Bacterial diversity in deep-sea sediment from northeastern Pacific Ocean

The development of culture-independent technique using nucleic acids has led to many new findings in studies of microbial ecology.The 16S rDNA sequencing method is one of the effectively used culture-independent techniques in recent years.In this study,16S rDNA sequencing method was used to investigate the bacterial diversity in deep-sea sediment from Northeast Pacific polymetallic nodule province(145.3968 W,8.3751 N,water depth of 5307m).Sediment samples were collected by a TV-multicorer and total DNA was extracted using two different methods(chemical method and DNA extracting kit method).After purification genomic DNA was amplified using the universal primers(27F and 1492R).PCR products(1.5kb) were recovered and cloned into pMD18-T vector(TaKaRa).Clones were randomly selected and sequenced.After the sequences were checked using the Chimera Check program of the RDP database,a bacterial 16S rDNA gene library of 79 clones was established.Phylogenetic analysis using Mega3.1 indicated that 79 clones can be divided into 11 phylotypes.Gamma proteobacteria(22.8%) and Alpha proteobacteria(16.5%) were the dominant components of the sediment bacterial community,followed by Planctomycetacia(7.6%),Delta proteobacteria(6.3%),Nitrospira(6.3%),Actinobacteria(6.3%),Beta proteobacteria(5%),Acidobacteria(5.1%),Sphingobacteria(3.8%),Firmicutes(2.5%) and Other bacteria(17.7%).Gamma proteobacteria also dominated at layer 0-2cm and 4-6cm.Different layers had different types of bacteria,but Alpha proteobacteria,Gamma proteobacteria,Delta proteobacteria,Planctomycetacia,Nitrospira,Actinobacteria and Acidobacteria appeared in all layers.Pseudomonas is common in many different deep-sea environments.In this study,it accounted for 22.2% of total Gamma proteobacteria.