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Hying ZT, Miller TJ, Loh CY, Bazurto JV. Glycine betaine metabolism is enabled in Methylorubrum extorquens PA1 by alterations to dimethylglycine dehydrogenase. Appl Environ Microbiol 2024; 90:e0209023. [PMID: 38534142 PMCID: PMC11267896 DOI: 10.1128/aem.02090-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/22/2024] [Indexed: 03/28/2024] Open
Abstract
Low nutrient availability is a key characteristic of the phyllosphere (the aerial surface of plants). Phyllospheric bacteria utilize a wide array of carbon sources generated by plant hosts. Glycine betaine (GB) is a plant-derived compound that can be metabolized by certain members of the phyllosphere microbiota. Metabolism of glycine betaine generates formaldehyde, an intermediate of methylotrophic metabolism, leading us to investigate how the ubiquitous plant colonizing bacterium Methylorubrum extorquens PA1 might metabolize GB encountered in its native environment. M. extorquens PA1 cannot utilize GB as a sole carbon source. Through suppressor mutation analysis, we show that M. extorquens PA1 encodes a conserved GB utilization pathway that can be activated by single point mutations conferring GB utilization as a carbon source. We identified the gene cluster encoding the GB catabolic enzymes and found that gene expression was induced in the presence of GB. We show that utilization of GB is conserved among representative Methylobacterium species and generates the one-carbon metabolism intermediate formaldehyde, which M. extorquens utilizes as a source of energy. Our results support a model where suppressor mutations in Mext_3745 or ftsH (Mext_4840) prevent the degradation of the dimethylglycine dehydrogenase subunit DgcB by the membrane integral protease FtsH, conferring the ability to utilize GB by either (i) restoring stable membrane topology of DgcB or (ii) decreasing FtsH protease activity, respectively. Both mutations alleviate the bottleneck at the second step of GB degradation catalyzed by DgcAB.IMPORTANCEOvercoming low nutrient availability is a challenge many bacteria encounter in the environment. Facultative methylotrophs are able to utilize one-carbon and multi-carbon compounds as carbon and energy sources. The utilization of plant-derived glycine betaine (GB) represents a possible source of multi-carbon and one-carbon substrates. The metabolism of glycine betaine produces formaldehyde and glycine, which may be used simultaneously by facultative methylotrophs. However, the genes required for the utilization of GB in the ubiquitous plant-associated bacterium Methylorubrum extorquens have yet to be identified or described. Our work identifies and validates the genes required for glycine betaine metabolism in M. extorquens and shows that it directly intersects with methylotrophic metabolism through the production of formaldehyde.
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Affiliation(s)
- Zachary T. Hying
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Tyler J. Miller
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Chin Yi Loh
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Jannell V. Bazurto
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
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Baruah N, Haajanen R, Rahman MT, Pirttilä AM, Koskimäki JJ. Biosynthesis of polyhydroxybutyrate by Methylorubrum extorquens DSM13060 is essential for intracellular colonization in plant endosymbiosis. FRONTIERS IN PLANT SCIENCE 2024; 15:1302705. [PMID: 38390299 PMCID: PMC10883064 DOI: 10.3389/fpls.2024.1302705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Methylorubrum extorquens DSM13060 is an endosymbiont that lives in the cells of shoot tip meristems. The bacterium is methylotrophic and consumes plant-derived methanol for the production of polyhydroxybutyrate (PHB). The PHB provides protection against oxidative stress for both host and endosymbiont cells through its fragments, methyl-esterified 3-hydroxybutyrate (ME-3HB) oligomers. We evaluated the role of the genes involved in the production of ME-3HB oligomers in the host colonization by the endosymbiont M. extorquens DSM13060 through targeted genetic mutations. The strains with deletions in PHB synthase (phaC), PHB depolymerase (phaZ1), and a transcription factor (phaR) showed altered PHB granule characteristics, as ΔphaC had a significantly low number of granules, ΔphaR had a significantly increased number of granules, and ΔphaZ1 had significantly large PHB granules in the bacterial cells. When the deletion strains were exposed to oxidative stress, the ΔphaC strain was sensitive to 10 mM HO· and 20 mM H2O2. The colonization of the host, Scots pine (Pinus sylvestris L.), by the deletion strains varied greatly. The deletion strain ΔphaR colonized the host mainly intercellularly, whereas the ΔphaZ1 strain was a slightly poorer colonizer than the control. The deletion strain ΔphaC lacked the colonization potential, living mainly on the surfaces of the epidermis of pine roots and shoots in contrast to the control, which intracellularly colonized all pine tissues within the study period. In earlier studies, deletions within the PHB metabolic pathway have had a minor effect on plant colonization by rhizobia. We have previously shown the association between ME-3HB oligomers, produced by PhaC and PhaZ1, and the ability to alleviate host-generated oxidative stress during plant infection by the endosymbiont M. extorquens DSM13060. Our current results show that the low capacity for PHB synthesis leads to poor tolerance of oxidative stress and loss of colonization potential by the endosymbiont. Altogether, our findings demonstrate that the metabolism of PHB in M. extorquens DSM13060 is an important trait in the non-rhizobial endosymbiosis.
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Affiliation(s)
- Namrata Baruah
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roosa Haajanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Mohammad Tanvir Rahman
- Disease Networks, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Janne J Koskimäki
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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Jahan R, McDonald IR. Diversity of Methylobacterium species associated with New Zealand native plants. FEMS Microbiol Lett 2023; 370:fnad124. [PMID: 37985695 PMCID: PMC10699869 DOI: 10.1093/femsle/fnad124] [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: 05/24/2023] [Revised: 09/26/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023] Open
Abstract
Methylobacterium species are abundant colonizers of the phyllosphere due to the availability of methanol, a waste product of pectin metabolism during plant cell division. The phyllosphere is an extreme environment, with a landscape that is heterogeneous and continuously changing as the plant grows and is exposed to high levels of ultraviolet irradiation. Geographically, New Zealand (NZ) has been isolated for over a million years, has a biologically diverse flora, and is considered a biodiversity hotspot, with most native plants being endemic. We therefore hypothesize that the phyllosphere of NZ native plants harbor diverse groups of Methylobacterium species. Leaf imprinting using methanol-supplemented agar medium was used to isolate bacteria, and diversity was determined using ARDRA and 16S rRNA gene sequencing. Methylobacterium species were successfully isolated from the phyllosphere of 18 of the 20 native NZ plant species in this study, and six different species were identified: M. marchantiae, M. mesophilicum, M. adhaesivum, M. komagatae, M. extorquens, and M. phyllosphaerae. Other α, β, and γ-Proteobacteria, Actinomycetes, Bacteroidetes, and Firmicutes were also isolated, highlighting the presence of other potentially novel methanol utilizers within this ecosystem. This study identified that Methylobacterium are abundant members of the NZ phyllosphere, with species diversity and composition dependent on plant species.
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Affiliation(s)
- Rowshan Jahan
- Te Aka Mātuatua—School of Science, Te Whare Wānanga o Waikato—University of Waikato, Private Bag 3105, Hamilton 3240, Aotearoa, New Zealand
| | - Ian R McDonald
- Te Aka Mātuatua—School of Science, Te Whare Wānanga o Waikato—University of Waikato, Private Bag 3105, Hamilton 3240, Aotearoa, New Zealand
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Changes in Ambient Bacterial Community in Northern Taiwan during Long-Range Transport: Asian Dust Storm and Frontal Pollution. ATMOSPHERE 2022. [DOI: 10.3390/atmos13050841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Long-range transport (LRT) can carry air pollutants to downwind areas. However, studies about the impacts of LRT on bacterial communities are few. This study investigated the influence of Asian dust storms (ADS) and frontal pollution (FP) on bacterial communities in ambient air using next-generation sequencing (NGS) and Terminal Restriction Fragment Length Polymorphism (T-RFLP). Air samples were collected at Cape Fugui (CF) and National Taiwan University (NTU) in northern Taiwan before (or background days), during, and after LRTs from November 2013 to March 2015. The richness, H index, and evenness increased during FPs and then decreased after FPs. During and after ADS and FP, the prevalence of the phylum Proteobacteria decreased, but that of Firmicutes increased. The dominant class of Proteobacteria changed from Alphaproteobacteria on background days to Betaproteobacteria during LRTs. At the genus level, the high abundance of Ralstonia and Bacillus during FP and Clostridium during ADS were detected at both locations. Additionally, Ralstonia was dominant at CF during ADS. In conclusion, FP and ADS both changed the bacterial community. The indicator genus was Clostridium and Ralstonia for ADS as well as Bacillus and Ralstonia for FP. Given the potential health threats posed by the bioaerosols transported, people should avoid outdoor activities during LRTs.
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Alessa O, Ogura Y, Fujitani Y, Takami H, Hayashi T, Sahin N, Tani A. Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species. Front Microbiol 2021; 12:740610. [PMID: 34737731 PMCID: PMC8561711 DOI: 10.3389/fmicb.2021.740610] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/06/2021] [Indexed: 01/06/2023] Open
Abstract
The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.
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Affiliation(s)
- Ola Alessa
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Hideto Takami
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nurettin Sahin
- Egitim Fakultesi, Mugla Sitki Kocman University, Mugla, Turkey
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
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Capacity of soil bacteria to reach the phyllosphere and convergence of floral communities despite soil microbiota variation. Proc Natl Acad Sci U S A 2021; 118:2100150118. [PMID: 34620708 PMCID: PMC8521660 DOI: 10.1073/pnas.2100150118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
The role of flowers as environmental filters for bacterial communities and the provenance of bacteria in the phyllosphere are currently poorly understood. We experimentally tested the effect of induced variation in soil communities on the microbiota of plant organs. We identified soil-derived bacteria in the phyllosphere and show a strong convergence of floral communities with an enrichment of members of the Burkholderiaceae family. This finding highlights a potential role of the flower in shaping the interaction between plants and a bacterial family known to harbor both plant pathogens and growth-promoting strains. Because the flower involves host–symbiont feedback, the selection of specific bacteria by the reproductive organs of angiosperms could be relevant for the modulation of fruit and seed production. Leaves and flowers are colonized by diverse bacteria that impact plant fitness and evolution. Although the structure of these microbial communities is becoming well-characterized, various aspects of their environmental origin and selection by plants remain uncertain, such as the relative proportion of soilborne bacteria in phyllosphere communities. Here, to address this issue and to provide experimental support for bacteria being filtered by flowers, we conducted common-garden experiments outside and under gnotobiotic conditions. We grew Arabidopsis thaliana in a soil substitute and added two microbial communities from natural soils. We estimated that at least 25% of the phyllosphere bacteria collected from the plants grown in the open environment were also detected in the controlled conditions, in which bacteria could reach leaves and flowers only from the soil. These taxa represented more than 40% of the communities based on amplicon sequencing. Unsupervised hierarchical clustering approaches supported the convergence of all floral microbiota, and 24 of the 28 bacteria responsible for this pattern belonged to the Burkholderiaceae family, which includes known plant pathogens and plant growth-promoting members. We anticipate that our study will foster future investigations regarding the routes used by soil microbes to reach leaves and flowers, the ubiquity of the environmental filtering of Burkholderiaceae across plant species and environments, and the potential functional effects of the accumulation of these bacteria in the reproductive organs of flowering plants.
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Mass spectrometry-based approaches to study lanthanides and lanthanide-dependent proteins in the phyllosphere. Methods Enzymol 2021; 650:215-236. [PMID: 33867023 DOI: 10.1016/bs.mie.2021.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Rare-earth elements (REEs) were recently discovered to be biologically significant. The finding was originally made with the methanol dehydrogenase XoxF, which depends on REEs for its activity, and reports of lanthanide-utilizing bacteria have since expanded. Environmental proteomics allows the identification of proteins specifically induced by the presence of lanthanides or can provide insights into the preferred use of lanthanide-dependent and -independent isoenzymes, for example. Here we describe protocols for the growth and subsequent mass spectrometry-based proteome analysis of bacteria obtained from controlled artificial media and from the phyllosphere of the model plant Arabidopsis thaliana. In addition, the use of inductively coupled plasma mass spectrometry (ICP-MS) is described for the quantification of REEs in biological samples.
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Meena KK, Bitla UM, Sorty AM, Singh DP, Gupta VK, Wakchaure GC, Kumar S. Mitigation of Salinity Stress in Wheat Seedlings Due to the Application of Phytohormone-Rich Culture Filtrate Extract of Methylotrophic Actinobacterium Nocardioides sp. NIMMe6. Front Microbiol 2020; 11:2091. [PMID: 33071995 PMCID: PMC7531191 DOI: 10.3389/fmicb.2020.02091] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 08/08/2020] [Indexed: 01/02/2023] Open
Abstract
Salinity stress is an important plant growth limiting factor influencing crop productivity negatively. Microbial interventions for salinity stress mitigation have invited significant attention due to the promising impacts of interactive associations on the intrinsic mechanisms of plants. We report the impact of microbial inoculation of a halotolerant methylotrophic actinobacterium (Nocardioides sp. NIMMe6; LC140963) and seed coating of its phytohormone-rich bacterial culture filtrate extract (BCFE) on wheat seedlings grown under saline conditions. Different plant-growth-promoting (PGP) attributes of the bacterium in terms of its growth in N-limiting media and siderophore and phytohormone [indole-3-acetic acid (IAA) and salicylic acid] production influenced plant growth positively. Microbial inoculation and priming with BCFE resulted in improved germination (92% in primed seeds at 10 dS m–1), growth, and biochemical accumulation (total protein 42.01 and 28.75 mg g–1 in shoot and root tissues at 10 dS m–1 in BCFE-primed seeds) and enhanced the activity level of antioxidant enzymes (superoxide dismutase, catalase, peroxidase, and ascorbate peroxidase) to confer stress mitigation. Biopriming with BCFE proved impactful. The BCFE application has further influenced the overexpression of defense-related genes in the seedlings grown under salinity stress condition. Liquid chromatography–mass spectrometry-based characterization of the biomolecules in the BCFE revealed quantification of salicylate and indole-3-acetate (Rt 4.978 min, m/z 138.1 and 6.177 min, 129.1), respectively. The high tolerance limit of the bacterium to 10% NaCl in the culture media suggested its possible survival and growth under high soil salinity condition as microbial inoculant. The production of a high quantity of IAA (45.6 μg ml–1 of culture filtrate) by the bacterium reflected its capability to not only support plant growth under salinity condition but also mitigate stress due to the impact of phytohormone as defense mitigators. The study suggested that although microbial inoculation offers stress mitigation in plants, the phytohormone-rich BCFE from Nocardioides sp. NIMMe6 has potential implications for defense against salinity stress in wheat.
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Affiliation(s)
- Kamlesh K Meena
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
| | - Utkarsh M Bitla
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
| | - Ajay M Sorty
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
| | - Dhananjaya P Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Vijai K Gupta
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - G C Wakchaure
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
| | - Satish Kumar
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
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Macey MC, Pratscher J, Crombie AT, Murrell JC. Impact of plants on the diversity and activity of methylotrophs in soil. MICROBIOME 2020; 8:31. [PMID: 32156318 PMCID: PMC7065363 DOI: 10.1186/s40168-020-00801-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/10/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils. RESULTS Application of probes for methanol dehydrogenase genes (mxaF, xoxF, mdh2) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including Hyphomicrobium, Methylobacterium and members of the Comamonadaceae. The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using 13C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the 13C-labelled DNA revealed members of the Methylophilaceae as highly abundant and active in all soils examined. There was greater diversity of active members of the Methylophilaceae and Comamonadaceae and of the genus Methylobacterium in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a 13CO2 atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere. CONCLUSION In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle. Video abstract.
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Affiliation(s)
- Michael C. Macey
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, Buckinghamshire MK7 6AA UK
| | - Jennifer Pratscher
- The Lyell Centre, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Research Avenue South, Edinburgh, EH14 4AP UK
| | - Andrew T. Crombie
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
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Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria. Int J Mol Sci 2018; 19:ijms19010291. [PMID: 29351192 PMCID: PMC5796236 DOI: 10.3390/ijms19010291] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/13/2018] [Accepted: 01/15/2018] [Indexed: 11/16/2022] Open
Abstract
Metal contaminated soils are increasing worldwide. Metal-tolerant plants growing on metalliferous soils are fascinating genetic and microbial resources. Seeds can vertically transmit endophytic microorganisms that can assist next generations to cope with environmental stresses, through yet poorly understood mechanisms. The aims of this study were to identify the core seed endophyte microbiome of the pioneer metallophyte Crotalaria pumila throughout three generations, and to better understand the plant colonisation of the seed endophyte Methylobacterium sp. Cp3. Strain Cp3 was detected in C. pumila seeds across three successive generations and showed the most dominant community member. When inoculated in the soil at the time of flowering, strain Cp3 migrated from soil to seeds. Using confocal microscopy, Cp3-mCherry was demonstrated to colonise the root cortex cells and xylem vessels of the stem under metal stress. Moreover, strain Cp3 showed genetic and in planta potential to promote seed germination and seedling development. We revealed, for the first time, that the seed microbiome of a pioneer plant growing in its natural environment, and the colonisation behaviour of an important plant growth promoting systemic seed endophyte. Future characterization of seed microbiota will lead to a better understanding of their functional contribution and the potential use for seed-fortification applications.
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Peredo EL, Simmons SL. Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere. Front Microbiol 2018; 8:2669. [PMID: 29375531 PMCID: PMC5767230 DOI: 10.3389/fmicb.2017.02669] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/21/2017] [Indexed: 11/13/2022] Open
Abstract
Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents.
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Affiliation(s)
- Elena L Peredo
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
| | - Sheri L Simmons
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
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Correlated production and consumption of chloromethane in the Arabidopsis thaliana phyllosphere. Sci Rep 2017; 7:17589. [PMID: 29242530 PMCID: PMC5730606 DOI: 10.1038/s41598-017-17421-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/24/2017] [Indexed: 11/24/2022] Open
Abstract
Chloromethane (CH3Cl) is a toxic gas mainly produced naturally, in particular by plants, and its emissions contribute to ozone destruction in the stratosphere. Conversely, CH3Cl can be degraded and used as the sole carbon and energy source by specialised methylotrophic bacteria, isolated from a variety of environments including the phyllosphere, i.e. the aerial parts of vegetation. The potential role of phyllospheric CH3Cl-degrading bacteria as a filter for plant emissions of CH3Cl was investigated using variants of Arabidopsis thaliana with low, wild-type and high expression of HOL1 methyltransferase previously shown to be responsible for most of CH3Cl emissions by A. thaliana. Presence and expression of the bacterial chloromethane dehalogenase cmuA gene in the A. thaliana phyllosphere correlated with HOL1 genotype, as shown by qPCR and RT-qPCR. Production of CH3Cl by A. thaliana paralleled HOL1 expression, as assessed by a fluorescence-based bioreporter. The relation between plant production of CH3Cl and relative abundance of CH3Cl-degrading bacteria in the phyllosphere suggests that CH3Cl-degrading bacteria co-determine the extent of plant emissions of CH3Cl to the atmosphere.
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Li O, Xiao R, Sun L, Guan C, Kong D, Hu X. Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing. PLoS One 2017; 12:e0184717. [PMID: 28931073 PMCID: PMC5607135 DOI: 10.1371/journal.pone.0184717] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 08/29/2017] [Indexed: 01/22/2023] Open
Abstract
As an epiphyte orchid, Dendrobium catenatum relies on microorganisms for requisite nutrients. Metagenome pyrosequencing based on 16S rRNA and nifH genes was used to characterize the bacterial and diazotrophic communities associated with D. catenatum collected from 5 districts in China. Based on Meta-16S rRNA sequencing, 22 bacterial phyla and 699 genera were identified, distributed as 125 genera from 8 phyla and 319 genera from 10 phyla shared by all the planting bases and all the tissues, respectively. The predominant Proteobacteria varied from 71.81% (GZ) to 96.08% (YN), and Delftia (10.39-38.42%), Burkholderia (2.71-15.98%), Escherichia/Shigella (4.90-25.12%), Pseudomonas (2.68-30.72%) and Sphingomonas (1.83-2.05%) dominated in four planting bases. Pseudomonas (17.94-22.06%), Escherichia/Shigella (6.59-11.59%), Delftia (9.65-22.14%) and Burkholderia (3.12-11.05%) dominated in all the tissues. According to Meta-nifH sequencing, 4 phyla and 45 genera were identified, while 17 genera and 24 genera from 4 phyla were shared by all the planting bases and all the tissues, respectively. Burkholderia and Bradyrhizobium were the most popular in the planting bases, followed by Methylovirgula and Mesorhizobium. Mesorhizobium was the most popular in different tissues, followed by Beijerinckia, Xanthobacter, and Burkholderia. Among the genera, 39 were completely overlapped with the results based on the 16S rRNA gene. In conclusion, abundant bacteria and diazotrophs were identified in common in different tissues of D. catenatum from five planting bases, which might play a great role in the supply of nutrients such as nitrogen. The exact abundance of phylum and genus on the different tissues from different planting bases need deeper sequencing with more samples.
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Affiliation(s)
- Ou Li
- College of Life Science, Zhejiang Sci-Tech University, Xiasha, Hangzhou, PR China
| | - Rong Xiao
- College of Life Science, Zhejiang Sci-Tech University, Xiasha, Hangzhou, PR China
| | - Lihua Sun
- Zhejiang Academy of Medical Sciences, Hangzhou, PR China
| | - Chenglin Guan
- College of Life Science, Zhejiang Sci-Tech University, Xiasha, Hangzhou, PR China
| | - Dedong Kong
- Agricultural Experiment Station, Zhejiang Univesity, Hangzhou, PR China
| | - Xiufang Hu
- College of Life Science, Zhejiang Sci-Tech University, Xiasha, Hangzhou, PR China
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14
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Okumura M, Fujitani Y, Maekawa M, Charoenpanich J, Murage H, Kimbara K, Sahin N, Tani A. Cultivable Methylobacterium species diversity in rice seeds identified with whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis. J Biosci Bioeng 2016; 123:190-196. [PMID: 27720675 DOI: 10.1016/j.jbiosc.2016.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/03/2016] [Accepted: 09/05/2016] [Indexed: 11/17/2022]
Abstract
Methylobacterium species are methylotrophic bacteria that widely inhabit plant surfaces. In addition to studies on methylotrophs as model organisms, research has also been conducted on their mechanism of plant growth promotion as well as the species-species specificity of plant-microbe interaction. We employed whole-cell matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (WC-MS) analysis, which enables the rapid and accurate identification of bacteria at the species level, to identify Methylobacterium isolates collected from the rice seeds of different cultivars harvested in Japan, Thailand, and Kenya. Rice seeds obtained from diverse geographical locations showed different communities of Methylobacterium species. We found that M. fujisawaense, M. aquaticum, M. platani, and M. radiotolerans are the most frequently isolated species, but none were isolated as common species from 18 seed samples due to the highly biased communities in some samples. These findings will contribute to the development of formulations containing selected species that promote rice growth, though it may be necessary to customize the formulations depending on the cultivars and farm conditions.
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Affiliation(s)
- Marie Okumura
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Masahiko Maekawa
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Jittima Charoenpanich
- Department of Biochemistry, Faculty of Science, Burapha University, Bangsaen, Chonburi 20131, Thailand
| | - Hunja Murage
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
| | - Kazuhide Kimbara
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan; Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Kita-ku, Hamamatsu 432-8561, Japan
| | - Nurettin Sahin
- Egitim Fakultesi, Mugla Sitki Kocman University, 48170 Kotekli, Mugla, Turkey
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
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15
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Ueda Y, Frindte K, Knief C, Ashrafuzzaman M, Frei M. Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice. PLoS One 2016; 11:e0163178. [PMID: 27643794 PMCID: PMC5028031 DOI: 10.1371/journal.pone.0163178] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 09/02/2016] [Indexed: 12/23/2022] Open
Abstract
Microbes constitute a vital part of the plant holobiont. They establish plant-microbe or microbe-microbe associations, forming a unique microbiota with each plant species and under different environmental conditions. These microbial communities have to adapt to diverse environmental conditions, such as geographical location, climate conditions and soil types, and are subjected to changes in their surrounding environment. Elevated ozone concentration is one of the most important aspects of global change, but its effect on microbial communities living on plant surfaces has barely been investigated. In the current study, we aimed at elucidating the potential effect of elevated ozone concentrations on the phyllosphere (aerial part of the plant) and rhizoplane (surface of the root) microbiota by adopting next-generation 16S rRNA amplicon sequencing. A standard japonica rice cultivar Nipponbare and an ozone-tolerant breeding line L81 (Nipponbare background) were pre-grown in a greenhouse for 10 weeks and then exposed to ozone at 85 ppb for 7 h daily for 30 days in open top chambers. Microbial cells were collected from the phyllosphere and rhizoplane separately. The treatment or different genotypes did not affect various diversity indices. On the other hand, the relative abundance of some bacterial taxa were significantly affected in the rhizoplane community of ozone-treated plants. A significant effect of ozone was detected by homogeneity of molecular variance analysis in the phyllosphere, meaning that the community from ozone-treated phyllosphere samples was more variable than those from control plants. In addition, a weak treatment effect was observed by clustering samples based on the Yue and Clayton and weighted UniFrac distance matrices among samples. We therefore conclude that the elevated ozone concentrations affected the bacterial community structure of the phyllosphere and the rhizosplane as a whole, even though this effect was rather weak and did not lead to changes of the function of the communities.
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Affiliation(s)
- Yoshiaki Ueda
- Institute of Crop Science and Resource Conservation (INRES) – Plant Nutrition, University of Bonn, Bonn, Germany
| | - Katharina Frindte
- Institute of Crop Science and Resource Conservation (INRES) – Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation (INRES) – Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Md Ashrafuzzaman
- Institute of Crop Science and Resource Conservation (INRES) – Plant Nutrition, University of Bonn, Bonn, Germany
| | - Michael Frei
- Institute of Crop Science and Resource Conservation (INRES) – Plant Nutrition, University of Bonn, Bonn, Germany
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16
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Müller DB, Schubert OT, Röst H, Aebersold R, Vorholt JA. Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization. Mol Cell Proteomics 2016; 15:3256-3269. [PMID: 27457762 DOI: 10.1074/mcp.m116.058164] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 12/24/2022] Open
Abstract
Plants are colonized by a diverse community of microorganisms, the plant microbiota, exhibiting a defined and conserved taxonomic structure. Niche separation based on spatial segregation and complementary adaptation strategies likely forms the basis for coexistence of the various microorganisms in the plant environment. To gain insights into organism-specific adaptations on a molecular level, we selected two exemplary community members of the core leaf microbiota and profiled their proteomes upon Arabidopsis phyllosphere colonization. The highly quantitative mass spectrometric technique SWATH MS was used and allowed for the analysis of over two thousand proteins spanning more than three orders of magnitude in abundance for each of the model strains. The data suggest that Sphingomonas melonis utilizes amino acids and hydrocarbon compounds during colonization of leaves whereas Methylobacterium extorquens relies on methanol metabolism in addition to oxalate metabolism, aerobic anoxygenic photosynthesis and alkanesulfonate utilization. Comparative genomic analyses indicates that utilization of oxalate and alkanesulfonates is widespread among leaf microbiota members whereas, aerobic anoxygenic photosynthesis is almost exclusively found in Methylobacteria. Despite the apparent niche separation between these two strains we also found a relatively small subset of proteins to be coregulated, indicating common mechanisms, underlying successful leaf colonization. Overall, our results reveal for two ubiquitous phyllosphere commensals species-specific adaptations to the host environment and provide evidence for niche separation within the plant microbiota.
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Affiliation(s)
- Daniel B Müller
- From the ‡Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Olga T Schubert
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Hannes Röst
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland; ¶Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Julia A Vorholt
- From the ‡Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland;
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17
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Tani A, Sahin N, Fujitani Y, Kato A, Sato K, Kimbara K. Methylobacterium Species Promoting Rice and Barley Growth and Interaction Specificity Revealed with Whole-Cell Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF/MS) Analysis. PLoS One 2015; 10:e0129509. [PMID: 26053875 PMCID: PMC4460032 DOI: 10.1371/journal.pone.0129509] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/08/2015] [Indexed: 11/18/2022] Open
Abstract
Methylobacterium species frequently inhabit plant surfaces and are able to utilize the methanol emitted from plants as carbon and energy sources. As some of the Methylobacterium species are known to promote plant growth, significant attention has been paid to the mechanism of growth promotion and the specificity of plant-microbe interactions. By screening our Methylobacterium isolate collection for the high growth promotion effect in vitro, we selected some candidates for field and pot growth tests for rice and barley, respectively. We found that inoculation resulted in better ripening of rice seeds, and increased the size of barley grains but not the total yield. In addition, using whole-cell matrix-assister laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, we identified and classified Methylobacterium isolates from Methylobacterium-inoculated rice plants. The inoculated species could not be recovered from the rice plants, and in some cases, the Methylobacterium community structure was affected by the inoculation, but not with predomination of the inoculated species. The isolates from non-inoculated barley of various cultivars grown in the same field fell into just two species. These results suggest that there is a strong selection pressure at the species level of Methylobacterium residing on a given plant species, and that selection of appropriate species that can persist on the plant is important to achieve growth promotion.
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Affiliation(s)
- Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
- * E-mail:
| | - Nurettin Sahin
- Egitim Fakultesi, Mugla Sitki Kocman University, Mugla, Turkey
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Akiko Kato
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Kazuhide Kimbara
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
- Faculty of Engineering, Shizuoka University, Hamamatsu, Japan
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18
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Osawa A, Kaseya Y, Koue N, Schrader J, Knief C, Vorholt JA, Sandmann G, Shindo K. 4-[2-O-11Z-Octadecenoyl-β-glucopyranosyl]-4,4′-diapolycopene-4,4′-dioic acid and 4-[2-O-9Z-hexadecenoyl-β-glucopyranosyl]-4,4′-diapolycopene-4,4′-dioic acid: new C30-carotenoids produced by Methylobacterium. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.04.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Kolb S, Stacheter A. Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment. Front Microbiol 2013; 4:268. [PMID: 24046766 PMCID: PMC3763247 DOI: 10.3389/fmicb.2013.00268] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/19/2013] [Indexed: 01/06/2023] Open
Abstract
The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.
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Affiliation(s)
- Steffen Kolb
- Department of Ecological Microbiology, University of Bayreuth Bayreuth, Germany
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20
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Bal Krishna KC, Sathasivan A, Ginige MP. Microbial community changes with decaying chloramine residuals in a lab-scale system. WATER RESEARCH 2013; 47:4666-4679. [PMID: 23770481 DOI: 10.1016/j.watres.2013.04.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 04/13/2013] [Accepted: 04/18/2013] [Indexed: 06/02/2023]
Abstract
When chloramine is used as a disinfectant, managing an acceptable "residual" throughout the water distribution systems particularly once nitrification has set in is challenging. Managing chloramine decay prior to the onset of nitrification through effective control strategies is important and to-date the strategies developed around nitrification has been ineffective. This study aimed at developing a more holistic knowledge on how decaying chloramine and nitrification metabolites impact microbial communities in chloraminated systems. Five lab-scale reactors (connected in series) were operated to simulate a full-scale chloraminated distribution system. Culture independent techniques (cloning and qPCR) were used to characterise and quantify the mixed microbial communities in reactors maintaining a residual of high to low (2.18-0.03 mg/L). The study for the first time associates chloramine residuals and nitrification metabolites to different microbial communities. Bacterial classes Solibacteres, Nitrospira, Sphingobacteria and Betaproteobacteria dominated at low chloramine residuals whereas Actinobacteria and Gammaproteobacteria dominated at higher chloramine residuals. Prior to the onset of nitrification bacterial genera Pseudomonas, Methylobacterium and Sphingomonas were found to be dominant and Sphingomonas in particular increased with the onset of nitrification. Nitrosomonas urea, oligotropha, and two other novel ammonia-oxidizing bacteria were detected once the chloramine residuals had dropped below 0.65 mg/L. Additionally nitrification alone failed to explain chloramine decay rates observed in these reactors. The finding of this study is expected to re-direct the focus from nitrifiers to heterotrophic bacteria, which the authors believe could hold the key towards developing a control strategy that would enable better management of chloramine residuals.
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Affiliation(s)
- K C Bal Krishna
- Department of Civil and Construction Engineering, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
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21
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Buse HY, Lu J, Struewing IT, Ashbolt NJ. Eukaryotic diversity in premise drinking water using 18S rDNA sequencing: implications for health risks. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:6351-66. [PMID: 23589243 DOI: 10.1007/s11356-013-1646-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 03/13/2013] [Indexed: 05/08/2023]
Abstract
The goal of this study was to characterize microbial eukaryotes over a 12-month period to provide insight into the occurrence of potential bacterial predators and hosts in premise plumbing. Nearly 6,300 partial 18S rRNA gene sequences from 24 hot (36.9-39.0 °C) and cold (6.8-29.1 °C) drinking water samples were analyzed and classified into major eukaryotic groups. Each major group, consisting of free-living amoebae (FLA)/protozoa, algae, copepods, dinoflagellates, fungi, nematodes, and unique uncultured eukaryotic sequences, showed limited diversity dominated by a few distinct populations, which may be characteristic of oligotrophic environments. Changes in the relative abundance of predators such as nematodes, copepods, and FLA appear to be related to temperature and seasonal changes in water quality. Sequences nearly identical to FLA such as Hartmannella vermiformis, Echinamoeba thermarmum, Pseudoparamoeba pagei, Protacanthamoeba bohemica, Platyamoeba sp., and Vannella sp. were obtained. In addition to FLA, various copepods, rotifers, and nematodes have been reported to internalize viral and bacterial pathogens within drinking water systems thus potentially serving as transport hosts; implications of which are discussed further. Increasing the knowledge of eukaryotic occurrence and their relationship with potential pathogens should aid in assessing microbial risk associated with various eukaryotic organisms in drinking water.
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Affiliation(s)
- Helen Y Buse
- Dynamac c/o US Environmental Protection Agency, 26 W Martin Luther King Drive, Cincinnati, OH 45242, USA.
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22
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Isolation of optically targeted single bacteria by application of fluidic force microscopy to aerobic anoxygenic phototrophs from the phyllosphere. Appl Environ Microbiol 2013; 79:4895-905. [PMID: 23770907 DOI: 10.1128/aem.01087-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In their natural environment, bacteria often behave differently than they do under laboratory conditions. To gain insight into the physiology of bacteria in situ, dedicated approaches are required to monitor their adaptations and specific behaviors under environmental conditions. Optical microscopy is crucial for the observation of fundamental characteristics of bacteria, such as cell shape, size, and marker gene expression. Here, fluidic force microscopy (FluidFM) was exploited to isolate optically selected bacteria for subsequent identification and characterization. In this study, bacteriochlorophyll-producing bacteria, which can be visualized due to their characteristic fluorescence in the infrared range, were isolated from leaf washes. Bacterial communities from the phyllosphere were investigated because they harbor genes indicative of aerobic anoxygenic photosynthesis. Our data show that different species of Methylobacterium express their photosystem in planta, and they show a distinct pattern of bacteriochlorophyll production under laboratory conditions that is dependent on supplied carbon sources.
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23
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Aggregation of selected plant growth promoting Methylobacterium strains: role of cell surface components and hydrophobicity. Arch Microbiol 2013; 195:219-25. [DOI: 10.1007/s00203-013-0866-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 06/01/2012] [Accepted: 01/02/2013] [Indexed: 01/09/2023]
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24
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Wellner S, Lodders N, Glaeser SP, Kämpfer P. Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces. Int J Syst Evol Microbiol 2013; 63:2690-2699. [PMID: 23291886 DOI: 10.1099/ijs.0.047787-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three pink-pigmented, aerobic, Gram-stain-negative, rod-shaped and facultatively methylotrophic strains were isolated from the phyllosphere of Trifolium repens and Cerastium holosteoides. 16S rRNA gene sequence analysis support the affiliation of all strains to the genus Methylobacterium. The closest relatives of strains C34(T) and T5 were Methylobacterium gnaphalii 23e(T) (98.0 and 98.5 % sequence similarity, respectively) and Methylobacterium organophilum JCM 2833(T) (97.0 and 97.2 %, respectively). Strain TA73(T) showed the highest sequence similarities to Methylobacterium marchantiae JT1(T) and Methylobacterium bullatum F3.2(T) (both 97.9 %), followed by Methylobacterium phyllosphaerae CBMB27(T) and Methylobacterium brachiatum DSM 19569(T) (both 97.8 %), Methylobacterium cerastii C15(T) and Methylobacterium radiotolerans JCM 2831(T) (both 97.7 %). The major components in the fatty acid profiles were C18 : 1ω7c, C16 : 0 and one unknown fatty acid for strain TA73(T) and C18 : 1ω7c, C16 : 1ω7c/iso-C15 : 0 2-OH, C18 : 0 and C16 : 0 for strains C34(T) and T5. Physiological and biochemical analysis, including DNA-DNA hybridization, revealed clear differences between the investigated strains and their closest phylogenetic neighbours. DNA-DNA hybridization studies also showed high similarities between strains C34(T) and T5 (59.6-100 %). Therefore, the isolates represent two novel species within the genus Methylobacterium, for which the names Methylobacterium trifolii sp. nov. (type strain TA73(T) = LMG 25778(T) = CCM 7786(T)) and Methylobacterium thuringiense sp. nov. (type strain C34(T) = LMG 25777(T) = CCM 7787(T)) are proposed.
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Affiliation(s)
- S Wellner
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - N Lodders
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - S P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - P Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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25
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A catalytic role of XoxF1 as La3+-dependent methanol dehydrogenase in Methylobacterium extorquens strain AM1. PLoS One 2012; 7:e50480. [PMID: 23209751 PMCID: PMC3507691 DOI: 10.1371/journal.pone.0050480] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 10/24/2012] [Indexed: 12/02/2022] Open
Abstract
In the methylotrophic bacterium Methylobacterium extorquens strain AM1, MxaF, a Ca2+-dependent methanol dehydrogenase (MDH), is the main enzyme catalyzing methanol oxidation during growth on methanol. The genome of strain AM1 contains another MDH gene homologue, xoxF1, whose function in methanol metabolism has remained unclear. In this work, we show that XoxF1 also functions as an MDH and is La3+-dependent. Despite the absence of Ca2+ in the medium strain AM1 was able to grow on methanol in the presence of La3+. Addition of La3+ increased MDH activity but the addition had no effect on mxaF or xoxF1 expression level. We purified MDH from strain AM1 grown on methanol in the presence of La3+, and its N-terminal amino acid sequence corresponded to that of XoxF1. The enzyme contained La3+ as a cofactor. The ΔmxaF mutant strain could not grow on methanol in the presence of Ca2+, but was able to grow after supplementation with La3+. Taken together, these results show that XoxF1 participates in methanol metabolism as a La3+-dependent MDH in strain AM1.
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26
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High-throughput identification and screening of novel Methylobacterium species using whole-cell MALDI-TOF/MS analysis. PLoS One 2012; 7:e40784. [PMID: 22808262 PMCID: PMC3395638 DOI: 10.1371/journal.pone.0040784] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/13/2012] [Indexed: 11/28/2022] Open
Abstract
Methylobacterium species are ubiquitous α-proteobacteria that reside in the phyllosphere and are fed by methanol that is emitted from plants. In this study, we applied whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (WC-MS) to evaluate the diversity of Methylobacterium species collected from a variety of plants. The WC-MS spectrum was reproducible through two weeks of cultivation on different media. WC-MS spectrum peaks of M. extorquens strain AM1 cells were attributed to ribosomal proteins, but those were not were also found. We developed a simple method for rapid identification based on spectra similarity. Using all available type strains of Methylobacterium species, the method provided a certain threshold similarity value for species-level discrimination, although the genus contains some type strains that could not be easily discriminated solely by 16S rRNA gene sequence similarity. Next, we evaluated the WC-MS data of approximately 200 methylotrophs isolated from various plants with MALDI Biotyper software (Bruker Daltonics). Isolates representing each cluster were further identified by 16S rRNA gene sequencing. In most cases, the identification by WC-MS matched that by sequencing, and isolates with unique spectra represented possible novel species. The strains belonging to M. extorquens, M. adhaesivum, M. marchantiae, M. komagatae, M. brachiatum, M. radiotolerans, and novel lineages close to M. adhaesivum, many of which were isolated from bryophytes, were found to be the most frequent phyllospheric colonizers. The WC-MS technique provides emerging high-throughputness in the identification of known/novel species of bacteria, enabling the selection of novel species in a library and identification without 16S rRNA gene sequencing.
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Atamna-Ismaeel N, Finkel O, Glaser F, von Mering C, Vorholt JA, Koblížek M, Belkin S, Béjà O. Bacterial anoxygenic photosynthesis on plant leaf surfaces. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:209-16. [PMID: 23757275 DOI: 10.1111/j.1758-2229.2011.00323.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The aerial surface of plants, the phyllosphere, is colonized by numerous bacteria displaying diverse metabolic properties that enable their survival in this specific habitat. Recently, we reported on the presence of microbial rhodopsin harbouring bacteria on the top of leaf surfaces. Here, we report on the presence of additional bacterial populations capable of harvesting light as a means of supplementing their metabolic requirements. An analysis of six phyllosphere metagenomes revealed the presence of a diverse community of anoxygenic phototrophic bacteria, including the previously reported methylobacteria, as well as other known and unknown phototrophs. The presence of anoxygenic phototrophic bacteria was also confirmed in situ by infrared epifluorescence microscopy. The microscopic enumeration correlated with estimates based on metagenomic analyses, confirming both the presence and high abundance of these microorganisms in the phyllosphere. Our data suggest that the phyllosphere contains a phylogenetically diverse assemblage of phototrophic species, including some yet undescribed bacterial clades that appear to be phyllosphere-unique.
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Affiliation(s)
- Nof Atamna-Ismaeel
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel Bioinformatics Knowledge Unit, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel Faculty of Science, Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland Institute of Microbiology, Department of Phototrophic Microorganisms - ALGATECH, 379 81 Třeboň, Czech Republic
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Irvine IC, Brigham CA, Suding KN, Martiny JBH. The abundance of pink-pigmented facultative methylotrophs in the root zone of plant species in invaded coastal sage scrub habitat. PLoS One 2012; 7:e31026. [PMID: 22383990 PMCID: PMC3286463 DOI: 10.1371/journal.pone.0031026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 12/30/2011] [Indexed: 12/05/2022] Open
Abstract
Pink-pigmented facultative methylotrophic bacteria (PPFMs) are associated with the roots, leaves and seeds of most terrestrial plants and utilize volatile C(1) compounds such as methanol generated by growing plants during cell division. PPFMs have been well studied in agricultural systems due to their importance in crop seed germination, yield, pathogen resistance and drought stress tolerance. In contrast, little is known about the PPFM abundance and diversity in natural ecosystems, let alone their interactions with non-crop species. Here we surveyed PPFM abundance in the root zone soil of 5 native and 5 invasive plant species along ten invasion gradients in Southern California coastal sage scrub habitat. PPFMs were present in every soil sample and ranged in abundance from 10(2) to 10(5) CFU/g dry soil. This abundance varied significantly among plant species. PPFM abundance was 50% higher in the root zones of annual or biennial species (many invasives) than perennial species (all natives). Further, PPFM abundance appears to be influenced by the plant community beyond the root zone; pure stands of either native or invasive species had 50% more PPFMs than mixed species stands. In sum, PPFM abundance in the root zone of coastal sage scrub plants is influenced by both the immediate and surrounding plant communities. The results also suggest that PPFMs are a good target for future work on plant-microorganism feedbacks in natural ecosystems.
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Affiliation(s)
- Irina C Irvine
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America.
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Nakagawa T, Mitsui R, Tani A, Sasa K, Tashiro S, Iwama T, Hayakawa T, Kawai K. A catalytic role of XoxF1 as La3+-dependent methanol dehydrogenase in Methylobacterium extorquens strain AM1. PLoS One 2012. [PMID: 23209751 DOI: 10.1371/.pone.0050480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
In the methylotrophic bacterium Methylobacterium extorquens strain AM1, MxaF, a Ca(2+)-dependent methanol dehydrogenase (MDH), is the main enzyme catalyzing methanol oxidation during growth on methanol. The genome of strain AM1 contains another MDH gene homologue, xoxF1, whose function in methanol metabolism has remained unclear. In this work, we show that XoxF1 also functions as an MDH and is La(3+)-dependent. Despite the absence of Ca(2+) in the medium strain AM1 was able to grow on methanol in the presence of La(3+). Addition of La(3+) increased MDH activity but the addition had no effect on mxaF or xoxF1 expression level. We purified MDH from strain AM1 grown on methanol in the presence of La(3+), and its N-terminal amino acid sequence corresponded to that of XoxF1. The enzyme contained La(3+) as a cofactor. The ΔmxaF mutant strain could not grow on methanol in the presence of Ca(2+), but was able to grow after supplementation with La(3+). Taken together, these results show that XoxF1 participates in methanol metabolism as a La(3+)-dependent MDH in strain AM1.
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Affiliation(s)
- Tomoyuki Nakagawa
- Faculty of Applied Biological Science, Gifu University, Gifu, Japan.
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Trias R, García-Lledó A, Sánchez N, López-Jurado JL, Hallin S, Bañeras L. Abundance and composition of epiphytic bacterial and archaeal ammonia oxidizers of marine red and brown macroalgae. Appl Environ Microbiol 2012; 78:318-25. [PMID: 22081571 PMCID: PMC3255731 DOI: 10.1128/aem.05904-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 10/31/2011] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae's potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities on three species of macroalgae, Osmundaria volubilis, Phyllophora crispa, and Laminaria rodriguezii, from the Balearic Islands (western Mediterranean Sea). Quantitative PCR of bacterial and archaeal 16S rRNA and amoA genes was performed. In contrast to what has been shown for most other marine environments, the macroalgae's surfaces were dominated by bacterial amoA genes rather than those from the archaeal counterpart. On the basis of the sequences retrieved from AOB and AOA amoA gene clone libraries from each algal species, the bacterial ammonia-oxidizing communities were related to Nitrosospira spp. and to Nitrosomonas europaea and only 6 out of 15 operational taxonomic units (OTUs) were specific for the host species. Conversely, the AOA diversity was higher (43 OTUs) and algal species specific, with 17 OTUs specific for L. rodriguezii, 3 for O. volubilis, and 9 for P. crispa. Altogether, the results suggest that marine macroalgae may exert an ecological niche for AOB in marine environments, potentially through specific microbe-host interactions.
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MESH Headings
- Ammonia/metabolism
- Archaea/classification
- Archaea/genetics
- Archaea/metabolism
- Bacteria/classification
- Bacteria/genetics
- Bacteria/metabolism
- Biodiversity
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Laminaria/microbiology
- Mediterranean Sea
- Molecular Sequence Data
- Oxidation-Reduction
- Oxidoreductases/genetics
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Real-Time Polymerase Chain Reaction
- Rhodophyta/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Rosalia Trias
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, Universitat de Girona, Girona, Spain
| | - Arantzazu García-Lledó
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, Universitat de Girona, Girona, Spain
| | - Noemí Sánchez
- Botany, Faculty of Sciences, Universitat de Girona, Girona, Spain
| | | | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Microbiology, Uppsala, Sweden
| | - Lluís Bañeras
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, Universitat de Girona, Girona, Spain
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Wellner S, Lodders N, Kämpfer P. Diversity and biogeography of selected phyllosphere bacteria with special emphasis on Methylobacterium spp. Syst Appl Microbiol 2011; 34:621-30. [PMID: 22000032 DOI: 10.1016/j.syapm.2011.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/17/2011] [Accepted: 08/23/2011] [Indexed: 11/26/2022]
Abstract
On the basis of cultivation-dependent (isolation on mineral salt medium supplemented with 0.5% methanol) and -independent (DGGE analysis) methods, we investigated the influence of the host plant species Trifolium repens and Cerastium holosteoides, three geographic locations and the land-use types meadow, mown pasture and pasture on the abundance and community composition of selected phyllosphere bacteria with emphasis on Methylobacterium species. Methylobacterium abundance was significantly higher on leaves of T. repens (mean value 2.0×10(7) CFU PPFM per g leaf) than on leaves of C. holosteoides (mean value 2.0×10(6) CFU per g leaf). Leaves from the sampling site Schorfheide-Chorin showed slightly lower Methylobacterium numbers than leaves of the other sampling sites. Land-use and sampling period had no consistent influence on Methylobacterium community size. Methylobacterium community composition was very similar over both sampling periods, all three sampling sites, all land-use types and both plant species. Moreover, no relationship between geographic and genetic distance was observed. Community composition of selected Proteobacteria was influenced by plant species, geographic location and land-use. Often, differences in community composition could be observed between meadows, mown pastures and pastures but not between different kinds of meadows (cutted once versus three times) and mown pastures (fertilized versus non-fertilized). The results also indicate, that whether there are differences between land-use types or not strongly depends on the investigated host plant species and ecosystem. Besides Methylobacterium, representatives of Methylophilus were detected. The results indicate that Methylobacterium species are generally abundant and stable members of the phyllosphere community whereas other genera occur more occasionally, and that Methylobacterium clearly dominates the methylotrophic phyllosphere community.
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Affiliation(s)
- S Wellner
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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Knief C, Dengler V, Bodelier PLE, Vorholt JA. Characterization of Methylobacterium strains isolated from the phyllosphere and description of Methylobacterium longum sp. nov. Antonie van Leeuwenhoek 2011; 101:169-83. [DOI: 10.1007/s10482-011-9650-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 09/24/2011] [Indexed: 11/27/2022]
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Fedorov DN, Doronina NV, Trotsenko YA. Phytosymbiosis of aerobic methylobacteria: New facts and views. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711040047] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Yeast methylotrophy: metabolism, gene regulation and peroxisome homeostasis. Int J Microbiol 2011; 2011:101298. [PMID: 21754936 PMCID: PMC3132611 DOI: 10.1155/2011/101298] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 05/09/2011] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic methylotrophs, which are able to obtain all the carbon and energy needed for growth from methanol, are restricted to a limited number of yeast species. When these yeasts are grown on methanol as the sole carbon and energy source, the enzymes involved in methanol metabolism are strongly induced, and the membrane-bound organelles, peroxisomes, which contain key enzymes of methanol metabolism, proliferate massively. These features have made methylotrophic yeasts attractive hosts for the production of heterologous proteins and useful model organisms for the study of peroxisome biogenesis and degradation. In this paper, we describe recent insights into the molecular basis of yeast methylotrophy.
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Nadalig T, Farhan Ul Haque M, Roselli S, Schaller H, Bringel F, Vuilleumier S. Detection and isolation of chloromethane-degrading bacteria from the Arabidopsis thaliana phyllosphere, and characterization of chloromethane utilization genes. FEMS Microbiol Ecol 2011; 77:438-48. [PMID: 21545604 DOI: 10.1111/j.1574-6941.2011.01125.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Chloromethane gas is produced naturally in the phyllosphere, the compartment defined as the aboveground parts of vegetation, which hosts a rich bacterial flora. Chloromethane may serve as a growth substrate for specialized aerobic methylotrophic bacteria, which have been isolated from soil and water environments, and use cmu genes for chloromethane utilization. Evidence for the presence of chloromethane-degrading bacteria on the leaf surfaces of Arabidopsis thaliana was obtained by specific quantitative PCR of the cmuA gene encoding the two-domain methyltransferase corrinoid protein of chloromethane dehalogenase. Bacterial strains were isolated on a solid mineral medium with chloromethane as the sole carbon source from liquid mineral medium enrichment cultures inoculated with leaves of A. thaliana. Restriction analysis-based genotyping of cmuA PCR products was used to evaluate the diversity of chloromethane-degrading bacteria during enrichment and after strain isolation. The isolates obtained, affiliated to the genus Hyphomicrobium based on their 16S rRNA gene sequence and the presence of characteristic hyphae, dehalogenate chloromethane, and grow in a liquid culture with chloromethane as the sole carbon and energy source. The cmu genes of these isolates were analysed using new PCR primers, and their sequences were compared with those of previously reported aerobic chloromethane-degrading strains. The three isolates featured a colinear cmuBCA gene arrangement similar to that of all previously characterized strains, except Methylobacterium extorquens CM4 of known genome sequence.
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Affiliation(s)
- Thierry Nadalig
- Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France.
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Anda M, Ikeda S, Eda S, Okubo T, Sato S, Tabata S, Mitsui H, Minamisawa K. Isolation and genetic characterization of Aurantimonas and Methylobacterium strains from stems of hypernodulated soybeans. Microbes Environ 2011; 26:172-80. [PMID: 21512309 DOI: 10.1264/jsme2.me10203] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aims of this study were to isolate Aurantimonas and Methylobacterium strains that responded to soybean nodulation phenotypes and nitrogen fertilization rates in a previous culture-independent analysis (Ikeda et al. ISME J. 4:315-326, 2010). Two strategies were adopted for isolation from enriched bacterial cells prepared from stems of field-grown, hypernodulated soybeans: PCR-assisted isolation for Aurantimonas and selective cultivation for Methylobacterium. Thirteen of 768 isolates cultivated on Nutrient Agar medium were identified as Aurantimonas by colony PCR specific for Aurantimonas and 16S rRNA gene sequencing. Meanwhile, among 187 isolates on methanol-containing agar media, 126 were identified by 16S rRNA gene sequences as Methylobacterium. A clustering analysis (>99% identity) of the 16S rRNA gene sequences for the combined datasets of the present and previous studies revealed 4 and 8 operational taxonomic units (OTUs) for Aurantimonas and Methylobacterium, respectively, and showed the successful isolation of target bacteria for these two groups. ERIC- and BOX-PCR showed the genomic uniformity of the target isolates. In addition, phylogenetic analyses of Aurantimonas revealed a phyllosphere-specific cluster in the genus. The isolates obtained in the present study will be useful for revealing unknown legume-microbe interactions in relation to the autoregulation of nodulation.
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Affiliation(s)
- Mizue Anda
- Graduate School of Life Sciences, Tohoku University, Sendai 980–8577, Japan
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Knief C, Frances L, Vorholt JA. Competitiveness of diverse Methylobacterium strains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1. MICROBIAL ECOLOGY 2010; 60:440-452. [PMID: 20700590 DOI: 10.1007/s00248-010-9725-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 07/11/2010] [Indexed: 05/29/2023]
Abstract
Facultative methylotrophic bacteria of the genus Methylobacterium are consistently found in association with plants, particularly in the phyllosphere. To gain a better understanding of the mechanisms underlying the dispersal and occurrence of Methylobacterium on plants, diverse strains were isolated, identified, and studied with regard to their competitiveness on the model plant Arabidopsis thaliana. As a basis for this study a comprehensive collection of Methylobacterium isolates was established. Isolates were obtained from five different naturally grown A. thaliana populations and diverse other plant genera at these and further sites. They were classified using automated ribosomal internal spacer analysis (ARISA) and a representative subset was identified based on 16S rRNA gene sequence analysis. A comparison of their ARISA patterns with those generated based on a cultivation-independent approach from the same sampling material confirmed that the isolates were abundant colonizers of the studied plants. In competition experiments, colonization efficiency of the strains was found to be linked to phylogeny, rather than to the geographical origin or plant genus from which they were isolated. The most competitive colonizers were related to the species Methylobacterium tardum and Methylobacterium extorquens. Higher cell numbers were observed in the phyllosphere of A. thaliana when a mixture of different strains was applied relative to inoculation with only one strain, suggesting partial niche heterogeneity. Based on the results of the competition experiments, representative strains with different colonization efficiencies were selected, which will serve as models in future studies aiming at a better understanding of plant colonization by this bacterial genus. Among them is the meanwhile genome-sequenced strain M. extorquens PA1, which represents a competitive species of plant colonizers with a broad dispersal. This strain was characterized in more detail including physiological, morphological, and chemotaxonomical properties.
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Affiliation(s)
- Claudia Knief
- Institute of Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland.
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Schmidt S, Christen P, Kiefer P, Vorholt JA. Functional investigation of methanol dehydrogenase-like protein XoxF in Methylobacterium extorquens AM1. Microbiology (Reading) 2010; 156:2575-2586. [DOI: 10.1099/mic.0.038570-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methanol dehydrogenase-like protein XoxF of Methylobacterium extorquens AM1 exhibits a sequence identity of 50 % to the catalytic subunit MxaF of periplasmic methanol dehydrogenase in the same organism. The latter has been characterized in detail, identified as a pyrroloquinoline quinone (PQQ)-dependent protein, and shown to be essential for growth in the presence of methanol in this methylotrophic model bacterium. In contrast, the function of XoxF in M. extorquens AM1 has not yet been elucidated, and a phenotype remained to be described for a xoxF mutant. Here, we found that a xoxF mutant is less competitive than the wild-type during colonization of the phyllosphere of Arabidopsis thaliana, indicating a function for XoxF during plant colonization. A comparison of the growth parameters of the M. extorquens AM1 xoxF mutant with those of the wild-type during exponential growth revealed a reduced methanol uptake rate and a reduced growth rate for the xoxF mutant of about 30 %. Experiments with cells starved for carbon revealed that methanol oxidation in the xoxF mutant occurs less rapidly compared with the wild-type, especially in the first minutes after methanol addition. A distinct phenotype for the xoxF mutant was also observed when formate and CO2 production were measured after the addition of methanol or formaldehyde to starved cells. The wild-type, but not the xoxF mutant, accumulated formate upon substrate addition and had a 1 h lag in CO2 production under the experimental conditions. Determination of the kinetic properties of the purified enzyme showed a conversion capacity for both formaldehyde and methanol. The results suggest that XoxF is involved in one-carbon metabolism in M. extorquens AM1.
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Affiliation(s)
- Sabrina Schmidt
- Institute of Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Philipp Christen
- Institute of Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Julia A. Vorholt
- Institute of Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME JOURNAL 2010; 4:719-28. [PMID: 20164863 DOI: 10.1038/ismej.2010.9] [Citation(s) in RCA: 194] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The plant phyllosphere constitutes a habitat for numerous microorganisms; among them are members of the genus Methylobacterium. Owing to the ubiquitous occurrence of methylobacteria on plant leaves, they represent a suitable target for studying plant colonization patterns. The influence of the factor site, host plant species, time and the presence of other phyllosphere bacteria on Methylobacterium community composition and population size were evaluated in this study. Leaf samples were collected from Arabidopsis thaliana or Medicago truncatula plants and from the surrounding plant species at several sites. The abundance of cultivable Methylobacterium clearly correlated with the abundance of other phyllosphere bacteria, suggesting that methylobacteria constitute a considerable and rather stable fraction of the phyllosphere microbiota under varying environmental conditions. Automated ribosomal intergenic spacer analysis (ARISA) was applied to characterize the Methylobacterium community composition and showed the presence of similar communities on A. thaliana plants at most sites in 2 consecutive years of sampling. A substantial part of the observed variation in the community composition was explained by site and plant species, especially in the case of the plants collected at the Arabidopsis sites (50%). The dominating ARISA peaks that were detected on A. thaliana plants were found on other plant species grown at the same site, whereas some different peaks were detected on A. thaliana plants from other sites. This indicates that site-specific factors had a stronger impact on the Methylobacterium community composition than did plant-specific factors and that the Methylobacterium-plant association is not highly host plant species specific.
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Schäfer H, Myronova N, Boden R. Microbial degradation of dimethylsulphide and related C1-sulphur compounds: organisms and pathways controlling fluxes of sulphur in the biosphere. JOURNAL OF EXPERIMENTAL BOTANY 2009; 61:315-334. [PMID: 20007683 DOI: 10.1093/jxb/erp355] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Dimethylsulphide (DMS) plays a major role in the global sulphur cycle. It has important implications for atmospheric chemistry, climate regulation, and sulphur transport from the marine to the atmospheric and terrestrial environments. In addition, DMS acts as an info-chemical for a wide range of organisms ranging from micro-organisms to mammals. Micro-organisms that cycle DMS are widely distributed in a range of environments, for instance, oxic and anoxic marine, freshwater and terrestrial habitats. Despite the importance of DMS that has been unearthed by many studies since the early 1970s, the understanding of the biochemistry, genetics, and ecology of DMS-degrading micro-organisms is still limited. This review examines current knowledge on the microbial cycling of DMS and points out areas for future research that should shed more light on the role of organisms degrading DMS and related compounds in the biosphere.
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Gillevet PM, Sikaroodi M, Torzilli AP. Analyzing salt-marsh fungal diversity: comparing ARISA fingerprinting with clone sequencing and pyrosequencing. FUNGAL ECOL 2009. [DOI: 10.1016/j.funeco.2009.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Chou HH, Berthet J, Marx CJ. Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation. PLoS Genet 2009; 5:e1000652. [PMID: 19763169 PMCID: PMC2732905 DOI: 10.1371/journal.pgen.1000652] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 08/17/2009] [Indexed: 11/18/2022] Open
Abstract
Understanding the evolution of biological systems requires untangling the molecular mechanisms that connect genetic and environmental variations to their physiological consequences. Metal limitation across many environments, ranging from pathogens in the human body to phytoplankton in the oceans, imposes strong selection for improved metal acquisition systems. In this study, we uncovered the genetic and physiological basis of adaptation to metal limitation using experimental populations of Methylobacterium extorquens AM1 evolved in metal-deficient growth media. We identified a transposition mutation arising recurrently in 30 of 32 independent populations that utilized methanol as a carbon source, but not in any of the 8 that utilized only succinate. These parallel insertion events increased expression of a novel transporter system that enhanced cobalt uptake. Such ability ensured the production of vitamin B12, a cobalt-containing cofactor, to sustain two vitamin B12–dependent enzymatic reactions essential to methanol, but not succinate, metabolism. Interestingly, this mutation provided higher selective advantages under genetic backgrounds or incubation temperatures that permit faster growth, indicating growth-rate–dependent epistatic and genotype-by-environment interactions. Our results link beneficial mutations emerging in a metal-limiting environment to their physiological basis in carbon metabolism, suggest that certain molecular features may promote the emergence of parallel mutations, and indicate that the selective advantages of some mutations depend generically upon changes in growth rate that can stem from either genetic or environmental influences. Effects of mutations can change under different genetic backgrounds or environmental factors, also known as epistasis and genotype-by-environment interactions (G×E), respectively. Though epistasis and G×E are traditionally treated as distinct phenomena, our study of a beneficial mutation highlights their commonality. This mutation resulted from insertion of the same transposable element upstream of a novel cobalt transport system in 30 of 32 independent populations during evolution in metal-limited media. The resulting increased cobalt uptake provided a selective benefit that depended upon two environmental factors: cobalt limitation and growth substrates whose metabolism requires a particular vitamin B12 (which contains cobalt) -dependent biochemical pathway. Furthermore, this mutation exhibited epistatic and G×E interactions with other cellular processes in a generic way, such that its selective advantage increased as cells were able to grow faster. This growth-rate dependence accords with a simple model: the slowest of multiple physiological processes needed for growth exerts the greatest control over an organism's growth rate. It suggests that as growth results from the performance of the entire physiological system, genes or environmental factors that affect distinct physiological processes may thus interact through their convergent effects on growth phenotypes.
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Affiliation(s)
- Hsin-Hung Chou
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Julia Berthet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A 2009; 106:16428-33. [PMID: 19805315 DOI: 10.1073/pnas.0905240106] [Citation(s) in RCA: 516] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aerial plant surfaces represent the largest biological interface on Earth and provide essential services as sites of carbon dioxide fixation, molecular oxygen release, and primary biomass production. Rather than existing as axenic organisms, plants are colonized by microorganisms that affect both their health and growth. To gain insight into the physiology of phyllosphere bacteria under in situ conditions, we performed a culture-independent analysis of the microbiota associated with leaves of soybean, clover, and Arabidopsis thaliana plants using a metaproteogenomic approach. We found a high consistency of the communities on the 3 different plant species, both with respect to the predominant community members (including the alphaproteobacterial genera Sphingomonas and Methylo bacterium) and with respect to their proteomes. Observed known proteins of Methylobacterium were to a large extent related to the ability of these bacteria to use methanol as a source of carbon and energy. A remarkably high expression of various TonB-dependent receptors was observed for Sphingomonas. Because these outer membrane proteins are involved in transport processes of various carbohydrates, a particularly large substrate utilization pattern for Sphingomonads can be assumed to occur in the phyllosphere. These adaptations at the genus level can be expected to contribute to the success and coexistence of these 2 taxa on plant leaves. We anticipate that our results will form the basis for the identification of unique traits of phyllosphere bacteria, and for uncovering previously unrecorded mechanisms of bacteria-plant and bacteria-bacteria relationships.
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