Actinomadura sediminis sp. nov., a marine actinomycete isolated from mangrove sediment

Jie He, Ying Xu, Maloy Kumar Sahu, Xin-Peng Tian, Guo-Xing Nie, Qiong Xie, Si Zhang, Kannan Sivakumar, Wen-Jun Li

¹Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China

²Centre of Advanced Study in Marine Biology, Faculty of Marine Science, Annamalai University, Parangipettai 608 502, Tamilnadu, India

³CAS Key Laboratory of Marine Bio-Resources Sustainable Utilization, RNAM Center for Marine Microbiology, CAS Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China

⁴College of Life Science, Henan Normal University, Xinxiang 453007, PR China

⁵State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing 100094, PR China

⁶Key Laboratory of Biogeography and Bioresource in Arid Land, Xingjiang Institute of Ecology and Geography, Chinese Academy Of Sciences, Ürmqi 830011, PR China

Correspondence
Wen-Jun Li wjli{at}ynu.edu.cn Kannan Sivakumar oceanactino{at}gmail.com

International Journal of Systematic and Evolutionary Microbiology 2012; 62(Pt 5):1110–1116 · https://doi.org/10.1099/ijs.0.032979-0

Abstract

In this study, the taxonomic position of an actinobacterium, strain YIM M 10931^T, which was isolated from a mangrove sediment sample collected in Dugong Creek, Little Andaman, India, was determined by a polyphasic approach. This Gram-positive, aerobic strain produced branched substrate mycelium and aerial hyphae, which differentiated into short, hooked or spiral spore chains. The organism contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole cell sugars consisted of mannose, ribose, glucose, galactose and madurose. The cellular fatty acid profile mainly consisted of iso-C_16 : 0, 10-methyl C_18 : 0 and C_16 : 0. The quinone system was predominantly composed of MK-9(H₈) (45.5 %) and MK-9(H₆) (39 %). The phospholipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol and two unknown phospholipids. The organism showed a combination of morphological and chemotaxonomic properties typical of members of the genus Actinomadura. Moreover, phylogenetic analysis based on a 16S rRNA gene sequence generated from the strain identified its closest relatives as Actinomadura cremea DSM 43676^T (98.4 % sequence similarity), Actinomadura rifamycini DSM 43936^T (97.4 %) and Actinomadura apis IM17-1^T (96.9 %). It was obvious from the resulting phylogenetic trees that strain YIM M 10931^T belongs to a distinct subclade within the evolutionary radiation of the genus Actinomadura. DNA–DNA hybridizations of strain YIM M 10931^T with A. cremea DSM 43676^T and A. rifamycini DSM 43936^T were performed and further confirmed that the isolate represents a separate genomic species. Based on the phenotypic and genotypic characteristics presented, it is proposed that strain YIM M 10931^T represents a novel species within the genus Actinomadura, for which the name Actinomadura sediminis sp. nov. is proposed; the type strain is YIM M 10931^T ( = CCTCC AA 2010009^T = DSM 45500^T).