1
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Costa D, Tavares RM, Baptista P, Lino-Neto T. The influence of bioclimate on soil microbial communities of cork oak. BMC Microbiol 2022; 22:163. [PMID: 35739482 PMCID: PMC9219136 DOI: 10.1186/s12866-022-02574-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 06/02/2022] [Indexed: 12/25/2022] Open
Abstract
Background Soil microbiomes are important to maintain soil processes in forests and confer protection to plants against abiotic and biotic stresses. These microbiomes can be affected by environmental changes. In this work, soil microbial communities from different cork oak Portuguese forests under different edaphoclimatic conditions were described by using a metabarcoding strategy targeting ITS2 and 16S barcodes. Results A total of 11,974 fungal and 12,010 bacterial amplicon sequence variants (ASVs) were obtained, revealing rich and diverse microbial communities associated with different cork oak forests. Bioclimate was described as the major factor influencing variability in these communities (or bioclimates/cork oak forest for fungal community), followed by boron and granulometry. Also, pH explained variation of fungal communities, while C:N ratio contributed to bacterial variation. Fungal and bacterial biomarker genera for specific bioclimates were described. Their co-occurrence network revealed the existence of a complex and delicate balance among microbial communities. Conclusions The findings revealed that bacterial communities are more likely to be affected by different edaphoclimatic conditions than fungal communities, also predicting a higher impact of climate change on bacterial communities. The integration of cork oak fungal and bacterial microbiota under different bioclimates could be further explored to provide information about useful interactions for increasing cork oak forest sustainability in a world subject to climate changes. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02574-2.
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Affiliation(s)
- Daniela Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
| | - Rui M Tavares
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
| | - Paula Baptista
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Teresa Lino-Neto
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal.
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2
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Kalsoom Khan F, Kluting K, Tångrot J, Urbina H, Ammunet T, Eshghi Sahraei S, Rydén M, Ryberg M, Rosling A. Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi. IMA Fungus 2020; 11:23. [PMID: 33292867 PMCID: PMC7607712 DOI: 10.1186/s43008-020-00045-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/14/2020] [Indexed: 01/04/2023] Open
Abstract
Due to their submerged and cryptic lifestyle, the vast majority of fungal species are difficult to observe and describe morphologically, and many remain known to science only from sequences detected in environmental samples. The lack of practices to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here, we use environmental sequence data as taxonomical evidence and combine phylogenetic and ecological data to generate and test species hypotheses in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing from a well-studied Swedish pine forest podzol soil, we generate 68 distinct species hypotheses of Archaeorhizomycetes, of which two correspond to the only described species in the class. Nine of the species hypotheses represent 78% of the sequenced Archaeorhizomycetes community, and are supported by long read data that form the backbone for delimiting species hypothesis based on phylogenetic branch lengths. Soil fungal communities are shaped by environmental filtering and competitive exclusion so that closely related species are less likely to co-occur in a niche if adaptive traits are evolutionarily conserved. In soil profiles, distinct vertical horizons represent a testable niche dimension, and we found significantly differential distribution across samples for a well-supported pair of sister species hypotheses. Based on the combination of phylogenetic and ecological evidence, we identify two novel species for which we provide molecular diagnostics and propose names. While environmental sequences cannot be automatically translated to species, they can be used to generate phylogenetically distinct species hypotheses that can be further tested using sequences as ecological evidence. We conclude that in the case of abundantly and frequently observed species, environmental sequences can support species recognition in the absences of physical specimens, while rare taxa remain uncaptured at our sampling and sequencing intensity.
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Affiliation(s)
- Faheema Kalsoom Khan
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.,Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Kerri Kluting
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Jeanette Tångrot
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Umeå University, Umeå, Sweden
| | - Hector Urbina
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.,Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, Florida, 32608, USA
| | - Tea Ammunet
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Shadi Eshghi Sahraei
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Martin Rydén
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Martin Ryberg
- Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Anna Rosling
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
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3
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Mason LM, Eagar A, Patel P, Blackwood CB, DeForest JL. Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest. J Appl Microbiol 2020; 130:109-122. [PMID: 32619072 DOI: 10.1111/jam.14761] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 01/20/2023]
Abstract
AIMS The soil microbial community plays a critical role in increasing phosphorus (P) availability in low-P, weathered soils by "mining" recalcitrant organic P through the production of phosphatase enzymes. However, there is a lack of data on the fungal and bacterial taxa which are directly involved in P mining, which could also serve as potential microbial bioindicators of low P availability. METHODS AND RESULTS Leveraging a 5-year P enrichment experiment on low-P forest soils, high-throughput sequencing was used to profile the microbial community to determine which taxa associate closely with P availability. We hypothesized that there would be a specialized group of soil micro-organisms that could access recalcitrant P and whose presence could serve as a bioindicator of P mining. Community profiling revealed several candidate bioindicators of P mining (Russulales, Acidobacteria Subgroup 2, Acidobacteriales, Obscuribacterales and Solibacterales), whose relative abundance declined with elevated P and had a significant, positive association with phosphatase production. In addition, we identified candidate bioindicators of high P availability (Mytilinidales, Sebacinales, Chitinophagales, Cytophagales, Saccharimonadales, Opitulales and Gemmatales). CONCLUSIONS This research provides evidence that mitigating P limitation in this ecosystem may be a specialized trait and is mediated by a few microbial taxa. SIGNIFICANCE AND IMPACT OF THE STUDY Here, we characterize Orders of soil microbes associated with manipulated phosphorus availability in forest soils to determine bioindicator candidates for phosphorus. Likewise, we provide evidence that the microbial trait to utilize recalcitrant organic forms of P (e.g. P mining) is likely a specialized trait and not common to all members of the soil microbial community. This work further elucidates the role that a complex microbial community plays in the cycling of P in low-P soils, and provides evidence for future studies on microbial linkages to human-induced ecosystem changes.
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Affiliation(s)
- L M Mason
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, USA
| | - A Eagar
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - P Patel
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - C B Blackwood
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - J L DeForest
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, USA
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4
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Venneman J, De Tender C, Debode J, Audenaert K, Baert G, Vermeir P, Cremelie P, Bekaert B, Landschoot S, Thienpondt B, Djailo BD, Vereecke D, Haesaert G. Sebacinoids within rhizospheric fungal communities associated with subsistence farming in the Congo Basin: a needle in each haystack. FEMS Microbiol Ecol 2020; 95:5524361. [PMID: 31247636 DOI: 10.1093/femsec/fiz101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022] Open
Abstract
The unique ecosystem of the Congolese rainforest has only scarcely been explored for its plant-fungal interactions. Here, we characterized the root fungal communities of field-grown maize and of Panicum from adjacent borders in the Congo Basin and assessed parameters that could shape them. The soil properties indicated that comparable poor soil conditions prevailed in fields and borders, illustrating the low input character of local subsistence farming. The rhizosphere fungal communities, dominated by ascomycetous members, were structured by plant species, slash-and-burn practices and soil P, pH and C/N ratio. Examining fungi with potential plant growth-promoting abilities, the glomeromycotan communities appeared to be affected by the same parameters, whereas the inconspicuous symbionts of the order Sebacinales seemed less susceptible to environmental and anthropogenic factors. Notwithstanding the low abundances at which they were detected, sebacinoids occurred in 87% of the field samples, implying that they represent a consistent taxon within indigenous fungal populations across smallholder farm sites. Pending further insight into their ecosystem functionality, these data suggest that Sebacinales are robust root inhabitants that might be relevant for on-farm inoculum development within sustainable soil fertility management in the Sub-Saharan region.
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Affiliation(s)
- Jolien Venneman
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Krijgslaan 281, S9, BE-9000, Ghent, Belgium
| | - Jane Debode
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium
| | - Kris Audenaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Geert Baert
- Department of Environment, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Pieter Vermeir
- Department of Green Chemistry and Technology, Laboratory of Chemical Analysis (LCA), Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Pieter Cremelie
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium
| | - Boris Bekaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Sofie Landschoot
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Bert Thienpondt
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Benoît Dhed'a Djailo
- Faculty of Science and Agriculture, Kisangani University, B.P. 2012, Kisangani, Democratic Republic of Congo
| | - Danny Vereecke
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Geert Haesaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
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5
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Nguyen DQ, Schneider D, Brinkmann N, Song B, Janz D, Schöning I, Daniel R, Pena R, Polle A. Soil and root nutrient chemistry structure root-associated fungal assemblages in temperate forests. Environ Microbiol 2020; 22:3081-3095. [PMID: 32383336 DOI: 10.1111/1462-2920.15037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022]
Abstract
Root-associated fungi (RAF) link nutrient fluxes between soil and roots and thus play important roles in ecosystem functioning. To enhance our understanding of the factors that control RAF, we fitted statistical models to explain variation in RAF community structure using data from 150 temperate forest sites covering a broad range of environmental conditions and chemical root traits. We found that variation in RAF communities was related to both root traits (e.g., cations, carbohydrates, NO3 - ) and soil properties (pH, cations, moisture, C/N). The identified drivers were the combined result of distinct response patterns of fungal taxa (determined at the rank of orders) to biotic and abiotic factors. Our results support that RAF community variation is related to evolutionary adaptedness of fungal lineages and consequently, drivers of RAF communities are context-dependent.
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Affiliation(s)
- Dung Quang Nguyen
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany.,Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, Duc Thang Ward, Bac Tu Liem District, Hanoi, Vietnam
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Grisebachstraße 8, 37077, Germany
| | - Nicole Brinkmann
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany
| | - Bin Song
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany
| | - Dennis Janz
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany
| | - Ingo Schöning
- Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Grisebachstraße 8, 37077, Germany
| | - Rodica Pena
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany
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6
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Yuan QS, Xu J, Jiang W, Ou X, Wang H, Guo L, Xiao C, Wang Y, Wang X, Kang C, Zhou T. Insight to shape of soil microbiome during the ternary cropping system of Gastradia elata. BMC Microbiol 2020; 20:108. [PMID: 32370761 PMCID: PMC7201697 DOI: 10.1186/s12866-020-01790-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/16/2020] [Indexed: 11/18/2022] Open
Abstract
Background The ternary cropping system of Gastradia elata depends on a symbiotic relationship with the mycorrhizal fungi Armillaria mellea, which decays wood to assimilate nutrition for the growth of G. elata. The composition of microbe flora as key determinants of rhizoshere and mycorrhizoshere soil fertility and health was investigated to understand how G. elata and A. mellea impacted on its composition. The next generation pyrosequencing analysis was applied to assess the shift of structure of microbial community in rhizoshere of G. elata and mycorrhizoshere of A. mellea compared to the control sample under agriculture process. Results The root-associated microbe floras were significantly impacted by rhizocompartments (including rhizoshere and mycorrhizoshere) and agriculture process. Cropping process of G. elata enhanced the richness and diversity of the microbial community in rhizoshere and mycorrhizoshere soil. Furthermore, planting process of G. elata significantly reduced the abundance of phyla Basidiomycota, Firmicutes and Actinobacteria, while increased the abundance of phyla Ascomycota, Chloroflexi, Proteobacteria, Planctomycetes, and Gemmatimonadetes in rhizoshere and mycorrhizoshere. Besides, A. mellea and G. elata significantly enriched several members of saprophytoic and pathogenic fungus (i.e., Exophiala, Leptodontidium, Cosmospora, Cercophora, Metarhizium, Ilyonectria, and Sporothrix), which will enhance the possibility of G. elata disease incidence. At the same time, the ternary cropping system significantly deterred several members of beneficial ectomycorrhizal fungus (i.e., Russula, Sebacina, and Amanita), which will reduce the ability to protect G. elata from diseases. Conclusions In the ternary cropping system of G. elata, A. mellea and G. elata lead to imbalance of microbial community in rhizoshere and mycorrhizoshere soil, suggested that further studies on maintaining the balance of microbial community in A. mellea mycorrhizosphere and G. elata rhizosphere soil under field conditions may provide a promising avenue for high yield and high quality G. elata.
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Affiliation(s)
- Qing-Song Yuan
- Guizhou University of Traditional Chinese Medicine, Dongqingnan Road, Guiyang, 540025, Guizhou, China
| | - Jiao Xu
- Guizhou University of Traditional Chinese Medicine, Dongqingnan Road, Guiyang, 540025, Guizhou, China
| | - Weike Jiang
- Guizhou University of Traditional Chinese Medicine, Dongqingnan Road, Guiyang, 540025, Guizhou, China
| | - Xiaohong Ou
- Guizhou University of Traditional Chinese Medicine, Dongqingnan Road, Guiyang, 540025, Guizhou, China
| | - Hui Wang
- Guizhou University of Traditional Chinese Medicine, Dongqingnan Road, Guiyang, 540025, Guizhou, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Chenghong Xiao
- Guizhou University of Traditional Chinese Medicine, Dongqingnan Road, Guiyang, 540025, Guizhou, China
| | - Yanhong Wang
- Guizhou University of Traditional Chinese Medicine, Dongqingnan Road, Guiyang, 540025, Guizhou, China
| | - Xiao Wang
- Shandong Analysis and Test Center, Shandong Academic of Sciences, Jinan, 250014, Shandong, China
| | - Chuanzhi Kang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Tao Zhou
- Guizhou University of Traditional Chinese Medicine, Dongqingnan Road, Guiyang, 540025, Guizhou, China.
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7
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Robin A, Pradier C, Sanguin H, Mahé F, Lambais GR, de Araujo Pereira AP, Germon A, Santana MC, Tisseyre P, Pablo AL, Heuillard P, Sauvadet M, Bouillet JP, Andreote FD, Plassard C, de Moraes Gonçalves JL, Cardoso EJBN, Laclau JP, Hinsinger P, Jourdan C. How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation. MYCORRHIZA 2019; 29:637-648. [PMID: 31732817 DOI: 10.1007/s00572-019-00917-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 09/11/2019] [Indexed: 06/10/2023]
Abstract
Despite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pits differing by their water availability. A meta-barcoding approach based on Illumina sequencing of internal transcribed spacers (ITS1 and ITS2) was carried out on DNA extracted from root samples (fine roots and ECM root tips separately). ECM fungi dominated the root-associated fungal community, with more than 90% of sequences assigned to the genus Pisolithus. The morphological and barcoding results demonstrated, for the first time, the presence of ECM symbiosis down to 4-m. The molecular diversity of Pisolithus spp. was strongly dependent on depth, with soil pH and soil water content as primary drivers of the Pisolithus spp. structure. Altogether, our results highlight the importance to consider the ECM symbiosis in deep soil layers to improve our understanding of fine roots functioning in tropical soils.
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Affiliation(s)
- Agnès Robin
- CIRAD, UMR Eco&Sols, Piracicaba, SP, 13418-900, Brazil.
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France.
- ESALQ, University São Paulo, Piracicaba, SP, 13418-900, Brazil.
| | - Céline Pradier
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR Eco&Sols, F-34398, Montpellier, France
| | - Hervé Sanguin
- CIRAD, UMR BGPI, F-34398, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Frédéric Mahé
- CIRAD, UMR BGPI, F-34398, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | | | | | - Amandine Germon
- UNESP, University São Paulo, Botucatu, SP, 18610-300, Brazil
| | | | - Pierre Tisseyre
- LSTM, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Anne-Laure Pablo
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Pauline Heuillard
- INRA, US 1426, GeT-PlaGe, Genotoul, F-31320, Castanet-Tolosan, France
| | - Marie Sauvadet
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Jean-Pierre Bouillet
- CIRAD, UMR Eco&Sols, Piracicaba, SP, 13418-900, Brazil
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | | | - Claude Plassard
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | | | | | - Jean-Paul Laclau
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR Eco&Sols, F-34398, Montpellier, France
| | - Philippe Hinsinger
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Christophe Jourdan
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR Eco&Sols, F-34398, Montpellier, France
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8
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Schröter K, Wemheuer B, Pena R, Schöning I, Ehbrecht M, Schall P, Ammer C, Daniel R, Polle A. Assembly processes of trophic guilds in the root mycobiome of temperate forests. Mol Ecol 2018; 28:348-364. [PMID: 30276908 DOI: 10.1111/mec.14887] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/05/2018] [Accepted: 09/17/2018] [Indexed: 01/09/2023]
Abstract
Root-associated mycobiomes (RAMs) link plant and soil ecological processes, thereby supporting ecosystem functions. Understanding the forces that govern the assembly of RAMs is key to sustainable ecosystem management. Here, we dissected RAMs according to functional guilds and combined phylogenetic and multivariate analyses to distinguish and quantify the forces driving RAM assembly processes. Across large biogeographic scales (>1,000 km) in temperate forests (>100 plots), RAMs were taxonomically highly distinct but composed of a stable trophic structure encompassing symbiotrophic, ectomycorrhizal (55%), saprotrophic (7%), endotrophic (3%) and pathotrophic fungi (<1%). Taxonomic community composition of RAMs is explained by abiotic factors, forest management intensity, dominant tree family (Fagaceae, Pinaceae) and root resource traits. Local RAM assemblies are phylogenetically clustered, indicating stronger habitat filtering on roots in dry, acid soils and in conifer stands than in other forest types. The local assembly of ectomycorrhizal communities is driven by forest management intensity. At larger scales, root resource traits and soil pH shift the assembly process of ectomycorrhizal fungi from deterministic to neutral. Neutral or weak deterministic assembly processes are prevalent in saprotrophic and endophytic guilds. The remarkable consistency of the trophic composition of the RAMs suggests that temperate forests attract fungal assemblages that afford functional resilience under the current range of climatic and edaphic conditions. At local scales, the filtering processes that structure symbiotrophic assemblies can be influenced by forest management and tree selection, but at larger scales, environmental cues and host resource traits are the most prevalent forces.
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Affiliation(s)
- Kristina Schröter
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany.,Centre for Marine Bio-Innovation, School of Biological Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Rodica Pena
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Ingo Schöning
- Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Martin Ehbrecht
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Peter Schall
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Christian Ammer
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
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9
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Detection of a root-associated group of Hyaloscyphaceae (Helotiales) species that commonly colonizes Fagaceae roots and description of three new species in genus Glutinomyces. MYCOSCIENCE 2018. [DOI: 10.1016/j.myc.2018.02.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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McCormick MK, Whigham DF, Canchani-Viruet A. Mycorrhizal fungi affect orchid distribution and population dynamics. THE NEW PHYTOLOGIST 2018; 219:1207-1215. [PMID: 29790578 DOI: 10.1111/nph.15223] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/17/2018] [Indexed: 05/03/2023]
Abstract
Symbioses are ubiquitous in nature and influence individual plants and populations. Orchids have life history stages that depend fully or partially on fungi for carbon and other essential resources. As a result, orchid populations depend on the distribution of orchid mycorrhizal fungi (OMFs). We focused on evidence that local-scale distribution and population dynamics of orchids can be limited by the patchy distribution and abundance of OMFs, after an update of an earlier review confirmed that orchids are rarely limited by OMF distribution at geographic scales. Recent evidence points to a relationship between OMF abundance and orchid density and dormancy, which results in apparent density differences. Orchids were more abundant, less likely to enter dormancy, and more likely to re-emerge when OMF were abundant. We highlight the need for additional studies on OMF quantity, more emphasis on tropical species, and development and application of next-generation sequencing techniques to quantify OMF abundance in substrates and determine their function in association with orchids. Research is also needed to distinguish between OMFs and endophytic fungi and to determine the function of nonmycorrhizal endophytes in orchid roots. These studies will be especially important if we are to link orchids and OMFs in efforts to inform conservation.
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Affiliation(s)
- Melissa K McCormick
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD, 21037, USA
| | - Dennis F Whigham
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD, 21037, USA
| | - Armando Canchani-Viruet
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD, 21037, USA
- Universidad Metropolitana, Escuela de Ciencias y Tecnología, 1399 Avenida Ana G. Mendez, San Juan, 00926, Puerto Rico
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