Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags

Abstract

b Sediment, a special realm in aquatic environments, has high microbial diversity. While there are numerous reports about the microbial community in marine sediment, freshwater and intertidal sediment communities have been overlooked. The present study determined millions of Illumina reads for a comparison of bacterial communities in freshwater, intertidal wetland, and marine sediments along Pearl River, China, using a technically consistent approach. Our results show that both taxon richness and evenness were the highest in freshwater sediment, medium in intertidal sediment, and lowest in marine sediment. The high number of sequences allowed the determination of a wide variety of bacterial lineages in all sediments for reliable statistical analyses. Principal component analysis showed that the three types of communities could be well separated from phylum to operational taxonomy unit (OTU) levels, and the OTUs from abundant to rare showed satisfactory resolutions. Statistical analysis (LEfSe) demonstrated that the freshwater sediment was enriched with Acidobacteria, Nitrospira, Verrucomicrobia, Alphaproteobacteria, and Betaproteobacteria. The intertidal sediment had a unique community with diverse primary producers (such as Chloroflexi, Bacillariophyta, Gammaproteobacteria, and Epsilonproteobacteria) as well as saprophytic microbes (such as Actinomycetales, Bacteroidetes, and Firmicutes). The marine sediment had a higher abundance of Gammaproteobacteria and Deltaproteobacteria, which were mainly involved in sulfate reduction in anaerobic conditions. These results are helpful for a systematic understanding of bacterial communities in natural sediment environments.

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

“…These phyla have been always identified as dominant groups in sediment environments and were generally important contributors to biogeochemical processes (Durbin and Teske 2011;Wang et al 2012). Proteobacteria were dominant in most surface marine sediments, comprising >50 % of the microbial biomass (Bowman and McCuaig 2003), and it seems that γ-Proteobacteria was the most significant clade in marine sediments (Feng et al 2009;Wang et al 2012). Global distribution might be an important ecological characteristic of these marine bacteria groups, and many corresponding clusters included might have flexible adaptation to the various marine sediment environments.…”

“…Advances in sequencing technology are expanding our view of the microbial communities in unprecedented ways. New highthroughput pyrosequencing methods are increasing dramatically the number of sequences, allowing deeper coverage and improving our statistical power as well (Wang et al 2012;Hu et al 2013). A combination of more advanced methods may provide a comprehensive and complementary view in understanding of the marine sediment bacteria community.…”

Geographical variation in soil bacterial community structure in tropical forests in Southeast Asia and temperate forests in Japan based on pyrosequencing analysis of 16S rRNA

“…The present study shows that Acidobacteria and Proteobacteria are also predominant in the soil of tropical forests in Indonesia (Java and Sumatra) and Singapore in Southeast Asia. Acidobacteria and Proteobacteria are Gram-negative bacteria represented by many species that grow and survive under many environmental conditions (Stackebrandt et al, 1988;Quaiser et al, 2003); however, Acidobacteria are found primarily in soil (Sogins et al, 2006), while Proteobacteria are found in soil (Barns et al, 1999;Zinger et al, 2011;Wang et al, 2012), fresh water (Hugenholtz et al, 1998) and seawater (Hugenholtz et al, 1998;Venter et al, 2004;Zinger et al, 2011). In BKOman, an exceptional phylum composition was observed, characterized by high representation of Proteobacteria (≈40%) and low representation of Acidobacteria (4%).…”

The 16S rRNA gene in the study of marine microbial communities

“…Esto posiblemente sea influenciado por los nutrientes, las condiciones ambientales y la heterogeneidad del sustrato que se presentan en el bentos, lo que favorece las altas tasas de recambio de las poblaciones (Ramette et al 2009, Miller et al 2013, Gobet et al 2014. Las comunidades microbianas bentónicas son las responsables de los procesos de nitrificación y oxidación anaeróbica de amonio (Prabavathi y Mathivanan 2012, Wang et al 2012, Laverock et al 2014, Lipsewers et al 2014, Vigneron et al 2014, Bowen et al 2015, lo que permite la reutilización del nitrógeno orgánico.…”

“…These communities are very dynamic and the most diverse of the marine communities, most likely because of the high rates of population exchange promoted by the nutrients, environmental conditions, and substrate heterogeneity in the benthic zone (Ramette et al 2009, Miller et al 2013, Gobet et al 2014. They are capable of nitrification and anaerobic ammonium oxidation (Prabavathi and Mathivanan 2012, Wang et al 2012, Laverock et al 2014, Lipsewers et al 2014, Vigneron et al 2014, Bowen et al 2015, which allows the reuse of organic nitrogen.…”