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Huusko K, Manninen OH, Myrsky E, Stark S. Soil fungal and bacterial communities reflect differently tundra vegetation state transitions and soil physico-chemical properties. THE NEW PHYTOLOGIST 2024; 243:407-422. [PMID: 38750646 DOI: 10.1111/nph.19808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/23/2024] [Indexed: 06/07/2024]
Abstract
Strong disturbances may induce ecosystem transitions into new alternative states that sustain through plant-soil interactions, such as the transition of dwarf shrub-dominated into graminoid-dominated vegetation by herbivory in tundra. Little evidence exists on soil microbial communities in alternative states, and along the slow process of ecosystem return into the predisturbance state. We analysed vegetation, soil microbial communities and activities as well as soil physico-chemical properties in historical reindeer enclosures in northernmost Finland in the following plot types: control heaths in the surrounding tundra; graminoid-dominated; 'shifting'; and recovered dwarf shrub-dominated vegetation inside enclosures. Soil fungal communities followed changes in vegetation, whereas bacterial communities were more affected by soil physico-chemical properties. Graminoid plots were characterized by moulds, pathotrophs and dark septate endophytes. Ericoid mycorrhizal and saprotrophic fungi were typical for control and recovered plots. Soil microbial communities inside the enclosures showed historical contingency, as their spatial variation was high in recovered plots despite the vegetation being more homogeneous. Self-maintaining feedback loops between plant functional types, soil microbial communities, and carbon and nutrient mineralization act effectively to stabilize alternative vegetation states, but once predisturbance vegetation reestablishes itself, soil microbial communities and physico-chemical properties return back towards their predisturbance state.
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Affiliation(s)
- Karoliina Huusko
- Arctic Center, University of Lapland, PO Box 122, Rovaniemi, FI-96101, Finland
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, Oulu, FI-90014, Finland
| | - Outi H Manninen
- Arctic Center, University of Lapland, PO Box 122, Rovaniemi, FI-96101, Finland
| | - Eero Myrsky
- Arctic Center, University of Lapland, PO Box 122, Rovaniemi, FI-96101, Finland
| | - Sari Stark
- Arctic Center, University of Lapland, PO Box 122, Rovaniemi, FI-96101, Finland
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Alam M, Pandit B, Moin A, Iqbal UN. Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture. Indian J Microbiol 2024; 64:343-366. [PMID: 39011025 PMCID: PMC11246410 DOI: 10.1007/s12088-024-01225-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/07/2024] [Indexed: 07/17/2024] Open
Abstract
Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.
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Affiliation(s)
- Masrure Alam
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
| | - Baishali Pandit
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
- Department of Botany, Surendranath College, 24/2 MG Road, Kolkata, West Bengal 700009 India
| | - Abdul Moin
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
| | - Umaimah Nuzhat Iqbal
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
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Zhang JZ, Li XZ, Yin YB, Luo SC, Wang DX, Zheng H, Liu YX. High-throughput sequencing-based analysis of the composition and diversity of the endophyte community in roots of Stellera chamaejasme. Sci Rep 2024; 14:8607. [PMID: 38615120 PMCID: PMC11016073 DOI: 10.1038/s41598-024-59055-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/06/2024] [Indexed: 04/15/2024] Open
Abstract
Stellera chamaejasme (S. chamaejasme) is an important medicinal plant with heat-clearing, detoxifying, swelling and anti-inflammatory effects. At the same time, it is also one of the iconic plants of natural grassland degradation in northwest China, playing a key role in the invasion process. Plant endophytes live in healthy plant tissues and can synthesize substances needed for plant growth, induce disease resistance in host plants, and enhance plant resistance to environmental stress. Therefore, studying the root endophytes of S. chamaejasme is of great significance for mining beneficial microbial resources and biological prevention and control of S. chamaejasme. This study used Illumina MiSeq high-throughput sequencing technology to analyze the composition and diversity of endophytes in the roots of S. chamaejasme in different alpine grasslands (BGC, NMC and XGYZ) in Tibet. Research results show that the main phylum of endophytic fungi in the roots of S. chamaejasme in different regions is Ascomycota, and the main phyla of endophytic bacteria are Actinobacteria, Proteobacteria and Firmicutes (Bacteroidota). Overall, the endophyte diversity of the NMC samples was significantly higher than that of the other two sample sites. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) results showed significant differences in the composition of endophytic bacterial and fungal communities among BGC, NMC and XGYZ samples. Co-occurrence network analysis of endophytes showed that there were positive correlations between fungi and some negative correlations between bacteria, and the co-occurrence network of bacteria was more complex than that of fungi. In short, this study provides a vital reference for further exploring and utilizing the endophyte resources of S. chamaejasme and an in-depth understanding of the ecological functions of S. chamaejasme endophytes.
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Affiliation(s)
- Jun-Ze Zhang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Xin-Zhong Li
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Ye-Bing Yin
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Si-Cen Luo
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Dong-Xu Wang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Heng Zheng
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, China.
| | - Yi-Xuan Liu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China.
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4
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Ihalainen JA, Dogan B, Kurttila M, Zeng Y, van Elsas JD, Nissinen R. Multifaceted photoreceptor compositions in dual phototrophic systems - A genomic analysis. J Mol Biol 2024; 436:168412. [PMID: 38135178 DOI: 10.1016/j.jmb.2023.168412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
For microbes and their hosts, sensing of external cues is essential for their survival. For example, in the case of plant associated microbes, the light absorbing pigment composition of the plant as well as the ambient light conditions determine the well-being of the microbe. In addition to light sensing, some microbes can utilize xanthorhodopsin based proton pumps and bacterial photosynthetic complexes that work in parallel for energy production. They are called dual phototrophic systems. Light sensing requirements in these type of systems are obviously demanding. In nature, the photosensing machinery follows mainly the same composition in all organisms. However, the specific role of each photosensor in specific light conditions is elusive. In this study, we provide an overall picture of photosensors present in dual phototrophic systems. We compare the genomes of the photosensor proteins from dual phototrophs to those from similar microbes with "single" phototrophicity or microbes without phototrophicity. We find that the dual phototrophic bacteria obtain a larger variety of photosensors than their light inactive counterparts. Their rich domain composition and functional repertoire remains similar across all microbial photosensors. Our study calls further investigations of this particular group of bacteria. This includes protein specific biophysical characterization in vitro, microbiological studies, as well as clarification of the ecological meaning of their host microbial interactions.
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Affiliation(s)
- Janne A Ihalainen
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Batuhan Dogan
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland
| | - Moona Kurttila
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland
| | - Yonghui Zeng
- University of Copenhagen, Department of Plant and Environmental Sciences, 2100 Copenhagen, Denmark
| | - Jan Dirk van Elsas
- University of Groningen, Groningen Institute for Evolutionary Life Sciences, 9747 AG Groningen, the Netherlands
| | - Riitta Nissinen
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland; University of Turku, Department of Biology, 20500 Turku, Finland
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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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6
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Carper DL, Lawrence TJ, Quiroz D, Kueppers LM, Frank AC. Needle bacterial community structure across the species range of limber pine. ISME COMMUNICATIONS 2024; 4:ycae062. [PMID: 38800125 PMCID: PMC11128189 DOI: 10.1093/ismeco/ycae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 04/12/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024]
Abstract
Bacteria on and inside leaves can influence forest tree health and resilience. The distribution and limits of a tree species' range can be influenced by various factors, with biological interactions among the most significant. We investigated the processes shaping the bacterial needle community across the species distribution of limber pine, a widespread Western conifer inhabiting a range of extreme habitats. We tested four hypotheses: (i) Needle community structure varies across sites, with site-specific factors more important to microbial assembly than host species selection; (ii) dispersal limitation structures foliar communities across the range of limber pine; (iii) the relative significance of dispersal and selection differs across sites in the tree species range; and (iv) needle age structures bacterial communities. We characterized needle communities from the needle surface and tissue of limber pine and co-occurring conifers across 16 sites in the limber pine distribution. Our findings confirmed that site characteristics shape the assembly of bacterial communities across the host species range and showed that these patterns are not driven by dispersal limitation. Furthermore, the strength of selection by the host varied by site, possibly due to differences in available microbes. Our study, by focusing on trees in their natural setting, reveals real needle bacterial dynamics in forests, which is key to understanding the balance between stochastic and deterministic processes in shaping forest tree-microbe interactions. Such understanding will be necessary to predict or manipulate these interactions to support forest ecosystem productivity or assist plant migration and adaptation in the face of global change.
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Affiliation(s)
- Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
- Quantitative and Systems Biology Program, University of California, Merced, Merced, CA 95343, United States
| | - Travis J Lawrence
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Dianne Quiroz
- Energy & Resources Group, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Lara M Kueppers
- Energy & Resources Group, University of California, Berkeley, Berkeley, CA 94720, United States
- Sierra Nevada Research Institute, University of California, Merced, Merced, CA 95353, United States
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - A Carolin Frank
- Sierra Nevada Research Institute, University of California, Merced, Merced, CA 95353, United States
- Life and Environmental Sciences Department, School of Natural Sciences, University of California, Merced, 5200 Lake Rd, Merced, CA 95343, United States
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7
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Mathew SA, Fuchs B, Nissinen R, Helander M, Puigbò P, Saikkonen K, Muola A. Glyphosate-based herbicide use affects individual microbial taxa in strawberry endosphere but not the microbial community composition. J Appl Microbiol 2023; 134:6987274. [PMID: 36639128 DOI: 10.1093/jambio/lxad006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/30/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
AIMS In a field study, the effects of treatments of glyphosate-based herbicides (GBHs) in soil, alone and in combination with phosphate fertilizer, were examined on the performance and endophytic microbiota of garden strawberry. METHODS AND RESULTS The root and leaf endophytic microbiota of garden strawberries grown in GBH-treated and untreated soil, with and without phosphate fertilizer, were analyzed. Next, bioinformatics analysis on the type of 5-enolpyruvylshikimate-3-phosphate synthase enzyme was conducted to assess the potential sensitivity of strawberry-associated bacteria and fungi to glyphosate, and to compare the results with field observations. GBH treatments altered the abundance and/or frequency of several operational taxonomic units (OTUs), especially those of root-associated fungi and bacteria. These changes were partly related to their sensitivity to glyphosate. Still, GBH treatments did not shape the overall community structure of strawberry microbiota or affect plant performance. Phosphate fertilizer increased the abundance of both glyphosate-resistant and glyphosate-sensitive bacterial OTUs, regardless of the GBH treatments. CONCLUSIONS These findings demonstrate that although the overall community structure of strawberry endophytic microbes is not affected by GBH use, some individual taxa are.
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Affiliation(s)
- Suni Anie Mathew
- Department of Biology, University of Turku, 20014 Turku, Finland
| | - Benjamin Fuchs
- Biodiversity Unit, University of Turku, 20014 Turku, Finland
| | - Riitta Nissinen
- Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Marjo Helander
- Department of Biology, University of Turku, 20014 Turku, Finland
| | - Pere Puigbò
- Department of Biology, University of Turku, 20014 Turku, Finland.,Nutrition and Health Unit, Eurecat Technology Centre of Catalonia, 43204 Reus, Catalonia.,Department of Biochemistry and Biotechnology, Rovira i Virgili University, 43007 Tarragona, Catalonia
| | - Kari Saikkonen
- Biodiversity Unit, University of Turku, 20014 Turku, Finland
| | - Anne Muola
- Biodiversity Unit, University of Turku, 20014 Turku, Finland.,Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, 9016 Tromsø, Norway
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8
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Adeleke BS, Babalola OO. Meta-omics of endophytic microbes in agricultural biotechnology. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102332] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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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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10
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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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11
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Kalinowska A, Jankowska K, Fudala-Ksiazek S, Pierpaoli M, Luczkiewicz A. The microbial community, its biochemical potential, and the antimicrobial resistance of Enterococcus spp. in Arctic lakes under natural and anthropogenic impact (West Spitsbergen). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:142998. [PMID: 33213908 DOI: 10.1016/j.scitotenv.2020.142998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/04/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
The sustainable management of small human communities in the Arctic is challenging. In this study, both a water supply system (Lake 1) under the natural impact of a bird-nesting area, and a wastewater receiver (Lake 2) were analysed in the vicinity of the Polish Polar Station on West Spitsbergen. Microbial community composition, abundance and activity were assessed in samples of the treated wastewater, lake water and sediments using next-generation sequencing and direct microscope counts. Special attention was given to the faecal indicator, Enterococcus spp., whose occurrence and antimicrobial resistance were tested in water and wastewater samples. The results indicate that Lake 1, at a tundra stream discharge (L-TS) and a water supply point (L-WS) were dominated by three phyla: Proteobacteria (57-58%) Bacteroidetes (27-29%) and Actinobacteria (9-10%), showing similar microbial composition up to the genus level. This suggests that nutrient-rich runoff from the bird colony was retained by surrounding tundra vegetation and reached Lake 1 at L-TS to a limited extent. Lake 2, being the wastewater recipient (WW-R), mirrors to some extent the core phyla of treated wastewater (WW-E), but in different shares. This suggests the possible washout of wastewater-related bacteria with activated sludge flocs, which was also supported by the microscopic observations. Compared to Lake 1, in WW-R an increase in all tested parameters was noted: total prokaryotic cell number, average cell volume, prokaryotic biomass and live cell percentage. The presence of Enterococcus spp. antibiotic resistance patterns highlight the importance of human associated microbiome and resistome dissemination via wastewater discharge. Moreover, it can be expected that temperature-related biochemical processes (e.g. nutrient cycling) may be accelerated by the ongoing climate change. Thus, proper wastewater treatment requires locally adapted solutions in increasingly visited and inhabited polar regions. Additionally, microbial community discharged to the environment with the treated wastewater, requires critical attention.
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Affiliation(s)
- Agnieszka Kalinowska
- Department of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Katarzyna Jankowska
- Department of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Sylwia Fudala-Ksiazek
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Mattia Pierpaoli
- Department of Metrology and Optoelectronics, Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Aneta Luczkiewicz
- Department of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
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12
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Aghdam SA, Brown AMV. Deep learning approaches for natural product discovery from plant endophytic microbiomes. ENVIRONMENTAL MICROBIOME 2021; 16:6. [PMID: 33758794 PMCID: PMC7972023 DOI: 10.1186/s40793-021-00375-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/21/2021] [Indexed: 05/10/2023]
Abstract
Plant microbiomes are not only diverse, but also appear to host a vast pool of secondary metabolites holding great promise for bioactive natural products and drug discovery. Yet, most microbes within plants appear to be uncultivable, and for those that can be cultivated, their metabolic potential lies largely hidden through regulatory silencing of biosynthetic genes. The recent explosion of powerful interdisciplinary approaches, including multi-omics methods to address multi-trophic interactions and artificial intelligence-based computational approaches to infer distribution of function, together present a paradigm shift in high-throughput approaches to natural product discovery from plant-associated microbes. Arguably, the key to characterizing and harnessing this biochemical capacity depends on a novel, systematic approach to characterize the triggers that turn on secondary metabolite biosynthesis through molecular or genetic signals from the host plant, members of the rich 'in planta' community, or from the environment. This review explores breakthrough approaches for natural product discovery from plant microbiomes, emphasizing the promise of deep learning as a tool for endophyte bioprospecting, endophyte biochemical novelty prediction, and endophyte regulatory control. It concludes with a proposed pipeline to harness global databases (genomic, metabolomic, regulomic, and chemical) to uncover and unsilence desirable natural products. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s40793-021-00375-0.
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Affiliation(s)
- Shiva Abdollahi Aghdam
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX 79409 USA
| | - Amanda May Vivian Brown
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX 79409 USA
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13
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Isolation and Characterization of Cold-Tolerant Hyper-ACC-Degrading Bacteria from the Rhizosphere, Endosphere, and Phyllosphere of Antarctic Vascular Plants. Microorganisms 2020; 8:microorganisms8111788. [PMID: 33202619 PMCID: PMC7697395 DOI: 10.3390/microorganisms8111788] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/03/2020] [Accepted: 11/12/2020] [Indexed: 12/25/2022] Open
Abstract
1-Aminociclopropane-1-carboxylate (ACC)-degrading bacteria having been widely studied for their use in alleviating abiotic stresses in plants. In the present study, we isolated and characterized ACC-degrading bacteria from the rhizosphere, phyllosphere, and endosphere of the Antarctic vascular plants Deschampsia antarctica and Colobanthus quitensis. One hundred and eighty of the 578 isolates (31%) were able to grow on minimal medium containing ACC, with 101 isolates (23, 37, and 41 endosphere-, phyllosphere- and rhizosphere-associated isolates, respectively) identified as being genetically unique by enterobacterial repetitive intergenic consensus (ERIC)-PCR. Subsequently, freeze/thaw treatments and ice-recrystallization-inhibition (IRI) activity assays were performed, the results of which revealed that 77 (13%) of cold-tolerant isolates exhibited putative ACC deaminase activity. Significant (p ≤ 0.05) differences in IRI activity were also observed between the studied plant niches. Surprisingly, all the cold-tolerant isolates showed ACC deaminase activity, independent of the plant niches, with 12 isolates showing the highest ACC deaminase activities of 13.21-39.56 mmol α KB mg protein-1 h-1. These isolates were categorized as 'cold-tolerant hyper-ACC-degrading bacteria', and identified as members of Pseudomonas, Serratia, and Staphylococcus genera. The results revealed the occurrence of cold-tolerant hyper-ACC-degrading bacteria in diverse plant niches of Antarctic vascular plants, that could be investigated as novel microbial inoculants to alleviate abiotic stresses in plants.
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14
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Papik J, Folkmanova M, Polivkova-Majorova M, Suman J, Uhlik O. The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity. Biotechnol Adv 2020; 44:107614. [PMID: 32858117 DOI: 10.1016/j.biotechadv.2020.107614] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/14/2020] [Accepted: 08/15/2020] [Indexed: 10/25/2022]
Abstract
Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.
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Affiliation(s)
- Jakub Papik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Magdalena Folkmanova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Marketa Polivkova-Majorova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic.
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15
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Tosi M, Gaiero J, Linton N, Mafa-Attoye T, Castillo A, Dunfield K. Bacterial Endophytes: Diversity, Functional Importance, and Potential for Manipulation. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-981-15-6125-2_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Fadiji AE, Babalola OO. Exploring the potentialities of beneficial endophytes for improved plant growth. Saudi J Biol Sci 2020; 27:3622-3633. [PMID: 33304173 PMCID: PMC7714962 DOI: 10.1016/j.sjbs.2020.08.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 11/23/2022] Open
Abstract
Pathogen affects plant growth, host health and productivity. Endophytes, presumed to live inside the plant tissues, might be helpful in sustaining the future of agriculture. Although recent studies have proven that endophytes can be pathogenic, commensal, non-pathogenic, and/or beneficial, this review will focus on the beneficial category only. Beneficial endophytes produce a number of compounds which are useful for protecting plants from environmental conditions, enhancing plant growth and sustainability, while living conveniently inside the hosts. The population of endophytes is majorly controlled by location, and climatic conditions where the host plant grows. Often the most frequently isolated endophytes from the tissues of the plant are fungi, but sometimes greater numbers of bacteria are isolated. Beneficial endophytes stand a chance to replace the synthetic chemicals currently being used for plant growth promotion if carefully explored by researchers and embraced by policymakers. However, the roles of endophytes in plant growth improvement and their behavior in the host plant have not been fully understood. This review presents the current development of research into beneficial endophytes and their effect in improving plant growth.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, Private Mail Bag X2046, North-West University, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, Private Mail Bag X2046, North-West University, South Africa
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17
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Huang CL, Sarkar R, Hsu TW, Yang CF, Chien CH, Chang WC, Chiang TY. Endophytic Microbiome of Biofuel Plant Miscanthus sinensis (Poaceae) Interacts with Environmental Gradients. MICROBIAL ECOLOGY 2020; 80:133-144. [PMID: 31832698 DOI: 10.1007/s00248-019-01467-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
Miscanthus in Taiwan occupies a cline along altitude and adapts to diverse environments, e.g., habitats of high salinity and volcanoes. Rhizospheric and endophytic bacteria may help Miscanthus acclimate to those stresses. The relative contributions of rhizosphere vs. endosphere compartments to the adaptation remain unknown. Here, we used targeted metagenomics to compare the microbial communities in the rhizosphere and endosphere among ecotypes of M. sinensis that dwell habitats under different stresses. Proteobacteria and Actinobacteria predominated in the endosphere. Diverse phyla constituted the rhizosphere microbiome, including a core microbiome found consistently across habitats. In endosphere, the predominance of the bacteria colonizing from the surrounding soil suggests that soil recruitment must have subsequently determined the endophytic microbiome in Miscanthus roots. In endosphere, the bacterial diversity decreased with the altitude, likely corresponding to rising limitation to microorganisms according to the species-energy theory. Specific endophytes were associated with different environmental stresses, e.g., Pseudomonas spp. for alpine and Agrobacterium spp. for coastal habitats. This suggests Miscanthus actively recruits an endosphere microbiome from the rhizosphere it influences.
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Affiliation(s)
- Chao-Li Huang
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Rakesh Sarkar
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Tsai-Wen Hsu
- Endemic Species Research Institute, Nantou, 55244, Taiwan
| | - Chia-Fen Yang
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Chia-Hung Chien
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Wen-Chi Chang
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
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18
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Deciphering the Root Endosphere Microbiome of the Desert Plant Alhagi sparsifolia for Drought Resistance-Promoting Bacteria. Appl Environ Microbiol 2020; 86:AEM.02863-19. [PMID: 32220847 DOI: 10.1128/aem.02863-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/21/2020] [Indexed: 01/28/2023] Open
Abstract
Drought is among the most destructive abiotic stresses limiting crop growth and yield worldwide. Although most research has focused on the contribution of plant-associated microbial communities to plant growth and disease suppression, far less is known about the microbes involved in drought resistance among desert plants. In the present study, we applied 16S rRNA gene amplicon sequencing to determine the structure of rhizosphere and root endosphere microbiomes of Alhagi sparsifolia Compared to those of the rhizosphere, endosphere microbiomes had lower diversity but contained several taxa with higher relative abundance; many of these taxa were also present in the roots of other desert plants. We isolated a Pseudomonas strain (LTGT-11-2Z) that was prevalent in root endosphere microbiomes of A. sparsifolia and promoted drought resistance during incubation with wheat. Complete genome sequencing of LTGT-11-2Z revealed 1-aminocyclopropane-1-carboxylate deaminases, siderophore, spermidine, and colanic acid biosynthetic genes, as well as type VI secretion system (T6SS) genes, which are likely involved in biofilm formation and plant-microbe interactions. Together, these results indicate that drought-enduring plants harbor bacterial endophytes favorable to plant drought resistance, and they suggest that novel endophytic bacterial taxa and gene resources may be discovered among these desert plants.IMPORTANCE Understanding microbe-mediated plant resistance to drought is important for sustainable agriculture. We performed 16S rRNA gene amplicon sequencing and culture-dependent functional analyses of Alhagi sparsifolia rhizosphere and root endosphere microbiomes and identified key endophytic bacterial taxa and their genes facilitating drought resistance in wheat. This study improves our understanding of plant drought resistance and provides new avenues for drought resistance improvement in crop plants under field conditions.
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19
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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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20
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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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21
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Acuña-Rodríguez IS, Newsham KK, Gundel PE, Torres-Díaz C, Molina-Montenegro MA. Functional roles of microbial symbionts in plant cold tolerance. Ecol Lett 2020; 23:1034-1048. [PMID: 32281227 DOI: 10.1111/ele.13502] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/14/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022]
Abstract
In this review, we examine the functional roles of microbial symbionts in plant tolerance to cold and freezing stresses. The impacts of symbionts on antioxidant activity, hormonal signaling and host osmotic balance are described, including the effects of the bacterial endosymbionts Burkholderia, Pseudomonas and Azospirillum on photosynthesis and the accumulation of carbohydrates such as trehalose and raffinose that improve cell osmotic regulation and plasma membrane integrity. The influence of root fungal endophytes and arbuscular mycorrhizal fungi on plant physiology at low temperatures, for example their effects on nutrient acquisition and the accumulation of indole-3-acetic acid and antioxidants in tissues, are also reviewed. Meta-analyses are presented showing that aspects of plant performance (shoot biomass, relative water content, sugar and proline concentrations and Fv /Fm ) are enhanced in symbiotic plants at low (-1 to 15 °C), but not at high (20-26 °C), temperatures. We discuss the implications of microbial symbionts for plant performance at low and sub-zero temperatures in the natural environment and propose future directions for research into the effects of symbionts on the cold and freezing tolerances of plants, concluding that further studies should routinely incorporate symbiotic microbes in their experimental designs.
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Affiliation(s)
- Ian S Acuña-Rodríguez
- Laboratorio de Biología Vegetal, Instituto de Ciencias Biológicas, Universidad de Talca, Campus Lircay, Talca, Chile
| | | | - Pedro E Gundel
- IFEVA, CONICET, Universidad de Buenos Aires, Facultad de Agronomía, Buenos Aires, Argentina
| | - Cristian Torres-Díaz
- Grupo de Biodiversidad y Cambio Global (BCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Campus Fernando May, Chillán, Chile
| | - Marco A Molina-Montenegro
- Laboratorio de Biología Vegetal, Instituto de Ciencias Biológicas, Universidad de Talca, Campus Lircay, Talca, Chile.,Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.,Centro de Investigación en Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Campus San Miguel, Talca, Chile
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22
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Lopez-Echartea E, Strejcek M, Mukherjee S, Uhlik O, Yrjälä K. Bacterial succession in oil-contaminated soil under phytoremediation with poplars. CHEMOSPHERE 2020; 243:125242. [PMID: 31995861 DOI: 10.1016/j.chemosphere.2019.125242] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/13/2019] [Accepted: 10/26/2019] [Indexed: 05/18/2023]
Abstract
Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soil, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils experienced succession of bacteria over time, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.
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Affiliation(s)
- Eglantina Lopez-Echartea
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Michal Strejcek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Shinjini Mukherjee
- KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Leuven, Belgium
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Kim Yrjälä
- University of Helsinki, Department of Forest Sciences, Helsinki, Finland; Zhejiang A&F University, State Key Laboratory of Subtropical Silviculture, Zhejiang, China.
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Kushwaha P, Kashyap PL, Bhardwaj AK, Kuppusamy P, Srivastava AK, Tiwari RK. Bacterial endophyte mediated plant tolerance to salinity: growth responses and mechanisms of action. World J Microbiol Biotechnol 2020; 36:26. [PMID: 31997078 DOI: 10.1007/s11274-020-2804-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/22/2020] [Indexed: 12/18/2022]
Abstract
Salinity stress is one of the key constraints for sustainable crop production. It has gained immense importance in the backdrop of climate change induced imbalanced terrestrial water budgets. The traditional agronomic approaches and breeding salt-tolerant genotypes have often proved insufficient to alleviate salinity stress. Newer approaches like the use of bacterial endophytes associated with agricultural crops have occupied center place recently, owing to their advantageous role in improving crop growth, health and yield. Research evidences have revealed that bacterial endophytes can promote plant growth by accelerating availability of mineral nutrients, helping in production of phytohormones, siderophores, and enzymes, and also by activating systemic resistance against insect pest and pathogens in plants. These research developments have opened an innovative boulevard in agriculture for capitalizing bacterial endophytes, single species or consortium, to enhance plant salt tolerance capabilities, and ultimately lead to translational refinement of crop-production business under salty environments. This article reviews the latest research progress on the identification and functional characterization of salt tolerant endophytic bacteria and illustrates various mechanisms triggered by them for plant growth promotion under saline environment.
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Affiliation(s)
- Prity Kushwaha
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Mau, 275103, India
| | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, India.
| | - Ajay Kumar Bhardwaj
- ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, 132001, India.
| | - Pandiyan Kuppusamy
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Mau, 275103, India
| | - Alok Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Mau, 275103, India
| | - Rajesh Kumar Tiwari
- AMITY University, Uttar Pradesh Lucknow Campus, Malhaur, Gomti Nagar Extension, Lucknow, 227105, India
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24
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Schenkel D, Deveau A, Niimi J, Mariotte P, Vitra A, Meisser M, Buttler A, Splivallo R. Linking soil's volatilome to microbes and plant roots highlights the importance of microbes as emitters of belowground volatile signals. Environ Microbiol 2019; 21:3313-3327. [PMID: 30895716 DOI: 10.1111/1462-2920.14599] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/13/2019] [Accepted: 03/19/2019] [Indexed: 01/08/2023]
Abstract
Plants and microbes release a plethora of volatiles that act as signals in plant-microbe interactions. Characterizing soil's volatilome and microbiome might shed light on the nature of relevant volatile signals and on their emitters. This hypothesis was tested by characterizing plant cover, soil's volatilome, nutrient content and microbiomes in three grasslands of the Swiss Jura Mountains. The fingerprints of soil's volatiles were generated by solid-phase micro-extraction gas chromatography/mass spectrometry, whereas high-throughput sequencing was used to create a snapshot of soil's microbial communities. A high similarity was observed in plant communities of two out of three sites, which was mirrored by the soil's volatilome. Multiple factor analysis evidenced a strong association among soil's volatilome, plant and microbial communities. The proportion of volatiles correlated to single bacterial and fungal taxa was higher than for plants. This suggests that those organisms might be major contributors to the volatilome of grassland soils. These findings illustrate that key volatiles in grassland soils might be emitted by a handful of organisms that include specific plants and microbes. Further work will be needed to unravel the structure of belowground volatiles and understand their implications for plant health and development.
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Affiliation(s)
- Denis Schenkel
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster, 60325, Frankfurt, Germany
| | - Aurélie Deveau
- Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280, Champenoux, France
| | - Jun Niimi
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Pierre Mariotte
- Laboratory of Ecological Systems (ECOS), Station 2, École Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), 1015, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Site Lausanne, Case postale 96, 1015, Lausanne, Switzerland
| | - Amarante Vitra
- Laboratory of Ecological Systems (ECOS), Station 2, École Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), 1015, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Site Lausanne, Case postale 96, 1015, Lausanne, Switzerland
| | - Marco Meisser
- Agroscope, Route de Duillier 50, Case Postale 1012, 1260, Nyon, Switzerland
| | - Alexandre Buttler
- Laboratory of Ecological Systems (ECOS), Station 2, École Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), 1015, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Site Lausanne, Case postale 96, 1015, Lausanne, Switzerland.,Laboratoire de Chrono-Environnement, UMR CNRS 6249, UFR des Sciences et Techniques, 16 route de Gray, Université de Franche-Comté, F-25030, Besançon, France
| | - Richard Splivallo
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster, 60325, Frankfurt, Germany.,Laboratory of Ecological Systems (ECOS), Station 2, École Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), 1015, Lausanne, Switzerland
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Akyol TY, Niwa R, Hirakawa H, Maruyama H, Sato T, Suzuki T, Fukunaga A, Sato T, Yoshida S, Tawaraya K, Saito M, Ezawa T, Sato S. Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields. Microbes Environ 2019; 34:23-32. [PMID: 30584188 PMCID: PMC6440726 DOI: 10.1264/jsme2.me18109] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/22/2018] [Indexed: 12/22/2022] Open
Abstract
Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields. Inoculation changed the abundance of indigenous AM fungi and other fungal members in a field-dependent manner. Inoculation consistently enriched several bacterial OTUs by changing the abundance of indigenous bacteria and introducing new bacteria. Some inoculum-associated bacteria closely interacted with the introduced AM fungi, some of which belonged to the genera Burkholderia, Cellulomonas, Microbacterium, Sphingomonas, and Streptomyces and may be candidate mycorrhizospheric bacteria that contribute to the establishment and/or function of the introduced AM fungi. Inoculated AM fungi also co-occurred with several indigenous bacteria with putative beneficial traits, suggesting that inoculated AM fungi may recruit specific taxa to confer better plant performance. The bacterial families Methylobacteriaceae, Acetobacteraceae, Armatimonadaceae, and Alicyclobacillaceae were consistently reduced by the inoculation, possibly due to changes in the host plant status caused by the inoculum. To the best of our knowledge, this is the first large-scale study to investigate interactions between AM fungal inoculation and indigenous root microbial communities in agricultural fields.
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Affiliation(s)
| | - Rieko Niwa
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization (NARO)2–1–18 Kannondai, Tsukuba 305–8666Japan
| | | | - Hayato Maruyama
- Graduate School of Agriculture, Hokkaido UniversitySapporo 060–8589Japan
| | - Takumi Sato
- Faculty of Agriculture, Yamagata UniversityTsuruoka 997–8555Japan
| | - Takae Suzuki
- Field Science Center, Graduate School of Agriculture, Tohoku UniversityOsaki 989–6711Japan
| | - Ayako Fukunaga
- Western Region Agricultural Research Center, NAROAyabe 623–0035Japan
| | - Takashi Sato
- Faculty of Bioresource Sciences, Akita Prefectural UniversityAkita 010–0195Japan
| | - Shigenobu Yoshida
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization (NARO)2–1–18 Kannondai, Tsukuba 305–8666Japan
| | - Keitaro Tawaraya
- Faculty of Agriculture, Yamagata UniversityTsuruoka 997–8555Japan
| | - Masanori Saito
- Field Science Center, Graduate School of Agriculture, Tohoku UniversityOsaki 989–6711Japan
- Department of Innovation Research, Japan Science and Technology AgencyTokyo, 102–0076Japan
| | - Tatsuhiro Ezawa
- Graduate School of Agriculture, Hokkaido UniversitySapporo 060–8589Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku UniversitySendai 980–8577Japan
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Inside the plant: addressing bacterial endophytes in biotic stress alleviation. Arch Microbiol 2019; 201:415-429. [PMID: 30834947 DOI: 10.1007/s00203-019-01642-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/06/2018] [Accepted: 02/26/2019] [Indexed: 12/28/2022]
Abstract
Bacterial endophytes are the internal association of bacteria with the plants, cherished whole or any part of their life cycle inside the plant. They are reported to improve plant health against the biotic stresses via de novo synthesis of structural compounds and stimulation of plant immunity. They are found to be vital in development of host resistance against phytopathogens and capable in reducing and elimination of deleterious effects of plant pathogens. Fungal-, bacterial-, viral-, insect- and nematode-associated negative effect can be reduced by the bacterial endophytes. They are also reported to control plant pathogens through several defense mechanisms such as by producing antimicrobial compounds and antibiotics, de novo synthesis of structural compounds, keeping out of pathogens by niche competition and induction of plant immunity or induced systemic resistance. In this review, an effort is made to summarize the exploitation of endophytic bacteria as a biological substitute to control biotic stresses in agricultural practices.
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Kosek K, Luczkiewicz A, Kozioł K, Jankowska K, Ruman M, Polkowska Ż. Environmental characteristics of a tundra river system in Svalbard. Part 1: Bacterial abundance, community structure and nutrient levels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:1571-1584. [PMID: 30545665 DOI: 10.1016/j.scitotenv.2018.11.378] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/24/2018] [Accepted: 11/25/2018] [Indexed: 06/09/2023]
Abstract
The Arctic hosts a set of unique ecosystems, characterised by extreme environmental conditions and undergoing a rapid change resulting from the average temperature rising. We present a study on an aquatic ecosystem of the Revelva catchment (Spitsbergen), based on samples collected from the lake, river and their tributaries, in the summer of 2016. The landscape variety of the study site and the seasonal change in the hydrological regime modify the availability of nutrients. In general, the upper part of the catchment consists of the mountain rocky slopes which are especially abundant in iron minerals, sulphides and phosphorus minerals. The lower part of the catchment is covered by plants - lichens, saxifrages and bryophytes, which are a different source of nutrients. In the analysed water samples, the maximum concentrations of nutrients such as iron, boron and phosphorus were 0.28 μg L-1, 4.52 μg L-1 and 1.91 μg L-1, respectively, in June, while in September, Fe and B reached the concentrations of 1.32 μg L-1 and 2.71 μg L-1, respectively. The concentration of P in September was below the detection limit of 1.00 μg L-1, which may be explained by the necessity of bacteria to consume it immediately on current needs. We noted also an increase in TOC concentration between the June and September samples, which could originate both from the biomass accumulation in the catchment and the permafrost melting contributing to the hydrological regime of the river. The bacterial community developed in this environment consisted mainly of Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes phylum, while the presence of Acidobacteria was less pronounced than in other tundra-related environments. The described catchment shows that despite the relatively small amount of bioavailable nutrients, the Revelva system is biodiverse and one of the most significant biogeochemical changes occurs there in response to seasonally switching water sources.
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Affiliation(s)
- Klaudia Kosek
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Aneta Luczkiewicz
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Krystyna Kozioł
- Institute of Geography, Faculty of Geography and Biology, Pedagogical University in Cracow, Podchorążych 2 St., Cracow 30-084, Poland; Institute of Geophysics, Polish Academy of Sciences, 64 Księcia Janusza St., Warsaw 01-452, Poland
| | - Katarzyna Jankowska
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Marek Ruman
- Faculty of Earth Sciences, University of Silesia,60 Będzińska St., Sosnowiec 41-200, Poland
| | - Żaneta Polkowska
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
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Botnen SS, Davey ML, Halvorsen R, Kauserud H. Sequence clustering threshold has little effect on the recovery of microbial community structure. Mol Ecol Resour 2018; 18:1064-1076. [PMID: 29673081 DOI: 10.1111/1755-0998.12894] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/21/2018] [Accepted: 04/11/2018] [Indexed: 11/27/2022]
Abstract
Analysis of microbial community structure by multivariate ordination methods, using data obtained by high-throughput sequencing of amplified markers (i.e., DNA metabarcoding), often requires clustering of DNA sequences into operational taxonomic units (OTUs). Parameters for the clustering procedure tend not to be justified but are set by tradition rather than being based on explicit knowledge. In this study, we explore the extent to which ordination results are affected by variation in parameter settings for the clustering procedure. Amplicon sequence data from nine microbial community studies, representing different sampling designs, spatial scales and ecosystems, were subjected to clustering into OTUs at seven different similarity thresholds (clustering thresholds) ranging from 87% to 99% sequence similarity. The 63 data sets thus obtained were subjected to parallel DCA and GNMDS ordinations. The resulting community structures were highly similar across all clustering thresholds. We explain this pattern by the existence of strong ecological structuring gradients and phylogenetically diverse sets of abundant OTUs that are highly stable across clustering thresholds. Removing low-abundance, rare OTUs had negligible effects on community patterns. Our results indicate that microbial data sets with a clear gradient structure are highly robust to choice of sequence clustering threshold.
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Affiliation(s)
- Synnøve Smebye Botnen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
- The University Centre in Svalbard, Longyearbyen, Norway
| | - Marie Louise Davey
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Rune Halvorsen
- Department of Research and Collections, Natural History Museum, University of Oslo, Oslo, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
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29
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Aydogan EL, Moser G, Müller C, Kämpfer P, Glaeser SP. Long-Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field-Experiment. Front Microbiol 2018; 9:144. [PMID: 29487575 PMCID: PMC5816784 DOI: 10.3389/fmicb.2018.00144] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
Global warming is currently a much discussed topic with as yet largely unexplored consequences for agro-ecosystems. Little is known about the warming effect on the bacterial microbiota inhabiting the plant surface (phyllosphere), which can have a strong impact on plant growth and health, as well as on plant diseases and colonization by human pathogens. The aim of this study was to investigate the effect of moderate surface warming on the diversity and composition of the bacterial leaf microbiota of the herbaceous plant Galium album. Leaves were collected from four control and four surface warmed (+2°C) plots located at the field site of the Environmental Monitoring and Climate Impact Research Station Linden in Germany over a 6-year period. Warming had no effect on the concentration of total number of cells attached to the leaf surface as counted by Sybr Green I staining after detachment, but changes in the diversity and phylogenetic composition of the bacterial leaf microbiota analyzed by bacterial 16S rRNA gene Illumina amplicon sequencing were observed. The bacterial phyllosphere microbiota were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Warming caused a significant higher relative abundance of members of the Gammaproteobacteria, Actinobacteria, and Firmicutes, and a lower relative abundance of members of the Alphaproteobacteria and Bacteroidetes. Plant beneficial bacteria like Sphingomonas spp. and Rhizobium spp. occurred in significantly lower relative abundance in leaf samples of warmed plots. In contrast, several members of the Enterobacteriaceae, especially Enterobacter and Erwinia, and other potential plant or human pathogenic genera such as Acinetobacter and insect-associated Buchnera and Wolbachia spp. occurred in higher relative abundances in the phyllosphere samples from warmed plots. This study showed for the first time the long-term impact of moderate (+2°C) surface warming on the phyllosphere microbiota on plants. A reduction of beneficial bacteria and an enhancement of potential pathogenic bacteria in the phyllosphere of plants may indicate that this aspect of the ecosystem which has been largely neglected up till now, can be a potential risk for pathogen transmission in agro-ecosystems in the near future.
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Affiliation(s)
- Ebru L. Aydogan
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Gerald Moser
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph Müller
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefanie P. Glaeser
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
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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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Niku J, Warton DI, Hui FKC, Taskinen S. Generalized Linear Latent Variable Models for Multivariate Count and Biomass Data in Ecology. JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2017. [DOI: 10.1007/s13253-017-0304-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Foster ZSL, Sharpton TJ, Grünwald NJ. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput Biol 2017; 100:1738-50. [PMID: 28222096 DOI: 10.3732/ajb.1200572] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/07/2017] [Accepted: 02/10/2017] [Indexed: 05/20/2023] Open
Abstract
Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual.
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Affiliation(s)
- Zachary S L Foster
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, Oregon, United States of America
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Kumar M, Brader G, Sessitsch A, Mäki A, van Elsas JD, Nissinen R. Plants Assemble Species Specific Bacterial Communities from Common Core Taxa in Three Arcto-Alpine Climate Zones. Front Microbiol 2017; 8:12. [PMID: 28174556 PMCID: PMC5258723 DOI: 10.3389/fmicb.2017.00012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 01/03/2017] [Indexed: 02/01/2023] Open
Abstract
Evidence for the pivotal role of plant-associated bacteria to plant health and productivity has accumulated rapidly in the last years. However, key questions related to what drives plant bacteriomes remain unanswered, among which is the impact of climate zones on plant-associated microbiota. This is particularly true for wild plants in arcto-alpine biomes. Here, we hypothesized that the bacterial communities associated with pioneer plants in these regions have major roles in plant health support, and this is reflected in the formation of climate and host plant specific endophytic communities. We thus compared the bacteriomes associated with the native perennial plants Oxyria digyna and Saxifraga oppositifolia in three arcto-alpine regions (alpine, low Arctic and high Arctic) with those in the corresponding bulk soils. As expected, the bulk soil bacterial communities in the three regions were significantly different. The relative abundances of Proteobacteria decreased progressively from the alpine to the high-arctic soils, whereas those of Actinobacteria increased. The candidate division AD3 and Acidobacteria abounded in the low Arctic soils. Furthermore, plant species and geographic region were the major determinants of the structures of the endophere communities. The plants in the alpine region had higher relative abundances of Proteobacteria, while plants from the low- and high-arctic regions were dominated by Firmicutes. A highly-conserved shared set of ubiquitous bacterial taxa (core bacteriome) was found to occur in the two plant species. Burkholderiales, Actinomycetales and Rhizobiales were the main taxa in this core, and they were also the main contributors to the differences in the endosphere bacterial community structures across compartments as well as regions. We postulate that the composition of this core is driven by selection by the two plants.
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Affiliation(s)
- Manoj Kumar
- Department of Microbial Ecology, University of GroningenGroningen, Netherlands
- Department of Biological and Environmental Science, University of JyväskyläJyväskylä, Finland
| | - Günter Brader
- Health and Environment Department, AIT Austrian Institute of TechnologyTulln, Austria
| | - Angela Sessitsch
- Health and Environment Department, AIT Austrian Institute of TechnologyTulln, Austria
| | - Anita Mäki
- Department of Biological and Environmental Science, University of JyväskyläJyväskylä, Finland
| | - Jan D. van Elsas
- Department of Microbial Ecology, University of GroningenGroningen, Netherlands
| | - Riitta Nissinen
- Department of Biological and Environmental Science, University of JyväskyläJyväskylä, Finland
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Dombrowski JE, Hollenbeck VG, Martin RC. Isolation and Identification of Bacterial Endophytes from Grasses along the Oregon Coast. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/ajps.2017.83040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Root microbiota dynamics of perennial Arabis alpina are dependent on soil residence time but independent of flowering time. ISME JOURNAL 2016; 11:43-55. [PMID: 27482927 PMCID: PMC5097464 DOI: 10.1038/ismej.2016.109] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 06/27/2016] [Accepted: 07/03/2016] [Indexed: 11/08/2022]
Abstract
Recent field and laboratory experiments with perennial Boechera stricta and annual Arabidopsis thaliana suggest that the root microbiota influences flowering time. Here we examined in long-term time-course experiments the bacterial root microbiota of the arctic-alpine perennial Arabis alpina in natural and controlled environments by 16S rRNA gene profiling. We identified soil type and residence time of plants in soil as major determinants explaining up to 15% of root microbiota variation, whereas environmental conditions and host genotype explain maximally 11% of variation. When grown in the same soil, the root microbiota composition of perennial A. alpina is largely similar to those of its annual relatives A. thaliana and Cardamine hirsuta. Non-flowering wild-type A. alpina and flowering pep1 mutant plants assemble an essentially indistinguishable root microbiota, thereby uncoupling flowering time from plant residence time-dependent microbiota changes. This reveals the robustness of the root microbiota against the onset and perpetual flowering of A. alpina. Together with previous studies, this implies a model in which parts of the root microbiota modulate flowering time, whereas, after microbiota acquisition during vegetative growth, the established root-associated bacterial assemblage is structurally robust to perturbations caused by flowering and drastic changes in plant stature.
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Kielak AM, Cipriano MAP, Kuramae EE. Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria. Arch Microbiol 2016; 198:987-993. [PMID: 27339258 PMCID: PMC5080364 DOI: 10.1007/s00203-016-1260-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/09/2016] [Accepted: 06/15/2016] [Indexed: 11/26/2022]
Abstract
Acidobacteria is one of the most abundant phyla in soils and has been detected in rhizosphere mainly based on cultivation-independent approaches such as 16S rRNA gene survey. Although putative interaction of Acidobacteria with plants was suggested, so far no plant–bacterial interactions were shown. Therefore, we performed several in vitro tests to evaluate Acidobacteria–plant interactions and the possible mechanisms involved in such interaction. We observed that Arabidopsis thaliana inoculated with three strains belonging to Acidobacteria subdivision 1 showed increase in biomass of roots and shoots as well as morphological changes in root system. Our results indicate that the plant hormone indole-3-acetic acid production and iron acquisition are plausibly involved in the plant and Acidobacteria interactions. Here, we confirm for the first time that Acidobacteria can actively interact with plants and act as plant growth-promoting bacteria. In addition, we show that Acidobacteria strains produce exopolysaccharide which supports the adhesion of bacteria to the root surfaces.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Matheus A P Cipriano
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
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Ballhausen MB, Vandamme P, de Boer W. Trait Differentiation within the Fungus-Feeding (Mycophagous) Bacterial Genus Collimonas. PLoS One 2016; 11:e0157552. [PMID: 27309848 PMCID: PMC4911057 DOI: 10.1371/journal.pone.0157552] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/01/2016] [Indexed: 12/02/2022] Open
Abstract
The genus Collimonas consists of facultative, fungus-feeding (mycophagous) bacteria. To date, 3 species (C. fungivorans, C. pratensis and C. arenae) have been described and over 100 strains have been isolated from different habitats. Functional traits of Collimonas bacteria that are potentially involved in interactions with soil fungi mostly negatively (fungal inhibition e.g.), but also positively (mineral weathering e.g.), affect fungal fitness. We hypothesized that variation in such traits between Collimonas strains leads to different mycophagous bacterial feeding patterns. We investigated a) whether phylogenetically closely related Collimonas strains possess similar traits, b) how far phylogenetic resolution influences the detection of phylogenetic signal (possession of similar traits by related strains) and c) if there is a pattern of co-occurrence among the studied traits. We measured genetically encoded (nifH genes, antifungal collimomycin gene cluster e.g.) as well as phenotypically expressed traits (chitinase- and siderophore production, fungal inhibition and others) and related those to a high-resolution phylogeny (MLSA), constructed by sequencing the housekeeping genes gyrB and rpoB and concatenating those with partial 16S rDNA sequences. Additionally, high-resolution and 16S rDNA derived phylogenies were compared. We show that MLSA is superior to 16SrDNA phylogeny when analyzing trait distribution and relating it to phylogeny at fine taxonomic resolution (a single bacterial genus). We observe that several traits involved in the interaction of collimonads and their host fungus (fungal inhibition e.g.) carry phylogenetic signal. Furthermore, we compare Collimonas trait possession with sister genera like Herbaspirillum and Janthinobacterium.
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Affiliation(s)
- Max-Bernhard Ballhausen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Peter Vandamme
- Laboratory for Microbiology, Gent University, Gent, Belgium
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
- Department of Soil Quality, Wageningen University, Wageningen, the Netherlands
- * E-mail:
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Carrell AA, Carper DL, Frank AC. Subalpine conifers in different geographical locations host highly similar foliar bacterial endophyte communities. FEMS Microbiol Ecol 2016; 92:fiw124. [DOI: 10.1093/femsec/fiw124] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2016] [Indexed: 12/14/2022] Open
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Brabcová V, Nováková M, Davidová A, Baldrian P. Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community. THE NEW PHYTOLOGIST 2016; 210:1369-1381. [PMID: 26832073 DOI: 10.1111/nph.13849] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/07/2015] [Indexed: 06/05/2023]
Abstract
Turnover of fungal biomass in forest litter and soil represents an important process in the environment. To date, knowledge of mycelial decomposition has been derived primarily from short-term studies, and the guild of mycelium decomposers has been poorly defined. Here, we followed the fate of the fruiting bodies of an ectomycorrhizal fungus in litter and soil of a temperate forest over 21 wk. The community of associated microbes and enzymatic processes in this specific substrate were described. The decomposition of fungal fruiting bodies exhibited biphasic kinetics. The rapid initial phase, which included the disappearance of DNA, was followed by a slower turnover of the recalcitrant fraction. Compared with the surrounding litter and soil, the mycelium represented a hotspot of activity of several biopolymer-degrading enzymes and high bacterial biomass. Specific communities of bacteria and fungi were associated with decomposing mycelium. These communities differed between the initial and late phases of decomposition. The bacterial community associated with decomposing mycelia typically contained the genera Pedobacter, Pseudomonas, Variovorax, Chitinophaga, Ewingella and Stenotrophomonas, whereas the fungi were mostly nonbasidiomycetous r-strategists of the genera Aspergillus, Penicillium, Mortierella, Cladosporium and several others. Decomposing ectomycorrhizal fungal mycelium exhibits high rates of decomposition and represents a specific habitat supporting a specific microbial community.
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Affiliation(s)
- Vendula Brabcová
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Monika Nováková
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Anna Davidová
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 14220, Praha 4, Czech Republic
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Miyambo T, Makhalanyane TP, Cowan DA, Valverde A. Plants of the fynbos biome harbour host species-specific bacterial communities. FEMS Microbiol Lett 2016; 363:fnw122. [DOI: 10.1093/femsle/fnw122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2016] [Indexed: 12/28/2022] Open
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Carrell AA, Frank AC. Bacterial endophyte communities in the foliage of coast redwood and giant sequoia. Front Microbiol 2015; 6:1008. [PMID: 26441933 PMCID: PMC4585279 DOI: 10.3389/fmicb.2015.01008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/07/2015] [Indexed: 12/11/2022] Open
Abstract
The endophytic bacterial microbiome, with an emerging role in plant nutrient acquisition and stress tolerance, is much less studied in natural plant populations than in agricultural crops. In a previous study, we found consistent associations between trees in the pine family and acetic acid bacteria (AAB) occurring at high relative abundance inside their needles. Our objective here was to determine if that pattern may be general to conifers, or alternatively, is more likely restricted to pines or conifers growing in nutrient limited and exposed environments. We used 16S rRNA pyrosequencing to characterize the foliar endophyte communities of two conifers in the Cupressaceae family: Two coast redwood (CR; Sequoia sempervirens) populations and one giant sequoia (GS; Sequoiadendron giganteum) population were sampled. Similar to the pines, the endophyte communities of the giant trees were dominated by Proteobacteria, Firmicutes, Acidobacteria, and Actinobacteria. However, although some major operational taxonomic units (OTUs) occurred at a high relative abundance of 10–40% in multiple samples, no specific group of bacteria dominated the endophyte community to the extent previously observed in high-elevation pines. Several of the dominating bacterial groups in the CR and GS foliage (e.g., Bacillus, Burkholderia, Actinomycetes) are known for disease- and pest suppression, raising the possibility that the endophytic microbiome protects the giant trees against biotic stress. Many of the most common and abundant OTUs in our dataset were most similar to 16S rRNA sequences from bacteria found in lichens or arctic plants. For example, an OTU belonging to the uncultured Rhizobiales LAR1 lineage, which is commonly associated with lichens, was observed at high relative abundance in many of the CR samples. The taxa shared between the giant trees, arctic plants, and lichens may be part of a broadly defined endophyte microbiome common to temperate, boreal, and tundra ecosystems.
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Affiliation(s)
- Alyssa A Carrell
- Life and Environmental Sciences, School of Natural Sciences, University of California, Merced Merced, CA, USA ; Department of Biology, Duke University Durham, NC, USA ; Environmental Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Anna C Frank
- Life and Environmental Sciences, School of Natural Sciences, University of California, Merced Merced, CA, USA ; Sierra Nevada Research Institute, University of California, Merced Merced, CA, USA
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Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A. The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 2015; 79:293-320. [PMID: 26136581 PMCID: PMC4488371 DOI: 10.1128/mmbr.00050-14] [Citation(s) in RCA: 1077] [Impact Index Per Article: 119.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
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Affiliation(s)
- Pablo R. Hardoim
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | | | - Gabriele Berg
- Institute for Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Stéphane Compant
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Andrea Campisano
- Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | | | - Angela Sessitsch
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
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The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 2015. [PMID: 26136581 DOI: 10.1128/mmbr.00050-14.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
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Zhang T, Yao YF. Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific. PLoS One 2015; 10:e0130051. [PMID: 26067836 PMCID: PMC4466372 DOI: 10.1371/journal.pone.0130051] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 05/16/2015] [Indexed: 11/24/2022] Open
Abstract
This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems.
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Affiliation(s)
- Tao Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yi-Feng Yao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Poosakkannu A, Nissinen R, Kytöviita MM. Culturable endophytic microbial communities in the circumpolar grass, Deschampsia flexuosa in a sub-Arctic inland primary succession are habitat and growth stage specific. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:111-122. [PMID: 25721603 DOI: 10.1111/1758-2229.12195] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Little is known about endophytic microbes in cold climate plants and how their communities are formed.We compared culturable putative endophytic bacteria and fungi in the ecologically important circumpolargrass, Deschampsia flexuosa growing in two successional stages of subarctic sand dune (68°29′N).Sequence analyses of partial 16S rRNA and internal transcribed spacer (ITS) sequences of culturable endophytes showed that diverse bacteria and fungi inhabit different tissues of D. flexuosa. A total of 178 bacterial isolates representing seven taxonomic divisions, Alpha, Beta and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Acidobacteria, and 30 fungal isolates representing the phylum Ascomycota were identified. Several endophytes were affiliated with specific plant tissues or successional stages. This first report of bacterial endophytes in D. flexuosa revealed that the genus Pseudomonas is tightly associated with D. flexuosa, and encompassed 39% of the bacterial isolates, and 58% of seed isolates. Based on 16S rRNA and ITS sequence data, most of the D. flexuosa endophytes were closely related to microbes from other cold environments. The majority of seed endophytic bacterial isolates were able to solubilize organic form of phosphate suggesting that these endophytes could play a role in resource mobilization in germinating seeds in nutrient-poor habitat.
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Affiliation(s)
- Anbu Poosakkannu
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
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Bragina A, Cardinale M, Berg C, Berg G. Vertical transmission explains the specific Burkholderia pattern in Sphagnum mosses at multi-geographic scale. Front Microbiol 2013; 4:394. [PMID: 24391630 PMCID: PMC3866706 DOI: 10.3389/fmicb.2013.00394] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/03/2013] [Indexed: 11/13/2022] Open
Abstract
The betaproteobacterial genus Burkholderia is known for its versatile interactions with its hosts that can range from beneficial to pathogenic. A plant-beneficial-environmental (PBE) Burkholderia cluster was recently separated from the pathogen cluster, yet still little is known about burkholderial diversity, distribution, colonization, and transmission patterns on plants. In our study, we applied a combination of high-throughput molecular and microscopic methods to examine the aforementioned factors for Burkholderia communities associated with Sphagnum mosses - model plants for long-term associations - in Austrian and Russian bogs. Analysis of 16S rRNA gene amplicons libraries revealed that most of the Burkholderia are part of the PBE group, but a minor fraction was closely related to B. glathei and B. andropogonis from the pathogen cluster. Notably, Burkholderia showed highly similar composition patterns for each moss species independent of the geographic region, and Burkholderia-specific fluorescent in situ hybridization of Sphagnum gametophytes exhibited similar colonization patterns in different Sphagnum species at multi-geographic scales. To explain these patterns, we compared the compositions of the surrounding water, gametophyte-, and sporophyte-associated microbiome at genus level and discovered that Burkholderia were present in the Sphagnum sporophyte and gametophyte, but were absent in the flark water. Therefore, Burkholderia is a part of the core microbiome transmitted from the moss sporophyte to the gametophyte. This suggests a vertical transmission of Burkholderia strains, and thus underlines their importance for the plants themselves.
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Affiliation(s)
- Anastasia Bragina
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | - Massimiliano Cardinale
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
- Institute of Plant Sciences, Karl-Franzens University of GrazGraz, Austria
| | - Christian Berg
- Institute of Plant Sciences, Karl-Franzens University of GrazGraz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
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