Community Structure, Abundance and Potential Functions of Bacteria and Archaea in the Sansha Yongle Blue Hole, Xisha, South China Sea

Abstract

The Sansha Yongle Blue Hole is the deepest blue hole in the world and exhibits unique environmental characteristics. In this paper, Illumina sequencing and qPCR analysis were conducted to obtain the microbial information in this special ecosystem. The results showed that the richness and diversity of bacterial communities in the hole was greater than those of archaeal communities, and bacterial and archaeal communities were dominated by Proteobacteria and Euryarchaeota, respectively. Temperature and nitrate concentration significantly contributed to the heterogeneous distribution of major bacterial clades; salinity explained most variations of the archaeal communities, but not significant. A sudden increase of bacterial 16S rRNA, archaeal 16S rRNA, ANAMMOX 16S rRNA, nirS and dsrB gene was noticed from 90 to 100 m in the hole probably due to more phytoplankton at this depth. Sulfur oxidation and nitrate reduction were the most abundant predicted ecological functions in the hole, while lots of archaea were predicted to be involved in aerobic ammonia oxidation and methanogenesis. The co-occurrence network analysis illustrated that a synergistic effect between sulfate reduction and sulfur oxidation, and between nitrogen fixation and denitrification, a certain degree of coupling between sulfur and nitrogen cycle was also observed in the hole. The comparisons of bacterial and archaeal communities between the hole and other caves in the world (or other areas of the South China Sea) suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal communities.

Keywords: 16S rRNA gene sequencing; community characteristics; extremophiles; microbial ecology; the Sansha Yongle Blue Hole.

FIGURE 1

Relative abundance of the dominant bacteria and archaea at different levels in the water from the Sansha Yongle Blue Hole and the outer reef slope. (A) Relative abundance of the dominant bacteria at the phylum level. (B) Relative abundance of the Proteobacteria at the class level. (C) Relative abundance of the dominant archaea at the phylum level. (D) Relative abundance of the dominant archaea at the genus level.

FIGURE 2

Heatmap of the dominant bacteria at the genus level in the water from the Sansha Yongle Blue Hole and the outer reef slope. Clades are given at a higher taxonomic level if the sequences could not be assigned to a genus.

FIGURE 3

RDA ordination plots of the relationship between environmental factors and microbial community structure. (A) RDA targeting the dominant bacterial genera in the Sansha Yongle Blue Hole. (B) RDA targeting the archaeal genera in the Sansha Yongle Blue Hole.

FIGURE 4

The predicted ecological functions of bacterial (A) and archaeal (B) communities based on 16S rRNA genes. Nitrogen fixation, nitrification, aerobic nitrite oxidation, denitrification, nitrate denitrification, nitrite denitrification, nitrogen respiration, nitrite respiration, nitrite ammonification, nitrate respiration, nitrate reduction, nitrous oxide denitrification, nitrate ammonification are parts of nitrogen cycle. Sulfur respiration, sulfite respiration, sulfate respiration, respiration of sulfur compounds, dark thiosulfate oxidation, dark sulfur oxidation, dark sulfide oxidation, dark oxidation of sulfur compounds and thiosulfate respiration are parts of sulfur cycle. Methylotrophy, methanotrophy and methanogenesis are parts of carbon cycle.

FIGURE 5

Co-occurrence network analyses of the bacterial genera (A), the functional groups (B) and the archaeal genera (C) with a Spearman’s coefficient > 0.6 or <–0.6 and for which P < 0.05. The bacterial genera with relative abundance of more than 0.1% were selected. Each line represents a significant correlation between two genera. The red lines represent positive correlations, and the green lines represent negative correlations. The node size is proportional to the number of connections. SOB, sulfur-oxidizing bacteria; SRB, sulfate-reducing bacteria; NOB, nitrite-oxidizing bacteria; NFB, nitrogen-fixing bacteria. MGI, Marine Group I; MCG, Miscellaneous Crenarchaeotic Group; DHVEG_6, Deep Sea Hydrothermal Vent Group 6; SCG, Soil Crenarchaeotic Group; MBGB, Marine Benthic Group B; MGII, Marine Group II.

FIGURE 6

Quantitative analysis of bacterial 16S rRNA, archaeal 16S rRNA and functional genes (ANAMMOX 16S rRNA, nirS and dsrB genes) in the Sansha Yongle Blue Hole. The error bars represent the standard deviations of triplicate quantifications.

FIGURE 7

ANAMMOX 16S rRNA and nirS gene copy numbers and the dissolved inorganic nitrogen (ammonium, nitrite, and nitrate) concentrations in the portion of the water column between 80 and 100 m in the Sansha Yongle Blue Hole.