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Phylogenetic Study of Methanol Oxidizers from Chilika-Lake Sediments Using Genomic and Metagenomic Approaches

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Abstract

Group-wise diversity of sediment methylotrophs of Chilika lake (Lat. 19°28′–19°54′N; Long. 85°06′–85°35′E) Odisha, India at various identified sites was studied. Both the culturable and unculturable (metagenome) methylotrophs were investigated in the lake sediments employing both mxaF and 16S rRNA genes as markers. ARDRA profiling, 16S rRNA gene sequencing, PAGE profiling of HaeIII, EcoRI restricted mxaF gene and the mxaF gene sequences using culture-dependent approach revealed the relatedness of α-proteobacteria and Methylobacterium, Hyphomicrobium and Ancyclobacter sp. The total viable counts of the culturable aerobic methylotrophs were relatively higher in sediments near the sea mouth (S3; Panaspada), also demonstrated relatively high salinity (0.1 M NaCl) tolerance. Metagenomic DNA from the sediments, amplified using GC clamp mxaF primers and resolved through DGGE, revealed the diversity within the unculturable methylotrophic bacterium Methylobacterium organophilum, Ancyclobacter aquaticus, Burkholderiales and Hyphomicrobium sp. Culture-independent analyses revealed that up to 90 % of the methylotrophs were unculturable. The study enhances the general understandings of the metagenomic methylotrophs from such a special ecological niche.

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Acknowledgments

The authors are thankful to the ICAR (Indian Council of Agricultural Research), India for providing the financial and research support. The authors also would like to acknowledge their respective institutional Directors.

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  1. Kamlesh K. Meena

    Present address: National Institute of Abiotic Stress Management, Malegaon, Baramati, Pune, Maharashtra, India

Authors and Affiliations

  1. National Bureau of Agriculturally Important Microorganisms, Mau Nath Bhanjan, 275 101, UP, India

    Kamlesh K. Meena & Manish Kumar

  2. School of Biotechnology, KIIT University, Campus-11, Bhubaneswar, 751024, Odisha, India

    Snehasish Mishra & Sanjay Kumar Ojha

  3. National Institute of Abiotic Stress Management, Baramati, Pune, 413115, Maharashtra, India

    Goraksha C. Wakchaure & Biplab Sarkar

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  1. Kamlesh K. Meena
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Correspondence to Kamlesh K. Meena.

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The authors Kamlesh Kumar Meena, Snehasish Mishra and Manish Kumar should be regarded as the joint first authors.

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Meena, K.K., Kumar, M., Mishra, S. et al. Phylogenetic Study of Methanol Oxidizers from Chilika-Lake Sediments Using Genomic and Metagenomic Approaches. Indian J Microbiol 55, 151–162 (2015). https://doi.org/10.1007/s12088-015-0510-3

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