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Roldán DM, Menes RJ. Characterisation of 'Candidatus Methylobacter titanis' sp. nov., a putative novel species of Methylobacter clade 2 and their distribution in sediments of freshwater lakes in maritime Antarctica. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01840-1. [PMID: 37227602 DOI: 10.1007/s10482-023-01840-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/07/2023] [Indexed: 05/26/2023]
Abstract
Global warming has a strong impact on the polar regions, in particular, the Antarctic Peninsula and nearby islands. Methane (CH4) is a major factor in climate change and mitigation of CH4 emissions can be accomplished through microbial oxidation by methanotrophic bacteria. Understanding this biological process is crucial given the shortage of research carried out in this geographical area. The aim of this study was to characterise psychrophilic enrichment cultures of aerobic methanotrophs obtained from lake sediments of the Fildes Peninsula (King George Island, South Shetland Islands) and revealing the distribution of the genus Methylobacter in different lake sediments of the peninsula. Four stable methanotrophic enrichment cultures were obtained and analysed by metagenome-assembled genomes (MAGs). The phylogeny of methanotroph MAGs recovered from these enrichment cultures based on the 16S rRNA gene showed that K-2018 MAG008 and D1-2020 MAG004Ts clustered within the Methylobacter clade 2, with high similarity to Methylobacter tundripaludum SV96T (97.88 and 98.56% respectively). However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with M. tundripaludum were < 95% (84.8 and 85.0%, respectively) and < 70% (30.2 and 30.3%, respectively), suggesting that they represent a putative novel species for which the name 'Ca. Methylobacter titanis' is proposed. This is the first species of clade 2 of the genus Methylobacter obtained from Antarctica. The bacterial diversity assessed by 16S rRNA gene sequencing of 21 samples of different lakes (water column and sediments) revealed 54 ASVs associated with methanotrophs and the genus Methylobacter as the most abundant. These results suggest that aerobic methanotrophs belonging to the Methylobacter clade 2 would be the main responsible for CH4 oxidation in these sediments.
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Affiliation(s)
- Diego M Roldán
- Laboratorio de Ecología Microbiana Medioambiental, Microbiología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Rodolfo Javier Menes
- Laboratorio de Ecología Microbiana Medioambiental, Microbiología, Facultad de Química, Universidad de la República, Montevideo, Uruguay.
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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Rahalkar MC, Khatri K, Pandit P, Bahulikar RA, Mohite JA. Cultivation of Important Methanotrophs From Indian Rice Fields. Front Microbiol 2021; 12:669244. [PMID: 34539593 PMCID: PMC8447245 DOI: 10.3389/fmicb.2021.669244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/09/2021] [Indexed: 11/15/2022] Open
Abstract
Methanotrophs are aerobic to micro-aerophilic bacteria, which oxidize and utilize methane, the second most important greenhouse gas. The community structure of the methanotrophs in rice fields worldwide has been studied mainly using culture-independent methods. Very few studies have focused on culturing methanotrophs from rice fields. We developed a unique method for the cultivation of methanotrophs from rice field samples. Here, we used a modified dilute nitrate mineral salts (dNMS) medium, with two cycles of dilution till extinction series cultivation with prolonged incubation time, and used agarose in the solid medium. The cultivation approach resulted in the isolation of methanotrophs from seven genera from the three major groups: Type Ia (Methylomonas, Methylomicrobium, and Methylocucumis), Type Ib (Methylocaldum and Methylomagnum), and Type II (Methylocystis and Methylosinus). Growth was obtained till 10–6–10–8 dilutions in the first dilution series, indicating the culturing of dominant methanotrophs. Our study was supported by 16S rRNA gene-based next-generation sequencing (NGS) of three of the rice samples. Our analyses and comparison with the global scenario suggested that the cultured members represented the major detected taxa. Strain RS1, representing a putative novel species of Methylomicrobium, was cultured; and the draft genome sequence was obtained. Genome analysis indicated that RS1 represented a new putative Methylomicrobium species. Methylomicrobium has been detected globally in rice fields as a dominant genus, although no Methylomicrobium strains have been isolated from rice fields worldwide. Ours is one of the first extensive studies on cultured methanotrophs from Indian rice fields focusing on the tropical region, and a unique method was developed. A total of 29 strains were obtained, which could be used as models for studying methane mitigation from rice fields and for environmental and biotechnological applications.
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Affiliation(s)
- Monali C Rahalkar
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Kumal Khatri
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Pranitha Pandit
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Rahul A Bahulikar
- Central Research Station, BAIF Development Research Foundation, Pune, India
| | - Jyoti A Mohite
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
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Methane utilizing plant growth-promoting microbial diversity analysis of flooded paddy ecosystem of India. World J Microbiol Biotechnol 2021; 37:56. [PMID: 33619649 DOI: 10.1007/s11274-021-03018-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/01/2021] [Indexed: 01/10/2023]
Abstract
Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH4) emission. We hypothesize that efficient MUB having plant growth-promoting (PGP) attributes can be used for developing novel bio-inoculant for flooded paddy ecosystem which might not only reduce methane emission but also assist in improving the plant growth parameters. Hence, soil and plant samples were collected from the phyllosphere, rhizosphere, and non-rhizosphere of five rice-growing regions of India at the tillering stage and investigated for efficient methane-oxidizing and PGP bacteria. Based on the monooxygenase activity and percent methane utilization on NMS medium with methane as the sole C source, 123 isolates were identified and grouped phylogenetically into 13 bacteria and 2 yeast genera. Among different regions, a significantly higher number of isolates were obtained from lowland flooded paddy ecosystems of Aduthurai (33.33%) followed by Ernakulum (20.33%) and Brahmaputra valley (19.51%) as compared to upland irrigated regions of Gaya (17.07%) and Varanasi (8.94%). Among sub-samples, a significantly higher number of isolates were found inhabiting the phyllosphere (58.54%) followed by non-rhizosphere (25.20%) and rhizosphere (15.45%). Significantly higher utilization of methane and PGP attributes were observed in 30 isolates belonging to genera Hyphomicrobium, Burkholderia, Methylobacterium, Paenibacillus, Pseudomonas, Rahnella, and Meyerozyma. M. oryzae MNL7 showed significantly better growth with 74.33% of CH4 utilization at the rate of 302.9 ± 5.58 and exhibited half-maximal growth rate, Ks of 1.92 ± 0.092 mg CH4 L-1. Besides the ability to utilize CH4, P. polymyxa MaAL70 possessed PGP attributes such as solubilization of P, K, and Zn, fixation of atmospheric N and production of indole acetic acid (IAA). Both these promising isolates can be explored in the future for developing novel biofertilizers for flooded paddies.
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Tian HJ, Feng J, Zhang LM, He JZ, Liu YR. Ecological drivers of methanotrophic communities in paddy soils around mercury mining areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 721:137760. [PMID: 32169650 DOI: 10.1016/j.scitotenv.2020.137760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Methanotrophs play a crucial role in mitigating methane (CH4) emission by oxidizing produced CH4 in paddy soils; however, ecological drivers of methanotrophic community in the soils around heavy metal contaminated areas remain unclear. In this study, we evaluated the effects of heavy metal pollution and soil properties on the abundance, diversity and composition of methanotrophic community in paddy soils from two typical mercury (Hg) mining regions in southwest China. The results of random forest and structure equation models suggest that both heavy metal content and soil nutrients greatly influenced the attributes of methanotrophic community. In general, the abundance and diversity of methanotrophs were negatively related to soil Hg content, but showed positive correlation with soil organic carbon content. However, the other metals (cadmium (Cd), nickel (Ni), lead (Pb), arsenic (As), zinc (Zn)) had inconsistent associations with the microbial indexes of methanotrophic community in the soil. Elevated levels of heavy metal and nutrients in the soils shifted the community composition of methanotrophs. For example, Pb, As and Zn contents had negative associations with the relative abundance of Methylocaldum. In addition, changes in the relative abundance of ecological clusters within the co-occurrence network of methanotrophs were related to metal contents and soil properties. Together, our findings provide novel insights into understanding ecological drivers of methanotrophic community in paddy soils around Hg mining regions, with important implications for mitigating CH4 emissions in terrestrial ecosystems.
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Affiliation(s)
- Hua-Jing Tian
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiao Feng
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yu-Rong Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
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Rahalkar MC, Pandit PS, Dhakephalkar PK, Pore S, Arora P, Kapse N. Genome Characteristics of a Novel Type I Methanotroph (Sn10-6) Isolated from a Flooded Indian Rice Field. MICROBIAL ECOLOGY 2016; 71:519-523. [PMID: 26547566 DOI: 10.1007/s00248-015-0699-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
Flooded rice fields are important sources of atmospheric methane. Aerobic methanotrophs living in the vicinity of rice roots oxidize methane and act as environmental filters. Here, we present genome characteristics of a gammaproteobacterial methanotroph, isolate Sn10-6, which was isolated from a rice rhizosphere of a flooded field in India. Sn10-6 has been identified as a member of a putative novel genus and species within the family Methylococcaceae (Type I methanotrophs). The draft genome of Sn10-6 showed pathways for the following: methane oxidation, formaldehyde assimilation (RuMP), nitrogen fixation, conversion of nitrite to nitrous oxide, and other interesting genes including the ones responsible for survival in the rhizosphere environment. The majority of genes found in this genome were most similar to Methylovulum miyakonese which is a forest isolate. This draft genome provided insight into the physiology, ecology, and phylogeny of this gammaproteobacterial methanotroph.
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Affiliation(s)
- Monali C Rahalkar
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India.
| | - Pranitha S Pandit
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India
| | | | - Soham Pore
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India
| | - Preeti Arora
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India
| | - Neelam Kapse
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India
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Pandit PS, Rahalkar MC, Dhakephalkar PK, Ranade DR, Pore S, Arora P, Kapse N. Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches. MICROBIAL ECOLOGY 2016; 71:634-644. [PMID: 26547567 DOI: 10.1007/s00248-015-0697-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Methanotrophs play a crucial role in filtering out methane from habitats, such as flooded rice fields. India has the largest area under rice cultivation in the world; however, to the best of our knowledge, methanotrophs have not been isolated and characterized from Indian rice fields. A cultivation strategy composing of a modified medium, longer incubation time, and serial dilutions in microtiter plates was used to cultivate methanotrophs from a rice rhizosphere sample from a flooded rice field in Western India. We compared the cultured members with the uncultured community as revealed by three culture-independent methods. A novel type Ia methanotroph (Sn10-6), at the rank of a genus, and a putative novel species of a type II methanotroph (Sn-Cys) were cultivated from the terminal positive dilution (10(-6)). From lower dilution (10(-4)), a strain of Methylomonas spp. was cultivated. All the three culture-independent analyses, i.e., pmoA clone library, terminal restriction fragment length polymorphism (T-RFLP), and metagenomics approach, revealed the dominance of type I methanotrophs. Only metagenomic analysis showed significant presence of type II methanotrophs, albeit in lower proportion (37 %). All the three isolates showed relevance to the methanotrophic community as depicted by uncultured methods; however, the cultivated members might not be the most dominant ones. In conclusion, a combined cultivation and cultivation-independent strategy yielded us a broader picture of the methanotrophic community from rice rhizospheres of a flooded rice field in India.
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Affiliation(s)
- Pranitha S Pandit
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Monali C Rahalkar
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
| | | | - Dilip R Ranade
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Microbial Culture Collection, NCCS, Sai-Trinity Building Garware Circle, Pashan, Pune, Maharashtra, 411021, India
| | - Soham Pore
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Preeti Arora
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Neelam Kapse
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
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7
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Bellini MI, Gutiérrez L, Tarlera S, Scavino AF. Isolation and functional analysis of denitrifiers in an aquifer with high potential for denitrification. Syst Appl Microbiol 2013; 36:505-16. [DOI: 10.1016/j.syapm.2013.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 07/04/2013] [Accepted: 07/06/2013] [Indexed: 10/26/2022]
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Morris BEL, Henneberger R, Huber H, Moissl-Eichinger C. Microbial syntrophy: interaction for the common good. FEMS Microbiol Rev 2013; 37:384-406. [PMID: 23480449 DOI: 10.1111/1574-6976.12019] [Citation(s) in RCA: 446] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 11/30/2022] Open
Abstract
Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds.
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Affiliation(s)
- Brandon E L Morris
- Microbiology, Institute for Biology II, University of Freiburg, Freiburg, Germany
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Lüke C, Frenzel P, Ho A, Fiantis D, Schad P, Schneider B, Schwark L, Utami SR. Macroecology of methane-oxidizing bacteria: the β-diversity ofpmoAgenotypes in tropical and subtropical rice paddies. Environ Microbiol 2013; 16:72-83. [DOI: 10.1111/1462-2920.12190] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claudia Lüke
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
- Radboud University Nijmegen; Heyendaalsweg 135 Nijmegen 6525 AJ The Netherlands
| | - Peter Frenzel
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
| | - Adrian Ho
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
- Laboratory for Microbial Ecology and Technology (LabMET); Faculty of Bioscience Engineering; Coupure Links 653 Ghent 9000 Belgium
| | - Dian Fiantis
- Department of Soil Science; Faculty of Agriculture; Andalas University; Kampus Unand Limau Manis Padang 25163 Indonesia
| | - Peter Schad
- Department Ecology and Ecosystem Management; Center of Life and Food Sciences Weihenstephan; Technische Universität München; Lehrstuhl für Bodenkunde Freising-Weihenstephan D-85350 Germany
| | - Bellinda Schneider
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
| | - Lorenz Schwark
- Institute of Geosciences; University Kiel; Ludewig-Meyn-Straße 10 Kiel 24118 Germany
- WA-OIGC; Curtin University; Perth WA 6845 Australia
| | - Sri Rahayu Utami
- Department of Soil Science; Faculty of Agriculture; Brawijaya University; Jalan Veteran Malang 65145 East Java Indonesia
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Oldham AL, Drilling HS, Stamps BW, Stevenson BS, Duncan KE. Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities. AMB Express 2012; 2:60. [PMID: 23168231 PMCID: PMC3539857 DOI: 10.1186/2191-0855-2-60] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 11/16/2012] [Indexed: 12/20/2022] Open
Abstract
The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources.
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Affiliation(s)
- Athenia L Oldham
- The Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval GLCH #136, Norman, OK 73019, USA
- University of Oklahoma Biocorrosion Center, Norman, OK 73019, USA
- The Institute for Energy and the Environment, University of Oklahoma, 100 E. Boyd Street, Norman, OK, 73019, USA
| | - Heather S Drilling
- The Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval GLCH #136, Norman, OK 73019, USA
- University of Oklahoma Biocorrosion Center, Norman, OK 73019, USA
| | - Blake W Stamps
- The Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval GLCH #136, Norman, OK 73019, USA
- University of Oklahoma Biocorrosion Center, Norman, OK 73019, USA
| | - Bradley S Stevenson
- The Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval GLCH #136, Norman, OK 73019, USA
- University of Oklahoma Biocorrosion Center, Norman, OK 73019, USA
| | - Kathleen E Duncan
- The Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval GLCH #136, Norman, OK 73019, USA
- University of Oklahoma Biocorrosion Center, Norman, OK 73019, USA
- The Institute for Energy and the Environment, University of Oklahoma, 100 E. Boyd Street, Norman, OK, 73019, USA
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Meng X, Wang L, Long X, Liu Z, Zhang Z, Zed R. Influence of nitrogen fertilization on diazotrophic communities in the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.). Res Microbiol 2012; 163:349-56. [PMID: 22564556 DOI: 10.1016/j.resmic.2012.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Accepted: 03/28/2012] [Indexed: 11/28/2022]
Abstract
Diazotrophs in the soil may be influenced by plant factors as well as nitrogen (N) fertilization. In this study, we investigated potential diazotrophic communities in the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.) supplied with differing amounts of N. The community structure of N(2)-fixing bacteria was profiled using the length heterogeneity polymerase chain reaction (LH-PCR) and terminal restriction fragment length polymorphism (T-RFLP) based on a variation in the nifH gene. Higher numbers of diazotrophs were detected by T-RFLP compared to LH-PCR. The lowest number of N(2)-fixing bacteria was observed in the rhizosphere soil with high N fertilization. T-RFLP was a better method than LH-PCR for profiling microbial diversity of diazotrophs using multidimensional scaling (MDS) and analysis of similarity (ANOSIM) of fingerprints as well as diversity measures. The supply of N fertilizer appeared to negatively influence the abundance of diazotrophs in the rhizophere of the Jerusalem artichoke.
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Affiliation(s)
- Xianfa Meng
- Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.
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Analysis and comparison of the microflora isolated from fresco surface and from surrounding air environment through molecular and biodegradative assays. World J Microbiol Biotechnol 2012; 28:2015-27. [DOI: 10.1007/s11274-012-1004-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 01/07/2012] [Indexed: 01/11/2023]
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13
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Dianou D, Ueno C, Ogiso T, Kimura M, Asakawa S. Diversity of cultivable methane-oxidizing bacteria in microsites of a rice paddy field: investigation by cultivation method and fluorescence in situ hybridization (FISH). Microbes Environ 2012; 27:278-87. [PMID: 22446309 PMCID: PMC4036049 DOI: 10.1264/jsme2.me11327] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The diversity of cultivable methane-oxidizing bacteria (MOB) in the rice paddy field ecosystem was investigated by combined culture-dependent and fluorescence in situ hybridization (FISH) techniques. Seven microsites of a Japanese rice paddy field were the focus of the study: floodwater, surface soil, bulk soil, rhizosphere soil, root, basal stem of rice plant, and rice stumps of previous harvest. Based on pmoA gene analysis and transmission electron microscopy (TEM), four type I, and nine type II MOB isolates were obtained from the highest dilution series of enrichment cultures. The type I MOB isolates included a novel species in the genus Methylomonas from floodwater and this is the first type I MOB strain isolated from floodwater of a rice paddy field. In the type I MOB, two isolates from stumps were closely related to Methylomonas spp.; one isolate obtained from rhizosphere soil was most related to Methyloccocus-Methylocaldum-Methylogaea clade. Almost all the type II MOB isolates were related to Methylocystis methanotrophs. FISH confirmed the presence of both types I and II MOB in all the microsites and in the related enrichment cultures. The study reported, for the first time, the diversity of cultivable methanotrophs including a novel species of type I MOB in rice paddy field compartments. Refining growth media and culture conditions, in combination with molecular approaches, will allow us to broaden our knowledge on the MOB community in the rice paddy field ecosystem and consequently to implement strategies for mitigating CH4 emission from this ecosystem.
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Affiliation(s)
- Dayéri Dianou
- Centre National de la Recherche Scientifique et Technologique, 03BP7192 Ouagadougou, Burkina Faso
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Geymonat E, Ferrando L, Tarlera SE. Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field. Int J Syst Evol Microbiol 2011; 61:2568-2572. [DOI: 10.1099/ijs.0.028274-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel methanotroph, designated strain E10T, was isolated from a rice paddy field in Uruguay. Strain E10T grew on methane and methanol as sole carbon and energy sources. Cells were Gram-negative, non-motile, non-pigmented, slightly curved rods showing type I intracytoplasmic membranes arranged in stacks. The strain was neutrophilic and mesophilic; optimum growth occurred at 30–35 °C with no growth above 37 °C. The strain possessed only a particulate methane monooxygenase (pmoA). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the moderately thermophilic strains Methylocaldum szegediense OR2T (91.6 % sequence similarity) and Methylococcus capsulatus Bath (91.5 %). Comparative sequence analysis of pmoA genes also confirmed that strain E10T formed a new lineage among the genera Methylocaldum and Methylococcus with 89 and 84 % derived amino acid sequence identity to Methylococcus capsulatus Bath and Methylocaldum gracile VKM-14LT, respectively. The DNA G+C content was 63.1 mol% and the major cellular fatty acid was C16 : 0 (62.05 %). Thus, strain E10T ( = JCM 16910T = DSM 23452T) represents the type strain of a novel species within a new genus, for which the name Methylogaea oryzae gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Estefanía Geymonat
- Cátedra de Microbiología, Facultad de Química y Facultad de Ciencias, Universidad de la República-UDELAR, CC1157 Montevideo, Uruguay
| | - Lucía Ferrando
- Cátedra de Microbiología, Facultad de Química y Facultad de Ciencias, Universidad de la República-UDELAR, CC1157 Montevideo, Uruguay
| | - Silvana E. Tarlera
- Cátedra de Microbiología, Facultad de Química y Facultad de Ciencias, Universidad de la República-UDELAR, CC1157 Montevideo, Uruguay
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Detection, isolation, and characterization of acidophilic methanotrophs from Sphagnum mosses. Appl Environ Microbiol 2011; 77:5643-54. [PMID: 21724892 DOI: 10.1128/aem.05017-11] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sphagnum peatlands are important ecosystems in the methane cycle. Methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. Yet little is known about the diversity and identity of the methanotrophs present in and on Sphagnum mosses of peatlands, and only a few isolates are known. The methanotrophic community in Sphagnum mosses, originating from a Dutch peat bog, was investigated using a pmoA microarray. A high biodiversity of both gamma- and alphaproteobacterial methanotrophs was found. With Sphagnum mosses as the inoculum, alpha- and gammaproteobacterial acidophilic methanotrophs were isolated using established and newly designed media. The 16S rRNA, pmoA, pxmA, and mmoX gene sequences showed that the alphaproteobacterial isolates belonged to the Methylocystis and Methylosinus genera. The Methylosinus species isolated are the first acid-tolerant members of this genus. Of the acidophilic gammaproteobacterial strains isolated, strain M5 was affiliated with the Methylomonas genus, and the other strain, M200, may represent a novel genus, most closely related to the genera Methylosoma and Methylovulum. So far, no acidophilic or acid-tolerant methanotrophs in the Gammaproteobacteria class are known. All strains showed the typical features of either type I or II methanotrophs and are, to the best of our knowledge, the first isolated (acidophilic or acid-tolerant) methanotrophs from Sphagnum mosses.
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Lüke C, Krause S, Cavigiolo S, Greppi D, Lupotto E, Frenzel P. Biogeography of wetland rice methanotrophs. Environ Microbiol 2009; 12:862-72. [DOI: 10.1111/j.1462-2920.2009.02131.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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