Environmental DNA Sequencing Reveals a Highly Complex Eukaryote Community in Sansha Yongle Blue Hole, Xisha, South China Sea

Abstract

We report an Illumina high-throughput sequencing protocol of eukaryotic microbes in the world’s deepest marine blue hole, Sansha Yongle Blue Hole, Xisha, South China Sea. The variable V9 region of small subunit (SSU) rDNA, was sequenced using this approach from the waters of blue hole and outer reef slope. 917,771 unique eukaryotic 18S rRNA gene sequences and 6093 operational taxonomic units (OTUs) were identified. Significant differences in the eukaryotic composition were observed between the blue hole and outer reef slope, and the richness in the blue hole was much higher than that in the outer reef slope. The richness and diversity of eukaryotes in the blue hole were both lowest at 60 m and highest at 100 m depth. Eukaryotic microalgae assemblages dominated by Dinophyceae were the most abundant in the 10–20 m water column in the hole. Fauna was the main group at and below a depth of 60 m, where Araneae and Cyclopoida were dominant in the 60 m and 80 m water layer, respectively. There was a large number of Entoprocta at a depth of 180 m in the hole, where little oxygen was detected. Turbidity and nitrite concentration had a significant effect on the eukaryote community structure (p < 0.01).

Microeukaryotic and Prokaryotic Diversity of Anchialine Caves from Eastern Adriatic Sea Islands

“…Most anchialine cave studies documented endemism among eukaryotes [12]. Relatively few studies have attempted to record the full diversity of microbial communities in anchialine ecosystems [13][14][15], even though these studies resulted in descriptions of new species using novel molecular tools. In the region of the eastern Adriatic Sea, the majority of anchialine ecological studies have been based on the taxonomic research of stygobiotic metazoans [16], the distribution of trace metals [17], and iodine species and nutrients [18].…”

Metabarcoding reveals the differential sensitivity of planktonic microbiome to environmental filtering and biointeraction in Sansha Yongle blue hole

“…Depth partitioning of plankton microbiome in the SYBH Environmental heterogeneity is regarded as a universal driver of biodiversity (Stein et al, 2014), thus the strong vertically heterogeneous environment in the SYBH explained its higher plankton diversity than that in outer reef slope and other Chinese marginal seas (He et al, 2019;Liu et al, 2019;Li et al, 2020b). In this study, our joint analysis of microeukaryotic and prokaryotic plankton found that planktonic microbiome above 150 m in the SYBH was vertically structured along the abiotic gradients and grouped into three clusters as upper oxic layer (0-20 m), middle oxic layer (40-80 m) and suboxic-anoxic layer (90-150 m) (Figures 1D, 3).…”

“…In aquatic ecosystems, plankton serve as one of the sensitive indicators of biodiversity and environmental changes, and underpin important ecosystem functions (e.g., Ibarbalz et al, 2019;Sunagawa et al, 2020), thus scientists have started to explore the community composition of plankton and its relationship with environmental variables in SYBH. Prokaryotic plankton including bacteria and archaea community (He et al, 2019;Zhang et al, 2021), microeukaryotic plankton (Liu et al, 2019), microphytoplankton (Ge et al, 2020) and mesozooplankton (Chen et al, 2018) in SYBH have been investigated separately, with some lineages such as a genus of gram-negative bacteria Vibrio (Li et al, 2020a) and foraminifera (Li et al, 2020b) being addressed. However, the assembly mechanism of plankton microbiome, the role of subcommunities of different abundance and the potential microbial biointeraction remain elusive, which is crucial for understanding the ecological processes in SYBH.…”

Extremofiles 2.0

“…This, for several reasons, some, fundamental and related with the search for the limits of life [ 2 ], and others, more pragmatic and focused on the biotechnological potential of extremophiles, has sparked a marked growth of interest in the ecology of extreme environments [ 3 ]. The 2019–2020 version of Extremofiles 2.0, a Special Issue of Microorganisms devoted to extremophiles, has gathered eleven papers dealing with different aspects of microorganisms that thrive in extreme environments: five on halophiles [ 4 , 5 , 6 , 7 , 8 ], three on acidophiles [ 9 , 10 , 11 ], one on thermophiles [ 12 ], one on psycrophiles [ 13 ] and one on metal resistant microorganisms [ 14 ].…”

“…Liu et al analyzed the complex eukaryotic community in the world’s deepest marine blue hole in the South China Sea, where significant differences were observed at different depths, and the most abundant microalgae assemblages detected were Dinophyceae at 10–20 m water column [ 4 ].…”