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Methane oxidation by methanotrophs is a very important environmental process in the mitigation of methane. Methylobacter (Mtb.) clade 2 members have been reported as dominant methane oxidisers in soils and sediments worldwide. We enriched and purified a methanotroph from a tropical rice field soil sample from India. The highly enriched culture showed the presence of motile, long and thick rods (3-5 µm × 0.9-1.2 µm) and minor presence of short, thin rods. The culture was purified on agarose medium and formed yellow colonies which showed the presence of only thick and long rods, henceforth termed as strain KRF1. Based on 16S rRNA gene sequence analysis, strain KRF1 shows close phylogenetic affiliation to Methylobacter tundripaludum SV96 T (98.6% similarity). Due to the taxonomic novelty, and being the first member of Mtb. related to Mtb. tundripaludum from the tropics, the draft genome was sequenced. From the blastx analysis of the contigs, it was clear that the culture still had contamination of another organism, a Methylophilus species. The data binned in two clear bins: Mtb. related contigs and Methylophilus-related contigs. The binned draft genome of KRF1 shows features including the typical pathways for methane metabolism, denitrification and the presence of molybdenum iron and vanadium-iron nitrogenase genes. KRF1 is phylogenetically distinct from the five strains of Mtb. tundripaludum including SV96 T , Lake Washington strains and OWC strains, showing ~ 26% DDH and ~ 81% ANIb values and a unique position in a phylogenomic tree. Subsequently, KRF1 has been completely purified from its methylotrophic partner and a pure culture has been established and maintained in a WDCM approved culture collection, the MACS Collection of Microorganisms (as MCM 1471). KRF1 is thus the first cultured member of a putative novel species of Methylobacter clade 2 isolated from the tropics.

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.

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.

A total of 31 Acinetobacter isolates were obtained from the rhizosphere of Pennisetum glaucum and evaluated for their plant-growth-promoting traits. Two isolates, namely Acinetobacter sp. PUCM1007 and A. baumannii PUCM1029, produced indole acetic acid (10-13 microgram/ml). A total of 26 and 27 isolates solubilized phosphates and zinc oxide, respectively. Among the mineral-solubilizing strains, A. calcoaceticus PUCM1006 solubilized phosphate most efficiently (84 mg/ml), whereas zinc oxide was solubilized by A. calcoaceticus PUCM1025 at the highest solubilization efficiency of 918%. All the Acinetobacter isolates, except PUCM1010, produced siderophores. The highest siderophore production (85.0 siderophore units) was exhibited by A. calcoaceticus PUCM1016. Strains PUCM1001 and PUCM1019 (both A. calcoaceticus) and PUCM1022 (Acinetobacter sp.) produced both hydroxamate- and catechol-type siderophores, whereas all the other strains only produced catechol-type siderophores. In vitro inhibition of Fusarium oxysporum under iron-limited conditions was demonstrated by the siderophore-producing Acinetobacter strains, where PUCM1018 was the most potent inhibitor of the fungal phytopathogen. Acinetobacter sp. PUCM1022 significantly enhanced the shoot height, root length, and root dry weights of pearl millet seedlings in pot experiments when compared with controls, underscoring the plant-growth-promoting potential of these isolates.