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Lofgren L, Nguyen NH, Kennedy P, Pérez-Pazos E, Fletcher J, Liao HL, Wang H, Zhang K, Ruytinx J, Smith AH, Ke YH, Cotter HVT, Engwall E, Hameed KM, Vilgalys R, Branco S. Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. THE NEW PHYTOLOGIST 2024; 242:1448-1475. [PMID: 38581203 PMCID: PMC11045321 DOI: 10.1111/nph.19700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulating Suillus fungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled by Suillus, present a suite of protocols for working with the genus, and discuss how Suillus is emerging as an important model to elucidate the ecology and evolution of ECM interactions.
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Affiliation(s)
- Lotus Lofgren
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawai‘i at Māno, 3190 Maile Way, Honolulu, HI 96822, USA
| | - Peter Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Eduardo Pérez-Pazos
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Jessica Fletcher
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Haihua Wang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Kaile Zhang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
| | - Joske Ruytinx
- Research Group of Microbiology and Plant Genetics, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium, USA
| | - Alexander H. Smith
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Yi-Hong Ke
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109, USA
| | - H. Van T. Cotter
- University of North Carolina at Chapel Hill Herbarium, 120 South Road, Chapel Hill, NC 27599, USA
| | - Eiona Engwall
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599, USA
| | - Khalid M. Hameed
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
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Liu XL, Zhao H, Wang YX, Liu XY, Jiang Y, Tao MF, Liu XY. Detecting and characterizing new endofungal bacteria in new hosts: Pandoraea sputorum and Mycetohabitans endofungorum in Rhizopus arrhizus. Front Microbiol 2024; 15:1346252. [PMID: 38486702 PMCID: PMC10939042 DOI: 10.3389/fmicb.2024.1346252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
The fungus Rhizopus arrhizus (=R. oryzae) is commonly saprotrophic, exhibiting a nature of decomposing organic matter. Additionally, it serves as a crucial starter in food fermentation and can act as a pathogen causing mucormycosis in humans and animals. In this study, two distinct endofungal bacteria (EFBs), associated with individual strains of R. arrhizus, were identified using live/dead staining, fluorescence in situ hybridization, transmission electron microscopy, and 16S rDNA sequencing. The roles of these bacteria were elucidated through antibiotic treatment, pure cultivation, and comparative genomics. The bacterial endosymbionts, Pandoraea sputorum EFB03792 and Mycetohabitans endofungorum EFB03829, were purified from the host fungal strains R. arrhizus XY03792 and XY03829, respectively. Notably, this study marks the first report of Pandoraea as an EFB genus. Compared to its free-living counterparts, P. sputorum EFB03792 exhibited 28 specific virulence factor-related genes, six specific CE10 family genes, and 74 genes associated with type III secretion system (T3SS), emphasizing its pivotal role in invasion and colonization. Furthermore, this study introduces R. arrhizus as a new host for EFB M. endofungorum, with EFB contributing to host sporulation. Despite a visibly reduced genome, M. endofungorum EFB03829 displayed a substantial number of virulence factor-related genes, CE10 family genes, T3SS genes, mobile elements, and significant gene rearrangement. While EFBs have been previously identified in R. arrhizus, their toxin-producing potential in food fermentation has not been explored until this study. The discovery of these two new EFBs highlights their potential for toxin production within R. arrhizus, laying the groundwork for identifying suitable R. arrhizus strains for fermentation processes.
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Affiliation(s)
- Xiao-Ling Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Heng Zhao
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yi-Xin Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xin-Ye Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yang Jiang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Meng-Fei Tao
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Pang W, Zhang P, Zhang Y, Zhang X, Huang Y, Zhang T, Liu B. The Ectomycorrhizal Fungi and Soil Bacterial Communities of the Five Typical Tree Species in the Junzifeng National Nature Reserve, Southeast China. PLANTS (BASEL, SWITZERLAND) 2023; 12:3853. [PMID: 38005750 PMCID: PMC10675191 DOI: 10.3390/plants12223853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023]
Abstract
To explore the contribution of microorganisms to forest ecosystem function, we studied the ectomycorrhizal (ECM) fungal and soil bacterial community of the five typical tree species (Pinus massoniana, PM; Castanopsis carlesii, CC; Castanopsis eyrei, CE; Castanopsis fargesii, CF; and Keteleeria cyclolepis, KC) at the Junzifeng National Nature Reserve. The results indicated that the ECM fungal and soil bacterial diversity of CC and CF was similar, and the diversity rates of CC and CF were higher than those of PM, CE, and KC. Cenococcum geophilum and unclassified_Cortinariaceae II were the most prevalent occurring ECM fungi species in the five typical tree species, followed by unclassified_Cortinariaceae I and Lactarius atrofuscus. In bacteria, the dominant bacterial genera were Acidothermus, Bradyrhizobium, Acidibacter, Candidatus_Solibacter, Candidatus_Koribacter, Roseiarcus, and Bryobacter. EMF fungi and soil bacteria were correlated with edaphic factors, especially the soil pH, TP, and TK, caused by stand development. The results show that the community characteristics of ECM fungi and bacteria in the typical tree species of the Junzifeng National Nature Reserve reflect the critical role of soil microorganisms in stabilizing forest ecosystems.
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Affiliation(s)
- Wenbo Pang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Panpan Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Yuhu Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Xiao Zhang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yanbin Huang
- Administration Bureau of Fujian Junzifeng National Nature Reserve, Mingxi 365200, China;
| | - Taoxiang Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Bao Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
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Wilhelm RC, Muñoz-Ucros J, Weikl F, Pritsch K, Goebel M, Buckley DH, Bauerle TL. The effects of mixed-species root zones on the resistance of soil bacteria and fungi to long-term experimental and natural reductions in soil moisture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162266. [PMID: 36822431 DOI: 10.1016/j.scitotenv.2023.162266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 06/18/2023]
Abstract
Mixed forest stands tend to be more resistant to drought than species-specific stands partially due to complementarity in root ecology and physiology. We asked whether complementary differences in the drought resistance of soil microbiomes might contribute to this phenomenon. We experimented on the effects of reduced soil moisture on bacterial and fungal community composition in species-specific (single species) and mixed-species root zones of Norway spruce and European beech forests in a 5-year-old throughfall-exclusion experiment and across seasonal (spring-summer-fall) and latitudinal moisture gradients. Bacteria were most responsive to changes in soil moisture, especially members of Rhizobiales, while fungi were largely unaffected, including ectomycorrhizal fungi (EMF). Community resistance was higher in spruce relative to beech root zones, corresponding with the proportions of drought-favored (more in spruce) and drought-sensitive bacterial taxa (more in beech). The spruce soil microbiome also exhibited greater resistance to seasonal changes between spring (wettest) and fall (driest). Mixed-species root zones contained a hybrid of beech- and spruce-associated microbiomes. Several bacterial populations exhibited either enhanced resistance or greater susceptibility to drought in mixed root zones. Overall, patterns in the relative abundances of soil bacteria closely tracked moisture in seasonal and latitudinal precipitation gradients and were more predictive of soil water content than other environmental variables. We conclude that complementary differences in the drought resistance of soil microbiomes can occur and the likeliest form of complementarity in mixed-root zones coincides with the enrichment of drought-tolerant bacteria associated with spruce and the sustenance of EMF by beech.
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Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA; Agronomy Department, Lilly Hall of Life Sciences, Purdue University, West Lafayette, IN, 47904, USA
| | - Juana Muñoz-Ucros
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Fabian Weikl
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany; Technical University of Munich, Professorship of Land Surface Atmosphere Interactions, Freising, Germany
| | - Karin Pritsch
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marc Goebel
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Taryn L Bauerle
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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Rivera-Orduña FN, Pineda-Mendoza RM, Vega-Correa B, López MF, Cano-Ramírez C, Zhang XX, Chen WF, Zúñiga G. A polyphasic taxonomy analysis reveals the presence of an ecotype of Rahnella contaminans associated with the gut of Dendroctonus-bark beetles. Front Microbiol 2023; 14:1171164. [PMID: 37180241 PMCID: PMC10174453 DOI: 10.3389/fmicb.2023.1171164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
Species belonging to the genus Rahnella are dominant members of the core gut bacteriome of Dendroctonus-bark beetles, a group of insects that includes the most destructive agents of pine forest in North and Central America, and Eurasia. From 300 isolates recovered from the gut of these beetles, 10 were selected to describe an ecotype of Rahnella contaminans. The polyphasic approach conducted with these isolates included phenotypic characteristics, fatty acid analysis, 16S rRNA gene, multilocus sequence analyses (gyrB, rpoB, infB, and atpD genes), and complete genome sequencing of two isolates, ChDrAdgB13 and JaDmexAd06, representative of the studied set. Phenotypic characterization, chemotaxonomic analysis, phylogenetic analyses of the 16S rRNA gene, and multilocus sequence analysis showed that these isolates belonged to Rahnella contaminans. The G + C content of the genome of ChDrAdgB13 (52.8%) and JaDmexAd06 (52.9%) was similar to those from other Rahnella species. The ANI between ChdrAdgB13 and JaDmexAd06 and Rahnella species including R. contaminans, varied from 84.02 to 99.18%. The phylogenomic analysis showed that both strains integrated a consistent and well-defined cluster, together with R. contaminans. A noteworthy observation is the presence of peritrichous flagella and fimbriae in the strains ChDrAdgB13 and JaDmexAd06. The in silico analysis of genes encoding the flagellar system of these strains and Rahnella species showed the presence of flag-1 primary system encoding peritrichous flagella, as well as fimbriae genes from the families type 1, α, β and σ mainly encoding chaperone/usher fimbriae and other uncharacterized families. All this evidence indicates that isolates from the gut of Dendroctonus-bark beetles are an ecotype of R. contaminans, which is dominant and persistent in all developmental stages of these bark beetles and one of the main members of their core gut bacteriome.
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Affiliation(s)
- Flor N. Rivera-Orduña
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Rosa María Pineda-Mendoza
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Brenda Vega-Correa
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - María Fernanda López
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Claudia Cano-Ramírez
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Xiao Xia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wen Feng Chen
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Gerardo Zúñiga
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
- *Correspondence: Gerardo Zúñiga,
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Huang L, Li Y, Yuan J, Wan S, Colinas C, He X, Shi X, Wang Y, Yu F. Tuber indicum and T. lijiangense colonization differentially regulates plant physiological responses and mycorrhizosphere bacterial community of Castanopsis rockii seedlings. FRONTIERS IN PLANT SCIENCE 2023; 14:1134446. [PMID: 37123847 PMCID: PMC10130384 DOI: 10.3389/fpls.2023.1134446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Abstract
Black truffles and white truffles are widely studied around the world, but their effects on plant growth and physiological responses, and on the mycorrhizosphere bacterial community of the host plant remain unclear. Here, mycorrhizal colonization of Castanopsis rockii by Tuber indicum (Chinese black truffle) and T. lijiangense (Chinese white truffle), respectively, was induced in a greenhouse study, and their effects on host growth, physiological responses and mycorrhizosphere bacterial communities were compared. The results show that colonization of both Tuber species significantly increased leaf photosynthetic rate, leaf P concentration and mycorrhizosphere acid phosphatase activity, as well as richness of mycorrhizosphere bacterial communities of C. rockii seedlings. However, T. indicum colonization on the one hand significantly decreased tartrate content, bacterial acid phosphatase, phoC gene abundance in the mycorrhizosphere, and peroxidase (POD) activity of ectomycorrhizal root tips, but on the other hand increased mycorrhizosphere pH and superoxide dismutase (SOD) of ectomycorrhizal root tips, compared to T. lijiangense colonization. Moreover, principal coordinate and β-diversity analyses show significant differences in mycorrhizosphere bacterial community composition between T. indicum and T. lijiangese colonized C. rockii seedlings. Finally, the relative abundance of the bacterium Agromyces cerinus significantly correlated to mycorrhizosphere acid phosphatase activity and leaf P concentration, suggesting that this bacterium might play an important role in P mobilization and acquisition. Overall, these results suggest that T. indicum and T. lijiangense differently regulate their host plant's physiological responses and mycorrhizosphere bacterial community.
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Affiliation(s)
- Lanlan Huang
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yongmei Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Jing Yuan
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Shanping Wan
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Carlos Colinas
- Department of Crop and Forest Science, University of Lleida, Lleida, Spain
| | - Xinhua He
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Centre of Excellence for Soil Biology, College of Resources and Environment, and Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, China
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Xiaofei Shi
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Guizhou Kangqunyuan Biotechnology Co., LTD, Liupanshui, Guizhou, China
| | - Yanliang Wang
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- *Correspondence: Yanliang Wang, ; Fuqiang Yu,
| | - Fuqiang Yu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- *Correspondence: Yanliang Wang, ; Fuqiang Yu,
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Transcriptional Profiles of a Foliar Fungal Endophyte ( Pestalotiopsis, Ascomycota) and Its Bacterial Symbiont ( Luteibacter, Gammaproteobacteria) Reveal Sulfur Exchange and Growth Regulation during Early Phases of Symbiotic Interaction. mSystems 2022; 7:e0009122. [PMID: 35293790 PMCID: PMC9040847 DOI: 10.1128/msystems.00091-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Symbiosis with bacteria is widespread among eukaryotes, including fungi. Bacteria that live within fungal mycelia (endohyphal bacteria) occur in many plant-associated fungi, including diverse Mucoromycota and Dikarya. Pestalotiopsis sp. strain 9143 is a filamentous ascomycete isolated originally as a foliar endophyte of Platycladus orientalis (Cupressaceae). It is infected naturally with the endohyphal bacterium Luteibacter sp. strain 9143, which influences auxin and enzyme production by its fungal host. Previous studies have used transcriptomics to examine similar symbioses between endohyphal bacteria and root-associated fungi such as arbuscular mycorrhizal fungi and plant pathogens. However, currently there are no gene expression studies of endohyphal bacteria of Ascomycota, the most species-rich fungal phylum. To begin to understand such symbioses, we developed methods for assessing gene expression by Pestalotiopsis sp. and Luteibacter sp. when grown in coculture and when each was grown axenically. Our assays showed that the density of Luteibacter sp. in coculture was greater than in axenic culture, but the opposite was true for Pestalotiopsis sp. Dual-transcriptome sequencing (RNA-seq) data demonstrate that growing in coculture modulates developmental and metabolic processes in both the fungus and bacterium, potentially through changes in the balance of organic sulfur via methionine acquisition. Our analyses also suggest an unexpected, potential role of the bacterial type VI secretion system in symbiosis establishment, expanding current understanding of the scope and dynamics of fungal-bacterial symbioses. IMPORTANCE Interactions between microbes and their hosts have important outcomes for host and environmental health. Foliar fungal endophytes that infect healthy plants can harbor facultative endosymbionts called endohyphal bacteria, which can influence the outcome of plant-fungus interactions. These bacterial-fungal interactions can be influential but are poorly understood, particularly from a transcriptome perspective. Here, we report on a comparative, dual-RNA-seq study examining the gene expression patterns of a foliar fungal endophyte and a facultative endohyphal bacterium when cultured together versus separately. Our findings support a role for the fungus in providing organic sulfur to the bacterium, potentially through methionine acquisition, and the potential involvement of a bacterial type VI secretion system in symbiosis establishment. This work adds to the growing body of literature characterizing endohyphal bacterial-fungal interactions, with a focus on a model facultative bacterial-fungal symbiosis in two species-rich lineages, the Ascomycota and Proteobacteria.
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Biodiversity and Metabolic Potential of Bacteria in Bulk Soil from the Peri-Root Zone of Black Alder (Alnus glutinosa), Silver Birch (Betula pendula) and Scots Pine (Pinus sylvestris). Int J Mol Sci 2022; 23:ijms23052633. [PMID: 35269777 PMCID: PMC8910737 DOI: 10.3390/ijms23052633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
The formation of specific features of forest habitats is determined by the physical, chemical, and biological properties of the soil. The aim of the study was to determine the structural and functional biodiversity of soil microorganisms inhabiting the bulk soil from the peri-root zone of three tree species: Alnus glutinosa, Betula pendula, and Pinus sylvestris. Soil samples were collected from a semi-deciduous forest located in an area belonging to the Agricultural Experimental Station IUNG-PIB in Osiny, Poland. The basic chemical and biological parameters of soils were determined, as well as the structural diversity of bacteria (16S ribosomal RNA (rRNA) sequencing) and the metabolic profile of microorganisms (Biolog EcoPlates). The bulk soils collected from peri-root zone of A. glutinosa were characterized by the highest enzymatic activities. Moreover, the highest metabolic activities on EcoPlates were observed in bulk soil collected in the proximity of the root system the A. glutinosa and B. pendula. In turn, the bulk soil collected from peri-root zone of P. sylvestris had much lower biological activity and a lower metabolic potential. The most metabolized compounds were L-phenylalanine, L-asparagine, D-mannitol, and gamma-hydroxy-butyric acid. The highest values of the diversity indicators were in the soils collected in the proximity of the root system of A. glutinosa and B. pendula. The bulk soil collected from P. sylvestris peri-root zone was characterized by the lowest Shannon’s diversity index. In turn, the evenness index (E) was the highest in soils collected from the P. sylvestris, which indicated significantly lower diversity in these soils. The most abundant classes of bacteria in all samples were Actinobacteria, Acidobacteria_Gp1, and Alphaproteobacteria. The classes Bacilli, Thermoleophilia, Betaproteobacteria, and Subdivision3 were dominant in the B. pendula bulk soil. Streptosporangiales was the most significantly enriched order in the B. pendula soil compared with the A. glutinosa and P. sylvestris. There was a significantly higher mean proportion of aerobic nitrite oxidation, nitrate reduction, sulphate respiration, and sulfur compound respiration in the bulk soil of peri-root zone of A. glutinosa. Our research confirms that the evaluation of soil biodiversity and metabolic potential of bacteria can be of great assistance in a quality and health control tool in the soils of forested areas and in the forest production. Identification of bacteria that promote plant growth and have a high biotechnological potential can be assume a substantial improvement in the ecosystem and use of the forest land.
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Bastías DA, Johnson LJ, Card SD. Symbiotic bacteria of plant-associated fungi: friends or foes? CURRENT OPINION IN PLANT BIOLOGY 2020; 56:1-8. [PMID: 31786411 DOI: 10.1016/j.pbi.2019.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
Many bacteria form symbiotic associations with plant-associated fungi. The effects of these symbionts on host fitness usually depend on symbiont or host genotypes and environmental conditions. However, bacterial endosymbionts, that is those living within fungal cells, may positively regulate host performance as their survival is often heavily dependent on host fitness. Contrary to this, bacteria that establish ectosymbiotic associations with fungi, that is those located on the hyphal surface or in close vicinity to fungal mycelia, may not have an apparent net effect on fungal performance due to the low level of fitness dependency on their host. Our analysis supports the hypothesis that endosymbiotic bacteria of fungi are beneficial symbionts, and that effects of ectosymbiotic bacteria on fungal performance depends on the bacterial type involved in the interaction (e.g. helper versus pathogen of fungi). Ecological scenarios, where the presence of beneficial bacterial endosymbionts of fungi could be compromised, are also discussed.
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Affiliation(s)
- Daniel A Bastías
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
| | - Linda J Johnson
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Stuart D Card
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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Garcia-Lemos AM, Gobbi A, Nicolaisen MH, Hansen LH, Roitsch T, Veierskov B, Nybroe O. Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development. Front Microbiol 2020; 11:198. [PMID: 32194515 PMCID: PMC7064441 DOI: 10.3389/fmicb.2020.00198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/28/2020] [Indexed: 01/01/2023] Open
Abstract
Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growth–promoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.
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Affiliation(s)
- Adriana M Garcia-Lemos
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Alex Gobbi
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Mette Haubjerg Nicolaisen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark.,Department of Adaptive Biotechnologies, Global Change Research Institute, CAS, Brno, Czechia
| | - Bjarke Veierskov
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ole Nybroe
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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11
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Garcia-Lemos AM, Großkinsky DK, Stokholm MS, Lund OS, Nicolaisen MH, Roitsch TG, Veierskov B, Nybroe O. Root-Associated Microbial Communities of Abies nordmanniana: Insights Into Interactions of Microbial Communities With Antioxidative Enzymes and Plant Growth. Front Microbiol 2019; 10:1937. [PMID: 31507556 PMCID: PMC6714061 DOI: 10.3389/fmicb.2019.01937] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
Abies nordmanniana is a major Christmas tree species in Europe, but their uneven and prolonged growth slows down their production. By a 16S and 18S rRNA gene amplicon sequencing approach, we performed a characterization of root-associated bacterial and fungal communities for three-year-old A. nordmanniana plants collected from two nurseries in Denmark and Germany and displaying different growth patterns (small versus tall plants). Proteobacteria had the highest relative abundance at both sampling sites and plant sizes, and Ascomycota was the most abundant fungal phylum. At the order level, Acidobacteriales, Actinomycetales, Burkholderiales, Rhizobiales, and Xanthomonadales represented the bacterial core microbiome of A. nordmanniana, independently of the sampling site or plant size, while the fungal core microbiome included members of the Agaricales, Hypocreales, and Pezizales. Principal Coordinate Analysis indicated that both bacterial and fungal communities clustered according to the sampling site pointing to the significance of soil characteristics and climatic conditions for the composition of root-associated microbial communities. Major differences between communities from tall and small plants were a dominance of the potential pathogen Fusarium (Hypocreales) in the small plants from Germany, while Agaricales, that includes reported beneficial ectomycorrhizal fungi, dominated in the tall plants. An evaluation of plant root antioxidative enzyme profiles showed higher levels of the antioxidative enzymes ascorbate peroxidase, peroxidase, and superoxide dismutase in small plants compared to tall plants. We suggest that the higher antioxidative enzyme activities combined with the growth arrest phenotype indicate higher oxidative stress levels in the small plants. Additionally, the correlations between the relative abundances of specific taxa of the microbiome with the plant antioxidative enzyme profiles were established. The main result was that many more bacterial taxa correlated positively than negatively with one or more antioxidative enzyme activity. This may suggest that the ability of bacteria to increase plant antioxidative enzyme defenses is widespread.
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Affiliation(s)
- Adriana M. Garcia-Lemos
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Dominik K. Großkinsky
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Michaela S. Stokholm
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ole S. Lund
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Mette Haubjerg Nicolaisen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Thomas G. Roitsch
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Bjarke Veierskov
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ole Nybroe
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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12
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Sakoda S, Aisu K, Imagami H, Matsuda Y. Comparison of Actinomycete Community Composition on the Surface and Inside of Japanese Black Pine (Pinus thunbergii) Tree Roots Colonized by the Ectomycorrhizal Fungus Cenococcum geophilum. MICROBIAL ECOLOGY 2019; 77:370-379. [PMID: 29946784 DOI: 10.1007/s00248-018-1221-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
Various bacteria are associated with ectomycorrhizal roots, which are symbiotic complexes formed between plant roots and fungi. Among these associated bacteria, actinomycetes have received attention for their ubiquity and diverse roles in forest ecosystems. Here, to examine the association of actinomycetes with ectomycorrhizal root tips, we compared the bacterial and actinomycete communities on the surface and inside of root tips of coastal Japanese black pine (Pinus thunbergii) colonized by the fungus Cenococcum geophilum. Next-generation sequences of 16S rDNA of bacteria communities using the Ion Torrent Personal Genome Machine showed that the number of bacterial classes in the surface of C. geophilum ECM roots was significantly higher than that in non-ECM roots. The bacterial community structure of surface, inside, and non-ECM roots was significantly discriminated each other. For an isolation method, a total of 762 and 335 actinomycete isolates were obtained from the surface and inside of the roots, respectively. In addition, the isolation ratio of actinomycetes in these root tips varied depending on the age of the tree and the season. Identification of the isolates based on partial 16S rDNA sequencing revealed that the isolates belonged to nine genera of the order Actinomycetales. On the surface of the roots, most of the isolates belonged to genus Streptomyces (90.4%); inside of the roots, most of the isolates belonged to genus Actinoallomurus (40.0%), which is a relatively new taxon. Our results suggest that actinomycetes as well as bacteria are ubiquitously associated with C. geophilum ectomycorrhizal roots of P. thunbergii, although their communities can vary either surface or inside of individual root tips.
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Affiliation(s)
- Shoyo Sakoda
- Laboratory of Forest Mycology, Graduate School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan.
| | - Kana Aisu
- Laboratory of Forest Pathology and Mycology, Faculty of Bioresources, Mie University, Tsu, Japan
| | - Hiroki Imagami
- Laboratory of Forest Pathology and Mycology, Faculty of Bioresources, Mie University, Tsu, Japan
| | - Yosuke Matsuda
- Laboratory of Forest Mycology, Graduate School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan.
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13
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Obase K. Bacterial community on ectomycorrhizal roots of Laccaria laccata in a chestnut plantation. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2018.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Paul C, Filippidou S, Jamil I, Kooli W, House GL, Estoppey A, Hayoz M, Junier T, Palmieri F, Wunderlin T, Lehmann A, Bindschedler S, Vennemann T, Chain PSG, Junier P. Bacterial spores, from ecology to biotechnology. ADVANCES IN APPLIED MICROBIOLOGY 2018; 106:79-111. [PMID: 30798805 DOI: 10.1016/bs.aambs.2018.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The production of a highly specialized cell structure called a spore is a remarkable example of a survival strategy displayed by bacteria in response to challenging environmental conditions. The detailed analysis and description of the process of sporulation in selected model organisms have generated a solid background to understand the cellular processes leading to the formation of this specialized cell. However, much less is known regarding the ecology of spore-formers. This research gap needs to be filled as the feature of resistance has important implications not only on the survival of spore-formers and their ecology, but also on the use of spores for environmental prospection and biotechnological applications.
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Affiliation(s)
- Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Sevasti Filippidou
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Isha Jamil
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Wafa Kooli
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mathilda Hayoz
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Tina Wunderlin
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Anael Lehmann
- Laboratory of stable isotope geochemistry, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Torsten Vennemann
- Laboratory of stable isotope geochemistry, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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15
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Root-associated bacteria influencing mycelial growth of Tricholoma matsutake (pine mushroom). J Microbiol 2018; 56:399-407. [PMID: 29858828 DOI: 10.1007/s12275-018-7491-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/19/2018] [Accepted: 04/06/2018] [Indexed: 10/14/2022]
Abstract
Tricholoma matsutake is an ectomycorrhizal fungus usually associated with Pinus densiflora in South Korea. Fruiting bodies (mushrooms) of T. matsutake are economically important due to their attractive aroma; yet, T. matsutake is uncultivatable and its habitat is rapidly being eradicated due to global climate change. Root-associated bacteria can influence the growth of ectomycorrhizal fungi that co-exist in the host rhizosphere and distinctive bacterial communities are associated with T. matsutake. In this study, we investigated how these bacterial communities affect T. matsutake growth by isolating bacteria from the roots of P. densiflora colonized by ectomycorrhizae of T. matsutake and co-culturing rootassociated bacteria with T. matsutake isolates. Thirteen species of bacteria (27 isolates) were found in pine roots, all belonging to the orders Bacillales or Burkholderiales. Two species in the genus Paenibacillus promoted the growth of T. matsutake in glucose poor conditions, likely using soluble metabolites. In contrast, other bacteria suppressed the growth of T. matsutake using both soluble and volatile metabolites. Antifungal activity was more frequent in glucose poor conditions. In general, pine rhizospheres harbored many bacteria that had a negative impact on T. matsutake growth and the few Paenibacillus species that promoted T. matsutake growth. Paenibacillus species, therefore, may represent a promising resource toward successful cultivation of T. matsutake.
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16
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Epps MJ, Arnold AE. Quantifying beetle-macrofungal associations in a temperate biodiversity hot spot. Mycologia 2018; 110:269-285. [DOI: 10.1080/00275514.2018.1430439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Mary Jane Epps
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona 85721
| | - A. Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona 85721
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17
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Wang R, Dong L, Chen Y, Qu L, Wang Q, Zhang Y. Esteya Vermicola, a Nematophagous Fungus Attacking the Pine Wood Nematode, Harbors a Bacterial Endosymbiont Affiliated with Gammaproteobacteria. Microbes Environ 2017; 32:201-209. [PMID: 28824050 PMCID: PMC5606689 DOI: 10.1264/jsme2.me16167] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/19/2017] [Indexed: 11/12/2022] Open
Abstract
Symbioses have played pivotal roles in biological, ecological, and evolutionary diversification. Symbiotic bacteria affect the biology of hosts in a number of ways. Esteya vermicola, an endoparasitic nematophagous fungus, has high infectivity in the pine wood nematode (PWN), which causes devastating ecological damage and economic losses in Asia and Europe. An integration of molecular, phylogenetic, and morphological analyses revealed that surface-sterilized E. vermicola with septate hyphae from different geographic locations harbor bacterial endosymbionts. 16S rRNA gene sequences from four fungal strains all clustered in a well-supported monophyletic clade that was the most closely related to Pseudomonas stutzeri and affiliated with Gammaproteobacteria. The existence and intracellular location of endobacteria was revealed by fluorescent in situ hybridization (FISH). Our results showed that endobacteria were coccoid, vertically inherited, as yet uncultured, and essential symbionts. Ultrastructural observations indicated that young and old endobacteria differed in cell size, cell wall thickness, and the degree of reproduction. The results of the present study provide a fundamental understanding of the endobacteria inside E. vermicola and raise questions regarding the impact of endobacteria on the biology, ecology, and evolution of their fungal host.
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Affiliation(s)
- Ruizhen Wang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of ForestryChina
| | - Leiming Dong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of ForestryChina
| | - Yuequ Chen
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of ForestryChina
- Forestry Resources Protection Institute, Jilin Provincial Academy of Forestry SciencesChina
| | - Liangjian Qu
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of ForestryChina
| | - Qinghua Wang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of ForestryChina
| | - Yongan Zhang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of ForestryChina
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18
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Martinez-Klimova E, Rodríguez-Peña K, Sánchez S. Endophytes as sources of antibiotics. Biochem Pharmacol 2017; 134:1-17. [DOI: 10.1016/j.bcp.2016.10.010] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/25/2016] [Indexed: 11/27/2022]
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19
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Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
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20
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Zagryadskaya YA. Comparative characteristics of the bacterial complex in the hyphosphere of basidial macromycetes. BIOL BULL+ 2017. [DOI: 10.1134/s1062359017030116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change. Microbiol Mol Biol Rev 2017; 81:81/2/e00063-16. [PMID: 28404790 DOI: 10.1128/mmbr.00063-16] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.
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22
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Shaffer JP, U'Ren JM, Gallery RE, Baltrus DA, Arnold AE. An Endohyphal Bacterium ( Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum ( F. solani Species Complex, Nectriaceae). Front Microbiol 2017; 8:350. [PMID: 28382021 PMCID: PMC5361657 DOI: 10.3389/fmicb.2017.00350] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 02/20/2017] [Indexed: 01/12/2023] Open
Abstract
Bacterial endosymbionts occur in diverse fungi, including members of many lineages of Ascomycota that inhabit living plants. These endosymbiotic bacteria (endohyphal bacteria, EHB) often can be removed from living fungi by antibiotic treatment, providing an opportunity to assess their effects on functional traits of their fungal hosts. We examined the effects of an endohyphal bacterium (Chitinophaga sp., Bacteroidetes) on substrate use by its host, a seed-associated strain of the fungus Fusarium keratoplasticum, by comparing growth between naturally infected and cured fungal strains across 95 carbon sources with a Biolog® phenotypic microarray. Across the majority of substrates (62%), the strain harboring the bacterium significantly outperformed the cured strain as measured by respiration and hyphal density. These substrates included many that are important for plant- and seed-fungus interactions, such as D-trehalose, myo-inositol, and sucrose, highlighting the potential influence of EHB on the breadth and efficiency of substrate use by an important Fusarium species. Cases in which the cured strain outperformed the strain harboring the bacterium were observed in only 5% of substrates. We propose that additive or synergistic substrate use by the fungus-bacterium pair enhances fungal growth in this association. More generally, alteration of the breadth or efficiency of substrate use by dispensable EHB may change fungal niches in short timeframes, potentially shaping fungal ecology and the outcomes of fungal-host interactions.
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Affiliation(s)
| | - Jana M U'Ren
- School of Plant Sciences, University of ArizonaTucson, AZ, USA; Department of Agricultural and Biosystems Engineering, University of ArizonaTucson, AZ, USA
| | - Rachel E Gallery
- School of Natural Resources and the Environment, University of ArizonaTucson, AZ, USA; Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
| | - David A Baltrus
- School of Plant Sciences, University of Arizona Tucson, AZ, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of ArizonaTucson, AZ, USA; Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
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23
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Halsey JA, de Cássia Pereira E Silva M, Andreote FD. Bacterial selection by mycospheres of Atlantic Rainforest mushrooms. Antonie van Leeuwenhoek 2016; 109:1353-65. [PMID: 27411813 DOI: 10.1007/s10482-016-0734-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/05/2016] [Indexed: 01/12/2023]
Abstract
This study focuses on the selection exerted on bacterial communities in the mycospheres of mushrooms collected in the Brazilian Atlantic Rainforest. A total of 24 paired samples (bulk soil vs. mycosphere) were assessed to investigate potential interactions between fungi and bacteria present in fungal mycospheres. Prevalent fungal families were identified as Marasmiaceae and Lepiotaceae (both Basidiomycota) based on ITS partial sequencing. We used culture-independent techniques to analyze bacterial DNA from soil and mycosphere samples. Bacterial communities in the samples were distinguished based on overall bacterial, alphaproteobacterial, and betaproteobacterial PCR-DGGE patterns, which were different in fungi belonging to different taxa. These results were confirmed by pyrosequencing the V4 region of the 16S rRNA gene (based on five bulk soil vs. mycosphere pairs), which revealed the most responsive bacterial families in the different conditions generated beneath the mushrooms, identified as Bradyrhizobiaceae, Burkholderiaceae, and Pseudomonadaceae. The bacterial families Acetobacteraceae, Chrhoniobacteraceae, Planctomycetaceae, Conexibacteraceae, and Burkholderiaceae were found in all mycosphere samples, composing the core mycosphere microbiome. Similarly, some bacterial groups identified as Koribacteriaceae, Acidobacteria (Solibacteriaceae) and an unclassified group of Acidobacteria were preferentially present in the bulk soil samples (found in all of them). In this study we depict the mycosphere effect exerted by mushrooms inhabiting the Brazilian Atlantic Rainforest, and identify the bacteria with highest response to such a specific niche, possibly indicating the role bacteria play in mushroom development and dissemination within this yet-unexplored environment.
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Affiliation(s)
- Joshua Andrew Halsey
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Avenida Pádua Dias, 11, Piracicaba, SP, CEP 13418-900, Brazil
| | - Michele de Cássia Pereira E Silva
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Avenida Pádua Dias, 11, Piracicaba, SP, CEP 13418-900, Brazil.
| | - Fernando Dini Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Avenida Pádua Dias, 11, Piracicaba, SP, CEP 13418-900, Brazil
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24
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Arendt KR, Hockett KL, Araldi-Brondolo SJ, Baltrus DA, Arnold AE. Isolation of Endohyphal Bacteria from Foliar Ascomycota and In Vitro Establishment of Their Symbiotic Associations. Appl Environ Microbiol 2016; 82:2943-2949. [PMID: 26969692 PMCID: PMC4959084 DOI: 10.1128/aem.00452-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/03/2016] [Indexed: 12/16/2022] Open
Abstract
Endohyphal bacteria (EHB) can influence fungal phenotypes and shape the outcomes of plant-fungal interactions. Previous work has suggested that EHB form facultative associations with many foliar fungi in the Ascomycota. These bacteria can be isolated in culture, and fungi can be cured of EHB using antibiotics. Here, we present methods for successfully introducing EHB into axenic mycelia of strains representing two classes of Ascomycota. We first establish in vitro conditions favoring reintroduction of two strains of EHB (Luteibacter sp.) into axenic cultures of their original fungal hosts, focusing on fungi isolated from healthy plant tissue as endophytes: Microdiplodia sp. (Dothideomycetes) and Pestalotiopsis sp. (Sordariomycetes). We then demonstrate that these EHB can be introduced into a novel fungal host under the same conditions, successfully transferring EHB between fungi representing different classes. Finally, we manipulate conditions to optimize reintroduction in a focal EHB-fungal association. We show that EHB infections were initiated and maintained more often under low-nutrient culture conditions and when EHB and fungal hyphae were washed with MgCl2 prior to reassociation. Our study provides new methods for experimental assessment of the effects of EHB on fungal phenotypes and shows how the identity of the fungal host and growth conditions can define the establishment of these widespread and important symbioses.
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Affiliation(s)
- Kayla R Arendt
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Kevin L Hockett
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | | | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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Nguyen NH, Bruns TD. The Microbiome of Pinus muricata Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses. MICROBIAL ECOLOGY 2015; 69:914-921. [PMID: 25687126 DOI: 10.1007/s00248-015-0574-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 01/22/2015] [Indexed: 06/04/2023]
Abstract
Bacteria have been observed to grow with fungi, and those that associate with ectomycorrhizal fungi have often been thought of as symbionts that may either increase or decrease ectomycorrhizal formation rate or provide other unaccounted benefits. To explore this symbiosis from a community ecology perspective, we sampled ectomycorrhizal root tips over a 3-year period and used 454 pyrosequencing to identify the bacteria that live inside the ectomycorrhizal root tips. The results showed that fungal community composition within the same soil core and fungal taxonomic identity had a stronger effect on bacterial community composition than sample year or site. Members of the Burkholderiales and Rhizobiales were most highly represented, reflecting many previous reports of these bacteria in association with fungi. The repeated occurrences of these two bacterial orders suggest that they may be symbiotic with their fungal hosts, although the nature of such mechanisms, be it symbiotic diazotrophy or otherwise, remains to be thoroughly tested.
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Affiliation(s)
- Nhu H Nguyen
- Department of Plant Biology, University of Minnesota, St. Paul, MN, 55108, USA,
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26
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Churchland C, Grayston SJ. Specificity of plant-microbe interactions in the tree mycorrhizosphere biome and consequences for soil C cycling. Front Microbiol 2014; 5:261. [PMID: 24917855 PMCID: PMC4042908 DOI: 10.3389/fmicb.2014.00261] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 05/13/2014] [Indexed: 01/22/2023] Open
Abstract
Mycorrhizal associations are ubiquitous and form a substantial component of the microbial biomass in forest ecosystems and fluxes of C to these belowground organisms account for a substantial portion of carbon assimilated by forest vegetation. Climate change has been predicted to alter belowground plant-allocated C which may cause compositional shifts in soil microbial communities, and it has been hypothesized that this community change will influence C mitigation in forest ecosystems. Some 10,000 species of ectomycorrhizal fungi are currently recognized, some of which are host specific and will only associate with a single tree species, for example, Suillus grevillei with larch. Mycorrhizae are a strong sink for plant C, differences in mycorrhizal anatomy, particularly the presence and extent of emanating hyphae, can affect the amount of plant C allocated to these assemblages. Mycorrhizal morphology affects not only spatial distribution of C in forests, but also differences in the longevity of these diverse structures may have important consequences for C sequestration in soil. Mycorrhizal growth form has been used to group fungi into distinctive functional groups that vary qualitatively and spatially in their foraging and nutrient acquiring potential. Through new genomic techniques we are beginning to understand the mechanisms involved in the specificity and selection of ectomycorrhizal associations though much less is known about arbuscular mycorrhizal associations. In this review we examine evidence for tree species- mycorrhizal specificity, and the mechanisms involved (e.g., signal compounds). We also explore what is known about the effects of these associations and interactions with other soil organisms on the quality and quantity of C flow into the mycorrhizosphere (the area under the influence of mycorrhizal root tips), including spatial and seasonal variations. The enormity of the mycorrhizosphere biome in forests and its potential to sequester substantial C belowground highlights the vital importance of increasing our knowledge of the dynamics of the different mycorrhizal functional groups in diverse forests.
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Affiliation(s)
| | - Sue J. Grayston
- Belowground Ecosystem Group, Department of Forest and Conservation Sciences, University of British ColumbiaVancouver, BC, Canada
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Vik U, Logares R, Blaalid R, Halvorsen R, Carlsen T, Bakke I, Kolstø AB, Økstad OA, Kauserud H. Different bacterial communities in ectomycorrhizae and surrounding soil. Sci Rep 2013; 3:3471. [PMID: 24326907 PMCID: PMC3858787 DOI: 10.1038/srep03471] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 11/25/2013] [Indexed: 02/01/2023] Open
Abstract
Several eukaryotic symbioses have shown to host a rich diversity of prokaryotes that interact with their hosts. Here, we study bacterial communities associated with ectomycorrhizal root systems of Bistorta vivipara compared to bacterial communities in bulk soil using pyrosequencing of 16S rRNA amplicons. A high richness of Operational Taxonomic Units (OTUs) was found in plant roots (3,571 OTUs) and surrounding soil (3,476 OTUs). The community composition differed markedly between these two environments. Actinobacteria, Armatimonadetes, Chloroflexi and OTUs unclassified at phylum level were significantly more abundant in plant roots than in soil. A large proportion of the OTUs, especially those in plant roots, presented low similarity to Sanger 16S rRNA reference sequences, suggesting novel bacterial diversity in ectomycorrhizae. Furthermore, the bacterial communities of the plant roots were spatially structured up to a distance of 60 cm, which may be explained by bacteria using fungal hyphae as a transport vector. The analyzed ectomycorrhizae presents a distinct microbiome, which likely influence the functioning of the plant-fungus symbiosis.
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Affiliation(s)
- Unni Vik
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, P.O. 1066 Blindern, 0316 Oslo, Norway
| | - Ramiro Logares
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003 Barcelona, Spain
| | - Rakel Blaalid
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, P.O. 1066 Blindern, 0316 Oslo, Norway
| | - Rune Halvorsen
- Natural History Museum, Department of research and collections, University of Oslo, P.O. 1172 Blindern, 0318 OSLO, Norway
| | - Tor Carlsen
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, P.O. 1066 Blindern, 0316 Oslo, Norway
| | - Ingrid Bakke
- NTNU/Norwegian University of Science and Technology, Department of Biotechnology, Sem Sælands vei 8, 7491 Trondheim, Norway
| | - Anne-Brit Kolstø
- Laboratory for Microbial Dynamics, School of Pharmacy, University of Oslo, P.O. 1068 Blindern, 0316 Oslo, Norway
| | - Ole Andreas Økstad
- Laboratory for Microbial Dynamics, School of Pharmacy, University of Oslo, P.O. 1068 Blindern, 0316 Oslo, Norway
| | - Håvard Kauserud
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, P.O. 1066 Blindern, 0316 Oslo, Norway
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Abstract
Rahnella aquatilis CIP 78.65 is a gammaproteobacterium isolated from a drinking water source in Lille, France. Here we report the complete genome sequence of Rahnella aquatilis CIP 78.65, the type strain of R. aquatilis.
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Morales-Jiménez J, Zúñiga G, Ramírez-Saad HC, Hernández-Rodríguez C. Gut-associated bacteria throughout the life cycle of the bark beetle Dendroctonus rhizophagus Thomas and Bright (Curculionidae: Scolytinae) and their cellulolytic activities. MICROBIAL ECOLOGY 2012; 64:268-78. [PMID: 22234511 DOI: 10.1007/s00248-011-9999-0] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 12/13/2011] [Indexed: 05/25/2023]
Abstract
Dendroctonus rhizophagus Thomas and Bright (Curculionidae: Scolytinae) is an endemic economically important insect of the Sierra Madre Occidental in Mexico. This bark beetle has an atypical behavior within the genus because just one beetle couple colonizes and kills seedlings and young trees of 11 pine species. In this work, the bacteria associated with the Dendroctonus rhizophagus gut were analyzed by culture-dependent and culture-independent methods. Analysis of 16S rRNA sequences amplified directly from isolates of gut bacteria suggests that the bacterial community associated with Dendroctonus rhizophagus, like that of other Dendroctonus spp. and Ips pini, is limited in number. Nine bacterial genera of γ-Proteobacteria and Actinobacteria classes were detected in the gut of Dendroctonus rhizophagus. Stenotrophomonas and Rahnella genera were the most frequently found bacteria from Dendroctonus rhizophagus gut throughout their life cycle. Stenotrophomonas maltophilia, Ponticoccus gilvus, and Kocuria marina showed cellulolytic activity in vitro. Stenotrophomonas maltophilia, Rahnella aquatilis, Raoultella terrigena, Ponticoccus gilvus, and Kocuria marina associated with larvae or adults of Dendroctonus rhizophagus could be implicated in nitrogen fixation and cellulose breakdown, important roles associated to insect development and fitness, especially under the particularly difficult life conditions of this beetle.
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Affiliation(s)
- Jesús Morales-Jiménez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Distrito Federal, CP, Mexico
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Izumi H, Finlay RD. Ectomycorrhizal roots select distinctive bacterial and ascomycete communities in Swedish subarctic forests. Environ Microbiol 2010; 13:819-30. [PMID: 21176055 DOI: 10.1111/j.1462-2920.2010.02393.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Ectomycorrhizal (ECM) roots represent important niches for interactions with bacteria and ascomycete fungi, since they have a large surface area and receive a direct supply of plant assimilates from their tree hosts. We tested the hypothesis that the roots colonized by specific ECM fungi harbour distinct bacteria/ascomycete communities. Roots were collected from two different locations in a subarctic shrub forest dominated by Betula pubescens. Bacterial and ascomycete communities were analysed by PCR-DGGE and sequencing, in roots colonized by five frequently observed ECM fungi, Leccinum variicolor, Piloderma fallax, Tomentellopsis submollis, Lactarius torminosus and Pseudotomentella tristis. The bacterial communities associated with P. fallax- or P. tristis-colonized roots were distinct from those associated with roots colonized by three other ECM fungi at both sampling locations. Bacterial communities associated with T. submollis-, L. torminosus- and L. variicolor-colonized roots were more similar to each other. Lactarius- and Pseudotomentella-colonized roots hosted distinct ascomycete communities at one site while only the community associated with Lactarius was distinct at the second location. The results thus suggest that while the community structure of bacteria colonizing ECM roots can be influenced by the local soil environment, there can also be a strong selective effect of particular fungal symbionts.
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Affiliation(s)
- Hironari Izumi
- Uppsala BioCenter, Department of Forest Mycology & Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.
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Rigamonte TA, Pylro VS, Duarte GF. The role of mycorrhization helper bacteria in the establishment and action of ectomycorrhizae associations. Braz J Microbiol 2010; 41:832-40. [PMID: 24031563 PMCID: PMC3769757 DOI: 10.1590/s1517-83822010000400002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 03/02/2010] [Accepted: 04/26/2010] [Indexed: 01/18/2023] Open
Abstract
More than 95 % short roots of most terrestrial plants are colonized by mycorrhizal fungi as soon as they emerge in the upper soil profiles. The establishment of mycorrhizal association involves profound morphological and physiological changes in root and fungus. It is affected by other rhizospheric microorganisms, specifically by the bacteria. Bacteria may have developed mechanisms of selective interaction with surrounding microorganisms, with neutral or positive effects on mycorrhizal associations, but negative effect on root pathogens in general. Because of the beneficial effect of bacteria on mycorrhizae, the concept of Mycorrhization Helper Bacteria (MHB) was created. Five main actions of MHB on mycorrhizae were proposed: in the receptivity of root to the mycobiont, in root-fungus recognition, in fungal growth, in the modification of rhizospheric soil and in the germination of fungal propagules. MHB appear to develop a gradation of specificity for the mycobiont, but little or no specificity for the host plant in symbiosis. One of the main groups of MHB is the fluorescent Pseudomonas, well represented in diversity and cell density studies of mycorrhizal associations. This review covers the activity of MHB in the establishment of ectomycorrhizae, taking as model the effects of Pseudomonas sp. described in scientific literature.
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Affiliation(s)
| | - Victor Satler Pylro
- Universidade Federal de Viçosa, Departamento de Microbiologia, Viçosa, MG, Brasil
| | - Gabriela Frois Duarte
- Universidade Federal de Ouro Preto, Departamento de Ciências Biológicas, Ouro Preto, MG, Brasil
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32
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Adams AS, Adams SM, Currie CR, Gillette NE, Raffa KF. Geographic variation in bacterial communities associated with the red turpentine beetle (Coleoptera: Curculionidae). ENVIRONMENTAL ENTOMOLOGY 2010; 39:406-414. [PMID: 20388269 DOI: 10.1603/en09221] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Bacterial communities are known to play important roles in insect life histories, yet their consistency or variation across populations is poorly understood. Bacteria associated with the bark beetle Dendroctonus valens LeConte from eight populations, ranging from Wisconsin to Oregon, were evaluated and compared. We used the culture-independent technique of denaturing gradient gel electrophoresis to visualize bacterial diversity, or individual operational taxonomic units (OTUs), from individual beetles. One-way analysis of similarities was used to test for differences of bacterial communities between sites. Analysis of community profiles showed that individual beetles on average contained 10 OTUs, with frequency of association from 2 to 100% of beetles. OTU sequences most closely matched beta- and gamma-proteobacteria, and one each matched Bacilli and Actinobacteria. Several OTUs were particularly abundant, most notably an Actinobacterium from 100% and two Proteobacteria from 60% of beetles sampled. Some OTUs were similar to previously described bacteria with known biochemical capabilities and ecological functions, suggesting that some bacterial associates of D. valens may contribute to its ability to exploit a resource low in nutrients and high in defensive compounds. There were significant differences of bacterial communities between sites. The strength of these differences was positively correlated with distance between sites, although additional unexplained factors also contribute to the variation.
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Affiliation(s)
- Aaron S Adams
- Department of Entomology, University of Wisconsin, 237 Russell Labs, Madison, WI 53706, USA.
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Otsuka Y, Muramatsu Y, Nakagawa Y, Matsuda M, Nakamura M, Murata H. Burkholderia oxyphila sp. nov., a bacterium isolated from acidic forest soil that catabolizes (+)-catechin and its putative aromatic derivatives. Int J Syst Evol Microbiol 2010; 61:249-254. [PMID: 20207808 DOI: 10.1099/ijs.0.017368-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated strain OX-01(T), was isolated from acidic soil, taxonomically investigated and identified as an agent that catabolizes (+)-catechin into taxifolin. Strain OX-01(T) is a Gram-reaction-negative, aerobic, non-sporulating, non-motile and rod-shaped bacterium. 16S rRNA gene sequence analysis identified this strain as a member of the genus Burkholderia and occupying a phylogenetic position closest to, but clearly distinct from, Burkholderia sacchari. Strain OX-01(T) does not have any nif genes, which are required for N(2)-fixation, in its genome, a feature that is similar to B. sacchari, which lacks nifH, but is distinct from the N(2)-fixing features of many other phylogenetically related taxa, such as Burkholderia ferrariae, B. heleia, B. mimosarum, B. nodosa, B. silvatlantica, B. tropica and B. unamae. Strain OX-01(T) has the following chemotaxonomic characteristics: the major ubiquinone is Q-8, the DNA G+C content is 64 mol% and the major fatty acids are C(16 : 0), C(17 : 0) cyclo and C(18 : 1)ω7c. It also has a unique profile of carbohydrate utilization among other species of the genus Burkholderia. The strain cannot assimilate many pentoses, hexoses and oligosaccharides, whereas it can catabolize (+)-catechin and its putative aromatic derivatives, such as 4-hydroxy-3-methoxycinnamic acid, protocatechuic acid, p-hydroxybenzoic acid, trans-p-coumaric acid and vanillic acid. Based on its morphological, physiological and chemotaxonomic characteristics, together with DNA-DNA relatedness values and 16S rRNA gene sequence comparison data, we show that strain OX-O1(T) represents a novel species of the genus Burkholderia, for which the name Burkholderia oxyphila sp. nov. is proposed. The type strain is OX-01(T) (=NBRC 105797(T) =DSM 22550(T)).
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Affiliation(s)
- Yuichiro Otsuka
- Department of Biomass Chemistry, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, Ibaraki 305-8687, Japan
| | - Yuki Muramatsu
- Resource Collection Division, NITE Biological Resource Centre Department of Biotechnology, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Yasuyoshi Nakagawa
- Resource Collection Division, NITE Biological Resource Centre Department of Biotechnology, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Motoki Matsuda
- Toyama Prefectural University, Kurokawa 5180, Imizu, Toyama 939-0398, Japan
| | - Masaya Nakamura
- Department of Applied Microbiology and Mushroom Sciences, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, lbaraki 305-8687, Japan
| | - Hitoshi Murata
- Department of Applied Microbiology and Mushroom Sciences, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, lbaraki 305-8687, Japan
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Scheublin TR, Sanders IR, Keel C, van der Meer JR. Characterisation of microbial communities colonising the hyphal surfaces of arbuscular mycorrhizal fungi. ISME JOURNAL 2010; 4:752-63. [PMID: 20147983 DOI: 10.1038/ismej.2010.5] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are symbiotic soil fungi that are intimately associated with the roots of the majority of land plants. They colonise the interior of the roots and the hyphae extend into the soil. It is well known that bacterial colonisation of the rhizosphere can be crucial for many pathogenic as well as symbiotic plant-microbe interactions. However, although bacteria colonising the extraradical AMF hyphae (the hyphosphere) might be equally important for AMF symbiosis, little is known regarding which bacterial species would colonise AMF hyphae. In this study, we investigated which bacterial communities might be associated with AMF hyphae. As bacterial-hyphal attachment is extremely difficult to study in situ, we designed a system to grow AMF hyphae of Glomus intraradices and Glomus proliferum and studied which bacteria separated from an agricultural soil specifically attach to the hyphae. Characterisation of attached and non-attached bacterial communities was performed using terminal restriction fragment length polymorphism and clone library sequencing of 16S ribosomal RNA (rRNA) gene fragments. For all experiments, the composition of hyphal attached bacterial communities was different from the non-attached communities, and was also different from bacterial communities that had attached to glass wool (a non-living substratum). Analysis of amplified 16S rRNA genes indicated that in particular bacteria from the family of Oxalobacteraceae were highly abundant on AMF hyphae, suggesting that they may have developed specific interactions with the fungi.
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Affiliation(s)
- Tanja R Scheublin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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Morales-Jiménez J, Zúñiga G, Villa-Tanaca L, Hernández-Rodríguez C. Bacterial community and nitrogen fixation in the red turpentine beetle, Dendroctonus valens LeConte (Coleoptera: Curculionidae: Scolytinae). MICROBIAL ECOLOGY 2009; 58:879-91. [PMID: 19543937 DOI: 10.1007/s00248-009-9548-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 05/27/2009] [Indexed: 05/25/2023]
Abstract
The red turpentine beetle, Dendroctonus valens LeConte (Coleoptera: Curculionidae: Scolytinae), colonizes all pines species within its native range throughout North and Central America. Recently, this species was accidentally introduced to China, where it has caused severe damage in pine forests. It belongs to a group of beetles that spend most of their lives between the tree bark and sapwood, where it feeds on phloem: a poor substrate with very low nutritional value of nitrogen and toxic properties due to its high content of secondary defensive compounds. The aim of this study was to characterize the bacterial community of the D. valens gut by culture-dependent and -independent methods. Polymerase chain reaction denaturing gradient gel electrophoresis and ribosomal gene library analyses revealed that species diversity in the D. valens gut was relatively low, containing between six and 17 bacterial species. The bacterial community associated with larvae and adults was dominated by members of the following genera: Lactococcus, Acinetobacter, Pantoea, Rahnella, Stenothrophomonas, Erwinia, Enterobacter, Serratia, Janibacter, Leifsonia, Cellulomonas, and Cellulosimicrobium. The members of the last four genera showed cellulolytic activity in vitro and could be involved in cellulose breakdown in the insect gut. Finally, nitrogen fixation was demonstrated in live larvae and adults; however, capacity of nitrogen fixing in vitro was not found among enterobacterial species isolated in nitrogen-free media; neither were nifD nor nifH genes detected. In contrast, nifD gen was detected in metagenomic DNA from insect guts. The identification of bacterial species and their potential physiological capacities will allow exploring the role of gut symbiotic bacteria in the adaptation and survival of D. valens in a harsh chemical habitat poor in nitrogen sources.
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Affiliation(s)
- Jesús Morales-Jiménez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. De Carpio y Plan de Ayala. Col. Sto. Tomas, Mexico, Distrito Federal, CP 11340, Mexico
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Tanaka M, Nara K. Phylogenetic diversity of non-nodulating Rhizobiumâ associated with pine ectomycorrhizae. FEMS Microbiol Ecol 2009; 69:329-43. [DOI: 10.1111/j.1574-6941.2009.00720.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Uroz S, Calvaruso C, Turpault MP, Frey-Klett P. Mineral weathering by bacteria: ecology, actors and mechanisms. Trends Microbiol 2009; 17:378-87. [PMID: 19660952 DOI: 10.1016/j.tim.2009.05.004] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 05/15/2009] [Accepted: 05/26/2009] [Indexed: 12/31/2022]
Affiliation(s)
- Stéphane Uroz
- Institut National de la Recherche Agronomique (INRA), Nancy Université, UMR 1136 Interactions Arbres Micro-organismes, Centre INRA de Nancy, 54280 Champenoux, France.
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Warmink JA, van Elsas JD. Migratory response of soil bacteria to Lyophyllum sp. strain Karsten in soil microcosms. Appl Environ Microbiol 2009; 75:2820-30. [PMID: 19286795 PMCID: PMC2681705 DOI: 10.1128/aem.02110-08] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 03/05/2009] [Indexed: 12/12/2022] Open
Abstract
In this study, the selection of bacteria on the basis of their migration via fungal hyphae in soil was investigated in microcosm experiments containing Lyophyllum sp. strain Karsten (DSM2979). One week following inoculation with a bacterial community obtained from soil, selection of a few specific bacterial types was noticed at 30 mm in the growth direction of Lyophyllum sp. strain Karsten in sterile soil. Cultivation-based analyses showed that the migration-proficient types encompassed 10 bacterial groups, as evidenced by (GTG)(5) genomic fingerprinting as well as 16S rRNA gene sequencing. These were (>97% similarity) Burkholderia terrae BS001, Burkholderia sordidicola BS026, Burkholderia sediminicola BS010, and Burkholderia phenazinium BS028; Dyella japonica BS013, BS018, and BS021; "Sphingoterrabacterium pocheensis" BS024; Sphingobacterium daejeonense BS025; and Ralstonia basilensis BS017. Migration as single species was subsequently found for B. terrae BS001, D. japonica BS018 and BS021, and R. basilensis BS017. Typically, migration occurred only when these organisms were introduced at the fungal growth front and only in the direction of hyphal growth. Migration proficiency showed a one-sided correlation with the presence of the hrcR gene, used as a marker for the type III secretion system (TTSS), as all single-strain migrators were equipped with this system and most non-single-strain migrators were not. The presence of the TTSS stood in contrast to the low prevalence of TTSSs within the bacterial community used as an inoculum (<3%). Microscopic examination of B. terrae BS001 in contact with Lyophyllum sp. strain Karsten hyphae revealed the development of a biofilm surrounding the hyphae. Migration-proficient bacteria interacting with Lyophyllum sp. strain Karsten may show complex behavior (biofilm formation) at the fungal tip, leading to their translocation and growth in novel microhabitats in soil.
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MESH Headings
- Agaricales
- Bacteria/classification
- Bacteria/genetics
- Bacteria/growth & development
- Bacteria/isolation & purification
- Bacterial Physiological Phenomena
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Locomotion
- Molecular Sequence Data
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
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Affiliation(s)
- J A Warmink
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Kerklaan 30, 9750RA Haren, The Netherlands
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40
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Kretzer AM, King ZR, Bai S. Bacterial communities associated with tuberculate ectomycorrhizae of Rhizopogon spp. MYCORRHIZA 2009; 19:277-282. [PMID: 19066986 DOI: 10.1007/s00572-008-0213-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Accepted: 11/21/2008] [Indexed: 05/27/2023]
Abstract
We have previously reported the design of a new PCR primer pair that allows amplification of a broad range of eubacterial 16S rDNA sequences from ectomycorrhizae (ECM) without co-amplification of plastid or mitochondrial sequences. Here, we report using a similar primer combination to generate three small 16S rDNA libraries from tuberculate ECM of Rhizopogon spp., two from R. vinicolor ECM (libraries Rvi18 and Rvi24) and one from R. vesiculosus ECM (library Rve13). At the class level, libraries were dominated by sequences from the Alphaproteobacteria, Gammaproteobacteria, and Acidobacteria, with some Sphingobacteria, Actinobacteria, Planctomycetacia, and Verrucomicrobiae present as well. Based on the parsimony test implemented in TreeClimber, libraries Rvi18 and Rvi24 were significantly different from Rve13 at the alpha = 0.05 level, while they were only borderline significantly different from each other (p = 0.07). Differences between Rvi and Rve libraries were primarily due to differences in the number of Alphaproteobacteria sequences and specifically sequences from the Rhizobiales, which were more common in the Rve13 library. It is currently unknown what drives these differences between eubacterial communities. Amplification success for eubacterial 16S rDNA sequences was generally low in this study indicating low abundance of bacteria on tuberculate ECM. Attempts to amplify nitrogenase reductase (nifH) sequences were unsuccessful.
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Affiliation(s)
- Annette M Kretzer
- College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA.
| | - Zachary R King
- College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Shasha Bai
- College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
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41
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Warmink JA, Nazir R, van Elsas JD. Universal and species-specific bacterial ‘fungiphiles’ in the mycospheres of different basidiomycetous fungi. Environ Microbiol 2009; 11:300-12. [DOI: 10.1111/j.1462-2920.2008.01767.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Graham RI, Zahner V, Lucarotti CJ. An intracellular symbiont and other microbiota associated with field-collected populations of sawflies (Hymenoptera: Symphyta). Can J Microbiol 2008; 54:758-68. [DOI: 10.1139/w08-067] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Six species of sawfly (Hymenoptera: Symphyta) from four taxonomic families (Agridae, Diprionidae, Pamphiliidae, and Tenthredinidae) were collected from locations across Canada and surveyed for their associated microbiota. Total DNA was extracted from individual insects, and polymerase chain reaction (PCR) was used to amplify the conserved 16S rRNA gene from microbiota. Denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) were undertaken to separate bacterial clones associated with the host insect. Sequencing of the PCR–DGGE and PCR–RFLP products revealed a dominance of α- and γ-Proteobacteria, with most sequences showing high similarity to bacteria previously identified from other insect species and environmental samples. Additionally, a strain of the bacterial endosymbiont Wolbachia and a Wolbachia bacteriophage were identified from the mountain ash sawfly ( Pristiphora geniculata ).
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Affiliation(s)
- Robert I. Graham
- Population Ecology Group, Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 6C2, Canada
- Department of Biochemistry and Molecular Biology, Oswaldo Cruz Institute-FIOCRUZ, Manguinhos CEP 21045-900, Rio de Janeiro, RJ, Brazil
- Canadian Forest Service, Atlantic Forestry Centre, Natural Resources Canada, P.O. Box 4000, Fredericton, NB E3B 5P7, Canada
| | - Viviane Zahner
- Population Ecology Group, Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 6C2, Canada
- Department of Biochemistry and Molecular Biology, Oswaldo Cruz Institute-FIOCRUZ, Manguinhos CEP 21045-900, Rio de Janeiro, RJ, Brazil
- Canadian Forest Service, Atlantic Forestry Centre, Natural Resources Canada, P.O. Box 4000, Fredericton, NB E3B 5P7, Canada
| | - Christopher J. Lucarotti
- Population Ecology Group, Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 6C2, Canada
- Department of Biochemistry and Molecular Biology, Oswaldo Cruz Institute-FIOCRUZ, Manguinhos CEP 21045-900, Rio de Janeiro, RJ, Brazil
- Canadian Forest Service, Atlantic Forestry Centre, Natural Resources Canada, P.O. Box 4000, Fredericton, NB E3B 5P7, Canada
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43
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Uroz S, Heinonsalo J. Degradation of N-acyl homoserine lactone quorum sensing signal molecules by forest root-associated fungi. FEMS Microbiol Ecol 2008; 65:271-8. [DOI: 10.1111/j.1574-6941.2008.00477.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Offre P, Pivato B, Mazurier S, Siblot S, Berta G, Lemanceau P, Mougel C. Microdiversity of Burkholderiales associated with mycorrhizal and nonmycorrhizal roots of Medicago truncatula. FEMS Microbiol Ecol 2008; 65:180-92. [PMID: 18507681 DOI: 10.1111/j.1574-6941.2008.00504.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The genetic diversity of bacterial communities associated with mycorrhizal and nonmycorrhizal roots of Medicago truncatula was characterized by two approaches. Firstly, phylogenetic analysis was performed on 164 partial 16S rRNA gene-intergenic spacer (IGS) sequences from operational taxonomic units previously shown to be preferentially associated with mycorrhizal roots. These sequences were distributed into three branches corresponding to Comamonadaceae, Oxalobacteraceae and Rubrivivax subgroups. Most sequences were obtained from mycorrhizal roots, indicating the preferential association of the corresponding families with mycorrhizal roots. A second phylogenetic analysis was performed on the partial 16S rRNA gene-IGS sequences of 173 isolates among a large collection of isolates, from mycorrhizal and nonmycorrhizal roots, belonging to Comamonadaceae and Oxalobacteraceae on the basis of their positive hybridization with a partial 16S rRNA gene-IGS probe obtained in this study. Sequence analysis confirmed the affiliation of 166 isolates to Comamonadaceae and seven to Oxalobacteraceae. Oxalobacteraceae isolates were more abundant in mycorrhizal (five) than in nonmycorrhizal (two) roots, whereas Comamonadaceae isolates were more abundant in nonmycorrhizal (109) than mycorrhizal roots (57). Further analysis of Comamonadaceae isolates by BOX-PCR showed that the genetic structure of culturable populations belonging to this family differed significantly in mycorrhizal and nonmycorrhizal roots, as indicated by distributions in different BOX types, differences being significantly explained by BOX types only including isolates from mycorrhizal roots. These data are discussed in an ecological context.
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Affiliation(s)
- Pierre Offre
- INRA, Université de Bourgogne, UMR1229 Microbiologie du Sol et de l'Environnement, CMSE, BP, Dijon, France
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Izumi H, Anderson IC, Killham K, Moore ERB. Diversity of predominant endophytic bacteria in European deciduous and coniferous trees. Can J Microbiol 2008; 54:173-9. [PMID: 18388988 DOI: 10.1139/w07-134] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The diversity of endophytic bacteria residing in root, stem, and leaf tissues was examined in coniferous and deciduous tree species, Scots pine (Pinus sylvestris L.), silver birch (Betula pendula Roth), and rowan (Sorbus aucuparia L.). Using cultivation-dependent and -independent analyses, the bacterial communities were observed to be significantly different in the belowground (roots and rhizosphere) and aboveground (leaves and stems) samples of the respective host trees. No significant differences, with respect to the different tree species, were observed in the associated communities. Predominant cultivable endophytes isolated included bacteria closely related to Bacillus subtilis, Bacillus licheniformis, Paenibacillus spp., and Acinetobacter calcoaceticus. Comparisons of the most abundant cultivable bacteria in the rhizosphere and root samples suggested that root endophytic bacteria may be in residence through processes of selection or active colonization rather than by passive diffusion from the rhizosphere.
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Affiliation(s)
- Hironari Izumi
- The Macaulay Institute, Craigiebuckler, Aberdeen AB15 8QH, Scotland, UK.
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Izumi H, Cairney JWG, Killham K, Moore E, Alexander IJ, Anderson IC. Bacteria associated with ectomycorrhizas of slash pine (Pinus elliottii) in south-eastern Queensland, Australia. FEMS Microbiol Lett 2008; 282:196-204. [PMID: 18355286 DOI: 10.1111/j.1574-6968.2008.01122.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Bacterial communities associated with ectomycorrhizal and uncolonized roots of Pinus elliottii (slash pine) collected from a plantation in south-east Queensland, Australia, were investigated, using cultivation-dependent and -independent methods. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene PCR products obtained using a cultivation-independent approach revealed that bacterial communities associated with ectomycorrhizal root tips differed significantly from those associated with roots uncolonized by ectomycorrhizal fungi. DGGE analysis of cultivable bacterial communities revealed no significant difference between ectomycorrhizal and uncolonized roots. Neither analytical approach revealed significant differences between the bacterial communities associated with ectomycorrhizal roots colonized by a Suillus sp. or an Atheliaceae taxon. Cloned bacterial 16S rRNA genes revealed sequence types closely related with that of Burkholderia phenazinium, common in both ectomycorrhizal-colonized and -uncolonized roots, while sequence types most similar to the potentially phyopathogenic bacteria Burkholderia andropogonis and Pantoea ananatis were only detected in ectomycorrhizal roots. These results highlight the possibility of global movement of microorganisms, including putative pathogens, as a result of the introduction of exotic pine plantations.
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Affiliation(s)
- Hironari Izumi
- The Macaulay Institute, Craigiebuckler, Aberdeen, Scotland, UK.
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47
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de Boer W, van der Wal A. Chapter 8 Interactions between saprotrophic basidiomycetes and bacteria. BRITISH MYCOLOGICAL SOCIETY SYMPOSIA SERIES 2008. [DOI: 10.1016/s0275-0287(08)80010-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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48
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Izumi H, Anderson IC, Alexander IJ, Killham K, Moore ERB. Diversity and expression of nitrogenase genes (nifH) from ectomycorrhizas of Corsican pine (Pinus nigra). Environ Microbiol 2007; 8:2224-30. [PMID: 17107563 DOI: 10.1111/j.1462-2920.2006.01104.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The diversity of bacterial nitrogenase genes (nifH) and their mRNA transcription in ectomycorrhizas of Corsican pine (Pinus nigra) were examined. DNA and RNA were extracted from surface-sterilized and non-sterilized Corsican pine roots colonized by the ectomycorrhizal (ECM) fungi, Suillus variegatus and Tomentellopsis submollis. DNA-derived nifH polymerase chain reaction (PCR) products were obtained from all samples, but only a few reverse transcription PCRs for nifH mRNA were successful, suggesting that nitrogenase genes were not always transcribed. Several different nifH sequences were detected and the bacteria actively transcribing nifH were different from those whose genes were detected through DNA-based PCR. Putative nitrogenase amino acid sequences revealed that more than half of the nifH products were derived from methylotrophic bacteria, such as Methylocella spp. The next most frequent sequence types were similar to those from Burkholderia.
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Affiliation(s)
- Hironari Izumi
- The Macaulay Institute, Craigiebuckler, Aberdeen AB15 8QH, Scotland, UK.
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49
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Abstract
In natural conditions, mycorrhizal fungi are surrounded by complex microbial communities, which modulate the mycorrhizal symbiosis. Here, the focus is on the so-called mycorrhiza helper bacteria (MHB). This concept is revisited, and the distinction is made between the helper bacteria, which assist mycorrhiza formation, and those that interact positively with the functioning of the symbiosis. After considering some examples of MHB from the literature, the ecological and evolutionary implications of the relationships of MHB with mycorrhizal fungi are discussed. The question of the specificity of the MHB effect is addressed, and an assessment is made of progress in understanding the mechanisms of the MHB effect, which has been made possible through the development of genomics. Finally, clear evidence is presented suggesting that some MHB promote the functioning of the mycorrhizal symbiosis. This is illustrated for three critical functions of practical significance: nutrient mobilization from soil minerals, fixation of atmospheric nitrogen, and protection of plants against root pathogens. The review concludes with discussion of future research priorities regarding the potentially very fruitful concept of MHB.
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Affiliation(s)
- P Frey-Klett
- INRA, UMR1136 INRA-UHP 'Interactions Arbres/Micro-organismes', IFR 110, Centre de Nancy, 54280 Champenoux, France
| | - J Garbaye
- INRA, UMR1136 INRA-UHP 'Interactions Arbres/Micro-organismes', IFR 110, Centre de Nancy, 54280 Champenoux, France
| | - M Tarkka
- UFZ-Department of Soil Ecology, Helmholz Centre for Environmental Research, Theodor-Lieser-Strasse 4, 06120 Halle, Germany
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50
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Bending GD, Aspray TJ, Whipps JM. Significance of Microbial Interactions in the Mycorrhizosphere. ADVANCES IN APPLIED MICROBIOLOGY 2006; 60:97-132. [PMID: 17157634 DOI: 10.1016/s0065-2164(06)60004-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Gary D Bending
- Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom.
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