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Fasusi OA, Amoo AE, Babalola OO. Propagation and characterization of viable arbuscular mycorrhizal fungal spores within maize plant (Zea mays L.). J Sci Food Agric 2021; 101:5834-5841. [PMID: 33788958 DOI: 10.1002/jsfa.11235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/18/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The harmful effect of chemical fertilizer application on human health and the environment as a modern method of meeting the food demand of the increasing world population demands an urgent alternative that is environmentally friendly, which will pose no harm to human health and the environment. Arbuscular mycorrhizal fungi (AMF) are beneficial soil microorganisms that provide various ecological functions in increasing soil fertility and enhancing plant growth. This present study aimed to propagate, characterize and examine the effect of viable arbuscular mycorrhizal fungal spores on maize (Zea mays L) hosts using molecular methods. The propagation of AMF in the host plant using sterile soil and vermiculite was conducted in the greenhouse. RESULT The effect of AMF inoculation revealed a significant difference (P > 0.05) in maize growth, root colonization and AMF spore count when compared with the control. In all the parameters measured in this study, all the AMF spores propagated had a positive effect on the maize plant over the control, with the highest value mostly recorded in Rhizophagus irregularis AOB1. The molecular characterization of the spore using a specific universal primer for Glomeromycota established the success of the propagation process, which enhanced the classification of the AMF species into Rhizophagus irregularis OAB1, Glomus mosseae OAB2 and Paraglomus occultum OAB3. CONCLUSION This finding will be a starting point in producing arbuscular mycorrhizal inoculum as a biofertilizer to enhance plant growth promotion. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Oluwaseun Adeyinka Fasusi
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, North-West University, Mmabatho, South Africa
| | - Adenike Eunice Amoo
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, North-West University, Mmabatho, South Africa
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Paz C, Öpik M, Bulascoschi L, Bueno CG, Galetti M. Dispersal of Arbuscular Mycorrhizal Fungi: Evidence and Insights for Ecological Studies. Microb Ecol 2021; 81:283-292. [PMID: 32920663 DOI: 10.1007/s00248-020-01582-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Dispersal is a critical ecological process that modulates gene flow and contributes to the maintenance of genetic and taxonomic diversity within ecosystems. Despite an increasing global understanding of the arbuscular mycorrhizal (AM) fungal diversity, distribution and prevalence in different biomes, we have largely ignored the main dispersal mechanisms of these organisms. To provide a geographical and scientific overview of the available data, we systematically searched for the direct evidence on the AM fungal dispersal agents (abiotic and biotic) and different propagule types (i.e. spores, extraradical hyphae or colonized root fragments). We show that the available data (37 articles) on AM fungal dispersal originates mostly from North America, from temperate ecosystems, from biotic dispersal agents (small mammals) and AM fungal spores as propagule type. Much lesser evidence exists from South American, Asian and African tropical systems and other dispersers such as large-bodied birds and mammals and non-spore propagule types. We did not find strong evidence that spore size varies across dispersal agents, but wind and large animals seem to be more efficient dispersers. However, the data is still too scarce to draw firm conclusions from this finding. We further discuss and propose critical research questions and potential approaches to advance the understanding of the ecology of AM fungi dispersal.
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Affiliation(s)
- Claudia Paz
- Department of Ecology, Institute of Biosciences, São Paulo State University, Av 24A 1515, Rio Claro, SP, 13506-900, Brazil.
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40 Street, 51005, Tartu, Estonia.
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40 Street, 51005, Tartu, Estonia
| | - Leticia Bulascoschi
- Department of Ecology, Institute of Biosciences, São Paulo State University, Av 24A 1515, Rio Claro, SP, 13506-900, Brazil
| | - C Guillermo Bueno
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40 Street, 51005, Tartu, Estonia
| | - Mauro Galetti
- Department of Ecology, Institute of Biosciences, São Paulo State University, Av 24A 1515, Rio Claro, SP, 13506-900, Brazil
- Department of Biology, University of Miami, Coral Gables, Miami, FL, 33146, USA
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Xi G, Shi J, Li J, Han Z. Isolation and identification of beneficial orchid mycorrhizal fungi in Bletilla striata (Thunb.) Rchb.f.(Orchidaceae). Plant Signal Behav 2020; 15:1816644. [PMID: 32897833 PMCID: PMC7671041 DOI: 10.1080/15592324.2020.1816644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Orchid mycorrhizal fungi (OMF) are essential for orchids growth. Bletilla striata (Thunb.) Rchb.f.(Orchidaceae) has high ornamental and medicinal value. Beneficial OMF isolation is crucial to improve the survival rate of B. striata tissue culture and transplanting. In this study, we isolated and identified the beneficial OMF in B. striata from the roots of sterilized wild B. striata seedlings by culturing in four different mediums. The germination states of B. striata seeds inoculated with diverse OMF were classified and calculated. Fresh and dry weight increments of B. striata seedlings inoculated with diverse OMF were recorded after 90 d of culturing on 1/2 MS medium. ITS sequences of beneficial fungi were amplified by PCR and taxonomically identified using BLAST against the GenBank nucleotide database. Ten kinds of OMF strains were isolated from B. striata and named R1 to R10. R6 significantly promoted B. striata seeds germination (p < .01). R3 and R6 significantly promoted both the fresh and dry weight increments of B. striata seedlings (p < .05). The ITS sequence of R6 was most similar to the sequence of Serendipita. R3 was identified as Schizothecium fimbriatum by 100% ITS identity. R6 and R3 were beneficial OMF in B. striata.
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Affiliation(s)
- Gangjun Xi
- Biological Engineering Technology Center, Jiangsu Vocational College of Agriculture and Forestry, Jurong, Jiangsu, China
- CONTACT Gangjun Xi Biological Engineering Technology Center, Jiangsu Polytechnic College of Agriculture and Forestry, No. 19 Wenchang Road (East), Jurong, Jiangsu, 212400, China
| | - Jun Shi
- Biological Engineering Technology Center, Jiangsu Vocational College of Agriculture and Forestry, Jurong, Jiangsu, China
| | - Jingbao Li
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Zhengmin Han
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Zhengmin Han College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
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Luo Y, Wang Z, He Y, Li G, Lv X, Zhuang L. High-throughput sequencing analysis of the rhizosphere arbuscular mycorrhizal fungi (AMF) community composition associated with Ferula sinkiangensis. BMC Microbiol 2020; 20:335. [PMID: 33143657 PMCID: PMC7640387 DOI: 10.1186/s12866-020-02024-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/27/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Ferula sinkiangensis is an increasingly endangered medicinal plant. Arbuscular mycorrhiza fungi (AMF) are symbiotic microorganisms that live in the soil wherein they enhance nutrient uptake, stress resistance, and pathogen defense in host plants. While such AMF have the potential to contribute to the cultivation of Ferula sinkiangensis, the composition of AMF communities associated with Ferula sinkiangensis and the relationship between these fungi and other pertinent abiotic factors still remains to be clarified. RESULTS Herein, we collected rhizosphere and surrounding soil samples at a range of depths (0-20, 20-40, and 40-60 cm) and a range of slope positions (bottom, middle, top). These samples were then subjected to analyses of soil physicochemical properties and high-throughput sequencing (Illumina MiSeq). We determined that Glomus and Diversispora species were highly enriched in all samples. We further found that AMF diversity and richness varied significantly as a function of slope position, with this variation primarily being tied to differences in relative Glomus and Diversispora abundance. In contrast, no significant relationship was observed between soil depth and overall AMF composition, although some AMF species were found to be sensitive to soil depth. Many factors significantly affected AMF community composition, including organic matter content, total nitrogen, total potassium, ammonium nitrogen, nitrate nitrogen, available potassium, total dissolvable salt levels, pH, soil water content, and slope position. We further determined that Shannon diversity index values in these communities were positively correlated with total phosphorus, nitrate-nitrogen levels, and pH values (P < 0.05), whereas total phosphorus, total dissolvable salt levels, and pH were positively correlated with Chao1 values (P < 0.05). CONCLUSION In summary, our data revealed that Glomus and Diversispora are key AMF genera found within Ferula sinkiangensis rhizosphere soil. These fungi are closely associated with specific environmental and soil physicochemical properties, and these soil sample properties also differed significantly as a function of slope position (P < 0.05). Together, our results provide new insights regarding the relationship between AMF species and Ferula sinkiangensis, offering a theoretical basis for further studies of their development.
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Affiliation(s)
- Yunfeng Luo
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China
| | - Zhongke Wang
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China
| | - Yaling He
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China
| | - Guifang Li
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China
| | - Xinhua Lv
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China
| | - Li Zhuang
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China.
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Pecoraro L, Wang X, Venturella G, Gao W, Wen T, Gafforov Y, Gupta VK. Molecular evidence supports simultaneous association of the achlorophyllous orchid Chamaegastrodia inverta with ectomycorrhizal Ceratobasidiaceae and Russulaceae. BMC Microbiol 2020; 20:236. [PMID: 32746782 PMCID: PMC7397628 DOI: 10.1186/s12866-020-01906-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/14/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Achlorophyllous orchids are mycoheterotrophic plants, which lack photosynthetic ability and associate with fungi to acquire carbon from different environmental sources. In tropical latitudes, achlorophyllous forest orchids show a preference to establish mycorrhizal relationships with saprotrophic fungi. However, a few of them have been recently found to associate with ectomycorrhizal fungi and there is still much to be learned about the identity of fungi associated with tropical orchids. The present study focused on mycorrhizal diversity in the achlorophyllous orchid C. inverta, an endangered species, which is endemic to southern China. The aim of this work was to identify the main mycorrhizal partners of C. inverta in different plant life stages, by means of morphological and molecular methods. RESULTS Microscopy showed that the roots of analysed C. inverta samples were extensively colonized by fungal hyphae forming pelotons in root cortical cells. Fungal ITS regions were amplified by polymerase chain reaction, from DNA extracted from fungal mycelia isolated from orchid root samples, as well as from total root DNA. Molecular sequencing and phylogenetic analyses showed that the investigated orchid primarily associated with ectomycorrhizal fungi belonging to a narrow clade within the family Ceratobasidiaceae, which was previously detected in a few fully mycoheterotrophic orchids and was also found to show ectomycorrhizal capability on trees and shrubs. Russulaceae fungal symbionts, showing high similarity with members of the ectomycorrhizal genus Russula, were also identified from the roots of C. inverta, at young seedling stage. Ascomycetous fungi including Chaetomium, Diaporthe, Leptodontidium, and Phomopsis genera, and zygomycetes in the genus Mortierella were obtained from orchid root isolated strains with unclear functional role. CONCLUSIONS This study represents the first assessment of root fungal diversity in the rare, cryptic and narrowly distributed Chinese orchid C. inverta. Our results provide new insights on the spectrum of orchid-fungus symbiosis suggesting an unprecedented mixed association between the studied achlorophyllous forest orchid and ectomycorrhizal fungi belonging to Ceratobasidiaceae and Russulaceae. Ceratobasidioid fungi as dominant associates in the roots of C. inverta represent a new record of the rare association between the identified fungal group and fully mycoheterotrophic orchids in nature.
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Affiliation(s)
- Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Health Sciences Platform, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China.
| | - Xiao Wang
- School of Pharmaceutical Science and Technology, Health Sciences Platform, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Giuseppe Venturella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Health Sciences Platform, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Tingchi Wen
- The Engineering Research Center of Southwest Bio-Pharmaceutical Resources, Ministry of Education, Guizhou University, Guiyang, China
| | - Yusufjon Gafforov
- Laboratory of Mycology, Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Vijai Kumar Gupta
- AgroBioSciences and Chemical & Biochemical Sciences Department, University Mohammed VI Polytechnic, Hay Moulay Rachid, Ben Guerir, Morocco
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Savary R, Dupuis C, Masclaux FG, Mateus ID, Rojas EC, Sanders IR. Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava. ISME J 2020; 14:1333-1344. [PMID: 32066875 PMCID: PMC7242447 DOI: 10.1038/s41396-020-0606-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 01/16/2020] [Accepted: 01/30/2020] [Indexed: 12/19/2022]
Abstract
Most land plants form symbioses with arbuscular mycorrhizal fungi (AMF). Diversity of AMF increases plant community productivity and plant diversity. For decades, it was known that plants trade carbohydrates for phosphate with their fungal symbionts. However, recent studies show that plant-derived lipids probably represent the most essential currency of exchange. Understanding the regulation of plant genes involved in the currency of exchange is crucial to understanding stability of this mutualism. Plants encounter many different AMF genotypes that vary greatly in the benefit they confer to plants. Yet the role that fungal genetic variation plays in the regulation of this currency has not received much attention. We used a high-resolution phylogeny of one AMF species (Rhizophagus irregularis) to show that fungal genetic variation drives the regulation of the plant fatty acid pathway in cassava (Manihot esculenta); a pathway regulating one of the essential currencies of trade in the symbiosis. The regulation of this pathway was explained by clearly defined patterns of fungal genome-wide variation representing the precise fungal evolutionary history. This represents the first demonstrated link between the genetics of AMF and reprogramming of an essential plant pathway regulating the currency of exchange in the symbiosis. The transcription factor RAM1 was also revealed as the dominant gene in the fatty acid plant gene co-expression network. Our study highlights the crucial role of variation in fungal genomes in the trade of resources in this important symbiosis and also opens the door to discovering characteristics of AMF genomes responsible for interactions between AMF and cassava that will lead to optimal cassava growth.
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Affiliation(s)
- Romain Savary
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Cindy Dupuis
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Ivan D Mateus
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Edward C Rojas
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Copenhagen, Denmark
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
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Malicka M, Magurno F, Piotrowska-Seget Z, Chmura D. Arbuscular mycorrhizal and microbial profiles of an aged phenol-polynuclear aromatic hydrocarbon-contaminated soil. Ecotoxicol Environ Saf 2020; 192:110299. [PMID: 32058165 DOI: 10.1016/j.ecoenv.2020.110299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are ubiquitous, obligatory plant symbionts that have a beneficial influence on plants in contaminated environments. This study focused on evaluating the biomass and biodiversity of the AMF and microbial communities associated with Poa trivialis and Phragmites australis plants sampled at an aged site contaminated with phenol and polynuclear aromatic hydrocarbons (PAHs) and an uncontaminated control site. We analyzed the soil phospholipid fatty acid profile to describe the general structure of microbial communities. PCR-denaturing gradient gel electrophoresis with primers targeting the 18S ribosomal RNA gene was used to characterize the biodiversity of the AMF communities and identify dominant AMF species associated with the host plants in the polluted and control environments. The root mycorrhizal colonization and AMF biomass in the soil were negatively affected by the presence of PAHs and phenol, with no significant differences between the studied plant species, whereas the biodiversity of the AMF communities were influenced by the soil contamination and plant species. Soil contamination was more detrimental to the biodiversity of AMF communities associated with Ph. australis, compared to P. trivialis. Both species favored the development of different AMF species, which might be related to the specific features of their different root systems and soil microbial communities. The contaminated site was dominated by AMF generalists like Funneliformis and Rhizophagus, whereas in the control site Dominikia, Archaeospora, Claroideoglomus, Glomus, and Diversispora were also detected.
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Affiliation(s)
- Monika Malicka
- Institute of Biology Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28 Street, 40-032, Katowice, Poland.
| | - Franco Magurno
- Institute of Biology Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28 Street, 40-032, Katowice, Poland
| | - Zofia Piotrowska-Seget
- Institute of Biology Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28 Street, 40-032, Katowice, Poland
| | - Damian Chmura
- Institute of Environmental Protection and Engineering, University of Bielsko-Biala, 2 Willowa Street, 43-309 Bielsko-Biała, Poland
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Abstract
Isotope labeling enables the detection and quantification of nutrient fluxes between soil and plants through arbuscular mycorrhizal (AM) fungi. Here we describe the use of radioactive isotopes, 33P and 32P, to study the uptake of P from soil by AM fungal mycelium and its transfer to the host plant through the mycorrhizal pathway.
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Affiliation(s)
- Carla Cruz-Paredes
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Mayra E Gavito
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico.
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Koizumi T, Nara K. Ectomycorrhizal fungal communities in ice-age relict forests of Pinus pumila on nine mountains correspond to summer temperature. ISME J 2020; 14:189-201. [PMID: 31611652 PMCID: PMC6908592 DOI: 10.1038/s41396-019-0524-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 11/09/2022]
Abstract
Ectomycorrhizal (ECM) fungi are critical symbionts of major forest trees, and their communities are affected by various environmental factors including temperature. However, previous knowledge concerning temperature effects does not exclude the effects of host species and coexisting plants, which usually change with temperature, and should be rigorously tested under the same vegetation type. Herein we examined ECM fungal communities in ice-age relict forests dominated by a single host species (Pinus pumila) distributed on nine mountains across >1000 km in Japan. Direct sequencing of rDNA ITS regions identified 154 ECM fungal species from 4134 ECM root-tip samples. Gradient analyses revealed a large contribution of temperature, especially summer temperature, to ECM fungal communities. Additionally, we explored global sequence records of each fungal species to infer its potential temperature niche, and used it to estimate the temperature of the observed communities. The estimated temperature was significantly correlated with the actual temperature of the research sites, especially in summer seasons, indicating inherent temperature niches of the fungal components could determine their distribution among the sites. These results indicate that temperature is still a significant determinant in structuring ECM fungal communities after excluding the effects of host species and coexisting plants. The results also imply that the rising temperature under global warming may have been affecting soil microbes unnoticeably, while such microbial community change may have been contributing to the resilience of the same vegetation.
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Affiliation(s)
- Takahiko Koizumi
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8563, Japan.
- Department of Biosciences, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo, 156-8550, Japan.
| | - Kazuhide Nara
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8563, Japan
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Hartmann M, Voß S, Requena N. Host-Induced Gene Silencing of Arbuscular Mycorrhizal Fungal Genes via Agrobacterium rhizogenes-Mediated Root Transformation in Medicago truncatula. Methods Mol Biol 2020; 2146:239-248. [PMID: 32415608 DOI: 10.1007/978-1-0716-0603-2_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Host-induced gene silencing (HIGS) is a methodology that allows the downregulation of genes in organisms living in close association with a host and that are not amenable or recalcitrant to genetic modifications. This method has been particularly used for oomycetes and for filamentous fungi interacting with plants, including the fungi of the arbuscular mycorrhizal symbiosis. Here, we present a protocol developed in our laboratory to downregulate genes from the obligate symbiont Rhizophagus irregularis in symbiosis with Medicago truncatula plants.
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Affiliation(s)
- Meike Hartmann
- Molecular Phytopathology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Stefanie Voß
- Molecular Phytopathology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Natalia Requena
- Molecular Phytopathology, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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Vieira LC, da Silva DKA, de Melo MAC, Escobar IEC, Oehl F, da Silva GA. Edaphic Factors Influence the Distribution of Arbuscular Mycorrhizal Fungi Along an Altitudinal Gradient of a Tropical Mountain. Microb Ecol 2019; 78:904-913. [PMID: 30976842 DOI: 10.1007/s00248-019-01354-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/04/2019] [Indexed: 06/09/2023]
Abstract
Changes in relief in montane areas, with increasing altitude, provide different biotic and abiotic conditions, acting on the species of arbuscular mycorrhizal fungi (AMF). The objective of this work was to determine the influence of altitude, edaphic factors, and vegetation on the AMF species in a mountainous area. The list of AMF species was obtained from morphological identification of the spores, with 72 species recovered from field samples and trap cultures. Lower levels of Shannon's diversity occurred only at lower altitude; however, there was no difference in AMF richness. The structure of the AMF assembly between the two highest altitudes was similar and differed in relation to the lower altitude. There was variation in the distribution of AMF species, which was related to soil texture and chemical factors along the altitude gradient. Some species, genera, and families were indicative of a certain altitude, showing the preference of fungi for certain environmental conditions, which may aid in decisions to conserve montane ecosystems.
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Affiliation(s)
- Larissa Cardoso Vieira
- Departamento de Micologia, Laboratório de Micorrizas, Universidade Federal de Pernambuco, Av. Prof. Nelson Chaves s/n. Cidade Universitária, CEP 50670-420, Recife, Pernambuco, Brazil.
| | - Danielle Karla Alves da Silva
- Centro de Ciências Aplicadas e Educação, Campus IV, Departamento de Engenharia e Meio Ambiente, Universidade Federal da Paraíba, Av. Santa Elizabete s/n. CEP 56300-990, Rio Tinto, Paraíba, Brazil
| | - Mayara Alice Correia de Melo
- Departamento de Micologia, Laboratório de Micorrizas, Universidade Federal de Pernambuco, Av. Prof. Nelson Chaves s/n. Cidade Universitária, CEP 50670-420, Recife, Pernambuco, Brazil
| | - Indra Elena Costa Escobar
- Departamento de Micologia, Laboratório de Micorrizas, Universidade Federal de Pernambuco, Av. Prof. Nelson Chaves s/n. Cidade Universitária, CEP 50670-420, Recife, Pernambuco, Brazil
| | - Fritz Oehl
- Agroscope, Competence Division for Plants and Plant Products, Ecotoxicology, Schloss 1, CH-8820, Wädenswil, Switzerland
| | - Gladstone Alves da Silva
- Departamento de Micologia, Laboratório de Micorrizas, Universidade Federal de Pernambuco, Av. Prof. Nelson Chaves s/n. Cidade Universitária, CEP 50670-420, Recife, Pernambuco, Brazil
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Gazdag O, Kovács R, Parádi I, Füzy A, Ködöböcz L, Mucsi M, Szili-Kovács T, Inubushi K, Takács T. Density and Diversity of Microbial Symbionts under Organic and Conventional Agricultural Management. Microbes Environ 2019; 34:234-243. [PMID: 31189767 PMCID: PMC6759338 DOI: 10.1264/jsme2.me18138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 04/01/2019] [Indexed: 12/23/2022] Open
Abstract
The influence of organic and conventional farming and agroecology on the diversity and functioning of indigenous soil microbial communities was examined using a multifactorial analysis based on an extended minimum data set of classical status and functional tests. Main soil physicochemical properties and selected microbiological indicators, the quantity of heterotrophic or aerobic spore-forming bacteria, basal and substrate-induced respiration, catabolic activity with MicroResp™, and fluorescein diacetate enzyme activity were characterized. A pot experiment applying the most probable number method was designed with soil dilution series using Pisum sativum L. and Triticum spelta L. to assess the symbiotic infectivity and genetic diversity of key indicator groups of the plant microbiome, e.g. nitrogen-fixing bacteria (rhizobia) and arbuscular mycorrhizal fungi. Soil pH, humus content, CFU, enzyme activity, and soil respiration were significantly higher in organic soils. The activity of soil microorganisms was mainly related to clay, humus, calcium, and magnesium parameters. A redundancy analysis test of catabolic activities showed that samples were grouped according to different substrate utilization patterns and land uses were also clearly separated from each other. Farming practice influenced the abundance and diversity of microbial populations. Dark septate endophytic fungi were only found in conventional soils. In addition to confirming soil health improvements by organic management, our results highlight the importance of a complex evaluation including both classical status and functional parameters of soil microbiota, which may more reliably indicate a shift in the quality status of soils.
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Affiliation(s)
- Orsolya Gazdag
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - Ramóna Kovács
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - István Parádi
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
- Department of Plant Physiology and Molecular Plant Biology, Eötvös Loránd UniversityH 1117, Pázmány Péter sétány 1/C., BudapestHungary
| | - Anna Füzy
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - László Ködöböcz
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - Márton Mucsi
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - Tibor Szili-Kovács
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - Kazuyuki Inubushi
- Graduate School of Horticulture, Chiba UniversityMatsudo, ChibaJapan
| | - Tünde Takács
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
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Helbert, Turjaman M, Nara K. Ectomycorrhizal fungal communities of secondary tropical forests dominated by Tristaniopsis in Bangka Island, Indonesia. PLoS One 2019; 14:e0221998. [PMID: 31498844 PMCID: PMC6733470 DOI: 10.1371/journal.pone.0221998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/19/2019] [Indexed: 11/19/2022] Open
Abstract
In Southeast Asia, primary tropical rainforests are usually dominated by ectomycorrhizal (ECM) trees belonging to Dipterocarpaceae, although arbuscular mycorrhizal trees often outcompete them after disturbances such as forest fires and clear-cutting, thus preventing dipterocarp regeneration. In some secondary tropical forests, however, potentially ECM trees belonging to Tristaniopsis (Myrtaceae) become dominant and may help ECM dipterocarp forests to recover. However, we have no information about their mycorrhizal status in these settings. In this study, we analyzed ECM fungal communities in tropical secondary forests dominated by Tristaniopsis and investigated which ECM fungal species are shared with other tropical or temperate areas. In total, 100 samples were collected from four secondary forests dominated by Tristaniopsis on Bangka Island. ECM tips in the soil samples were subjected to molecular analyses to identify both ECM and host species. Based on a >97% ITS sequence similarity threshold, we identified 56 ECM fungal species dominated by Thelephoraceae, Russulaceae, and Clavulinaceae. Some of the ECM fungal species were shared between dominant Tristaniopsis and coexisting Eucalyptus or Quercus trees, including 5 common to ECM fungi recorded in a primary mixed dipterocarp forest at Lambir Hill, Malaysia. In contrast, no ECM fungal species were shared with other geographical regions, even with Tristaniopsis in New Caledonia. These results imply that secondary tropical forests dominated by Tristaniopsis harbor diverse ECM fungi, including those that inhabit primary dipterocarp forests in the same geographical region. They may function as refugia for ECM fungi, given that dipterocarp forests are disappearing quickly due to human activity.
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Affiliation(s)
- Helbert
- Department of Natural Environmental Studies, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Maman Turjaman
- Forest Research and Development Centre (FRDC), Environment and Forestry Research, Development, Innovation Agency (FORDA), the Ministry of Environment and Forestry, Bogor, Indonesia
| | - Kazuhide Nara
- Department of Natural Environmental Studies, The University of Tokyo, Kashiwa, Chiba, Japan
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Haug I, Setaro S, Suárez JP. Species composition of arbuscular mycorrhizal communities changes with elevation in the Andes of South Ecuador. PLoS One 2019; 14:e0221091. [PMID: 31419262 PMCID: PMC6697372 DOI: 10.1371/journal.pone.0221091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/30/2019] [Indexed: 12/24/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are the most prominent mycobionts of plants in the tropics, yet little is known about their diversity, species compositions and factors driving AMF distribution patterns. To investigate whether elevation and associated vegetation type affect species composition, we sampled 646 mycorrhizal samples in locations between 1000 and 4000 m above sea level (masl) in the South of Ecuador. We estimated diversity, distribution and species compositions of AMF by cloning and Sanger sequencing the 18S rDNA (the section between AML1 and AML2) and subsequent derivation of fungal OTUs based on 99% sequence similarity. In addition, we analyzed the phylogenetic structure of the sites by computing the mean pairwise distance (MPD) and the mean nearest taxon difference (MNTD) for each elevation level. It revealed that AMF species compositions at 1000 and 2000 masl differ from 3000 and 4000 masl. Lower elevations (1000 and 2000 masl) were dominated by members of Glomeraceae, whereas Acaulosporaceae were more abundant in higher elevations (3000 and 4000 masl). Ordination of OTUs with respect to study sites revealed a correlation to elevation with a continuous turnover of species from lower to higher elevations. Most of the abundant OTUs are not endemic to South Ecuador. We also found a high proportion of rare OTUs at all elevations: 79-85% of OTUs occurred in less than 5% of the samples. Phylogenetic community analysis indicated clustering and evenness for most elevation levels indicating that both, stochastic processes and habitat filtering are driving factors of AMF community compositions.
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Affiliation(s)
- Ingeborg Haug
- Evolutionary Ecology of Plants, Eberhard-Karls-University, Tübingen, Germany
| | - Sabrina Setaro
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Juan Pablo Suárez
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
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15
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Sendek A, Karakoç C, Wagg C, Domínguez-Begines J, do Couto GM, van der Heijden MGA, Naz AA, Lochner A, Chatzinotas A, Klotz S, Gómez-Aparicio L, Eisenhauer N. Drought modulates interactions between arbuscular mycorrhizal fungal diversity and barley genotype diversity. Sci Rep 2019; 9:9650. [PMID: 31273222 PMCID: PMC6609766 DOI: 10.1038/s41598-019-45702-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/07/2019] [Indexed: 01/31/2023] Open
Abstract
Droughts associated with climate change alter ecosystem functions, especially in systems characterized by low biodiversity, such as agricultural fields. Management strategies aimed at buffering climate change effects include the enhancement of intraspecific crop diversity as well as the diversity of beneficial interactions with soil biota, such as arbuscular mycorrhizal fungi (AMF). However, little is known about reciprocal relations of crop and AMF diversity under drought conditions. To explore the interactive effects of plant genotype richness and AMF richness on plant yield under ambient and drought conditions, we established fully crossed diversity gradients in experimental microcosms. We expected highest crop yield and drought tolerance at both high barley and AMF diversity. While barley richness and AMF richness altered the performance of both barley and AMF, they did not mitigate detrimental drought effects on the plant and AMF. Root biomass increased with mycorrhiza colonization rate at high AMF richness and low barley richness. AMF performance increased under higher richness of both barley and AMF. Our findings indicate that antagonistic interactions between barley and AMF may occur under drought conditions, particularly so at higher AMF richness. These results suggest that unexpected alterations of plant-soil biotic interactions could occur under climate change.
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Affiliation(s)
- Agnieszka Sendek
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Strasse 4, 06120, Halle, Germany.
- Department of Geobotany and Botanical Garden, Martin Luther University of Halle-Wittenberg, Am Kirchweg 2, 06108, Halle, Germany.
| | - Canan Karakoç
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Cameron Wagg
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstr. 190, Zürich, CH-8057, Switzerland
- Fredericton Research and Development Center, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Jara Domínguez-Begines
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Natural Resources and Agrobiology of Seville (IRNAS), CSIC, LINCGlobal, Avenida Reina Mercedes, 10, 41012, Sevilla, Spain
| | - Gabriela Martucci do Couto
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Department of Agroecology and Environment, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Ali Ahmad Naz
- Crop Genetics and Biotechnology Unit, Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Alfred Lochner
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Antonis Chatzinotas
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Stefan Klotz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Strasse 4, 06120, Halle, Germany
| | - Lorena Gómez-Aparicio
- Institute of Natural Resources and Agrobiology of Seville (IRNAS), CSIC, LINCGlobal, Avenida Reina Mercedes, 10, 41012, Sevilla, Spain
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103, Leipzig, Germany
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Banerjee S, Walder F, Büchi L, Meyer M, Held AY, Gattinger A, Keller T, Charles R, van der Heijden MGA. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J 2019; 13:1722-1736. [PMID: 30850707 PMCID: PMC6591126 DOI: 10.1038/s41396-019-0383-2] [Citation(s) in RCA: 367] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/04/2019] [Accepted: 02/17/2019] [Indexed: 01/28/2023]
Abstract
Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences the structure and complexity of microbial communities. We investigated the impact of conventional, no-till, and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harbored a much more complex fungal network with significantly higher connectivity than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. We also found a strong negative association (R2 = 0.366; P < 0.0001) between agricultural intensification and root fungal network connectivity. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH, and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiome.
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Affiliation(s)
- Samiran Banerjee
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland.
| | - Florian Walder
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland.
| | - Lucie Büchi
- Agroscope, Plant Production Systems, Route de Duillier 50, 1260, Nyon, Switzerland
- Natural Resources Institute, University of Greenwich, London, UK
| | - Marcel Meyer
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
| | - Alain Y Held
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
| | - Andreas Gattinger
- Research Institute of Organic Agriculture FiBL, 5070, Frick, Switzerland
- Justus-Liebig University Giessen, Organic Farming with focus on Sustainable Soil Use, Karl-Glöckner-Str. 21C, 35394, Giessen, Germany
| | - Thomas Keller
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Swedish University of Agricultural Sciences, Department of Soil & Environment, Box 7014, 75007, Uppsala, Sweden
| | - Raphael Charles
- Agroscope, Plant Production Systems, Route de Duillier 50, 1260, Nyon, Switzerland
- Research Institute of Organic Agriculture FiBL, Jordils 3, 1001, Lausanne, Switzerland
| | - Marcel G A van der Heijden
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, 8008, Zürich, Switzerland
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Reazin C, Baird R, Clark S, Jumpponen A. Chestnuts bred for blight resistance depart nursery with distinct fungal rhizobiomes. Mycorrhiza 2019; 29:313-324. [PMID: 31129728 DOI: 10.1007/s00572-019-00897-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Restoration of the American chestnut (Castanea dentata) is underway using backcross breeding that confers chestnut blight disease resistance from Asian chestnuts (most often Castanea mollissima) to the susceptible host. Successful restoration will depend on blight resistance and performance of hybrid seedlings, which can be impacted by below-ground fungal communities. We compared fungal communities in roots and rhizospheres (rhizobiomes) of nursery-grown, 1-year-old chestnut seedlings from different genetic families of American chestnut, Chinese chestnut, and hybrids from backcross breeding generations as well as those present in the nursery soil. We specifically focused on the ectomycorrhizal (EcM) fungi that may facilitate host performance in the nursery and aid in seedling establishment after outplanting. Seedling rhizobiomes and nursery soil communities were distinct and seedlings recruited heterogeneous communities from shared nursery soil. The rhizobiomes included EcM fungi as well as endophytes, putative pathogens, and likely saprobes, but their relative proportions varied widely within and among the chestnut families. Notably, hybrid seedlings that hosted few EcM fungi hosted a large proportion of potential pathogens and endophytes, with possible consequences in outplanting success. Our data show that chestnut seedlings recruit divergent rhizobiomes and depart nurseries with communities that may facilitate or compromise the seedling performance in the field.
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Affiliation(s)
| | - Richard Baird
- BCH-EPP Department, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Stacy Clark
- Southern Research Station, USDA Forest Service, Knoxville, TN, 37996, USA
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
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18
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Veresoglou SD, Verbruggen E, Makarova O, Mansour I, Sen R, Rillig MC. Arbuscular Mycorrhizal Fungi Alter the Community Structure of Ammonia Oxidizers at High Fertility via Competition for Soil NH 4. Microb Ecol 2019; 78:147-158. [PMID: 30402724 DOI: 10.1007/s00248-018-1281-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/24/2018] [Indexed: 05/20/2023]
Abstract
Nitrification represents a central process in the cycling of nitrogen (N) which in high-fertility habitats can occasionally be undesirable. Here, we explore how arbuscular mycorrhiza (AM) impacts nitrification when N availability is not limiting to plant growth. We wanted to test which of the mechanisms that have been proposed in the literature best describes how AM influences nitrification. We manipulated the growth settings of Plantago lanceolata so that we could control the mycorrhizal state of our plants. AM induced no changes in the potential nitrification rates or the estimates of ammonium oxidizing (AO) bacteria. However, we could observe a moderate shift in the community of ammonia-oxidizers, which matched the shift we saw when comparing hyphosphere to rhizosphere soil samples and mirrored well changes in the availability of ammonium in soil. We interpret our results as support that it is competition for N that drives the interaction between AM and AO. Our experiment sheds light on an understudied interaction which is pertinent to typical management practices in agricultural systems.
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Affiliation(s)
- Stavros D Veresoglou
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany.
| | - Erik Verbruggen
- Department of Plant and Vegetation Ecology, University of Antwerp, Antwerp, Belgium
| | - Olga Makarova
- Institute of Animal Hygiene and Environmental Health, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - India Mansour
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany
| | - Robin Sen
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, M1 5GD, UK
| | - Matthias C Rillig
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany
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19
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Zwiazek JJ, Equiza MA, Karst J, Senorans J, Wartenbe M, Calvo-Polanco M. Role of urban ectomycorrhizal fungi in improving the tolerance of lodgepole pine (Pinus contorta) seedlings to salt stress. Mycorrhiza 2019; 29:303-312. [PMID: 30982089 DOI: 10.1007/s00572-019-00893-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/02/2019] [Indexed: 05/27/2023]
Abstract
With large forested urban areas, the city of Edmonton, Alberta, Canada, faces high annual costs of replacing trees injured by deicing salts that are commonly used for winter road maintenance. Ectomycorrhizal fungi form symbiotic associations with tree roots that allow trees to tolerate the detrimental effects of polluted soils. Here, we examined mycorrhizal colonization of Pinus contorta by germinating seeds in soils collected from different locations: (1) two urban areas within the city of Edmonton, and (2) an intact pine forest just outside Edmonton. We then tested the responses of seedlings to 0-, 60-, and 90-mM NaCl. Our results showed lower abundance and diversity of ectomycorrhizal fungi in seedlings colonized with the urban soils compared to those from the pine forest soil. However, when subsequently exposed to NaCl treatments, only seedlings inoculated with one of the urban soils containing fungi from the genera Tuber, Suillus, and Wilcoxina, showed reduced shoot Na accumulation and higher growth rates. Our results indicate that local ectomycorrhizal fungi that are adapted to challenging urban sites may offer a potential suitable source for inoculum for conifer trees designated for plating in polluted urban environments.
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Affiliation(s)
- Janusz J Zwiazek
- Department of Renewable Resources, University of Alberta, 4-42 Earth Sciences Building, Edmonton, AB, T6G 2E3, Canada
| | - Maria A Equiza
- Department of Renewable Resources, University of Alberta, 4-42 Earth Sciences Building, Edmonton, AB, T6G 2E3, Canada
| | - Justine Karst
- Department of Renewable Resources, University of Alberta, 4-42 Earth Sciences Building, Edmonton, AB, T6G 2E3, Canada
| | - Jorge Senorans
- Department of Renewable Resources, University of Alberta, 4-42 Earth Sciences Building, Edmonton, AB, T6G 2E3, Canada
| | - Mark Wartenbe
- City of Edmonton, P.O. Box 2359, Edmonton, AB, T5J 2R7, Canada
| | - Monica Calvo-Polanco
- Department of Renewable Resources, University of Alberta, 4-42 Earth Sciences Building, Edmonton, AB, T6G 2E3, Canada.
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Faggioli V, Menoyo E, Geml J, Kemppainen M, Pardo A, Salazar MJ, Becerra AG. Soil lead pollution modifies the structure of arbuscular mycorrhizal fungal communities. Mycorrhiza 2019; 29:363-373. [PMID: 31016370 DOI: 10.1007/s00572-019-00895-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/08/2019] [Indexed: 05/09/2023]
Abstract
The impact of lead (Pb) pollution on native communities of arbuscular mycorrhizal fungi (AMF) was assessed in soil samples from the surroundings of an abandoned Pb smelting factory. To consider the influence of host identity, bulk soil surrounding plant roots soil samples of predominant plant species (Sorghum halepense, Bidens pilosa, and Tagetes minuta) growing in Pb-polluted soils and in an uncontaminated site were selected. Molecular diversity was assessed by sequencing the 18S rDNA region with primers specific to AMF (AMV4.5NF/AMDGR) using Illumina MiSeq. A total of 115 virtual taxa (VT) of AMF were identified in this survey. Plant species did not affect AMF diversity patterns. However, soil Pb content was negatively correlated with VT richness per sample. Paraglomeraceae and Glomeraceae were the predominant families while Acaulosporaceae, Ambisporaceae, Archaeosporaceae, Claroideoglomeraceae, Diversisporaceae, and Gigasporaceae were less abundant. Acaulosporaceae and Glomeraceae were negatively affected by soil Pb, but Paraglomeraceae relative abundance increased under increasing soil Pb content. Overall, 26 indicator taxa were identified; four of them were previously reported in Pb-polluted soils (VT060; VT222; VT004; VT380); and five corresponded to cultured spores of Scutellospora castaneae (VT041), Diversispora spp. and Tricispora nevadensis (VT060), Diversispora epigaea (VT061), Glomus proliferum (VT099), and Gl. indicum (VT222). Even though AMF were present in Pb-polluted soils, community structure was strongly altered via the differential responses of taxonomic groups of AMF to Pb pollution. These taxon-specific differences in tolerance to soil Pb content should be considered for future phytoremediation strategies based on the selection and utilization of native Glomeromycota.
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Affiliation(s)
- Valeria Faggioli
- Instituto Nacional de Tecnología Agropecuaria, EEA Marcos Juárez, Ruta 12 km 36, 2580, Marcos Juárez, Argentina
| | - Eugenia Menoyo
- Grupo de Estudios Ambientales (GEA), Instituto de Matemática Aplicada San Luis (IMASL)-CONICET, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700, San Luis, Argentina
| | - József Geml
- Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, Vondellaan 55, 2332 AA, Leiden, The Netherlands
| | - Minna Kemppainen
- Laboratorio de Micología Molecular, Instituto de Microbiología Básica y Aplicada (IMBA), Departamento de Ciencia y Tecnología, y CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña, 352, Bernal, Provincia de Buenos Aires, Argentina
| | - Alejandro Pardo
- Laboratorio de Micología Molecular, Instituto de Microbiología Básica y Aplicada (IMBA), Departamento de Ciencia y Tecnología, y CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña, 352, Bernal, Provincia de Buenos Aires, Argentina
| | - M Julieta Salazar
- Instituto Multidisciplinario de Biología Vegetal (IMBIV)-CONICET, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sársfield, 1611, Córdoba, Argentina
| | - Alejandra G Becerra
- Instituto Multidisciplinario de Biología Vegetal (IMBIV)-CONICET, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sársfield, 1611, Córdoba, Argentina.
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21
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Thoen E, Aas AB, Vik U, Brysting AK, Skrede I, Carlsen T, Kauserud H. A single ectomycorrhizal plant root system includes a diverse and spatially structured fungal community. Mycorrhiza 2019; 29:167-180. [PMID: 30929039 DOI: 10.1007/s00572-019-00889-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/19/2019] [Indexed: 05/11/2023]
Abstract
Although only a relatively small proportion of plant species form ectomycorrhizae with fungi, it is crucial for growth and survival for a number of widespread woody plant species. Few studies have attempted to investigate the fine scale spatial structure of entire root systems of adult ectomycorrhizal (EcM) plants. Here, we use the herbaceous perennial Bistorta vivipara to map the entire root system of an adult EcM plant and investigate the spatial structure of its root-associated fungi. All EcM root tips were sampled, mapped and identified using a direct PCR approach and Sanger sequencing of the internal transcribed spacer region. A total of 32.1% of all sampled root tips (739 of 2302) were successfully sequenced and clustered into 41 operational taxonomic units (OTUs). We observed a clear spatial structuring of the root-associated fungi within the root system. Clusters of individual OTUs were observed in the younger parts of the root system, consistent with observations of priority effects in previous studies, but were absent from the older parts of the root system. This may suggest a succession and fragmentation of the root-associated fungi even at a very fine scale, where competition likely comes into play at different successional stages within the root system.
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Affiliation(s)
- Ella Thoen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway.
| | - Anders B Aas
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
- Bymiljøetaten Oslo Kommune, PO box 636, Løren, 0507, Oslo, Norway
| | - Unni Vik
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
| | - Anne K Brysting
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
| | - Tor Carlsen
- The Natural History museum, University of Oslo, PO box 1172, Blindern, 0318, Oslo, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
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22
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Garcés‐Ruiz M, Senés‐Guerrero C, Declerck S, Cranenbrouck S. Community composition of arbuscular mycorrhizal fungi associated with native plants growing in a petroleum-polluted soil of the Amazon region of Ecuador. Microbiologyopen 2019; 8:e00703. [PMID: 30117306 PMCID: PMC6529925 DOI: 10.1002/mbo3.703] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/25/2018] [Accepted: 06/28/2018] [Indexed: 11/09/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are worldwide distributed plant symbionts. However, their occurrence in hydrocarbon-polluted environments is less investigated, although specific communities may be present with possible interest for remediation strategies. Here, we investigated the AMF community composition associated with the roots of diverse plant species naturally recolonizing a weathered crude oil pond in the Amazon region of Ecuador. Next generation 454 GS-Junior sequencing of an 800 bp LSU rRNA gene PCR amplicon was used. PCR amplicons were affiliated to a maximum-likelihood phylogenetic tree computed from 1.5 kb AMF reference sequences. A high throughput phylogenetic annotation approach, using an evolutionary placement algorithm (EPA) allowed the characterization of sequences to the species level. Fifteen species were detected. Acaulospora species were identified as dominant colonizers, with 73% of relative read abundance, Archaeospora (19.6%) and several genera from the Glomeraceae (Rhizophagus, Glomus macrocarpum-like, Sclerocystis, Dominikia and Kamienskia) were also detected. Although, a diverse community belonging to Glomeraceae was revealed, they represented <10% of the relative abundance in the Pond. Seventy five % of the species could not be identified, suggesting possible new species associated with roots of plants under highly hydrocarbon-polluted conditions.
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Affiliation(s)
- Mónica Garcés‐Ruiz
- Laboratory of MycologyEarth and Life InstituteUniversité catholique de LouvainLouvain‐la‐NeuveBelgium
- Laboratorio de micologíaCarrera de Microbiología, Facultad de Ciencia Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
| | | | - Stéphane Declerck
- Laboratory of MycologyEarth and Life InstituteUniversité catholique de LouvainLouvain‐la‐NeuveBelgium
| | - Sylvie Cranenbrouck
- Laboratory of MycologyEarth and Life InstituteUniversité catholique de LouvainLouvain‐la‐NeuveBelgium
- Laboratory of MycologyMycothèque de l'Université catholique de Louvain (MUCL/BCCM)Earth and Life Institute, Université catholique de LouvainLouvain‐la‐NeuveBelgium
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23
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Saw AK, Raj G, Das M, Talukdar NC, Tripathy BC, Nandi S. Alignment-free method for DNA sequence clustering using Fuzzy integral similarity. Sci Rep 2019; 9:3753. [PMID: 30842590 PMCID: PMC6403383 DOI: 10.1038/s41598-019-40452-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/28/2019] [Indexed: 12/28/2022] Open
Abstract
A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with the alignment-based method for sequence comparison. So, there is a high need for faster sequence analysis algorithms. In this study, we developed an alignment-free algorithm for faster sequence analysis. The novelty of our approach is the inclusion of fuzzy integral with Markov chain for sequence analysis in the alignment-free model. The method estimate the parameters of a Markov chain by considering the frequencies of occurrence of all possible nucleotide pairs from each DNA sequence. These estimated Markov chain parameters were used to calculate similarity among all pairwise combinations of DNA sequences based on a fuzzy integral algorithm. This matrix is used as an input for the neighbor program in the PHYLIP package for phylogenetic tree construction. Our method was tested on eight benchmark datasets and on in-house generated datasets (18 s rDNA sequences from 11 arbuscular mycorrhizal fungi (AMF) and 16 s rDNA sequences of 40 bacterial isolates from plant interior). The results indicate that the fuzzy integral algorithm is an efficient and feasible alignment-free method for sequence analysis on the genomic scale.
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Affiliation(s)
- Ajay Kumar Saw
- Institute of Advanced Study in Science and Technology, Mathematical Sciences Division, Guwahati, 781035, India
| | - Garima Raj
- Institute of Advanced Study in Science and Technology, Life Science Division, Guwahati, 781035, India
| | - Manashi Das
- Institute of Advanced Study in Science and Technology, Life Science Division, Guwahati, 781035, India
| | - Narayan Chandra Talukdar
- Institute of Advanced Study in Science and Technology, Life Science Division, Guwahati, 781035, India
| | | | - Soumyadeep Nandi
- Institute of Advanced Study in Science and Technology, Life Science Division, Guwahati, 781035, India.
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24
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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. Microb Ecol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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Lin LC, Ye YS, Lin WR. Characteristics of root-cultivable endophytic fungi from Rhododendron ovatum Planch. Braz J Microbiol 2019; 50:185-193. [PMID: 30637639 PMCID: PMC6863216 DOI: 10.1007/s42770-018-0011-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 08/23/2018] [Indexed: 11/26/2022] Open
Abstract
Ericoid mycorrhiza can improve the competitiveness of their host plants at the ecosystem level. The ability of ericoid mycorrhizal fungi to thrive under harsh environmental conditions suggests that they are capable of decomposing plant organic matter. This study aims to characterize 2 strains of root-cultivable endophytic fungi, RooDK1 and RooDK6, from Rhododendron ovatum Planch using colony and hyphal morphology, molecular analysis, observations of mycorrhiza, and investigations of adaptation to different sources of organic matter. Nitrogen utilization was also investigated by assessing protease production and growth on different nitrogen sources. Morphological studies indicated that both species are ericoid mycorrhizal fungi; our molecular studies confirmed RooDK1 as Oidiodendron maius and classified RooDK6 as Pezicula ericae. We observed that only RooDK1 can assist in host plant survival by degrading organic matter. This species also secretes protease and has the highest nitrate reductase activity of these 2 endophytes. Thus, RooDK1 has a greater ability to help the host plants thrive in a harsh habitat.
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Affiliation(s)
- Lei-Chen Lin
- Department of Forestry and Natural Resources, National Chiayi University, Chiayi, 60004, Taiwan.
| | - Yu-Sin Ye
- Department of Forestry and Natural Resources, National Chiayi University, Chiayi, 60004, Taiwan
| | - Wan-Rou Lin
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute (FIRDI), No. 331, Shih-Pin Road, Hsinchu, 30062, Taiwan
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26
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De Castro O, Avino M, Di Maio A, Menale B, Guida M. Sanger and next generation sequencing in the characterisation of arbuscular mycorrhizal fungi (AMF) in Pancratium maritimum L. (Amaryllidaceae), a representative plant species of Mediterranean sand dunes. Planta 2018; 248:1443-1453. [PMID: 30128603 DOI: 10.1007/s00425-018-2981-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
An interesting AMF colonization microcosm has been detected in the roots of Pancratium maritimum (sea daffodil). Both sequencing techniques (Sanger and NGS) have been used for AMF characterisation, showing a balanced trade-off between pros and cons. By Sanger and next generation sequencing of rRNA nuclear molecular markers (SSU-ITS-LSU and ITS2, respectively), the presence of AMF communities in the roots of P. maritimum was evaluated. Our results shed light on the presence of AMF in sea daffodil and the diversity of assemblages of AMF detected after Sanger sequencing of the SSU-ITS-LSU marker is much higher than that determined following NGS sequencing of ITS2 alone.
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Affiliation(s)
- Olga De Castro
- Department of Biology, University of Naples Federico II, Via Foria 223, Botanical Garden, 80139, Naples, Italy.
- DNATech srl, Spin-off Company of the University of Naples Federico II, Botanical Garden, Via Foria 223, 80139, Naples, Italy.
| | - Mariano Avino
- Department of Pathology and Laboratory Medicine, Western University, Dental Sciences Building, London, N6A 5C1, Canada
| | - Antonietta Di Maio
- DNATech srl, Spin-off Company of the University of Naples Federico II, Botanical Garden, Via Foria 223, 80139, Naples, Italy
| | - Bruno Menale
- Department of Biology, University of Naples Federico II, Via Foria 223, Botanical Garden, 80139, Naples, Italy
| | - Marco Guida
- DNATech srl, Spin-off Company of the University of Naples Federico II, Botanical Garden, Via Foria 223, 80139, Naples, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126, Naples, Italy
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27
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Symanczik S, Lehmann MF, Wiemken A, Boller T, Courty PE. Effects of two contrasted arbuscular mycorrhizal fungal isolates on nutrient uptake by Sorghum bicolor under drought. Mycorrhiza 2018; 28:779-785. [PMID: 30006910 DOI: 10.1007/s00572-018-0853-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
Drought is a limiting factor for crop production, especially in arid and semi-arid climates. In this study, Sorghum bicolor plants were inoculated, or not, with Rhizophagus irregularis, an arbuscular mycorrhizal (AM) strain typical for temperate climates, or Rhizophagus arabicus, a strain endemic to hyper-arid ecosystems. Plants were grown under well-watered or drought conditions in compartmented microcosms. Transpiration rates, plant growth, and nutrient uptake (using 15N as a tracer) were determined to assess the impact of drought stress on sorghum plants in AM symbiosis. Although AM colonization did not affect the bulk biomass of host plants, R. arabicus improved their transpiration efficiency and drought tolerance more than R. irregularis. Moreover, R. arabicus was able to extract more 15N from the soil under both water regimes, and AM-driven enhancement of the nitrogen and phosphorus content of sorghum, especially when water was limiting, was greater for R. arabicus-inoculated plants than for R. irregularis-inoculated plants. Our work demonstrates close links between AM hyphal phosphorus and nitrogen transport and uptake by AM plants for both AM fungal species. It also underscores that, under the drought stress conditions we applied, R. arabicus transfers significantly more nitrogen to sorghum than R. irregularis.
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Affiliation(s)
- Sarah Symanczik
- Zurich Basel Plant Science Center, Department of Environmental Sciences, University of Basel, Hebelstrasse 1, 4056, Basel, Switzerland
- Department of Soil Sciences, Research Institute of Organic Agriculture, Ackerstrasse 113, 5070, Frick, Switzerland
| | - Moritz F Lehmann
- Department of Environmental Sciences; Aquatic and Stable Isotope Biogeochemistry, University of Basel, Basel, Switzerland
| | - Andres Wiemken
- Zurich Basel Plant Science Center, Department of Environmental Sciences, University of Basel, Hebelstrasse 1, 4056, Basel, Switzerland
| | - Thomas Boller
- Zurich Basel Plant Science Center, Department of Environmental Sciences, University of Basel, Hebelstrasse 1, 4056, Basel, Switzerland
| | - Pierre-Emmanuel Courty
- Zurich Basel Plant Science Center, Department of Environmental Sciences, University of Basel, Hebelstrasse 1, 4056, Basel, Switzerland.
- Agroécologie, AgroSupDijon, CNRS, INRA, Université de Bourgogne Franche-Comté, 21000, Dijon, France.
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28
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Hugoni M, Luis P, Guyonnet J, Haichar FEZ. Plant host habitat and root exudates shape fungal diversity. Mycorrhiza 2018; 28:451-463. [PMID: 30109473 DOI: 10.1007/s00572-018-0857-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/25/2018] [Indexed: 05/06/2023]
Abstract
The rhizospheric microbiome is clearly affected by plant species and certain of their functional traits. These functional traits allow plants to adapt to their environmental conditions by acquiring or conserving nutrients, thus defining different ecological resource-use plant strategies. In the present study, we investigated whether plants with one of the two nutrient-use strategies (conservative versus exploitative) could influence fungal communities involved in soil organic matter degradation and root exudate assimilation, as well as those colonizing root tissues. We applied a DNA-based, stable-isotope probing (DNA-SIP) approach to four grass species distributed along a gradient of plant nutrient resource strategies, ranging from conservative to exploitative species, and analyzed their associated mycobiota composition using a fungal internal transcribed spacer (ITS) and Glomeromycotina 18S rRNA gene metabarcoding approach. Our results demonstrated that fungal taxa associated with exploitative and conservative plants could be separated into two general categories according to their location: generalists, which are broadly distributed among plants from each strategy and represent the core mycobiota of soil organic matter degraders, root exudate consumers in the root-adhering soil, and root colonizers; and specialists, which are locally abundant in one species and more specifically involved in soil organic matter degradation or root exudate assimilation on the root-adhering soil and the root tissues. Interestingly, for arbuscular mycorrhizal fungi analysis, all plant roots were mainly colonized by Glomus species, whereas an increased diversity of Glomeromycotina genera was observed for the exploitative plant species Dactylis glomerata.
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Affiliation(s)
- Mylène Hugoni
- CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Patricia Luis
- CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Julien Guyonnet
- CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Feth El Zahar Haichar
- CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France.
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29
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Argüelles-Moyao A, Garibay-Orijel R. Ectomycorrhizal fungal communities in high mountain conifer forests in central Mexico and their potential use in the assisted migration of Abies religiosa. Mycorrhiza 2018; 28:509-521. [PMID: 29948411 DOI: 10.1007/s00572-018-0841-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Abies religiosa forests in central Mexico are the only overwinter refuge of the monarch butterfly and provide important ecosystem services. These forests have lost 55% of their original area and as a consequence, diversity and biotic interactions in these ecosystems are in risk. The aim of this study was to compare the soil fungal diversity and community structure in the Abies religiosa forests and surrounding Pinus montezumae, Pinus hartwegii, and coniferous mixed forest plant communities to provide data on ecology of mycorrhizal interactions for the assisted migration of A. religiosa. We sampled soil from five coniferous forests, extracted total soil DNA, and sequenced the ITS2 region by Illumina MiSeq. The soil fungi community was integrated by 1746 taxa with a species turnover ranging from 0.280 to 0.461 between sampling sites. In the whole community, the more abundant and frequent species were Russula sp. (aff. olivobrunnea), Mortierella sp.1, and Piloderma sp. (aff. olivacearum). The ectomycorrhizal fungi were the more frequent and abundant functional group. A total of 298 species (84 ectomycorrhizal) was shared in the five conifer forests; these widely distributed species were dominated by Russulaceae and Clavulinaceae. The fungal community composition was significantly influenced by altitude and the lowest species turnover happened between the two A. religiosa forests even though they have different soil types. As Pinus montezumae forests have a higher altitudinal distribution adjacent to A. religiosa and share the largest number of ectomycorrhizal fungi with it, we suggest these forests as a potential habitat for new A. religiosa populations.
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Affiliation(s)
- Andrés Argüelles-Moyao
- Laboratorio de Sistemática, Ecología y Aprovechamiento de Hongos Ectomicorrízicos, Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria. Del. Coyoacán, C.P. 04510, Mexico City, CDMX, Mexico
- Posgrado en Ciencias Biológicas, Edificio B, 1° Piso, Unidad de Posgrado, Circuito de Posgrados, Universidad Nacional Autónoma de México, Ciudad Universitaria, Del. Coyoacán, C.P. 04510, Mexico City, CDMX, Mexico
| | - Roberto Garibay-Orijel
- Laboratorio de Sistemática, Ecología y Aprovechamiento de Hongos Ectomicorrízicos, Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria. Del. Coyoacán, C.P. 04510, Mexico City, CDMX, Mexico.
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30
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De Vita P, Avio L, Sbrana C, Laidò G, Marone D, Mastrangelo AM, Cattivelli L, Giovannetti M. Genetic markers associated to arbuscular mycorrhizal colonization in durum wheat. Sci Rep 2018; 8:10612. [PMID: 30006562 PMCID: PMC6045686 DOI: 10.1038/s41598-018-29020-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/04/2018] [Indexed: 11/09/2022] Open
Abstract
In this work we investigated the variability and the genetic basis of susceptibility to arbuscular mycorrhizal (AM) colonization of wheat roots. The mycorrhizal status of wild, domesticated and cultivated tetraploid wheat accessions, inoculated with the AM species Funneliformis mosseae, was evaluated. In addition, to detect genetic markers in linkage with chromosome regions involved in AM root colonization, a genome wide association analysis was carried out on 108 durum wheat varieties and two AM fungal species (F. mosseae and Rhizoglomus irregulare). Our findings showed that a century of breeding on durum wheat and the introgression of Reduced height (Rht) genes associated with increased grain yields did not select against AM symbiosis in durum wheat. Seven putative Quantitative Trait Loci (QTLs) linked with durum wheat mycorrhizal susceptibility in both experiments, located on chromosomes 1A, 2B, 5A, 6A, 7A and 7B, were detected. The individual QTL effects (r2) ranged from 7 to 16%, suggesting a genetic basis for this trait. Marker functional analysis identified predicted proteins with potential roles in host-parasite interactions, degradation of cellular proteins, homeostasis regulation, plant growth and disease/defence. The results of this work emphasize the potential for further enhancement of root colonization exploiting the genetic variability present in wheat.
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Affiliation(s)
- Pasquale De Vita
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy.
| | - Luciano Avio
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | | | - Giovanni Laidò
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy
| | - Daniela Marone
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy
| | - Anna M Mastrangelo
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, S.S. 673 km 25 + 200, 71121, Foggia, Italy
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, Via Stezzano 24, 24126, Bergamo, Italy
| | - Luigi Cattivelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Genomica e Bioinformatica, Via San Protaso 302, 29017, Fiorenzuola d'Arda, (PC), Italy
| | - Manuela Giovannetti
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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31
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Huang J, Han Q, Li J. Soil propagule bank of ectomycorrhizal fungi associated with Masson pine (Pinus massoniana) grown in a manganese mine wasteland. PLoS One 2018; 13:e0198628. [PMID: 29870548 PMCID: PMC5988271 DOI: 10.1371/journal.pone.0198628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/22/2018] [Indexed: 11/19/2022] Open
Abstract
Ectomycorrhizal (ECM) fungal propagule bank could facilitate the regeneration and plantation of seedlings in disturbed area. In this study, Masson pine (Pinus massoniana) seedlings were used to bait the ECM fungal propagule bank buried in the soils collected from a manganese (Mn) mine wasteland and a non-polluted area in China. After 6-month growth, we found the seedlings grown in the Mn mine soil (Mn:3200 mg kg-1) did not display any toxicity symptoms. Based on morphotyping and ITS-PCR sequencing, we identified a total of 16 ECM fungal OTUs (operative taxonomic units) at 97% similarity threshold, among which 11 OTUs were recovered in the Mn mine soils and 14 in the non-polluted soil. Two soil types shared 9 OTUs and both of them were dominated by a Tylospora sp. Based on those soil propagule banks in Masson pine forests reported in previous, we speculated that some Atheliaceae species may be preferred in the soil propagule bank of some pine species, such as Masson pine. In addition, NMDS ordination displayed geographical position effects on soil propagule banks in five Masson pine forest from three sites at regional scale. In conclusion, Masson pine ECM seedlings could grow well in the Mn wasteland as a suitable tree species used for reforestation application in Mn mineland, in addition, Mn pollution did not alter the dominant ECM fungal species in the soil propagule banks.
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Affiliation(s)
- Jian Huang
- College of Forestry, Northwest A&F University, Yangling, China
| | - Qisheng Han
- College of Forestry, Northwest A&F University, Yangling, China
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang, China
| | - Junjian Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
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Zhang T, Chen HYH, Ruan H. Global negative effects of nitrogen deposition on soil microbes. ISME J 2018; 12:1817-1825. [PMID: 29588494 PMCID: PMC6018792 DOI: 10.1038/s41396-018-0096-y] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/13/2018] [Accepted: 02/20/2018] [Indexed: 11/08/2022]
Abstract
Soil microbes comprise a large portion of the genetic diversity on Earth and influence a large number of important ecosystem processes. Increasing atmospheric nitrogen (N) deposition represents a major global change driver; however, it is still debated whether the impacts of N deposition on soil microbial biomass and respiration are ecosystem-type dependent. Moreover, the extent of N deposition impacts on microbial composition remains unclear. Here we conduct a global meta-analysis using 1408 paired observations from 151 studies to evaluate the responses of soil microbial biomass, composition, and function to N addition. We show that nitrogen addition reduced total microbial biomass, bacterial biomass, fungal biomass, biomass carbon, and microbial respiration. Importantly, these negative effects increased with N application rate and experimental duration. Nitrogen addition reduced the fungi to bacteria ratio and the relative abundances of arbuscular mycorrhizal fungi and gram-negative bacteria and increased gram-positive bacteria. Our structural equation modeling showed that the negative effects of N application on soil microbial abundance and composition led to reduced microbial respiration. The effects of N addition were consistent across global terrestrial ecosystems. Our results suggest that atmospheric N deposition negatively affects soil microbial growth, composition, and function across all terrestrial ecosystems, with more pronounced effects with increasing N deposition rate and duration.
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Affiliation(s)
- Tian'an Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Han Y H Chen
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Road, Thunder Bay, ON, P7B 5E1, Canada.
| | - Honghua Ruan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
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Smith GR, Steidinger BS, Bruns TD, Peay KG. Competition-colonization tradeoffs structure fungal diversity. ISME J 2018; 12:1758-1767. [PMID: 29491493 PMCID: PMC6018791 DOI: 10.1038/s41396-018-0086-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/28/2018] [Accepted: 02/07/2018] [Indexed: 01/13/2023]
Abstract
Findings of immense microbial diversity are at odds with observed functional redundancy, as competitive exclusion should hinder coexistence. Tradeoffs between dispersal and competitive ability could resolve this contradiction, but the extent to which they influence microbial community assembly is unclear. Because fungi influence the biogeochemical cycles upon which life on earth depends, understanding the mechanisms that maintain the richness of their communities is critically important. Here, we focus on ectomycorrhizal fungi, which are microbial plant mutualists that significantly affect global carbon dynamics and the ecology of host plants. Synthesizing theory with a decade of empirical research at our study site, we show that competition-colonization tradeoffs structure diversity in situ and that models calibrated only with empirically derived competition-colonization tradeoffs can accurately predict species-area relationships in this group of key eukaryotic microbes. These findings provide evidence that competition-colonization tradeoffs can sustain the landscape-scale diversity of microbes that compete for a single limiting resource.
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Affiliation(s)
- Gabriel R Smith
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
| | | | - Thomas D Bruns
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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Courty PE, Buée M, Tech JJT, Brulé D, Colin Y, Leveau JHJ, Uroz S. Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino. Mycorrhiza 2018; 28:343-356. [PMID: 29574496 DOI: 10.1007/s00572-018-0829-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/27/2018] [Indexed: 06/08/2023]
Abstract
Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical parent material and having the same climate conditions are particularly useful, as they isolate the factor of time from other factors controlling the character of soils. In our study, we considered a natural succession of uplifted marine terraces in Mendocino, CA, ranging from highly fertile in the younger terrace (about 100,000 years old) to infertile in the older terraces (about 300,000 years old). Using ITS amplicon pyrosequencing, we analysed and compared the diversity and composition of the soil fungal communities across the first terraces (T1 to T3), with a specific focus in the forested terraces (T2 and T3) on soil samples collected below trees of the same species (Pinus muricata) and of the same age. While diversity and richness indices were highest in the grassland (youngest) terrace (T1), they were higher in the older forested terrace (T3) compared to the younger forested terrace (T2). Interestingly, the most abundant ectomycorrhizal (ECM) taxa that we found within these fungal communities showed high homology with ITS Sanger sequences obtained previously directly from ECM root tips from trees in the same study site, revealing a relative conservation of ECM diversity over time. Altogether, our results provide new information about the diversity and composition of the fungal communities as well as on the dominant ECM species in the soil chronosequence of Mendocino in relation to soil age and ecosystem development.
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Affiliation(s)
- P E Courty
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - M Buée
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France
| | - J J T Tech
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - D Brulé
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Y Colin
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France
| | - J H J Leveau
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - S Uroz
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France.
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France.
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Cui J, Bai L, Liu X, Jie W, Cai B. Arbuscular mycorrhizal fungal communities in the rhizosphere of a continuous cropping soybean system at the seedling stage. Braz J Microbiol 2018; 49:240-247. [PMID: 29254630 PMCID: PMC5914137 DOI: 10.1016/j.bjm.2017.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/08/2017] [Accepted: 03/01/2017] [Indexed: 11/16/2022] Open
Abstract
Arbuscular mycorrhizae (AM) fungi play a crucial role in the growth of soybean; however, the planting system employed is thought to have an effect on AM fungal communities in the rhizosphere. This study was performed to explore the influence of continuous soybean cropping on the diversity of Arbuscular mycorrhizal (AM) fungi, and to identify the dominant AM fungus during the seedling stage. Three soybean cultivars were planted under two and three years continuous cropping, respectively. The diversity of AM fungi in the rhizosphere soil at the seedling stage was subsequently analyzed using polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE). The results showed that an increase in cropping years improved the colonization rate of AM in all three soybean cultivars. Moreover, the dominant species were found to be Funneliformis mosseae and Glomus species. The results of cluster analysis further confirmed that the number of years of continuous cropping significantly affected the composition of rhizospheric AM fungal communities in different soybean cultivars.
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Affiliation(s)
- Jiaqi Cui
- Heilongjiang University, College of Life Sciences, Harbin, China
| | - Li Bai
- Heilongjiang University, College of Life Sciences, Harbin, China
| | - Xiaorui Liu
- Heilongjiang University, College of Life Sciences, Harbin, China
| | - Weiguang Jie
- Heilongjiang University, College of Life Sciences, Harbin, China
| | - Baiyan Cai
- Heilongjiang University, College of Life Sciences, Harbin, China; Key Laboratory of Microbiology, Harbin, China.
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Vašutová M, Edwards-Jonášová M, Veselá P, Effenberková L, Fleischer P, Cudlín P. Management regime is the most important factor influencing ectomycorrhizal species community in Norway spruce forests after windthrow. Mycorrhiza 2018; 28:221-233. [PMID: 29352412 DOI: 10.1007/s00572-018-0820-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/05/2018] [Indexed: 06/07/2023]
Abstract
Ectomycorrhizal (ECM) fungi, as symbionts of many tree species in temperate forests, are thought to play an important role in forest regeneration processes after large disturbances. Their reaction to different disturbance and management regimes was studied in spruce forests (Lariceto-Piceetum) 10 years after a severe windthrow in the Tatra National Park (Slovak Republic). ECM community structure was compared between different "management types″-cleared area (EXT), area affected by wildfire (FIRE), uncleared area left for natural development (NEX), and mature forest as a control (REF). Based on Illumina sequencing of soil samples, we determined that the percentage of sequences assigned to ECM fungi decreased with increasing disturbance and management intensity (REF → NEX → EXT → FIRE). Similarly, the total number of ECM species per each of ten sampling points per plot (100 ha) differed between managed (EXT-11 species, FIRE-9) and unmanaged (NEX-16, REF-14) treatments. On the other hand, the percentage of sequences belonging to ericoid mycorrhizal fungi increased. Management type significantly influenced the composition of the ECM community, while vegetation and soil characteristics explained less data variation. The ECM species assemblage of the unmanaged site (NEX) was the most similar to the mature forest, while that of the burnt site was the most different. Thelephora terrestris dominated in all treatments affected by windthrow, accompanied by Tylospora fibrillosa (NEX) and Tylospora asterophora (EXT and FIRE). Management regime was also the most important factor affecting ECM species composition on the roots of spruce seedlings assessed by Sanger sequencing.
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Affiliation(s)
- Martina Vašutová
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, 37005, České Budějovice, Czech Republic.
- Global Change Research Institute, Czech Academy of Sciences, Lipová 1789/9, 37005, České Budějovice, Czech Republic.
| | - Magda Edwards-Jonášová
- Global Change Research Institute, Czech Academy of Sciences, Lipová 1789/9, 37005, České Budějovice, Czech Republic
| | - Petra Veselá
- Global Change Research Institute, Czech Academy of Sciences, Lipová 1789/9, 37005, České Budějovice, Czech Republic
| | - Lenka Effenberková
- Global Change Research Institute, Czech Academy of Sciences, Lipová 1789/9, 37005, České Budějovice, Czech Republic
| | - Peter Fleischer
- Faculty of Forestry, Technical University in Zvolen, T. G. Masaryka 2117/24, 960 53, Zvolen, Slovakia
- Research Station of TANAP, State Forest of TANAP, 059 60, Tatranská Lomnica, Slovakia
| | - Pavel Cudlín
- Global Change Research Institute, Czech Academy of Sciences, Lipová 1789/9, 37005, České Budějovice, Czech Republic
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Kohout P, Charvátová M, Štursová M, Mašínová T, Tomšovský M, Baldrian P. Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots. ISME J 2018; 12:692-703. [PMID: 29335638 PMCID: PMC5864242 DOI: 10.1038/s41396-017-0027-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/01/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022]
Abstract
Forest management practices often severely affect forest ecosystem functioning. Tree removal by clearcutting is one such practice, producing severe impacts due to the total reduction of primary productivity. Here, we assessed changes to fungal community structure and decomposition activity in the soil, roots and rhizosphere of a Picea abies stand for a 2-year period following clearcutting compared to data from before tree harvest. We found that the termination of photosynthate flow through tree roots into soil is associated with profound changes in soil, both in decomposition processes and fungal community composition. The rhizosphere, representing an active compartment of high enzyme activity and high fungal biomass in the living stand, ceases to exist and starts to resemble bulk soil. Decomposing roots appear to separate from bulk soil and develop into hotspots of decomposition and important fungal biomass pools. We found no support for the involvement of ectomycorrhizal fungi in the decomposition of roots, but we found some evidence that root endophytic fungi may have an important role in the early stages of this process. In soil, activity of extracellular enzymes also decreased in the long term following the end of rhizodeposition by tree roots.
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Affiliation(s)
- Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 142 20, Praha 4, Czech Republic
- Department of Mycorrhizal Symbiosis, Institute of Botany of the CAS, Zámek 1, 252 43, Průhonice, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Praha 2, Czech Republic
| | - Markéta Charvátová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 142 20, Praha 4, Czech Republic
| | - Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 142 20, Praha 4, Czech Republic
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 142 20, Praha 4, Czech Republic
| | - Michal Tomšovský
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 142 20, Praha 4, Czech Republic.
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38
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Sousa NMF, Veresoglou SD, Oehl F, Rillig MC, Maia LC. Predictors of Arbuscular Mycorrhizal Fungal Communities in the Brazilian Tropical Dry Forest. Microb Ecol 2018; 75:447-458. [PMID: 28779294 DOI: 10.1007/s00248-017-1042-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi with a broad distribution, and many taxa have physiological and ecological adaptations to specific environments, including semiarid ecosystems. Our aim was to address regional distribution patterns of AMF communities in such semiarid environments based on spore morphological techniques. We assessed AMF spores at the bottom and top of inselbergs distributed throughout the tropical dry forest in the Northeast region of Brazil. Across 10 replicate inselbergs and the surrounding area, spanning a range of altitude between 140 and 2000 m, we scored the AMF soil diversity and properties in 52 plots. We fitted parsimonious ordination analyses and variance partitioning models to determine the environmental factors which explained the variation in AMF community, based on morphological spore analysis. The diversity of AMF was similar at the bottom and top of inselbergs; however, we detected high variation in abundance and richness across sites. We formulated a parsimonious richness model that used physical soil factors as predictors. The AMF community structure could be best explained through the variables coarse and total sand, iron, organic matter, potassium, silt, and sodium which together accounted for 17.8% of total variance. Several AMF species were indicators of either deficiency or high values of specific soil properties. We demonstrated that habitat isolation of the inselbergs compared with surrounding areas did not trigger differences in AMF communities in semiarid regions of Brazil. At the regional scale, soil predictors across sites drove the distribution of symbiotic mycorrhizal fungi.
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Affiliation(s)
- Natália M F Sousa
- Programa de Pós-Graduação em Ciências Biológicas, Departamento de Micologia, Universidade Federal de Pernambuco, Av. da Engenharia s/n, Cidade Universitária, Recife, Pernambuco, Brazil.
| | - Stavros D Veresoglou
- Institut für Biologie, Freie Universität Berlin, Altensteinstr 6, 14195, Berlin, Germany
| | - Fritz Oehl
- Ecotoxicology, Agroscope Reckenholz-Agroscope, Wädenswil, CH-8820, Zürich, Switzerland
| | - Matthias C Rillig
- Ecotoxicology, Agroscope Reckenholz-Agroscope, Wädenswil, CH-8820, Zürich, Switzerland
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14196, Berlin, Germany
| | - Leonor C Maia
- Programa de Pós-Graduação em Ciências Biológicas, Departamento de Micologia, Universidade Federal de Pernambuco, Av. da Engenharia s/n, Cidade Universitária, Recife, Pernambuco, Brazil
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39
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Mucha J, Peay KG, Smith DP, Reich PB, Stefański A, Hobbie SE. Effect of Simulated Climate Warming on the Ectomycorrhizal Fungal Community of Boreal and Temperate Host Species Growing Near Their Shared Ecotonal Range Limits. Microb Ecol 2018; 75:348-363. [PMID: 28741266 PMCID: PMC5742605 DOI: 10.1007/s00248-017-1044-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/13/2017] [Indexed: 05/05/2023]
Abstract
Ectomycorrhizal (ECM) fungi can influence the establishment and performance of host species by increasing nutrient and water absorption. Therefore, understanding the response of ECM fungi to expected changes in the global climate is crucial for predicting potential changes in the composition and productivity of forests. While anthropogenic activity has, and will continue to, cause global temperature increases, few studies have investigated how increases in temperature will affect the community composition of ectomycorrhizal fungi. The effects of global warming are expected to be particularly strong at biome boundaries and in the northern latitudes. In the present study, we analyzed the effects of experimental manipulations of temperature and canopy structure (open vs. closed) on ectomycorrhizal fungi identified from roots of host seedlings through 454 pyrosequencing. The ecotonal boundary site selected for the study was between the southern boreal and temperate forests in northern Minnesota, USA, which is the southern limit range for Picea glauca and Betula papyrifera and the northern one for Pinus strobus and Quercus rubra. Manipulations that increased air and soil temperature by 1.7 and 3.4 °C above ambient temperatures, respectively, did not change ECM richness but did alter the composition of the ECM community in a manner dependent on host and canopy structure. The prediction that colonization of boreal tree species with ECM symbionts characteristic of temperate species would occur was not substantiated. Overall, only a small proportion of the ECM community appears to be strongly sensitive to warming.
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Affiliation(s)
- Joanna Mucha
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland.
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Dylan P Smith
- University of California, California Institute for Quantitative Biosciences, Berkeley, CA, USA
| | - Peter B Reich
- Department of Forest Resources, University of Minnesota, St. Paul, MN, USA
- Western Sydney University, Hawkesbury Institute for the Environment, Penrith, NSW, Australia
| | - Artur Stefański
- Department of Forest Resources, University of Minnesota, St. Paul, MN, USA
| | - Sarah E Hobbie
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
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Harris-Valle C, Esqueda M, Gutiérrez A, Castellanos AE, Gardea AA, Berbara R. Physiological response of Cucurbita pepo var. pepo mycorrhized by Sonoran desert native arbuscular fungi to drought and salinity stresses. Braz J Microbiol 2018; 49:45-53. [PMID: 28887008 PMCID: PMC5790584 DOI: 10.1016/j.bjm.2017.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 03/31/2017] [Accepted: 04/05/2017] [Indexed: 11/21/2022] Open
Abstract
Plants response to symbiosis with arbuscular mycorrhizal fungi (AMF) under water stress is important to agriculture. Under abiotic stress conditions native fungi are more effective than exotics in improving plant growth and water status. Mycorrhization efficiency is related to soil fungi development and energy cost-benefit ratio. In this study, we assessed the effect on growth, water status and energy metabolism of Cucurbita pepo var. pepo when inoculated with native AMF from the Sonoran desert Mexico (mixed isolate and field consortium), and compared with an exotic species from a temperate region, under drought, low and high salinity conditions. Dry weights, leaf water content, water and osmotic potentials, construction costs, photochemistry and mycorrhization features were quantified. Under drought and low salinity conditions, the mixed isolate increased plant growth and leaf water content. Leaf water potential was increased only by the field consortium under drought conditions (0.5-0.9MPa). Under high salinity, the field consortium increased aerial dry weight (more than 1g) and osmotic potential (0.54MPa), as compared to non-mycorrhized controls. Plants inoculated with native AMF, which supposedly diminish the effects of stress, exhibited low construction costs, increased photochemical capacity, and grew larger external mycelia in comparison to the exotic inoculum.
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Affiliation(s)
| | - Martín Esqueda
- Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico.
| | - Aldo Gutiérrez
- Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
| | | | - Alfonso A Gardea
- Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
| | - Ricardo Berbara
- Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Savary R, Masclaux FG, Wyss T, Droh G, Cruz Corella J, Machado AP, Morton JB, Sanders IR. A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis. ISME J 2018; 12:17-30. [PMID: 29027999 PMCID: PMC5739010 DOI: 10.1038/ismej.2017.153] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/20/2017] [Accepted: 08/21/2017] [Indexed: 11/26/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF; phylum Gomeromycota) associate with plants forming one of the most successful microbe-plant associations. The fungi promote plant diversity and have a potentially important role in global agriculture. Plant growth depends on both inter- and intra-specific variation in AMF. It was recently reported that an unusually large number of AMF taxa have an intercontinental distribution, suggesting long-distance gene flow for many AMF species, facilitated by either long-distance natural dispersal mechanisms or human-assisted dispersal. However, the intercontinental distribution of AMF species has been questioned because the use of very low-resolution markers may be unsuitable to detect genetic differences among geographically separated AMF, as seen with some other fungi. This has been untestable because of the lack of population genomic data, with high resolution, for any AMF taxa. Here we use phylogenetics and population genomics to test for intra-specific variation in Rhizophagus irregularis, an AMF species for which genome sequence information already exists. We used ddRAD sequencing to obtain thousands of markers distributed across the genomes of 81 R. irregularis isolates and related species. Based on 6 888 variable positions, we observed significant genetic divergence into four main genetic groups within R. irregularis, highlighting that previous studies have not captured underlying genetic variation. Despite considerable genetic divergence, surprisingly, the variation could not be explained by geographical origin, thus also supporting the hypothesis for at least one AMF species of widely dispersed AMF genotypes at an intercontinental scale. Such information is crucial for understanding AMF ecology, and how these fungi can be used in an environmentally safe way in distant locations.
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Affiliation(s)
- Romain Savary
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tania Wyss
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Germain Droh
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
- Laboratoire de Génétique, Unité de Formation et de Recherche en Biosciences, Université Félix Houphouet Boigny, Abidjan, Ivory Coast
| | - Joaquim Cruz Corella
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Joseph B Morton
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Ian R Sanders
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
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Thavamani P, Samkumar RA, Satheesh V, Subashchandrabose SR, Ramadass K, Naidu R, Venkateswarlu K, Megharaj M. Microbes from mined sites: Harnessing their potential for reclamation of derelict mine sites. Environ Pollut 2017; 230:495-505. [PMID: 28688926 DOI: 10.1016/j.envpol.2017.06.056] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/12/2017] [Accepted: 06/17/2017] [Indexed: 05/11/2023]
Abstract
Derelict mines pose potential risks to environmental health. Several factors such as soil structure, organic matter, and nutrient content are the greatly affected qualities in mined soils. Soil microbial communities are an important element for successful reclamation because of their major role in nutrient cycling, plant establishment, geochemical transformations, and soil formation. Yet, microorganisms generally remain an undervalued asset in mined sites. The microbial diversity in derelict mine sites consists of diverse species belonging to four key phyla: Proteobacteria, Acidobacteria, Firmicutes, and Bacteroidetes. The activity of plant symbiotic microorganisms including root-colonizing rhizobacteria and ectomycorrhizal fungi of existing vegetation in the mined sites is very high since most of these microbes are extremophiles. This review outlines the importance of microorganisms to soil health and the rehabilitation of derelict mines and how microbial activity and diversity can be exploited to better plan the soil rehabilitation. Besides highlighting the major breakthroughs in the application of microorganisms for mined site reclamation, we provide a critical view on plant-microbiome interactions to improve revegetation at the mined sites. Also, the need has been emphasized for deciphering the molecular mechanisms of adaptation and resistance of rhizosphere and non-rhizosphere microbes in abandoned mine sites, understanding their role in remediation, and subsequent harnessing of their potential to pave the way in future rehabilitation strategies for mined sites.
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Affiliation(s)
- Palanisami Thavamani
- Global Centre for Environmental Remediation, University of Newcastle, Australia.
| | - R Amos Samkumar
- ICAR- National Research Centre on Plant Biotechnology, Pusa, New Delhi 110012, India
| | - Viswanathan Satheesh
- ICAR- National Research Centre on Plant Biotechnology, Pusa, New Delhi 110012, India
| | | | - Kavitha Ramadass
- Future Industries Institute, University of South Australia, Australia
| | - Ravi Naidu
- Global Centre for Environmental Remediation, University of Newcastle, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapur 515055, India
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Hannula SE, Morriën E, de Hollander M, van der Putten WH, van Veen JA, de Boer W. Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. ISME J 2017; 11:2294-2304. [PMID: 28585935 PMCID: PMC5607372 DOI: 10.1038/ismej.2017.90] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/20/2017] [Accepted: 04/28/2017] [Indexed: 12/14/2022]
Abstract
Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands. Intact soil cores were collected from nine fields that represent three stages of land abandonment and pulse labeled with 13CO2. The fungal contribution to metabolization of plant-derived carbon was evaluated using phospholipid analysis combined with stable isotope probing (SIP), whereas fungal diversity was analyzed using DNA-SIP combined with 454-sequencing. We show that in recently abandoned fields most of the root-derived 13C was taken up by bacteria but that in long-term abandoned fields most of the root-derived 13C was found in fungal biomass. Furthermore, the composition of the active functional fungal community changed from one composed of fast-growing and pathogenic fungal species to one consisting of beneficial and slower-growing fungal species, which may have essential consequences for the carbon flow through the soil food web and consequently nutrient cycling and plant succession.
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Affiliation(s)
- S Emilia Hannula
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Elly Morriën
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, Department of Ecosytem and Landscape Dynamics (IBED-ELD), University of Amsterdam, Amsterdam, The Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Insititute of Biology, Leiden University, Leiden, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Soil Quality, Wageningen University & Research, Wageningen, The Netherlands
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44
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Mäkipää R, Rajala T, Schigel D, Rinne KT, Pennanen T, Abrego N, Ovaskainen O. Interactions between soil- and dead wood-inhabiting fungal communities during the decay of Norway spruce logs. ISME J 2017; 11:1964-1974. [PMID: 28430188 PMCID: PMC5563949 DOI: 10.1038/ismej.2017.57] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/18/2017] [Accepted: 03/03/2017] [Indexed: 11/25/2022]
Abstract
We investigated the interaction between fungal communities of soil and dead wood substrates. For this, we applied molecular species identification and stable isotope tracking to both soil and decaying wood in an unmanaged boreal Norway spruce-dominated stand. Altogether, we recorded 1990 operational taxonomic units, out of which more than 600 were shared by both substrates and 589 were found to exclusively inhabit wood. On average the soil was more species-rich than the decaying wood, but the species richness in dead wood increased monotonically along the decay gradient, reaching the same species richness and community composition as soil in the late stages. Decaying logs at all decay stages locally influenced the fungal communities from soil, some fungal species occurring in soil only under decaying wood. Stable isotope analyses suggest that mycorrhizal species colonising dead wood in the late decay stages actively transfer nitrogen and carbon between soil and host plants. Most importantly, Piloderma sphaerosporum and Tylospora sp. mycorrhizal species were highly abundant in decayed wood. Soil- and wood-inhabiting fungal communities interact at all decay phases of wood that has important implications in fungal community dynamics and thus nutrient transportation.
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Affiliation(s)
- Raisa Mäkipää
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Tiina Rajala
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Dmitry Schigel
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Katja T Rinne
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Taina Pennanen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Nerea Abrego
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Otso Ovaskainen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
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Crahay C, Munaut F, Colpaert JV, Huret S, Declerck S. Genetic stability of ectomycorrhizal fungi is not affected by cryopreservation at -130 °C or cold storage with repeated sub-cultivations over a period of 2 years. Mycorrhiza 2017; 27:595-601. [PMID: 28361204 DOI: 10.1007/s00572-017-0770-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 03/23/2017] [Indexed: 06/07/2023]
Abstract
Cryopreservation is considered the most reliable method for storage of filamentous fungi including ectomycorrhizal (ECM) fungi. A number of studies, however, have reported genetic changes in fungus cultures following cryopreservation. In the present study, the genetic stability of six ECM fungus isolates was analyzed using amplified fragment length polymorphism (AFLP). The isolates were preserved for 2 years either by cryopreservation (at -130 °C) or by storage at 4 °C with regular sub-cultivation. A third preservation treatment consisting of isolates maintained on Petri dishes at 22-23 °C for 2 years (i.e., without any sub-cultivation) was included and used as a control. The differences observed in AFLP patterns between the three preservation methods remained within the range of the total error generated by the AFLP procedure (6.85%). Therefore, cryopreservation at -130 °C and cold storage with regular sub-cultivation did not affect the genetic stability of the ECM fungus isolates, and both methods can be used for the routine storage of ECM fungus isolates over a period of 2 years.
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Affiliation(s)
- Charlotte Crahay
- Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Croix du Sud 2, bte L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Françoise Munaut
- Earth and Life Institute, Applied Microbiology, Phytopathology, Université catholique de Louvain, Croix du Sud 2, bte L7.05.03, 1348, Louvain-la-Neuve, Belgium
| | - Jan V Colpaert
- Center for Environmental Sciences, Environmental Biology Group, Universiteit Hasselt, Agoralaan, Gebouw D, 3590, Diepenbeek, Belgium
| | - Stéphanie Huret
- Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Mycothèque de l'Université catholique de Louvain (MUCL), Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Croix du Sud 2, bte L7.05.06, 1348, Louvain-la-Neuve, Belgium.
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Ruytinx J, Coninx L, Nguyen H, Smisdom N, Morin E, Kohler A, Cuypers A, Colpaert JV. Identification, evolution and functional characterization of two Zn CDF-family transporters of the ectomycorrhizal fungus Suillus luteus. Environ Microbiol Rep 2017; 9:419-427. [PMID: 28557335 DOI: 10.1111/1758-2229.12551] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
Two genes, SlZnT1 and SlZnT2, encoding Cation Diffusion Facilitator (CDF) family transporters were isolated from Suillus luteus mycelium by genome walking. Both gene models are very similar and phylogenetic analysis indicates that they are most likely the result of a recent gene duplication event. Comparative sequence analysis of the deduced proteins predicts them to be Zn transporters. This function was confirmed by functional analysis in yeast for SlZnT1. SlZnT1 was able to restore growth of the highly Zn sensitive yeast mutant Δzrc1 and localized to the vacuolar membrane. Transformation of Δzrc1 yeast cells with SlZnT1 resulted in an increased accumulation of Zn compared to empty vector transformed Δzrc1 yeast cells and equals Zn accumulation in wild type yeast cells. We were not able to express functional SlZnT2 in yeast. In S. luteus, both SlZnT genes are constitutively expressed whatever the external Zn concentrations. A labile Zn pool was detected in the vacuoles of S. luteus free-living mycelium. Therefore we conclude that SlZnT1 is indispensable for maintenance of Zn homeostasis by transporting excess Zn into the vacuole.
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Affiliation(s)
- Joske Ruytinx
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Agoralaan building D, Diepenbeek, 3590, Belgium
| | - Laura Coninx
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Agoralaan building D, Diepenbeek, 3590, Belgium
| | - Hoai Nguyen
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Agoralaan building D, Diepenbeek, 3590, Belgium
| | - Nick Smisdom
- Biomedical Research Institute, Hasselt University, Agoralaan building C, Diepenbeek, 3590, Belgium
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique, UMR1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Champenoux, 54280, France
| | - Annegret Kohler
- Institut National de la Recherche Agronomique, UMR1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Champenoux, 54280, France
| | - Ann Cuypers
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Agoralaan building D, Diepenbeek, 3590, Belgium
| | - Jan V Colpaert
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Agoralaan building D, Diepenbeek, 3590, Belgium
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47
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Koizumi T, Nara K. Communities of Putative Ericoid Mycorrhizal Fungi Isolated from Alpine Dwarf Shrubs in Japan: Effects of Host Identity and Microhabitat. Microbes Environ 2017; 32:147-153. [PMID: 28529264 PMCID: PMC5478538 DOI: 10.1264/jsme2.me16180] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/29/2017] [Indexed: 01/26/2023] Open
Abstract
Dwarf shrubs of the family Ericaceae are common in arctic and alpine regions. Many of these plants are associated with ericoid mycorrhizal (ERM) fungi, which allow them to take nutrients and water from the soil under harsh environmental conditions and, thus, affect host plant survival. Despite the importance of ERM fungi to alpine plant communities, limited information is available on the effects of microhabitat and host identity on ERM fungal communities. We investigated the communities of putative ERM fungi isolated from five dwarf shrub species (Arcterica nana, Diapensia lapponica, Empetrum nigrum, Loiseleuria procumbens, and Vaccinium vitis-idaea) that co-occur in an alpine region of Japan, with reference to distinct microhabitats provided by large stone pine (Pinus pumila) shrubs (i.e. bare ground, the edge of stone pine shrubs, and the inside of stone pine shrubs). We obtained 703 fungal isolates from 222 individual plants. These isolates were classified into 55 operational taxonomic units (OTUs) based on the sequencing of internal transcribed spacer regions in ribosomal DNA. These putative ERM fungal communities were dominated by Helotiales fungi for all host species. Cistella and Trimmatostroma species, which have rarely been detected in ERM roots in previous studies, were abundant. ERM fungal communities were significantly different among microhabitats (R2=0.28), while the host effect explained less variance in the fungal communities after excluding the microhabitat effect (R2=0.17). Our results suggest that the host effect on ERM fungal communities is minor and the distributions of hosts and fungal communities may be assessed based on microhabitat conditions.
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Affiliation(s)
- Takahiko Koizumi
- Department of Natural Environmental Studies, Graduate School of Frontier Science, The University of Tokyo5–1–5 Kashiwanoha, Kashiwa, Chiba, 277–8563Japan
| | - Kazuhide Nara
- Department of Natural Environmental Studies, Graduate School of Frontier Science, The University of Tokyo5–1–5 Kashiwanoha, Kashiwa, Chiba, 277–8563Japan
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Herrera H, Valadares R, Contreras D, Bashan Y, Arriagada C. Mycorrhizal compatibility and symbiotic seed germination of orchids from the Coastal Range and Andes in south central Chile. Mycorrhiza 2017; 27:175-188. [PMID: 27796595 DOI: 10.1007/s00572-016-0733-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/15/2016] [Indexed: 06/06/2023]
Abstract
Little is known about Orchidaceae plants in Chile and their mycorrhizal associations, a key issue for designing protective actions for endangered species. We investigated root fungi from seven terrestrial orchid species to identify potential mycorrhizal fungi. The main characteristics of Rhizoctonia-like fungi were observed under light microscopy, and isolates were identified through PCR-ITS sequencing. Molecular identification of fungal sequences showed a high diversity of fungi colonizing roots. Fungal ability to germinate seeds of different orchids was determined in symbiotic germination tests; 24 fungal groups were isolated, belonging to the genera Tulasnella, Ceratobasidium, and Thanatephorus. Furthermore, dark septate and other endophytic fungi were identified. The high number of Rhizoctonia-like fungi obtained from adult orchids from the Coastal mountain range suggests that, after germination, these orchids may complement their nutritional demands through mycoheterotrophy. Nonetheless, beneficial associations with other endophytic fungi may also co-exist. In this study, isolated mycorrhizal fungi had the ability to induce seed germination at different efficiencies and with low specificity. Germin ation rates were low, but protocorms continued to develop for 60 days. A Tulasnella sp. isolated from Chloraea gavilu was most effective to induce seed germination of different species. The dark septate endophytic (DSE) fungi did not show any effect on seed development; however, their widespread occurrence in some orchids suggests a putative role in plant establishment.
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Affiliation(s)
- Hector Herrera
- Departamento de Ciencias Forestales, Laboratorio de Biorremediación, Facultad de Ciencias Agropecuarias y Forestales, Universidad de La Frontera, Av. Francisco Salazar, 01145, Temuco, Chile
| | - Rafael Valadares
- Vale Institute of Technology - Sustainable Development, Rua Boaventura da silva 955, Cep 66050-090, Belém, PA, Brazil
| | - Domingo Contreras
- Facultad de Ciencias Básicas, Universidad Católica del Maule, Avenida San Miguel 3605, Casilla 617, Talca, Chile
| | - Yoav Bashan
- The Bashan Institute of Science, 1730 Post Oak Court, Auburn, AL, 36830, USA
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL, 36849, USA
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Av. IPN 195, La Paz, B.C.S. 23096, Mexico
| | - Cesar Arriagada
- Departamento de Ciencias Forestales, Laboratorio de Biorremediación, Facultad de Ciencias Agropecuarias y Forestales, Universidad de La Frontera, Av. Francisco Salazar, 01145, Temuco, Chile.
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Yamamoto K, Endo N, Degawa Y, Fukuda M, Yamada A. First detection of Endogone ectomycorrhizas in natural oak forests. Mycorrhiza 2017; 27:295-301. [PMID: 27817000 DOI: 10.1007/s00572-016-0740-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/10/2016] [Accepted: 10/25/2016] [Indexed: 05/27/2023]
Abstract
The order Endogonales in Mucoromycotina, an early divergent lineage of fungi, includes ectomycorrhizal (EM) fungi. This order is therefore considered a key taxon for elucidation of the evolution of EM associations. Recent studies have revealed high diversity of EM lineages of Basidiomycota and Ascomycota; however, EM associations of Endogonales and its relatives remain largely unknown. In this study, EM root tips with a unique fungal sheath, with aseptate and highly branched hyphae of variable widths, were identified in Quercus acutissima and Quercus crispula forests in the temperate zone of Japan. The mycobionts were confirmed as Endogone sp., which were placed as a sister clade of Endogone pisiformis, based on phylogenetic analyses of the small and large subunits of the nuclear ribosomal RNA and elongation factor-1α genes. This is the first report of EM of Endogone in natural forests of the Northern Hemisphere and the first finding on Quercus.
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Affiliation(s)
- Kohei Yamamoto
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, 8304, Minami-minowa, Nagano, 399-4598, Japan.
| | - Naoki Endo
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University, 4-101, Koyama, Tottori, 680-8553, Japan
| | - Yousuke Degawa
- Sugadaira Montane Research Center, University of Tsukuba, 1278-294, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | - Masaki Fukuda
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Shinshu University, 8304, Minami-minowa, Nagano, 399-4598, Japan
| | - Akiyoshi Yamada
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, 8304, Minami-minowa, Nagano, 399-4598, Japan
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Shinshu University, 8304, Minami-minowa, Nagano, 399-4598, Japan
- Division of Terrestrial Ecosystem, Institute of Mountain Science, Shinshu University, 8304, Minami-minowa, Nagano, 399-4598, Japan
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Mrak T, Kühdorf K, Grebenc T, Štraus I, Münzenberger B, Kraigher H. Scleroderma areolatum ectomycorrhiza on Fagus sylvatica L. Mycorrhiza 2017; 27:283-293. [PMID: 27913893 PMCID: PMC5352769 DOI: 10.1007/s00572-016-0748-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/17/2016] [Indexed: 05/17/2023]
Abstract
Despite its broad host range and distribution and its potential applications in commercial plantation forests, comprehensive descriptions of Scleroderma ectomycorrhizae are available only for Scleroderma citrinum, Scleroderma bovista and Scleroderma sinnamariense. This study provides a morphological and anatomical description of tree nursery derived ectomycorrhizae of Scleroderma areolatum on Fagus sylvatica, grown for several years in a climatized room. Ectomycorrhizae of S. areolatum were silvery white with abundant rhizomorphs; all mantle layers were plectenchymatous, rhizomorphs of type E, with prominent emanating hyphae with thick cell wall. The distal ends of emanating hyphae of rhizomorphs were inflated and often merged with other emanating hyphae. All parts of the mycorrhiza were clampless. In hyphae of the outer mantle layer, rhizomorphs and emanating hyphae, oily droplets were observed that did not stain in sulfo-vanillin and disappeared in lactic acid after a few hours. Although the phylogenetic analysis positioned the newly described ectomycorrhiza together with Scleroderma verrucosum and Scleroderma cepa in a single clade with a taxon name SH005470.07FU, the ectomycorrhizae of these three species can be morphologically well separated based on rhizomorph type.
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Affiliation(s)
- Tanja Mrak
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, Slovenia.
| | - Katja Kühdorf
- Institute of Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Strasse 84, 15374, Müncheberg, Germany
| | - Tine Grebenc
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, Slovenia
| | - Ines Štraus
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, Slovenia
| | - Babette Münzenberger
- Institute of Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Strasse 84, 15374, Müncheberg, Germany
| | - Hojka Kraigher
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, Slovenia
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