1
|
Mohite JA, Manvi SS, Pardhi K, Bahulikar RA, Deshpande S, Patange S, Joshi M, Kulkarni S, Rahalkar MC. Diverse type I and type II methanotrophs cultivated from an Indian freshwater wetland habitat. Int Microbiol 2024; 27:607-614. [PMID: 37556066 DOI: 10.1007/s10123-023-00415-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/26/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023]
Abstract
Wetlands are the main natural sources of methane emissions, which make up a significant portion of greenhouse gas emissions. Such wetland patches serve as rich habitats for aerobic methanotrophs. Limited knowledge of methanotrophs from tropical wetlands widens the scope of study from these habitats. In the present study, a freshwater wetland in a tropical region in India was sampled and serially diluted to obtain methanotrophs in culture. This was followed by the isolation of methanotrophs on agarose-containing plates, incubated under methane: air atmosphere. Methanotrophs are difficult to cultivate, and very few cultures of methanotrophs are available from tropical wetlands. Our current study reports the cultivation of a diverse community of methanotrophs from six genera, namely, Methylomonas, Methylococcus, Methylomagnum, Methylocucumis (type I methanotrophs) along with Methylocystis, Methylosinus (type II methanotrophs). A high abundance of methanotrophs (106-1010 methanotrophs/g fresh weight) was observed in the samples. A Methylococcus strain could represent a putative novel species that was also isolated. Cultures of Methylomagnum and Methylocucumis, two newly described type I methanotrophs exclusively found in rice fields, were obtained. A large number of Methylomonas koyamae strains were cultured. Our study is pioneering in the documentation of culturable methanotrophs from a typical tropical wetland patch. The isolated methanotrophs can act as models for studying methanotroph-based methane mitigation from wetland habitats and can be used for various mitigation and valorization applications.
Collapse
Affiliation(s)
- Jyoti A Mohite
- C2-83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Shubha S Manvi
- C2-83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Kajal Pardhi
- C2-83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Rahul A Bahulikar
- BAIF Development Research Foundation, Central Research Station, Urulikanchan, Pune, 412202, India
| | | | - Sanjana Patange
- Modern College, Shivajinagar, Pune, Maharashtra, 411005, India
| | - Mansi Joshi
- Fergusson College, F. C. Road, Pune, Maharashtra, 411004, India
| | | | - Monali C Rahalkar
- C2-83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
- Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India.
| |
Collapse
|
2
|
Mohite JA, Manvi SS, Pardhi K, Khatri K, Bahulikar RA, Rahalkar MC. Thermotolerant methanotrophs belonging to the Methylocaldum genus dominate the methanotroph communities in biogas slurry and cattle dung: A culture-based study from India. ENVIRONMENTAL RESEARCH 2023; 228:115870. [PMID: 37060990 DOI: 10.1016/j.envres.2023.115870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/27/2023] [Accepted: 04/08/2023] [Indexed: 05/16/2023]
Abstract
Biogas reactors run on various types of waste, with cattle dung and agricultural wastes being the primary sources in India. As biogas contains 50-60% methane, there is a possibility that the reactors harbour methanotrophs or methane-oxidizing bacteria. We set up serial endpoint dilution enrichments for the cultivation of methanotrophs using slurry from a small biogas reactor and cattle dung samples and obtained cultures of Methylocaldum gracile, a thermotolerant methanotroph. The study was expanded by sampling reactors of another small reactor of 20 L capacity and two 1000 L reactors. Dung samples were obtained from two Indian cattle breeds (Tharparkar and Gir). Pulverized rice straw used for feeding the biogas was also used for experiments. All the enrichment bottles were incubated at 39 °C, the reactors' in-situ temperature, and the rumen gut temperature. Our study isolated four pure cultures most related to Methylocaldum gracile VKM-14LT, two strains from cattle dung samples, and two from reactors. The study also resulted in the cultivation of four additional cultures of Methylocaldum gracile and Methylocaldum tepidum, which were non-axenic and identified by pmoA gene sequencing. Pure cultures Methylocaldum gracile RS-9 and CDP-2 were studied for optimum temperature and oxygen. Both the strains were thermotolerant and grew in the temperature range of 25-45 °C with the optimum between 37 and 45 °C. The cultures could grow with minimal oxygen (0.5%-1%) in the headspace, with growth up to 10% oxygen. To summarize, we report the cultivation and isolation of methanotrophs from biogas slurries and cattle dung samples. Methylocaldum was the dominant methanotroph cultured, probably due to its thermotolerant nature and the ability to grow under variable oxygen conditions. The present study also expands the existing knowledge about habitats known for the genus Methylocaldum. An analysis of the isolated cultures would help us design strategies for methane mitigation from ruminants.
Collapse
Affiliation(s)
- Jyoti A Mohite
- C2 Block, Room 83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India; Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India
| | - Shubha S Manvi
- C2 Block, Room 83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India; Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India
| | - Kajal Pardhi
- C2 Block, Room 83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India; Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India
| | - Kumal Khatri
- C2 Block, Room 83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India; Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India
| | - Rahul A Bahulikar
- BAIF Development Research Foundation, Central Research Station, Urulikanchan, Pune, 412202, India
| | - Monali C Rahalkar
- C2 Block, Room 83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India; Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Roldán DM, Carrizo D, Sánchez-García L, Menes RJ. Diversity and Effect of Increasing Temperature on the Activity of Methanotrophs in Sediments of Fildes Peninsula Freshwater Lakes, King George Island, Antarctica. Front Microbiol 2022; 13:822552. [PMID: 35369426 PMCID: PMC8969513 DOI: 10.3389/fmicb.2022.822552] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Global warming has a strong impact on polar regions. Particularly, the Antarctic Peninsula and nearby islands have experienced a marked warming trend in the past 50 years. Therefore, higher methane (CH4) emissions from this area could be expected in the future. Since mitigation of these emissions can be carried out by microbial oxidation, understanding this biological process is crucial since to our knowledge, no related studies have been performed in this area before. In this work, the aerobic CH4 oxidation potential of five freshwater lake sediments of Fildes Peninsula (King George Island, South Shetland Islands) was determined with values from 0.07 to 10 μmol CH4 gdw–1 day–1 and revealed up to 100-fold increase in temperature gradients (5, 10, 15, and 20°C). The structure and diversity of the bacterial community in the sediments were analyzed by next-generation sequencing (Illumina MiSeq) of 16S rRNA and pmoA genes. A total of 4,836 ASVs were identified being Proteobacteria, Actinobacteriota, Acidobacteriota, and Bacteroidota the most abundant phyla. The analysis of the pmoA gene identified 200 ASVs of methanotrophs, being Methylobacter Clade 2 (Type I, family Methylococcaceae) the main responsible of the aerobic CH4 oxidation. Moreover, both approaches revealed the presence of methanotrophs of the classes Gammaproteobacteria (families Methylococcaceae and Crenotrichaceae), Alphaproteobacteria (family Methylocystaceae), Verrucomicrobia (family Methylacidiphilaceae), and the candidate phylum of anaerobic methanotrophs Methylomirabilota. In addition, bacterial phospholipid fatty acids (PLFA) biomarkers were studied as a proxy for aerobic methane-oxidizing bacteria and confirmed these results. Methanotrophic bacterial diversity was significantly correlated with pH. In conclusion, our findings suggest that aerobic methanotrophs could mitigate in situ CH4 emissions in a future scenario with higher temperatures in this climate-sensitive area. This study provides new insights into the diversity of methanotrophs, as well as the influence of temperature on the CH4 oxidation potential in sediments of freshwater lakes in polar regions of the southern hemisphere.
Collapse
Affiliation(s)
- Diego M. Roldán
- Laboratorio de Ecología Microbiana Medioambiental, 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
| | - Daniel Carrizo
- Centro de Astrobiología, Consejo Superior de Investigaciones Científicas-Instituto Nacional de Técnica Aeroespacial (CSIC-INTA), Madrid, Spain
| | - Laura Sánchez-García
- Centro de Astrobiología, Consejo Superior de Investigaciones Científicas-Instituto Nacional de Técnica Aeroespacial (CSIC-INTA), Madrid, Spain
| | - Rodolfo Javier Menes
- Laboratorio de Ecología Microbiana Medioambiental, 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
- *Correspondence: Rodolfo Javier Menes,
| |
Collapse
|
5
|
Oren A, Garrity GM. CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35100104 DOI: 10.1099/ijsem.0.005186] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Isolation, Description and Genome Analysis of a Putative Novel Methylobacter Species (‘Ca. Methylobacter coli’) Isolated from the Faeces of a Blackbuck (Indian Antelope). MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12020035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Enteric fermentation of methane by ruminant animals represents a major source of anthropogenic methane. Significantly less information is available on the existence of methanotrophs in the gut of ruminants. Therefore, detailed strain descriptions of methanotrophs isolated from ruminant faeces or gut are rare. We present a first report on the enrichment and isolation of a methanotroph, strain BlB1, from the faeces of an Indian antelope (blackbuck). The 16S rRNA gene sequence of strain BlB1 showed the highest identity (98.40% identity) to Methylobacter marinus A45T and Methylobacter luteus NCIMB 11914T. Strain BlB1 showed coccoidal cells (1.5–2 µm in diameter), which formed chains or aggregates of 3–4 cells of light yellow-coloured colonies on agarose when incubated with methane in the gas phase. The draft genome of BlB1 (JADMKV01) is 4.87 Mbp in size, with a G + C content of 51.3%. The draft genome showed 27.4% digital DNA-DNA hybridization (DDH) and 83.07% average nucleotide identity (ANIb) values with that of its closest phylogenetic neighbour, Methylobacter marinus A45T. Due to the lower values of DDH and ANIb with the nearest species, and <98.7% 16S rRNA gene sequence identity, we propose that strain BlB1 belongs to a novel species of Methylobacter. However, as the culture has to be maintained live and resisted cryopreservation, deposition in culture collections was not possible and hence we propose a Candidatus species name, ‘Ca. Methylobacter coli’ BlB1. ‘Ca. Methylobacter coli’ BlB1 would be the first described methanotroph from ruminants worldwide, with a sequenced draft genome. This strain could be used as a model for studies concerning methane mitigation from ruminants.
Collapse
|
8
|
Hogendoorn C, Picone N, van Hout F, Vijverberg S, Poghosyan L, van Alen TA, Frank J, Pol A, Gagliano AL, Jetten MSM, D'Alessandro W, Quatrini P, Op den Camp HJM. Draft genome of a novel methanotrophic Methylobacter sp. from the volcanic soils of Pantelleria Island. Antonie van Leeuwenhoek 2021; 114:313-324. [PMID: 33566237 PMCID: PMC7902576 DOI: 10.1007/s10482-021-01525-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/22/2021] [Indexed: 11/27/2022]
Abstract
The genus Methylobacter is considered an important and often dominant group of aerobic methane-oxidizing bacteria in many oxic ecosystems, where members of this genus contribute to the reduction of CH4 emissions. Metagenomic studies of the upper oxic layers of geothermal soils of the Favara Grande, Pantelleria, Italy, revealed the presence of various methane-oxidizing bacteria, and resulted in a near complete metagenome assembled genome (MAG) of an aerobic methanotroph, which was classified as a Methylobacter species. In this study, the Methylobacter sp. B2 MAG was used to investigate its metabolic potential and phylogenetic affiliation. The MAG has a size of 4,086,539 bp, consists of 134 contigs and 3955 genes were found, of which 3902 were protein coding genes. All genes for CH4 oxidation to CO2 were detected, including pmoCAB encoding particulate methane monooxygenase (pMMO) and xoxF encoding a methanol dehydrogenase. No gene encoding a formaldehyde dehydrogenase was present and the formaldehyde to formate conversion follows the tetrahydromethanopterin (H4MPT) pathway. “Ca. Methylobacter favarea” B2 uses the Ribulose-Mono-Phosphate (RuMP) pathway for carbon fixation. Analysis of the MAG indicates that Na+/H+ antiporters and the urease system might be important in the maintenance of pH homeostasis of this strain to cope with acidic conditions. So far, thermoacidophilic Methylobacter species have not been isolated, however this study indicates that members of the genus Methylobacter can be found in distinct ecosystems and their presence is not restricted to freshwater or marine sediments.
Collapse
Affiliation(s)
- Carmen Hogendoorn
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Nunzia Picone
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Femke van Hout
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Sophie Vijverberg
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lianna Poghosyan
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Theo A van Alen
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jeroen Frank
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Antonia L Gagliano
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Palerma, Via U. La Malfa 153, 90146, Palermo, Italy
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Walter D'Alessandro
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Palerma, Via U. La Malfa 153, 90146, Palermo, Italy
| | - Paola Quatrini
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| |
Collapse
|
9
|
Zhu P, Cheng M, Pei D, Liu Y, Yan X. Methylomonas rhizoryzae sp. nov., a type I methanotroph isolated from the rhizosphere soil of rice. Antonie van Leeuwenhoek 2020; 113:2167-2176. [PMID: 33145620 DOI: 10.1007/s10482-020-01487-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
Abstract
A gammaproteobacterial methanotroph, strain GJ1T, was isolated from a rhizosphere soil sample of rice in Nanjing, China. The cells were Gram-negative, motile rods with a single polar flagellum, and they contained type I intracytoplasmic membranes. The cells formed pink colonies. The strain possessed both the particulate methane monooxygenase enzyme (pMMO) and the soluble methane monooxygenase enzyme (sMMO). pxmABC, encoding a divergent methane monooxygenase (pXMO), and nifH, which encodes dinitrogenase reductase, were also present. Methane and methanol were utilized as sole carbon sources, while other carbon sources, including acetate, pyruvate, succinate, citrate, malate, glucose, urea, methylamine, ethanol and formate, could not be utilized by strain GJ1T. Cell grew optimally at 25-33 °C (range 16-37 °C), pH 6.0-8.0 (range 5.5-8.5) and 0-1.2% NaCl (no growth above 1.5% NaCl). Phylogenetic analyses based on the 16S rRNA gene, pmoA and nifH showed that the isolate belongs to the genus Methylomonas of the family Methylococcaceae within the class Gammaproteobacteria. The major quinone was determined to be MQ-8, and the major fatty acids were observed to be C16:1 and C14:0. The genome size of strain GJ1T is about 4.55 Mb, and the DNA G + C content of the strain was determined to be 53.67 mol% within the range of the genus Methylomonas (47-58 mol%) reported at present. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain GJ1T and Methylomonas koyamae Fw12E-YT among the genus Methylomonas were the highest, and they were only 74.66% and 21.40%, respectively. In consequence, results of phenotypic characterization and phylogenetic analyses support strain GJ1T as a novel species within the genus Methylomonas, namely, Methylomonas rhizoryzae sp. nov.. The type strain is GJ1T (= ACCC 61706).
Collapse
Affiliation(s)
- Pingping Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Minggen Cheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Dongmei Pei
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yongchuang Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| |
Collapse
|
10
|
Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus. Microorganisms 2020; 8:microorganisms8050768. [PMID: 32443820 PMCID: PMC7285482 DOI: 10.3390/microorganisms8050768] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 01/21/2023] Open
Abstract
The Methylocystis and Methylosinus are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing methane fluxes from soils and wetlands. The original separation of these methanotrophs in two distinct genera was based mainly on their differences in cell morphology. Further comparative studies that explored various single-gene-based phylogenies suggested the monophyletic nature of each of these genera. Current availability of genome sequences from members of the Methylocystis/Methylosinus clade opens the possibility for in-depth comparison of the genomic potentials of these methanotrophs. Here, we report the finished genome sequence of Methylocystis heyeri H2T and compare it to 23 currently available genomes of Methylocystis and Methylosinus species. The phylogenomic analysis confirmed that members of these genera form two separate clades. The Methylocystis/Methylosinus pan-genome core comprised 1173 genes, with the accessory genome containing 4941 and 11,192 genes in the shell and the cloud, respectively. Major differences between the genome-encoded environmental traits of these methanotrophs include a variety of enzymes for methane oxidation and dinitrogen fixation as well as genomic determinants for cell motility and photosynthesis.
Collapse
|