Extracellular and mixotrophic symbiosis in the whale-fall mussel Adipicola pacifica: a trend in evolution from extra- to intracellular symbiosis

Scallop-bacteria symbiosis from the deep sea reveals strong genomic coupling in the absence of cellular integration

Previous studies have revealed tight metabolic complementarity between bivalves and their endosymbiotic chemosynthetic bacteria, but little is known about their interactions with ectosymbionts. Our analysis of the ectosymbiosis between a deep-sea scallop (Catillopecten margaritatus) and a gammaproteobacterium showed that bivalves could be highly interdependent with their ectosymbionts as well. Our microscopic observation revealed abundant sulfur-oxidizing bacteria (SOB) on the surfaces of the gill epithelial cells. Microbial 16S rRNA gene amplicon sequencing of the gill tissues showed the dominance of the SOB. An analysis of the SOB genome showed that it is substantially smaller than its free-living relatives and has lost cellular components required for free-living. Genomic and transcriptomic analyses showed that this ectosymbiont relies on rhodanese-like proteins and SOX multienzyme complex for energy generation, mainly on the Calvin-Benson-Bassham (CBB) cycle and peripherally on a phosphoenolpyruvate carboxylase for carbon assimilation. Besides, the symbiont encodes an incomplete tricarboxylic acid (TCA) cycle. Observation of the scallop's digestive gland and its nitrogen metabolism pathways indicates it does not fully rely on the ectosymbiont for nutrition. Analysis of the host's gene expression provided evidence that it could offer intermediates for the ectosymbiont to complete its TCA cycle and some amino acid synthesis pathways using exosomes, and its phagosomes, endosomes, and lysosomes might be involved in harvesting nutrients from the symbionts. Overall, our study prompts us to rethink the intimacy between the hosts and ectosymbionts in Bivalvia and the evolution of chemosymbiosis in general.

Marinagarivorans cellulosilyticus sp. nov., a cellulolytic bacterium isolated from the deep-sea off Noma-misaki, Japan

Cells from strain GE09^T, isolated from an artificially immersed nanofibrous cellulose plate in the deep sea, were Gram-stain-negative, motile, aerobic cells that could grow with cellulose as their only nutrient. Strain GE09^T was placed among members of Cellvibrionaceae, in the Gammaproteobacteria, with Marinagarivorans algicola Z1^T, a marine degrader of agar, as the closest relative (97.4 % similarity). The average nucleotide identity and digital DNA-DNA hybridization values between GE09^T and M. algicola Z1^T were 72.5 and 21.2 %, respectively. Strain GE09^T degraded cellulose, xylan and pectin, but not starch, chitin and agar. The different carbohydrate-active enzymes encoded in the genomes of strain GE09^T and M. algicola Z1^T highlights their differences in terms of target energy sources and reflects their isolation environments. The major cellular fatty acids of strain GE09^T were C_18 : 1  ω7c, C_16 : 0 and C_16 : 1  ω7c. The polar lipid profile showed phosphatidylglycerol and phosphatidylethanolamine. The major respiratory quinone was Q-8. Based on these distinct taxonomic characteristics, strain GE09^T represents a new species in the genus Marinagarivorans, for which we propose the name Marinagarivorans cellulosilyticus sp. nov. (type strain GE09^T=DSM 113420^T=JCM 35003^T).

Microbiomes and Obligate Symbiosis of Deep-Sea Animals

Microbial communities associated with deep-sea animals are critical to the establishment of novel biological communities in unusual environments. Over the past few decades, rapid exploration of the deep sea has enabled the discovery of novel microbial communities, some of which form symbiotic relationships with animal hosts. Symbiosis in the deep sea changes host physiology, behavior, ecology, and evolution over time and space. Symbiont diversity within a host is often aligned with diverse metabolic pathways that broaden the environmental niche for the animal host. In this review, we focus on microbiomes and obligate symbionts found in different deep-sea habitats and how they facilitate survival of the organisms that live in these environments. In addition, we discuss factors that govern microbiome diversity, host specificity, and biogeography in the deep sea. Finally, we highlight the current limitations of microbiome research and draw a road map for future directions to advance our knowledge of microbiomes in the deep sea. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Multispecies populations of methanotrophic Methyloprofundus and cultivation of a likely dominant species from the Iheya North deep-sea hydrothermal field

The Methyloprofundus clade is represented by uncultivated methanotrophic bacterial endosymbionts of deep-sea bathymodiolin mussels, but only a single free-living species has been cultivated to date. This study reveals the existence of free-living Methyloprofundus variants in the Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough. A clade-targeted amplicon analysis of the particulate methane monooxygenase gene (pmoA) detected 647 amplicon sequence variants (ASVs) of the Methyloprofundus clade in microbial communities newly formed in in situ colonization systems. Such systems were deployed at colonies of bathymodiolin mussels and a galatheoid crab in diffuse-flow areas. These ASVs were classified into 161 species-like groups. The proportion of the species-like groups representing endosymbionts of mussels was unexpectedly low. A methanotrophic bacterium designated INp10, a likely dominant species in the Methyloprofundus population in this field, was enriched in a biofilm formed in a methane-fed cultivation system operated at 10°C. Genomic characterization with the gene transcription data set of INp10 from the biofilm suggested traits advantageous to niche competition in environments, such as mobility, chemotaxis, biofilm formation, offensive and defensive systems, and hypoxia tolerance. The notable metabolic traits that INp10 shares with some Methyloprofundus members are the use of lanthanide-dependent XoxF as the sole methanol dehydrogenase due to the absence of the canonical MxaFI, the glycolytic pathway using fructose-6-phosphate aldolase instead of fructose-1,6-bisphosphate aldolase, and the potential to perform partial denitrification from nitrate under oxygen-limited conditions. These findings help us better understand the ecological strategies of this possibly widespread marine-specific methanotrophic clade.

IMPORTANCE The Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough is characterized by abundant methane derived from organic-rich sediments and diverse chemosynthetic animal species, including those harboring methanotrophic bacterial symbionts, such as bathymodiolin mussels Bathymodiolus japonicus and “Bathymodiolus” platifrons and a galatheoid crab, Shinkaia crosnieri. Symbiotic methanotrophs have attracted significant attention, and yet free-living methanotrophs in this environment have not been studied in detail. We focused on the free-living Methyloprofundus spp. that thrive in this hydrothermal field and identified an unexpectedly large number of species-like groups in this clade. Moreover, we enriched and characterized a methanotroph whose genome sequence indicated that it corresponds to a new species in the genus Methyloprofundus. This species might be a dominant member of the indigenous Methyloprofundus population. New information on free-living Methyloprofundus populations suggests that the hydrothermal field is a promising locale at which to investigate the adaptive capacity and associated genetic diversity of Methyloprofundus spp.

Inside or out? Clonal thiotrophic symbiont populations occupy deep-sea mussel bacteriocytes with pathways connecting to the external environment

Deep-sea Bathymodiolus mussels are generally thought to harbour chemosynthetic symbiotic bacteria in gill epithelial cells called bacteriocytes. However, previously observed openings at the apical surface of bacteriocytes have not been conclusively explained and investigated as to whether the Bathymodiolus symbiosis is intracellular or extracellular. In this study, we show that almost all the membranous chambers encompassing symbionts in a single bacteriocyte of Bathymodiolus septemdierum are interconnected and have pathways connecting to the external environment. Furthermore, the symbiont population colonising a single bacteriocyte is mostly clonal. This study hypothesises on a novel model of cellular localization at the interface between extra- and intracellular symbiosis, and the cellular-level process of symbiont acquisition in Bathymodiolus mussels.

Cryptic fungal diversity revealed in deep-sea sediments associated with whale-fall chemosynthetic ecosystems

In this study, sediments from whale-fall chemosynthetic ecosystems (two different sites, one naturally occurring at 4200 m water depth in South Atlantic Ocean and one artificially immersed at 100 m water depth in Kagoshima Bay, Japan) were investigated by Ion Torrent PGM sequencing of the ITS region of ribosomal RNA to reveal fungal communities in these unique marine environments. As a result, a total of 107 (897 including singletons) Operational Taxonomic Units (OTUs) were obtained from the samples explored. Composition of the 107 OTUs at the phylum level among the five samples from two different whale-fall sites was assigned to Ascomycota (46%), Basidiomycota (7%), unidentified fungi (21%), non-fungi (10%), and sequences with no affiliation to any organisms in the public database (No-match) (16%). The high detection of the unidentified fungi and unassigned fungi was revealed in the whale-fall environments in this study. Some of these unidentified fungi are allied to early diverging fungi and they were more abundant in the sediments not directly in contact with whalebone. This study suggests that a cryptic fungal community exists in unique whale-fall ecosystems.

Molecular characterization of Bathymodiolus mussels and gill symbionts associated with chemosynthetic habitats from the U.S. Atlantic margin

Mussels of the genus Bathymodiolus are among the most widespread colonizers of hydrothermal vent and cold seep environments, sustained by endosymbiosis with chemosynthetic bacteria. Presumed species of Bathymodiolus are abundant at newly discovered cold seeps on the Mid-Atlantic continental slope, however morphological taxonomy is challenging, and their phylogenetic affinities remain unestablished. Here we used mitochondrial sequence to classify species found at three seep sites (Baltimore Canyon seep (BCS; ~400m); Norfolk Canyon seep (NCS; ~1520m); and Chincoteague Island seep (CTS; ~1000m)). Mitochondrial COI (N = 162) and ND4 (N = 39) data suggest that Bathymodiolus childressi predominates at these sites, although single B. mauritanicus and B. heckerae individuals were detected. As previous work had suggested that methanotrophic and thiotrophic interactions can both occur at a site, and within an individual mussel, we investigated the symbiont communities in gill tissues of a subset of mussels from BCS and NCS. We constructed metabarcode libraries with four different primer sets spanning the 16S gene. A methanotrophic phylotype dominated all gill microbial samples from BCS, but sulfur-oxidizing Campylobacterota were represented by a notable minority of sequences from NCS. The methanotroph phylotype shared a clade with globally distributed Bathymodiolus spp. symbionts from methane seeps and hydrothermal vents. Two distinct Campylobacterota phylotypes were prevalent in NCS samples, one of which shares a clade with Campylobacterota associated with B. childressi from the Gulf of Mexico and the other with Campylobacterota associated with other deep-sea fauna. Variation in chemosynthetic symbiont communities among sites and individuals has important ecological and geochemical implications and suggests shifting reliance on methanotrophy. Continued characterization of symbionts from cold seeps will provide a greater understanding of the ecology of these unique environments as well and their geochemical footprint in elemental cycling and energy flux.

A specific and widespread association between deep-sea Bathymodiolus mussels and a novel family of Epsilonproteobacteria

Bathymodiolus mussels dominate animal communities at many hydrothermal vents and cold seeps. Essential to the mussels' ecological and evolutionary success is their association with symbiotic methane- and sulfur-oxidizing gammaproteobacteria, which provide them with nutrition. In addition to these well-known gammaproteobacterial endosymbionts, we found epsilonproteobacterial sequences in metatranscriptomes, metagenomes and 16S rRNA clone libraries as well as by polymerase chain reaction screening of Bathymodiolus species sampled from vents and seeps around the world. These epsilonproteobacterial sequences were closely related, indicating that the association is highly specific. The Bathymodiolus-associated epsilonproteobacterial 16S rRNA sequences were at most 87.6% identical to the closest cultured relative, and 91.2% identical to the closest sequences in public databases. This clade therefore represents a novel family within the Epsilonproteobacteria. Fluorescence in situ hybridization and transmission electron microscopy showed that the bacteria are filamentous epibionts associated with the gill epithelia in two Bathymodiolus species. In animals that host highly specific symbioses with one or a few types of endosymbionts, other less-abundant members of the microbiota can be easily overlooked. Our work highlights how widespread and specific associations with less-abundant microbes can be. Possibly, these microbes play an important role in the survival and health of their animal hosts.

Identification of Associations between Bacterioplankton and Photosynthetic Picoeukaryotes in Coastal Waters

Photosynthetic picoeukaryotes are significant contributors to marine primary productivity. Associations between marine bacterioplankton and picoeukaryotes frequently occur and can have large biogeochemical impacts. We used flow cytometry to sort cells from seawater to identify non-eukaryotic phylotypes that are associated with photosynthetic picoeukaryotes. Samples were collected at the Santa Cruz wharf on Monterey Bay, CA, USA during summer and fall, 2014. The phylogeny of associated microbes was assessed through 16S rRNA gene amplicon clone and Illumina MiSeq libraries. The most frequently detected bacterioplankton phyla within the photosynthetic picoeukaryote sorts were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) and Bacteroidetes. Intriguingly, the presence of free-living bacterial genera in the photosynthetic picoeukaryote sorts could suggest that some of the photosynthetic picoeukaryotes were mixotrophs. However, the occurrence of bacterial sequences, which were not prevalent in the corresponding bulk seawater samples, indicates that there was also a selection for specific OTUs in association with photosynthetic picoeukaryotes suggesting specific functional associations. The results show that diverse bacterial phylotypes are found in association with photosynthetic picoeukaryotes. Taxonomic identification of these associations is a prerequisite for further characterizing and to elucidate their metabolic pathways and ecological functions.

Deep-sea whale fall fauna from the Atlantic resembles that of the Pacific Ocean

Whale carcasses create remarkable habitats in the deep-sea by producing concentrated sources of organic matter for a food-deprived biota as well as places of evolutionary novelty and biodiversity. Although many of the faunal patterns on whale falls have already been described, the biogeography of these communities is still poorly known especially from basins other than the NE Pacific Ocean. The present work describes the community composition of the deepest natural whale carcass described to date found at 4204 m depth on Southwest Atlantic Ocean with manned submersible Shinkai 6500. This is the first record of a natural whale fall in the deep Atlantic Ocean. The skeleton belonged to an Antarctic Minke whale composed of only nine caudal vertebrae, whose degradation state suggests it was on the bottom for 5–10 years. The fauna consisted mainly of galatheid crabs, a new species of the snail Rubyspira and polychaete worms, including a new Osedax species. Most of the 41 species found in the carcass are new to science, with several genera shared with NE Pacific whale falls and vent and seep ecosystems. This similarity suggests the whale-fall fauna is widespread and has dispersed in a stepping stone fashion, deeply influencing its evolutionary history.

Adapted to change: The rapid development of symbiosis in newly settled, fast-maturing chemosymbiotic mussels in the deep sea

Symbioses between microbiota and marine metazoa occur globally at chemosynthetic habitats facing imminent threat from anthropogenic disturbance, yet little is known concerning the role of symbiosis during early development in chemosymbiotic metazoans: a critical period in any benthic species' lifecycle. The emerging symbiosis of Idas (sensu lato) simpsoni mussels undergoing development is assessed over a post-larval-to-adult size spectrum using histology and fluorescence in situ hybridisation (FISH). Post-larval development shows similarities to that of both heterotrophic and chemosymbiotic mussels. Data from newly settled specimens confirm aposymbiotic, planktotrophic larval development. Sulphur-oxidising (SOX) symbionts subsequently colonise multiple exposed, non-ciliated epithelia shortly after metamorphosis, but only become abundant on gills as these expand with greater host size. This wide-spread bathymodiolin recorded from sulphidic wood, bone and cold-seep habitats, displays a suite of adaptive traits that could buffer against anthropogenic disturbance.

Post-capture immune gene expression studies in the deep-sea hydrothermal vent mussel Bathymodiolus azoricus acclimatized to atmospheric pressure

Deep-sea hydrothermal vents are extreme habitats that are distributed worldwide in association with volcanic and tectonic events, resulting thus in the establishment of particular environmental conditions, in which high pressure, steep temperature gradients, and potentially toxic concentrations of sulfur, methane and heavy metals constitute driving factors for the foundation of chemosynthetic-based ecosystems. Of all the different macroorganisms found at deep-sea hydrothermal vents, the mussel Bathymodiolus azoricus is the most abundant species inhabiting the vent ecosystems from the Mid-Atlantic Ridge (MAR). In the present study, the effect of long term acclimatization at atmospheric pressure on host-symbiotic associations were studied in light of the ensuing physiological adaptations from which the immune and endosymbiont gene expressions were concomitantly quantified by means of real-time PCR. The expression of immune genes at 0 h, 12 h, 24 h, 36 h, 48 h, 72 h, 1 week and 3 weeks post-capture acclimatization was investigated and their profiles compared across the samples tested. The gene signal distribution for host immune and bacterial genes followed phasic changes in gene expression at 24 h, 1 week and 3 weeks acclimatization when compared to other time points tested during this temporal expression study. Analyses of the bacterial gene expression also suggested that both bacterial density and activity could contribute to shaping the intricate association between endosymbionts and host immune genes whose expression patterns seem to be concomitant at 1 week acclimatization. Fluorescence in situ hybridization was used to assess the distribution and prevalence of endosymbiont bacteria within gill tissues confirming the gradual loss of sulfur-oxidizing (SOX) and methane-oxidizing (MOX) bacteria during acclimatization. The present study addresses the deep-sea vent mussel B. azoricus as a model organism to study how acclimatization in aquaria and the prevalence of symbiotic bacteria are driving the expression of host immune genes. Tight associations, unseen thus far, suggest that host immune and bacterial gene expression patterns reflect distinct physiological responses over the course of acclimatization under aquarium conditions.

Bioenergetic evolution in proteobacteria and mitochondria

Mitochondria are the energy-producing organelles of our cells and derive from bacterial ancestors that became endosymbionts of microorganisms from a different lineage, together with which they formed eukaryotic cells. For a long time it has remained unclear from which bacteria mitochondria actually evolved, even if these organisms in all likelihood originated from the α lineage of proteobacteria. A recent article (Degli Esposti M, et al. 2014. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One 9:e96566) has presented novel evidence indicating that methylotrophic bacteria could be among the closest living relatives of mitochondrial ancestors. Methylotrophs are ubiquitous bacteria that live on single carbon sources such as methanol and methane; in the latter case they are called methanotrophs. In this review, I examine their possible ancestry to mitochondria within a survey of the common features that can be found in the central and terminal bioenergetic systems of proteobacteria and mitochondria. I also discuss previously overlooked information on methanotrophic bacteria, in particular their intracytoplasmic membranes resembling mitochondrial cristae and their capacity of establishing endosymbiotic relationships with invertebrate animals and archaic plants. This information appears to sustain the new idea that mitochondrial ancestors could be related to extant methanotrophic proteobacteria, a possibility that the genomes of methanotrophic endosymbionts will hopefully clarify.

Whale-fall ecosystems: recent insights into ecology, paleoecology, and evolution

Whale falls produce remarkable organic- and sulfide-rich habitat islands at the seafloor. The past decade has seen a dramatic increase in studies of modern and fossil whale remains, yielding exciting new insights into whale-fall ecosystems. Giant body sizes and especially high bone-lipid content allow great-whale carcasses to support a sequence of heterotrophic and chemosynthetic microbial assemblages in the energy-poor deep sea. Deep-sea metazoan communities at whale falls pass through a series of overlapping successional stages that vary with carcass size, water depth, and environmental conditions. These metazoan communities contain many new species and evolutionary novelties, including bone-eating worms and snails and a diversity of grazers on sulfur bacteria. Molecular and paleoecological studies suggest that whale falls have served as hot spots of adaptive radiation for a specialized fauna; they have also provided evolutionary stepping stones for vent and seep mussels and could have facilitated speciation in other vent/seep taxa.

Physiological and genomic features of a novel sulfur-oxidizing gammaproteobacterium belonging to a previously uncultivated symbiotic lineage isolated from a hydrothermal vent

Strain Hiromi 1, a sulfur-oxidizing gammaproteobacterium was isolated from a hydrothermal vent chimney in the Okinawa Trough and represents a novel genus that may include a phylogenetic group found as endosymbionts of deep-sea gastropods. The SSU rRNA gene sequence similarity between strain Hiromi 1 and the gastropod endosymbionts was approximately 97%. The strain was shown to grow both chemolithoautotrophically and chemolithoheterotrophically with an energy metabolism of sulfur oxidation and O₂ or nitrate reduction. Under chemolithoheterotrophic growth conditions, the strain utilized organic acids and proteinaceous compounds as the carbon and/or nitrogen sources but not the energy source. Various sugars did not support growth as a sole carbon source. The observation of chemolithoheterotrophy in this strain is in line with metagenomic analyses of endosymbionts suggesting the occurrence of chemolithoheterotrophy in gammaproteobacterial symbionts. Chemolithoheterotrophy and the presence of homologous genes for virulence- and quorum sensing-related functions suggest that the sulfur-oxidizing chomolithotrophic microbes seek animal bodies and microbial biofilm formation to obtain supplemental organic carbons in hydrothermal ecosystems.

The contrasted evolutionary fates of deep-sea chemosynthetic mussels (Bivalvia, Bathymodiolinae)

Bathymodiolinae are giant mussels that were discovered at hydrothermal vents and harboring chemosynthetic symbionts. Due to their close phylogenetic relationship with seep species and tiny mussels from organic substrates, it was hypothesized that they gradually evolved from shallow to deeper environments, and specialized in decaying organic remains, then in seeps, and finally colonized deep-sea vents. Here, we present a multigene phylogeny that reveals that most of the genera are polyphyletic and/or paraphyletic. The robustness of the phylogeny allows us to revise the genus-level classification. Organic remains are robustly supported as the ancestral habitat for Bathymodiolinae. However, rather than a single step toward colonization of vents and seeps, recurrent habitat shifts from organic substrates to vents and seeps occurred during evolution, and never the reverse. This new phylogenetic framework challenges the gradualist scenarios “from shallow to deep.” Mussels from organic remains tolerate a large range of ecological conditions and display a spectacular species diversity contrary to vent mussels, although such habitats are yet underexplored compared to vents and seeps. Overall, our data suggest that for deep-sea mussels, the high specialization to vent habitats provides ecological success in this harsh habitat but also brings the lineage to a kind of evolutionary dead end.

Adaptive radiation of chemosymbiotic deep-sea mussels

Adaptive radiations present fascinating opportunities for studying the evolutionary process. Most cases come from isolated lakes or islands, where unoccupied ecological space is filled through novel adaptations. Here, we describe an unusual example of an adaptive radiation: symbiotic mussels that colonized island-like chemosynthetic environments such as hydrothermal vents, cold seeps and sunken organic substrates on the vast deep-sea floor. Our time-calibrated molecular phylogeny suggests that the group originated and acquired sulfur-oxidizing symbionts in the Late Cretaceous, possibly while inhabiting organic substrates and long before its major radiation in the Middle Eocene to Early Oligocene. The first appearance of intracellular and methanotrophic symbionts was detected only after this major radiation. Thus, contrary to expectations, the major radiation may have not been triggered by the evolution of novel types of symbioses. We hypothesize that environmental factors, such as increased habitat availability and/or increased dispersal capabilities, sparked the radiation. Intracellular and methanotrophic symbionts were acquired in several independent lineages and marked the onset of a second wave of diversification at vents and seeps. Changes in habitat type resulted in adaptive trends in shell lengths (related to the availability of space and energy, and physiological trade-offs) and in the successive colonization of greater water depths.

Integrative biology of Idas iwaotakii (Habe, 1958), a 'model species' associated with sunken organic substrates

The giant bathymodioline mussels from vents have been studied as models to understand the adaptation of organisms to deep-sea chemosynthetic environments. These mussels are closely related to minute mussels associated to organic remains decaying on the deep-sea floor. Whereas biological data accumulate for the giant mussels, the small mussels remain poorly studied. Despite this lack of data for species living on organic remains it has been hypothesized that during evolution, contrary to their relatives from vents or seeps, they did not acquire highly specialized biological features. We aim at testing this hypothesis by providing new biological data for species associated with organic falls. Within Bathymodiolinae a close phylogenetic relationship was revealed between the Bathymodiolus sensu stricto lineage (i.e. “thermophilus” lineage) which includes exclusively vent and seep species, and a diversified lineage of small mussels, attributed to the genus Idas, that includes mostly species from organic falls. We selected Idas iwaotakii (Habe, 1958) from this latter lineage to analyse population structure and to document biological features. Mitochondrial and nuclear markers reveal a north-south genetic structure at an oceanic scale in the Western Pacific but no structure was revealed at a regional scale or as correlated with the kind of substrate or depth. The morphology of larval shells suggests substantial dispersal abilities. Nutritional features were assessed by examining bacterial diversity coupled by a microscopic analysis of the digestive tract. Molecular data demonstrated the presence of sulphur-oxidizing bacteria resembling those identified in other Bathymodiolinae. In contrast with most Bathymodiolus s.s. species the digestive tract of I. iwaotakii is not reduced. Combining data from literature with the present data shows that most of the important biological features are shared between Bathymodiolus s.s. species and its sister-lineage. However Bathymodiolus s.s. species are ecologically more restricted and also display a lower species richness than Idas species.

Isolation and characterization of a thermophilic, obligately anaerobic and heterotrophic marine Chloroflexi bacterium from a Chloroflexi-dominated microbial community associated with a Japanese shallow hydrothermal system, and proposal for Thermomarinilinea lacunofontalis gen. nov., sp. nov

A novel marine thermophilic and heterotrophic Anaerolineae bacterium in the phylum Chloroflexi, strain SW7^T, was isolated from an in situ colonization system deployed in the main hydrothermal vent of the Taketomi submarine hot spring field located on the southern part of Yaeyama Archipelago, Japan. The microbial community associated with the hydrothermal vent was predominated by thermophilic heterotrophs such as Thermococcaceae and Anaerolineae, and the next dominant population was thermophilic sulfur oxidizers. Both aerobic and anaerobic hydrogenotrophs including methanogens were detected as minor populations. During the culture-dependent viable count analysis in this study, an Anaerolineae strain SW7^T was isolated from an enrichment culture at a high dilution rate. Strain SW7^T was an obligately anaerobic heterotroph that grew with fermentation and had non-motile thin rods 3.5–16.5 μm in length and 0.2 μm in width constituting multicellular filaments. Growth was observed between 37–65°C (optimum 60°C), pH 5.5–7.3 (optimum pH 6.0), and 0.5–3.5% (w/v) NaCl concentration (optimum 1.0%). Based on the physiological and phylogenetic features of a new isolate, we propose a new species representing a novel genus Thermomarinilinea: the type strain of Thermomarinilinea lacunofontalis sp. nov., is SW7^T (=JCM15506^T=KCTC5908^T).

A novel alveolate in bivalves with chemosynthetic bacteria inhabiting deep-sea methane seeps

It has recently been unveiled that a wide variety of microbial eukaryotes (protists) occur in chemosynthetic ecosystems, such as hydrothermal vents and methane seeps. However, there is little knowledge regarding protists associated with endemic animals inhabiting these environments. In the present study, utilizing PCR techniques, we detected fragments of the small subunit ribosomal RNA gene (SSU rRNA gene) from a particular protist from gill tissues of a significant fraction of the vesicomyid clams Calyptogena soyoae and C. okutanii complex and of the mussel Bathymodiolus platifrons and B. japonicus, all of which harbor chemosynthetic endosymbiont bacteria and dominate methane seeps in Sagami Bay, Japan. Based on the phylogeny of SSU rRNA gene, the organism in question was shown to belong to Alveolata. It is noteworthy that this protist did not affiliate with any known alveolate group, although being deeply branched within the lineage of Syndiniales, for which the monophyly was constantly recovered, but not robustly supported. In addition, the protist detected using PCR followed by sequencing was localized within gill epithelial cells of B. platifrons with whole-mount fluorescence in situ hybridization. This protist may be an endoparasite or an endocommensal of Calyptogena spp. and Bathymodiolus spp., and possibly have physiological and ecological impacts on these bivalves.

On the evolutionary ecology of symbioses between chemosynthetic bacteria and bivalves

Mutualistic associations between bacteria and eukaryotes occur ubiquitously in nature, forming the basis for key ecological and evolutionary innovations. Some of the most prominent examples of these symbioses are chemosynthetic bacteria and marine invertebrates living in the absence of sunlight at deep-sea hydrothermal vents and in sediments rich in reduced sulfur compounds. Here, chemosynthetic bacteria living in close association with their hosts convert CO₂ or CH₄ into organic compounds and provide the host with necessary nutrients. The dominant macrofauna of hydrothermal vent and cold seep ecosystems all depend on the metabolic activity of chemosynthetic bacteria, which accounts for almost all primary production in these complex ecosystems. Many of these enigmatic mutualistic associations are found within the molluscan class Bivalvia. Currently, chemosynthetic symbioses have been reported from five distinct bivalve families (Lucinidae, Mytilidae, Solemyidae, Thyasiridae, and Vesicomyidae). This brief review aims to provide an overview of the diverse physiological and genetic adaptations of symbiotic chemosynthetic bacteria and their bivalve hosts.

Reproductive traits of the cold-seep symbiotic mussel Idas modiolaeformis: gametogenesis and larval biology

We describe the first reproductive features of a chemosynthetic mussel collected at cold seeps from the eastern Mediterranean Sea. Idas modiolaeformis (Bivalvia, Mytilidae) is a hermaphroditic species in which production of male and female gametes likely alternates, a feature regarded as an adaptation to patchy and ephemeral habitats. By using fluorescent in situ hybridization, we demonstrate that bacterial symbionts, while present within the gills, are absent within acini that enclose female gametes and male gametes. This supports the hypothesis of environmental acquisition of symbionts in chemosynthetic mytilids. Prodissoconch I (PI) is relatively small compared to prodissoconch II (PII), suggesting a planktotrophic larval stage. Diameters of the two larval shells are in the range of sizes reported for mytilids, with a PII size between that of the shallow Mytilus edulis and that of the cold-seep mussel "Bathymodiolus" childressi.

Metatranscriptomic analysis of sulfur oxidation genes in the endosymbiont of solemya velum

Thioautotrophic endosymbionts in the Domain Bacteria mediate key sulfur transformations in marine reducing environments. However, the molecular pathways underlying symbiont metabolism and the extent to which these pathways are expressed in situ are poorly characterized for almost all symbioses. This is largely due to the difficulty of culturing symbionts apart from their hosts. Here, we use pyrosequencing of community RNA transcripts (i.e., the metatranscriptome) to characterize enzymes of dissimilatory sulfur metabolism in the model symbiosis between the coastal bivalve Solemya velum and its intracellular thioautotrophic symbionts. High-throughput sequencing of total RNA from the symbiont-containing gill of a single host individual generated 1.6 million sequence reads (500 Mbp). Of these, 43,735 matched Bacteria protein-coding genes in BLASTX searches of the NCBI database. The taxonomic identities of the matched genes indicated relatedness to diverse species of sulfur-oxidizing Gammaproteobacteria, including other thioautotrophic symbionts and the purple sulfur bacterium Allochromatium vinosum. Manual querying of these data identified 28 genes from diverse pathways of sulfur energy metabolism, including the dissimilatory sulfite reductase (Dsr) pathway for sulfur oxidation to sulfite, the APS pathway for sulfite oxidation, and the Sox pathway for thiosulfate oxidation. In total, reads matching sulfur energy metabolism genes represented 7% of the Bacteria mRNA pool. Together, these data highlight the dominance of thioautotrophy in the context of symbiont community metabolism, identify the likely pathways mediating sulfur oxidation, and illustrate the utility of metatranscriptome sequencing for characterizing community gene transcription of uncultured symbionts.