Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea

Abstract

Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea. Overall, high-throughput sequencing of the dsrB and soxB genes achieved almost complete coverage (>99%) and revealed the high diversity, richness, and operational taxonomic unit (OTU) numbers of the SRB and SOB communities, which suggest the existence of an active sulfur cycle in the study area. Further analysis demonstrated that rare species make vital contributions to the high richness, diversity, and OTU numbers obtained. Depth-based distributions of the dsrB, soxB, and 16S rRNA gene abundances indicated that the SRB abundance might be more sensitive to the sedimentary dynamic environment than those of total bacteria and SOB. In addition, the results of unweighted pair group method with arithmetic mean (UPGMA) clustering analysis and redundancy analysis revealed that environmental parameters, such as depth and dissolved inorganic nitrogen concentrations, and the sedimentary dynamic environment, which differed between the two sampling stations, can significantly influence the community structures of total bacteria, SRB, and SOB. This study provided further comprehensive information regarding the characteristics of SRB and SOB communities.

Analysis of viral and bacterial communities in groundwater associated with contaminated land

“…Sulfur oxidizers were abundant at the site. These include Halothiobacillaceae (Táncsics et al, 2018), Hydrogenophilaceae (Táncsics et al, 2018), Rhodocyclaceae (Táncsics et al, 2018), Helicobacteraceae (Ihara et al, 2017) and Spirochaetaceae (Zhang et al, 2017). Halothiobacillaceae was abundant at the C1 sampling station (0.56-4.21%) and Spirochaetaceae was most abundant in C3 bacterial communities.…”

Microbial Communities and Sulfate-Reducing Microorganisms Abundance and Diversity in Municipal Anaerobic Sewage Sludge Digesters from a Wastewater Treatment Plant (Marrakech, Morocco)

“…Desulfomicrobium and Desulfovibrio was widely discovered in natural environments and anaerobic reactors, which degraded lactic into acetate [95][96][97]. The Desulfobacteraceae and Desulfurellaceae OTUs found in anaerobic digesters were considered as key players in the carbon-and sulfur-cycling in organic carbon-and sulfate-rich reduction [98]. Their potential in treating industrial waste and drainage has been investigated under various settings [13].…”

Impacts of Human Activities on the Composition and Abundance of Sulfate-Reducing and Sulfur-Oxidizing Microorganisms in Polluted River Sediments

“…Both SRM and SOM differ in abundance and diversity among environments and are substantially influenced by environmental factors, such as temperature, organic matter, sulfides, geochemical gradients, and sampling depth (Varon-Lopez et al, 2014; Robador et al, 2016; Edwardson and Hollibaugh, 2017; Meier et al, 2017; Zhang M.J. et al, 2017; Zhang Y. et al, 2017). Generally, SRM are dominated by Deltaproteobacteria and Firmicutes (Haller et al, 2011; Mueller et al, 2015; Robador et al, 2016; Zhang Y. et al, 2017), while Gammaproteobacteria and Epsilonproteobacteria are considered dominant SOM on aquatic sediment surfaces (Lenk et al, 2012; Meier et al, 2017). However, some genera (e.g., Desulfitobacterium and Desulfitibacter in Firmicutes and Pyrobaculum in Archaea) of SRM have functional genes for sulfate reduction but cannot use sulfate as a terminal electron acceptor (Mueller et al, 2015; Edwardson and Hollibaugh, 2017).…”

“…Various molecular methods have been used to characterize the community diversity and structure of SRM and SOM based on functional gene markers (Varon-Lopez et al, 2014; Angermeyer et al, 2016; Tian et al, 2017; Zhang Y. et al, 2017). However, traditional molecular methods are limited for characterizing diverse SRM and SOM communities for the following reasons: (i) incomplete databases of functional genes; (ii) low-throughput analysis and lack of complete cover the complex microbial community; and (iii) low amplification efficiency (Varon-Lopez et al, 2014; Angermeyer et al, 2016; Zhang Y. et al, 2017). High-throughput sequencing constitutes a powerful approach for achieving complete coverage of microbial communities (Zhou et al, 2011; Zhang Y. et al, 2017).…”

“…However, traditional molecular methods are limited for characterizing diverse SRM and SOM communities for the following reasons: (i) incomplete databases of functional genes; (ii) low-throughput analysis and lack of complete cover the complex microbial community; and (iii) low amplification efficiency (Varon-Lopez et al, 2014; Angermeyer et al, 2016; Zhang Y. et al, 2017). High-throughput sequencing constitutes a powerful approach for achieving complete coverage of microbial communities (Zhou et al, 2011; Zhang Y. et al, 2017). The community structure and diversity of SRM and SOM have been effectively evaluated by the high-throughput sequencing of 16S rRNA (Haller et al, 2011; Hausmann et al, 2016; Robador et al, 2016; Edwardson and Hollibaugh, 2017; Meier et al, 2017; Tian et al, 2017).…”