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Sharavin DY, Belyaeva PG. Biotechnological potential of psychrotolerant methylobacteria isolated from biotopes of Antarctic oases. Arch Microbiol 2024; 206:323. [PMID: 38907777 DOI: 10.1007/s00203-024-04056-7] [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: 04/03/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Ten strains of psychrotolerant methylotrophic bacteria were isolated from the samples collected in Larsemann and Bunger Hills (Antarctica). Most of the isolates are assigned to the genus Pseudomonas, representatives of the genera Janthinobacterium, Massilia, Methylotenera and Flavobacterium were also found. Majority of isolates were able to grow on a wide range of sugars, methylamines and other substrates. Optimal growth temperatures for the isolated strains varied from 6 °C to 28 °C. The optimal concentration of NaCl was 0.5-2.0%. The optimal pH values of the medium were 6-7. It was found that three strains synthesized indole-3-acetic acid on a medium with L-tryptophan reaching 11-12 μg/ml. The values of intracellular carbohydrates in several strains exceeded 50 μg/ml. Presence of calcium-dependent and lanthanum-dependent methanol dehydrogenase have been shown for some isolates. Strains xBan7, xBan20, xBan37, xBan49, xPrg27, xPrg48, xPrg51 showed the presence of free amino acids. Bioprospection of Earth cryosphere for such microorganisms has a potential in biotechnology.
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Affiliation(s)
- Dmitry Yuryevich Sharavin
- Laboratory of Cellular Immunology and Nanobiotechnology, Institute of Ecology and Genetics of Microorganisms (IEGM), 13, Golev st., Perm, 614081, Russia.
| | - Polina Gennadievna Belyaeva
- Laboratory of Cellular Immunology and Nanobiotechnology, Institute of Ecology and Genetics of Microorganisms (IEGM), 13, Golev st., Perm, 614081, Russia
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Gamit HA, Amaresan N. Methylobacterium spp. mitigation of UV stress in mung bean (Vigna radiata L.). Photochem Photobiol Sci 2023; 22:2839-2850. [PMID: 37838625 DOI: 10.1007/s43630-023-00490-6] [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: 04/21/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Methylotrophs are a diverse group of bacteria that abundantly colonize the phyllosphere and have great potential to withstand UV irradiation because of their pigmented nature and ability to promote plant growth through various mechanisms. The present study investigated the effects of UVB radiation on plant growth-promoting (PGP) properties of methylotrophic bacteria and the growth of Vigna radiata L. A total of 55 methylotrophic bacteria were isolated from desert plants, and 15 methylotrophs were resistant to UVB radiation for 4 h. All UVB-resistant methylotrophs possess a methyldehydrogenase gene. Identification based on 16S rRNA gene sequencing revealed that all 15 UVB-resistant methylotrophs belonged to the genera Methylorubrum (07), Methylobacterium (07), and Rhodococcus (01). Screening of methylotrophs for PGP activity in the presence and absence of UVB radiation revealed that all isolates showed ACC deaminase activity and growth on a nitrogen-free medium. Furthermore, the production of IAA-like substances ranged from 8.62 to 85.76 µg/mL, siderophore production increased from 3.47 to 65.75% compared to the control. Seed germination assay with V. radiata L. (mung bean) exposed to UVB radiation revealed that methylotrophs improved seed germination, root length, and shoot length compared to the control. The present findings revealed that the isolates SD3, SD2, KD1, KD5, UK1, and UK3 reduced the deleterious effects of UVB radiation on mung bean plants and can be used to protect seedlings from UVB radiation for sustainable agriculture.
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Affiliation(s)
- Harshida A Gamit
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India
| | - Natarajan Amaresan
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India.
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Mohanty SR, Mahawar H, Bajpai A, Dubey G, Parmar R, Atoliya N, Devi MH, Singh AB, Jain D, Patra A, Kollah B. Methylotroph bacteria and cellular metabolite carotenoid alleviate ultraviolet radiation-driven abiotic stress in plants. Front Microbiol 2023; 13:899268. [PMID: 36687662 PMCID: PMC9853530 DOI: 10.3389/fmicb.2022.899268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/30/2022] [Indexed: 01/07/2023] Open
Abstract
Increasing UV radiation in the atmosphere due to the depletion of ozone layer is emerging abiotic stress for agriculture. Although plants have evolved to adapt to UV radiation through different mechanisms, but the role of phyllosphere microorganisms in counteracting UV radiation is not well studied. The current experiment was undertaken to evaluate the role of phyllosphere Methylobacteria and its metabolite in the alleviation of abiotic stress rendered by ultraviolet (UV) radiation. A potential pink pigmenting methylotroph bacterium was isolated from the phylloplane of the rice plant (oryzae sativa). The 16S rRNA gene sequence of the bacterium was homologous to the Methylobacter sp. The isolate referred to as Methylobacter sp N39, produced beta-carotene at a rate (μg ml-1 d-1) of 0.45-3.09. Biosynthesis of beta-carotene was stimulated by brief exposure to UV for 10 min per 2 days. Carotenoid biosynthesis was predicted as y = 3.09 × incubation period + 22.151 (r 2 = 0.90). The carotenoid extract of N39 protected E. coli from UV radiation by declining its death rate from 14.67% min-1 to 4.30% min-1 under UV radiation. Application of N39 cells and carotenoid extract also protected rhizobium (Bradyrhizobium japonicum) cells from UV radiation. Scanning electron microscopy indicated that the carotenoid extracts protected E. coli cells from UV radiation. Foliar application of either N39 cells or carotenoid extract enhanced the plant's (Pigeon pea) resistance to UV irradiation. This study highlight that Methylobacter sp N39 and its carotenoid extract can be explored to manage UV radiation stress in agriculture.
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Affiliation(s)
- Santosh Ranjan Mohanty
- ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, India,*Correspondence: Santosh Ranjan Mohanty, ,
| | - Himanshu Mahawar
- ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, India,ICAR -s Directorate of Weed Research, Jabalpur, Madhya Pradesh, India,Himanshu Mahawar,
| | - Apekcha Bajpai
- ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, India
| | - Garima Dubey
- ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, India
| | - Rakesh Parmar
- ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, India
| | - Nagvanti Atoliya
- ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, India
| | | | | | - Devendra Jain
- Department of Molecular Biology and Biotechnology, Maharana Pratap University of Agriculture and Technology, Udaipur, Rajasthan, India
| | - Ashok Patra
- ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, India
| | - Bharati Kollah
- ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, India,Bharati Kollah, ,
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Medison RG, Tan L, Medison MB, Chiwina KE. Use of beneficial bacterial endophytes: A practical strategy to achieve sustainable agriculture. AIMS Microbiol 2022; 8:624-643. [PMID: 36694581 PMCID: PMC9834078 DOI: 10.3934/microbiol.2022040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/30/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
Beneficial endophytic bacteria influence their host plant to grow and resist pathogens. Despite the advantages of endophytic bacteria to their host, their application in agriculture has been low. Furthermore, many plant growers improperly use synthetic chemicals due to having no or little knowledge of the role of endophytic bacteria in plant growth, the prevention and control of pathogens and poor access to endobacterial bioproducts. These synthetic chemicals have caused soil infertility, environmental contamination, disruption to ecological cycles and the emergence of resistant pests and pathogens. There is more that needs to be done to explore alternative ways of achieving sustainable plant production while maintaining environmental health. In recent years, the use of beneficial endophytic bacteria has been noted to be a promising tool in promoting plant growth and the biocontrol of pathogens. Therefore, this review discusses the roles of endophytic bacteria in plant growth and the biocontrol of plant pathogens. Several mechanisms that endophytic bacteria use to alleviate plant biotic and abiotic stresses by helping their host plants acquire nutrients, enhance plant growth and development and suppress pathogens are explained. The review also indicates that there is a gap between research and general field applications of endophytic bacteria and suggests a need for collaborative efforts between growers at all levels. Furthermore, the presence of scientific and regulatory frameworks that promote advanced biotechnological tools and bioinoculants represents major opportunities in the applications of endophytic bacteria. The review provides a basis for future research in areas related to understanding the interactions between plants and beneficial endophytic microorganisms, especially bacteria.
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Affiliation(s)
| | - Litao Tan
- College of Agriculture, Yangtze University, Jingzhou Hubei 434025, China
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Chemodurova AA, Reshetnikov AS, Agafonova NV, Doronina NV. Genes of NAD+-Dependent Formate Dehydrogenases in Taxonomy of Aerobic Methylotrophic Bacteria of the Genus Ancylobacter. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722601932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Dhar K, Panneerselvan L, Venkateswarlu K, Megharaj M. Efficient bioremediation of PAHs-contaminated soils by a methylotrophic enrichment culture. Biodegradation 2022; 33:575-591. [PMID: 35976498 PMCID: PMC9581816 DOI: 10.1007/s10532-022-09996-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/05/2022] [Indexed: 01/13/2023]
Abstract
Bioaugmentation effectively enhances microbial bioremediation of hazardous polycyclic aromatic hydrocarbons (PAHs) from contaminated environments. While screening for pyrene-degrading bacteria from a former manufactured gas plant soil (MGPS), the mixed enrichment culture was found to be more efficient in PAHs biodegradation than the culturable pure strains. Interestingly, analysis of 16S rRNA sequences revealed that the culture was dominated by a previously uncultured member of the family Rhizobiaceae. The culture utilized C1 and other methylotrophic substrates, including dimethylformamide (DMF), which was used as a solvent for supplementing the culture medium with PAHs. In the liquid medium, the culture rapidly degraded phenanthrene, pyrene, and the carcinogenic benzo(a)pyrene (BaP), when provided as the sole carbon source or with DMF as a co-substrate. The efficiency of the culture in the bioremediation of PAHs from the MGPS and a laboratory waste soil (LWS) was evaluated in bench-scale slurry systems. After 28 days, 80% of Σ16 PAHs were efficiently removed from the inoculated MGPS. Notably, the bioaugmentation achieved 90% removal of four-ringed and 60% of highly recalcitrant five- and six-ringed PAHs from the MGPS. Likewise, almost all phenanthrene, pyrene, and 65% BaP were removed from the bioaugmented LWS. This study highlights the application of the methylotrophic enrichment culture dominated by an uncultured bacterium for the efficient bioremediation of PAHs.
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Affiliation(s)
- Kartik Dhar
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
| | - Logeshwaran Panneerselvan
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia.,Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, ATC Building, Callaghan, NSW, 2308, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, 515003, India
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia. .,Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, ATC Building, Callaghan, NSW, 2308, Australia.
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Wang J, Chu YX, Schäfer H, Tian G, He R. CS 2 increasing CH 4-derived carbon emissions and active microbial diversity in lake sediments. ENVIRONMENTAL RESEARCH 2022; 208:112678. [PMID: 34999031 DOI: 10.1016/j.envres.2022.112678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Lakes are important methane (CH4) sources to the atmosphere, especially eutrophic lakes with cyanobacterial blooms accompanied by volatile sulfur compound (VSC) emissions. CH4 oxidation is a key strategy to mitigate CH4 emission from lakes. In this study, we characterized the fate of CH4-derived carbon and active microbial communities in lake sediments with CS2 used as a typical VSC, based on the investigation of CH4 and VSC fluxes from Meiliang Bay in Lake Taihu. Stable isotope probing microcosm incubation showed that the efficiency of CH4-derived carbon incorporated into organic matter was 21.1% in the sediment with CS2 existence, which was lower than that without CS2 (27.3%). SO42--S was the main product of CS2 oxidation under aerobic condition, accounting for 59.3-62.7% of the input CS2-S. CS2 and CH4 coexistence led to a decrease of methanotroph and methylotroph abundances and stimulated the production of extracellular polymeric substances. CS2 and its metabolites including total sulfur, SO42- and acid volatile sulfur acted as the main drivers influencing the active microbial community structure in the sediments. Compared with α-proteobacteria methanotrophs, γ-proteobacteria methanotrophs Methylomicrobium, Methylomonas, Crenothrix and Methylosarcina were more dominant in the sediments. CH4-derived carbon mainly flowed into methylotrophs in the first stage. With CH4 consumption, more CH4-derived carbon flowed into non-methylotrophs. CS2 could prompt more CH4-derived carbon flowing into non-methanotrophs and non-methylotrophs, such as sulfur-metabolizing bacteria. These findings can help elucidate the influence of VSCs on microorganisms and provide insights to carbon fluxes from eutrophic lake systems.
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Affiliation(s)
- Jing Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yi-Xuan Chu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Guangming Tian
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China.
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8
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Wang S, Liu Q, Li J, Wang Z. Methane in wastewater treatment plants: status, characteristics, and bioconversion feasibility by methane oxidizing bacteria for high value-added chemicals production and wastewater treatment. WATER RESEARCH 2021; 198:117122. [PMID: 33865027 DOI: 10.1016/j.watres.2021.117122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/23/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Methane is a type of renewable fuel that can generate many types of high value-added chemicals, however, besides heat and power production, there is little methane utilization in most of the wastewater treatment plants (WWTPs) all round the world currently. In this review, the status of methane production performance from WWTPs was firstly investigated. Subsequently, based on the identification and classification of methane oxidizing bacteria (MOB), the key enzymes and metabolic pathway of MOB were presented in depth. Then the production, extraction and purification process of high value-added chemicals, including methanol, ectoine, biofuel, bioplastic, methane protein and extracellular polysaccharides, were introduced in detail, which was conducive to understand the bioconversion process of methane. Finally, the use of methane in wastewater treatment process, including nitrogen removal, emerging contaminants removal as well as resource recovery was extensively explored. These findings could provide guidance in the development of sustainable economy and environment, and facilitate biological methane conversion by using MOB in further attempts.
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Affiliation(s)
- Shuo Wang
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China; Jiangsu College of Water Treatment Technology and Material Collaborative Innovation Center, Suzhou 215009, China
| | - Qixin Liu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Ji Li
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China; Jiangsu College of Water Treatment Technology and Material Collaborative Innovation Center, Suzhou 215009, China.
| | - Zhiwu Wang
- Department of Civil and Environmental Engineering, Virginia Tech, Manassas, VA 20110, USA.
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Senthilkumar M, Pushpakanth P, Arul Jose P, Krishnamoorthy R, Anandham R. Diversity and functional characterization of endophytic Methylobacterium isolated from banana cultivars of South India and its impact on early growth of tissue culture banana plantlets. J Appl Microbiol 2021; 131:2448-2465. [PMID: 33891792 DOI: 10.1111/jam.15112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/28/2021] [Accepted: 04/11/2021] [Indexed: 11/27/2022]
Abstract
AIMS This study aimed at determining the distribution, colonization and growth promoting nature of Methylobacterium spp. in tissue culture banana plantlets. METHODS AND RESULTS Leaf samples from different field grown banana cultivars were used for Methylobacterium spp., isolation. Metabolic profile and functional characterization for plant growth-promoting traits of the isolates were assessed. The isolates were confirmed using 16S rRNA gene sequencing analysis, which resulted in six distinct species of Methylobacterium namely M. radiotolerans, M. salsuginis, M. thiocyanatum, M. rhodesianum, M. rhodinum and M. populi. Methylobacterium spp. inoculation experiment was conducted under hydroponic system in tissue culture banana plantlets (germ free) with eight selected isolates. A significant increase in growth parameters of Methylobacterium treated plantlets compared to uninoculated control was observed. Methylobacterium salsuginis TNMB03-gfp29 was developed and colonization micrograph was obtained using confocal laser scanning microscopy (CLSM) and scanning electron microscopy in different parts of banana plantlets (root, stem and leaves). CONCLUSION Field grown banana plants found to harbour diverse endophytic Methylobacterium population. Our finding suggests that endophytic Methylobacterium species may provide significant plant growth promoting compounds/nutrients to the banana plants. The experimental results demonstrated the efficacy of Methylobacterium spp. as a potential bioinoculant and can be exploited as a phyllosphere and rhizosphere based bioinoculant for the initial establishment and growth of tissue culture banana plantlets. SIGNIFICANCE AND IMPACT OF THE STUDY This study extended our knowledge on the distribution of Methylobacterium spp. in banana plants and endophytic colonization nature of this particular genus in plants. In addition, efficient isolate (M. salsuginis TNMB03) identified in this study may be promoted as bio-inoculants for banana plants after field evaluation.
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Affiliation(s)
- M Senthilkumar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P Pushpakanth
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P Arul Jose
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Madurai, Tamil Nadu, India
| | - R Krishnamoorthy
- Department of Crop Management, Vanavarayar Institute of Agriculture, Pollachi, Tamil Nadu, India
| | - R Anandham
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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A Novel Moderately Thermophilic Facultative Methylotroph within the Class Alphaproteobacteria. Microorganisms 2021; 9:microorganisms9030477. [PMID: 33668875 PMCID: PMC7996495 DOI: 10.3390/microorganisms9030477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/25/2022] Open
Abstract
Methylotrophic bacteria (non-methanotrophic methanol oxidizers) consuming reduced carbon compounds containing no carbon–carbon bonds as their sole carbon and energy source have been found in a great variety of environments. Here, we report a unique moderately thermophilic methanol-oxidising bacterium (strain LS7-MT) that grows optimally at 55 °C (with a growth range spanning 30 to 60 °C). The pure isolate was recovered from a methane-utilizing mixed culture enrichment from an alkaline thermal spring in the Ethiopia Rift Valley, and utilized methanol, methylamine, glucose and a variety of multi-carbon compounds. Phylogenetic analysis of the 16S rRNA gene sequences demonstrated that strain LS7-MT represented a new facultatively methylotrophic bacterium within the order Hyphomicrobiales of the class Alphaproteobacteria. This new strain showed 94 to 96% 16S rRNA gene identity to the two methylotroph genera, Methyloceanibacter and Methyloligella. Analysis of the draft genome of strain LS7-MT revealed genes for methanol dehydrogenase, essential for methanol oxidation. Functional and comparative genomics of this new isolate revealed genomic and physiological divergence from extant methylotrophs. Strain LS7-MT contained a complete mxaF gene cluster and xoxF1 encoding the lanthanide-dependent methanol dehydrogenase (XoxF). This is the first report of methanol oxidation at 55 °C by a moderately thermophilic bacterium within the class Alphaproteobacteria. These findings expand our knowledge of methylotrophy by the phylum Proteobacteria in thermal ecosystems and their contribution to global carbon and nitrogen cycles.
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Discovery of lanthanide-dependent methylotrophy and screening methods for lanthanide-dependent methylotrophs. Methods Enzymol 2021; 650:1-18. [PMID: 33867018 DOI: 10.1016/bs.mie.2021.01.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The lanthanide elements (Lns) affect the physiology and growth of certain microorganisms known as "Ln-responsive microorganisms." Among them, in 2011, it was first reported that strains of Methylobacterium exhibited high methanol dehydrogenase (MDH) activity when grown in the presence of Lns; the purified Ln-inducible MDH was identified as XoxF-type MDH, whose catalytic function had previously been unknown. XoxF was the first enzyme to be identified as Ln-dependent, and its function in methylotrophy is more fundamental and important than that of the corresponding Ca2+-dependent MDH MxaFI. XoxF is encoded in the genomes of methylotrophic as well as non-methylotrophic bacteria. Thus, Lns are among the most fascinating and important growth factors for bacteria that potentially utilize methanol. Bacteria that require Lns for methanol growth are called "Ln-dependent methylotrophs." Recent findings indicate that these microorganisms comprise an "Ln-dependent ecosystem" that we have not been able to reconstruct under laboratory conditions without Lns. In this chapter, we summarize methods for (1) screening of Ln-responsive microorganisms, (2) purification of native XoxFs from Ln-dependent methylotrophs, and (3) screening of Ln-dependent methylotrophs from natural environments, while providing a history of the discovery of the Ln-dependent methylotrophs.
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Jawaharraj K, Sudha Dhiman S, Bedwell S, Vemuri B, Islam J, Sani RK, Gadhamshetty V. Electricity from methane by Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. BIORESOURCE TECHNOLOGY 2021; 321:124398. [PMID: 33257167 DOI: 10.1016/j.biortech.2020.124398] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/31/2020] [Accepted: 11/06/2020] [Indexed: 06/12/2023]
Abstract
Given the difficulties valorizing methane (CH4) via catalytic routes, this study explores use of CH4-oxidizing bacteria ("methanotrophs") for generating electricity directly from CH4. A preconditioned methanotrophic biofilm on 3D nickel foam with reduced graphene oxide (rGO/Ni) was used as the anode in two-compartment microbial fuel cells (MFCs). This study demonstrates a proof of concept for turning CH4 into electricity by two model methanotrophs including Methylosinus trichosposium OB3b and Methylococcus capsulatus (Bath). Both OB3b (205 mW.m-2) and Bath (110 mW.m-2) strains yielded a higher electricity from CH4 when grown on rGO/Ni compared to graphite felt electrodes. Based on electrochemistry tests, molecular dynamics simulations, genome annotations and interaction analysis, a mechanistic understanding of reasons behind enhanced performance of methanotrophs grown on rGO/Ni are presented.
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Affiliation(s)
- Kalimuthu Jawaharraj
- Department of Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; 2D-materials for Biofilm Engineering, Science and Technology (2DBEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA
| | - Saurabh Sudha Dhiman
- BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; Chemical and Biological Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA; 2D-materials for Biofilm Engineering, Science and Technology (2DBEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA
| | - Sierra Bedwell
- Department of Microbiology and Immunology, Montana State University, Culbertson Hall, 100, Bozeman, MT 59717, USA
| | - Bhuvan Vemuri
- Department of Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA
| | - Jamil Islam
- Department of Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA
| | - Rajesh Kumar Sani
- BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; Chemical and Biological Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA; 2D-materials for Biofilm Engineering, Science and Technology (2DBEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA
| | - Venkataramana Gadhamshetty
- Department of Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; BuG ReMeDEE Consortia, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, USA; 2D-materials for Biofilm Engineering, Science and Technology (2DBEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD 57701, USA.
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Legein M, Smets W, Vandenheuvel D, Eilers T, Muyshondt B, Prinsen E, Samson R, Lebeer S. Modes of Action of Microbial Biocontrol in the Phyllosphere. Front Microbiol 2020; 11:1619. [PMID: 32760378 PMCID: PMC7372246 DOI: 10.3389/fmicb.2020.01619] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
A fast-growing field of research focuses on microbial biocontrol in the phyllosphere. Phyllosphere microorganisms possess a wide range of adaptation and biocontrol factors, which allow them to adapt to the phyllosphere environment and inhibit the growth of microbial pathogens, thus sustaining plant health. These biocontrol factors can be categorized in direct, microbe-microbe, and indirect, host-microbe, interactions. This review gives an overview of the modes of action of microbial adaptation and biocontrol in the phyllosphere, the genetic basis of the mechanisms, and examples of experiments that can detect these mechanisms in laboratory and field experiments. Detailed insights in such mechanisms are key for the rational design of novel microbial biocontrol strategies and increase crop protection and production. Such novel biocontrol strategies are much needed, as ensuring sufficient and consistent food production for a growing world population, while protecting our environment, is one of the biggest challenges of our time.
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Affiliation(s)
- Marie Legein
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Wenke Smets
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Dieter Vandenheuvel
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Tom Eilers
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Babette Muyshondt
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Els Prinsen
- Laboratory for Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Roeland Samson
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Sarah Lebeer
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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Feng GD, Chen W, Zhang XJ, Zhang J, Wang SN, Zhu H. Methylobacterium nonmethylotrophicum sp. nov., isolated from tungsten mine tailing. Int J Syst Evol Microbiol 2020; 70:2867-2872. [PMID: 32207677 DOI: 10.1099/ijsem.0.004112] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel pink-pigmented strain, designated 6HR-1T, was isolated from tungsten mine tailings in Jiangxi Province, PR China. Cells were Gram-stain-negative, aerobic, non-spore-forming, rod-shaped and motile with a polar flagellum (monotrichous). It could not utilize methanol, methylamine, formaldehyde or formate as a sole carbon source. The methanol dehydrogenase mxaF gene was absent but the xoxF gene was present. Phylogenomic and 16S rRNA gene phylogenetic analyses clearly showed that strain 6HR-1T was affiliated to the genus Methylobacterium and closely related to 'Methylobacterium terrae' 17Sr1-28T (98.6 %), Methylobacterium platani JCM 14648T (97.7 %), Methylobacterium variabile DSM 16961T (97.7 %) and Methylobacterium currus KACC 19662T (97.4 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain 6HR-1T and its closely related type species were 87.4-88.7 and 33.2-36.3 %, respectively. It had summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) as the major fatty acid and ubiquinone 10 as the predominant respiratory quinone. Polyphasic characterization supported that strain 6HR-1T represents a novel species of the genus Methylobacterium, for which the name Methylobacterium nonmethylotrophicum sp. nov. is proposed with the type strain 6HR-1T (=GDMCC 1.662T=KCTC 42760T).
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Affiliation(s)
- Guang-Da Feng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Wendi Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Xian-Jiao Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Jun Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Sheng-Nan Wang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
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15
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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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16
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Vadivukkarasi P, Bhai RS. Phyllosphere-associated Methylobacterium: a potential biostimulant for ginger (Zingiber officinale Rosc.) cultivation. Arch Microbiol 2020; 202:369-375. [PMID: 31673721 DOI: 10.1007/s00203-019-01753-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 10/25/2022]
Abstract
Methanol, a by-product associated with plant metabolism, is a substrate for pink pigmented facultative methylotrophs (PPFMs) of phyllosphere. The symbiotic interaction of PPFMs has many desirable effects on plant growth and disease resistance. The present study investigated the potential of native PPFMs for mitigating biotic stress and plant growth promotion in ginger. PPFMs were isolated from ginger phyllosphere by leaf imprint technique and screened against major fungal phytopathogens of ginger viz. Macrophomina phaseolina, Sclerotium rolfsii, Pythium myriotylum, Colletotrichum gloeosporioides and Fusarium oxysporum. Among the 60 PPFMs, IISRGPPFM13 was selected for its highly inhibitory activity against the target pathogens. The isolate was useful for mineral solubility, production of IAA, siderophores and hydrolytic enzymes like cellulase, pectinase, lipase, amylase and chitinase. On in planta experiments revealed that IISRGPPFM13 considerably increased plant growth parameters when the bacterium was applied as soil drenching cum foliar spraying. Methanol utilization potential of the isolate was confirmed by mxaF gene analysis where the sequence showing 95.51% identity towards Methylobacterium platani and M. iners. Further, 16S rRNA gene sequence showing 98.73% identity with M. komagatae 002-079 T (AB252201). This is the first report of its kind that a genus of Methylobacterium with biostimulant potential isolated from the phyllosphere of ginger.
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Affiliation(s)
- Ponnusamy Vadivukkarasi
- Division of Crop Protection, ICAR-Indian Institute of Spices Research (IISR), Marikunnu P.O., Kozhikode, Kerala, 673012, India
| | - R Suseela Bhai
- Division of Crop Protection, ICAR-Indian Institute of Spices Research (IISR), Marikunnu P.O., Kozhikode, Kerala, 673012, India.
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17
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Wang S, An Z, Wang ZW. Bioconversion of methane to chemicals and fuels by methane-oxidizing bacteria. ADVANCES IN BIOENERGY 2020. [DOI: 10.1016/bs.aibe.2020.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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18
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Lanthanide-Dependent Methylotrophs of the Family Beijerinckiaceae: Physiological and Genomic Insights. Appl Environ Microbiol 2019; 86:AEM.01830-19. [PMID: 31604774 DOI: 10.1128/aem.01830-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/07/2019] [Indexed: 01/07/2023] Open
Abstract
Methylotrophic bacteria use methanol and related C1 compounds as carbon and energy sources. Methanol dehydrogenases are essential for methanol oxidation, while lanthanides are important cofactors of many pyrroloquinoline quinone-dependent methanol dehydrogenases and related alcohol dehydrogenases. We describe here the physiological and genomic characterization of newly isolated Beijerinckiaceae bacteria that rely on lanthanides for methanol oxidation. A broad physiological diversity was indicated by the ability to metabolize a wide range of multicarbon substrates, including various sugars, and organic acids, as well as diverse C1 substrates such as methylated amines and methylated sulfur compounds. Methanol oxidation was possible only in the presence of low-mass lanthanides (La, Ce, and Nd) at submicromolar concentrations (>100 nM). In a comparison with other Beijerinckiaceae, genomic and transcriptomic analyses revealed the usage of a glutathione- and tetrahydrofolate-dependent pathway for formaldehyde oxidation and channeling methyl groups into the serine cycle for carbon assimilation. Besides a single xoxF gene, we identified two additional genes for lanthanide-dependent alcohol dehydrogenases, including one coding for an ExaF-type alcohol dehydrogenase, which was so far not known in Beijerinckiaceae Homologs for most of the gene products of the recently postulated gene cluster linked to lanthanide utilization and transport could be detected, but for now it remains unanswered how lanthanides are sensed and taken up by our strains. Studying physiological responses to lanthanides under nonmethylotrophic conditions in these isolates as well as other organisms is necessary to gain a more complete understanding of lanthanide-dependent metabolism as a whole.IMPORTANCE We supplemented knowledge of the broad metabolic diversity of the Beijerinckiaceae by characterizing new members of this family that rely on lanthanides for methanol oxidation and that possess additional lanthanide-dependent enzymes. Considering that lanthanides are critical resources for many modern applications and that recovering them is expensive and puts a heavy burden on the environment, lanthanide-dependent metabolism in microorganisms is an exploding field of research. Further research into how isolated Beijerinckiaceae and other microbes utilize lanthanides is needed to increase our understanding of lanthanide-dependent metabolism. The diversity and widespread occurrence of lanthanide-dependent enzymes make it likely that lanthanide utilization varies in different taxonomic groups and is dependent on the habitat of the microbes.
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19
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Zakharenko AS, Galachyants YP, Morozov IV, Shubenkova OV, Morozov AA, Ivanov VG, Pimenov NV, Krasnopeev AY, Zemskaya TI. Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal. MICROBIAL ECOLOGY 2019; 78:269-285. [PMID: 30483839 DOI: 10.1007/s00248-018-1299-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.
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Affiliation(s)
- Aleksandra S Zakharenko
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia.
| | - Yuriy P Galachyants
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Igor V Morozov
- Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Olga V Shubenkova
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Alexey A Morozov
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Vyacheslav G Ivanov
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Nikolay V Pimenov
- Research Center of Biotechnology, Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Andrey Y Krasnopeev
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Tamara I Zemskaya
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
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20
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Taubert M, Grob C, Crombie A, Howat AM, Burns OJ, Weber M, Lott C, Kaster AK, Vollmers J, Jehmlich N, von Bergen M, Chen Y, Murrell JC. Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy. Environ Microbiol 2019; 21:3780-3795. [PMID: 31267680 DOI: 10.1111/1462-2920.14728] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/14/2019] [Accepted: 06/29/2019] [Indexed: 11/29/2022]
Abstract
The release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the sediment-water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with 13 C-methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalysing the first reaction step to methanol. We observed a transfer of carbon to methanol-oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment per day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment-water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane-oxidizing community supported a complex trophic network. Our results provide valuable eco-physiological insights into this specialized microbial community performing an ecosystem function of global relevance.
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Affiliation(s)
- Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159 07743, Jena, Germany.,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Carolina Grob
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew Crombie
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Alexandra M Howat
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Oliver J Burns
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Miriam Weber
- HYDRA Marine Sciences GmbH, Sinzheim, Germany.,HYDRA Field Station Elba, Italy.,Microsensor Group, Max Plank Institute for Marine Microbiology, 28359, Celsiusstr. 1, Bremen, Germany
| | - Christian Lott
- HYDRA Marine Sciences GmbH, Sinzheim, Germany.,HYDRA Field Station Elba, Italy.,Department of Symbiosis, Max Plank Institute for Marine Microbiology, 28359, Celsiusstr. 1, Bremen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Karlsruhe, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124, Inhoffenstrasse 7B, Braunschweig, Germany
| | - John Vollmers
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Karlsruhe, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, 04103, Brüderstraße 32, Leipzig, Germany.,Department of Chemistry and Bioscience, University of Aalborg, 9220, Fredrik Bajers Vej 7H, Aalborg East, Denmark
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - John Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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21
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Methylopila carotae sp. nov., a facultative methylotroph, isolated from a root of Daucus carota L. Antonie van Leeuwenhoek 2019; 112:1307-1316. [DOI: 10.1007/s10482-019-01263-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/06/2019] [Indexed: 10/27/2022]
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22
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Shahzad R, Khan AL, Waqas M, Ullah I, Bilal S, Kim YH, Asaf S, Kang SM, Lee IJ. Metabolic and proteomic alteration in phytohormone-producing endophytic Bacillus amyloliquefaciens RWL-1 during methanol utilization. Metabolomics 2019; 15:16. [PMID: 30830445 DOI: 10.1007/s11306-018-1467-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/20/2018] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Methanol utilization by bacteria is important for various industrial processes. Methylotrophic bacteria are taxonomically diverse and some species promote plant growth and induce stress tolerance. However, methylotrophic potential of bacterial endophytes is poorly understood. OBJECTIVE The current study aimed to evaluate the metabolomic and proteomic changes in endophytic Bacillus amyloliquefaciens RWL-1 caused by its methanol utilization and the resultant influence on its phytohormone production. METHODS B. amyloliquefaciens RWL-1 was grown in LB medium with different concentrations [0 (control), 0.5, 1, 1.5, 2, 2.5, 3, 3.5, and 4%) of methanol to examine its methylotrophic potential. SDS-PAGE analysis was carried out for bacterial protein confirmation. Moreover, the phytohormones (indole 3 acetic acid (IAA), gibberellins (GAs), abscisic acid (ABA)) produced by RWL-1 in methanol supplemented medium were quantified by GC-MS/SIM (6890N Network GC system, and 5973 Network Mass Selective Detector; Agilent Technologies, Santa Clara, CA, USA), while the antioxidants were estimated spectrophotometrically (T60 UV-VIS spectrophotometer, Leicester, UK). The amino acid quantification was carried out by amino acid analyzer (HITACHI L-8900, Japan). Furthermore, Nano-liquid chromatography (LC)-MS/MS analysis was performed with an Agilent system (Wilmington, DE, USA) for proteomic analysis while mascot algorithm (Matrix science, USA) was used to identify peptide sequences present in the protein sequence database. RESULTS RWL-1 showed significant growth in media supplemented with 2 and 3.5% methanol, when compared with other concentrations. Mass spectroscopy analysis revealed that RWL-1 utilizes methanol efficiently as a carbon source. In the presence of methanol, RWL-1 produced significantly higher levels of IAA but lower levels of ABA, when compared with the control. Further, enzymatic antioxidants and functional amino acids were significantly up-regulated, with predominant expression of glutamic acid and alanine. Nano-liquid chromatography, quadrupole time-of-flight analysis, and quantitative analysis of methanol-treated bacterial cells showed expression of eight different types of proteins, including detoxification proteins, unrecognized and unclassified enzymes with antioxidant properties, proteases, metabolism enzymes, ribosomal proteins, antioxidant proteins, chaperones, and heat shock proteins. CONCLUSION Results demonstrate that RWL-1 can significantly enhance its growth by utilizing methanol, and could produce phytohormones when growing in methanol-supplemented media, with increased expression of specific proteins and different biochemicals. These results will be useful in devising strategies for utilizing methylotrophic bacterial endophytes as alternative promoters of plant growth. Understanding RWL-1 ability to utilize methanol. The survival and phytohormones production by Bacillus amyloliquefaciens RWL-1 in methanol supplemented media whistle inducing metabolic and proteomic changes.
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Affiliation(s)
- Raheem Shahzad
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Abdul Latif Khan
- Natural and Medical Science Research Center, University of Nizwa, Nizwa, Oman
| | - Muhammad Waqas
- Department of Agriculture Extension, Buner, Khyber Pakhtunkhwa, Pakistan
| | - Ihsan Ullah
- Department of Biological Sciences, Faculty of science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saqib Bilal
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yoon-Ha Kim
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sajjad Asaf
- Natural and Medical Science Research Center, University of Nizwa, Nizwa, Oman
| | - Sang-Mo Kang
- Institute of Agricultural Science and Technology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Kaparullina EN, Agafonova NV, Trotsenko YA, Doronina NV. Methylophilus aquaticus sp. nov., a New Aerobic Methylotrophic Bacterium Isolated from a Freshwater Reservoir. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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van Kruistum H, Bodelier PLE, Ho A, Meima-Franke M, Veraart AJ. Resistance and Recovery of Methane-Oxidizing Communities Depends on Stress Regime and History; A Microcosm Study. Front Microbiol 2018; 9:1714. [PMID: 30108568 PMCID: PMC6080070 DOI: 10.3389/fmicb.2018.01714] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/09/2018] [Indexed: 11/21/2022] Open
Abstract
Although soil microbes are responsible for important ecosystem functions, and soils are under increasing environmental pressure, little is known about their resistance and resilience to multiple stressors. Here, we test resistance and recovery of soil methane-oxidizing communities to two different, repeated, perturbations: soil drying, ammonium addition and their combination. In replicated soil microcosms we measured methane oxidation before and after perturbations, while monitoring microbial abundance and community composition using quantitative PCR assays for the bacterial 16S rRNA and pmoA gene, and sequencing of the bacterial 16S rRNA gene. Although microbial community composition changed after soil drying, methane oxidation rates recovered, even after four desiccation events. Moreover, microcosms subjected to soil drying recovered significantly better from ammonium addition compared to microcosms not subjected to soil drying. Our results show the flexibility of microbial communities, even if abundances of dominant populations drop, ecosystem functions can recover. In addition, a history of stress may induce changes in community composition and functioning, which may in turn affect its future tolerance to different stressors.
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Affiliation(s)
- Henri van Kruistum
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Paul L E Bodelier
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Adrian Ho
- Institut für Mikrobiologie, Leibniz Universität Hannover, Hanover, Germany
| | - Marion Meima-Franke
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Annelies J Veraart
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Department Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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25
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Green PN, Ardley JK. Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov. Int J Syst Evol Microbiol 2018; 68:2727-2748. [PMID: 30024371 DOI: 10.1099/ijsem.0.002856] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Methylobacterium, when first proposed by Patt et al. in 1976, was a monospecific genus created to accommodate a single pink pigmented facultatively methylotrophic bacterium. The genus now has over 50 validly published species, however, the percentage 16S rRNA sequence divergence within Methylobacterium questions whether or not they can still be accommodated within one genus. Additionally, several strains are described as belonging to Methylobacterium, but nodulate legumes and in some cases are unable to utilize methanol as a sole carbon source. This study reviews and discusses the current taxonomic status of Methylobacterium. Based on 16S rRNA gene, multi-locus sequence analysis, genomic and phenotypic data, the 52 Methylobacterium species can no longer be retained in one genus. Consequently, a new genus, Methylorubrum gen. nov., is proposed to accommodate 11 species previously held in Methylobacterium. The reclassified species names are proposed as: Methylorubrum aminovorans comb. nov. (type strain TH-15T=NCIMB 13343T=DSM 8832T), Methylorubrum extorquens comb. nov. (type strain NCIMB 9399T=DSM 1337T), Methylorubrum podarium comb. nov. (type strain FM4T=NCIMB 14856T=DSM 15083T), Methylorubrum populi comb. nov. (type strain BJ001T=NCIMB 13946T=ATCC BAA-705T), Methylorubrum pseudosasae comb. nov. (type strain BL44T=ICMP 17622T=NBRC 105205T), Methylorubrum rhodesianum comb. nov. (type strain NCIMB 12249T=DSM 5687T), Methylorubrum rhodinum comb. nov. (type strain NCIMB 9421T=DSM 2163T), Methylorubrum salsuginis comb. nov. (type strain MRT=NCIMB 14847T=NCCB 100140T), Methylorubrum suomiense comb. nov. (type strain F20T=NCIMB 13778T=DSM 14458T), Methylorubrum thiocyanatum comb. nov. (type strain ALL/SCN-PT=NCIMB 13651T=DSM 11490T) and Methylorubrum zatmanii comb. nov. (type strain NCIMB 12243T=DSM 5688T). The taxonomic position of several remaining species is also discussed.
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Affiliation(s)
- Peter N Green
- 1NCIMB, Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen AB21 9YA, UK
| | - Julie K Ardley
- 2School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia
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26
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Howat AM, Vollmers J, Taubert M, Grob C, Dixon JL, Todd JD, Chen Y, Kaster AK, Murrell JC. Comparative Genomics and Mutational Analysis Reveals a Novel XoxF-Utilizing Methylotroph in the Roseobacter Group Isolated From the Marine Environment. Front Microbiol 2018; 9:766. [PMID: 29755426 PMCID: PMC5934484 DOI: 10.3389/fmicb.2018.00766] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/04/2018] [Indexed: 11/13/2022] Open
Abstract
The Roseobacter group comprises a significant group of marine bacteria which are involved in global carbon and sulfur cycles. Some members are methylotrophs, using one-carbon compounds as a carbon and energy source. It has recently been shown that methylotrophs generally require a rare earth element when using the methanol dehydrogenase enzyme XoxF for growth on methanol. Addition of lanthanum to methanol enrichments of coastal seawater facilitated the isolation of a novel methylotroph in the Roseobacter group: Marinibacterium anthonyi strain La 6. Mutation of xoxF5 revealed the essential nature of this gene during growth on methanol and ethanol. Physiological characterization demonstrated the metabolic versatility of this strain. Genome sequencing revealed that strain La 6 has the largest genome of all Roseobacter group members sequenced to date, at 7.18 Mbp. Multilocus sequence analysis (MLSA) showed that whilst it displays the highest core gene sequence similarity with subgroup 1 of the Roseobacter group, it shares very little of its pangenome, suggesting unique genetic adaptations. This research revealed that the addition of lanthanides to isolation procedures was key to cultivating novel XoxF-utilizing methylotrophs from the marine environment, whilst genome sequencing and MLSA provided insights into their potential genetic adaptations and relationship to the wider community.
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Affiliation(s)
- Alexandra M. Howat
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - John Vollmers
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Carolina Grob
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - J. C. Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
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27
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Agafonova NV, Kaparullina EN, Doronina NV, Trotsenko YA. Methylobacillus caricis sp. nov., an obligate methylotroph isolated from roots of sedge (Carex sp.). Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717060042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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28
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Agafonova NV, Kaparullina EN, Trotsenko YA, Doronina NV. Ancylobacter sonchi sp. nov., a novel methylotrophic bacterium frоm roots of Sonchus arvensis L. Int J Syst Evol Microbiol 2017; 67:4552-4558. [PMID: 28984222 DOI: 10.1099/ijsem.0.002330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic facultatively methylotrophic bacterium was isolated from roots of Sonchus arvensis L. and designated strain OsotT The cells of this strain were Gram-stain-negative, asporogenous, motile short rods multiplying by binary fisson. They utilized methanol, methylamines and a variety of polycarbon compounds as the carbon and energy sources. Methanol was assimilated after sequential oxidation to formaldehyde and CO2 via the ribulose bisphosphate pathway. The organism grew optimally at 22-29 °C and pH 7.5-8.0. The dominant phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol (cardiolipin). The major cellular fatty acids of strain OsotT cells grown in R2A medium were C18 : 1ω7c (49.0 %), C19 : 0ω8c cyclo (38.3 %) and C16 : 0 (8.4 %). The major ubiquinone was Q-10. The DNA G+C content of strain OsotT was 66.1 mol% (Tm). On the basis of 16S rRNA gene sequence analysis strain OsotT is phylogenetically related to the members of genus Ancylobacter (97.1-98.8 % sequence similarity). Based on 16S rRNA gene sequence analysis and DNA-DNA relatedness (27-29 %) with type strains of the genus Ancylobacter, the novel isolate is classified as a new species of this genus and named Ancylobacter sonchi sp. nov.; the type strain is OsotT (=VKM B-3145T=JCM 32039T).
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Affiliation(s)
| | - Elena N Kaparullina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow region, 142290, Russia
| | - Yuri A Trotsenko
- Pushchino State Institute of Natural Sciences, Pushchino, Russia.,G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow region, 142290, Russia
| | - Nina V Doronina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow region, 142290, Russia
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29
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A novel methanotroph in the genus Methylomonas that contains a distinct clade of soluble methane monooxygenase. J Microbiol 2017; 55:775-782. [DOI: 10.1007/s12275-017-7317-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/25/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
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30
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Del Rocío Bustillos-Cristales M, Corona-Gutierrez I, Castañeda-Lucio M, Águila-Zempoaltécatl C, Seynos-García E, Hernández-Lucas I, Muñoz-Rojas J, Medina-Aparicio L, Fuentes-Ramírez LE. Culturable Facultative Methylotrophic Bacteria from the Cactus Neobuxbaumia macrocephala Possess the Locus xoxF and Consume Methanol in the Presence of Ce 3+ and Ca 2. Microbes Environ 2017; 32:244-251. [PMID: 28855445 PMCID: PMC5606694 DOI: 10.1264/jsme2.me17070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Methanol-consuming culturable bacteria were isolated from the plant surface, rhizosphere, and inside the stem of Neobuxbaumia macrocephala. All 38 isolates were facultative methylotrophic microorganisms. Their classification included the Classes Actinobacteria, Sphingobacteriia, Alpha-, Beta-, and Gammaproteobacteria. The deduced amino acid sequences of methanol dehydrogenase obtained by PCR belonging to Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria showed high similarity to rare-earth element (REE)-dependent XoxF methanol dehydrogenases, particularly the group XoxF5. The sequences included Asp301, the REE-coordinating amino acid, present in all known XoxF dehydrogenases and absent in MxaF methanol dehydrogenases. The quantity of the isolates showed positive hybridization with a xoxF probe, but not with a mxaF probe. Isolates of all taxonomic groups showed methylotrophic growth in the presence of Ce3+ or Ca2+. The presence of xoxF-like sequences in methylotrophic bacteria from N. macrocephala and its potential relationship with their adaptability to xerophytic plants are discussed.
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31
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Morawe M, Hoeke H, Wissenbach DK, Lentendu G, Wubet T, Kröber E, Kolb S. Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil. Front Microbiol 2017; 8:1361. [PMID: 28790984 PMCID: PMC5523551 DOI: 10.3389/fmicb.2017.01361] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 07/05/2017] [Indexed: 02/03/2023] Open
Abstract
Methanol is an abundant atmospheric volatile organic compound that is released from both living and decaying plant material. In forest and other aerated soils, methanol can be consumed by methanol-utilizing microorganisms that constitute a known terrestrial sink. However, the environmental factors that drive the biodiversity of such methanol-utilizers have been hardly resolved. Soil-derived isolates of methanol-utilizers can also often assimilate multicarbon compounds as alternative substrates. Here, we conducted a comparative DNA stable isotope probing experiment under methylotrophic (only [13C1]-methanol was supplemented) and combined substrate conditions ([12C1]-methanol and alternative multi-carbon [13Cu]-substrates were simultaneously supplemented) to (i) identify methanol-utilizing microorganisms of a deciduous forest soil (European beech dominated temperate forest in Germany), (ii) assess their substrate range in the soil environment, and (iii) evaluate their trophic links to other soil microorganisms. The applied multi-carbon substrates represented typical intermediates of organic matter degradation, such as acetate, plant-derived sugars (xylose and glucose), and a lignin-derived aromatic compound (vanillic acid). An experimentally induced pH shift was associated with substantial changes of the diversity of active methanol-utilizers suggesting that soil pH was a niche-defining factor of these microorganisms. The main bacterial methanol-utilizers were members of the Beijerinckiaceae (Bacteria) that played a central role in a detected methanol-based food web. A clear preference for methanol or multi-carbon substrates as carbon source of different Beijerinckiaceae-affiliated phylotypes was observed suggesting a restricted substrate range of the methylotrophic representatives. Apart from Bacteria, we also identified the yeasts Cryptococcus and Trichosporon as methanol-derived carbon-utilizing fungi suggesting that further research is needed to exclude or prove methylotrophy of these fungi.
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Affiliation(s)
- Mareen Morawe
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany
| | - Henrike Hoeke
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental ResearchLeipzig, Germany.,Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of LeipzigLeipzig, Germany
| | - Dirk K Wissenbach
- Institute of Forensic Medicine, University Hospital JenaJena, Germany
| | - Guillaume Lentendu
- Department of Ecology, University of KaiserslauternKaiserslautern, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental ResearchLeipzig, Germany
| | - Eileen Kröber
- Institute of Landscape Biogeochemistry, Leibniz Centre for Landscape ResearchMüncheberg, Germany
| | - Steffen Kolb
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany.,Institute of Landscape Biogeochemistry, Leibniz Centre for Landscape ResearchMüncheberg, Germany
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32
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Agafonova NV, Doronina NV, Kaparullina EN, Fedorov DN, Gafarov AB, Sazonova OI, Sokolov SL, Trotsenko YA. A novel Delftia plant symbiont capable of autotrophic methylotrophy. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717010039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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33
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Kaparullina EN, Trotsenko YA, Doronina NV. Methylobacillus methanolivorans sp. nov., a novel non-pigmented obligately methylotrophic bacterium. Int J Syst Evol Microbiol 2017; 67:425-431. [DOI: 10.1099/ijsem.0.001646] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Elena N. Kaparullina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow region 142290, Russian Federation
| | - Yuri A. Trotsenko
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow region 142290, Russian Federation
| | - Nina V. Doronina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow region 142290, Russian Federation
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34
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Doronina NV, Kaparullina EN, Trotsenko YA. Emended description of Methylovorus glucosotrophus govorukhina and trotsenko 1991. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716050040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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35
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Islam T, Torsvik V, Larsen Ø, Bodrossy L, Øvreås L, Birkeland NK. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps. Front Microbiol 2016; 7:851. [PMID: 27379029 PMCID: PMC4908921 DOI: 10.3389/fmicb.2016.00851] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 05/23/2016] [Indexed: 11/13/2022] Open
Abstract
Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2–7.5 (optimal 5.5–6.0) and at a temperature range of 30–60°C (optimal 51–55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1–94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems.
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Affiliation(s)
- Tajul Islam
- Department of Biology, University of Bergen Bergen, Norway
| | - Vigdis Torsvik
- Department of Biology, University of Bergen Bergen, Norway
| | - Øivind Larsen
- Department of Biology, University of BergenBergen, Norway; Uni Environment, Uni ResearchBergen, Norway
| | | | - Lise Øvreås
- Department of Biology, University of Bergen Bergen, Norway
| | - Nils-Kåre Birkeland
- Department of Biology, University of BergenBergen, Norway; Centre for Geobiology, University of BergenBergen, Norway
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36
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Genomic features of uncultured methylotrophs in activated-sludge microbiomes grown under different enrichment procedures. Sci Rep 2016; 6:26650. [PMID: 27221669 PMCID: PMC4879533 DOI: 10.1038/srep26650] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 05/06/2016] [Indexed: 11/21/2022] Open
Abstract
Methylotrophs are organisms that are able to grow on C1 compounds as carbon and energy sources. They play important roles in the global carbon cycle and contribute largely to industrial wastewater treatment. To identify and characterize methylotrophs that are involved in methanol degradation in wastewater-treatment plants, methanol-fed activated-sludge (MAS) microbiomes were subjected to phylogenetic and metagenomic analyses, and genomic features of dominant methylotrophs in MAS were compared with those preferentially grown in laboratory enrichment cultures (LECs). These analyses consistently indicate that Hyphomicrobium plays important roles in MAS, while Methylophilus occurred predominantly in LECs. Comparative analyses of bin genomes reconstructed for the Hyphomicrobium and Methylophilus methylotrophs suggest that they have different C1-assimilation pathways. In addition, function-module analyses suggest that their cell-surface structures are different. Comparison of the MAS bin genome with genomes of closely related Hyphomicrobium isolates suggests that genes unnecessary in MAS (for instance, genes for anaerobic respiration) have been lost from the genome of the dominant methylotroph. We suggest that genomic features and coded functions in the MAS bin genome provide us with insights into how this methylotroph adapts to activated-sludge ecosystems.
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37
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Taubert M, Grob C, Howat AM, Burns OJ, Chen Y, Neufeld JD, Murrell JC. Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies. Methods Mol Biol 2016; 1399:235-255. [PMID: 26791507 DOI: 10.1007/978-1-4939-3369-3_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Methylotrophs are microorganisms ubiquitous in the environment that can metabolize one-carbon (C1) compounds as carbon and/or energy sources. The activity of these prokaryotes impacts biogeochemical cycles within their respective habitats and can determine whether these habitats act as sources or sinks of C1 compounds. Due to the high importance of C1 compounds, not only in biogeochemical cycles, but also for climatic processes, it is vital to understand the contributions of these microorganisms to carbon cycling in different environments. One of the most challenging questions when investigating methylotrophs, but also in environmental microbiology in general, is which species contribute to the environmental processes of interest, or "who does what, where and when?" Metabolic labeling with C1 compounds substituted with (13)C, a technique called stable isotope probing, is a key method to trace carbon fluxes within methylotrophic communities. The incorporation of (13)C into the biomass of active methylotrophs leads to an increase in the molecular mass of their biomolecules. For DNA-based stable isotope probing (DNA-SIP), labeled and unlabeled DNA is separated by isopycnic ultracentrifugation. The ability to specifically analyze DNA of active methylotrophs from a complex background community by high-throughput sequencing techniques, i.e. targeted metagenomics, is the hallmark strength of DNA-SIP for elucidating ecosystem functioning, and a protocol is detailed in this chapter.
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Affiliation(s)
- Martin Taubert
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
- Institute for Ecology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - Carolina Grob
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Alexandra M Howat
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Oliver J Burns
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, Canada, N2L 3G1
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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38
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Dedysh SN, Didriksen A, Danilova OV, Belova SE, Liebner S, Svenning MM. Methylocapsa palsarum sp. nov., a methanotroph isolated from a subArctic discontinuous permafrost ecosystem. Int J Syst Evol Microbiol 2015; 65:3618-3624. [DOI: 10.1099/ijsem.0.000465] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic methanotrophic bacterium was isolated from a collapsed palsa soil in northern Norway and designated strain NE2T. Cells of this strain were Gram-stain-negative, non-motile, non-pigmented, slightly curved thick rods that multiplied by normal cell division. The cells possessed a particulate methane monooxygenase enzyme (pMMO) and utilized methane and methanol. Strain NE2T grew in a wide pH range of 4.1–8.0 (optimum pH 5.2–6.5) at temperatures between 6 and 32 °C (optimum 18–25 °C), and was capable of atmospheric nitrogen fixation under reduced oxygen tension. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C16 : 1ω7c, and the DNA G+C content was 61.7 mol%. The isolate belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and was most closely related to the facultative methanotroph Methylocapsa aurea KYGT (98.3 % 16S rRNA gene sequence similarity and 84 % PmoA sequence identity). However, strain NE2T differed from Methylocapsa aurea KYGT by cell morphology, the absence of pigmentation, inability to grow on acetate, broader pH growth range, and higher tolerance to NaCl. Therefore, strain NE2T represents a novel species of the genus Methylocapsa, for which we propose the name Methylocapsa palsarum sp. nov. The type strain is NE2T ( = LMG 28715T = VKM B-2945T).
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Affiliation(s)
- Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Alena Didriksen
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, 9037 Tromsø, Norway
| | - Olga V. Danilova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Svetlana E. Belova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Mette M. Svenning
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, 9037 Tromsø, Norway
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39
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Chao H, Wu B, Shen P. Overexpression of the methanol dehydrogenase gene mxaF
in Methylobacterium
sp. MB200 enhances L-serine production. Lett Appl Microbiol 2015; 61:390-6. [DOI: 10.1111/lam.12467] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/09/2015] [Accepted: 07/10/2015] [Indexed: 12/01/2022]
Affiliation(s)
- H. Chao
- College of Life Science and Technology; Guangxi University; Nanning China
- Key Laboratory of Agricultural and Environmental Microbiology; Wuhan Institute of Virology; Chinese Academy of Sciences; Wuhan China
| | - B. Wu
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics; Nanning China
| | - P. Shen
- College of Life Science and Technology; Guangxi University; Nanning China
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics; Nanning China
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40
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Ramachandran A, Walsh DA. Investigation of XoxF methanol dehydrogenases reveals new methylotrophic bacteria in pelagic marine and freshwater ecosystems. FEMS Microbiol Ecol 2015; 91:fiv105. [DOI: 10.1093/femsec/fiv105] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2015] [Indexed: 11/14/2022] Open
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41
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Agafonova NV, Kaparullina EN, Doronina NV, Trotsenko YA. Methylopila turkiensis sp. nov., a new aerobic facultatively methylotrophic phytosymbiont. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715040025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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42
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Grob C, Taubert M, Howat AM, Burns OJ, Dixon JL, Richnow HH, Jehmlich N, von Bergen M, Chen Y, Murrell JC. Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph. Environ Microbiol 2015; 17:4007-18. [PMID: 26033676 DOI: 10.1111/1462-2920.12935] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/20/2015] [Accepted: 05/28/2015] [Indexed: 11/26/2022]
Abstract
A variety of culture-independent techniques have been developed that can be used in conjunction with culture-dependent physiological and metabolic studies of key microbial organisms in order to better understand how the activity of natural populations influences and regulates all major biogeochemical cycles. In this study, we combined deoxyribonucleic acid-stable isotope probing (DNA-SIP) with metagenomics and metaproteomics to characterize an uncultivated marine methylotroph that actively incorporated carbon from (13) C-labeled methanol into biomass. By metagenomic sequencing of the heavy DNA, we retrieved virtually the whole genome of this bacterium and determined its metabolic potential. Through protein-stable isotope probing, the RuMP cycle was established as the main carbon assimilation pathway, and the classical methanol dehydrogenase-encoding gene mxaF, as well as three out of four identified xoxF homologues were found to be expressed. This proof-of-concept study is the first in which the culture-independent techniques of DNA-SIP and protein-SIP have been used to characterize the metabolism of a naturally occurring Methylophaga-like bacterium in the marine environment (i.e. Methylophaga thiooxydans L4) and thus provides a powerful approach to access the genome and proteome of uncultivated microbes involved in key processes in the environment.
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Affiliation(s)
- Carolina Grob
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Martin Taubert
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Alexandra M Howat
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Oliver J Burns
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Joanna L Dixon
- Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth, Devon, PL1 3DH, UK
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Nico Jehmlich
- Department of Proteomics, Helmholtz-Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Martin von Bergen
- Department of Proteomics, Helmholtz-Centre for Environmental Research-UFZ, Leipzig, Germany.,Department of Metabolomics, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.,Department of Chemistry and Bioscience, University of Aalborg, Fredrik Bajers Vej 7H, Aalborg East, 9220, Denmark
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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43
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Dourado MN, Aparecida Camargo Neves A, Santos DS, Araújo WL. Biotechnological and agronomic potential of endophytic pink-pigmented methylotrophic Methylobacterium spp. BIOMED RESEARCH INTERNATIONAL 2015; 2015:909016. [PMID: 25861650 PMCID: PMC4377440 DOI: 10.1155/2015/909016] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/31/2014] [Accepted: 01/29/2015] [Indexed: 11/17/2022]
Abstract
The genus Methylobacterium is composed of pink-pigmented facultative methylotrophic (PPFM) bacteria, which are able to synthesize carotenoids and grow on reduced organic compounds containing one carbon (C1), such as methanol and methylamine. Due to their high phenotypic plasticity, these bacteria are able to colonize different habitats, such as soil, water, and sediment, and different host plants as both endophytes and epiphytes. In plant colonization, the frequency and distribution may be influenced by plant genotype or by interactions with other associated microorganisms, which may result in increasing plant fitness. In this review, different aspects of interactions with the host plant are discussed, including their capacity to fix nitrogen, nodule the host plant, produce cytokinins, auxin and enzymes involved in the induction of systemic resistance, such as pectinase and cellulase, and therefore plant growth promotion. In addition, bacteria belonging to this group can be used to reduce environmental contamination because they are able to degrade toxic compounds, tolerate high heavy metal concentrations, and increase plant tolerance to these compounds. Moreover, genome sequencing and omics approaches have revealed genes related to plant-bacteria interactions that may be important for developing strains able to promote plant growth and protection against phytopathogens.
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Affiliation(s)
| | | | - Daiene Souza Santos
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Welington Luiz Araújo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Brazil
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44
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Yoo YS, Han JS, Ahn CM, Kim CG. Comparative enzyme inhibitive methanol production by Methylosinus sporium from simulated biogas. ENVIRONMENTAL TECHNOLOGY 2015; 36:983-991. [PMID: 25267420 DOI: 10.1080/09593330.2014.971059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Methane in a simulated biogas converting to methanol under aerobic condition was comparatively assessed by inhibiting the activity of methanol dehydrogenase (MDH) of Methylosinus sporium using phosphate, NaCl, NH4Cl or EDTA in their varying concentrations. The highest amount of methane was indistinguishably diverted at the typical conditions regardless of the types of inhibitors: 35°C and pH 7 under a 0.4% (v/v) of biogas, specifically for <40 mM phosphate, 50 mM NaCl, 40 mM NH4Cl or 150 µM EDTA. The highest level of methanol was obtained for the addition of 40 mM phosphate, 100 mM NaCl, 40 mM NH4Cl or 50 µM EDTA. In other words, 0.71, 0.60, 0.66 and 0.66 mmol methanol was correspondingly generated by the oxidation of 1.3, 0.67, 0.74 and 1.3 mmol methane. It gave a methanol conversion rate of 54.7%, 89.9%, 89.6% and 47.8%, respectively. Among them, the maximum rate of methanol production was observed at 6.25 µmol/mg h for 100 mM NaCl. Regardless of types or concentrations of inhibitors differently used, methanol production could be nonetheless identically maximized when the MDH activity was limitedly hampered by up to 35%.
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Affiliation(s)
- Yeon-Sun Yoo
- a Department of Environmental Engineering , Inha University , Incheon , Republic of Korea
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45
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Rajala P, Bomberg M, Kietäväinen R, Kukkonen I, Ahonen L, Nyyssönen M, Itävaara M. Rapid Reactivation of Deep Subsurface Microbes in the Presence of C-1 Compounds. Microorganisms 2015; 3:17-33. [PMID: 27682076 PMCID: PMC5023232 DOI: 10.3390/microorganisms3010017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/26/2015] [Accepted: 01/29/2015] [Indexed: 11/30/2022] Open
Abstract
Microorganisms in the deep biosphere are believed to conduct little metabolic activity due to low nutrient availability in these environments. However, destructive penetration to long-isolated bedrock environments during construction of underground waste repositories can lead to increased nutrient availability and potentially affect the long-term stability of the repository systems, Here, we studied how microorganisms present in fracture fluid from a depth of 500 m in Outokumpu, Finland, respond to simple carbon compounds (C-1 compounds) in the presence or absence of sulphate as an electron acceptor. C-1 compounds such as methane and methanol are important intermediates in the deep subsurface carbon cycle, and electron acceptors such as sulphate are critical components of oxidation processes. Fracture fluid samples were incubated in vitro with either methane or methanol in the presence or absence of sulphate as an electron acceptor. Metabolic response was measured by staining the microbial cells with fluorescent dyes that indicate metabolic activity and transcriptional response with RT-qPCR. Our results show that deep subsurface microbes exist in dormant states but rapidly reactivate their transcription and respiration systems in the presence of C-1 substrates, particularly methane. Microbial activity was further enhanced by the addition of sulphate as an electron acceptor. Sulphate- and nitrate-reducing microbes were particularly responsive to the addition of C-1 compounds and sulphate. These taxa are common in deep biosphere environments and may be affected by conditions disturbed by bedrock intrusion, as from drilling and excavation for long-term storage of hazardous waste.
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Affiliation(s)
- Pauliina Rajala
- Technical Research Centre of Finland (VTT), Kemistintie 3/Tietotie 2, FI-02044, Espoo, Finland.
| | - Malin Bomberg
- Technical Research Centre of Finland (VTT), Kemistintie 3/Tietotie 2, FI-02044, Espoo, Finland.
| | - Riikka Kietäväinen
- Geological Survey of Finland (GTK), P.O. Box 96, FI-02151, Espoo, Finland.
| | - Ilmo Kukkonen
- University of Helsinki, P.O. Box 33, University of Helsinki, FI-00014, Helsinki, Finland.
| | - Lasse Ahonen
- Geological Survey of Finland (GTK), P.O. Box 96, FI-02151, Espoo, Finland.
| | - Mari Nyyssönen
- Technical Research Centre of Finland (VTT), Kemistintie 3/Tietotie 2, FI-02044, Espoo, Finland.
| | - Merja Itävaara
- Technical Research Centre of Finland (VTT), Kemistintie 3/Tietotie 2, FI-02044, Espoo, Finland.
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46
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Meena KK, Kumar M, Mishra S, Ojha SK, Wakchaure GC, Sarkar B. Phylogenetic study of methanol oxidizers from chilika-lake sediments using genomic and metagenomic approaches. Indian J Microbiol 2015; 55:151-62. [PMID: 25805901 DOI: 10.1007/s12088-015-0510-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/03/2015] [Indexed: 01/13/2023] Open
Abstract
Group-wise diversity of sediment methylotrophs of Chilika lake (Lat. 19°28'-19°54'N; Long. 85°06'-85°35'E) Odisha, India at various identified sites was studied. Both the culturable and unculturable (metagenome) methylotrophs were investigated in the lake sediments employing both mxaF and 16S rRNA genes as markers. ARDRA profiling, 16S rRNA gene sequencing, PAGE profiling of HaeIII, EcoRI restricted mxaF gene and the mxaF gene sequences using culture-dependent approach revealed the relatedness of α-proteobacteria and Methylobacterium, Hyphomicrobium and Ancyclobacter sp. The total viable counts of the culturable aerobic methylotrophs were relatively higher in sediments near the sea mouth (S3; Panaspada), also demonstrated relatively high salinity (0.1 M NaCl) tolerance. Metagenomic DNA from the sediments, amplified using GC clamp mxaF primers and resolved through DGGE, revealed the diversity within the unculturable methylotrophic bacterium Methylobacterium organophilum, Ancyclobacter aquaticus, Burkholderiales and Hyphomicrobium sp. Culture-independent analyses revealed that up to 90 % of the methylotrophs were unculturable. The study enhances the general understandings of the metagenomic methylotrophs from such a special ecological niche.
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Affiliation(s)
- Kamlesh K Meena
- National Bureau of Agriculturally Important Microorganisms, Mau Nath Bhanjan, 275 101 UP India ; National Institute of Abiotic Stress Management, Malegaon, Baramati, Pune, Maharashtra India
| | - Manish Kumar
- National Bureau of Agriculturally Important Microorganisms, Mau Nath Bhanjan, 275 101 UP India
| | - Snehasish Mishra
- School of Biotechnology, KIIT University, Campus-11, Bhubaneswar, 751024 Odisha India
| | - Sanjay Kumar Ojha
- School of Biotechnology, KIIT University, Campus-11, Bhubaneswar, 751024 Odisha India
| | - Goraksha C Wakchaure
- National Institute of Abiotic Stress Management, Baramati, Pune, 413115 Maharashtra India
| | - Biplab Sarkar
- National Institute of Abiotic Stress Management, Baramati, Pune, 413115 Maharashtra India
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47
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Poroshina MN, Doronina NV, Kaparullina EN, Trotsenko YA. Advenella kashmirensis subsp. methylica PK1, a facultative methylotroph from carex rhizosphere. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715010117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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48
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Wang YN, Tian WY, He WH, Chen GC, An ML, Jia B, Liu L, Zhou Y, Liu SJ. Methylopila henanense sp. nov., a novel methylotrophic bacterium isolated from tribenuron methyl-contaminated wheat soil. Antonie van Leeuwenhoek 2014; 107:329-36. [DOI: 10.1007/s10482-014-0331-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/05/2014] [Indexed: 11/30/2022]
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49
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Tavormina PL, Hatzenpichler R, McGlynn S, Chadwick G, Dawson KS, Connon SA, Orphan VJ. Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs. Int J Syst Evol Microbiol 2014; 65:251-259. [PMID: 25342114 DOI: 10.1099/ijs.0.062927-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1(T), 'whale fall 1') that shares 98 % 16S rRNA gene sequence identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep-sea mussels, ≤94.6 % 16S rRNA gene sequence identity with species of the genus Methylobacter and ≤93.6 % 16S rRNA gene sequence identity with species of the genera Methylomonas and Methylosarcina. Strain WF1(T) represents the first cultivar from the 'deep sea-1' clade of marine methanotrophs, which includes members that participate in methane oxidation in sediments and the water column in addition to mussel endosymbionts. Cells of strain WF1(T) were elongated cocci, approximately 1.5 µm in diameter, and occurred singly, in pairs and in clumps. The cell wall was Gram-negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic DNA G+C content of WF1(T) was 40.5 mol%, significantly lower than that of currently described cultivars, and the major fatty acids were 16 : 0, 16 : 1ω9c, 16 : 1ω9t, 16 : 1ω8c and 16 : 2ω9,14. Growth occurred in liquid media at an optimal temperature of 23 °C, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1(T), a capacity that had not been functionally demonstrated previously in members of Methylobacter. On the basis of its unique morphological, physiological and phylogenetic properties, this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti gen. nov., sp. nov. The type strain of Methyloprofundus sedimenti is WF1(T) ( = LMG 28393(T) = ATCC BAA-2619(T)).
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Affiliation(s)
- Patricia L Tavormina
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Shawn McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Grayson Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Stephanie A Connon
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
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50
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Madhaiyan M, Poonguzhali S. Methylobacterium pseudosasicola sp. nov. and Methylobacterium phyllostachyos sp. nov., isolated from bamboo leaf surfaces. Int J Syst Evol Microbiol 2014; 64:2376-2384. [DOI: 10.1099/ijs.0.057232-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Two strains of Gram-negative, methylotrophic bacteria, isolated because of their abilities to promote plant growth, were subjected to a polyphasic taxonomic study. The isolates were strictly aerobic, motile, pink-pigmented, facultatively methylotrophic, non-spore-forming rods. The chemotaxonomic characteristics of the isolates included the presence of C18 : 1ω7c as the major cellular fatty acid. The DNA G+C contents of strains BL36T and BL47T were 69.4 and 69.8 mol%, respectively. 16S rRNA gene sequence analysis of strains BL36T and BL47T placed them under the genus
Methylobacterium,
with the pairwise sequence similarity between them and the type strains of closely related species ranging from 97.2 to 99.0 %. On the basis of their phenotypic and phylogenetic distinctiveness and the results of DNA–DNA hybridization analysis, the isolates represent two novel species within the genus
Methylobacterium
, for which the names Methylobacterium pseudosasicola sp. nov. (type strain BL36T = NBRC 105203T = ICMP 17621T) and Methylobacterium phyllostachyos sp. nov. (type strain BL47T = NBRC 105206T = ICMP 17619T) are proposed.
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Affiliation(s)
- Munusamy Madhaiyan
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
| | - Selvaraj Poonguzhali
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
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