Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts

Abstract

Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R2 = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.

Population genetic structure and implication for adaptive differentiation of the snail (Gastropoda, Provannidae) in deep‐sea chemosynthetic ecosystems

“…It has been shown that there are differences in concentration of chemical composition, temperature range and bacteria compositions between hydrothermal vent in Okinawa Trough and methane seep in the South China Sea (summarized in Hui et al, 2022). Therefore, excluding geographical factors and limited larval dispersal ability that may hinder the connectivity of populations, the snail P. glabra , as a common species in hydrothermal vent and methane seep, may have undergone local adaptive differentiation, which blocks the genetic exchange between populations.…”

“…Chemotrophic microbes play important roles in the survival of animals in seep and vent. It has been revealed that more abundant methane‐oxidizing bacteria are in shrimp gill from the seep of the South China Sea than in the hydrothermal vent of Okinawa Trough, while sulfur‐oxidizing bacteria are dominant in the vent samples (Hui et al, 2022). Therefore, findings in this study imply that the selection of these outlier‐containing immune genes may be the result of the long‐term interaction of the snail P. glabra with different epibiotic, water or sediment microbe communities and other environmental factors.…”

“…Vents are usually richer in H 2 S and heavy metals than those of seeps. For example, the content of H 2 S (0.45–2 Mm) is especially higher in the water column of hydrothermal vent in Okinawa Trough than in Formosa Ridge seep (summarized in Hui et al, 2022). In addition, the temperature of the hydrothermal fluid can reach over 400°C with a wide range by mix of the vent fluid and surrounding seawater (Koschinsky et al, 2008), while in seeps, temperatures maintain in low ~4°C.…”

“…One of the outlier genes IRAK1, a serine/threonine kinase, has been reported to have the ability to activate the important immune-related toll-like receptor signalling pathway (Flannery & Bowie, 2010;4.3.3 | DNA repair and processing of genetic material Vents are usually richer in H 2 S and heavy metals than those of seeps. For example, the content of H 2 S (0.45-2 Mm) is especially higher in the water column of hydrothermal vent in Okinawa Trough than in Formosa Ridge seep (summarized in Hui et al, 2022). In addition, the temperature of the hydrothermal fluid can reach over 400°C with a wide range by mix of the vent fluid and surrounding seawater (Koschinsky et al, 2008), while in seeps, temperatures maintain in low ~4°C.…”

Presence of an ultra-small microbiome in fermented cabbages

“…SMRT sequencing, a synthetic long-read sequencing technology based on full-length 16S rRNA, is widely used to study microbial communities in various environments, including food. It has been used to analyze microbial diversity in various samples ( Pootakham et al, 2017 ; Jeong et al, 2021 ; Hui et al, 2022 ; Liang et al, 2022 ). SMRT sequencing is advantageous over general Illumina sequencing because it provides accurate classification at a taxonomic level using full-length 16S rRNA sequences instead of short amplicons ( Mosher et al, 2014 ; Jeong et al, 2021 ); in this study, SMRT sequencing was used to confirm the microbial composition of fermented cabbage, including NM and USM samples.…”