A Gram-positive, non-motile, rod-shaped bacterium strain NIO-1018T isolated from a mangrove sediment sample of the Chorao Island, Goa, India, was subjected to a detailed polyphasic taxonomic study. The strain designated as NIO-1018T matched with most of the phenotypic and chemotaxonomic properties of the genus Agromyces and represents a novel species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1018T fell within the cluster comprising species of the genus Agromyces, clustering with Agromyces soli (98.1 %), Agromyces flavus (97.9 %), Agromyces aurantiacus (97.7 %) and Agromyces ulmi (97.3 %). The predominant menaquinone was MK-12, and the major cellular fatty acids were anteiso-C15:0, iso-C16:0, anteiso-C17:0 and iso-C15:0. The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content of strain NIO-1018T was 71.8 mol%. The combination of phylogenetic analysis, DNA–DNA relatedness, phenotypic characteristics and chemotaxonomic data supported the view that strain NIO-1018T represents a novel species of the genus Agromyces, for which the name Agromyces indicus sp. nov. is proposed. The type strain is NIO-1018 (=JCM 17573T = CCTCC AB2011122T).
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Chen J, Chen HM, Zhang YQ, Wei YZ, Li QP, Liu HY, Su J, Zhang YQ, Yu LY (2011) Agromyces flavus sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 61:1705–1709
De Ley P, Cattoir H, Reeynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142
Dorofeeva LV, Krausova VI, Evtushenko LI, Tiedje JM (2003) Agromyces albus sp. nov., isolated from a plant (Androsace sp.). Int J Syst Evol Microbiol 53:1435–1438
Felsenstein J (1985) Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Gledhill WE, Casida LE (1969) Predominant catalase negative soil bacteria. III. Agromyces gen. nov., microorganisms intermediary to Actinomyces and Nocardia. Appl Microbiol 18:340–349
Hayakawa M, Nonomura H (1987) Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65:501–509
Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469
Jung SY, Lee SY, Oh TK, Yoon JH (2007) Agromyces allii sp. nov., isolated from the rhizosphere of Allium victorialis var. platyphyllum. Int J Syst Evol Microbiol 57:588–593
Jurado V, Groth I, Gonzalez JM, Laiz L, Saiz-Jimenez C (2005a) Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov. Int J Syst Evol Microbiol 55:153–157, 293
Jurado V, Groth I, Gonzalez JM, Laiz L, Saiz-Jimenez C (2005b) Agromyces subbeticus sp. nov., isolated from a cave in southern Spain. Int J Syst Evol Microbiol 55:1897–1901
Jurado V, Groth I, Gonzalez JM, Laiz L, Schuetze B, Saiz-Jimenez C (2005c) Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 55:871–875
Kelly KL (1964) Inter-Society Color Council–National Bureau of Standards color-name charts illustrated with centroid colors. US Government Printing Office, Washington
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163
Lanyi B (1987) Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67
Lee MJ, Ten LN, Woo SJ, Park JH (2011) Agromyces soli sp. nov., isolated from farm soil. Int J Syst Evol Microbiol 61:1286–1292
Li WJ, Zhang LP, Xu P, Cui XL, Xu LH, Zhang Z, Schumann P, Stackebrandt E, Jiang CL (2003) Agromyces aurantiacus sp. nov., isolated from a Chinese primeval forest. Int J Syst Evol Microbiol 53:303–307
Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China) and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57:1424–1428
MacKenzie SL (1987) Gas chromatographic analysis of amino acids as the N-heptafluoro butyryl isobutyl esters. J Assoc Off Anal Chem 70:151–160
Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
Ortiz-Martinez A, Gonzalez JM, Evtushenko LI, Jurado V, Laiz L, Groth I, Saiz-Jimenez C (2004) Reclassification of Agromyces fucosus subsp. hippuratus as Agromyces hippuratus sp. nov., comb. nov. and emended description of Agromyces fucosus. Int J Syst Evol Microbiol 54:1553–1556
Park EJ, Kim MS, Jung MJ, Roh SW, Chang HW, Shin KS, Bae JW (2010) Agromyces atrinae sp. nov., isolated from fermented seafood. Int J Syst Evol Microbiol 60:1056–1059
Rivas R, Trujillo ME, Mateos PF, Martínez-Molina E, Velázquez E (2004) Agromyces ulmi sp. nov., xylanolytic bacteria from Ulmus nigra in Spain. Int J Syst Evol Microbiol 54:1987–1990
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sasser M (1990) Identification of bacteria through fatty acid analysis. In: Klement Z, Rudolph K, Sands DC (eds) Methods in phytobacteriology. Akademiai Kaido, Budapest, pp 199–204
Schleifer KH (1985) Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156
Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477
Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340
Smibert RM, Krieg NR (1994) Phenotypic characterization methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC
Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species dentition in bacteriology. Int J Syst Bacteriol 44:846–849
Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231
Suzuki K, Sasaki J, Uramoto M, Nakase T, Komagata K (1996) Agromyces mediolanus sp. nov., nom. rev., comb. nov, a species for ‘Corynebacterium mediolanum’ Mamoli 1939 and for some aniline-assimilating bacteria which contain 2,4-diaminobutyric acid in the cell wall peptidoglycan. Int J Syst Bacteriol 46:88–93
Takeuchi M, Hatano K (2001) Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov. and Agromyces bracchium sp. nov., from the mangrove rhizosphere. Int J Syst Evol Microbiol 51:1529–1537
Thawai C, Tanasupawat S, Suwanborirux K, Kudo T (2011) Agromyces tropicus sp. nov., isolated from soil. Int J Syst Evol Microbiol 61:605–609
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The clustal × windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882
Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE (1987) International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464
Williams ST, Goodfellow M, Alderson G (1989) Genus Streptomyces waksman and henrici 1943. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams & Wilkins, Baltimore, pp 2452–2492
Yoon JH, Schumann P, Kang SJ, Park S, Oh TK (2008) Agromyces terreus sp. nov., isolated from soil. Int J Syst Evol Microbiol 58:1308–1312
Zgurskaya HI, Evtushenko LI, Akimov VN, Voyevoda HV, Dobrovolskaya TG, Lysak LV, Kalakoutskii LV (1992) Emended description of the genus Agromyces and description of Agromyces cerinus subsp. cerinus sp. nov., subsp. nov., Agromyces cerinus subsp. nitratus sp. nov., subsp. nov., Agromyces fucosus subsp. fucosus sp. nov., subsp. nov., and Agromyces fucosus subsp. hippuratus sp. nov., subsp. nov. Int J Syst Bacteriol 42:635–641
Zhang DC, Schumann P, Liu HC, Xin YH, Zhou YG, Schinner F, Margesin R (2010) Agromyces bauzanensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 60:2341–2345
Author thanks Dr. S. R. Shetye, Director, National Institute of Oceanography for facilities and encouragement. This work was supported from the grants under OLP0001 from the Council for Scientific and Industrial Research (CSIR), New Delhi. This is NIO contribution number 5162.
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Dastager, S.G., Qiang, ZL., Damare, S. et al. Agromyces indicus sp. nov., isolated from mangroves sediment in Chorao Island, Goa, India. Antonie van Leeuwenhoek 102, 345–352 (2012). https://doi.org/10.1007/s10482-012-9744-9
- Agromyces indicus sp. nov.
- 16S rRNA
- Mangrove sediment