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Abstract
Shotgun metagenome sequencing provides the opportunity to recover underexplored rare populations and identify difficult-to-elucidate biochemical pathways. However, information on sulfur genes, including their sequences, is scattered in public databases. Here, we introduce SMDB (https://smdb.gxu.edu.cn/)—a manually curated database of sulfur genes based on an in-depth review of the scientific literature and orthology database. The SMDB contained a total of 175 genes and covered 11 sulfur metabolism processes with 395,737 representative sequences affiliated with 110 phyla and 2340 genera of bacteria/archaea. The SMDB was applied to characterize the sulfur cycle from five habitats and compared the microbial diversity of mangrove sediments with that of other habitats. The structure and composition of microorganism communities and sulfur genes were significantly different among the five habitats. Our results show that microorganism alpha diversity in mangrove sediments was significantly higher than in other habitats. Genes involved in dissimilatory sulfate reduction were abundant in subtropical marine mangroves and deep-sea sediments. The neutral community model results showed that microbial dispersal was higher in the marine mangrove ecosystem than in others habitats. The Flavilitoribacter of sulfur-metabolizing microorganism becomes a reliable biomarker in the five habitats. SMDB will assist researchers to analyze genes of sulfur cycle from the metagenomic efficiently.
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1 Guangxi Academy of Sciences, National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Nanning, China (GRID:grid.418329.5) (ISNI:0000 0004 1774 8517); Guangxi University, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Nanning, China (GRID:grid.256609.e) (ISNI:0000 0001 2254 5798)
2 Guangxi Academy of Sciences, National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Nanning, China (GRID:grid.418329.5) (ISNI:0000 0004 1774 8517); Guangxi Academy of Sciences, Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai, China (GRID:grid.418329.5) (ISNI:0000 0004 1774 8517)
3 Guangxi Academy of Sciences, Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai, China (GRID:grid.418329.5) (ISNI:0000 0004 1774 8517)
4 Guangxi University, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Nanning, China (GRID:grid.256609.e) (ISNI:0000 0001 2254 5798)
5 Beibu Gulf University, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, China (GRID:grid.508037.9) (ISNI:0000 0004 8002 2532)
6 Nanning Normal University, Guangxi Key Lab of Human-Machine Interaction and Intelligent Decision, Nanning, China (GRID:grid.411856.f) (ISNI:0000 0004 1800 2274); Soochow University, State Key Laboratory of Radiation Medicine and Protection, Suzhou, China (GRID:grid.263761.7) (ISNI:0000 0001 0198 0694)
7 Guangxi Academy of Sciences, National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Nanning, China (GRID:grid.418329.5) (ISNI:0000 0004 1774 8517); Guangxi University, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Nanning, China (GRID:grid.256609.e) (ISNI:0000 0001 2254 5798); Beibu Gulf University, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, China (GRID:grid.508037.9) (ISNI:0000 0004 8002 2532)