ece3.10065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/22/2023] [Indexed: 05/25/2023] Open
Abstract
The distribution and community assembly of above- and belowground microbial communities associated with individual plants remain poorly understood, despite its consequences for plant-microbe interactions and plant health. Depending on how microbial communities are structured, we can expect different effects of the microbial community on the health of individual plants and on ecosystem processes. Importantly, the relative role of different factors will likely differ with the scale examined. Here, we address the driving factors at a landscape level, where each individual unit (oak trees) is accessible to a joint species pool. This allowed to quantify the relative effect of environmental factors and dispersal on the distribution of two types of fungal communities: those associated with the leaves and those associated with the soil of Quercus robur trees in a landscape in southwestern Finland. Within each community type, we compared the role of microclimatic, phenological, and spatial variables, and across community types, we examined the degree of association between the respective communities. Most of the variation in the foliar fungal community was found within trees, whereas soil fungal community composition showed positive spatial autocorrelation up to 50 m. Microclimate, tree phenology, and tree spatial connectivity explained little variation in the foliar and soil fungal communities. Foliar and soil fungal communities differed strongly in community structure, with no significant concordance detected between them. We provide evidence that foliar and soil fungal communities assemble independent of each other and are structured by different ecological processes.
Collapse
Affiliation(s)
- Maria Faticov
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- Département de biologieUniversité de SherbrookeSherbrookeQuebecCanada
| | - Ahmed Abdelfattah
- Leibniz Institute of Agricultural Engineering and Bio‐economyPotsdamGermany
| | - Peter Hambäck
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Tomas Roslin
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Ayco J. M. Tack
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| |
Collapse
|
8
|
Maciá-Vicente JG, Francioli D, Weigelt A, Albracht C, Barry KE, Buscot F, Ebeling A, Eisenhauer N, Hennecke J, Heintz-Buschart A, van Ruijven J, Mommer L. The structure of root-associated fungal communities is related to the long-term effects of plant diversity on productivity. Mol Ecol 2023. [PMID: 37081579 DOI: 10.1111/mec.16956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 04/22/2023]
Abstract
Root-associated fungi could play a role in determining both the positive relationship between plant diversity and productivity in experimental grasslands, and its strengthening over time. This hypothesis assumes that specialized pathogenic and mutualistic fungal communities gradually assemble over time, enhancing plant growth more in species-rich than in species-poor plots. To test this hypothesis, we used high-throughput amplicon sequencing to characterize root-associated fungal communities in experimental grasslands of 1 and 15 years of age with varying levels of plant species richness. Specifically, we tested whether the relationship between fungal communities and plant richness and productivity becomes stronger with the age of the experimental plots. Our results showed that fungal diversity increased with plant diversity, but this relationship weakened rather than strengthened over the two time points. Contrastingly, fungal community composition showed increasing associations with plant diversity over time, suggesting a gradual build-up of specific fungal assemblages. Analyses of different fungal guilds showed that these changes were particularly marked in pathogenic fungi, whose shifts in relative abundance are consistent with the pathogen dilution hypothesis in diverse plant communities. Our results suggest that root-associated fungal pathogens play more specific roles in determining the diversity-productivity relationship than other root-associated plant symbionts.
Collapse
Affiliation(s)
- Jose G Maciá-Vicente
- Plant Ecology and Nature Conservation, Wageningen University & Research, Wageningen, The Netherlands
| | - Davide Francioli
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Alexandra Weigelt
- Institute of Biology, Leipzig University, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Cynthia Albracht
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Kathryn E Barry
- Ecology and Biodiversity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Soil Ecology Department, Helmholtz Center for Environmental Research (UFZ), Halle (Saale), Germany
| | - Anne Ebeling
- Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany
| | - Justus Hennecke
- Institute of Biology, Leipzig University, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jasper van Ruijven
- Plant Ecology and Nature Conservation, Wageningen University & Research, Wageningen, The Netherlands
| | - Liesje Mommer
- Plant Ecology and Nature Conservation, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
9
|
Qu S, Shen C, Zhang L, Wang J, Zhang LM, Chen B, Sun GX, Ge Y. Dispersal limitation and host selection drive geo-specific and plant-specific differentiation of soil bacterial communities in the Tibetan alpine ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160944. [PMID: 36526178 DOI: 10.1016/j.scitotenv.2022.160944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Soil bacteria, which are active in shrub encroachment, play key roles in regulating ecosystem structure and function. However, the differentiation characteristics and assembly process of bacterial communities in scrubbed grasslands remain unknown. Taking the Qinghai-Tibet Plateau, a hotspot of shrub encroachment, as the study area, we collected 192 soils near nine natural typical shrubs' roots on a trans-longitude transect (about 1800 km) and investigated the bacterial communities using 16S rRNA amplicon sequencing. We found that the bacterial communities exhibited plant-specific and geographic-specific differentiation. On the one hand, bacterial communities differed significantly across plant species, with widely distributed shrubs harboring high diversity communities but few plant-specific taxa, and narrowly distributed shrubs possessing low diversity communities but more plant-specific taxa. Besides, there was a significant negative correlation between bacterial community similarity and plant phylogenetic distance. On the other hand, bacterial communities differed across geographic sites, with a significant decay in bacterial community similarity with geographic distance. The bacterial alpha diversity varied in an inverted V-shape from west to east, peaking at 91°E, which could be largely driven by mean annual temperature, soil pH and soil total carbon content. Community differentiation increased with the heterogeneity degree of assembly processes, and the dominant assembly process in these two specific differentiations differed. Dominated by stochastic and deterministic forces, respectively, geography diverged bacterial communities primarily through increased dispersal limitation, whereas plants diverged bacterial communities primarily through increased variable selection. Our study provides new insight into the characteristics and mechanisms of root-surrounding soil bacteria differentiation in scrubbed grasslands, contributing to the scientific management of degraded grasslands and the prediction of bacterial community structure and ecosystem function in response to global change.
Collapse
Affiliation(s)
- Sai Qu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Zhang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guo-Xin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
10
|
Blaalid R, Davey ML. Habitat Protection Approaches Facilitate Conservation of Overlooked Fungal Diversity - A Case Study From the Norwegian Coastal Heathland System. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:886685. [PMID: 37746238 PMCID: PMC10512255 DOI: 10.3389/ffunb.2022.886685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/02/2022] [Indexed: 09/26/2023]
Abstract
European coastal heathlands are distinct ecosystems shaped by land use tradition and they have experienced an 80% area reduction from their historical maximum. These mosaics of mires and wind exposed patches have ericaceous shrub dominated vegetation, and soils within coastal heathlands are characterized by low pH and high levels of recalcitrant debris. Using a culture-based approach with molecular identification of isolates, we characterized root-associated fungal communities of six ericaceous species in eight heathland localities along Norway's western coast. Site-level alpha diversity ranged from 21-38 OTUs, while the total estimated gamma diversity for culturable heathland root fungi was 190-231 OTUs. Most species recovered are previously reported at low abundance in Norway, suggesting the biodiversity in this community is underreported, rather than novel for science. The fungi recovered were primarily Ascomycota, specifically endophytic Phialocephala, and Pezicula, and no host specificity was observed in the communities. The fungal communities exhibited high turnover and low nestedness, both between ericaceous hosts and across heathland sites. We observed no spatial patterns in fungal betadiversity, and this heterogeneity may be a product of the unique historic land use practices at each locality creating a distinct mycofloral "fingerprint". Robust diversity estimates will be key for managing fungal biodiversity in coastal heathlands. Our results indicate that sampling schemes that maximize the number of host plants sampled per site, rather than the number of cultures per plant yield improved alpha diversity estimates. Similarly, gamma diversity estimates are improved by maximizing the total number of localities sampled, rather than increasing the number of plants sampled per locality. We argue that while the current protected status of coastal heathland habitats and restoration efforts have knock-on effects for the conservation of fungal biodiversity, fungi have a vital functional role in the ecosystem and holistic conservation plans that consider fungal biodiversity would be beneficial.
Collapse
Affiliation(s)
- Rakel Blaalid
- Department of Natural History, University Museum of Bergen, Bergen, Norway
- Norwegian Institute for Nature Research, NINA Bergen, Bergen, Norway
| | - Marie L. Davey
- Norwegian Institute for Nature Research, Terrestrial Biodiversity Department, Trondheim, Norway
| |
Collapse
|