Geographical Isolation, Buried Depth, and Physicochemical Traits Drive the Variation of Species Diversity and Prokaryotic Community in Three Typical Hypersaline Environments

Abstract

The prokaryotic community composition, species diversity and the distribution patterns at various taxonomic levels in a salt lake (Chaka salt lake), solar salterns (Taipei saltworks and Dongfang saltworks), and salt mines (Yuanyongjing salt mine, Xiangyan salt mine, and Dinyuan salt mine) were investigated using clone library or Illumina MiSeq sequencing. The clone library approach revealed that the salt lake harbors low species diversity (H' = 0.98) as compared to the solar saltern (H' = 4.36) and salt mine (H' = 3.57). The dominant group in the salt lake is a species from the genus Haloparvum which constitutes about 85% of the total sequences analyzed. The species diversities in salt salterns and salt mines are richer than in the salt lake, and the dominant group is less significant in terms of total percentage. High-throughput sequencing showed that geographical isolation greatly impacted on the microbial community (phyla level) and species diversity (operational taxonomic units (OTUs) level) of salt mines. Species of the genus Natronomonas are found in all three types of environments investigated. In addition, the microbial community and species diversity of different stratums of the salt mine are very similar. Furthermore, species of the genus Halorubrum flourish in the newest stratum of salt mine and have become the dominant group. This study provides some new knowledge on the species diversity and prokaryotic community composition of three typical hypersaline environments.

Keywords: 16S rRNA gene; clone library; high-throughput sequencing; hypersaline environment; microbial community; species diversity.

Figure 1

Location of the sampling sites. (a) Large scale map including sampling sites. (b) Close-up of the sampling area showing six different sampling sites from S1 to S6. These six sampling sites were grouped into three types: salt lake, salt mine, and solar saltern. S1: salt lake; S2, S3, and S5: salt mine; S4 and S6: solar saltern. The distances between each site of S2, S3, and S5 are shown.

Figure 2

Microbial community varies from different types of hypersaline environments. (a) Rarefaction curve generated for 16S rRNA genes in bacterial and archaeal clones’ libraries with clusterization stringency at 97% from the salt lake (blue line), solar saltern (green line), and salt mine (red line). (b) Venn diagram showing the shared and unique operational taxonomic units (OTUs) (97% similarity cut off) between salt lake (blue), solar saltern (green), and salt mine (red). Analysis and diagram generation were performed using the MOTHUR v 1.3 suite of programs (http://www.mothur.org/). (c) Relative abundance of bacterial and archaeal community obtained from 16S rRNA gene clones’ libraries at genus level.

Figure 3

Microbial community varies from different types of salt mines. (a) Rarefaction curve generated from the 16S rRNA genes pyro-sequencing (97% similarity cut off). (b) Venn diagram showing the shared and unique OTUs (97% similarity cut off). (c) Principal components analysis (PCA) of three salt mines with a different location. (d) Clustering analysis with un-weighted pair-group method with arithmetic means (UPGMA). (e) Heatmap analysis showing relative abundance of microbial community of three different salt mines, as determined by high-throughput sequencing. The color code indicates the range of relative abundance for a given phylum. (f) Relative abundance of microbial community at the phylum level obtained from the 16S rRNA gene pyrosequencing in three different salt mines. Legends with major relative abundances (>0.1%) are shown in the figure. (g) Relative abundance of haloarchaeal genera in the phylum Euryarchaeota.

Figure 4

Microbial community varies from buried depths of a salt mine sample. (a) Rarefaction curve generated from the 16S rRNA genes pyro-sequencing (97% similarity cut off). (b) Venn diagram showing the shared and unique OTUs (97% similarity cut off). (c) Heatmap analysis showing relative abundance of microbial community of three different salt mines determined by high-throughput sequencing. The color code indicates the range of relative abundance for a given phylum. (d) Relative abundance of microbial community at the phylum level obtained from the 16S rRNA gene pyrosequencing in three different salt mines. Legends with major relative abundances (>0.1%) are shown in the figure. (e) Relative abundance of haloarchaeal genera in the phylum Euryarchaeota.