Cultivation of Important Methanotrophs From Indian Rice Fields
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 cultu...
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| Format: | Article |
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Frontiers Media S.A.
2021-09-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.669244/full |
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| author | Monali C. Rahalkar Monali C. Rahalkar Kumal Khatri Kumal Khatri Pranitha Pandit Pranitha Pandit Rahul A. Bahulikar Jyoti A. Mohite Jyoti A. Mohite |
| author_facet | Monali C. Rahalkar Monali C. Rahalkar Kumal Khatri Kumal Khatri Pranitha Pandit Pranitha Pandit Rahul A. Bahulikar Jyoti A. Mohite Jyoti A. Mohite |
| author_sort | Monali C. Rahalkar |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-17T12:13:45Z |
| format | Article |
| id | doaj.art-2b81c099cf744c35a3f809d632b774c2 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-17T12:13:45Z |
| publishDate | 2021-09-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-2b81c099cf744c35a3f809d632b774c22022-12-21T21:49:16ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-09-011210.3389/fmicb.2021.669244669244Cultivation of Important Methanotrophs From Indian Rice FieldsMonali C. Rahalkar0Monali C. Rahalkar1Kumal Khatri2Kumal Khatri3Pranitha Pandit4Pranitha Pandit5Rahul A. Bahulikar6Jyoti A. Mohite7Jyoti A. Mohite8C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, IndiaDepartment of Microbiology, Savitribai Phule Pune University, Pune, IndiaC2, Bioenergy Group, MACS Agharkar Research Institute, Pune, IndiaDepartment of Microbiology, Savitribai Phule Pune University, Pune, IndiaC2, Bioenergy Group, MACS Agharkar Research Institute, Pune, IndiaDepartment of Microbiology, Savitribai Phule Pune University, Pune, IndiaCentral Research Station, BAIF Development Research Foundation, Pune, IndiaC2, Bioenergy Group, MACS Agharkar Research Institute, Pune, IndiaDepartment of Microbiology, Savitribai Phule Pune University, Pune, IndiaMethanotrophs 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.https://www.frontiersin.org/articles/10.3389/fmicb.2021.669244/fullmethanenovelIndiarice fieldscultivationmetagenomics |
| spellingShingle | Monali C. Rahalkar Monali C. Rahalkar Kumal Khatri Kumal Khatri Pranitha Pandit Pranitha Pandit Rahul A. Bahulikar Jyoti A. Mohite Jyoti A. Mohite Cultivation of Important Methanotrophs From Indian Rice Fields Frontiers in Microbiology methane novel India rice fields cultivation metagenomics |
| title | Cultivation of Important Methanotrophs From Indian Rice Fields |
| title_full | Cultivation of Important Methanotrophs From Indian Rice Fields |
| title_fullStr | Cultivation of Important Methanotrophs From Indian Rice Fields |
| title_full_unstemmed | Cultivation of Important Methanotrophs From Indian Rice Fields |
| title_short | Cultivation of Important Methanotrophs From Indian Rice Fields |
| title_sort | cultivation of important methanotrophs from indian rice fields |
| topic | methane novel India rice fields cultivation metagenomics |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.669244/full |
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