Actinobacterial Diversity In The South China Sea Sediments And Identification Of A Novel Actinomycet Species

The South China Sea is the largest sea in the four major seas of China with thedeepest depth and abundant of natural bioresources. However, we know little aboutthe actinbacterial diversity in the special marine ecosystem. So the actinobacterialdiversity analysis is very necessary and will be of agreat significance for the isolationof actinomycetes strains and the further exploitation of the novel medicinal microbialresources.The diversity of actinomycetes in abyssal sea sediments of the South ChinaSea was studied by culture-independent approach. The antinobacterial16S rDNAclone libraries of the two samples N40-4and site N63-4which were collected from3235m and4242m depth were built and analyzed. The two samples showed highgenetic diversities, which both contained Actinomycetes, Acidimicrobiia,Nitriliruptoria and Thermoleophilia four classes. The dominant populations of siteN40-4were the order Nitriliruptorales and Streptomycetales, the dominantpopulations of site N63-4were Nitriliruptorales and Acidimicrobiales. The populationstructures of the two sites are different, and both of them are also different from thepopulation structures of terrestrial actinomycetes. The N-J phylogenetic tree showedthat many sequences of those two sites formed independent branches and had a longgenetic distance with known species sequences. It indicate that the sediments of theSouth China Sea harbor a lot of resources of new species, the species and communitystructure of actinomycetes are abundant and diverse.7media were used to the isolate actinomycetes strains from18sedimentssamples and41strains were obtained. According to the morphological characteristicscomparition,19strains were selected to sequence the16S rDNA. Sequence analysisand blast the results in the EzBioCloud data showed that these strains belong to12different species.14strains were originated from the abyssal sea, which indicate the abundant and huge resources diversity of the sediments in the South China Sea. Themaximum homology identity of the OAct400strain with the known type strain is97.73%， which means it is a potential novel species. The maximum homologyidentity of the OAct415strain with the known type strain is98.96%，which means itcould be a novel sub-species, however, the physiologic and biochemical index and thechemical identification index need to be determined to confirm these strains. TheNeighbor-Joining phylogenetic tree was constructed from the alignments of thesequences between all these strains and maximum homology strains, which showedthat Strrptomyces was only a small and independent branch, which illustrated thatStrrptomyces was not the dominant population. Actinobacterial population structuresof the sediments in the South China Sea is different from which of the terrestrialenvironment. The actinobacterial diversity is abundant and massive new speicesresources are contained.A Gram-staining-positive, non-endospore-forming, dirty white-coloured strain,strain OAct400was isolated from a sediment sample collected at site N42-5with thedepths of2093m in the South China Sea, China. Phylogenetic analysis based on16SrDNA gene sequences showed strain OAct400was most closely related to membersof established species in the genus Microbacterium with sequence similarities ofapproximately94.%–97.73%, particularly Microbacterium amylolyticum N5T(97.73%), Microbacterium gubbeenense LMG19263T(97.44%) and Microbacteriumgubbeenense CIPT(97.43%). DNA–DNA hybridization studies showed none of theDNA–DNA relatedness values between strain OAct400and members of the genusMicrobacterium exceeded40%. The genomic DNA G+C content of the novel strainwas68mol%. The chemotaxonomic characteristics of strain OAct400, which hadMK-12and MK-11as its major menaquinones and anteiso-C15:0, anteiso-C16:0,anteiso-C17:0and iso-C16:0as its predominant fatty acid were consistent withclassification in the genus Microbacterium. Peptidoglycan in the novel straincontained alanine, glycine and glutamic acid. The polar lipid profile of strainOAct400comprised diphosphatidyl glycerol, phosphatidyly glycerol, phosphatidylyethanolamine and an unknown glycolipid. The novel strain’s major cell-wall sugars were arabinose, glucose and galactose. Based on the phylogenetic, DNA–DNAhybridization, chemotaxonomic and phenotypic data, strain OAct400represents anovel species within the genus Microbacterium for which the name Microbacteriumnanhaiensis sp.nov. is proposed; the type strain is OAct400~T(=DSM26811~T=KCTC29185~T).