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Singavarapu B, Ul Haq H, Darnstaedt F, Nawaz A, Beugnon R, Cesarz S, Eisenhauer N, Du J, Xue K, Wang Y, Bruelheide H, Wubet T. Influence of tree mycorrhizal type, tree species identity, and diversity on forest root-associated mycobiomes. THE NEW PHYTOLOGIST 2024; 242:1691-1703. [PMID: 38659111 DOI: 10.1111/nph.19722] [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: 07/14/2023] [Accepted: 02/20/2024] [Indexed: 04/26/2024]
Abstract
Understanding the complex interactions between trees and fungi is crucial for forest ecosystem management, yet the influence of tree mycorrhizal types, species identity, and diversity on tree-tree interactions and their root-associated fungal communities remains poorly understood. Our study addresses this gap by investigating root-associated fungal communities of different arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) tree species pairs (TSPs) in a subtropical tree diversity experiment, spanning monospecific, two-species, and multi-species mixtures, utilizing Illumina sequencing of the ITS2 region. The study reveals that tree mycorrhizal type significantly impacts the alpha diversity of root-associated fungi in monospecific stands. Meanwhile, tree species identity's influence is modulated by overall tree diversity. Tree-related variables and spatial distance emerged as major drivers of variations in fungal community composition. Notably, in multi-species mixtures, compositional differences between root fungal communities of AM and EcM trees diminish, indicating a convergence of fungal communities irrespective of mycorrhizal type. Interestingly, dual mycorrhizal fungal communities were observed in these multi-species mixtures. This research underscores the pivotal role of mycorrhizal partnerships and the interplay of biotic and abiotic factors in shaping root fungal communities, particularly in varied tree diversity settings, and its implications for effective forest management and biodiversity conservation.
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Affiliation(s)
- Bala Singavarapu
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle (Saale), Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
| | - Hafeez Ul Haq
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle (Saale), Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
| | - Friedrich Darnstaedt
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle (Saale), Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108, Halle, Germany
| | - Ali Nawaz
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle (Saale), Germany
- Department of Digital Health Sciences and Biomedicine, School of Life Sciences, University of Siegen, Am Eichenhang 50, 57076, Siegen, Germany
| | - Rémy Beugnon
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919, route de Mende, F-34293, Montpellier Cedex 5, France
- Leipzig Institute for Meteorology, Universität Leipzig, Stephanstraße 3, 04103, Leipzig, Germany
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
| | - Jianqing Du
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources, Chinese Academy of Sciences, 100101, Beijing, China
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
| | - Tesfaye Wubet
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
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Gacura MD, Zak DR, Blackwood CB. From individual leaves to forest stands: importance of niche, distance decay, and stochasticity vary by ecosystem type and functional group for fungal community composition. FEMS Microbiol Ecol 2024; 100:fiae016. [PMID: 38373845 PMCID: PMC10913062 DOI: 10.1093/femsec/fiae016] [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: 09/01/2023] [Revised: 01/26/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024] Open
Abstract
Community assembly is influenced by environmental niche processes as well as stochastic processes that can be spatially dependent (e.g. dispersal limitation) or independent (e.g. priority effects). Here, we sampled senesced tree leaves as unit habitats to investigate fungal community assembly at two spatial scales: (i) small neighborhoods of overlapping leaves from differing tree species and (ii) forest stands of differing ecosystem types. Among forest stands, ecosystem type explained the most variation in community composition. Among adjacent leaves within stands, variability in fungal composition was surprisingly high. Leaf type was more important in stands with high soil fertility and dominated by differing tree mycorrhizal types (sugar maple vs. basswood or red oak), whereas distance decay was more important in oak-dominated forest stands with low soil fertility. Abundance of functional groups was explained by environmental factors, but predictors of taxonomic composition within differing functional groups were highly variable. These results suggest that fungal community assembly processes are clearest for functional group abundances and large spatial scales. Understanding fungal community assembly at smaller spatial scales will benefit from further study focusing on differences in drivers for different ecosystems and functional groups, as well as the importance of spatially independent factors such as priority effects.
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Affiliation(s)
- Matthew D Gacura
- Department of Biological Sciences, Kent State University, 800 E. Summit St., Kent, OH 44242, United States
- Biology Department, Gannon University, 109 University Square, Erie, PA 16541, United States
| | - Donald R Zak
- School for Environment and Sustainability, University of Michigan, 440 Church St., Ann Arbor, MI 48109, United States
| | - Christopher B Blackwood
- Department of Biological Sciences, Kent State University, 800 E. Summit St., Kent, OH 44242, United States
- Department of Plant, Soil, and Microbial Sciences and Department of Plant Biology, Michigan State University, 1066 Bogue St., East Lansing, MI 48842, United States
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Davison J, Gerz M, Hiiesalu I, Moora M, Semchenko M, Zobel M. Niche types and community assembly. Ecol Lett 2024; 27:e14327. [PMID: 37819920 DOI: 10.1111/ele.14327] [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: 04/13/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Studies of niche differentiation and biodiversity often focus on a few niche dimensions due to the methodological challenge of describing hyperdimensional niche space. However, this may limit our understanding of community assembly processes. We used the full spectrum of realized niche types to study arbuscular mycorrhizal fungal communities: distinguishing abiotic and biotic, and condition and resource, axes. Estimates of differentiation in relation to different niche types were only moderately correlated. However, coexisting taxon niches were consistently less differentiated than expected, based on a regional null model, indicating the importance of habitat filtering at that scale. Nonetheless, resource niches were relatively more differentiated than condition niches, which is consistent with the effect of a resource niche-based coexistence mechanism. Considering niche types, and in particular distinguishing resource and condition niches, provides a more complete understanding of community assembly, compared with studying individual niche axes or the full niche.
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Affiliation(s)
- John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maret Gerz
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Yurkov AP, Kryukov AA, Gorbunova AO, Kudriashova TR, Kovalchuk AI, Gorenkova AI, Bogdanova EM, Laktionov YV, Zhurbenko PM, Mikhaylova YV, Puzanskiy RK, Bagrova TN, Yakhin OI, Rodionov AV, Shishova MF. Diversity of Arbuscular Mycorrhizal Fungi in Distinct Ecosystems of the North Caucasus, a Temperate Biodiversity Hotspot. J Fungi (Basel) 2023; 10:11. [PMID: 38248921 PMCID: PMC10817546 DOI: 10.3390/jof10010011] [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: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Investigations that are focused on arbuscular mycorrhizal fungus (AMF) biodiversity is still limited. The analysis of the AMF taxa in the North Caucasus, a temperate biodiversity hotspot, used to be limited to the genus level. This study aimed to define the AMF biodiversity at the species level in the North Caucasus biotopes. METHODS The molecular genetic identification of fungi was carried out with ITS1 and ITS2 regions as barcodes via sequencing using Illumina MiSeq, the analysis of phylogenetic trees for individual genera, and searches for operational taxonomic units (OTUs) with identification at the species level. Sequences from MaarjAM and NCBI GenBank were used as references. RESULTS We analyzed >10 million reads in soil samples for three biotopes to estimate fungal biodiversity. Briefly, 50 AMF species belonging to 20 genera were registered. The total number of the AM fungus OTUs for the "Subalpine Meadow" biotope was 171/131, that for "Forest" was 117/60, and that for "River Valley" was 296/221 based on ITS1/ITS2 data. The total number of the AM fungus species (except for virtual taxa) for the "Subalpine Meadow" biotope was 24/19, that for "Forest" was 22/13, and that for "River Valley" was 28/24 based on ITS1/ITS2 data. Greater AMF diversity, as well as number of OTUs and species, in comparison with that of forest biotopes, characterized valley biotopes (disturbed ecosystems; grasslands). The correlation coefficient between "Percentage of annual plants" and "Glomeromycota total reads" r = 0.76 and 0.81 for ITS1 and ITS2, respectively, and the correlation coefficient between "Percentage of annual plants" and "OTUs number (for total species)" was r = 0.67 and 0.77 for ITS1 and ITS2, respectively. CONCLUSION High AMF biodiversity for the river valley can be associated with a higher percentage of annual plants in these biotopes and the active development of restorative successional processes.
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Affiliation(s)
- Andrey P. Yurkov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Alexey A. Kryukov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Anastasiia O. Gorbunova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Tatyana R. Kudriashova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, 194064 St. Petersburg, Russia
| | - Anastasia I. Kovalchuk
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, 194064 St. Petersburg, Russia
| | - Anastasia I. Gorenkova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ekaterina M. Bogdanova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Yuri V. Laktionov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Peter M. Zhurbenko
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Yulia V. Mikhaylova
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Roman K. Puzanskiy
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia;
- Faculty of Ecology, Russian State Hydrometeorological University, 192007 St. Petersburg, Russia;
| | - Tatyana N. Bagrova
- Faculty of Ecology, Russian State Hydrometeorological University, 192007 St. Petersburg, Russia;
| | - Oleg I. Yakhin
- Institute of Biochemistry and Genetics, The Ufa Federal Research Center of the Russian Academy of Sciences, 450054 Ufa, Russia;
| | - Alexander V. Rodionov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Maria F. Shishova
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
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Veresoglou SD, Johnson D. Species-area relationships in microbial-mediated mutualisms. Trends Microbiol 2023; 31:1111-1117. [PMID: 37301688 DOI: 10.1016/j.tim.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Symbioses involving microorganisms prevail in nature and are key to regulating numerous ecosystem processes and in driving evolution. A major concern in understanding the ecology of symbioses involving microorganisms arises in the effectiveness of sampling strategies to capture the contrasting size of organisms involved. In many mutualisms, including mycorrhizas and gut systems, hosts interact simultaneously with multiple smaller sized mutualists, the identity of which determines success for the host. This complicates quantifying the diversity of mutualisms because sampling techniques fail to capture effectively the diversity of each partner. Here we propose the use of species-area relationships (SARs) to explicitly consider the spatial scale of microbial partners in symbioses, which we propose will improve our understanding of the ecology of mutualisms.
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Affiliation(s)
- Stavros D Veresoglou
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China.
| | - David Johnson
- Department of Earth and Environmental Sciences, Michael Smith Building, University of Manchester, Manchester, M139PT, UK
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Population Structure of Pyrola chlorantha (Family Ericaceae) at the Southern Range Margin (Samara Region, Russia). INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2022. [DOI: 10.3390/ijpb13040051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The population structure of endangered species is one of the main criteria for assessing their state in their habitats. Representatives of the Ericaceae family are sensitive to environmental changes, including anthropogenic pressure; thus, they are considered the indicator species in assessing phytocenose stability. The population structure and density of the threatened species green-flowered wintergreen, Pyrola chlorantha Sw., have been described at the southern range margin (south-east of the European part of Russia, Samara Region). The observations were performed here in 2006–2021, and the main parameters of the age and spatial structure of P. chlorantha populations were revealed for the first time. Green-flowered wintergreen populations were studied at monitoring study sites and at temporarily established study plots. A bush part (ramet) was set as a counting unit. In total, 27 sub-populations were surveyed, with 1520 individuals registered. The age structure of populations was characterized using common demographic indicators: the recovery index and the population age index. The age structure of the population was associated with the efficiency of both vegetative and seed reproduction. Generally, the share of pre-generative individuals was 32.3%, generative, 66.9%, and senile, 1.8%. The studied populations were stable due to low anthropogenic impact at the growth sites.
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Guo Y, Bei Q, Dzomeku BM, Martin K, Rasche F. Genetic diversity and community composition of arbuscular mycorrhizal fungi associated with root and rhizosphere soil of the pioneer plant Pueraria phaseoloides. IMETA 2022; 1:e51. [PMID: 38867903 PMCID: PMC10989906 DOI: 10.1002/imt2.51] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/22/2022] [Accepted: 08/10/2022] [Indexed: 06/14/2024]
Abstract
The pioneering plant Pueraria phaseoloides had a strong modulation effect on arbuscular mycorrhizal fungi (AMF) communities. Irrespective of geographical location, community composition of AMF in rhizosphere soil differed from that of the root. Co-occurrence network analysis revealed two AMF keystone species in rhizosphere soil (Acaulospora) and roots (Rhizophagus) of P. phaseoloides.
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Affiliation(s)
- Yaqin Guo
- Department of Agronomy in the Tropics and Subtropics, Institute of Agricultural Sciences in the Tropics (Hans‐Ruthenberg‐Institute)University of HohenheimStuttgartGermany
| | - Qicheng Bei
- Department of Soil EcologyHelmholtz Center for Environmental Research ‐ UFZLeipzigGermany
| | | | - Konrad Martin
- Department of Agronomy in the Tropics and Subtropics, Institute of Agricultural Sciences in the Tropics (Hans‐Ruthenberg‐Institute)University of HohenheimStuttgartGermany
| | - Frank Rasche
- Department of Agronomy in the Tropics and Subtropics, Institute of Agricultural Sciences in the Tropics (Hans‐Ruthenberg‐Institute)University of HohenheimStuttgartGermany
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Zhou Y, Chen K, Muneer MA, Li C, Shi H, Tang Y, Zhang J, Ji B. Soil moisture and pH differentially drive arbuscular mycorrhizal fungal composition in the riparian zone along an alpine river of Nam Co watershed. Front Microbiol 2022; 13:994918. [PMID: 36246247 PMCID: PMC9561679 DOI: 10.3389/fmicb.2022.994918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
The riparian zone is an important ecological corridor connecting the upstream and downstream rivers. Its highly complex biological and physical environments significantly affect the biogeographical pattern of species and various ecosystem functions. However, in alpine riparian ecosystems, the distribution patterns and drivers of arbuscular mycorrhizal (AM) fungi, a group of functionally important root-associated microorganisms, remain poorly understood. In this study, we investigated the AM fungal diversity and community composition in near-bank (wetland) and far-bank (alpine meadows) soils along the Niaqu River in the Nam Co watershed, and assessed the relative importance of abiotic and biotic filtering in shaping these distributions. Overall, 184 OTUs were identified in the riparian ecosystem, predominantly belonging to the genus Glomus, especially in the downstream soils, and Claroideoglomus in near-bank soils. AM fungal colonization, spore density, and α diversity showed an overall increasing trend along the river, while the extraradical hyphae declined dramatically from the middle of the river. AM fungal communities significantly varied between the wetland and alpine meadows in the riparian zone, mainly driven by the geographic distance, soil water content, soil pH, and plant communities. Specifically, soil pH was the principal predictor of AM fungal community in near-bank wetland soils, while soil water content had a most substantial direct effect in alpine meadows. These findings indicate that abiotic factors are the most important divers in shaping AM fungal communities at the watershed scale, which could be helpful in alpine riparian biodiversity conservation and management.
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Affiliation(s)
- Yaxing Zhou
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Keyu Chen
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Muhammad Atif Muneer
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Congcong Li
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Hailan Shi
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yu Tang
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Jing Zhang
- School of Grassland Science, Beijing Forestry University, Beijing, China
- *Correspondence: Jing Zhang,
| | - Baoming Ji
- School of Grassland Science, Beijing Forestry University, Beijing, China
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Whitehead J, Roy J, Hempel S, Rillig MC. Soil microbial communities shift along an urban gradient in Berlin, Germany. Front Microbiol 2022; 13:972052. [PMID: 36033838 PMCID: PMC9412169 DOI: 10.3389/fmicb.2022.972052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
The microbial communities inhabiting urban soils determine the functioning of these soils, in regards to their ability to cycle nutrients and support plant communities. In an increasingly urbanized world these properties are of the utmost importance, and the microbial communities responsible are worthy of exploration. We used 53 grassland sites spread across Berlin to describe and explain the impacts of urbanity and other environmental parameters upon the diversity and community composition of four microbial groups. These groups were (i) the Fungi, with a separate dataset for (ii) the Glomeromycota, (iii) the Bacteria, and (iv) the protist phylum Cercozoa. We found that urbanity had distinct impacts on fungal richness, which tended to increase. Geographic distance between sites and soil chemistry, in addition to urbanity, drove microbial community composition, with site connectivity being important for Glomeromycotan communities, potentially due to plant host communities. Our findings suggest that many microbial species are well adapted to urban soils, as supported by an increase in diversity being a far more common result of urbanity than the reverse. However, we also found distinctly separate distributions of operational taxonomic unit (OTU)s from the same species, shedding doubt of the reliability of indicator species, and the use of taxonomy to draw conclusion on functionality. Our observational study employed an extensive set of sites across an urbanity gradient, in the region of the German capital, to produce a rich microbial dataset; as such it can serve as a blueprint for other such investigations.
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Affiliation(s)
- James Whitehead
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Julien Roy
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stefan Hempel
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Matthias C. Rillig
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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Fu W, Chen B, Rillig MC, Jansa J, Ma W, Xu C, Luo W, Wu H, Hao Z, Wu H, Zhao A, Yu Q, Han X. Community response of arbuscular mycorrhizal fungi to extreme drought in a cold-temperate grassland. THE NEW PHYTOLOGIST 2022; 234:2003-2017. [PMID: 34449895 DOI: 10.1111/nph.17692] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Climate extremes pose enormous threats to natural ecosystems. Arbuscular mycorrhizal (AM) fungi are key plant symbionts that can affect plant community dynamics and ecosystem stability. However, knowledge about how AM fungal communities respond to climate extremes in natural ecosystems remains elusive. Based on a grassland extreme drought experiment in Inner Mongolia, we investigated the response of AM fungal communities to extreme drought in association with plant communities. The experiment simulated two types of extreme drought (chronic/intense) of once-in-20-year occurrence. AM fungal richness and community composition exhibited high sensitivity to extreme drought and were more sensitive to intense drought than chronic drought. This community sensitivity (i.e. decline in richness and shifts in community composition) of AM fungi can be jointly explained by soil moisture, plant richness, and aboveground productivity. Notably, the robustness of the plant-AM fungal community co-response increased with drought intensity. Our results indicate that AM fungal communities are sensitive to climate extremes, and we propose that the plant community mediates AM fungal community responses. Given the ubiquitous nature of AM associations, their climate sensitivity may have profound consequences on plant communities and ecosystem stability under climate change.
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Affiliation(s)
- Wei Fu
- 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
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
| | - Jan Jansa
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, Prague 4, 14220, Czech Republic
| | - Wang Ma
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Erguna Forest-Steppe Ecotone Research Station, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| | - Chong Xu
- Ministry of Agriculture Key Laboratory of Crop Nutrition and Fertilization, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Wentao Luo
- Erguna Forest-Steppe Ecotone Research Station, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| | - Honghui Wu
- Ministry of Agriculture Key Laboratory of Crop Nutrition and Fertilization, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhipeng Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hui Wu
- 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
| | - Aihua Zhao
- 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
| | - Qiang Yu
- National Hulunber Grassland Ecosystem Observation and Research Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Xingguo Han
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Erguna Forest-Steppe Ecotone Research Station, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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11
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Tedersoo L, Bahram M, Zinger L, Nilsson RH, Kennedy PG, Yang T, Anslan S, Mikryukov V. Best practices in metabarcoding of fungi: From experimental design to results. Mol Ecol 2022; 31:2769-2795. [PMID: 35395127 DOI: 10.1111/mec.16460] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023]
Abstract
The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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12
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Xu X, Qiu Y, Zhang K, Yang F, Chen M, Luo X, Yan X, Wang P, Zhang Y, Chen H, Guo H, Jiang L, Hu S. Climate warming promotes deterministic assembly of arbuscular mycorrhizal fungal communities. GLOBAL CHANGE BIOLOGY 2022; 28:1147-1161. [PMID: 34668627 DOI: 10.1111/gcb.15945] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) significantly contribute to plant resource acquisition and play important roles in mediating plant interactions and soil carbon (C) dynamics. However, it remains unclear how AMF communities respond to climate change. We assessed impacts of warming and precipitation alterations (30% increase or decrease) on soil AMF communities, and examined major ecological processes shaping the AMF community assemblage in a Tibetan alpine meadow. Our results showed that warming significantly increased root biomass, and available nitrogen (N) and phosphorus (P) in soil. While precipitation alterations increased AMF abundances, they did not significantly affect the composition or diversity of AMF communities. In contrast, warming altered the composition of AMF communities and reduced their Shannon-Wiener index and Pielou's evenness. In particular, warming shifted the AMF community composition in favor of Diversisporaceae over Glomeraceae, likely through its impact on soil N and P availability. In addition, AMF communities were phylogenetically random in the unwarmed control but clustered in warming plots, implying more deterministic community assembly under climate warming. Warming enhancement of root growth, N and P availability likely reduced plant C-allocation to AMF, imposing stronger environmental filtering on AMF communities. We further proposed a conceptual framework that integrates biological and geochemical processes into a mechanistic understanding of warming and precipitation changes' effects on AMF. Taken together, these results suggest that soil AMF communities may be more sensitive to warming than expected, highlighting the need to monitor their community structure and associated functional consequences on plant communities and soil C dynamics under the future warmer climate.
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Affiliation(s)
- Xinyu Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Kangcheng Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fei Yang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mengfei Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xi Luo
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xuebin Yan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Peng Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yi Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Huaihai Chen
- School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Hui Guo
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Shuijin Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
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13
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Dong Q, Guo X, Chen K, Ren S, Muneer MA, Zhang J, Li Y, Ji B. Phylogenetic Correlation and Symbiotic Network Explain the Interdependence Between Plants and Arbuscular Mycorrhizal Fungi in a Tibetan Alpine Meadow. FRONTIERS IN PLANT SCIENCE 2021; 12:804861. [PMID: 34975995 PMCID: PMC8718876 DOI: 10.3389/fpls.2021.804861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Plants and arbuscular mycorrhizal fungi (AMF) can form complex symbiotic networks based on functional trait selection, contributing to the maintenance of ecosystem biodiversity and stability. However, the selectivity of host plants on AMF and the characteristics of plant-AMF networks remain unclear in Tibetan alpine meadows. In this study, we studied the AMF communities in 69 root samples from 23 plant species in a Tibetan alpine meadow using Illumina-MiSeq sequencing of the 18S rRNA gene. The results showed a significant positive correlation between the phylogenetic distances of plant species and the taxonomic dissimilarity of their AMF community. The plant-AMF network was characterized by high connectance, high nestedness, anti-modularity, and anti-specialization, and the phylogenetic signal from plants was stronger than that from AMF. The high connected and nested plant-AMF network potentially promoted the interdependence and stability of the plant-AMF symbioses in Tibetan alpine meadows. This study emphasizes that plant phylogeny and plant-AMF networks play an important role in the coevolution of host plants and their mycorrhizal partners and enhance our understanding of the interactions between aboveground and belowground communities.
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Affiliation(s)
- Qiang Dong
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Xin Guo
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Keyu Chen
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Shijie Ren
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Muhammad Atif Muneer
- College of Resources and Environment, International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Zhang
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yaoming Li
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Baoming Ji
- School of Grassland Science, Beijing Forestry University, Beijing, China
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14
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Harrower JT, Gilbert GS. Parasitism to mutualism continuum for Joshua trees inoculated with different communities of arbuscular mycorrhizal fungi from a desert elevation gradient. PLoS One 2021; 16:e0256068. [PMID: 34449786 PMCID: PMC8396742 DOI: 10.1371/journal.pone.0256068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 07/31/2021] [Indexed: 11/19/2022] Open
Abstract
Most desert plants form symbiotic relationships with arbuscular mycorrhizal fungi (AMF), yet fungal identity and impacts on host plants remain largely unknown. Despite widespread recognition of the importance of AMF relationships for plant functioning, we do not know how fungal community structure changes across a desert climate gradient, nor the impacts of different fungal communities on host plant species. Because climate change can shape the distribution of species through effects on species interactions, knowing how the ranges of symbiotic partners are geographically structured and the outcomes of those species interactions informs theory and improves management recommendations. Here we used high throughput sequencing to examine the AMF community of Joshua trees along a climate gradient in Joshua Tree National Park. We then used a range of performance measures and abiotic factors to evaluate how different AMF communities may affect Joshua tree fitness. We found that fungal communities change with elevation resulting in a spectrum of interaction outcomes from mutualism to parasitism that changed with the developmental stage of the plant. Nutrient accumulation and the mycorrhizal growth response of Joshua tree seedlings inoculated with fungi from the lowest (warmest) elevations was first negative, but after 9 months had surpassed that of plants with other fungal treatments. This indicates that low elevation fungi are costly for the plant to initiate symbiosis, yet confer benefits over time. The strong relationship between AMF community and plant growth suggests that variation in AMF community may have long term consequences for plant populations along an elevation gradient.
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Affiliation(s)
- Jennifer T. Harrower
- Department of Environmental Studies, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Gregory S. Gilbert
- Department of Environmental Studies, University of California, Santa Cruz, Santa Cruz, California, United States of America
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15
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Rincón C, Droh G, Villard L, Masclaux FG, N'guetta A, Zeze A, Sanders IR. Hierarchical spatial sampling reveals factors influencing arbuscular mycorrhizal fungus diversity in Côte d'Ivoire cocoa plantations. MYCORRHIZA 2021; 31:289-300. [PMID: 33638731 PMCID: PMC8068719 DOI: 10.1007/s00572-020-01019-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
While many molecular studies have documented arbuscular mycorrhizal fungi (AMF) communities in temperate ecosystems, very few studies exist in which molecular techniques have been used to study tropical AMF communities. Understanding the composition of AMF communities in tropical areas gains special relevance as crop productivity in typically low fertility tropical soils can be improved with the use of AMF. We used a hierarchical sampling approach in which we sampled soil from cocoa (Theobroma cacao L.) plantations nested in localities, and in which localities were nested within each of three regions of Côte d'Ivoire. This sampling strategy, combined with 18S rRNA gene sequencing and a dedicated de novo OTU-picking model, allowed us to study AMF community composition and how it is influenced at different geographical scales and across environmental gradients. Several factors, including pH, influenced overall AMF alpha diversity and differential abundance of specific taxa and families of the Glomeromycotina. Assemblages and diversity metrics at the local scale did not reliably predict those at regional scales. The amount of variation explained by soil, climate, and geography variables left a large proportion of the variance to be explained by other processes, likely happening at smaller scales than the ones considered in this study. Gaining a better understanding of processes involved in shaping tropical AMF community composition and AMF establishment are much needed and could allow for the development of sustainable, productive tropical agroecosystems.
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Affiliation(s)
- Cristian Rincón
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Germain Droh
- Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Lucas Villard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Assanvo N'guetta
- Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Adolphe Zeze
- Laboratoire de Biotechnologies Végétale Et Microbienne, Unité Mixte de Recherche Et D'Innovation en Sciences Agronomiques Et Génie Rual, Institut National Polytechnique Félix Houphouet-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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16
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Arbuscular mycorrhizal fungal community assembly in agroforestry systems from the Southern Brazil. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00700-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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17
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Okiobe ST, Rillig MC, Mola M, Augustin J, Parolly G, Veresoglou SD. Arbuscular mycorrhiza has little influence on N2O potential emissions compared to plant diversity in experimental plant communities. FEMS Microbiol Ecol 2020; 96:5685959. [PMID: 31868885 DOI: 10.1093/femsec/fiz208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/19/2019] [Indexed: 11/14/2022] Open
Abstract
Denitrification is an ecosystem process linked to ongoing climate change, because it releases nitrous oxide (N2O) into the atmosphere. To date, the literature covers mostly how aboveground (i.e. plant community structure) and belowground (i.e. plant-associated soil microbes) biota separately influence denitrification in isolation of each other. We here present a mesocosm experiment where we combine a manipulation of belowground biota (i.e. addition of Rhizophagus irregularis propagules to the indigenous mycorrhizal community) with a realized gradient in plant diversity. We used a seed mix containing plant species representative of mesophytic European grasslands and by stochastic differences in species establishment across the sixteen replicates per treatment level a spontaneously established gradient in plant diversity. We address mycorrhizal-induced and plant-diversity mediated changes on denitrification potential parameters and how these differ from the existing literature that studies them independently of each other. We show that unlike denitrification potential, N2O potential emissions do not change with mycorrhiza and depend instead on realized plant diversity. By linking mycorrhizal ecology to an N-cycling process, we present a comprehensive assessment of terrestrial denitrification dynamics when diverse plants co-occur.
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Affiliation(s)
- Simon T Okiobe
- Freie Universität Berlin, Institut für Biologie, Altensteinstraße 6, D-14195 Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstraße 6, D-14195 Berlin, Germany
| | - Matthias C Rillig
- Freie Universität Berlin, Institut für Biologie, Altensteinstraße 6, D-14195 Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstraße 6, D-14195 Berlin, Germany
| | - Magkdi Mola
- Freie Universität Berlin, Institut für Biologie, Altensteinstraße 6, D-14195 Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstraße 6, D-14195 Berlin, Germany
| | - Jürgen Augustin
- Research Area 1 "Landscape Functioning", Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany
| | - Gerald Parolly
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Strasse 6-8, 14195 Berlin, Germany
| | - Stavros D Veresoglou
- Freie Universität Berlin, Institut für Biologie, Altensteinstraße 6, D-14195 Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstraße 6, D-14195 Berlin, Germany
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18
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Sandoz FA, Bindschedler S, Dauphin B, Farinelli L, Grant JR, Hervé V. Biotic and abiotic factors shape arbuscular mycorrhizal fungal communities associated with the roots of the widespread fern Botrychium lunaria (Ophioglossaceae). ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:342-354. [PMID: 32216046 DOI: 10.1111/1758-2229.12840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 06/10/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) play central roles in terrestrial ecosystems by interacting with both above and belowground communities as well as by influencing edaphic properties. The AMF communities associated with the roots of the fern Botrychium lunaria (Ophioglossaceae) were sampled in four transects at 2400 m a.s.l. in the Swiss Alps and analyzed using metabarcoding. Members of five Glomeromycota genera were identified across the 71 samples. Our analyses revealed the existence of a core microbiome composed of four abundant Glomus operational taxonomic units (OTUs), as well as a low OTU turnover between samples. The AMF communities were not spatially structured, which contrasts with most studies on AMF associated with angiosperms. pH, microbial connectivity and humus cover significantly shaped AMF beta diversity but only explained a minor fraction of variation in beta diversity. AMF OTUs associations were found to be significant by both cohesion and co-occurrence analyses, suggesting a role for fungus-fungus interactions in AMF community assembly. In particular, OTU co-occurrences were more frequent between different genera than among the same genus, rising the hypothesis of functional complementarity among the AMF associated to B. lunaria. Altogether, our results provide new insights into the ecology of fern symbionts in alpine grasslands.
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Affiliation(s)
- Frédéric Alexandre Sandoz
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Conservatoire et Jardin botaniques de la Ville de Genève, Chambésy-Genève, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Benjamin Dauphin
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Jason R Grant
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Laboratory of Biogeosciences, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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19
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Goldmann K, Boeddinghaus RS, Klemmer S, Regan KM, Heintz‐Buschart A, Fischer M, Prati D, Piepho H, Berner D, Marhan S, Kandeler E, Buscot F, Wubet T. Unraveling spatiotemporal variability of arbuscular mycorrhizal fungi in a temperate grassland plot. Environ Microbiol 2020; 22:873-888. [PMID: 31087598 PMCID: PMC7065148 DOI: 10.1111/1462-2920.14653] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022]
Abstract
Soils provide a heterogeneous environment varying in space and time; consequently, the biodiversity of soil microorganisms also differs spatially and temporally. For soil microbes tightly associated with plant roots, such as arbuscular mycorrhizal fungi (AMF), the diversity of plant partners and seasonal variability in trophic exchanges between the symbionts introduce additional heterogeneity. To clarify the impact of such heterogeneity, we investigated spatiotemporal variation in AMF diversity on a plot scale (10 × 10 m) in a grassland managed at low intensity in southwest Germany. AMF diversity was determined using 18S rDNA pyrosequencing analysis of 360 soil samples taken at six time points within a year. We observed high AMF alpha- and beta-diversity across the plot and at all investigated time points. Relationships were detected between spatiotemporal variation in AMF OTU richness and plant species richness, root biomass, minimal changes in soil texture and pH. The plot was characterized by high AMF turnover rates with a positive spatiotemporal relationship for AMF beta-diversity. However, environmental variables explained only ≈20% of the variation in AMF communities. This indicates that the observed spatiotemporal richness and community variability of AMF was largely independent of the abiotic environment, but related to plant properties and the cooccurring microbiome.
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Affiliation(s)
- Kezia Goldmann
- Department of Soil EcologyUFZ – Helmholtz Centre for Environmental ResearchTheodor‐Lieser‐Straße 4, 06120Halle (Saale)Germany
| | - Runa S. Boeddinghaus
- Department of Soil Biology, Institute of Soil Science and Land EvaluationUniversity of HohenheimEmil‐Wolff‐Straße 27, 70599StuttgartGermany
| | - Sandra Klemmer
- Department of Soil EcologyUFZ – Helmholtz Centre for Environmental ResearchTheodor‐Lieser‐Straße 4, 06120Halle (Saale)Germany
| | - Kathleen M. Regan
- Department of Soil Biology, Institute of Soil Science and Land EvaluationUniversity of HohenheimEmil‐Wolff‐Straße 27, 70599StuttgartGermany
- Ecosystems CenterMarine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Anna Heintz‐Buschart
- Department of Soil EcologyUFZ – Helmholtz Centre for Environmental ResearchTheodor‐Lieser‐Straße 4, 06120Halle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigDeutscher Platz 5e, 04103LeipzigGermany
| | - Markus Fischer
- Institute of Plant Sciences and Botanical GardenUniversity of BernAltenbergrain 21, 3013BernSwitzerland
| | - Daniel Prati
- Institute of Plant Sciences and Botanical GardenUniversity of BernAltenbergrain 21, 3013BernSwitzerland
| | - Hans‐Peter Piepho
- Institute of Crop Science, Biostatistics UnitUniversity of HohenheimFruwirthstraße 23, 70599StuttgartGermany
| | - Doreen Berner
- Department of Soil Biology, Institute of Soil Science and Land EvaluationUniversity of HohenheimEmil‐Wolff‐Straße 27, 70599StuttgartGermany
| | - Sven Marhan
- Department of Soil Biology, Institute of Soil Science and Land EvaluationUniversity of HohenheimEmil‐Wolff‐Straße 27, 70599StuttgartGermany
| | - Ellen Kandeler
- Department of Soil Biology, Institute of Soil Science and Land EvaluationUniversity of HohenheimEmil‐Wolff‐Straße 27, 70599StuttgartGermany
| | - François Buscot
- Department of Soil EcologyUFZ – Helmholtz Centre for Environmental ResearchTheodor‐Lieser‐Straße 4, 06120Halle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigDeutscher Platz 5e, 04103LeipzigGermany
| | - Tesfaye Wubet
- Department of Soil EcologyUFZ – Helmholtz Centre for Environmental ResearchTheodor‐Lieser‐Straße 4, 06120Halle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigDeutscher Platz 5e, 04103LeipzigGermany
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20
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Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat Rev Microbiol 2020; 17:95-109. [PMID: 30442909 DOI: 10.1038/s41579-018-0116-y] [Citation(s) in RCA: 404] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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Affiliation(s)
- R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Sten Anslan
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Leho Tedersoo
- Natural History Museum of Tartu University, Tartu, Estonia
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21
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Roy J, Mazel F, Sosa-Hernández MA, Dueñas JF, Hempel S, Zinger L, Rillig MC. The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution. THE NEW PHYTOLOGIST 2019; 224:936-948. [PMID: 31355954 DOI: 10.1111/nph.16080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
The phylogenetic depth at which arbuscular mycorrhizal (AM) fungi harbor a coherent ecological niche is unknown, which has consequences for operational taxonomic unit (OTU) delineation from sequence data and the study of their biogeography. We tested how changes in AM fungi community composition across habitats (beta diversity) vary with OTU phylogenetic resolution. We inferred exact sequence variants (ESVs) to resolve phylotypes at resolutions finer than provided by traditional sequence clustering and analyzed beta diversity profiles up to order-level sequence clusters. At the ESV level, we detected the environmental predictors revealed with traditional OTUs or at higher genetic distances. However, the correlation between environmental predictors and community turnover steeply increased at a genetic distance of c. 0.03 substitutions per site. Furthermore, we observed a turnover of either closely or distantly related taxa (respectively at or above 0.03 substitutions per site) along different environmental gradients. This study suggests that different axes of AM fungal ecological niche are conserved at different phylogenetic depths. Delineating AM fungal phylotypes using DNA sequences should screen different phylogenetic resolutions to better elucidate the factors that shape communities and predict the fate of AM symbioses in a changing environment.
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Affiliation(s)
- Julien Roy
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Florent Mazel
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Moisés A Sosa-Hernández
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Juan F Dueñas
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Stefan Hempel
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Lucie Zinger
- Ecole Normale Supérieure, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), PSL Research University, F-75005, Paris, France
| | - Matthias C Rillig
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
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22
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Haug I, Setaro S, Suárez JP. Species composition of arbuscular mycorrhizal communities changes with elevation in the Andes of South Ecuador. PLoS One 2019; 14:e0221091. [PMID: 31419262 PMCID: PMC6697372 DOI: 10.1371/journal.pone.0221091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/30/2019] [Indexed: 12/24/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are the most prominent mycobionts of plants in the tropics, yet little is known about their diversity, species compositions and factors driving AMF distribution patterns. To investigate whether elevation and associated vegetation type affect species composition, we sampled 646 mycorrhizal samples in locations between 1000 and 4000 m above sea level (masl) in the South of Ecuador. We estimated diversity, distribution and species compositions of AMF by cloning and Sanger sequencing the 18S rDNA (the section between AML1 and AML2) and subsequent derivation of fungal OTUs based on 99% sequence similarity. In addition, we analyzed the phylogenetic structure of the sites by computing the mean pairwise distance (MPD) and the mean nearest taxon difference (MNTD) for each elevation level. It revealed that AMF species compositions at 1000 and 2000 masl differ from 3000 and 4000 masl. Lower elevations (1000 and 2000 masl) were dominated by members of Glomeraceae, whereas Acaulosporaceae were more abundant in higher elevations (3000 and 4000 masl). Ordination of OTUs with respect to study sites revealed a correlation to elevation with a continuous turnover of species from lower to higher elevations. Most of the abundant OTUs are not endemic to South Ecuador. We also found a high proportion of rare OTUs at all elevations: 79-85% of OTUs occurred in less than 5% of the samples. Phylogenetic community analysis indicated clustering and evenness for most elevation levels indicating that both, stochastic processes and habitat filtering are driving factors of AMF community compositions.
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Affiliation(s)
- Ingeborg Haug
- Evolutionary Ecology of Plants, Eberhard-Karls-University, Tübingen, Germany
| | - Sabrina Setaro
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Juan Pablo Suárez
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
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23
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Wilkinson TDJ, Miranda JP, Ferrari J, Hartley SE, Hodge A. Aphids Influence Soil Fungal Communities in Conventional Agricultural Systems. FRONTIERS IN PLANT SCIENCE 2019; 10:895. [PMID: 31354767 PMCID: PMC6640087 DOI: 10.3389/fpls.2019.00895] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/24/2019] [Indexed: 05/12/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) form symbioses with the roots of most plant species, including cereals. AMF can increase the uptake of nutrients including nitrogen (N) and phosphorus (P), and of silicon (Si) as well as increase host resistance to various stresses. Plants can simultaneously interact with above-ground insect herbivores such as aphids, which can alter the proportion of plant roots colonized by AMF. However, it is unknown if aphids impact the structure of AMF communities colonizing plants or the extent of the extraradical mycelium produced in the soil, both of which can influence the defensive and nutritional benefit a plant derives from the symbiosis. This study investigated the effect of aphids on the plant-AMF interaction in a conventionally managed agricultural system. As plants also interact with other soil fungi, the non-AMF fungal community was also investigated. We hypothesized that aphids would depress plant growth, and reduce intraradical AMF colonization, soil fungal hyphal density and the diversity of AM and non-AM fungal communities. To test the effects of aphids, field plots of barley enclosed with insect proof cages were inoculated with Sitobion avenae or remained uninoculated. AMF specific and total fungal amplicon sequencing assessed root fungal communities 46 days after aphid addition. Aphids did not impact above-ground plant biomass, but did increase the grain N:P ratio. Whilst aphid presence had no impact on AMF intraradical colonization, soil fungal hyphal length density, or AMF community characteristics, there was a trend for the aphid treatment to increase vesicle numbers and the relative abundance of the AMF family Gigasporaceae. Contrary to expectations, the aphid treatment also increased the evenness of the total fungal community. This suggests that aphids can influence soil communities in conventional arable systems, a result that could have implications for multitrophic feedback loops between crop pests and soil organisms across the above-below-ground interface.
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Affiliation(s)
| | | | - Julia Ferrari
- Department of Biology, University of York, York, United Kingdom
| | - Sue E. Hartley
- Department of Biology, University of York, York, United Kingdom
- York Environmental Sustainability Institute, University of York, York, United Kingdom
| | - Angela Hodge
- Department of Biology, University of York, York, United Kingdom
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24
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Herrera P, Suárez JP, Sánchez-Rodríguez A, Molina MC, Prieto M, Méndez M. Many broadly-shared mycobionts characterize mycorrhizal interactions of two coexisting epiphytic orchids in a high elevation tropical forest. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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25
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Hempel S. Passengers and drivers of arbuscular mycorrhizal fungal communities at different scales. THE NEW PHYTOLOGIST 2018; 220:952-953. [PMID: 30408218 DOI: 10.1111/nph.15139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Stefan Hempel
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, Berlin, Germany
- Berlin Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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26
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Berruti A, Bianciotto V, Lumini E. Seasonal variation in winter wheat field soil arbuscular mycorrhizal fungus communities after non-mycorrhizal crop cultivation. MYCORRHIZA 2018; 28:535-548. [PMID: 29931405 DOI: 10.1007/s00572-018-0845-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Intensive farming practices that implement deep and frequent tillage, high input inorganic fertilization, cultivation with non-host species, and pesticide use are widely reported to be detrimental for arbuscular mycorrhizal fungi (AMF), which are one of the most important plant biofertilizers. The effect of the reduction of agricultural input on AMF community dynamics following conversion from conventional non-mycorrhizal to lower input mycorrhizal crop cultivation has not yet been fully elucidated. We investigated the effect of the reduction of agricultural input, rotation, and season on AMF communities in winter wheat field soil after conversion from long-term (more than 20 years) non-mycorrhizal (sugar beet) crop cultivation. We described AMF communities from bulk soil samples by specifically targeting the 18S ribosomal gene using a combination of AMF specific primers and 454 pyrosequencing. No effect was found after 3 years' reduction of agricultural input, and only marginal effects were due to rotation with specific crops preceding winter wheat. Instead, season and year of sampling had the most appreciable influence on the AMF community. We suggest that, after conversion from long-term non-mycorrhizal to mycorrhizal crop cultivation, AMF diversity is low if compared to similar agroecosystems. Seasonal and successional dynamics play an important role as determinants of community structure.
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Affiliation(s)
- Andrea Berruti
- Institute for Sustainable Plant Protection -Turin unit, National Research Council, Viale Mattioli 25, 10125, Torino, Italy
| | - Valeria Bianciotto
- Institute for Sustainable Plant Protection -Turin unit, National Research Council, Viale Mattioli 25, 10125, Torino, Italy
| | - Erica Lumini
- Institute for Sustainable Plant Protection -Turin unit, National Research Council, Viale Mattioli 25, 10125, Torino, Italy.
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27
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Egan CP, Rummel A, Kokkoris V, Klironomos J, Lekberg Y, Hart M. Using mock communities of arbuscular mycorrhizal fungi to evaluate fidelity associated with Illumina sequencing. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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28
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Christian N, Bever JD. Carbon allocation and competition maintain variation in plant root mutualisms. Ecol Evol 2018; 8:5792-5800. [PMID: 29938093 PMCID: PMC6010867 DOI: 10.1002/ece3.4118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 02/02/2018] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
Plants engage in multiple root symbioses that offer varying degrees of benefit. We asked how variation in partner quality persists using a resource-ratio model of population growth. We considered the plant's ability to preferentially allocate carbon to mutualists and competition for plant carbon between mutualist and nonmutualist symbionts. We treated carbon as two nutritionally interchangeable, but temporally separated, resources-carbon allocated indiscriminately for the construction of the symbiosis, and carbon preferentially allocated to the mutualist after symbiosis establishment and assessment. This approach demonstrated that coexistence of mutualists and nonmutualists is possible when fidelity of the plant to the mutualist and the cost of mutualism mediate resource competition. Furthermore, it allowed us to trace symbiont population dynamics given varying degrees of carbon allocation. Specifically, coexistence occurs at intermediate levels of preferential allocation. Our findings are consistent with previous empirical studies as well the application of biological market theory to plantroot symbioses.
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Affiliation(s)
- Natalie Christian
- Evolution, Ecology and Behavior ProgramDepartment of BiologyIndiana UniversityBloomingtonIndiana
| | - James D. Bever
- Department of Ecology and Evolutionary BiologyThe University of KansasLawrenceKansas
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29
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Xu Z, Wu Y, Jiang Y, Zhang X, Li J, Ban Y. Arbuscular mycorrhizal fungi in two vertical-flow wetlands constructed for heavy metal-contaminated wastewater bioremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:12830-12840. [PMID: 29476370 DOI: 10.1007/s11356-018-1527-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
Over the last three decades, the presence of arbuscular mycorrhizal fungi (AMF) in wetland habitats had been proven, and their roles played in wetland ecosystems and potential functions in wastewater bioremediation technical installations are interesting issues. To increase knowledge on the functions of AMF in the plant-based bioremediation of wastewater, we constructed two vertical-flow wetlands planting with Phragmites australis and investigated AMF distribution in plant roots and their roles played in purification of wastewater polluted by heavy metals (HMs), utilizing the Illumina sequencing technique. A total of 17 operational taxonomic units (OTUs) from 33,031 AMF sequences were obtained, with Glomus being the most dominant. P. australis living in the two vertical-flow constructed wetlands (CWs) harbored diverse AMF comparable with the AM fungal communities in upland habitats. The AMF composition profiles of CW1 (vegetated with non-inoculated plants) and CW2 (vegetated with mycorrhizal plants inoculated with Rhizophagus intraradices) were significantly different. CW1 (15 OTUs) harbored more diverse AMF than CW2 (7 OTUs); however, CW2 harbored much more OTU13 than CW1. In addition, a zipf species abundance distribution (SAD), which might due to the heavy overdominance of OTU13, was observed across AM fugal taxa in P. australis roots of the two CWs. CW1 and CW2 showed high (> 70%) removal capacity of HMs. CW2 exhibited significant higher Cd and Zn removal efficiencies than CW1 (CK) (p = 0.005 and p = 0.008, respectively). It was considered that AMF might play a role in HM removal in CWs.
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Affiliation(s)
- Zhouying Xu
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Yang Wu
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Yinghe Jiang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Xiangling Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Junli Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Yihui Ban
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, Hubei, 430070, China.
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30
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Tylianakis JM, Martínez-García LB, Richardson SJ, Peltzer DA, Dickie IA. Symmetric assembly and disassembly processes in an ecological network. Ecol Lett 2018; 21:896-904. [PMID: 29611321 DOI: 10.1111/ele.12957] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/24/2018] [Accepted: 03/02/2018] [Indexed: 02/03/2023]
Abstract
The processes whereby ecological networks emerge, persist and decay throughout ecosystem development are largely unknown. Here we study networks of plant and arbuscular mycorrhizal fungal (AMF) communities along a 120 000 year soil chronosequence, as they undergo assembly (progression) and then disassembly (retrogression). We found that network assembly and disassembly were symmetrical, self-reinforcing processes that together were capable of generating key attributes of network architecture. Plant and AMF species that had short indirect paths to others in the community (i.e. high centrality), rather than many direct interaction partners (i.e. high degree), were best able to attract new interaction partners and, in the case of AMF species, also to retain existing interactions with plants during retrogression. We then show using simulations that these non-random patterns of attachment and detachment promote nestedness of the network. These results have implications for predicting extinction sequences, identifying focal points for invasions and suggesting trajectories for restoration.
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Affiliation(s)
- Jason M Tylianakis
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK.,Bio-protection Research Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Laura B Martínez-García
- Landcare Research, PO Box 69040, Lincoln, 7640, New Zealand.,Department of Soil Quality, Wageningen University, P.O. Box 47, Wageningen, 6700 AA, The Netherlands
| | | | | | - Ian A Dickie
- Bio-protection Research Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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31
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House GL, Bever JD. Disturbance reduces the differentiation of mycorrhizal fungal communities in grasslands along a precipitation gradient. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2018; 28:736-748. [PMID: 29314434 DOI: 10.1002/eap.1681] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/22/2017] [Accepted: 12/11/2017] [Indexed: 05/14/2023]
Abstract
Given that mycorrhizal fungi play key roles in shaping plant communities, greater attention should be focused on factors that determine the composition of mycorrhizal fungal communities and their sensitivity to anthropogenic disturbance. We investigate changes in arbuscular mycorrhizal (AM) fungal community composition across a precipitation gradient in North American grasslands as well as changes occurring with varying degrees of site disturbance that have resulted in invasive plant establishment. We find strong differentiation of AM fungal communities in undisturbed remnant grasslands across the precipitation gradient, whereas communities in disturbed grasslands were more homogeneous. These changes in community differentiation with disturbance are consistent with more stringent environmental filtering of AM fungal communities in undisturbed sites that may also be promoted by more rigid functional constraints imposed on AM fungi by the native plant communities in these areas. The AM fungal communities in eastern grasslands were particularly sensitive to anthropogenic disturbance, with disturbed sites having low numbers of AM fungal operational taxonomic units (OTUs) commonly found in undisturbed sites, and also the proliferation of AM fungal OTUs in disturbed sites. This proliferation of AM fungi in eastern disturbed sites coincided with increased soil phosphorus availability and is consistent with evidence suggesting the fungi represented by these OTUs would provide reduced benefits to native plants. The differentiation of AM fungal communities along the precipitation gradient in undisturbed grasslands but not in disturbed sites is consistent with AM fungi aiding plant adaptation to climate, and suggests they may be especially important targets for conservation and restoration in order to help maintain or re-establish diverse grassland plant communities.
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Affiliation(s)
- Geoffrey L House
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, Indiana, 47405, USA
| | - James D Bever
- Department of Ecology and Evolutionary Biology and Kansas Biological Survey, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
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32
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Camenzind T, Hammer EC, Lehmann J, Solomon D, Horn S, Rillig MC, Hempel S. Arbuscular mycorrhizal fungal and soil microbial communities in African Dark Earths. FEMS Microbiol Ecol 2018. [PMID: 29538644 DOI: 10.1093/femsec/fiy033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The socio-economic values of fertile and carbon-rich Dark Earth soils are well described from the Amazon region. Very recently, Dark Earth soils were also identified in tropical West Africa, with comparable beneficial soil properties and plant growth-promoting effects. The impact of this management technique on soil microbial communities, however, is less well understood, especially with respect to the ecologically relevant group of arbuscular mycorrhizal (AM) fungi. Thus, we tested the hypotheses that (1) improved soil quality in African Dark Earth (AfDE) will increase soil microbial biomass and shift community composition and (2) concurrently increased nutrient availability will negatively affect AM fungal communities. Microbial communities were distinct in AfDE in comparison to adjacent sites, with an increased fungal:bacterial ratio of 71%, a pattern mainly related to shifts in pH. AM fungal abundance and diversity, however, did not differ despite clearly increased soil fertility in AfDE, with 3.7 and 1.7 times greater extractable P and total N content, respectively. The absence of detrimental effects on AM fungi, often seen following applications of inorganic fertilizers, and the enhanced role of saprobic fungi relevant for mineralization and C sequestration support previous assertions of this management type as a sustainable alternative agricultural practice.
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Affiliation(s)
- Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Altensteinstr. 34, 14195 Berlin, Germany
| | - Edith C Hammer
- Department of Biology, Lund University, Box 118, 22100 Lund, Sweden
| | - Johannes Lehmann
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, 909 Bradfield Hall, Ithaca, New York, US
- Atkinson Center for a Sustainable Future, Cornell University, 200 Rice Hall, Ithaca, New York, USA
- Institute for Advanced Studies, Technical University Munich, Lichtenbergstr. 2a, 85748 Garching, Germany
| | - Dawit Solomon
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, 909 Bradfield Hall, Ithaca, New York, US
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), East Africa Box 30709, Nairobi, Kenya
| | - Sebastian Horn
- Hawkesbury Institute for the Environment, Western Sydney University, Science Rd, Richmond NSW 2753, Australia
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Altensteinstr. 34, 14195 Berlin, Germany
| | - Stefan Hempel
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Altensteinstr. 34, 14195 Berlin, Germany
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33
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López-García Á, Varela-Cervero S, Vasar M, Öpik M, Barea JM, Azcón-Aguilar C. Plant traits determine the phylogenetic structure of arbuscular mycorrhizal fungal communities. Mol Ecol 2017; 26:6948-6959. [DOI: 10.1111/mec.14403] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/09/2017] [Accepted: 10/16/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Álvaro López-García
- Department of Soil Microbiology and Symbiotic Systems; Estación Experimental del Zaidín; CSIC; Granada Spain
| | - Sara Varela-Cervero
- Department of Soil Microbiology and Symbiotic Systems; Estación Experimental del Zaidín; CSIC; Granada Spain
| | - Martti Vasar
- Department of Botany; University of Tartu; Tartu Estonia
| | - Maarja Öpik
- Department of Botany; University of Tartu; Tartu Estonia
| | - José M. Barea
- Department of Soil Microbiology and Symbiotic Systems; Estación Experimental del Zaidín; CSIC; Granada Spain
| | - Concepción Azcón-Aguilar
- Department of Soil Microbiology and Symbiotic Systems; Estación Experimental del Zaidín; CSIC; Granada Spain
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34
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Berruti A, Desirò A, Visentin S, Zecca O, Bonfante P. ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:658-667. [PMID: 28799720 DOI: 10.1111/1758-2229.12574] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 05/17/2017] [Accepted: 08/03/2017] [Indexed: 05/26/2023]
Abstract
ITS primers commonly used to describe soil fungi are flawed for AMF although it is unknown the extent to which they distort the interpretation of community patterns. Here, we focus on how the use of a specific ITS2 fungal barcoding primer pair biased for AMF changes the interpretation of AMF community patterns from three mountain vineyards compared to a novel AMF-specific approach on the 18S. We found that although discrepancies were present in the taxonomic composition of the two resulting datasets, the estimation of diversity patterns among AMF communities was similar and resulted in both primer systems being able to correctly assess the community-structuring effect of location, compartment (root vs. soil) and environment. Both methodologies made it possible to detect the same alpha-diversity trend among the locations under study but not between root and soil transects. We show that the ITS2 primer system for fungal barcoding provides a good estimate of both AMF community structure and relation to environmental variables. However, this primer system does not fit in with cross-compartment surveys (roots vs. soil) as it can underestimate AMF diversity in soil samples. When specifically focusing on AMF, the 18S primer system resulted in wide coverage and marginal non-target amplification.
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Affiliation(s)
- Andrea Berruti
- Department of Life Sciences and System Biology, University of Torino, viale Mattioli 25, Torino 10125, Italy
- Institute for Sustainable Plant Protection, UOS Torino - National Research Council, viale Mattioli 25, Torino 10125, Italy
| | - Alessandro Desirò
- Department of Life Sciences and System Biology, University of Torino, viale Mattioli 25, Torino 10125, Italy
| | - Stefano Visentin
- Department of Life Sciences and System Biology, University of Torino, viale Mattioli 25, Torino 10125, Italy
| | - Odoardo Zecca
- Institut Agricole Re´gional, strada la Rochere 1, Aosta 11100, Italy
| | - Paola Bonfante
- Department of Life Sciences and System Biology, University of Torino, viale Mattioli 25, Torino 10125, Italy
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35
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Ban Y, Jiang Y, Li M, Zhang X, Zhang S, Wu Y, Xu Z. Homogenous stands of a wetland grass living in heavy metal polluted wetlands harbor diverse consortia of arbuscular mycorrhizal fungi. CHEMOSPHERE 2017; 181:699-709. [PMID: 28477526 DOI: 10.1016/j.chemosphere.2017.04.135] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 04/08/2017] [Accepted: 04/26/2017] [Indexed: 06/07/2023]
Abstract
Over the last three decades, the presence of arbuscular mycorrhizal (AM) fungi in wetland habitats had received increased attention, however, their distribution and functions have not been studied intensively. Using Illumina sequencing technology, we examined the AM fungal communities in roots of Phragmites australis living in 3 heavy metals (HMs) polluted wetlands located in Hubei Province, China. A total of 258 operational taxonomic units (OTUs) from 235,213 sequences affiliated with 6 Glomeromycota families (Glomeraceae, Paraglomeraceae, Claroideoglomeraceae, Ambisporaceae, Archaeosporaceae, and Diversisporaceae) were obtained, with Glomeraceae and Paraglomeraceae being the most and second-most dominant family, respectively. P. australis living in the HMs polluted wetlands harbored diverse AM fungi, including many non-recorded species in upland habitats, and the OTU number which we obtained in this study was higher than most of the records of upland habitats. Dry and waterlogged samples had common OTUs, however, AM fungal communities at different levels in dry and corresponding waterlogged P. australis roots were significant different. In addition, results from this study suggested that a preemption (geometric model) species abundance distributions (SAD), which might due to the distinctive features, e.g. heavy overdominance and difference in the most dominant taxon of each sample, was observed across AM fugal taxa in P. australis roots of the 3 HMs polluted wetlands.
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Affiliation(s)
- Yihui Ban
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, Hubei, China
| | - Yinghe Jiang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, Hubei, China
| | - Meng Li
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, Hubei, China
| | - Xiangling Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, Hubei, China
| | - Shiyang Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, Hubei, China
| | - Yang Wu
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, Hubei, China
| | - Zhouying Xu
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, Hubei, China.
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36
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Jarvis KJ, Allan GJ, Craig AJ, Beresic-Perrins RK, Wimp G, Gehring CA, Whitham TG. Arthropod communities on hybrid and parental cottonwoods are phylogenetically structured by tree type: Implications for conservation of biodiversity in plant hybrid zones. Ecol Evol 2017; 7:5909-5921. [PMID: 28808554 PMCID: PMC5551273 DOI: 10.1002/ece3.3146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/17/2017] [Indexed: 02/03/2023] Open
Abstract
Although hybridization in plants has been recognized as an important pathway in plant speciation, it may also affect the ecology and evolution of associated communities. Cottonwood species (Populus angustifolia and P. fremontii) and their naturally occurring hybrids are known to support different plant, animal, and microbial communities, but no studies have examined community structure within the context of phylogenetic history. Using a community composed of 199 arthropod species, we tested for differences in arthropod phylogenetic patterns within and among hybrid and parental tree types in a common garden. Three major patterns emerged. (1) Phylogenetic diversity (PD) was significantly different between arthropod communities on hybrids and Fremont cottonwood when pooled by tree type. (2) Mean phylogenetic distance (MPD) and net relatedness index (NRI) indicated that communities on hybrid trees were significantly more phylogenetically overdispersed than communities on either parental tree type. (3) Community distance (Dpw) indicated that communities on hybrids were significantly different than parental species. Our results show that arthropod communities on parental and hybrid cottonwoods exhibit significantly different patterns of phylogenetic structure. This suggests that arthropod community assembly is driven, in part, by plant-arthropod interactions at the level of cottonwood tree type. We discuss potential hypotheses to explain the effect of plant genetic dissimilarity on arthropod phylogenetic community structure, including the role of competition and environmental filtering. Our findings suggest that cottonwood species and their hybrids function as evolutionarily significant units (ESUs) that affect the assembly and composition of associated arthropod communities and deserve high priority for conservation.
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Affiliation(s)
- Karl J Jarvis
- School of Forestry Northern Arizona University Flagstaff AZ USA.,Biology Department Southern Utah University Cedar City UT USA
| | - Gerard J Allan
- Department of Biological Sciences Northern Arizona University Flagstaff AZ USA.,Merriam-Powell Center for Environmental Research Flagstaff AZ USA
| | - Ashley J Craig
- Department of Biological Sciences Northern Arizona University Flagstaff AZ USA
| | | | - Gina Wimp
- Department of Biology Georgetown University Washington DC USA
| | - Catherine A Gehring
- Department of Biological Sciences Northern Arizona University Flagstaff AZ USA.,Merriam-Powell Center for Environmental Research Flagstaff AZ USA
| | - Thomas G Whitham
- Department of Biological Sciences Northern Arizona University Flagstaff AZ USA.,Merriam-Powell Center for Environmental Research Flagstaff AZ USA
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37
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Bouffaud ML, Bragalini C, Berruti A, Peyret-Guzzon M, Voyron S, Stockinger H, van Tuinen D, Lumini E, Wipf D, Plassart P, Lemanceau P, Bianciotto V, Redecker D, Girlanda M. Arbuscular mycorrhizal fungal community differences among European long-term observatories. MYCORRHIZA 2017; 27:331-343. [PMID: 27942957 DOI: 10.1007/s00572-016-0753-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/25/2016] [Indexed: 06/06/2023]
Abstract
Arbuscular mycorrhizal fungal (AMF) communities have been demonstrated to respond to a variety of biotic and abiotic factors, including various aspects of land management. Numerous studies have specifically addressed the impact of land use on AMF communities, but usually have been confined to one or a few sites. In this study, soil AMF assemblages were described in four different long-term observatories (LTOs) across Europe, each of which included a site-specific high-intensity and a low-intensity land use. AMF communities were characterized on the basis of 454 sequencing of the internal transcribed spacer 2 (ITS2) rDNA region. The primary goals of this study were (i) to determine the main factors that shape AMF communities in differentially managed sites in Europe and (ii) to identify individual AMF taxa or combinations of taxa suitable for use as biomarkers of land use intensification. AMF communities were distinct among LTOs, and we detected significant effects of management type and soil properties within the sites, but not across all sites. Similarly, indicator species were identified for specific LTOs and land use types but not universally for high- or low-intensity land uses. Different subsets of soil properties, including several chemical and physical variables, were found to be able to explain an important fraction of AMF community variation alone or together with other examined factors in most sites. The important factors were different from those for other microorganisms studied in the same sites, highlighting particularities of AMF biology.
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Affiliation(s)
- M-L Bouffaud
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
- Helmholtz Center for Environmental Research - UFZ, Halle, Germany, German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - C Bragalini
- Department of Life Sciences and System Biology (DBios), University of Torino, 25 Viale Mattioli, 10125, Torino, Italy
- Université Claude Bernard Lyon1, Lyon, France
| | - A Berruti
- CNR-Istituto per la Protezione Sostenibile delle Piante, UOS Turin (CNR-IPSP), Torino, Italy
| | - M Peyret-Guzzon
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - S Voyron
- Department of Life Sciences and System Biology (DBios), University of Torino, 25 Viale Mattioli, 10125, Torino, Italy
| | - H Stockinger
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - D van Tuinen
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - E Lumini
- CNR-Istituto per la Protezione Sostenibile delle Piante, UOS Turin (CNR-IPSP), Torino, Italy
| | - D Wipf
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - P Plassart
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - P Lemanceau
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - V Bianciotto
- CNR-Istituto per la Protezione Sostenibile delle Piante, UOS Turin (CNR-IPSP), Torino, Italy
| | - D Redecker
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France.
| | - M Girlanda
- Department of Life Sciences and System Biology (DBios), University of Torino, 25 Viale Mattioli, 10125, Torino, Italy.
- Université Claude Bernard Lyon1, Lyon, France.
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38
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Egan CP, Callaway RM, Hart MM, Pither J, Klironomos J. Phylogenetic structure of arbuscular mycorrhizal fungal communities along an elevation gradient. MYCORRHIZA 2017; 27:273-282. [PMID: 27909817 DOI: 10.1007/s00572-016-0752-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
Despite the importance of arbuscular mycorrhizal (AM) fungi within terrestrial ecosystems, we know little about how natural AM fungal communities are structured. To date, the majority of studies examining AM fungal community diversity have focused on single habitats with similar environmental conditions, with relatively few studies having assessed the diversity of AM fungi over large-scale environmental gradients. In this study, we characterized AM fungal communities in the soil along a high-elevation gradient in the North American Rocky Mountains. We focused on phylogenetic patterns of AM fungal communities to gain insight into how AM fungal communities are naturally assembled. We found that alpine AM fungal communities had lower phylogenetic diversity relative to lower elevation communities, as well as being more heterogeneous in composition than either treeline or subalpine communities. AM fungal communities were phylogenetically clustered at all elevations sampled, suggesting that environmental filtering, either selection by host plants or fungal niches, is the primary ecological process structuring communities along the gradient.
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Affiliation(s)
- Cameron P Egan
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada.
| | - Ragan M Callaway
- Division of Biological Sciences and the Institute on Ecosystems, University of Montana, Missoula, MT, 59812, USA
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Jason Pither
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada
| | - John Klironomos
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada
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39
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Chen L, Zheng Y, Gao C, Mi XC, Ma KP, Wubet T, Guo LD. Phylogenetic relatedness explains highly interconnected and nested symbiotic networks of woody plants and arbuscular mycorrhizal fungi in a Chinese subtropical forest. Mol Ecol 2017; 26:2563-2575. [DOI: 10.1111/mec.14061] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 01/05/2017] [Accepted: 02/06/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Liang Chen
- State Key Laboratory of Mycology; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
- College of Life Sciences; University of Chinese Academy of Sciences; Beijing 100049 China
| | - Yong Zheng
- State Key Laboratory of Mycology; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Cheng Gao
- State Key Laboratory of Mycology; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Ke-Ping Ma
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Tesfaye Wubet
- Department of Soil Ecology; UFZ - Helmholtz Centre for Environmental Research; 06120 Halle (Saale) Germany
- The German Centre for Integrative Biodiversity Research (iDiv); University Leipzig; 04103 Leipzig Germany
| | - Liang-Dong Guo
- State Key Laboratory of Mycology; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
- College of Life Sciences; University of Chinese Academy of Sciences; Beijing 100049 China
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40
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Horn S, Hempel S, Verbruggen E, Rillig MC, Caruso T. Linking the community structure of arbuscular mycorrhizal fungi and plants: a story of interdependence? ISME JOURNAL 2017; 11:1400-1411. [PMID: 28244977 DOI: 10.1038/ismej.2017.5] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 12/14/2016] [Accepted: 12/19/2016] [Indexed: 11/09/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are crucial to plants and vice versa, but little is known about the factors linking the community structure of the two groups. We investigated the association between AMF and the plant community structure in the nearest neighborhood of Festuca brevipila in a semiarid grassland with steep environmental gradients, using high-throughput sequencing of the Glomeromycotina (former Glomeromycota). We focused on the Passenger, Driver and Habitat hypotheses: (i) plant communities drive AMF (passenger); (ii) AMF communities drive the plants (driver); (iii) the environment shapes both communities causing covariation. The null hypothesis is that the two assemblages are independent and this study offers a spatially explicit novel test of it in the field at multiple, small scales. The AMF community consisted of 71 operational taxonomic units, the plant community of 47 species. Spatial distance and spatial variation in the environment were the main determinants of the AMF community. The structure of the plant community around the focal plant was a poor predictor of AMF communities, also in terms of phylogenetic community structure. Some evidence supports the passenger hypothesis, but the relative roles of the factors structuring the two groups clearly differed, leading to an apparent decoupling of the two assemblages at the relatively small scale of this study. Community phylogenetic structure in AMF suggests an important role of within-assemblage interactions.
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Affiliation(s)
- Sebastian Horn
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stefan Hempel
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Institut für Biologie-Ökologie der Pflanzen, Freie Universität Berlin, Berlin, Germany
| | - Erik Verbruggen
- Department of Biology, Research group of Plant and Vegetation Ecology (PLECO), University of Antwerp, Wilrijk, Belgium
| | - Matthias C Rillig
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Institut für Biologie-Ökologie der Pflanzen, Freie Universität Berlin, Berlin, Germany
| | - Tancredi Caruso
- School of Biological Sciences and Institute for Global Food Security, Queen's University Belfast, Medical Biology Centre, Belfast, Northern Ireland, UK
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41
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Aguilar‐Trigueros CA, Rillig MC. Effect of different root endophytic fungi on plant community structure in experimental microcosms. Ecol Evol 2016; 6:8149-8158. [PMID: 27878084 PMCID: PMC5108266 DOI: 10.1002/ece3.2416] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 07/01/2016] [Accepted: 08/11/2016] [Indexed: 01/25/2023] Open
Abstract
Understanding the effects of root-associated microbes in explaining plant community patterns represents a challenge in community ecology. Although typically overlooked, several lines of evidence point out that nonmycorrhizal, root endophytic fungi in the Ascomycota may have the potential to drive changes in plant community ecology given their ubiquitous presence, wide host ranges, and plant species-specific fitness effects. Thus, we experimentally manipulated the presence of root endophytic fungal species in microcosms and measured its effects on plant communities. Specifically, we tested whether (1) three different root endophyte species can modify plant community structure; (2) those changes can also modified the way plant respond to different soil types; and (3) the effects are modified when all the fungi are present. As a model system, we used plant and fungal species that naturally co-occur in a temperate grassland. Further, the soil types used in our experiment reflected a strong gradient in soil texture that has been shown to drive changes in plant and fungal community structure in the field. Results showed that each plant species responded differently to infection, resulting in distinct patterns of plant community structure depending on the identity of the fungus present. Those effects depended on the soil type. For example, large positive effects due to presence of the fungi were able to compensate for less nutrients levels in one soil type. Further, host responses when all three fungi were present were different from the ones observed in single fungal inoculations, suggesting that endophyte-endophyte interactions may be important in structuring plant communities. Overall, these results indicate that plant responses to changes in the species identity of nonmycorrhizal fungal community species and their interactions can modify plant community structure.
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Affiliation(s)
- Carlos A. Aguilar‐Trigueros
- Plant EcologyInstitut für BiologieFreie Universität BerlinBerlinGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity ResearchBerlinGermany
| | - Matthias C. Rillig
- Plant EcologyInstitut für BiologieFreie Universität BerlinBerlinGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity ResearchBerlinGermany
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42
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Liu X, Liang M, Etienne RS, Gilbert GS, Yu S. Phylogenetic congruence between subtropical trees and their associated fungi. Ecol Evol 2016; 6:8412-8422. [PMID: 28031793 PMCID: PMC5167024 DOI: 10.1002/ece3.2503] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/23/2016] [Accepted: 08/30/2016] [Indexed: 11/29/2022] Open
Abstract
Recent studies have detected phylogenetic signals in pathogen–host networks for both soil‐borne and leaf‐infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next‐generation high‐throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK, rbcL, atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host–fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant–fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant–fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.
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Affiliation(s)
- Xubing Liu
- Department of Ecology School of Life Sciences/State Key Laboratory of Biocontrol Sun Yat-sen University Guangzhou China; Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen The Netherlands
| | - Minxia Liang
- Department of Ecology School of Life Sciences/State Key Laboratory of Biocontrol Sun Yat-sen University Guangzhou China
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen The Netherlands
| | - Gregory S Gilbert
- Department of Environmental Studies University of California Santa Cruz Santa Cruz CA USA
| | - Shixiao Yu
- Department of Ecology School of Life Sciences/State Key Laboratory of Biocontrol Sun Yat-sen University Guangzhou China
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43
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Vályi K, Mardhiah U, Rillig MC, Hempel S. Community assembly and coexistence in communities of arbuscular mycorrhizal fungi. THE ISME JOURNAL 2016; 10:2341-51. [PMID: 27093046 PMCID: PMC5030697 DOI: 10.1038/ismej.2016.46] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 02/04/2023]
Abstract
Arbuscular mycorrhizal fungi are asexual, obligately symbiotic fungi with unique morphology and genomic structure, which occupy a dual niche, that is, the soil and the host root. Consequently, the direct adoption of models for community assembly developed for other organism groups is not evident. In this paper we adapted modern coexistence and assembly theory to arbuscular mycorrhizal fungi. We review research on the elements of community assembly and coexistence of arbuscular mycorrhizal fungi, highlighting recent studies using molecular methods. By addressing several points from the individual to the community level where the application of modern community ecology terms runs into problems when arbuscular mycorrhizal fungi are concerned, we aim to account for these special circumstances from a mycocentric point of view. We suggest that hierarchical spatial structure of arbuscular mycorrhizal fungal communities should be explicitly taken into account in future studies. The conceptual framework we develop here for arbuscular mycorrhizal fungi is also adaptable for other host-associated microbial communities.
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Affiliation(s)
- Kriszta Vályi
- Department of Plant Ecology, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Ulfah Mardhiah
- Department of Plant Ecology, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Matthias C Rillig
- Department of Plant Ecology, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Stefan Hempel
- Department of Plant Ecology, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
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44
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Montiel-Rozas MDM, López-García Á, Kjøller R, Madejón E, Rosendahl S. Organic amendments increase phylogenetic diversity of arbuscular mycorrhizal fungi in acid soil contaminated by trace elements. MYCORRHIZA 2016; 26:575-585. [PMID: 27072359 DOI: 10.1007/s00572-016-0694-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
In 1998, a toxic mine spill polluted a 55-km(2) area in a basin southward to Doñana National Park (Spain). Subsequent attempts to restore those trace element-contaminated soils have involved physical, chemical, or biological methodologies. In this study, the restoration approach included application of different types and doses of organic amendments: biosolid compost (BC) and leonardite (LEO). Twelve years after the last addition, molecular analyses of arbuscular mycorrhizal (AM) fungal communities associated with target plants (Lamarckia aurea and Chrysanthemum coronarium) as well as analyses of trace element concentrations both in soil and in plants were performed. The results showed an improved soil quality reflected by an increase in soil pH and a decrease in trace element availability as a result of the amendments and dosages. Additionally, the phylogenetic diversity of the AM fungal community increased, reaching the maximum diversity at the highest dose of BC. Trace element concentration was considered the predominant soil factor determining the AM fungal community composition. Thereby, the studied AM fungal community reflects a community adapted to different levels of contamination as a result of the amendments. The study highlights the long-term effect of the amendments in stabilizing the soil system.
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Affiliation(s)
- María Del Mar Montiel-Rozas
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC) Avda. Reina Mercedes, 10 41012, Sevilla, Spain.
| | - Álvaro López-García
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
| | - Engracia Madejón
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC) Avda. Reina Mercedes, 10 41012, Sevilla, Spain
| | - Søren Rosendahl
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
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45
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Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering. Appl Environ Microbiol 2016; 82:4921-30. [PMID: 27260357 DOI: 10.1128/aem.00816-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/27/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus- and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample. IMPORTANCE Arbuscular mycorrhizal (AM) fungi form important mutualisms with the roots of most plant species. Individual AM fungi are genetically diverse, but it is unclear whether the level of this diversity differs among evolutionary lineages. We found that the amount of sequence variation in an rRNA gene that is commonly used to identify AM fungal species varied significantly between evolutionary groups that correspond to different genera, with the exception of two genera that are genetically indistinguishable from each other. When we clustered groups of similar sequences into operational taxonomic units (OTUs) using five different clustering methods, these patterns of sequence variation caused the number of OTUs to either over- or underestimate the actual number of AM fungal species, depending on the genus. Our results indicate that OTU-based inferences about AM fungal species composition from environmental sequences can be improved if they take these taxonomically structured patterns of sequence variation into account.
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López-García Á, Horn S, Rillig MC, Hempel S. Spatial and niche-based ecological processes drive the distribution of endophytic Sebacinales in soil and root of grassland communities. FEMS Microbiol Ecol 2016; 92:fiw079. [PMID: 27090761 DOI: 10.1093/femsec/fiw079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2016] [Indexed: 11/13/2022] Open
Abstract
The interest in endophytic sebacinalean communities has been increasing during the last decade due to the increased knowledge about their symbiotic life style and potential role for ecosystem functioning. Although they are present in many ecosystems, their abundance in individual plant roots is very limited. This fact affects their study: they are difficult to isolate and to detect in root DNA samples. To advance knowledge of the forces that shape their distribution, we approached the parallel study of sebacinalean communities in roots and soil of grassland. Using a small-scale spatially explicit sampling design, we analysed the contribution of spatial position, soil properties, plant community and phylogenetic components to the variation of sebacinalean communities. The results revealed the presence of 11 operational taxonomic units (OTUs) and a high coincidence between root and soil communities: on an average a single-OTU per sample was recorded for both sample types. Spatial distance was found to mainly drive the distribution of Sebacinales in soil, whereas phylogenetic plus environmental signatures mainly drove their presence in roots. Independently of the sample type, we found clear evidence of environmental filtering caused by soil pH which, furthermore, seemed to control the presence of a specialized sebacinalean OTU.
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Affiliation(s)
- Álvaro López-García
- Department of Plant Ecology, Institut für Biologie, Freie Universität Berlin, D-14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - Sebastian Horn
- Department of Soil Biology and Genomics, Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Matthias C Rillig
- Department of Plant Ecology, Institut für Biologie, Freie Universität Berlin, D-14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - Stefan Hempel
- Department of Plant Ecology, Institut für Biologie, Freie Universität Berlin, D-14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
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Deslippe JR, Hartmann M, Grayston SJ, Simard SW, Mohn WW. Stable isotope probing implicates a species of Cortinarius in carbon transfer through ectomycorrhizal fungal mycelial networks in Arctic tundra. THE NEW PHYTOLOGIST 2016; 210:383-90. [PMID: 26681156 DOI: 10.1111/nph.13797] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Julie R Deslippe
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Martin Hartmann
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Zuercherstrasse 111, CH-8903, Birmensdorf, Switzerland
- Molecular Ecology, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, CH-8046, Zurich, Switzerland
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Susan J Grayston
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Suzanne W Simard
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
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Barnes CJ, van der Gast CJ, Burns CA, McNamara NP, Bending GD. Temporally Variable Geographical Distance Effects Contribute to the Assembly of Root-Associated Fungal Communities. Front Microbiol 2016; 7:195. [PMID: 26941720 PMCID: PMC4766365 DOI: 10.3389/fmicb.2016.00195] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/05/2015] [Indexed: 11/16/2022] Open
Abstract
Root-associated fungi are key contributors to ecosystem functioning, however, the factors which determine community assembly are still relatively poorly understood. This study simultaneously quantified the roles of geographical distance, environmental heterogeneity and time in determining root-associated fungal community composition at the local scale within a short rotation coppice (SRC) willow plantation. Culture independent molecular analyses of the root-associated fungal community suggested a strong but temporally variable effect of geographical distance among fungal communities in terms of composition at the local geographical level. Whilst these distance effects were most prevalent on October communities, soil pH had an effect on structuring of the communities throughout the sampling period. Given the temporal variation in the effects of geographical distance and the environment for shaping root-associated fungal communities, there is clearly need for a temporal component to sampling strategies in future investigations of fungal ecology.
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Affiliation(s)
- Christopher J. Barnes
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
- Section of Evolutionary Genomics, National History Museum of Denmark, University of CopenhagenCopenhagen, Denmark
| | | | - Caitlin A. Burns
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
| | - Niall P. McNamara
- Natural Environment Research Council Centre for Ecology and Hydrology – Lancaster Environment CentreLancaster, UK
| | - Gary D. Bending
- School of Life Sciences, Gibbet Hill Campus, University of WarwickCoventry, UK
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Shifts in the phylogenetic structure of arbuscular mycorrhizal fungi in response to experimental nitrogen and carbon dioxide additions. Oecologia 2015; 179:175-85. [PMID: 25990297 DOI: 10.1007/s00442-015-3337-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
Abstract
Global N inputs and atmospheric CO2 concentrations have increased as a result of human activities, and are predicted to increase along with population growth, with potentially negative effects on biodiversity. Using taxonomic and phylogenetic measures, we examined the response of arbuscular mycorrhizal fungi (AMF) to experimental manipulations of N and CO2 at the Jasper Ridge Global Change Experiment. No significant interactions between N and CO2 were observed, but individual effects of N and CO2 were found. Elevated CO2 resulted in changes in phylogenetic similarity, and a shift to phylogenetic clustering of AMF communities. N addition resulted in higher phylogenetic diversity and evenness, with no shifts in community composition and no significant signal for phylogenetic clustering. N addition resulted in an increase in both available N and the N:P ratio in N-amended plots, which suggests that changing patterns of nutrient limitation could have lead to altered species interactions. These findings suggest that elevated levels of N and CO2 altered patterns of AMF community assembly, with potential effects on ecosystem function.
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Cheeke TE, Schütte UM, Hemmerich CM, Cruzan MB, Rosenstiel TN, Bever JD. Spatial soil heterogeneity has a greater effect on symbiotic arbuscular mycorrhizal fungal communities and plant growth than genetic modification with Bacillus thuringiensis toxin genes. Mol Ecol 2015; 24:2580-93. [PMID: 25827202 DOI: 10.1111/mec.13178] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/28/2015] [Accepted: 03/18/2015] [Indexed: 02/06/2023]
Abstract
Maize, genetically modified with the insect toxin genes of Bacillus thuringiensis (Bt), is widely cultivated, yet its impacts on soil organisms are poorly understood. Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots and may be uniquely sensitive to genetic changes within a plant host. In this field study, the effects of nine different lines of Bt maize and their corresponding non-Bt parental isolines were evaluated on AMF colonization and community diversity in plant roots. Plants were harvested 60 days after sowing, and data were collected on plant growth and per cent AMF colonization of roots. AMF community composition in roots was assessed using 454 pyrosequencing of the 28S rRNA genes, and spatial variation in mycorrhizal communities within replicated experimental field plots was examined. Growth responses, per cent AMF colonization of roots and AMF community diversity in roots did not differ between Bt and non-Bt maize, but root and shoot biomass and per cent colonization by arbuscules varied by maize cultivar. Plot identity had the most significant effect on plant growth, AMF colonization and AMF community composition in roots, indicating spatial heterogeneity in the field. Mycorrhizal fungal communities in maize roots were autocorrelated within approximately 1 m, but at greater distances, AMF community composition of roots differed between plants. Our findings indicate that spatial variation and heterogeneity in the field has a greater effect on the structure of AMF communities than host plant cultivar or modification by Bt toxin genes.
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Affiliation(s)
- Tanya E Cheeke
- Department of Biology, Portland State University, PO Box 751, Portland, OR, 97207, USA; Department of Biology, Indiana University, Bloomington, IN, 47405, USA; Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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