title: Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches.
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.
authors.affiliation: MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
authors.forename: Pranitha S
authors.initials: PS
authors.lastname: Pandit
authors.affiliation: MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India. monalirahalkar@aripune.org.
authors.forename: Monali C
authors.identifier: http://orcid.org/0000-0003-0945-4378
authors.initials: MC
authors.lastname: Rahalkar
authors.affiliation: MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
authors.forename: Prashant K
authors.initials: PK
authors.lastname: Dhakephalkar
authors.affiliation: 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.
authors.forename: Dilip R
authors.initials: DR
authors.lastname: Ranade
authors.affiliation: MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
authors.forename: Soham
authors.initials: S
authors.lastname: Pore
authors.affiliation: MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
authors.forename: Preeti
authors.initials: P
authors.lastname: Arora
authors.affiliation: MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
authors.forename: Neelam
authors.initials: N
authors.lastname: Kapse
mesh_terms: D001419:Bacteria / Q000145:classification / Q000254:growth & development / Q000302:isolation & purification* / Q000378:metabolism*; D007194:India; D008697:Methane / Q000378:metabolism*; D012275:Oryza / Q000254:growth & development / Q000382:microbiology*; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology; D058441:Rhizosphere; D012988:Soil Microbiology
chemical_list: D008697:Methane
keywords: Indian rice fields; Metagenome; Methanotrophs