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Molecular and culture dependent characterization of endolithic bacteria in two beach sand samples and description of Rhizobium endolithicum sp. nov.

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Abstract

Endolithic metagenome analysis of two beach samples collected form Chilika, Odisha, India indicated rich bacterial diversity. While the metagenome analysis of sample one yielded 16S rRNA gene sequences which represent six phyla and 16 genera, sample two yielded very rich diversity representing 17 phyla and 286 genera. Six species of bacteria were isolated from the endolithic enrichments and most of them have 16S rRNA gene sequence similarity of >99 % with known taxa, except for strain JC140T having <97 % sequence similarity with taxa with valid names. Strain JC140T is Gram-stain-negative and motile. 16S rRNA gene based EzTaxon-e BLAST analysis indicated that strain JC140T is closely related with the type strains of Rhizobium yanglingense SH22623T (96.8 %), R. alkalisoli CCBAU 01393T (96.3 %), R. vignae CCBAU 05176T (96.2 %), R. mesosinicum CCBAU 25010T (96.1 %) and other members of the genus Rhizobium with <96 % sequence similarity. Strain JC140T was characterized based on polyphasic taxonomic analysis. Strain JC140T could tolerate up to 5 % salinity, resistant to rifampicin (10 μg) and was positive for catalase and oxidase. The major fatty acid is summed feature 8 (C18:1ω7c/C18:1ω6c) with minor amounts of C19:0 cycloω8c, C16:0, C18:0, C17:0cyclo, summed feature 2 (C14:03OH/C16:1 isoI), summed feature 3 (C16:1ω7c/C16:1ω6c) and 2-hydroxyacid of C15:0. Diphosphatidylglycerol, phosphatidylethanol-amine, phosphatidylcholine, phosphatidylglycerol, unidentified lipids (L1, 2), unidentified phospholipid (PL1–4) constitute the polar lipids of strain JC140T. The strain has bacteriohopane derivative (BHD2), diplopterol and two unidentified hopanes (UH1, 2) as major hopanoids. Q-10 is the major quinone of strain JC140T. Based on polyphasic taxonomic analysis, strain JC140T represents a species in the genus Rhizobium for which, the name R. endolithicum sp. nov. is proposed. The type strain is JC140T (= KCTC32077T = CCUG64352T = MTCC11723T = HAMBI 2447T).

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Acknowledgments

MoES government of India is acknowledged for financial support. We thank Prof. J. Euzéby for his expert suggestion for correct species epithet and Latin etymology. We gratefully acknowledge LMG, Belgium for providing with the type strain of Rhizobium yanglingense LMG 19592T (= SH 22623T) as gratis and HAMBI, Finland for providing Rhizobium vignae HAMBI 3093T (= CCBAU 05176T) and Rhizobium alkalisoli HAMBI 3051T(= CCBAU 01393T) in exchange.

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Authors and Affiliations

  1. Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India

    B. Parag & Ch. V. Ramana

  2. Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad, 500 085, India

    Ch. Sasikala

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  1. B. Parag
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  2. Ch. Sasikala
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  3. Ch. V. Ramana
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Correspondence to Ch. V. Ramana.

Additional information

EMBL accession number for 16S rRNA and thrC gene sequences of strain JC140T are HE818072 and HG329718.

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Parag, B., Sasikala, C. & Ramana, C.V. Molecular and culture dependent characterization of endolithic bacteria in two beach sand samples and description of Rhizobium endolithicum sp. nov.. Antonie van Leeuwenhoek 104, 1235–1244 (2013). https://doi.org/10.1007/s10482-013-0046-7

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