海洋生物分类与系统演化实验室知识库

深海热液和冷泉化能生态系统具有高压、低氧、黑暗以及富含还原性气体等特点。在这种完全无光的生态系统中，初级生产者不是陆地上常见的光合生物，而是可以利用深海热液喷口或冷泉释放的硫化氢、氢气、甲烷等物质的化能自养微生物。阿尔文虾科（Alvinocarididae）物种是深海化能合成生态系统的特有物种之一，和这些生态系统中的许多其他物种一样，阿尔文虾在鳃腔和肠道中拥有重要的化能合成细菌群落。在冲绳热液区阿尔文虾科不同物种占据不同的生态位，其中光足深海阿尔文虾（Shinkaicaris leurokolos）栖息在热液喷口的“黑烟囱”壁上，而长角阿尔文虾（Alvinocaris longirostris）栖息在远离喷口的贻贝床上。此外，长角阿尔文虾是目前已发现的唯一在热液和冷泉区均有分布的阿尔文虾科物种。因此，阿尔文虾科物种为研究生物应对深海化能极端环境适应性进化机制提供了优良模型。
本研究首先利用三代结合二代高通量测序技术对冲绳热液的光足深海阿尔文虾和长角阿尔文虾进行了全长转录组的测定和比较。在光足深海阿尔文虾和长角阿尔文虾中分别得到了16,037和13,666条unigenes，其中分别有11,718（73.07%）和10,243（74.95%）条unigenes在NR、NT、KOG、KEGG、KO和GO数据库中得到注释，GC含量分别为46.5%和45.8%。进一步分析两种阿尔文虾的高表达基因发现：与硫化物和重金属解毒代谢相关的基因（SQR、ETHE1、TST和FRI）主要在光足深海阿尔文虾中高表达，而更多与免疫相关的基因（BGBP、CHIT、CHIA和ALPS）在长角阿尔文虾中高表达。除此之外，氧化应激和热应激相关的基因（SODM、GST、GPX、HSP70和HSP7D）在光足深海阿尔文虾中显著扩张，而和免疫相关的基因（CHIA和CHIT）在长角阿尔文虾中显著扩张。最终还发现了6个参与DNA损伤修复相关的基因（HIPK2、INT6、HEAT3、RUVB2、SMC1A和SIR1），5个参与氧化应激的基因（CCD51、RT05、DHC24、IMP2L和VA0E）和5个参与温度适应的基因（PPID、EXL1、L2EFL、NU155和TCPQ）在光足深海阿尔文虾中受到了正选择。这些特征可能与光足深海阿尔文虾和长角阿尔文虾对其不同热液微环境的适应相关。
阿尔文虾的共附生菌也在帮助其宿主适应极端环境方面扮演重要角色。利用三代全长16S扩增子测序技术对冲绳热液的长角阿尔文虾、光足深海阿尔文虾以及南海冷泉的长角阿尔文虾鳃相关细菌的群落组成多样性进行了分析。共聚类得到568个OTU，其中冷泉长角阿尔文虾鳃中得到的OTU数目最多（平均每个样品208个），热液光足深海阿尔文虾鳃中的OTU最少（平均每个样品92个）。多样性分析显示，冷泉长角阿尔文虾鳃菌群的多样性最高，而热液光足深海阿尔文虾鳃菌群的多样性最低，并且冷泉长角阿尔文虾和热液长角阿尔文虾鳃相关细菌群落组成更相似。多样性的差异可能是由于冷泉环境较热液更为温和、化学性质更稳定造成的，并且宿主的主动选择可能也在其中发挥了重要作用。
进一步的注释发现，三组虾鳃相关细菌都主要由Campylobacteria、Gammaproteobacteria和Alphaproteobacteria组成。但在科水平上，热液光足深海阿尔文虾鳃相关细菌几乎全部由硫氧化相关的Sulfurovaceae组成（94.05%），热液长角阿尔文虾鳃菌中除了Sulfurovaceae（69.21%）外，其他参与硫氧化的Gammaproteobacteria un-group（14.37%）和Thiotrichaceae（6.77%）也占到了比较高的丰度。而在冷泉长角阿尔文虾鳃中除这几类硫代谢相关菌外，具有甲烷氧化能力的Methylomonadaceae的相对丰度明显多于热液长角阿尔文虾和光足深海阿尔文虾（19.38% vs 0.32% vs 0.01%）。因此，研究认为栖息地环境的理化因素和阿尔文虾宿主对细菌的特异性稳定识别可能在其鳃相关菌群组成中发挥了重要作用。
综上，本研究通过对不同深海化能合成环境中不同阿尔文虾的全长转录组比较分析，以及虾鳃相关细菌的全长16S扩增子分析阐释了深海极端环境下阿尔文虾适应不同化能生态微环境的分子基础及鳃相关微生物多的样性，丰富了深海生物组学的数据资源，为深入揭示深海化能生态系统大型甲壳动物的适应性进化机制奠定了基础。

Deep-sea hydrothermal vents and cold seeps are chemosynthetic ecosystems characterized by high pressure, low oxygen, absence of light, and rich in reducing gases. In these completely lightless ecosystems, primary producers are not photosynthetic organisms commonly found on land, but chemoautotrophic bacteria that can utilize hydrogen sulfide, hydrogen, methane, etc. released from deep-sea hydrothermal vents or cold seeps. Shrimps of the family Alvinocarididae are endemic species of deep-sea chemosynthetic ecosystems. Like many other invertebrates in these ecosystems, alvinocaridid shrimps harbor important chemosynthetic bacterial communities in the gill chamber and gut. Different alvinocaridid species occupy different ecological niches in the Okinawa Through hydrothermal region, with Shinkaicaris leurokolos inhabiting the chimney walls of hydrothermal vents and Alvinocaris longirostris inhabiting the mussel beds far from vents. Moreover, the A. longirostris is the only alvinocaridid shrimps found co-distributed in hydrothermal vent and cold seep environment. Therefore, alvinocaridid shrimps have become an excellent model to study the adaptive evolution mechanism of extreme deep-sea chemosynthesis environment.
In this study, the full-length transcriptomes of S. leurokolos and A. longirostris in the Okinawa Through hydrothermal vent were sequenced and compared by using a combination of single-molecule real-time (SMRT) and Illumina RNA-seq technology technology. In total, 16,037 and 13,666 unigenes were obtained from S. leurokolos and A. longirostris, respectively, of which 11,718 (73.07%) and 10,243 (74.95%) unigenes were annotated with NR, NT, KOG, KEGG, KO, and GO databases. The GC contents of the transcriptomes were 46.5% and 45.8% in S. leurokolos and A. longirostris. Further analysis revealed that genes related to sulfide and heavy metal detoxification metabolism (SQR, ETHE1, TST, and FRI) were highly expressed in S. leurokolos, while more immune-related genes (BGBP, CHIT, CHIA and ALPS) were highly expressed in A. longirostris. In addition to this, genes related to oxidative and heat stress (SODM, GST, GPX, HSP70, and HSP7D) were significantly expanded in S. leurokolos, while genes related to immune defense genes (CHIA and CHIT) were significantly expanded in A. longirostris. Eventually, six genes involved in DNA damage repair-related genes (HIPK2, INT6, HEAT3, RUVB2, SMC1A, and SIR1), five genes involved in oxidative stress (CCD51, RT05, DHC24, IMP2L, and VA0E) and five genes involved in temperature stresses (PPID, EXL1, L2EFL, NU155, and TCPQ) were subjected to positive selection in S. leurokolos. These features may be related to the adaptability of S. leurokolos and A. longirostris to their microenvironments.
The symbionts of alvinocaridid shrimps also play an important role in helping hosts adapt to extreme environments. The third-generation full-length 16S amplicon sequencing technology was used to analyze the community composition and diversity of bacteria associated with the gills of the A. longirostris and S. leurokolos from the Okinawa Through hydrothermal vent and the A. longirostris from cold seeps in the South China Sea. In the end, a total of 568 OTUs were obtained by clustering, the number of OTUs on the gills of the cold seep A. longirostris, was the largest (average 208 per sample), and the number of OTUs in the hydrothermal vent S. leurokolos was the least (average 92 per sample). The analysis of diversity showed that the diversity of the gill-associated bacteria of the cold seep A. longirostris were the highest. In contrast, the lowest diversity was found in the hydrothermal vent S. leurokolos, and the gill-associated bacterial communities of cold seep A. longirostris and hydrothermal vent A. longirostris were more similar in composition. The difference in diversity may be due to the milder and more chemically stable environment of cold seeps than those of hydrothermal vents, and active selection by the host may also play an important role.
Further annotation found that the three groups of shrimp gill-associated bacteria were mainly composed of bacteria from the classes Campylobacteria, Gammaproteobacteria, and Alphaproteobacteria. However, at the family level, hydrothermal vent S. leurokolos gill-associated bacteria consisted almost entirely of sulfur oxidation-related Sulfurovaceae family (94.06%), and excluding Sulfurovaceae family (69.21%) in hydrothermal vent A. longirostris gill bacteria, Gammaproteobacteria un-group（14.37%）and Thiotrichaceae family (6.77%) involved in sulfur oxidation also accounted for a relatively high abundance. In comparison, the relative abundance of Methylomonadaceae family with methane oxidation capacity on the gills of cold seep A. longirostris was significantly more than that of the two hydrothermal vent A. longirostris and S. leurokolos (19.38% vs. 0.32% vs. 0.01%). In conclusion, we suggest that physicochemical factors of the habitat environments and the specific stable recognition of bacteria by the hosts may co-contribute to the composition of the gill-associated bacteria in alvinocaridid shrimps.
In summary, this study illustrates the molecular basis of adaptive evolution in alvinocaridid shrimps with different ecological niches and their gill-associated microbial diveristy through comparative full-length transcriptome analysis and full-length 16S amplicon sequencing. The results have greatly enriched the genetic resources of deep-sea life, and provided basis for further studies of adaptive evolution mechanisms of crustaceans from deep-sea chemosynthetic ecosystems.