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ABSTRACT: microbial diversity of cold seep sediment

PROVIDER: PRJNA724900 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR14320062_1.fastq.gz	Fastqsanger.gz
	SRR14320062_2.fastq.gz	Fastqsanger.gz
	SRR14320063_1.fastq.gz	Fastqsanger.gz
	SRR14320063_2.fastq.gz	Fastqsanger.gz
	SRR14320064.fastq.gz	Fastqsanger.gz

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Responses to different sulfur sources reveal the complicated and interlinked sulfur metabolism pathways of a deep-sea sulfate reducing bacterium

Project description:Sulfur metabolism in the deep-sea cold seep has been mentioned to have an important contribution to the biogeochemical cycle of sulfur in previous studies. And sulfate reducing bacteria have also been considered to be a dominant microbial population in the deep-sea cold seep and play a crucial role in this process. However, most of sulfate reducing bacteria from cold seep still cannot be purely cultured under laboratory conditions, therefore the actual sulfur metabolism pathways in sulfate reducing bacteria from the deep-sea cold seep have remained unclear. Here, we isolate and pure culture a typical sulfate reducing bacterium Desulfovibrio marinus CS1 from the sediment sample of the deep-sea cold seep in the South China Sea, which provides a probability to understand the sulfur metabolism in the cold seep.

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Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. Three groups of samples, A, B and C. Every group has 3 replicates.

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Project description:Zero-valent sulfur (ZVS) distributes widely in the deep-sea cold seep, which is important immediate in the active sulfur cycle of cold seep. In our preview work, a novel ZVS formation pathway discovered in the deep-sea cold weep bacterium Erythrobacter flavus 21-3 was described. However, whether this pathway worked and what function roles it played in the cold seep were unknown. In this study, E. flavus 21-3 was verified to produce zero-valent sulfur in the cold seep using genes soxB and tsdA as our preview report described. Based on proteomic data, stoichiometric methods and microscopic observation, this ZVS formation pathway benefited E. flavus 21-3 in the deep-sea cold seep. Notably, 30% metagenomes contained these two genes in the shallow sediments, which present the most abundant sulfur genes and active sulfur cycle in the cold seep sediments. It suggested that this sulfur formation pathway exist across many bacteria in the cold seep. This strongly indicates that this novel pathway might be frequently used by microbes and plays an important role in the biogeochemical sulfur cycle in cold seep.

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Study of microbial functional structure in Xiangjiang River sediment

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Thiosulfate oxidation in Erythrobacter flavus 21-3 provides novel clues to the source of element sulfur in the deep-sea cold seep

Project description:Zero-valent sulfur (ZVS) and thiosulfate are important intermediates in the biogeochemical cycle of sulfur. The former has been proved to be existed in the cold seep and hydrothermal systems. Three thiosulfate oxidation pathways are already identified and here we found a novel one in Erythrobacter, which was the first genus in the family Erythrobacteraceae that could accumulate ZVS during thiosulfate oxidation. Erythrobacter flavus 21-3 was isolated from the sediment of clod seep. Genomic analyses showed the typical genes encoding Sox multienzyme complex were absent in the genome of E. flavus 21-3. Through proteome and genome data, we identified a three gene involved pathway of thiosulfate oxidation, including thiosulfate dehydrogenase (tsdA), thiosulfohydrolase (soxB) and sulfur dioxygenases (sdo). For the first time, genetic operating system was constructed in Erythrobacter, and mutant strains ΔtsdA, ΔsoxB, ΔsdoA, ΔsdoB and ΔsdoAB were constructed. Stoichiometry was calculated and tetrathionate and ZVS were found to be the intermediates in this novel thiosulfate oxidation pathway. The diverse and distribution of these proteins were investigated and this novel thiosulfate oxidation pathway may exist in bacteria formerly ignored the function of ZVS production. The results give a powerful evidence for a new source of biogenetic ZVS in cold seep.

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