Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags - PubMed (original) (raw)

Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags

Yu Wang et al. Appl Environ Microbiol. 2012 Dec.

Abstract

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.

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Figures

Fig 1

Fig 1

α-Diversity comparison. Rarefaction curves for OTU (A) and Shannon index (B) were calculated using Mothur (v1.27.0) with reads normalized to 33,307 for each sample using 0.03 distance OTUs.

Fig 2

Fig 2

Phylum distribution. (Left) Relative abundance of the dominant bacterial phyla in the three types of sediments. (Right) Principal component analysis (PCA) of phylum abundance data using Canoco 4.5.

Fig 3

Fig 3

Canonical correspondence analysis (CCA) diagram illustrating the relationship between the genus-level community structure from different sampling sites and environmental variables.

Fig 4

Fig 4

Clustering of samples. Bray-Curis similarity index was calculated using the abundance of OTUs, and hierarchical clustering was calculated using average linkage algorithms using PRIMER 6. F means freshwater samples, I means intertidal samples, and M means marine samples.

Fig 5

Fig 5

Cladogram indicating the phylogenetic distribution of microbial lineages associated with the three types of sediments; lineages with LDA values of 3.5 or higher determined by LEfSe are displayed. Differences are represented in the color of the most abundant class (red indicating freshwater, green intertidal, purple marine, and yellow nonsignificant). Each circle's diameter is proportional to the taxon's abundance. The strategy of multiclass analysis is nonstrict (at least one class differential). Circles represent phylogenetic levels from domain to genus inside out. Labels are shown of the phylum and class levels.

Fig 6

Fig 6

Indicator microbial groups within the three types of sediments with LDA values higher than 4.

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