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Rodríguez-Albarracín HS, Demattê JAM, Rosin NA, Amorim MTA, Contreras AED, Andreote FD, Rosas JTF. Soil organic carbon sequestration potential explained by mineralogical and microbiological activity using spectral transfer functions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174652. [PMID: 38992377 DOI: 10.1016/j.scitotenv.2024.174652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 06/05/2024] [Accepted: 07/07/2024] [Indexed: 07/13/2024]
Abstract
The ability of soil to sequester carbon and reduce atmospheric CO2 concentrations is limited and depends on the soil minerals and their interaction with the microbiota. Microbial activities are closely associated with the types and amounts of soil organic matter (SOM) and clay minerals that have functional groups that interact with energy in Vis NIR-SWIR and Mid-IR wavelengths. The main objective of this research was to determine, based on these spectral ranges, the relation between mineralogical and organic compounds, as their sequestration and specialization in soils from Brazil. It was possible to map microbiological activity by spectral transfer functions and digital soil mapping reaching R2 from 0.77 to 0.85. Multiple regression equations were constructed to quantify enzymatic activity, microbial biomass carbon (MBC), particulate organic matter (POM), and resistant forms of carbon, and SOM associated with the mineral fraction (MAOM). All these properties were detected by specific bands obtained with the recursive feature elimination (RFE) algorithm, reaching correlations from 0.64 to 0.98 in specific ranges. The prediction model of the carbon sequestration potential was adjusted with microbiological and mineralogical variables from Vis-NIR-SWIR and the Mid-IR spectral range. A SARAR double autoregressive model was adjusted with r 0.61 and to a spatial error model (SEM) with r 0.7. The explanatory variables were associated with kaolinite, hematite, goethite, gibbsite, and the abundance of fungi, actinomycetes, vesico-arbuscular mycorrhizal fungi, enzymatic activity of beta-glucosidase, urease and phosphatase, and POM. Among the microbiological variables, the general abundance of fungi was the most important, in contrast to enzymatic activity that was the least important. The interaction between the different maps constructed and historical land use allowed the identification of areas that contribute to sequestering new carbon and could be the key to climate change mitigation strategies.
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Affiliation(s)
- Heidy Soledad Rodríguez-Albarracín
- Departament of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo 13418-900, Brazil.
| | - José A M Demattê
- Departament of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo 13418-900, Brazil.
| | - Nícolas Augusto Rosin
- Departament of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo 13418-900, Brazil.
| | - Merilyn Taynara Accorsi Amorim
- Departament of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo 13418-900, Brazil.
| | - Aquiles Enrique Darghan Contreras
- Faculty of Agricultural Sciences, Department of Agronomy, National University of Colombia, Carrera 30 núm. 45-03, Building 500, Bogotá, DC, Colombia.
| | - Fernando Dini Andreote
- Departament of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo 13418-900, Brazil.
| | - Jorge Tadeu Fim Rosas
- Departament of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo 13418-900, Brazil.
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Zhou J, Gui H, Yang S, Yang X, Shi L. Fungal Interactions Matter: Tricholoma matsutake Domination Affect Fungal Diversity and Function in Mountain Forest Soils. BIOLOGY 2021; 10:1051. [PMID: 34681150 PMCID: PMC8533266 DOI: 10.3390/biology10101051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022]
Abstract
Tricholoma matsutake forms a symbiotic association with coniferous trees, developing mycelial aggregations, called 'shiro', which are characterized by distinct chemical and physical properties from nearby forest bulk soil. The fungal diversity living in shiro soil play key roles in nutrient cycles for this economically important mushroom, but have not been profiled across large spatial and environmental gradients. Samples of shiro and non-shiro (nearby bulk soil) were taken from five field sites where sporocarps naturally formed. Phospholipid fatty acids (PLFA) and Illumina MiSeq sequencing were combined to identify fungal biomass and community structure. Matsutake dominated in the shiro, which had a significantly reduced saprotrophic fungi biomass compared to non-shiro soil. Fungal diversity was negatively correlated with the relative abundance of T. matsutake in the shiro soil. The fungal community in the shiro was characterized by similar fungal species composition in most samples regardless of forest types. Matsutake coexisted with a specific fungal community due to competition or nutrient interactions. Oidiodendron was positively correlated with the abundance of T. matsutake, commonly cohabitant in the shiro. In contrast, Helotiales and Mortierella were negatively correlated with T. matsutake, both of which commonly inhabit the non-shiro soil but do not occur in shiro soils. We conclude that T. matsutake generate a dominance effect to shape the fungal community and diversity in shiro soil across distinctive forest types.
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Affiliation(s)
- Jie Zhou
- Biogeochemistry of Agroecosystems, Department of Crop Science, Georg August University of Göttingen, 37075 Göttingen, Germany; (J.Z.); (L.S.)
| | - Heng Gui
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China;
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China;
| | - Shujiao Yang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China;
| | - Xuefei Yang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China;
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla 666303, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, China
| | - Lingling Shi
- Biogeochemistry of Agroecosystems, Department of Crop Science, Georg August University of Göttingen, 37075 Göttingen, Germany; (J.Z.); (L.S.)
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China;
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Distinct Compartmentalization of Microbial Community and Potential Metabolic Function in the Fruiting Body of Tricholoma matsutake. J Fungi (Basel) 2021; 7:jof7080586. [PMID: 34436125 PMCID: PMC8397075 DOI: 10.3390/jof7080586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 01/21/2023] Open
Abstract
The uniquely compartmentalized fruiting body structure of the ectomycorrhizal fungus (EMF) Tricholoma matsutake, is a hotspot of microbial habitation and interaction. However, microbial diversity within this microniche structure of the EMF is rarely investigated. Furthermore, there is limited information concerning microbiomes associated with sporomes belonging to the ubiquitous fungal phylum Basidiomycota, particularly with respect to fungus-EMF interactions. In this study, we conducted high throughput sequencing, using ITS (fungal) and 16S rRNA (bacterial) marker genes to characterize and compare fruiting body microbiomes in the outer (pileipellis and stipitipellis) and inner layers (pileum context, stipe context, and lamellae) of the fruiting body of T. matsutake. Our results show the number of unique bacterial operational taxonomic units (OTUs) among the different compartments ranged from 410 to 499 and was more than double that of the shared/common OTUs (235). Micrococcales, Bacillales, Caulobacter, and Sphingomonas were the primary significant bacterial taxa within the different compartments of the dissected T. matsutake fruiting body. Non-parametric multivariate analysis of variance showed significant compartmental differences for both the bacterial and the fungal community structure within the T. matsutake fruiting body. The metabolic profiling revealed putative metabolisms (of amino acids, carbohydrates, and nucleotides) and the biosynthesis of secondary metabolites to be highly enriched in outer layers; in the inner parts, the metabolisms of energy, cofactors, vitamins, and lipids were significantly higher. This study demonstrates for the first time the distinct compartmentalization of microbial communities and potential metabolic function profiles in the fruiting body of an economically important EMF T. matsutake.
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Carrasco J, García‐Delgado C, Lavega R, Tello ML, De Toro M, Barba‐Vicente V, Rodríguez‐Cruz MS, Sánchez‐Martín MJ, Pérez M, Preston GM. Holistic assessment of the microbiome dynamics in the substrates used for commercial champignon (Agaricus bisporus) cultivation. Microb Biotechnol 2020; 13:1933-1947. [PMID: 32716608 PMCID: PMC7533343 DOI: 10.1111/1751-7915.13639] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/09/2020] [Indexed: 11/30/2022] Open
Abstract
Microorganisms strongly influence and are required to generate the selective substrate that provides nutrients and support for fungal growth, and ultimately to induce mushroom fructification under controlled environmental conditions. In this work, the fungal and bacterial microbiota living in the different substrates employed in a commercial crop (compost phase I, II and III, flush 1 and 2, and casing material on day 1, 6 and 8 after compost casing and during flush 1 and 2) have been characterized along the different stages of cultivation by metataxonomic analysis (16S rRNA and ITS2), analysis of phospholipid fatty acid content (PLFAs) and RT-qPCR. Additionally, laccase activity and the content of lignin and complex carbohydrates in compost and casing have been quantified. The bacterial diversity in compost and casing increased throughout the crop cycle boosted by the connection of both substrates. As reflected by the PLFAs, the total living bacterial biomass appears to be negatively correlated with the mycelium of the crop. Agaricus bisporus was the dominant fungal species in colonized substrates, displacing the pre-eminent Ascomycota, accompanied by a sustained increase in laccase activity, which is considered to be a major product of protein synthesis during the mycelial growth of champignon. From phase II onwards, the metabolic machinery of the fungal crop degrades lignin and carbohydrates in compost, while these components are hardly degraded in casing, which reflects the minor role of the casing for nourishing the crop. The techniques employed in this study provide a holistic and detailed characterization of the changing microbial composition in commercial champignon substrates. The knowledge generated will contribute to improve compost formulations (selection of base materials) and accelerate compost production, for instance, through biotechnological interventions in the form of tailored biostimulants and to design environmentally sustainable bio-based casing materials.
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Affiliation(s)
- Jaime Carrasco
- Department of Plant SciencesUniversity of OxfordS Parks RdOxfordOX1 3RBUK
- Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH)AutolSpain
| | - Carlos García‐Delgado
- Departamento de Geología y GeoquímicaUniversidad Autónoma de MadridMadridSpain
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA‐CSIC)SalamancaSpain
| | - Rebeca Lavega
- Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH)AutolSpain
| | - María L. Tello
- Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH)AutolSpain
| | - María De Toro
- Plataforma de Genómica y BioinformáticaCentro de Investigación Biomédica de La Rioja (CIBIR)LogroñoSpain
| | - Víctor Barba‐Vicente
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA‐CSIC)SalamancaSpain
| | | | | | - Margarita Pérez
- Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH)AutolSpain
| | - Gail M. Preston
- Department of Plant SciencesUniversity of OxfordS Parks RdOxfordOX1 3RBUK
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Pratama AA, van Elsas JD. Gene mobility in microbiomes of the mycosphere and mycorrhizosphere -role of plasmids and bacteriophages. FEMS Microbiol Ecol 2020; 95:5454738. [PMID: 30980672 DOI: 10.1093/femsec/fiz053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/12/2019] [Indexed: 12/22/2022] Open
Abstract
Microbial activity in soil, including horizontal gene transfer (HGT), occurs in soil hot spots and at "hot moments". Given their capacities to explore soil for nutrients, soil fungi (associated or not with plant roots) can act as (1) selectors of myco(rrhizo)sphere-adapted organisms and (2) accelerators of HGT processes across the cell populations that are locally present. This minireview critically examines our current understanding of the drivers of gene mobility in the myco(rrhizo)sphere. We place a special focus on the role of two major groups of gene mobility agents, i.e. plasmids and bacteriophages. With respect to plasmids, there is mounting evidence that broad-host-range (IncP-1β and PromA group) plasmids are prominent drivers of gene mobility across mycosphere inhabitants. A role of IncP-1β plasmids in Fe uptake processes has been revealed. Moreover, a screening of typical mycosphere-inhabiting Paraburkholderia spp. revealed carriage of integrated plasmids, next to prophages, that presumably confer fitness enhancements. In particular, functions involved in biofilm formation and nutrient uptake were thus identified. The potential of the respective gene mobility agents to promote the movement of such genes is critically examined.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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Different Effects of Soil Fertilization on Bacterial Community Composition in the Penicillium canescens Hyphosphere and in Bulk Soil. Appl Environ Microbiol 2020; 86:AEM.02969-19. [PMID: 32144110 PMCID: PMC7205497 DOI: 10.1128/aem.02969-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/26/2020] [Indexed: 12/14/2022] Open
Abstract
P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil. This study investigated the effects of long-term soil fertilization on the composition and potential for phosphorus (P) and nitrogen (N) cycling of bacterial communities associated with hyphae of the P-solubilizing fungus Penicillium canescens. Using a baiting approach, hyphosphere bacterial communities were recovered from three soils that had received long-term amendment in the field with mineral or mineral plus organic fertilizers. P. canescens hyphae recruited bacterial communities with a decreased diversity and an increased abundance of Proteobacteria relative to what was observed in soil communities. As core bacterial taxa, Delftia and Pseudomonas spp. were present in all hyphosphere samples irrespective of soil fertilization. However, the type of fertilization showed significant impacts on the diversity, composition, and distinctive taxa/operational taxonomic units (OTUs) of hyphosphere communities. The soil factors P (Olsen method), exchangeable Mg, exchangeable K, and pH were important for shaping soil and hyphosphere bacterial community compositions. An increased relative abundance of organic P metabolism genes was found in hyphosphere communities from soil that had not received P fertilizers, which could indicate P limitation near the fungal hyphae. Additionally, P. canescens hyphae recruited bacterial communities with a higher abundance of N fixation genes than found in soil communities, which might imply a role of hyphosphere communities for fungal N nutrition. Furthermore, the relative abundances of denitrification genes were greater in several hyphosphere communities, indicating an at least partly anoxic microenvironment with a high carbon-to-N ratio around the hyphae. In conclusion, soil fertilization legacy shapes P. canescens hyphosphere microbiomes and their functional potential related to P and N cycling. IMPORTANCE P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil.
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Yu F, Liang JF, Song J, Wang SK, Lu JK. Bacterial Community Selection of Russula griseocarnosa Mycosphere Soil. Front Microbiol 2020; 11:347. [PMID: 32269551 PMCID: PMC7109302 DOI: 10.3389/fmicb.2020.00347] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/17/2020] [Indexed: 11/13/2022] Open
Abstract
Russula griseocarnosa is a wild, ectomycorrhizal, edible, and medicinal fungus with high economic value in southern China. R. griseocarnosa fruiting bodies cannot be artificially cultivated. To better understand the effects of abiotic and biotic factors on R. griseocarnosa growth, the physicochemical properties of R. griseocarnosa and its associated bacterial communities were investigated in two soil types (mycosphere and bulk soil) from Fujian, Guangdong, and Guangxi Provinces. The results revealed that the diversity, community structure, and functional characteristics of the dominant mycosphere bacteria in all geographical locations were similar. Soil pH and available nitrogen (AN) are the major factors influencing the mycosphere-soil bacterial communities' structure. The diversity of soil bacteria is decreased in R. griseocarnosa mycosphere when compared with the bulk soil. Burkholderia-Paraburkholderia, Mycobacterium, Roseiarcus, Sorangium, Acidobacterium, and Singulisphaera may also be mycorrhiza helper bacteria (MHB) of R. griseocarnosa. The functional traits related to the two-component system, bacterial secretion system, tyrosine metabolism, biosynthesis of unsaturated fatty acids, and metabolism of cofactors and vitamins were more abundant in R. griseocarnosa mycosphere soil. The mycosphere soil bacteria of R. griseocarnosa play a key role in R. griseocarnosa growth. Application of management strategies, such as N fertilizer and microbial fertilizer containing MHB, may promote the conservation, propagation promotion, and sustainable utilization of R. griseocarnosa.
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Affiliation(s)
| | - Jun-Feng Liang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
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Isolation and Whole-Genome Sequencing of 12 Mushroom-Associated Bacterial Strains: an Inquiry-Based Laboratory Exercise in a Genomics Course at the Rochester Institute of Technology. Microbiol Resour Announc 2020; 9:9/6/e01457-19. [PMID: 32029553 PMCID: PMC7005118 DOI: 10.1128/mra.01457-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the isolation, identification, and whole-genome sequences of 12 bacterial strains associated with four mushroom species. The study was done as an inquiry-based exercise in an undergraduate genomics course (BIOL 340) in the Thomas H. Gosnell School of Life Sciences at the Rochester Institute of Technology. Here, we report the isolation, identification, and whole-genome sequences of 12 bacterial strains associated with four mushroom species. The study was done as an inquiry-based exercise in an undergraduate genomics course (BIOL 340) in the Thomas H. Gosnell School of Life Sciences at the Rochester Institute of Technology.
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Hao X, Zhu YG, Nybroe O, Nicolaisen MH. The Composition and Phosphorus Cycling Potential of Bacterial Communities Associated With Hyphae of Penicillium in Soil Are Strongly Affected by Soil Origin. Front Microbiol 2020; 10:2951. [PMID: 31969866 PMCID: PMC6960115 DOI: 10.3389/fmicb.2019.02951] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 12/09/2019] [Indexed: 02/05/2023] Open
Abstract
Intimate fungal-bacterial interactions are widespread in nature. However the main drivers for the selection of hyphae-associated bacterial communities and their functional traits in soil systems remain elusive. In the present study, baiting microcosms were used to recover hyphae-associated bacteria from two Penicillium species with different phosphorus-solubilizing capacities in five types of soils. Based on amplicon sequencing of 16S rRNA genes, the composition of bacterial communities associated with Penicillium hyphae differed significantly from the soil communities, showing a lower diversity and less variation in taxonomic structure. Furthermore, soil origin had a significant effect on hyphae-associated community composition, whereas the two fungal species used in this study had no significant overall impact on bacterial community structure, despite their different capacities to solubilize phosphorus. However, discriminative taxa and specific OTUs were enriched in hyphae-associated communities of individual Penicillium species indicating that each hyphosphere represented a unique niche for bacterial colonization. Additionally, an increased potential of phosphorus cycling was found in hyphae-associated communities, especially for the gene phnK involved in phosphonate degradation. Altogether, it was established that the two Penicillium hyphae represent unique niches in which microbiome assemblage and phosphorus cycling potential are mainly driven by soil origin, with less impact made by fungal identity with a divergent capacity to utilize phosphorus.
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Affiliation(s)
- Xiuli Hao
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette H. Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
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Changey F, Meglouli H, Fontaine J, Magnin-Robert M, Tisserant B, Lerch TZ, Lounès-Hadj Sahraoui A. Initial microbial status modulates mycorrhizal inoculation effect on rhizosphere microbial communities. MYCORRHIZA 2019; 29:475-487. [PMID: 31506745 DOI: 10.1007/s00572-019-00914-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) play a central role in rhizosphere functioning as they interact with both plants and soil microbial communities. The conditions in which AMF modify plant physiology and microbial communities in the rhizosphere are still poorly understood. In the present study, four different plant species, (clover, alfalfa, ryegrass, tall fescue) were cultivated in either sterilized (γ ray) or non-sterilized soil and either inoculated with a commercial AMF (Glomus LPA Val 1.) or not. After 20 weeks of cultivation, the mycorrhizal rate and shoot and root biomasses were measured. The abundance and composition of bacteria, archaea, and fungi were analyzed, respectively, by quantitative PCR (qPCR) and fingerprinting techniques. Whilst sterilization did not change the AMF capacity to modify plant biomass, significant changes in microbial communities were observed, depending on the taxon and the associated plant. AMF inoculation decreases both bacterial and archaeal abundance and diversity, with a greatest extent in sterilized samples. These results also show that AMF exert different selections on soil microbial communities according to the plant species they are associated with. This study suggests that the initial abundance and diversity of rhizosphere microbial communities should be considered when introducing AMF to cultures.
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Affiliation(s)
- Frédérique Changey
- Unité de Chimie Environnementale et Interactions sur le Vivant) (UCEIV), EA 4492, SFR Condorcet FR CNRS 3417, Université du Littoral Côte d'Opale, 50 rue Ferdinand Buisson, 62228, Calais, France.
| | - Hacène Meglouli
- Unité de Chimie Environnementale et Interactions sur le Vivant) (UCEIV), EA 4492, SFR Condorcet FR CNRS 3417, Université du Littoral Côte d'Opale, 50 rue Ferdinand Buisson, 62228, Calais, France
| | - Joël Fontaine
- Unité de Chimie Environnementale et Interactions sur le Vivant) (UCEIV), EA 4492, SFR Condorcet FR CNRS 3417, Université du Littoral Côte d'Opale, 50 rue Ferdinand Buisson, 62228, Calais, France
| | - Maryline Magnin-Robert
- Unité de Chimie Environnementale et Interactions sur le Vivant) (UCEIV), EA 4492, SFR Condorcet FR CNRS 3417, Université du Littoral Côte d'Opale, 50 rue Ferdinand Buisson, 62228, Calais, France
| | - Benoit Tisserant
- Unité de Chimie Environnementale et Interactions sur le Vivant) (UCEIV), EA 4492, SFR Condorcet FR CNRS 3417, Université du Littoral Côte d'Opale, 50 rue Ferdinand Buisson, 62228, Calais, France
| | - Thomas Z Lerch
- Paris Institute of Ecology and Environnemental Sciences (IEES-Paris), UMR 7518 (CNRS- SU-INRA-UPEC- Paris Diderot-IRD), Université Paris-Est Créteil, 60 avenue du Général de Gaulle, 94010, Créteil Cedex, France
| | - Anissa Lounès-Hadj Sahraoui
- Unité de Chimie Environnementale et Interactions sur le Vivant) (UCEIV), EA 4492, SFR Condorcet FR CNRS 3417, Université du Littoral Côte d'Opale, 50 rue Ferdinand Buisson, 62228, Calais, France
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Carrasco J, Preston GM. Growing edible mushrooms: a conversation between bacteria and fungi. Environ Microbiol 2019; 22:858-872. [DOI: 10.1111/1462-2920.14765] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Jaime Carrasco
- Department of Plant SciencesUniversity of Oxford, S Parks Rd Oxford OX1 3RB UK
- Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH) Autol Spain
| | - Gail M. Preston
- Department of Plant SciencesUniversity of Oxford, S Parks Rd Oxford OX1 3RB UK
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Gong S, Chen C, Zhu J, Qi G, Jiang S. Effects of wine-cap Stropharia cultivation on soil nutrients and bacterial communities in forestlands of northern China. PeerJ 2018; 6:e5741. [PMID: 30324022 PMCID: PMC6183509 DOI: 10.7717/peerj.5741] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/12/2018] [Indexed: 01/21/2023] Open
Abstract
Background Cultivating the wine-cap mushroom (Stropharia rugosoannulata) on forestland has become popular in China. However, the effects of wine-cap Stropharia cultivation on soil nutrients and bacterial communities are poorly understood. Methods We employed chemical analyses and high-throughput sequencing to determine the impact of cultivating the wine-cap Stropharia on soil nutrients and bacterial communities of forestland. Results Cultivation regimes of Stropharia on forestland resulted in consistent increases of soil organic matter (OM) and available phosphorus (AP) content. Among the cultivation regimes, the greatest soil nutrient contents were found in the one-year interval cultivation regime, and the lowest total N and alkaline hydrolysable N contents were observed in the current-year cultivation regime. No significant differences were observed in alpha diversity among all cultivation regimes. Specific soil bacterial groups, such as Acidobacteria, increased in abundance after cultivation of Stropharia rugosoannulata. Discussion Given the numerous positive effects exerted by OM on soil physical and chemical properties, and the consistent increase in OM content for all cultivation regimes, we suggest that mushroom cultivation is beneficial to forest soil nutrient conditions through increasing OM content. Based on the fact that the one-year interval cultivation regime had the highest soil nutrient content as compared with other cultivation regimes, we recommend this regime for application in farming practice. The spent mushroom compost appeared to be more influential than the hyphae of S. rugosoannulata on the soil nutrients and bacterial communities; however, this requires further study. This research provides insight into understanding the effects of mushroom cultivation on the forest soil ecosystem and suggests a relevant cultivation strategy that reduces its negative impacts.
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Affiliation(s)
- Sai Gong
- College of Plant Protection, Shandong Province Key Laboratory of Agricultural Microbiology, Engineering Research Centre of Forest Pest Management of Shandong Province, Shandong Agricultural University, Taian, Shandong, China
| | - Chen Chen
- College of Plant Protection, Shandong Province Key Laboratory of Agricultural Microbiology, Engineering Research Centre of Forest Pest Management of Shandong Province, Shandong Agricultural University, Taian, Shandong, China
| | - Jingxian Zhu
- College of Plant Protection, Shandong Province Key Laboratory of Agricultural Microbiology, Engineering Research Centre of Forest Pest Management of Shandong Province, Shandong Agricultural University, Taian, Shandong, China
| | - Guangyao Qi
- College of Plant Protection, Shandong Province Key Laboratory of Agricultural Microbiology, Engineering Research Centre of Forest Pest Management of Shandong Province, Shandong Agricultural University, Taian, Shandong, China
| | - Shuxia Jiang
- College of Plant Protection, Shandong Province Key Laboratory of Agricultural Microbiology, Engineering Research Centre of Forest Pest Management of Shandong Province, Shandong Agricultural University, Taian, Shandong, China
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Bahram M, Vanderpool D, Pent M, Hiltunen M, Ryberg M. The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:155-166. [PMID: 29327481 DOI: 10.1111/1758-2229.12612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/19/2017] [Accepted: 01/04/2018] [Indexed: 06/07/2023]
Abstract
Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.
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Affiliation(s)
- Mohammad Bahram
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, 51005 Estonia
| | - Dan Vanderpool
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Mari Pent
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, 51005 Estonia
| | - Markus Hiltunen
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
| | - Martin Ryberg
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
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Pent M, Hiltunen M, Põldmaa K, Furneaux B, Hildebrand F, Johannesson H, Ryberg M, Bahram M. Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies. Environ Microbiol 2018; 20:1641-1650. [DOI: 10.1111/1462-2920.14069] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Mari Pent
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
| | - Markus Hiltunen
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
| | - Brendan Furneaux
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Falk Hildebrand
- Structural and Computational Biology, European Molecular Biology Laboratory; Heidelberg Germany
| | - Hanna Johannesson
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Martin Ryberg
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
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Ceballos SJ, Yu C, Claypool JT, Singer SW, Simmons BA, Thelen MP, Simmons CW, VanderGheynst JS. Development and characterization of a thermophilic, lignin degrading microbiota. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.08.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Ghodsalavi B, Svenningsen NB, Hao X, Olsson S, Nicolaisen MH, Al-Soud WA, Sørensen SJ, Nybroe O. A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil. PLoS One 2017; 12:e0187116. [PMID: 29077733 PMCID: PMC5659649 DOI: 10.1371/journal.pone.0187116] [Citation(s) in RCA: 14] [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: 06/29/2017] [Accepted: 10/13/2017] [Indexed: 11/18/2022] Open
Abstract
It is important to identify and recover bacteria associating with fungi under natural soil conditions to enable eco-physiological studies, and to facilitate the use of bacterial-fungal consortia in environmental biotechnology. We have developed a novel type of baiting microcosm, where fungal hyphae interact with bacteria under close-to-natural soil conditions; an advantage compared to model systems that determine fungal influences on bacterial communities in laboratory media. In the current approach, the hyphae are placed on a solid support, which enables the recovery of hyphae with associated bacteria in contrast to model systems that compare bulk soil and mycosphere soil. We used the baiting microcosm approach to determine, for the first time, the composition of the bacterial community associating in the soil with hyphae of the phosphate-solubilizer, Penicillium bilaii. By applying a cultivation-independent 16S rRNA gene-targeted amplicon sequencing approach, we found a hypha-associated bacterial community with low diversity compared to the bulk soil community and exhibiting massive dominance of Burkholderia OTUs. Burkholderia is known be abundant in soil environments affected by fungi, but the discovery of this massive dominance among bacteria firmly associating with hyphae in soil is novel and made possible by the current bait approach.
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Affiliation(s)
- Behnoushsadat Ghodsalavi
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Nanna Bygvraa Svenningsen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Xiuli Hao
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Stefan Olsson
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mette Haubjerg Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Waleed Abu Al-Soud
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- * E-mail:
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Oh SY, Fong JJ, Park MS, Lim YW. Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil. PLoS One 2016; 11:e0168573. [PMID: 27977803 PMCID: PMC5158061 DOI: 10.1371/journal.pone.0168573] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/03/2016] [Indexed: 02/01/2023] Open
Abstract
Tricholoma matsutake, the pine mushroom, is a valuable forest product with high economic value in Asia, and plays an important ecological role as an ectomycorrhizal fungus. Around the host tree, T. matsutake hyphae generate a distinctive soil aggregating environment called a fairy ring, where fruiting bodies form. Because T. matsutake hyphae dominate the soil near the fairy ring, this species has the potential to influence the microbial community. To explore the influence of T. matsutake on the microbial communities, we compared the microbial community and predicted bacterial function between two different soil types-T. matsutake dominant and T. matsutake minor. DNA sequence analyses showed that fungal and bacterial diversity were lower in the T. matsutake dominant soil compared to T. matsutake minor soil. Some microbial taxa were significantly more common in the T. matsutake dominant soil across geographic locations, many of which were previously identified as mycophillic or mycorrhiza helper bacteria. Between the two soil types, the predicted bacterial functional profiles (using PICRUSt) had significantly distinct KEGG modules. Modules for amino acid uptake, carbohydrate metabolism, and the type III secretion system were higher in the T. matsutake dominant soil than in the T. matsutake minor soil. Overall, similar microbial diversity, community structure, and bacterial functional profiles of the T. matsutake dominant soil across geographic locations suggest that T. matsutake may generate a dominance effect.
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Affiliation(s)
- Seung-Yoon Oh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jonathan J. Fong
- Science Unit, Lingnan University, Tuen Mun, New Territories, Hong Kong
| | - Myung Soo Park
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
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