Insights into the strategy of micro-environmental adaptation: Transcriptomic analysis of two alvinocaridid shrimps at a hydrothermal vent

Abstract

Diffusing fluid at a deep-sea hydrothermal vent creates rapid, acute physico-chemical gradients that correlate strongly with the distribution of the vent fauna. Two alvinocaridid shrimps, Alvinocaris longirostris and Shinkaicaris leurokolos occupy distinct microhabitats around these vents and exhibit different thermal preferences. S. leurokolos inhabits the central area closer to the active chimney, while A. longirostris inhabits the peripheral area. In this study, we screened candidate genes that might be involved in niche separation and microhabitat adaptation through comparative transcriptomics. The results showed that among the top 20% of overexpressed genes, gene families related to protein synthesis and structural components were much more abundant in S. leurokolos compared to A. longirostris. Moreover, 15 out of 25 genes involved in cellular carbohydrate metabolism were related to trehalose biosynthesis, versus 1 out of 5 in A. longirostris. Trehalose, a non-reducing disaccharide, is a multifunctional molecule and has been proven to act as a protectant responsible for thermotolerance in Saccharomyces cerevisiae. Putative positively selected genes involved in chitin metabolism and the immune system (lectin, serine protease and antimicrobial peptide) were enriched in S. leurokolos. In particular, one collagen and two serine proteases were found to have experienced strong positive selection. In addition, sulfotransferase-related genes were both overexpressed and positively selected in S. leurokolos. Finally, genes related to structural proteins, immune proteins and protectants were overexpressed or positively selected. These characteristics could represent adaptations of S. leurokolos to its microhabitat, which need to be confirmed by more evidence, such as data from large samples and different development stages of these alvinocaridid shrimps.

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

“…In addition, the water of hydrothermal vent area with lower pH (5.20 and 5.50) are more acidic than those of the seep. In this study, it has been revealed that Campylobacteria and Gammaproteobacteria are the most dominant microbial community compositions of the alvinocaridid gills, consisting with other studies in crustaceans from vent and seep environments ( Hügler et al, 2011 ; Sun et al, 2016 ; Zhang et al, 2018 ). Among them, Sulfurovaceae (all Sulfurovum ) is ubiquitous in all samples, which is usually sulfur oxidizer and reducer and plays a vital role in the sulfur, nitrogen, hydrogen cycles, and even bio-fixation of CO 2 in the deep sea ( Mino et al, 2014 ; Kwon et al, 2015 ; Jeon et al, 2017 ).…”

“…Moreover, vents are usually richer in hydrogen sulfide and heavy metals than those of seeps ( Cosson & Vivier, 1997 ; Miyazaki et al, 2013 ). In addition, the temperature of the hydrothermal fluid can reach over 400 °C, and a steep thermal gradient is specifically created by mix of the vent fluid and the surrounding seawater (∼2 °C) ( Koschinsky et al, 2008 ; Zhu et al, 2020 ), while in seeps, temperatures do not vary appreciably from those of the ambient deep-sea water.…”

Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences

“…Collagen is the main structural protein in the extracellular matrix of diverse connective tissues, playing important roles in tissue morphogenesis and the maintenance of tissue structural integrity ( Gelse et al., 2003 ). Previous studies uncovered that some collagens are positively selected in the deep-sea fish Aldrovandia affinis ( Lan et al., 2018 ) and the deep-sea alvinocaridid shrimp Shinkaicaris leurokolos ( Zhu et al., 2020 ), suggesting their potential roles in deep-sea adaptation. Herein, 86 collagen-encoding transcripts were identified, with 19 upregulated and 4 downregulated in the onboard fixed group ( Table S2 ).…”

Characteristics of Two Crustins from Alvinocaris longirostris in Hydrothermal Vents

“…The RNA extraction, sequencing, assembly, and annotation were performed according to our laboratory's published paper [33]. Based on the sequences of the annotated Crustins, two paired primers of Crustins, Al-crus 3 and Al-crus 7, were designed (Table S1).…”