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Bacterial community in deep subseafloor sediments from the western Pacific "warm pool"

science china Earth sciences 2008年第4期51卷 618-624页

作者： zhao jing1 & zeng runying2 1 college of oceanography and environmental science, xiamen university, xiamen 361005, china 2 Key Laboratory of Marine Biogenetic Resources, Third Institute of oceanography, State Oceanic Administration, xiamen 361005, china college of oceanography and environmental science Xiamen University Xiamen China Key Laboratory of Marine Biogenetic Resources Third Institute of Oceanography State Oceanic Administration Xiamen China

The bacterial community in deep subseafloor sediments at a depth of 230 cm from the western Pacific "warm pool" is studied by construction of 16S rDNA clone library and PCR-RFLP (Restriction Fragment Length Polymorphism) analysis. The results indicate that the bacterial community in these sediments is mainly composed of five groups: α-Proteobacteria, β-Proteobacteria, CFB group (Cytophaga / Flexi-bacteria / Bacteroides), Acidobacteria and gram positive bacteria, with a few genera detected in each group. The most abundant bacteria group is α-Proteobacteria, and the next is β-Proteobacteria. The dominant species in α-and β-Proteobacteria are Sphingomonas paucimobilis and Pseudomonas alca-ligenes respectively. The CFB group is simply composed of members belonging to Flavobacterium. The gram positive bacteria are rich, and mainly consists of the genus Geobacillus. The analysis of bacterial community indicates that organic matter is still abundant in the subseafloor sediments at the depth of 230 cm in the western Pacific "warm pool" . These bacteria in this deep biosphere may play an impor-tant role in the nitrogen cycle of deep sea sediments at "warm pool" .

关键词： western Pacific 'warm pool' deep subseafloor sediment bacterial community

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Phylogenetic diversity of TypeⅠpolyketide synthase genes from sediments of Ardley Island in Antarctica

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Acta Oceanologica Sinica 2011年第6期30卷 104-111页

作者： zhao jing YANG Ning CHEN Xinglin JIANG Qingru zeng runying Department of Marine Technology and Ocean Engineering College of Oceanography and Environmental Science Xiamen University Xiamen 361005 China Key Laboratory of Marine Biogenetic Resources Third Institute of Oceanography State Oceanic Administration Xiamen 361005 China

The diversity of modular polyketide synthase （PKS） genes in sediments of Ardley Island in Antarctica, was studied by restriction fragment length polymorphism （RFLP） analysis. Phylogenetic analysis of 14 amino acid （AA） sequences indicates that the identified ketosynthase （KS） domains were clustered with those from diverse bacterial groups, including Cyanobacteria, γ-Proteobacteria, Actinobacteria, Firmicutes, and some unidentified microorganisms from marine sponge, bryozoan and other environmental samples. The obtained KS domains showed 43%–81% similarity at the AA level to reference sequences in GenBank. Six identified KS domains showed diverse sequences of the motif （VQTACSTS） that was used to identify the hybrid PKS/nonribosomal peptide synthetase （NRPS） enzyme complex, and formed a new branch. These results reveal a high diversity and novelty of PKS genes in antarctic sediments.

关键词： polyketide synthase diversity Antarctica

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Coextraction of microbial metagenomic DNA and RNA from deep-sea sediment

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Acta Oceanologica Sinica 2007年第6期26卷 150-157页

作者： zhao jing YANG Xiangsheng zeng runying college of oceanography and environmental science Xiamen University Xiamen 361005 China School of Life sciences Xiamen University Xiamen 361005 China Key Laboratory of Marine Biogenetic Resources Third Institute of Oceanography State Oceanic Administration Xiamen 361005 China

A protocol to coextract the microbial metagenomic DNA and RNA from deep-sea sediment was developed for the microbiological study of environmental samples. The obtained pure metagenomic DNA with the size larger than 23 kb and stable RNA could be used directly for PCR and reverse transcription - PCR （ RT - PCR） respectively. The direct lysis including the treatments of SDS, proteinase and lysozyme was applied to acquiring the metagenomic DNA and RNA furthest. Prior to the lysis treatment, the glass bead and denaturing solution were added to enhance the lysis efficiency and keep the integrity of RNA respectively. Denaturing gradient gel electrophoresis （DGGE） was applied in accessing the microbial 16S rRNA diversity by PCR and RT -PCR amplification from a single extraction. The pattern obtained by this analysis revealed some differences between them, indicating the efficiency of the protocol in extracting the metagenomic DNA and total RNA from deep-sea sediment.

关键词： deep-sea sediment metagenomic DNA total RNA coextraction

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