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Mészárošová L, Kuťáková E, Kohout P, Münzbergová Z, Baldrian P. Plant effects on microbiome composition are constrained by environmental conditions in a successional grassland. ENVIRONMENTAL MICROBIOME 2024; 19:8. [PMID: 38268048 PMCID: PMC10809484 DOI: 10.1186/s40793-024-00550-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND Below-ground microbes mediate key ecosystem processes and play a vital role in plant nutrition and health. Understanding the composition of the belowground microbiome is therefore important for maintaining ecosystem stability. The structure of the belowground microbiome is largely determined by individual plants, but it is not clear how far their influence extends and, conversely, what the influence of other plants growing nearby is. RESULTS To determine the extent to which a focal host plant influences its soil and root microbiome when growing in a diverse community, we sampled the belowground bacterial and fungal communities of three plant species across a primary successional grassland sequence. The magnitude of the host effect on its belowground microbiome varied among microbial groups, soil and root habitats, and successional stages characterized by different levels of diversity of plant neighbours. Soil microbial communities were most strongly structured by sampling site and showed significant spatial patterns that were partially driven by soil chemistry. The influence of focal plant on soil microbiome was low but tended to increase with succession and increasing plant diversity. In contrast, root communities, particularly bacterial, were strongly structured by the focal plant species. Importantly, we also detected a significant effect of neighbouring plant community composition on bacteria and fungi associating with roots of the focal plants. The host influence on root microbiome varied across the successional grassland sequence and was highest in the most diverse site. CONCLUSIONS Our results show that in a species rich natural grassland, focal plant influence on the belowground microbiome depends on environmental context and is modulated by surrounding plant community. The influence of plant neighbours is particularly pronounced in root communities which may have multiple consequences for plant community productivity and stability, stressing the importance of plant diversity for ecosystem functioning.
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Affiliation(s)
- Lenka Mészárošová
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic.
- University of Chemistry and Technology, Technická 5, Praha 6, 166 28, Czech Republic.
| | - Eliška Kuťáková
- Institute of Botany of the CAS, v. v. i., Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Skogsmarksgränd 17, Umeå, 901 83, Sweden
| | - Petr Kohout
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic
| | - Zuzana Münzbergová
- Institute of Botany of the CAS, v. v. i., Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic
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Ahmad W, Coffman L, Weerasooriya AD, Crawford K, Khan AL. The silicon regulates microbiome diversity and plant defenses during cold stress in Glycine max L. FRONTIERS IN PLANT SCIENCE 2024; 14:1280251. [PMID: 38269137 PMCID: PMC10805835 DOI: 10.3389/fpls.2023.1280251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 12/14/2023] [Indexed: 01/26/2024]
Abstract
Introduction With climate change, frequent exposure of bioenergy and food crops, specifically soybean (Glycine max L.), to low-temperature episodes is a major obstacle in maintaining sustainable plant growth at early growth stages. Silicon (Si) is a quasi-essential nutrient that can help to improve stress tolerance; however, how Si and a combination of cold stress episodes influence plant growth, plant physiology, and microbiome diversity has yet to be fully discovered. Methods The soybean plants were exposed to cold stress (8-10°C) with or without applying Si, and the different plant organs (shoot and root) and rhizospheric soil were subjected to microbiome analysis. The plant growth, physiology, and gene expression analysis of plant defenses during stress and Si were investigated. Results and discussion We showed that cold stress significantly retarded soybean plants' growth and biomass, whereas, Si-treated plants showed ameliorated negative impacts on plant growth at early seedling stages. The beneficial effects of Si were also evident from significantly reduced antioxidant activities - suggesting lower cold-induced oxidative stress. Interestingly, Si also downregulated critical genes of the abscisic acid pathway and osmotic regulation (9-cis-epoxy carotenoid dioxygenase and dehydration-responsive element binding protein) during cold stress. Si positively influenced alpha and beta diversities of bacterial and fungal microbiomes with or without cold stress. Results showed significant variation in microbiome composition in the rhizosphere (root and soil) and phyllosphere (shoot) in Si-treated plants with or without cold stress exposures. Among microbiome phyla, Proteobacteria, Bacteroidota, and Ascomycota were significantly more abundant in Si treatments in cold stress than in control conditions. For the core microbiome, we identified 179 taxa, including 88 unique bacterial genera in which Edaphobacter, Haliangium, and Streptomyces were highly abundant. Enhanced extracellular enzyme activities in the cold and Si+cold treatments, specifically phosphatase and glucosidases, also reflected the microbiome abundance. In conclusion, this work elucidates cold-mediated changes in microbiome diversity and plant growth, including the positive impact Si can have on cold tolerance at early soybean growth stages - a step toward understanding crop productivity and stress tolerance.
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Affiliation(s)
- Waqar Ahmad
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
- Department of Biology and Biochemistry, College of Natural Science & Mathematics, University of Houston, Houston, TX, United States
| | - Lauryn Coffman
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Aruna D Weerasooriya
- Cooperative Agricultural Research Center, College of Agriculture & Human Sciences, Prairie View A&M University, Prairie View, TX, United States
| | - Kerri Crawford
- Department of Biology and Biochemistry, College of Natural Science & Mathematics, University of Houston, Houston, TX, United States
| | - Abdul Latif Khan
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
- Department of Biology and Biochemistry, College of Natural Science & Mathematics, University of Houston, Houston, TX, United States
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3
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Doherty SJ, Busby RR, Baker CCM, Barbato RA. Rhizosphere microbial community structure differs between constant subzero and freeze-thaw temperature regimes in a subarctic soil. FEMS Microbiol Ecol 2023; 99:fiad147. [PMID: 37962959 DOI: 10.1093/femsec/fiad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/13/2023] [Indexed: 11/16/2023] Open
Abstract
In the Arctic and subarctic, climate change is causing reduced snowpack extent and earlier snowmelt. Shallower snowpack decreases the thermal insulation of underlying soil and results in more freeze-thaw conditions reflective of dynamic air temperatures. The aim of this study was to determine the effect of alternative temperature regimes on overall microbial community structure and rhizosphere recruitment across representatives of three subarctic plant functional groups. We hypothesized that temperature regime would influence rhizosphere community structure more than plant type. Planted microcosms were established using a tree, forb, grass, or no plant control and subjected to either freeze-thaw cycling or static subzero temperatures. Our results showed rhizosphere communities exhibited reduced diversity compared to bulk soils, and were influenced by temperature conditions and to a lesser extent plant type. We found that plants have a core microbiome that is persistent under different winter temperature scenarios but also have temperature regime-specific rhizosphere microbes. Freeze-thaw cycling resulted in greater community shifts from the pre-incubation soils when compared to constant subzero temperature. This finding suggests that wintertime snowpack conditions may be a significant factor for plant-microbe interactions upon spring thaw.
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Affiliation(s)
- Stacey J Doherty
- United States Army, Engineer Research Development Center, Cold Regions Research and Engineering Laboratory, Hanover, NH 03755, United States
| | - Ryan R Busby
- United States Army, Engineer Research Development Center, Construction Engineering Research Laboratory, Champaign, IL 61826, United States
| | - Christopher C M Baker
- United States Army, Engineer Research Development Center, Cold Regions Research and Engineering Laboratory, Hanover, NH 03755, United States
| | - Robyn A Barbato
- United States Army, Engineer Research Development Center, Cold Regions Research and Engineering Laboratory, Hanover, NH 03755, United States
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Feng Y, Zhang Y, Shah OU, Luo K, Chen Y. Isolation and Identification of Endophytic Bacteria Bacillus sp. ME9 That Exhibits Biocontrol Activity against Xanthomonas phaseoli pv. manihotis. BIOLOGY 2023; 12:1231. [PMID: 37759630 PMCID: PMC10525512 DOI: 10.3390/biology12091231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023]
Abstract
In recent years, the bacterial blight of cassava has caused substantial economic losses to the Chinese cassava industry. Chemical control methods have become the primary approach to control this disease; however, their widespread usage and harmful residues have raised concerns about environmental pollution. In order to avoid this, it is urgent to seek a green ecological method to prevent and control it. Biological control through the utilization of microorganisms not only effectively inhibits the disease, but also gives consideration to environmental friendliness. Therefore, investigating an endophytic biological control method for cassava bacterial blight is of great importance. In this study, cassava leaf tissues were used as test specimens in order to isolate endophytic bacteria by using dilution and separation methods. Bacillus ME9, derived from cassava endophytic bacteria, exhibits good antagonism against a diverse range of pathogens, including Xpm11. Its genome consists of a series of genes encoding antibacterial lipopeptides, which may be directly related to its antibacterial capabilities. Furthermore, inoculation resulted in a substantial change in the diversity of the endophytic bacterial community, characterized by improved diversity, and displayed an obvious inhibition of pathogenic bacterial growth, demonstrating successful colonization within plants. The results laid a foundation and provided theoretical support for the development and utilization of cassava endophytic bacterial diversity and endogenous disease control strategies.
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Affiliation(s)
- Yating Feng
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China (O.U.S.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yijie Zhang
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China (O.U.S.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Obaid Ullah Shah
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China (O.U.S.)
- Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou 570228, China
| | - Kai Luo
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China (O.U.S.)
| | - Yinhua Chen
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China (O.U.S.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
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5
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Tao S, Yin H, Fang Y, Zhang Y, Zhang N, Qu L. Elevated O 3 concentrations alter the compartment-specific microbial communities inhabiting rust-infected poplars. Environ Microbiol 2022; 25:990-1006. [PMID: 36582119 DOI: 10.1111/1462-2920.16332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
Elevated ozone (O3 ) can affect the susceptivity of plants to rust pathogens. However, the collective role of microbiomes involved in such interaction remains largely elusive. We exposed two cultivated poplar clones exhibiting differential O3 sensitivities, to non-filtered ambient air (NF), NF + 40 ppb or NF + 60 ppb O3 -enriched air in field open-top chambers and then inoculated Melampsora larici-populina urediniospores to study their response to rust infection and to investigate how microbiomes inhabiting four compartments (phyllosphere, rhizosphere, root endosphere, bulk soil) are involved in this response. We found that hosts with higher O3 sensitivity had significantly lower rust severity than hosts with lower sensitivity. Furthermore, the effect of increased O3 on the diversity and composition of microbial communities was highly dependent on poplar compartments, with the microbial network complexity patterns being completely opposite between the two clones. Notably, microbial source analysis estimated that phyllosphere fungal communities predominately derived from root endosphere and vice versa, suggesting a potential transmission mechanism between plant above- and below-ground systems. These promising results suggest that further investigations are needed to better understand the interactions of abiotic and biotic stresses on plant performance and the role of the microbiome in driving these changes.
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Affiliation(s)
- Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China.,Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People's Republic of China
| | - Haiyue Yin
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Yue Fang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China.,Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People's Republic of China
| | - Laiye Qu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing, China
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6
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Wang Q, Liu Y, Su Y, Cheng C, Shang B, Agathokleous E, Feng Z. Effects of elevated ozone on bacterial communities inhabiting the phyllo- and endo-spheres of rice plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154705. [PMID: 35318051 DOI: 10.1016/j.scitotenv.2022.154705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
To explore the effects of elevated ozone (O3) on microbial communities inhabiting phyllo- and endo-spheres of Japonica rice leaves, cultivars Nangeng 5055 (NG5055) and Wuyujing 27 (WYJ27) were grown in either charcoal-filtered air (CF) or elevated O3 (ambient O3 + 40 ppb, E-O3) in field open-top chambers (OTCs) during a growing season. E-O3 increased the values of the Shannon (43-80%) and Simpson (34-51%) indexes of the phyllo-and endo-spheric bacterial communities in NG5055. E-O3 also increased the values of the phyllosphere Simpson index by 58% and the endosphere Shannon index by 54% in WYJ27. Both diversity indexes positively correlated with the contents of nitrogen, phosphorus, magnesium, and soluble sugar, and negatively correlated with the contents of starch and condensed tannins. The leaf-associated bacterial community composition significantly changed in both rice cultivars under E-O3. Moreover, the leaf-associated bacterial communities in NG5055 were more sensitive to E-O3 than those in WYJ27. The chemical properties explained 70% and 98% of variations in the phyllosphere and endosphere bacterial communities, respectively, suggesting a predominant role of chemical status for the endospheric bacterial community. Most variation (57.3%) in the endosphere bacterial community assembly was explained by phosphorus. Gammaproteobacteria and Pantoea were found to be the most abundant class (63-76%) and genus (38-48%) in the phyllosphere and endosphere, respectively. E-O3 significantly increased the relative abundance of Bacteroidetes in the phyllosphere bacterial community and decreased the relative abundance of Gammaproteobacteria in the endophytic community. In conclusion, elevated O3 increased the diversity of bacterial communities of leaf phyllosphere and endosphere, and leaf chemical properties had a more pronounced effect on the endosphere bacterial community.
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Affiliation(s)
- Qi Wang
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Yuanyuan Liu
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Yi Su
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Cheng Cheng
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Bo Shang
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Evgenios Agathokleous
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Zhaozhong Feng
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China.
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7
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The diversity of bacterial endophytes from Iris pseudacorus L. and their plant beneficial traits. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100133. [PMID: 35909614 PMCID: PMC9325737 DOI: 10.1016/j.crmicr.2022.100133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This study reports the diversity of cultivable endophytic bacteria associated with yellow iris (Iris pseudacorus L.) by using 16S rRNA gene analysis and their plant beneficial traits. The 16S rRNA sequence similarities of endophytic bacteria isolated from the leaves and roots of yellow iris showed that the isolates belonged to the genera Staphylococcus, Streptomyces, Variovorax, Pantoea, Paenibacillus, Bacillus, Janthinobacterium, Enterobacter, Brevibacterium, Agrobacterium, Rhizobium, Xanthomonas translucens, and Pseudomonas. The endophytic bacteria Pseudomonas gessardii HRT18, Brevibacterium frigoritolerans HRT8, Streptomyces atratus HRT13, and Bacillus toyonensis HST13 exhibited antimicrobial activity against five plant pathogenic fungi Fusarium, Rhizoctonia, Botrytis, Pythium, and Alternaria. They also demonstrated the capability to produce chitinase, protease, glucanase, lipase, HCN, and indole-3-acetic acid (IAA). Thirteen isolates (46%) produced IAA, and the most active IAA producers were Bacillus cereus, Agrobacterium tumefaciens, Agrobacterium vitis, Bacillus megaterium, and Bacillus aryabhattai. The IAA producing bacterial isolates stimulated root and shoot growth of garden cress. Our findings suggest that medicinal plants could be a promising source for isolating plant-beneficial bacteria that can be used to enhance the growth and protect plants against soil-borne pathogens.
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Marian M, Licciardello G, Vicelli B, Pertot I, Perazzolli M. Ecology and potential functions of plant-associated microbial communities in cold environments. FEMS Microbiol Ecol 2022; 98:fiab161. [PMID: 34910139 PMCID: PMC8769928 DOI: 10.1093/femsec/fiab161] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.
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Affiliation(s)
- Malek Marian
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Giorgio Licciardello
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Bianca Vicelli
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Ilaria Pertot
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Michele Perazzolli
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
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9
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von Cräutlein M, Helander M, Korpelainen H, Leinonen PH, Vázquez de Aldana BR, Young CA, Zabalgogeazcoa I, Saikkonen K. Genetic Diversity of the Symbiotic Fungus Epichloë festucae in Naturally Occurring Host Grass Populations. Front Microbiol 2021; 12:756991. [PMID: 34925265 PMCID: PMC8678516 DOI: 10.3389/fmicb.2021.756991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/29/2021] [Indexed: 11/20/2022] Open
Abstract
Epichloë festucae is a common symbiont of the perennial and widely distributed cool season grass, Festuca rubra. The symbiosis is highly integrated involving systemic growth of the fungus throughout above-ground host parts and vertical transmission from plant to its offspring via host seeds. However, the nature of symbiosis is labile ranging from antagonistic to mutualistic depending on prevailing selection pressures. Both the loss of fungus in the maternal host lineage and horizontal transmission through sexual spores within the host population may partly explain the detected variation in symbiosis in wild grass populations. Epichloë species are commonly considered as pathogens when they produce sexual spores and partly castrate their host plant. This is the pathogenic end of the continuum from antagonistic to mutualistic interactions. Here we examined the population genetic structure of E. festucae to reveal the gene flow, importance of reproduction modes, and alkaloid potential of the symbiotic fungus in Europe. Epichloë-species are highly dependent on the host in survival and reproduction whilst benefits to the host are largely linked to defensive mutualism attributable to fungal-origin bioactive alkaloids that negatively affect vertebrate and/or invertebrate herbivores. We detected decreased genetic diversity in previously glaciated areas compared to non-glaciated regions during the last glacial maximum period and found three major genetic clusters in E. festucae populations: southern, northeastern and northwestern Europe. Sexual reproduction may have a higher role than expected in Spanish E. festucae populations due to the predominance of unique genotypes and presence of both mating types in the region. In contrast, asexual reproduction via host seeds predominates in the Faroe Island and Finland in northern Europe due to the presence of biased mating-type ratios and large dominant genotypes in the E. festucae populations within the region. A substantially larger variation of alkaloid genotypes was observed in the fungal populations than expected, although the variability of the alkaloid genotypes within populations is considerably lower in northern than Spanish populations in southern Europe. E. festucae populations consist of different combinations of alkaloid classes from the gene clusters of ergot alkaloid and indole-terpenes, and from pyrrolopyrazine alkaloid gene. We suggest that the postglacial distribution history of the host grass, prevailing reproduction strategies of E. festucae, and local selection pressures likely explain a large part of the genetic variation observed in fungal populations among geographic regions. The identified alkaloid genotypes can be used by turfgrass breeders to improve resistance against herbivores in red fescue varieties and to develop new sustainable cultivars in Europe.
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Affiliation(s)
- Maria von Cräutlein
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke), Helsinki, Finland.,Biodiversity Unit, University of Turku, Turku, Finland
| | - Marjo Helander
- Department of Biology, University of Turku, Turku, Finland
| | - Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Päivi Helena Leinonen
- Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke), Helsinki, Finland.,Biodiversity Unit, University of Turku, Turku, Finland
| | - Beatriz R Vázquez de Aldana
- Institute of Natural Resources and Agrobiology of Salamanca, Spanish National Research Council (CSIC), Salamanca, Spain
| | | | - Iñigo Zabalgogeazcoa
- Institute of Natural Resources and Agrobiology of Salamanca, Spanish National Research Council (CSIC), Salamanca, Spain
| | - Kari Saikkonen
- Biodiversity Unit, University of Turku, Turku, Finland.,Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke), Turku, Finland
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10
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Juurakko CL, diCenzo GC, Walker VK. Cold Acclimation in Brachypodium Is Accompanied by Changes in Above-Ground Bacterial and Fungal Communities. PLANTS (BASEL, SWITZERLAND) 2021; 10:2824. [PMID: 34961295 PMCID: PMC8704670 DOI: 10.3390/plants10122824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 01/04/2023]
Abstract
Shifts in microbiota undoubtedly support host plants faced with abiotic stress, including low temperatures. Cold-resistant perennials prepare for freeze stress during a period of cold acclimation that can be mimicked by transfer from growing conditions to a reduced photoperiod and a temperature of 4 °C for 2-6 days. After cold acclimation, the model cereal, Brachypodium distachyon, was characterized using metagenomics supplemented with amplicon sequencing (16S ribosomal RNA gene fragments and an internal transcribed spacer region). The bacterial and fungal rhizosphere remained largely unchanged from that of non-acclimated plants. However, leaf samples representing bacterial and fungal communities of the endo- and phyllospheres significantly changed. For example, a plant-beneficial bacterium, Streptomyces sp. M2, increased more than 200-fold in relative abundance in cold-acclimated leaves, and this increase correlated with a striking decrease in the abundance of Pseudomonas syringae (from 8% to zero). This change is of consequence to the host, since P. syringae is a ubiquitous ice-nucleating phytopathogen responsible for devastating frost events in crops. We posit that a responsive above-ground bacterial and fungal community interacts with Brachypodium's low temperature and anti-pathogen signalling networks to help ensure survival in subsequent freeze events, underscoring the importance of inter-kingdom partnerships in the response to cold stress.
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Affiliation(s)
- Collin L. Juurakko
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; (G.C.d.); (V.K.W.)
| | - George C. diCenzo
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; (G.C.d.); (V.K.W.)
| | - Virginia K. Walker
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; (G.C.d.); (V.K.W.)
- Department of Biomedical and Molecular Sciences, School of Environmental Studies, Queen’s University, Kingston, ON K7L 3N6, Canada
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Singh RK, Singh P, Guo DJ, Sharma A, Li DP, Li X, Verma KK, Malviya MK, Song XP, Lakshmanan P, Yang LT, Li YR. Root-Derived Endophytic Diazotrophic Bacteria Pantoea cypripedii AF1 and Kosakonia arachidis EF1 Promote Nitrogen Assimilation and Growth in Sugarcane. Front Microbiol 2021; 12:774707. [PMID: 34975800 PMCID: PMC8714890 DOI: 10.3389/fmicb.2021.774707] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/12/2021] [Indexed: 11/15/2022] Open
Abstract
Excessive, long-term application of chemical fertilizers in sugarcane crops disrupts soil microbial flora and causes environmental pollution and yield decline. The role of endophytic bacteria in improving crop production is now well-documented. In this study, we have isolated and identified several endophytic bacterial strains from the root tissues of five sugarcane species. Among them, eleven Gram-negative isolates were selected and screened for plant growth-promoting characteristics, i.e., production of siderophores, indole-3-acetic acid (IAA), ammonia, hydrogen cyanide (HCN), and hydrolytic enzymes, phosphorus solubilization, antifungal activity against plant pathogens, nitrogen-fixation, 1-aminocyclopropane-1-carboxylic acid deaminase activity, and improving tolerance to different abiotic stresses. These isolates had nifH (11 isolates), acdS (8 isolates), and HCN (11 isolates) genes involved in N-fixation, stress tolerance, and pathogen biocontrol, respectively. Two isolates Pantoea cypripedii AF1and Kosakonia arachidis EF1 were the most potent strains and they colonized and grew in sugarcane plants. Both strains readily colonized the leading Chinese sugarcane variety GT42 and significantly increased the activity of nitrogen assimilation enzymes (glutamine synthetase, NADH glutamate dehydrogenase, and nitrate reductase), chitinase, and endo-glucanase and the content of phytohormones gibberellic acid, indole-3-acetic acid, and abscisic acid. The gene expression analysis of GT42 inoculated with isolates of P. cypripedii AF1 or K. arachidis EF1 showed increased activity of nifH and nitrogen assimilation genes. Also, the inoculated diazotrophs significantly increased plant nitrogen content, which was corroborated by the 15N isotope dilution analysis. Collectively, these findings suggest that P. cypripedii and K. arachidis are beneficial endophytes that could be used as a biofertilizer to improve plant nitrogen nutrition and growth of sugarcane. To the best of our knowledge, this is the first report of sugarcane growth enhancement and nitrogen fixation by Gram-negative sugarcane root-associated endophytic bacteria P. cypripedii and K. arachidis. These strains have the potential to be utilized as sugarcane biofertilizers, thus reducing nitrogen fertilizer use and improving disease management.
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Affiliation(s)
- Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Dao-Jun Guo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Dong-Ping Li
- Microbiology Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiang Li
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Mukesh Kumar Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Prakash Lakshmanan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- Interdisciplinary Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, China
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Li-Tao Yang
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
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12
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Glick BR, Gamalero E. Recent Developments in the Study of Plant Microbiomes. Microorganisms 2021; 9:microorganisms9071533. [PMID: 34361969 PMCID: PMC8306116 DOI: 10.3390/microorganisms9071533] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/11/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia with the collective being responsible for the positive effects on plant growth. Different plants attract different cross-sections of the bacteria and fungi in the soil, initially based on the composition of the unique root exudates from each plant. Thus, plants mostly attract those microorganisms that are beneficial to plants and exclude those that are potentially pathogenic. Beneficial bacterial consortia not only help to promote plant growth, these consortia also protect plants from a wide range of direct and indirect environmental stresses. Moreover, it is currently possible to engineer plant seeds to contain desired bacterial strains and thereby benefit the next generation of plants. In this way, it may no longer be necessary to deliver beneficial microbiota to each individual growing plant. As we develop a better understanding of beneficial bacterial microbiomes, it may become possible to develop synthetic microbiomes where compatible bacteria work together to facilitate plant growth under a wide range of natural conditions.
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Affiliation(s)
- Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel, 11, 15121 Alessandria, Italy
- Correspondence:
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13
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Liu J, Su J, Zhang M, Luo Z, Li X, Chai B. Bacterial Community Spacing Is Mainly Shaped by Unique Species in the Subalpine Natural Lakes of China. Front Microbiol 2021; 12:669131. [PMID: 34276600 PMCID: PMC8282455 DOI: 10.3389/fmicb.2021.669131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities have been described as early indicators of both regional and global climatic change and play a critical role in the global biogeochemical cycle. Exploring the mechanisms that determine the diversity patterns of bacterial communities and how they share different habitats along environmental gradients are, therefore, a central theme in microbial ecology research. We characterized the diversity patterns of bacterial communities in Pipahai Lake (PPH), Mayinghai Lake (MYH), and Gonghai Lake (GH), three subalpine natural lakes in Ningwu County, Shanxi, China, and analyzed the distribution of their shared and unique taxa (indicator species). Results showed that the species composition and structure of bacterial communities were significantly different among the three lakes. Both the structure of the entire bacterial community and the unique taxa were significantly influenced by the carbon content (TOC and IC) and space distance; however, the structure of the shared taxa was affected by conductivity (EC), pH, and salinity. The structure of the entire bacterial community and unique taxa were mainly affected by the same factors, suggesting that unique taxa may be important in maintaining the spatial distribution diversity of bacterial communities in subalpine natural freshwater lakes. Our results provide new insights into the diversity maintenance patterns of the bacterial communities in subalpine lakes, and suggest dispersal limitation on bacterial communities between adjacent lakes, even in a small local area. We revealed the importance of unique taxa in maintaining bacterial community structure, and our results are important in understanding how bacterial communities in subalpine lakes respond to environmental change in local habitats.
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Affiliation(s)
- Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Jiahe Su
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Zhengming Luo
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China.,Department of Geography, Xinzhou Teachers University, Xinzhou, China
| | - Xiaoqi Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
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14
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Huang K, Wang J, Huang J, Zhang S, Vogler AP, Liu Q, Li Y, Yang M, Li Y, Zhou X. Host Phylogeny and Diet Shape Gut Microbial Communities Within Bamboo-Feeding Insects. Front Microbiol 2021; 12:633075. [PMID: 34239504 PMCID: PMC8260032 DOI: 10.3389/fmicb.2021.633075] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome plays an important role in a host’s development and adaption to its dietary niche. In this study, a group of bamboo-feeding insects are used to explore the potential role of the gut microbiota in the convergent adaptation to extreme diet specialization. Specifically, using a 16S rRNA marker and an Illumina sequencing platform, we profiled the microbial communities of 76 gut samples collected from nine bamboo-feeding insects, including both hemimetabolous (Orthoptera and Hemiptera) and holometabolous (Coleoptera and Lepidoptera) species, which are specialized in three distinct dietary niches: bamboo leaf, shoot, and sap. The gut microbiota of these insects were dominated by Proteobacteria, Firmicutes, and Bacteroidetes and were clustered into solid (leaf and shoot) and liquid (sap) dietary niches. The gut bacterial communities of insects feeding on solid diet overlapped significantly, even though these insects belong to phylogenetically distant lineages representing different orders. In addition, the presence of cellulolytic bacterial communities within the gut microbiota allows bamboo-feeding insects to adapt to a highly specialized, fiber-rich diet. Although both phylogeny and diet can impact the structure and composition of gut microbiomes, phylogeny is the primary driving force underlying the convergent adaptation to a highly specialized diet, especially when the related insect species harbor similar gut microbiomes and share the same dietary niche over evolutionary timescales. These combined findings lay the foundation for future research on how convergent feeding strategies impact the interplays between hosts and their gut microbiomes and how the gut microbiota may facilitate convergent evolution in phylogenetically distant species in adaptation to the shared diet.
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Affiliation(s)
- Kuanguan Huang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Jie Wang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Junhao Huang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Shouke Zhang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London Silwood Park, Ascot, United Kingdom
| | - Quanquan Liu
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Yongchun Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Maowei Yang
- Institute of Forestry Investigation and Planning of Guangning, Guangning, China
| | - You Li
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, United States
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15
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Bolivar-Anillo HJ, González-Rodríguez VE, Cantoral JM, García-Sánchez D, Collado IG, Garrido C. Endophytic Bacteria Bacillus subtilis, Isolated from Zea mays, as Potential Biocontrol Agent against Botrytis cinerea. BIOLOGY 2021; 10:biology10060492. [PMID: 34205845 PMCID: PMC8229056 DOI: 10.3390/biology10060492] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/20/2022]
Abstract
Simple Summary Plant–microorganism associations date back more than 400 million years. Plants host microorganisms that establish many different relationships with them, some negative and others very positive for both organisms. A type of this relationship is established with microorganisms that live inside them, known as endophytic microorganisms; they can include bacteria, yeasts, and fungi. In this study, we isolate endophytic bacteria from maize plants, and we characterize them in order to check their potential for being used as biocontrol agents against Botrytis cinerea, one of the most important phytopathogenic fungi in the world. The endophytic bacteria showed this antagonistic effect during in vitro assay and also during in vivo assay in Phaseolus vulgaris. At the same time, they showed the capacity for promoting growth in Zea mays plants. Abstract Plant diseases are one of the main factors responsible for food loss in the world, and 20–40% of such loss is caused by pathogenic infections. Botrytis cinerea is the most widely studied necrotrophic phytopathogenic fungus. It is responsible for incalculable economic losses due to the large number of host plants affected. Today, B. cinerea is controlled mainly by synthetic fungicides whose frequent application increases risk of resistance, thus making them unsustainable in terms of the environment and human health. In the search for new alternatives for the biocontrol of this pathogen, the use of endophytic microorganisms and their metabolites has gained momentum in recent years. In this work, we isolated endophytic bacteria from Zea mays cultivated in Colombia. Several strains of Bacillus subtilis, isolated and characterized in this work, exhibited growth inhibition against B. cinerea of more than 40% in in vitro cultures. These strains were characterized by studying several of their biochemical properties, such as production of lipopeptides, potassium solubilization, proteolytic and amylolytic capacity, production of siderophores, biofilm assays, and so on. We also analyzed: (i) its capacity to promote maize growth (Zea mays) in vivo, and (ii) its capacity to biocontrol B. cinerea during in vivo infection in plants (Phaseolus vulgaris).
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Affiliation(s)
- Hernando José Bolivar-Anillo
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4 planta, Universidad de Cádiz, 11510 Puerto Real, Spain;
- Programa de Microbiología, Facultad de Ciencias Básicas y Biomédicas, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Victoria E. González-Rodríguez
- Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Spain; (V.E.G.-R.); (J.M.C.); (D.G.-S.)
| | - Jesús M. Cantoral
- Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Spain; (V.E.G.-R.); (J.M.C.); (D.G.-S.)
| | - Darío García-Sánchez
- Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Spain; (V.E.G.-R.); (J.M.C.); (D.G.-S.)
| | - Isidro G. Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4 planta, Universidad de Cádiz, 11510 Puerto Real, Spain;
- Correspondence: (I.G.C.); (C.G.)
| | - Carlos Garrido
- Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Spain; (V.E.G.-R.); (J.M.C.); (D.G.-S.)
- Correspondence: (I.G.C.); (C.G.)
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16
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Singh P, Singh RK, Guo DJ, Sharma A, Singh RN, Li DP, Malviya MK, Song XP, Lakshmanan P, Yang LT, Li YR. Whole Genome Analysis of Sugarcane Root-Associated Endophyte Pseudomonas aeruginosa B18-A Plant Growth-Promoting Bacterium With Antagonistic Potential Against Sporisorium scitamineum. Front Microbiol 2021; 12:628376. [PMID: 33613496 PMCID: PMC7894208 DOI: 10.3389/fmicb.2021.628376] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/12/2021] [Indexed: 12/20/2022] Open
Abstract
Sugarcane smut is a significant fungal disease that causes a major loss in sugar yield and quality. In this study, we isolated an endophytic strain B18 from a sugarcane root, which showed plant growth-promotion, hydrolytic enzyme production, antifungal activity against sugarcane pathogens (Sporisorium scitamineum, Ceratocystis paradoxa, Fusarium verticillioides), and the presence of nifH, acdS, and antibiotic genes (hcn, prn, and phCA) under in vitro conditions. BIOLOG(R) phenotypic profiling of B18 established its ability to use various carbon and nitrogen sources and tolerate a range of pH and osmotic and temperature stresses. Whole-genome analysis of B18, identified as Pseudomonas aeruginosa, showed that it consists of a single circular chromosome of 6,490,014 bp with 66.33% GC content. Genome annotation has identified 5,919 protein-coding genes, and 65 tRNA, and 12 rRNA genes. The P. aeruginosa B18 genome encodes genes related to ethylene, nitrogen (nifU, norBCDERQ, gltBDPS, and aatJMPQ), and phosphate (pstABCS and phoBDHRU) metabolism and produce indole-3-acetic acid and siderophores. This also includes genes encoding hydrolases and oxidoreductases, those associated with biocontrol mechanisms (hcnABC, phzA_B, phzDEFGMS, and pchA), colonization (minCDE and lysC), and biofilm formation (efp, hfq, flgBCDEFGHI, and motAB), and those associated with metabolism of secondary metabolites. Collectively, these results suggest a role for P. aeruginosa B18 in plant growth enhancement and biocontrol mechanisms. The P. aeruginosa B18 strain was found to be an efficient colonizer in sugarcane; it can improve growth through modulation of plant hormone production and enhanced host-plant resistance to smut pathogen S. scitamineum in a smut-susceptible sugarcane variety (Yacheng71-374). These biocontrol and plant growth promotion properties of P. aeruginosa B18 area are discussed in this report.
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Affiliation(s)
- Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Dao-Jun Guo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China.,College of Agriculture, Guangxi University, Nanning, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | | | - Dong-Ping Li
- Microbiology Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Mukesh K Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Prakash Lakshmanan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin (CAGD), College of Resources and Environment, Southwest University, Chongqing, China.,Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Li-Tao Yang
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China.,College of Agriculture, Guangxi University, Nanning, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China.,College of Agriculture, Guangxi University, Nanning, China
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17
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Tveit AT, Kiss A, Winkel M, Horn F, Hájek T, Svenning MM, Wagner D, Liebner S. Environmental patterns of brown moss- and Sphagnum-associated microbial communities. Sci Rep 2020; 10:22412. [PMID: 33376244 PMCID: PMC7772339 DOI: 10.1038/s41598-020-79773-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/02/2020] [Indexed: 11/08/2022] Open
Abstract
Northern peatlands typically develop through succession from fens dominated by the moss family Amblystegiaceae to bogs dominated by the moss genus Sphagnum. How the different plants and abiotic environmental conditions provided in Amblystegiaceae and Sphagnum peat shape the respective moss associated microbial communities is unknown. Through a large-scale molecular and biogeochemical study spanning Arctic, sub-Arctic and temperate regions we assessed how the endo- and epiphytic microbial communities of natural northern peatland mosses relate to peatland type (Sphagnum and Amblystegiaceae), location, moss taxa and abiotic environmental variables. Microbial diversity and community structure were distinctly different between Amblystegiaceae and Sphagnum peatlands, and within each of these two peatland types moss taxon explained the largest part of microbial community variation. Sphagnum and Amblystegiaceae shared few (< 1% of all operational taxonomic units (OTUs)) but strikingly abundant (up to 65% of relative abundance) OTUs. This core community overlapped by one third with the Sphagnum-specific core-community. Thus, the most abundant microorganisms in Sphagnum that are also found in all the Sphagnum plants studied, are the same OTUs as those few shared with Amblystegiaceae. Finally, we could confirm that these highly abundant OTUs were endophytes in Sphagnum, but epiphytes on Amblystegiaceae. We conclude that moss taxa and abiotic environmental variables associate with particular microbial communities. While moss taxon was the most influential parameter, hydrology, pH and temperature also had significant effects on the microbial communities. A small though highly abundant core community is shared between Sphagnum and Amblystegiaceae.
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Affiliation(s)
- Alexander Tøsdal Tveit
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, Tromsø, Norway
| | - Andrea Kiss
- GFZ German Research Center for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Matthias Winkel
- GFZ German Research Center for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Center for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Tomáš Hájek
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Mette Marianne Svenning
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, Tromsø, Norway
| | - Dirk Wagner
- GFZ German Research Center for Geosciences, Section Geomicrobiology, Potsdam, Germany
- University of Potsdam, Institute of Geosciences, Potsdam, Germany
| | - Susanne Liebner
- GFZ German Research Center for Geosciences, Section Geomicrobiology, Potsdam, Germany.
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany.
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18
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Mapelli F, Riva V, Vergani L, Choukrallah R, Borin S. Unveiling the Microbiota Diversity of the Xerophyte Argania spinosa L. Skeels Root System and Residuesphere. MICROBIAL ECOLOGY 2020; 80:822-836. [PMID: 32583006 PMCID: PMC7550381 DOI: 10.1007/s00248-020-01543-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
The microbiota associated to xerophyte is a "black box" that might include microbes involved in plant adaptation to the extreme conditions that characterize their habitat, like water shortage. In this work, we studied the bacterial communities inhabiting the root system of Argania spinosa L. Skeels, a tree of high economic value and ecological relevance in Northern Africa. Illumina 16S rRNA gene sequencing and cultivation techniques were applied to unravel the bacterial microbiota's structure in environmental niches associated to argan plants (i.e., root endosphere, rhizosphere, root-surrounding soil), not associated to the plant (i.e., bulk soil), and indirectly influenced by the plant being partially composed by its leafy residue and the associated microbes (i.e., residuesphere). Illumina dataset indicated that the root system portions of A. spinosa hosted different bacterial communities according to their degree of association with the plant, enriching for taxa typical of the plant microbiome. Similar alpha- and beta-diversity trends were observed for the total microbiota and its cultivable fraction, which included 371 isolates. In particular, the residuesphere was the niche with the highest bacterial diversity. The Plant Growth Promotion (PGP) potential of 219 isolates was investigated in vitro, assessing several traits related to biofertilization and biocontrol, besides the production of exopolysaccharides. Most of the multivalent isolates showing the higher PGP score were identified in the residuesphere, suggesting it as a habitat that favor their proliferation. We hypothesized that these bacteria can contribute, in partnership with the argan root system, to the litter effect played by this tree in its native arid lands.
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Affiliation(s)
- Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133, Milan, Italy.
| | - Valentina Riva
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133, Milan, Italy
| | - Lorenzo Vergani
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133, Milan, Italy
| | - Redouane Choukrallah
- Hassan II, Salinity and Plant Nutrition Laboratory, Institut Agronomique et Vétérinaire, Agadir, Morocco
| | - Sara Borin
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133, Milan, Italy
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19
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Guo DJ, Singh RK, Singh P, Li DP, Sharma A, Xing YX, Song XP, Yang LT, Li YR. Complete Genome Sequence of Enterobacter roggenkampii ED5, a Nitrogen Fixing Plant Growth Promoting Endophytic Bacterium With Biocontrol and Stress Tolerance Properties, Isolated From Sugarcane Root. Front Microbiol 2020; 11:580081. [PMID: 33072048 PMCID: PMC7536287 DOI: 10.3389/fmicb.2020.580081] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022] Open
Abstract
Sugarcane is the leading economic crop in China, requires huge quantities of nitrogen in the preliminary plant growth stages. However, the use of an enormous amount of nitrogen fertilizer increases the production price, and have detrimental results on the environment, causes severe soil and water pollution. In this study, a total of 175 endophytic strains were obtained from the sugarcane roots, belonging to five different species, i.e., Saccharum officinarum, Saccharum barberi, Saccharum robustum, Saccharum spontaneum, and Saccharum sinense. Among these, only 23 Enterobacter strains were chosen based on nitrogen fixation, PGP traits, hydrolytic enzymes production, and antifungal activities. Also, all selected strains were showed diverse growth range under different stress conditions, i.e., pH (5–10), temperature (20–45°C), and NaCl (7–12%) and 14 strains confirmed positive nifH, and 12 strains for acdS gene amplification, suggested that these strains could fix nitrogen along with stress tolerance properties. Out of 23 selected strains, Enterobacter roggenkampii ED5 was the most potent strain. Hence, this strain was further selected for comprehensive genome analysis, which includes a genome size of 4,702,851 bp and 56.05% of the average G + C content. Genome annotations estimated 4349 protein-coding with 83 tRNA and 25 rRNA genes. The CDSs number allocated to the KEGG, COG, and GO database were 2839, 4028, and 2949. We recognized a total set of genes that are possibly concerned with ACC deaminase activity, siderophores and plant hormones production, nitrogen and phosphate metabolism, symbiosis, root colonization, biofilm formation, sulfur assimilation and metabolism, along with resistance response toward a range of biotic and abiotic stresses. E. roggenkampii ED5 strain was also a proficient colonizer in sugarcane (variety GT11) and enhanced growth of sugarcane under the greenhouse. To the best of our knowledge, this is the first information on the whole-genome sequence study of endophytic E. roggenkampii ED5 bacterium associated with sugarcane root. And, our findings proposed that identification of predicted genes and metabolic pathways might describe this strain an eco-friendly bioresource to promote sugarcane growth by several mechanisms of actions under multi-stresses.
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Affiliation(s)
- Dao-Jun Guo
- College of Agriculture, Guangxi University, Nanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Dong-Ping Li
- Microbiology Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Yong-Xiu Xing
- College of Agriculture, Guangxi University, Nanning, China
| | - Xiu-Peng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Li-Tao Yang
- College of Agriculture, Guangxi University, Nanning, China
| | - Yang-Rui Li
- College of Agriculture, Guangxi University, Nanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
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20
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Liu Y, Li D, Qi J, Peng Z, Chen W, Wei G, Jiao S. Stochastic processes shape the biogeographic variations in core bacterial communities between aerial and belowground compartments of common bean. Environ Microbiol 2020; 23:949-964. [PMID: 32893947 DOI: 10.1111/1462-2920.15227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022]
Abstract
Although studies of biogeography in soil bacterial communities have attracted considerable attention, the generality of these patterns along with assembly processes and underlying drivers is poorly understood in the inner tissues of plants. Plant tissues provide unique ecological habitats for microorganisms, which play an essential role in plant performance. Here, we compared core bacterial communities among five soil-plant associated compartments of common bean across five sampling sites in China. Neutral and null modelling consistently suggested that stochastic processes dominated the core community assembly processes and escalated from the belowground compartments to the inner tissues of aerial plant parts. The multiple distance-decay relationships also varied and had flattened patterns in the stem endosphere, which were shaped by distinct environmental factors in each compartment. Coexistence patterns also varied in topological features, in addition with the sparsest networks in the stem endosphere resulted from the interaction with the stochastic processes. This study considerably expanded our understanding of various biogeographic patterns, assembly processes, and the underlying mechanisms of core bacterial communities between aerial and belowground compartments of common bean. That will provide a scientific basis for the reasonable regulation of core bacterial consortia to get better plant performance.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Da Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jiejun Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ziheng Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
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21
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Hough M, McClure A, Bolduc B, Dorrepaal E, Saleska S, Klepac-Ceraj V, Rich V. Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient. Front Microbiol 2020; 11:796. [PMID: 32499761 PMCID: PMC7243355 DOI: 10.3389/fmicb.2020.00796] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/03/2020] [Indexed: 02/01/2023] Open
Abstract
Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts in plant communities and soil microbiomes as permafrost thaws, and are potentially appreciable sources of climate change feedbacks due to their soil carbon (C) storage. We characterized phyllosphere and rhizosphere microbiomes of six plant species, and bulk peat, across a permafrost thaw progression (from intact permafrost, to partially- and fully-thawed stages) via 16S rRNA gene amplicon sequencing. We tested the hypothesis that the relative influence of biotic versus environmental filtering (the role of plant species versus thaw-defined habitat) in structuring microbial communities would differ among phyllosphere, rhizosphere, and bulk peat. Using both abundance- and phylogenetic-based approaches, we found that phyllosphere microbial composition was more strongly explained by plant associate, with little influence of habitat, whereas in the rhizosphere, plant and habitat had similar influence. Network-based community analyses showed that keystone taxa exhibited similar patterns with stronger responses to drivers. However, plant associates appeared to have a larger influence on organisms belonging to families associated with methane-cycling than the bulk community. Putative methanogens were more strongly influenced by plant than habitat in the rhizosphere, and in the phyllosphere putative methanotrophs were more strongly influenced by plant than was the community at large. We conclude that biotic effects can be stronger than environmental filtering, but their relative importance varies among microbial groups. For most microbes in this system, biotic filtering was stronger aboveground than belowground. However, for putative methane-cyclers, plant associations have a stronger influence on community composition than environment despite major hydrological changes with thaw. This suggests that plant successional dynamics may be as important as hydrological changes in determining microbial relevance to C-cycling climate feedbacks. By partitioning the degree that plant versus environmental filtering drives microbiome composition and function we can improve our ability to predict the consequences of warming for C-cycling in other arctic areas undergoing similar permafrost thaw transitions.
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Affiliation(s)
- Moira Hough
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Amelia McClure
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Benjamin Bolduc
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, United States
| | - Ellen Dorrepaal
- Climate Impacts Research Centre, Umeå University, Umeå, Sweden
| | - Scott Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Virginia Rich
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, United States
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22
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Given C, Häikiö E, Kumar M, Nissinen R. Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna. FRONTIERS IN PLANT SCIENCE 2020; 11:561. [PMID: 32528486 PMCID: PMC7247849 DOI: 10.3389/fpls.2020.00561] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
The rapid developments in the next-generation sequencing methods in the recent years have provided a wealth of information on the community structures and functions of endophytic bacteria. However, the assembly processes of these communities in different plant tissues are still currently poorly understood, especially in wild plants in natural settings. The aim of this study was to compare the composition of endophytic bacterial communities in leaves and roots of arcto-alpine pioneer plant Oxyria digyna, and investigate, how plant tissue (leaf or root) or plant origin affect the community assembly. To address this, we planted micropropagated O. digyna plants with low bacterial load (bait plants) in experimental site with native O. digyna population, in the Low Arctic. The endophytic bacterial community structures in the leaves and roots of the bait plants were analyzed after one growing season and one year in the field, and compared to those of the wild plants growing at the same site. 16S rRNA gene targeted sequencing revealed that endophytic communities in the roots were more diverse than in the leaves, and the diversity in the bait plants increased in the field, and was highest in the wild plants. Both tissue type and plant group had strong impact on the endophytic bacterial community structures. Firmicutes were highly abundant in the leaf communities of both plant types. Proteobacteria and Bacteroidetes were more abundant in the roots, albeit with different relative abundances in different plant groups. The community structures in the bait plants changed in the field over time, and increasingly resembled the wild plant endophytic communities. This was due to the changes in the relative abundances of several bacterial taxa, as well as species acquisition in the field, but with no species turnover. Several OTUs that were acquired by the bait plants in the field and represent phosphate solubilizing and diazotrophic bacterial taxa, suggesting major role in nutrient acquisition of these bacteria for this nonmycorrhizal plant, thriving in the nutrient poor arctic soils.
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Affiliation(s)
- Cindy Given
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Elina Häikiö
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Manoj Kumar
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Riitta Nissinen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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23
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Gadkari PS, McGuinness LR, Männistö MK, Kerkhof LJ, Häggblom MM. Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing. FEMS Microbiol Ecol 2019; 96:5645228. [DOI: 10.1093/femsec/fiz192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT
Arctic soils store vast amounts of carbon and are subject to intense climate change. While the effects of thaw on the composition and activities of Arctic tundra microorganisms has been examined extensively, little is known about the consequences of temperature fluctuations within the subzero range in seasonally frozen or permafrost soils. This study identified tundra soil bacteria active at subzero temperatures using stable isotope probing (SIP). Soils from Kilpisjärvi, Finland, were amended with 13C-cellobiose and incubated at 0, −4 and −16°C for up to 40 weeks. 16S rRNA gene sequence analysis of 13C-labelled DNA revealed distinct subzero-active bacterial taxa. The SIP experiments demonstrated that diverse bacteria, including members of Candidatus Saccharibacteria, Melioribacteraceae, Verrucomicrobiaceae, Burkholderiaceae, Acetobacteraceae, Armatimonadaceae and Planctomycetaceae, were capable of synthesising 13C-DNA at subzero temperatures. Differences in subzero temperature optima were observed, for example, with members of Oxalobacteraceae and Rhizobiaceae found to be more active at 0°C than at −4°C or −16°C, whereas Melioribacteriaceae were active at all subzero temperatures tested. Phylogeny of 13C-labelled 16S rRNA genes from the Melioribacteriaceae, Verrucomicrobiaceae and Candidatus Saccharibacteria suggested that these taxa formed subzero-active clusters closely related to members from other cryo-environments. This study demonstrates that subzero temperatures impact active bacterial community composition and activity, which may influence biogeochemical cycles.
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Affiliation(s)
- Preshita S Gadkari
- School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick NJ 08901, USA
| | - Lora R McGuinness
- Department of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Minna K Männistö
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Max M Häggblom
- School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick NJ 08901, USA
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24
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Oberhofer M, Hess J, Leutgeb M, Gössnitzer F, Rattei T, Wawrosch C, Zotchev SB. Exploring Actinobacteria Associated With Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Leontopodium nivale Subspecies alpinum. Front Microbiol 2019; 10:2531. [PMID: 31781058 PMCID: PMC6857621 DOI: 10.3389/fmicb.2019.02531] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/21/2019] [Indexed: 11/24/2022] Open
Abstract
The rhizosphere of plants is enriched in nutrients facilitating growth of microorganisms, some of which are recruited as endophytes. Endophytes, especially Actinobacteria, are known to produce a plethora of bioactive compounds. We hypothesized that Leontopodium nivale subsp. alpinum (Edelweiss), a rare alpine medicinal plant, may serve as yet untapped source for uncommon Actinobacteria associated with this plant. Rhizosphere soil of native Alpine plants was used, after physical and chemical pre-treatments, for isolating Actinobacteria. Isolates were selected based on morphology and identified by 16S rRNA gene-based barcoding. Resulting 77 Actinobacteria isolates represented the genera Actinokineospora, Kitasatospora, Asanoa, Microbacterium, Micromonospora, Micrococcus, Mycobacterium, Nocardia, and Streptomyces. In parallel, Edelweiss plants from the same location were surface-sterilized, separated into leaves, roots, rhizomes, and inflorescence and pooled within tissues before genomic DNA extraction. Metagenomic 16S rRNA gene amplicons confirmed large numbers of actinobacterial operational taxonomic units (OTUs) descending in diversity from roots to rhizomes, leaves and inflorescences. These metagenomic data, when queried with isolate sequences, revealed an overlap between the two datasets, suggesting recruitment of soil bacteria by the plant. Moreover, this study uncovered a profound diversity of uncultured Actinobacteria from Rubrobacteridae, Thermoleophilales, Acidimicrobiales and unclassified Actinobacteria specifically in belowground tissues, which may be exploited by a targeted isolation approach in the future.
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Affiliation(s)
- Martina Oberhofer
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Jaqueline Hess
- Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Marlene Leutgeb
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Florian Gössnitzer
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Christoph Wawrosch
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Sergey B. Zotchev
- Pharmaceutical Biotechnology, Department of Pharmacognosy, University of Vienna, Vienna, Austria
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25
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Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands. ISME JOURNAL 2019; 14:463-475. [PMID: 31659233 PMCID: PMC6976627 DOI: 10.1038/s41396-019-0543-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 12/25/2022]
Abstract
The active bacterial rhizobiomes and root exudate profiles of phytometers of six plant species growing in central European temperate grassland communities were investigated in three regions located up to 700 km apart, across diverse edaphic conditions and along a strong land use gradient. The recruitment process from bulk soil communities was identified as the major direct driver of the composition of active rhizosphere bacterial communities. Unexpectedly, the effect of soil properties, particularly soil texture, water content, and soil type, strongly dominated over plant properties and the composition of polar root exudates of the primary metabolism. While plant species-specific selection of bacteria was minor, the RNA-based composition of active rhizosphere bacteria substantially differed between rhizosphere and bulk soil. Although other variables could additionally be responsible for the consistent enrichment of particular bacteria in the rhizosphere, distinct bacterial OTUs were linked to the presence of specific polar root exudates independent of individual plant species. Our study also identified numerous previously unknown taxa that are correlated with rhizosphere dynamics and hence represent suitable targets for future manipulations of the plant rhizobiome.
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26
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Niku J, Hui FKC, Taskinen S, Warton DI. gllvm: Fast analysis of multivariate abundance data with generalized linear latent variable models in
r. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13303] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jenni Niku
- Department of Mathematics and Statistics University of Jyväskylä Jyväskylä Finland
| | - Francis K. C. Hui
- Research School of Finance Actuarial Studies & Statistics Australian National University Canberra Australia
| | - Sara Taskinen
- Department of Mathematics and Statistics University of Jyväskylä Jyväskylä Finland
| | - David I. Warton
- School of Mathematics and Statistics and Evolution & Ecology Research Centre UNSW Sydney Canberra Australia
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27
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Wu H, Gu Q, Xie Y, Lou Z, Xue P, Fang L, Yu C, Jia D, Huang G, Zhu B, Schneider A, Blom J, Lasch P, Borriss R, Gao X. Cold-adapted Bacilli isolated from the Qinghai-Tibetan Plateau are able to promote plant growth in extreme environments. Environ Microbiol 2019; 21:3505-3526. [PMID: 31233661 DOI: 10.1111/1462-2920.14722] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022]
Abstract
Nearly 1400 Bacillus strains growing in the plant rhizosphere were sampled from different sites on the Qinghai-Tibetan Plateau. Forty-five of the isolates, selected due to their biocontrol activity, were genome-sequenced and their taxonomic identification revealed that they were representatives of the Bacillus subtilis species complex (20) and the Bacillus cereus group (9). Majority of the remaining strains were found closely related to Bacillus pumilus, but their average nucleotide identity based on BLAST and electronic DNA/DNA hybridization values excluded closer taxonomic identification. A total of 45 different gene clusters involved in synthesis of secondary metabolites were detected by mining the genomes of the 45 selected strains. Except eight mesophilic strains, the 37 remaining strains were found either cold-adapted or psychrophilic, able to propagate at 10°C and below (Bacillus wiedmannii NMSL88 and Bacillus sp. RJGP41). Pot experiments performed at 10°C with winter wheat seedlings revealed that cold-adapted representatives of B. pumilus, B. safensis and B. atrophaeus promoted growth of the seedlings under cold conditions, suggesting that these bacilli isolated from a cold environment are promising candidates for developing of bioformulations useful for application in sustainable agriculture under environmental conditions unfavourable for the mesophilic bacteria presently in use.
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Affiliation(s)
- Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Qin Gu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Yongli Xie
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Zhiying Lou
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Pengqi Xue
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Liu Fang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Chenjie Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Dandan Jia
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Guochao Huang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Bichun Zhu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Andy Schneider
- Proteomics and Spectroscopy Unit (ZBS6) at the Centre for Biological Threats and Special Pathogens, Robert Koch-Institute, Berlin, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig Universität Giessen, Giessen, Germany
| | - Peter Lasch
- Proteomics and Spectroscopy Unit (ZBS6) at the Centre for Biological Threats and Special Pathogens, Robert Koch-Institute, Berlin, Germany
| | - Rainer Borriss
- Nordreet UG, Greifswald, Germany.,Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
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Zhang Q, Acuña JJ, Inostroza NG, Mora ML, Radic S, Sadowsky MJ, Jorquera MA. Endophytic Bacterial Communities Associated with Roots and Leaves of Plants Growing in Chilean Extreme Environments. Sci Rep 2019; 9:4950. [PMID: 30894597 PMCID: PMC6426880 DOI: 10.1038/s41598-019-41160-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/01/2019] [Indexed: 12/21/2022] Open
Abstract
Several studies have demonstrated the relevance of endophytic bacteria on the growth and fitness of agriculturally-relevant plants. To our knowledge, however, little information is available on the composition, diversity, and interaction of endophytic bacterial communities in plants struggling for existence in the extreme environments of Chile, such as the Atacama Desert (AD) and Patagonia (PAT). The main objective of the present study was to analyze and compare the composition of endophytic bacterial communities associated with roots and leaves of representative plants growing in Chilean extreme environments. The plants sampled were: Distichlis spicate and Pluchea absinthioides from the AD, and Gaultheria mucronata and Hieracium pilosella from PAT. The abundance and composition of their endophytic bacterial communities was determined by quantitative PCR and high–throughput sequencing of 16S rRNA, respectively. Results indicated that there was a greater abundance of 16S rRNA genes in plants from PAT (1013 to 1014 copies g−1 DNA), compared with those from AD (1010 to 1012 copies g−1 DNA). In the AD, a greater bacterial diversity, as estimated by Shannon index, was found in P. absinthioides, compared with D. spicata. In both ecosystems, the greater relative abundances of endophytes were mainly attributed to members of the phyla Proteobacteria (14% to 68%), Firmicutes (26% to 41%), Actinobacteria (6 to 23%) and Bacteroidetes (1% to 21%). Our observations revealed that most of operational taxonomic units (OTUs) were not shared between tissue samples of different plant species in both locations, suggesting the effect of the plant genotype (species) on the bacterial endophyte communities in Chilean extreme environments, where Bacillaceae and Enterobacteriacea could serve as keystone taxa as revealed our linear discriminant analysis.
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Affiliation(s)
- Qian Zhang
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Nitza G Inostroza
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - María Luz Mora
- Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Sergio Radic
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad de Magallanes, Ave. Bulnes 01855, Punta Arenas, Chile
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA.,Department of Soil, Water, and Climate, and Department of Plant and Microbial Biology, University of Minnesota, 439 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile. .,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.
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Cheng D, Tian Z, Feng L, Xu L, Wang H. Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range. PeerJ 2019; 6:e6162. [PMID: 30643678 PMCID: PMC6327885 DOI: 10.7717/peerj.6162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 11/25/2018] [Indexed: 11/20/2022] Open
Abstract
Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant-bacteria interactions in the invasion of this species in China.
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Affiliation(s)
- Dandan Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China
| | - Zhongsai Tian
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Liang Feng
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Lin Xu
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China
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30
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Qin S, Feng WW, Zhang YJ, Wang TT, Xiong YW, Xing K. Diversity of Bacterial Microbiota of Coastal Halophyte Limonium sinense and Amelioration of Salinity Stress Damage by Symbiotic Plant Growth-Promoting Actinobacterium Glutamicibacter halophytocola KLBMP 5180. Appl Environ Microbiol 2018; 84:e01533-18. [PMID: 30054358 PMCID: PMC6146988 DOI: 10.1128/aem.01533-18] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/20/2018] [Indexed: 11/20/2022] Open
Abstract
Plant-associated microorganisms are considered a key determinant of plant health and growth. However, little information is available regarding the composition and ecological function of the roots' and leaves' bacterial microbiota of halophytes. Here, using both culture-dependent and culture-independent techniques, we characterized the bacterial communities of the roots and leaves as well as the rhizosphere and bulk soils of the coastal halophyte Limonium sinense in Jiangsu Province, China. We identified 49 representative bacterial strains belonging to 17 genera across all samples, with Glutamicibacter as the most dominant genus. All Glutamicibacter isolates showed multiple potential plant growth promotion traits and tolerated a high concentration of NaCl and a wide pH range. Interestingly, further inoculation experiments showed that the Glutamicibacter halophytocola strain KLBMP 5180 isolated from root tissue significantly promoted host growth under NaCl stress. Indeed, KLBMP 5180 inoculation increased the concentrations of total chlorophyll, proline, antioxidative enzymes, flavonoids, K+, and Ca2+ in the leaves; the concentrations of malondialdehyde (MDA) and Na+ were reduced. A transcriptome analysis identified 1,359 and 328 differentially expressed genes (DEGs) in inoculated seedlings treated with 0 and 250 mM NaCl, respectively. We found that pathways related to phenylpropanoid and flavonoid biosynthesis and ion transport and metabolism might play more important roles in host salt stress tolerance induced by KLBMP 5180 inoculation compared to that in noninoculated leaves. Our results provide novel insights into the complex composition and function of the bacterial microbiota of the coastal halophyte L. sinense and suggest that halophytes might recruit specific bacteria to enhance their tolerance of harsh environments.IMPORTANCE Halophytes are important coastal plants often used for the remediation of saline coastal soils. Limonium sinense is well known for its medical properties and phytoremediation of saline soils. However, excessive exploitation and utilization have made the wild resource endangered. The use of endophytic and rhizosphere bacteria may be one of the suitable ways to solve the problem. This study was undertaken to develop approaches to improve the growth of L. sinense using endophytes. The application of actinobacterial endophytes ameliorated salt stress damage of the host via complex physiological and molecular mechanisms. The results also highlight the potential of using habitat-adapted, symbiotic, indigenous endophytic bacteria to enhance the growth and ameliorate abiotic stress damage of host plants growing in special habitats.
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Affiliation(s)
- Sheng Qin
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, People's Republic of China
| | - Wei-Wei Feng
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, People's Republic of China
| | - Yue-Ji Zhang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, People's Republic of China
| | - Tian-Tian Wang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, People's Republic of China
| | - You-Wei Xiong
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, People's Republic of China
| | - Ke Xing
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, People's Republic of China
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Exploitation of new endophytic bacteria and their ability to promote sugarcane growth and nitrogen nutrition. Antonie van Leeuwenhoek 2018; 112:283-295. [DOI: 10.1007/s10482-018-1157-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
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Branska B, Pechacova Z, Kolek J, Vasylkivska M, Patakova P. Flow cytometry analysis of Clostridium beijerinckii NRRL B-598 populations exhibiting different phenotypes induced by changes in cultivation conditions. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:99. [PMID: 29632557 PMCID: PMC5887253 DOI: 10.1186/s13068-018-1096-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/26/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND Biobutanol production by clostridia via the acetone-butanol-ethanol (ABE) pathway is a promising future technology in bioenergetics , but identifying key regulatory mechanisms for this pathway is essential in order to construct industrially relevant strains with high tolerance and productivity. We have applied flow cytometric analysis to C. beijerinckii NRRL B-598 and carried out comparative screening of physiological changes in terms of viability under different cultivation conditions to determine its dependence on particular stages of the life cycle and the concentration of butanol. RESULTS Dual staining by propidium iodide (PI) and carboxyfluorescein diacetate (CFDA) provided separation of cells into four subpopulations with different abilities to take up PI and cleave CFDA, reflecting different physiological states. The development of a staining pattern during ABE fermentation showed an apparent decline in viability, starting at the pH shift and onset of solventogenesis, although an appreciable proportion of cells continued to proliferate. This was observed for sporulating as well as non-sporulating phenotypes at low solvent concentrations, suggesting that the increase in percentage of inactive cells was not a result of solvent toxicity or a transition from vegetative to sporulating stages. Additionally, the sporulating phenotype was challenged with butanol and cultivation with a lower starting pH was performed; in both these experiments similar trends were obtained-viability declined after the pH breakpoint, independent of the actual butanol concentration in the medium. Production characteristics of both sporulating and non-sporulating phenotypes were comparable, showing that in C. beijerinckii NRRL B-598, solventogenesis was not conditional on sporulation. CONCLUSION We have shown that the decline in C. beijerinckii NRRL B-598 culture viability during ABE fermentation was not only the result of accumulated toxic metabolites, but might also be associated with a special survival strategy triggered by pH change.
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Affiliation(s)
- Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Zora Pechacova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
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Maksimov IV, Maksimova TI, Sarvarova ER, Blagova DK, Popov VO. Endophytic Bacteria as Effective Agents of New-Generation Biopesticides (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818020072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence. ISME JOURNAL 2018; 12:1188-1198. [PMID: 29335640 PMCID: PMC5931989 DOI: 10.1038/s41396-017-0026-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 11/02/2017] [Accepted: 11/15/2017] [Indexed: 11/23/2022]
Abstract
In mature soils, plant species and soil type determine the selection of root microbiota. Which of these two factors drives rhizosphere selection in barren substrates of developing desert soils has, however, not yet been established. Chronosequences of glacier forelands provide ideal natural environments to identify primary rhizosphere selection factors along the changing edaphic conditions of a developing soil. Here, we analyze changes in bacterial diversity in bulk soils and rhizospheres of a pioneer plant across a High Arctic glacier chronosequence. We show that the developmental stage of soil strongly modulates rhizosphere community assembly, even though plant-induced selection buffers the effect of changing edaphic factors. Bulk and rhizosphere soils host distinct bacterial communities that differentially vary along the chronosequence. Cation exchange capacity, exchangeable potassium, and metabolite concentration in the soil account for the rhizosphere bacterial diversity. Although the soil fraction (bulk soil and rhizosphere) explains up to 17.2% of the variation in bacterial microbiota, the soil developmental stage explains up to 47.7% of this variation. In addition, the operational taxonomic unit (OTU) co-occurrence network of the rhizosphere, whose complexity increases along the chronosequence, is loosely structured in barren compared with mature soils, corroborating our hypothesis that soil development tunes the rhizosphere effect.
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Kumar M, van Elsas JD, Nissinen R. Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia. Front Microbiol 2017; 8:1972. [PMID: 29081767 PMCID: PMC5645501 DOI: 10.3389/fmicb.2017.01972] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/25/2017] [Indexed: 12/31/2022] Open
Abstract
Arctic and alpine biomes are most often strongly nitrogen-limited, and hence biological nitrogen fixation is a strong driver of these ecosystems. Both biomes are characterized by low temperatures and short growing seasons, but they differ in seasonality of solar radiation and in soil water balance due to underlying permafrost in the Arctic. Arcto-alpine plant species are well-adapted to the low temperatures that prevail in their habitats, and plant growth is mainly limited by the availability of nutrients, in particular nitrogen, due to slow mineralization. Nitrogen fixing bacteria are likely important for plant growth in these habitats, but very little is known of these bacteria or forces shaping their communities. In this study, we characterized the potential nitrogen fixing bacterial (PNFB) communities associated with two arcto-alpine pioneer plant species, Oxyria digyna (mountain sorrel) and Saxifraga oppositifolia (blue saxifrage), in three climate regions. Both of these plants readily colonize low nutrient mineral soils. Our goal was to investigate how climate (region) and, on the other hand, host plant and plant species shape these communities. To our knowledge, this is the first comprehensive study describing PNFB communities associated with pioneer plants in different arcto-alpine biomes. Replicate samples were taken from two arctic regions, Kilpisjärvi and Ny-Ålesund, and one alpine region, Mayrhofen. In these, the PNFB communities in the bulk and rhizosphere soils and the plant endospheres were characterized by nifH-targeted PCR and massive parallel sequencing. The data revealed strong effects of climatic region on the dominating nitrogen fixers. Specifically, nifH sequences related to Geobacter (δ-Proteobacteria) were present in high relative abundances in the nitrogen-fixing communities in the Mayrhofen and Kilpisjärvi regions, while members of the Clostridiales prevailed in the Kilpisjärvi and Ny-Ålesund regions. The bulk and rhizosphere soil as well as the endosphere communities in the Mayrhofen region were all characterized by high relative abundances of nifH sequences related to Geobacter. In contrast, the endosphere and soil (bulk or rhizosphere soil) communities in the High Arctic were highly divergent: endosphere communities in the arctic regions were shaped by Clostridium spp., while nifH sequences representing δ-Proteobacteria, β-Proteobacteria, Cyanobacteria (in Ny-Ålesund), and Verrucomicrobia (in Kilpisjärvi) dominated the soil communities. Interestingly, the major PNFB genera identified in this study have been previously identified as members of conserved core microbiomes in the endospheres and seeds of these plants by 16S rRNA gene based analyses combined with bacterial isolation, suggesting a very tight interaction between diazotrophic bacteria and these arctic pioneer plants. Overall, anaerobic bacterial taxa dominated the PNFB communities of the endospheres and rhizospheres of the two plant species in all study sites. This could indicate anoxic conditions in and around plant roots at the time of sampling (early growth season), created by melting snow and underlying permafrost.
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Affiliation(s)
- Manoj Kumar
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Department of Microbial Ecology, University of Groningen, Groningen, Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, University of Groningen, Groningen, Netherlands
| | - Riitta Nissinen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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