The Diversity, Composition, and Putative Functions of Gill-Associated Bacteria of Bathymodiolin Mussel and Vesicomyid Clam from Haima Cold Seep, South China Sea

The Haima cold seep, which is one of the two active cold seeps in the South China Sea, is known for its great ecological importance. The seep bivalves are assumed to depend mainly on their bacterial symbiosis for survival and growth. However, information on the bacterial diversity, composition, and putative function of gill-associated of dominant dwelling animals in Haima cold seep remain elusive. Herein, we adopted a high-throughput sequencing of 16S rRNA gene amplicons, and function prediction methods (Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICURUSTs)) to purposely illustrate the taxonomic and phylogenetic diversity, composition, and putative functions of the symbionts in bathymodiolin mussel Gigantidas haimaensis (Bivalvia: Mytilidae: Gigantidas) and vesicomyid clam Archivesica marissinica (Bivalvia: Glossoidea: Vesicomyidae). The predominant microbes of both species were Proteobacteria and Gammaproteobacteria on the phylum and class level, respectively. The taxonomic and phylogenetic diversity of gill microbial communities in G. haimaensis were significantly different from those in A. marissinica (p < 0.05). Nine functional groups, including seven carbon-related biogeochemical groups, were identified through the FAPROTAX analysis. However, the most dominant groups for G. haimaensis and A. marissinica were both chemoheterotrophic. G. haimaensis and A. marissinica shared many pathways, however, 16 obtained Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups (42.11%) significantly differed between the two species (p < 0.05). These findings would provide insight into the functions of microbes in the element cycling and energy flow as well as the host-symbiont relationship of bivalves in the Haima cold seep environment.

Differences in cofactor, oxygen and sulfur requirements influence niche adaptation in deep-sea vesicomyid clam symbioses

Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that can provide insights into adaptation to divergent ecological niches. While patterns of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is relatively rare. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Differences in nitrogen and sulfur physiology between the two dominant symbiont groups, Ca. Ruthia and Ca. Vesicomyosocius, have been hypothesized to influence niche exploitation, which likely affects gene content evolution in these symbionts. However, genomic data are currently limited to confirm this assumption. In the present study we sequenced and compared 11 vesicomyid symbiont genomes with existing assemblies for Ca. Vesicomyosocius okutanii and Ca. Ruthia magnifica. Our analyses indicate that the two vesicomyid symbiont groups have a common core genome related to chemosynthetic metabolism, but differ in their potential for nitrate respiration and flexibility to environmental sulfide concentrations. Moreover, Ca. Vesicomyosocius and Ca. Ruthia have different enzymatic requirements for cobalamin and nickel and show contrasting capacities to acquire foreign genetic material. Tests for site-specific positive selection in metabolic candidate genes imply that the observed physiological differences are adaptive and thus likely correspond to ecological niches available to each symbiont group. These findings highlight the role of niche differentiation in creating divergent paths of reductive genome evolution in vertically transmitted symbionts.

Extreme Genomic Makeover: Evolutionary History of Maternally-transmitted Clam Symbionts

Given their recent switch to a vertically-transmitted intracellular lifestyle, the chemosynthetic bacteria associated with deep-sea vesicomyid clams are an excellent model system to study the processes underlying reductive genome evolution. In this study, we provide the first estimates of the relative contributions of drift, recombination and selection in shaping the ongoing reductive genome evolution in these symbionts. To do so, we compared the genomes of endosymbionts associated with 11 vesicomyid clam species to that of closely related free-living bacteria and their respective hosts’ mitochondria. Our investigation confirmed that neutral evolutionary processes were the dominant driver of reductive genome evolution in this group and highlighted the important role of horizontal gene transfer in mitigating genome erosion. Finally, a genome-wide screen for episodic positive selection across the symbiont phylogeny revealed the pervasive role of selective processes in maintaining symbiont functional integrity.

‘Pliocardia' krylovata, a new species of vesicomyid clam from cold seeps along the Costa Rica Margin

‘Pliocardia' krylovata, sp. nov. (Bivalvia: Vesicomyidae: Pliocardiinae) is described from cold seeps off the coast of the Nicoya Peninsula, Costa Rica (700–1000 m depth). The phylogenetic position of‘P.' krylovatawas assessed by both morphological comparisons as well as nucleotide data from the cytochrome c oxidase I gene. Within the vesicomyids,‘P.' krylovatabelongs to the Pliocardiinae and its closest relative is‘Calyptogena' ponderosa, which also bears some morphological resemblance to the genusPliocardia, perhaps suggesting a need for reanalysis of not only its generic designation, but also the entire Pliocardiinae subfamily.‘P.' krylovatahas morphological similarities to‘Pliocardia' bowdenianaand‘Vesicomya' crenulomarginata, recently reassigned to the genusPliocardia, including a thick shell, obvious rostrum, pointed posterior end, and a sculptured shell with concentric ribs on the outer surface, to name a few. It is morphologically distinguished, however, by having a complex pallial sinus and remarkably deep escutcheon.

Aerobic and anaerobic enzymatic activities ofCalyptogena gallardoi(Vesicomyidae): a clam associated with methane cold seeps off Chile

Calyptogena gallardoiis a recently described species of vesicomyid clam associated to the extensive gas-hydrate field reported for the Chilean margin along 35°S to 45°S. Enzymatic analysis in foot, gill and abductor muscle tissues ofC. gallardoicollected in central-south Chile (~36°21′S 73°44′W), show high activities for malate dehydrogenase (MDH), strombine dehydrogenase (STRDH) and alanopine dehydrogenase (ALPDH) and a low activity of citrate synthase (CS) and ETS (electron transport system). Positive significant correlations (log–log scale) were found between enzymatic activities involved in anaerobic metabolism (MDH versus LDH and ALPDH versus STRDH), as well as between CS and opines dehydrogenases. The ratio MDH/LDH or any other opine dehydrogenase assayed was >> 1 in all tissues analysed. These results indicate thatC. gallardoiis highly adapted to the harsh anaerobic conditions of marine chemosynthesis-based communities inhabiting a reduced environment.