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Gautier M, Moreau PA, Boury B, Richard F. Unravelling the French National Fungal Database: Geography, Temporality, Taxonomy and Ecology of the Recorded Diversity. J Fungi (Basel) 2022; 8:jof8090926. [PMID: 36135651 PMCID: PMC9504494 DOI: 10.3390/jof8090926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Large datasets are highly valuable resources to investigate multi-scale patterns of organisms, and lay foundations for citizen science-based conservation strategies. Here, we used 1,043,262 records from 1708 to 2021 to explore the geography, taxonomy, ecology and distribution patterns of 11,556 fungal taxa in metropolitan France. Our analysis reveals a four-phase pattern of temporal recording, with a main contribution of post-1977 observations in relation with the structuration of associative mycology. The dataset shows an uneven geography of fungal recording. Four clusters of high-intensity sampling scattered across France contrast with poorly documented areas, including the Mediterranean. Basidiomycota and Agaricales highly dominate the dataset, accounting for 88.8 and 50.4% of records, respectively. The dataset is composed of many rare taxa, with 61.2% of them showing fewer than 100 records, and 20.5% recorded only once. The analysis of metadata brings to light a preponderance of the mycorrhizal guild (44.6%), followed by litter saprotrophs (31.6%) and wood saprotrophs (18.1%). Highly documented forests (76.3% of records) contrast with poorly investigated artificial (6.43%) and open habitats (10.1%). This work provides the first comprehensive overview of fungal diversity in France and identifies the Mediterranean area and open habitats as priorities to integrate into a global strategy for fungal conservation in France.
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Affiliation(s)
- Montan Gautier
- Centre d’Ecologie Fonctionelle et Evolutive (UMR CEFE), University Montpellier-CNRS-EPHE-IRD, 1919 route de Mende, CEDEX 5, F-34293 Montpellier, France
| | - Pierre-Arthur Moreau
- Laboratoire de Génie Civil et géo-Environnement (ULR 4515-LGCgE), University Lille, F-59000 Lille, France
- Association pour le développement d’outils naturalistes et informatiques pour la Fonge (AdoniF), 3 rue du Pr Laguesse, F-59000 Lille, France
| | - Béatrice Boury
- Association pour le développement d’outils naturalistes et informatiques pour la Fonge (AdoniF), 3 rue du Pr Laguesse, F-59000 Lille, France
| | - Franck Richard
- Centre d’Ecologie Fonctionelle et Evolutive (UMR CEFE), University Montpellier-CNRS-EPHE-IRD, 1919 route de Mende, CEDEX 5, F-34293 Montpellier, France
- Correspondence:
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Authier L, Violle C, Richard F. Ectomycorrhizal Networks in the Anthropocene: From Natural Ecosystems to Urban Planning. FRONTIERS IN PLANT SCIENCE 2022; 13:900231. [PMID: 35845640 PMCID: PMC9280895 DOI: 10.3389/fpls.2022.900231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Trees acquire hydric and mineral soil resources through root mutualistic associations. In most boreal, temperate and Mediterranean forests, these functions are realized by a chimeric structure called ectomycorrhizae. Ectomycorrhizal (ECM) fungi are highly diversified and vary widely in their specificity toward plant hosts. Reciprocally, association patterns of ECM plants range from highly specialist to generalist. As a consequence, ECM symbiosis creates interaction networks, which also mediate plant-plant nutrient interactions among different individuals and drive plant community dynamics. Our knowledge of ECM networks essentially relies on a corpus acquired in temperate ecosystems, whereas the below-ground facets of both anthropogenic ECM forests and inter-tropical forests remain poorly investigated. Here, we successively (1) review the current knowledge of ECM networks, (2) examine the content of early literature produced in ECM cultivated forests, (3) analyze the recent progress that has been made in understanding the place of ECM networks in urban soils, and (4) provide directions for future research based on the identification of knowledge gaps. From the examined corpus of knowledge, we reach three main conclusions. First, the emergence of metabarcoding tools has propelled a resurgence of interest in applying network theory to ECM symbiosis. These methods revealed an unexpected interconnection between mutualistic plants with arbuscular mycorrhizal (AM) herbaceous plants, embedding ECM mycelia through root-endophytic interactions. This affinity of ECM fungi to bind VA and ECM plants, raises questions on the nature of the associated functions. Second, despite the central place of ECM trees in cultivated forests, little attention has been paid to these man-made landscapes and in-depth research on this topic is lacking. Third, we report a lag in applying the ECM network theory to urban soils, despite management initiatives striving to interconnect motile organisms through ecological corridors, and the highly challenging task of interconnecting fixed organisms in urban greenspaces is discussed. In particular, we observe a pauperized nature of resident ECM inoculum and a spatial conflict between belowground human pipelines and ECM networks. Finally, we identify the main directions of future research to make the needed link between the current picture of plant functioning and the understanding of belowground ECM networks.
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Affiliation(s)
- Louise Authier
- CEFE, Univ Montpellier - CNRS - EPHE - IRD, Montpellier, France
- Ilex Paysage + Urbanisme, Lyon, France
| | - Cyrille Violle
- CEFE, Univ Montpellier - CNRS - EPHE - IRD, Montpellier, France
| | - Franck Richard
- CEFE, Univ Montpellier - CNRS - EPHE - IRD, Montpellier, France
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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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Venice F, Vizzini A, Frascella A, Emiliani G, Danti R, Della Rocca G, Mello A. Localized reshaping of the fungal community in response to a forest fungal pathogen reveals resilience of Mediterranean mycobiota. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149582. [PMID: 34426333 DOI: 10.1016/j.scitotenv.2021.149582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/16/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
Mediterranean forests are facing the impact of pests such as the soilborne Phytophthora cambivora, the causal agent of Ink disease, and this impact is made more severe by global changes. The status and resilience of the soil microbial ecosystem in areas with such a disturbance are little known; however, the assessment of the microbial community is fundamental to preserve the ecosystem functioning under emerging challenges. We profile soil fungal communities in a chestnut stand affected by ink disease in Italy using metabarcoding, and couple high-throughput sequencing with physico-chemical parameters and dendrometric measurements. Since the site also includes an area where the disease symptoms seem to be suppressed, we performed several analyses to search for determinants that may contribute to such difference. We demonstrate that neither pathogen presence nor trees decline associate with the reduction of the residing community diversity and functions, but rather with microbial network reshaping through substitutions and new interactions, despite a conservation of core taxa. We predict interactions between taxa and parameters such as soil pH and C/N ratio, and suggest that disease incidence may also relate with disappearance of pathogen antagonists, including ericoid- and ectomycorrhizal (ECM) fungi. By combining metabarcoding and field studies, we infer the resilient status of the fungal community towards a biotic stressor, and provide a benchmark for the study of other threatened ecosystems.
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Affiliation(s)
- Francesco Venice
- Institute for Sustainable Plant Protection (IPSP)-SS Turin-National Research Council (CNR), Viale Mattioli 25, 10125 Turin, Italy
| | - Alfredo Vizzini
- Institute for Sustainable Plant Protection (IPSP)-SS Turin-National Research Council (CNR), Viale Mattioli 25, 10125 Turin, Italy; Department of Life Sciences and System Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Arcangela Frascella
- Institute for Sustainable Plant Protection (IPSP)-National Research Council (CNR), Via Madonna del Piano 10, 50019 Sesto F.no (FI), Italy
| | - Giovanni Emiliani
- Institute for Sustainable Plant Protection (IPSP)-National Research Council (CNR), Via Madonna del Piano 10, 50019 Sesto F.no (FI), Italy
| | - Roberto Danti
- Institute for Sustainable Plant Protection (IPSP)-National Research Council (CNR), Via Madonna del Piano 10, 50019 Sesto F.no (FI), Italy
| | - Gianni Della Rocca
- Institute for Sustainable Plant Protection (IPSP)-National Research Council (CNR), Via Madonna del Piano 10, 50019 Sesto F.no (FI), Italy
| | - Antonietta Mello
- Institute for Sustainable Plant Protection (IPSP)-SS Turin-National Research Council (CNR), Viale Mattioli 25, 10125 Turin, Italy.
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Lofgren LA, Stajich JE. Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes. Curr Biol 2021; 31:R1312-R1325. [PMID: 34637742 PMCID: PMC8516061 DOI: 10.1016/j.cub.2021.06.083] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic roles as difficult to treat human infections and devastating plant pathogens. Despite community efforts to estimate and catalog fungal diversity, we have only named and described a minute fraction of the fungal world. The identification, characterization, and conservation of fungal diversity is paramount to preserving fungal bioresources, and to understanding and predicting ecosystem cycling and the evolution and epidemiology of fungal disease. Although species and ecosystem conservation are necessarily the foundation of preserving this diversity, there is value in expanding our definition of conservation to include the protection of biological collections, ecological metadata, genetic and genomic data, and the methods and code used for our analyses. These definitions of conservation are interdependent. For example, we need metadata on host specificity and biogeography to understand rarity and set priorities for conservation. To aid in these efforts, we need to draw expertise from diverse fields to tie traditional taxonomic knowledge to data obtained from modern -omics-based approaches, and support the advancement of diverse research perspectives. We also need new tools, including an updated framework for describing and tracking species known only from DNA, and the continued integration of functional predictions to link genetic diversity to functional and ecological diversity. Here, we review the state of fungal diversity research as shaped by recent technological advancements, and how changing viewpoints in taxonomy, -omics, and systematics can be integrated to advance mycological research and preserve fungal biodiversity.
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Affiliation(s)
- Lotus A Lofgren
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA
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Baptista P, Guedes de Pinho P, Moreira N, Malheiro R, Reis F, Padrão J, Tavares R, Lino-Neto T. In vitro interactions between the ectomycorrhizal Pisolithus tinctorius and the saprotroph Hypholoma fasciculare fungi: morphological aspects and volatile production. Mycology 2021; 12:216-229. [PMID: 34552812 PMCID: PMC8451600 DOI: 10.1080/21501203.2021.1876778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ectomycorrhizal fungi are crucial for forests sustainability. For Castanea sativa, ectomycorrhizal fungus Pisolithus tinctorius is an important mutualist partner. Saprotrophic fungi Hypholoma fasciculare, although used for biocontrol of Armillaria root disease, it negatively affected the interaction between the P. tinctorius and plant host roots, by compromise the formation of P. tinctorius-C. sativa mycorrhizae. In this work, fungal morphology during inhibition of H. fasciculare against P. tinctorius was elucidated. P. tinctorius growth was strongly affected by H. fasciculare, which was significantly reduced after six days of co-culture and become even more significant through time. During this period, P. tinctorius developed vesicles and calcium oxalate crystals, which were described as mechanisms to stress adaption by fungi. H. fasciculare produced different volatile organic compounds in co-cultures over time and differ between single or in dual-species. H. fasciculare highly produced sesquiterpenes (namely, α-muurolene) and nitrogen-containing compounds, which are recognised as having antimicrobial activity.
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Affiliation(s)
- Paula Baptista
- Centro De Investigação De Montanha (CIMO), Instituto Politécnico De Bragança, Campus De Santa Apolónia, Bragança, Portugal
| | - Paula Guedes de Pinho
- UCIBIO-REQUIMTE/Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Nathalie Moreira
- UCIBIO-REQUIMTE/Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ricardo Malheiro
- Centro De Investigação De Montanha (CIMO), Instituto Politécnico De Bragança, Campus De Santa Apolónia, Bragança, Portugal
| | - Francisca Reis
- BioSystems & Integrative Sciences Institute (Bioisi), Plant Functional Biology Centre, University of Minho, Campus De Gualtar, Braga, Portugal
| | - Jorge Padrão
- BioSystems & Integrative Sciences Institute (Bioisi), Plant Functional Biology Centre, University of Minho, Campus De Gualtar, Braga, Portugal
| | - Rui Tavares
- BioSystems & Integrative Sciences Institute (Bioisi), Plant Functional Biology Centre, University of Minho, Campus De Gualtar, Braga, Portugal
| | - Teresa Lino-Neto
- BioSystems & Integrative Sciences Institute (Bioisi), Plant Functional Biology Centre, University of Minho, Campus De Gualtar, Braga, Portugal
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Rahmeh R, Akbar A, Kumar V, Al-Mansour H, Kishk M, Ahmed N, Al-Shamali M, Boota A, Al-Ballam Z, Shajan A, Al-Okla N. Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment. Evol Bioinform Online 2021; 17:11769343211016887. [PMID: 34163126 PMCID: PMC8191072 DOI: 10.1177/11769343211016887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/16/2021] [Indexed: 11/15/2022] Open
Abstract
Soil contamination by hydrocarbons due to oil spills has become a global concern and it has more implications in oil producing regions. Biostimulation is considered as one of the promising remediation techniques that can be adopted to enhance the rate of degradation of crude oil. The soil microbial consortia play a critical role in governing the biodegradation of total petroleum hydrocarbons (TPHs), in particular polycyclic aromatic hydrocarbons (PAHs). In this study, the degradation pattern of TPHs and PAHs of Kuwait soil biopiles was measured at three-month intervals. Then, the microbial consortium associated with oil degradation at each interval was revealed through 16S rRNA based next generation sequencing. Rapid degradation of TPHs and most of the PAHs was noticed at the first 3 months of biostimulation with a degradation rate of pyrene significantly higher compared to other PAHs counterparts. The taxonomic profiling of individual stages of remediation revealed that, biostimulation of the investigated soil favored the growth of Proteobacteria, Alphaprotobacteria, Chloroflexi, Chlorobi, and Acidobacteria groups. These findings provide a key step towards the restoration of oil-contaminated lands in the arid environment.
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Affiliation(s)
- Rita Rahmeh
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Abrar Akbar
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Vinod Kumar
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Hamad Al-Mansour
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Mohamed Kishk
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Nisar Ahmed
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Mustafa Al-Shamali
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Anwar Boota
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Zainab Al-Ballam
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Anisha Shajan
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Naser Al-Okla
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
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Jeong M, Choi DH, Cheon WJ, Kim JG. Pyrosequencing and Taxonomic Composition of the Fungal Community from Soil of Tricholoma matsutake in Gyeongju. J Microbiol Biotechnol 2021; 31:686-695. [PMID: 33782219 PMCID: PMC9705868 DOI: 10.4014/jmb.2103.03021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022]
Abstract
Tricholoma matsutake is an ectomycorrhizal fungus that has a symbiotic relationship with the root of Pinus densiflora. Soil microbial communities greatly affect the growth of T. matsutake, however, few studies have examined the characteristics of these communities. In the present study, we analyzed soil fungal communities from Gyeongju and Yeongdeok using metagenomic pyrosequencing to investigate differences in fungal species diversity, richness, and taxonomic composition between the soil under T. matsutake fruiting bodies (Sample 2) and soil where the fairy ring of T. matsutake was no longer present (Sample 1). The same spot was investigated three times at intervals of four months to observe changes in the community. In the samples from Yeongdeok, the number of valid reads was lower than that at Gyeongju. The operational taxonomic units of most Sample 2 groups were less than those of Sample 1 groups, indicating that fungal diversity was low in the T. matsutakedominant soil. The soil under the T. matsutake fruiting bodies was dominated by more than 51% T. matsutake. From fall to the following spring, the ratio of T. matsutake decreased. Basidiomycota was the dominant phylum in most samples. G-F1-2, G-F2-2, and Y-F1-2 had the genera Tricholoma, Umbelopsis, Oidiodendron, Sagenomella, Cladophialophora, and Phialocephala in common. G-F1-1, G-F2-1, and Y-F1-1 had 10 genera including Umbelopsis and Sagenomella in common. From fall to the following spring, the amount of phyla Basidiomycota and Mucoromycota gradually decreased but that of phylum Ascomycota increased. We suggest that the genus Umbelopsis is positively related to T. matsutake.
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Affiliation(s)
- Minji Jeong
- Department of Life Sciences and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Doo-Ho Choi
- Department of Life Sciences and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Woo-Jae Cheon
- Department of Forest Environment, Gyeongsangbuk-do Forest Environment Research Institute, Gyeong-ju 38174, Republic of Korea
| | - Jong-Guk Kim
- Department of Life Sciences and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea,Corresponding author Phone: +82-53-950-5379 Fax: +82-53-955-5379 E-mail:
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9
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Similarities and Differences among Soil Fungal Assemblages in Managed Forests and Formerly Managed Forest Reserves. FORESTS 2021. [DOI: 10.3390/f12030353] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Unlike the numerous works concerning the effect of management on the forest mycobiome, only a few studies have addressed how fungi from different trophic groups recover from natural and anthropogenic disturbances and develop structural features typical of unmanaged old-growth forests. Our objective is to compare the soil fungal assemblages represented by different functional/trophic groups in protected and managed stands located in European mixed forests dominated by Scots pine. Fungal communities were analyzed using high-throughput Illumina MiSeq sequencing of fungal internal transcribed spacer 1 (ITS1) amplicons. Formerly managed forest reserves (established around 50 years ago) and forests under standard forest management appeared to be similar in terms of total and mean species richness of all fungal operational taxonomic units (OTUs), as well as OTUs assigned to different functional trophic groups. Among the 599 recorded OTUs, 497 (83%) were shared between both management types, whereas 9.5% of taxa were unique to forest reserves and 7.5% were unique to managed stands. Ascomycota and Basidiomycota were the predominant phyla, comprising 88% of all identified fungi. The main functional components of soil fungal assemblages consisted of saprotrophic (42% fungal OTUs; 27% reads) and ectomycorrhizal fungi (16%; 47%). Two-way analysis of similarities (ANOSIM) revealed that both site and management strategy influenced the species composition of soil fungal communities, with site being a primary effect for saprotrophic and ectomycorrhizal fungi. Volume of coarse and very fine woody debris and soil pH significantly influenced the ectomycorrhizal fungal community, whereas saprotrophic fungi were influenced primarily by volume of coarse woody debris and soil nitrate concentration. Among the identified fungal OTUs, 18 red-listed fungal species were identified from both forest reserves and managed forests, comprising two ECM fungi and four saprotrophs from the category of endangered species. Our results suggest that the transformation of fungal diversity after cessation of forest management is rather slow, and that both forest reserves and managed forests help uphold fungal diversity.
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Santolamazza-Carbone S, Iglesias-Bernabé L, Sinde-Stompel E, Gallego PP. Ectomycorrhizal fungal community structure in a young orchard of grafted and ungrafted hybrid chestnut saplings. MYCORRHIZA 2021; 31:189-201. [PMID: 33502579 PMCID: PMC7910378 DOI: 10.1007/s00572-020-01015-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
Ectomycorrhizal (ECM) fungal community of the European chestnut has been poorly investigated, and mostly by sporocarp sampling. We proposed the study of the ECM fungal community of 2-year-old chestnut hybrids Castanea × coudercii (Castanea sativa × Castanea crenata) using molecular approaches. By using the chestnut hybrid clones 111 and 125, we assessed the impact of grafting on ECM colonization rate, species diversity, and fungal community composition. The clone type did not have an impact on the studied variables; however, grafting significantly influenced ECM colonization rate in clone 111. Species diversity and richness did not vary between the experimental groups. Grafted and ungrafted plants of clone 111 had a different ECM fungal species composition. Sequence data from ITS regions of rDNA revealed the presence of 9 orders, 15 families, 19 genera, and 27 species of ECM fungi, most of them generalist, early-stage species. Thirteen new taxa were described in association with chestnuts. The basidiomycetes Agaricales (13 taxa) and Boletales (11 taxa) represented 36% and 31%, of the total sampled ECM fungal taxa, respectively. Scleroderma citrinum, S. areolatum, and S. polyrhizum (Boletales) were found in 86% of the trees and represented 39% of total ECM root tips. The ascomycete Cenococcum geophilum (Mytilinidiales) was found in 80% of the trees but accounted only for 6% of the colonized root tips. These results could help to unveil the impact of grafting on fungal symbionts, improving management of chestnut agro-ecosystems and production of edible fungal species.
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Affiliation(s)
- Serena Santolamazza-Carbone
- Applied Plant & Soil Biology, Plant Biology and Soil Science Department, Biology Faculty, University of Vigo, E-36310, Vigo, Spain.
- CITACA - Agri-Food Research and Transfer Cluster, University of Vigo, Ourense, Spain.
| | - Laura Iglesias-Bernabé
- Applied Plant & Soil Biology, Plant Biology and Soil Science Department, Biology Faculty, University of Vigo, E-36310, Vigo, Spain
| | | | - Pedro Pablo Gallego
- Applied Plant & Soil Biology, Plant Biology and Soil Science Department, Biology Faculty, University of Vigo, E-36310, Vigo, Spain
- CITACA - Agri-Food Research and Transfer Cluster, University of Vigo, Ourense, Spain
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11
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Zanne AE, Abarenkov K, Afkhami ME, Aguilar-Trigueros CA, Bates S, Bhatnagar JM, Busby PE, Christian N, Cornwell WK, Crowther TW, Flores-Moreno H, Floudas D, Gazis R, Hibbett D, Kennedy P, Lindner DL, Maynard DS, Milo AM, Nilsson RH, Powell J, Schildhauer M, Schilling J, Treseder KK. Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. Biol Rev Camb Philos Soc 2019; 95:409-433. [PMID: 31763752 DOI: 10.1111/brv.12570] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 12/21/2022]
Abstract
Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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Affiliation(s)
- Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Michelle E Afkhami
- Department of Biology, University of Miami, Coral Gables, FL, 33146, U.S.A
| | - Carlos A Aguilar-Trigueros
- Freie Universität-Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany
| | - Scott Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, IN, 46391, U.S.A
| | | | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97330, U.S.A
| | - Natalie Christian
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, U.S.A.,Department of Biology, University of Louisville, Louisville, KY 40208, U.S.A
| | - William K Cornwell
- Evolution & Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Habacuc Flores-Moreno
- Department of Ecology, Evolution, and Behavior, and Department of Forest Resources, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Dimitrios Floudas
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Romina Gazis
- Department of Plant Pathology, Tropical Research & Education Center, University of Florida, Homestead, FL, 33031, U.S.A
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, 01610, U.S.A
| | - Peter Kennedy
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Daniel L Lindner
- US Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, Wisconsin, WI, 53726, U.S.A
| | - Daniel S Maynard
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Amy M Milo
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Rolf Henrik Nilsson
- University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Box 461, 405 30, Göteborg, Sweden
| | - Jeff Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Mark Schildhauer
- National Center for Ecological Analysis and Synthesis, 735 State Street, Suite 300, Santa Barbara, CA, 93101, U.S.A
| | - Jonathan Schilling
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, U.S.A
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Substrate Preference Determines Macrofungal Biogeography in the Greater Mekong Sub-Region. FORESTS 2019. [DOI: 10.3390/f10100824] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The availability and the quality of substrates are important drivers of macrofungal biogeography, and thus macrofungal species occurrence is potentially dependent on the availability of different substrates. However, few studies have explored the properties of macrofungal substrates and assessed the relationship between macrofungal diversity and substrate diversity at a landscape level. To address this issue, we conducted a landscape-scale survey of basidiocarp substrates in the Greater Mekong Subregion (GMS). A total of 957 macrofungal species distributed across 73 families and 189 genera were collected. Substrates of these macrofungi were categorized into four main groups (namely, litter, soil, root, and rare substrates) and referenced into 14 sub-substrate types (such as branches, leaves, and fruit). The results revealed that 50% of the observed macrofungal species were symbiotrophs living in ectomycorrhizal association with plant hosts, 30% were saprotrophs decomposing plant litter, 15% lived in soil organic matter, and 5% lived in rare substrates. The most abundant root symbiotic fungi were members of Russula, whereas most litter saprotrophic fungi belonged to Marasmius. Macrofungi commonly favored a single substrate. This specificity was not affected by changes in vegetation or climate. Less than 1% of macrofungi (e.g., Marasmius aff. maximus) could live on multiple substrates. Most of these unusual macrofungi were characterized as highly mobile and were generally found in successional areas. In secondary forests, our survey indicated that significant correlations exist between substrate preference and taxonomic diversity, reflected as higher substrate diversity generally accompanied by higher macrofungal diversity. In conclusion, substrate preference is an important factor driving macrofungal composition and distribution in the GMS. Macrofungi that thrive on multiple substrates constitute pioneer groups that have an important role in establishing macrofungal communities in new habitats. These observations have furthered our understanding of how substrate preferences could explain macrofungal biogeography.
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Taudière A, Bellanger JM, Carcaillet C, Hugot L, Kjellberg F, Lecanda A, Lesne A, Moreau PA, Scharmann K, Leidel S, Richard F. Diversity of foliar endophytic ascomycetes in the endemic Corsican pine forests. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Maghnia FZ, Abbas Y, Mahé F, Kerdouh B, Tournier E, Ouadji M, Tisseyre P, Prin Y, El Ghachtouli N, Bakkali Yakhlef SE, Duponnois R, Sanguin H. Habitat- and soil-related drivers of the root-associated fungal community of Quercus suber in the Northern Moroccan forest. PLoS One 2017; 12:e0187758. [PMID: 29155841 PMCID: PMC5695781 DOI: 10.1371/journal.pone.0187758] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 10/25/2017] [Indexed: 12/25/2022] Open
Abstract
Soil fungi associated with plant roots, notably ectomycorrhizal (EcM) fungi, are central in above- and below-ground interactions in Mediterranean forests. They are a key component in soil nutrient cycling and plant productivity. Yet, major disturbances of Mediterranean forests, particularly in the Southern Mediterranean basin, are observed due to the greater human pressures and climate changes. These disturbances highly impact forest cover, soil properties and consequently the root-associated fungal communities. The implementation of efficient conservation strategies of Mediterranean forests is thus closely tied to our understanding of root-associated fungal biodiversity and environmental rules driving its diversity and structure. In our study, the root-associated fungal community of Q. suber was analyzed using high-throughput sequencing across three major Moroccan cork oak habitats. Significant differences in root-associated fungal community structures of Q. suber were observed among Moroccan cork oak habitats (Maâmora, Benslimane, Chefchaoun) subjected to different human disturbance levels (high to low disturbances, respectively). The fungal community structure changes correlated with a wide range of soil properties, notably with pH, C:N ratio (P = 0.0002), and available phosphorus levels (P = 0.0001). More than 90 below-ground fungal indicators (P < 0.01)-either of a type of habitat and/or a soil property-were revealed. The results shed light on the ecological significance of ubiquitous ectomycorrhiza (Tomentella, Russula, Cenococcum), and putative sclerotia-associated/ericoid mycorrhizal fungal taxa (Cladophialophora, Oidiodendron) in the Moroccan cork oak forest, and their intraspecific variability regarding their response to land use and soil characteristics.
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Affiliation(s)
- Fatima Zahra Maghnia
- Forestry research center, Rabat, Morocco
- CIRAD, UMR LSTM, Montpellier, France
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
- IRD, UMR LSTM, Montpellier, France
| | - Younes Abbas
- Polyvalent Laboratory, Multidisciplinary Faculty, University of Sultan Moulay Slimane, Béni Mellal, Morocco
| | - Frédéric Mahé
- CIRAD, UMR LSTM, Montpellier, France
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Estelle Tournier
- CIRAD, UMR LSTM, Montpellier, France
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Pierre Tisseyre
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
- IRD, UMR LSTM, Montpellier, France
| | - Yves Prin
- CIRAD, UMR LSTM, Montpellier, France
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
| | - Naïma El Ghachtouli
- Laboratory of Microbial Biotechnology, Faculty of Sciences and Technology, University of Sidi Mohamed Ben Abdellah, Fez, Morocco
| | | | - Robin Duponnois
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
- IRD, UMR LSTM, Montpellier, France
| | - Hervé Sanguin
- CIRAD, UMR LSTM, Montpellier, France
- LSTM, Univ Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro, Montpellier, France
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15
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Michaëlla Ebenye HC, Taudière A, Niang N, Ndiaye C, Sauve M, Awana NO, Verbeken M, De Kesel A, Séne S, Diédhiou AG, Sarda V, Sadio O, Cissoko M, Ndoye I, Selosse MA, Bâ AM. Ectomycorrhizal fungi are shared between seedlings and adults in a monodominantGilbertiodendron dewevreirain forest in Cameroon. Biotropica 2016. [DOI: 10.1111/btp.12415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Helvyne C. Michaëlla Ebenye
- Laboratoire Commun de Microbiologie; IRD/UCAD/ISRA; BP 1386 Dakar Sénégal
- Institut de Systématique, Évolution, Biodiversité (ISYEB - UMR 7205 - CNRS MNHN, UPMC, EPHE); Muséum national d'Histoire naturelle; Sorbonne Universités; 57 rue Cuvier, CP50 75005 Paris France
- UMR 5175; CEFE - CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE; Montpellier France
- Department of Plant Taxonomy and Nature Conservation; University of Gdansk; Wita Stwosza 59 80-308 Gdansk Poland
- Laboratoire des Symbioses Tropicales et Méditerranéennes; UMR113- INRA/AGRO-M/CIRAD/IRD/UM2-TA10/J; Campus International de Baillarguet 34398 Montpellier Cedex 5 France. Laboratoire de Biologie et Physiologie Végétales; Faculté des Sciences Exactes et Naturelles; Université des Antilles; BP 592 97159 Pointe-à-Pitre Guadeloupe France
| | - Adrien Taudière
- UMR 5175; CEFE - CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE; Montpellier France
| | - Nogaye Niang
- Laboratoire Commun de Microbiologie; IRD/UCAD/ISRA; BP 1386 Dakar Sénégal
| | - Cheikh Ndiaye
- Laboratoire Commun de Microbiologie; IRD/UCAD/ISRA; BP 1386 Dakar Sénégal
| | - Mathieu Sauve
- UMR 5175; CEFE - CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE; Montpellier France
| | - Nérée Onguene Awana
- Soil, Water and Atmosphere Department; Institute of Agriculture Research for Development; BP. 2123 Yaoundé Cameroon
| | - Mieke Verbeken
- Department of Biology; Ghent University; K.L. Ledeganckstraat 35 9000 Ghent Belgium
| | - André De Kesel
- Botanic Garden Meise; Nieuwelaan 38 BE-1860 Meise Belgium
| | - Seynabou Séne
- Laboratoire Commun de Microbiologie; IRD/UCAD/ISRA; BP 1386 Dakar Sénégal
| | - Abdala G. Diédhiou
- Laboratoire Commun de Microbiologie; IRD/UCAD/ISRA; BP 1386 Dakar Sénégal
| | - Violette Sarda
- UMR 5175; CEFE - CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE; Montpellier France
| | - Omar Sadio
- IRD; UMR 195 LEMAR (UBO/CNRS/IRD/Ifremer); BP 1386, CP 18524 Dakar Sénégal
| | - Maïmouna Cissoko
- Laboratoire Commun de Microbiologie; IRD/UCAD/ISRA; BP 1386 Dakar Sénégal
| | - Ibrahima Ndoye
- Laboratoire Commun de Microbiologie; IRD/UCAD/ISRA; BP 1386 Dakar Sénégal
| | - Marc-André Selosse
- Institut de Systématique, Évolution, Biodiversité (ISYEB - UMR 7205 - CNRS MNHN, UPMC, EPHE); Muséum national d'Histoire naturelle; Sorbonne Universités; 57 rue Cuvier, CP50 75005 Paris France
- Department of Plant Taxonomy and Nature Conservation; University of Gdansk; Wita Stwosza 59 80-308 Gdansk Poland
| | - Amadou M. Bâ
- Laboratoire des Symbioses Tropicales et Méditerranéennes; UMR113- INRA/AGRO-M/CIRAD/IRD/UM2-TA10/J; Campus International de Baillarguet 34398 Montpellier Cedex 5 France
- Laboratoire de Biologie et Physiologie Végétales; Faculté des Sciences Exactes et Naturelles; Université des Antilles; BP 592 97159 Pointe-à-Pitre Guadeloupe France
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