Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions

Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans.     

Antarctic marine biodiversity and deep-sea hydrothermal vents

The diversity of many marine benthic groups is unlike that of most other taxa. Rather than declining from the tropics to the poles, much of the benthos shows high diversity in the Southern Ocean. Moreover, many species are unique to the Antarctic region. Recent work has shown that this is also true of the communities of Antarctic deep-sea hydrothermal vents. Vent ecosystems have been documented from many sites across the globe, associated with the thermally and chemically variable habitats found around these, typically high temperature, streams that are rich in reduced compounds and polymetallic sulphides. The animal communities of the East Scotia Ridge vent ecosystems are very different to those elsewhere, though the microbiota, which form the basis of vent food webs, show less differentiation. Much of the biological significance of deep-sea hydrothermal vents lies in their biodiversity, the diverse biochemistry of their bacteria, the remarkable symbioses among many of the marine animals and these bacteria, and the prospects that investigations of these systems hold for understanding the conditions that may have led to the first appearance of life. The discovery of diverse and unusual Antarctic hydrothermal vent ecosystems provides opportunities for new understanding in these fields. Moreover, the Antarctic vents south of 60°S benefit from automatic conservation under the Convention on the Conservation of Antarctic Marine Living Resources and the Antarctic Treaty. Other deep-sea hydrothermal vents located in international waters are not protected and may be threatened by growing interests in deep-sea mining.     

Expansion of the geographic distribution of a novel lineage of epsilon-Proteobacteria to a hydrothermal vent site on the Southern East Pacific Rise

The diversity associated with a microbial mat sample collected from a deep-sea hydrothermal vent on the Southern East Pacific Rise was determined using a molecular phylogenetic approach based on the comparison of sequences from the small subunit ribosomal RNA gene (16S rDNA). The DNA was extracted from the sample and the 16S rDNA was amplified by PCR. Sixteen different phylotypes were identified by restriction fragment length polymorphism analysis; four phylotypes were later identified as putative chimeras. Analysis of the 16S rDNA sequences placed all the phylotypes within the Proteobacteria. The majority of the sequences (98%) were most closely related to a new clade of epsilon-Proteobacteria that were initially identified from an in situ growth chamber deployed on a deep-sea hydrothermal vent on the Mid-Atlantic Ridge in 1995. The similarity between phylotypes identified from Atlantic and Pacific deep-sea hydrothermal vent sites indicates that this new clade of Proteobacteria may be endemic to and widely distributed among deep-sea hydrothermal vents.     

Deep-water chemosynthetic ecosystem research during the census of marine life decade and beyond: a proposed deep-ocean road map

The ChEss project of the Census of Marine Life (2002-2010) helped foster internationally-coordinated studies worldwide focusing on exploration for, and characterization of new deep-sea chemosynthetic ecosystem sites. This work has advanced our understanding of the nature and factors controlling the biogeography and biodiversity of these ecosystems in four geographic locations: the Atlantic Equatorial Belt (AEB), the New Zealand region, the Arctic and Antarctic and the SE Pacific off Chile. In the AEB, major discoveries include hydrothermal seeps on the Costa Rica margin, deepest vents found on the Mid-Cayman Rise and the hottest vents found on the Southern Mid-Atlantic Ridge. It was also shown that the major fracture zones on the MAR do not create barriers for the dispersal but may act as trans-Atlantic conduits for larvae. In New Zealand, investigations of a newly found large cold-seep area suggest that this region may be a new biogeographic province. In the Arctic, the newly discovered sites on the Mohns Ridge (71 °N) showed extensive mats of sulfur-oxidisng bacteria, but only one gastropod potentially bears chemosynthetic symbionts, while cold seeps on the Haakon Mossby Mud Volcano (72 °N) are dominated by siboglinid worms. In the Antarctic region, the first hydrothermal vents south of the Polar Front were located and biological results indicate that they may represent a new biogeographic province. The recent exploration of the South Pacific region has provided evidence for a sediment hosted hydrothermal source near a methane-rich cold-seep area. Based on our 8 years of investigations of deep-water chemosynthetic ecosystems worldwide, we suggest highest priorities for future research: (i) continued exploration of the deep-ocean ridge-crest; (ii) increased focus on anthropogenic impacts; (iii) concerted effort to coordinate a major investigation of the deep South Pacific Ocean - the largest contiguous habitat for life within Earth's biosphere, but also the world's least investigated deep-ocean basin.     

Microdistribution of Faunal Assemblages at Deep-Sea Hydrothermal Vents in the Southern Ocean

Chemosynthetic primary production by microbes supports abundant faunal assemblages at deep-sea hydrothermal vents, with zonation of invertebrate species typically occurring along physico-chemical gradients. Recently discovered vent fields on the East Scotia Ridge (ESR) in the Southern Ocean represent a new province of vent biogeography, but the spatial dynamics of their distinct fauna have yet to be elucidated. This study determines patterns of faunal zonation, species associations, and relationships between faunal microdistribution and hydrothermal activity in a vent field at a depth of 2,400 m on the ESR. Remotely operated vehicle (ROV) dives obtained high-definition imagery of three chimney structures with varying levels of hydrothermal activity, and a mosaic image of >250 m² of seafloor co-registered with temperature measurements. Analysis of faunal microdistribution within the mosaiced seafloor reveals a consistent pattern of faunal zonation with increasing distance from vent sources and peak temperatures. Assemblages closest to vent sources are visibly dominated by a new species of anomuran crab, Kiwa n. sp. (abundance >700 individuals m⁻²), followed by a peltospiroid gastropod (>1,500 individuals m⁻²), eolepadid barnacle (>1,500 individuals m⁻²), and carnivorous actinostolid anemone (>30 individuals m⁻²). Peripheral fauna are not dominated by a single taxon, but include predatory and scavenger taxa such as stichasterid seastars, pycnogonids and octopus. Variation in faunal microdistribution on chimneys with differing levels of activity suggests a possible successional sequence for vent fauna in this new biogeographic province. An increase in δ³⁴S values of primary consumers with distance from vent sources, and variation in their δ¹³C values also indicate possible zonation of nutritional modes of the vent fauna. By using ROV videography to obtain a high-resolution representation of a vent environment over a greater extent than previous studies, these results provide a baseline for determining temporal change and investigations of processes structuring faunal assemblages at Southern Ocean vents.     

Are hydrothermal vents oases for parasitic protists?

Two recent 18S ribosomal RNA-based surveys of protist diversity near hydrothermal vents in the Pacific and Atlantic oceans allowed the identification of a variety of sequences related to several parasitic protist lineages. These include the Apicomplexa, Perkinsozoa, Syndiniales and Kinetoplastida. This diversity of parasitic protists could be hosted by the dense animal populations that thrive around these hydrothermal vents which contrasts with the scarcely populated cold deep-sea waters. These protist parasites might explain some of the mysterious sudden mortality episodes affecting the hydrothermal vent fauna.     

Faunal changes and geographic crypticism indicate the occurrence of a biogeographic transition zone along the southern East Pacific Rise

Aim Deep‐sea hydrothermal vents have now been reported along all active mid‐ocean ridges and back‐arc basins, but the boundaries of biogeographic entities remain questionable owing to methodological issues. Here we examine biogeographic patterns of the vent fauna along the East Pacific Rise (EPR) and determine the relative roles of regional and local factors on the distribution of biodiversity associated with mussel beds along a poorly explored zone, the southern EPR (SEPR). Location East Pacific Rise. Methods A species list of macrobenthic invertebrates along the EPR was compiled from the literature and supplemented with data recovered during the French research cruise BIOSPEEDO carried out in 2004 along the SEPR. Biogeographic patterns were assessed by combining the identification of morphological species with a molecular barcoding approach. A multivariate regression tree (MRT) analysis was performed to identify any geographic breaks, and an empirical distribution of species richness was compared with predictions provided by a mid‐domain effect model. Macrofaunal community structure associated with mussel beds along the SEPR was analysed in relation to environmental factors using cluster and canonical redundancy analyses. Results Sequencing of the cytochrome c oxidase subunit I gene revealed the occurrence of several cryptic species complexes along the EPR, with the equator separating the southern and northern clades. Furthermore, during the BIOSPEEDO cruise at least 10 still unnamed species were collected between 7°25′ S and 21°33′ S. The shift in community structure identified by MRT analysis was located south of 17°34′ S or south of 13°59′ S, depending on the data used, suggesting that the southern part of the SEPR (17°25′–21°33′ S) constitutes a biogeographic transition zone in the vent fauna along the EPR. At a regional scale, latitude combined with the type of venting was significantly correlated with the community structure associated with mussel beds. Main conclusions Together, the molecular data, in situ observations, and the distribution of species suggest that the high diversity of vent fauna species presently observed between 17°25′ S and 21°33′ S is probably a result of the overlap of several distinct biogeographic provinces. We argue that this area thus constitutes a biogeographic vent fauna transition zone along the EPR.     

Observations on parasitism in deep-sea hydrothermal vent and seep limpets

Parasite burdens of shallow-water molluscs have been well documented, but little is known about parasite burdens of molluscs from deep-sea chemosynthetic environments (e.g. hydrothermal vents and seeps). Chemosynthetic habitats are characterized by high concentrations of reduced sulfur and, in the case of vents, high heavy metal concentrations. These compounds are noxious and even stress-inducing in some environments, but are part of the natural chemical milieu of vents and seeps. To examine parasite types and infection intensities in limpets from vents and seeps we documented parasite burdens in 4 limpet species from 4 hydrothermal vent fields (3 on the East Pacific Rise, 1 on the Mid-Atlantic Ridge) and 1 seep site (Florida Escarpment). Approximately 50 % of all limpets examined were infected with 1 or more types of parasites. Limpet parasites were predominantly rickettsia-like inclusions in the digestive and gill epithelia. Limpets collected from the vent field on the Mid-Atlantic Ridge were free of parasites. We detected no histopathological effects that we could attribute to parasites.     

Bacterial group II introns in a deep-sea hydrothermal vent environment

Group II introns are catalytic RNAs and mobile retrotransposable elements known to be present in the genomes of some nonmarine bacteria and eukaryotic organelles. Here we report the discovery of group II introns in a bacterial mat sample collected from a deep-sea hydrothermal vent near 9 degrees N on the East Pacific Rise. One of the introns was shown to self-splice in vitro. This is the first example of marine bacterial introns from molecular population structure studies of microorganisms that live in the proximity of hydrothermal vents. These types of mobile genetic elements may prove useful in improving our understanding of bacterial genome evolution and may serve as valuable markers in comparative studies of bacterial communities.     

Novel uncultured Epsilonproteobacteria dominate a filamentous sulphur mat from the 13 degrees N hydrothermal vent field, East Pacific Rise

Rapid growth of microbial sulphur mats have repeatedly been observed during oceanographic cruises to various deep-sea hydrothermal vent sites. The microorganisms involved in the mat formation have not been phylogenetically characterized, although the production of morphologically similar sulphur filaments by a Arcobacter strain coastal marine has been documented. An in situ collector deployed for 5 days at the 13 degrees N deep-sea hydrothermal vent site on the East Pacific Rise (EPR) was rapidly colonized by a filamentous microbial mat. Microscopic and chemical analyses revealed that the mat consisted of a network of microorganisms embedded in a mucous sulphur-rich matrix. Molecular surveys based on 16S rRNA gene and aclB genes placed all the environmental clone sequences within the Epsilonproteobacteria. Although few 16S rRNA gene sequences were affiliated with that of cultured organisms, the majority was related to uncultured representatives of the Arcobacter group (< or = 95% sequence similarity). A probe designed to target all of the identified lineages hybridized with more than 95% of the mat community. Simultaneous hybridizations with the latter probe and a probe specific to Arcobacter spp. confirmed the numerical dominance of Arcobacter-like bacteria. This study provides the first example of the prevalence and ecological significance of free-living Arcobacter at deep-sea hydrothermal vents.     

Comparative Population Structure of Two Deep-Sea Hydrothermal-Vent-Associated Decapods (Chorocaris sp. 2 and Munidopsis lauensis) from Southwestern Pacific Back-Arc Basins

Studies of genetic connectivity and population structure in deep-sea chemosynthetic ecosystems often focus on endosymbiont-hosting species that are directly dependent on chemical energy extracted from vent effluent for survival. Relatively little attention has been paid to vent-associated species that are not exclusively dependent on chemosynthetic ecosystems. Here we assess connectivity and population structure of two vent-associated invertebrates—the shrimp Chorocaris sp. 2 and the squat lobster Munidopsis lauensis—that are common at deep-sea hydrothermal vents in the western Pacific. While Chorocaris sp. 2 has only been observed at hydrothermal vent sites, M. lauensis can be found throughout the deep sea but occurs in higher abundance around the periphery of active vents We sequenced mitochondrial COI genes and deployed nuclear microsatellite markers for both species at three sites in Manus Basin and either North Fiji Basin (Chorocaris sp. 2) or Lau Basin (Munidopsis lauensis). We assessed genetic differentiation across a range of spatial scales, from approximately 2.5 km to more than 3000 km. Population structure for Chorocaris sp. 2 was comparable to that of the vent-associated snail Ifremeria nautilei, with a single seemingly well-mixed population within Manus Basin that is genetically differentiated from conspecifics in North Fiji Basin. Population structure for Munidopsis lauensis was more complex, with two genetically differentiated populations in Manus Basin and a third well-differentiated population in Lau Basin. The unexpectedly high level of genetic differentiation between M. lauensis populations in Manus Basin deserves further study since it has implications for conservation and management of diversity in deep-sea hydrothermal vent ecosystems.     

Prokaryote Diversity and Virus Abundance in Shallow Hydrothermal Vents of the Mediterranean Sea (Panarea Island) and the Pacific Ocean (North Sulawesi-Indonesia)

Despite their ubiquitous distribution in tectonically active coastal zones, shallow water hydrothermal vents have been less investigated than deep-sea vents. In the present study, we investigated the role of viral control and fluid emissions on prokaryote abundance, diversity, and community structure (total Archaea, total Bacteria, and sulphate-reducing bacteria) in waters and sediments surrounding the caldera of four different shallow-water hydrothermal vents (three located in the Mediterranean Sea and one in the Pacific Ocean). All vents, independent of their location, generally displayed a significant decrease of benthic prokaryote abundance, as well as its viable fraction, with increasing distance from the vent. Prokaryote assemblages were always dominated by Bacteria. Benthic Archaea accounted for 23–33% of total prokaryote abundance in the Mediterranean Sea and from 13 to 29% in the Pacific Ocean, whereas in the water column they accounted for 25–38%. The highest benthic bacterial ribotype richness was observed in close proximity of the vents (i.e., at 10-cm distance from the emissions), indicating that vent fluids might influence bacterial diversity in surrounding sediments. Virioplankton and viriobenthos abundances were low compared to other marine systems, suggesting that temperature and physical-chemical conditions might influence viral survival in these vent systems. We thus hypothesize that the high bacterial diversity observed in close proximity of the vents is related with the highly variable vent emissions, which could favor the coexistence of several prokaryotic species.     

Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance

Deep-sea vents support productive ecosystems driven primarily by chemoautotrophs. Chemoautotrophs are organisms that are able to fix inorganic carbon using a chemical energy obtained through the oxidation of reduced compounds. Following the discovery of deep-sea vent ecosystems in 1977, there has been an increasing knowledge that deep-sea vent chemoautotrophs display remarkable physiological and phylogenetic diversity. Cultivation-dependent and -independent studies have led to an emerging view that the majority of deep-sea vent chemoautotrophs have the ability to derive energy from a variety of redox couples other than the conventional sulfur-oxygen couple, and fix inorganic carbon via the reductive tricarboxylic acid cycle. In addition, recent genomic, metagenomic and postgenomic studies have considerably accelerated the comprehensive understanding of molecular mechanisms of deep-sea vent chemoautotrophy, even in yet uncultivable endosymbionts of vent fauna. Genomic analysis also suggested that there are previously unrecognized evolutionary links between deep-sea vent chemoautotrophs and important human/animal pathogens. This review summarizes chemoautotrophy in deep-sea vents, highlighting recent biochemical and genomic discoveries.     

Colonization of nascent, deep-sea hydrothermal vents by a novel Archaeal and Nanoarchaeal assemblage

Active deep-sea hydrothermal vents are areas of intense mixing and severe thermal and chemical gradients, fostering a biotope rich in novel hyperthermophilic microorganisms and metabolic pathways. The goal of this study was to identify the earliest archaeal colonizers of nascent hydrothermal chimneys, organisms that may be previously uncharacterized as they are quickly replaced by a more stable climax community. During expeditions in 2001 and 2002 to the hydrothermal vents of the East Pacific Rise (EPR) (9 degrees 50'N, 104 degrees 17'W), we removed actively venting chimneys and in their place deployed mineral chambers and sampling units that promoted the growth of new, natural hydrothermal chimneys and allowed their collection within hours of formation. These samples were compared with those collected from established hydrothermal chimneys from EPR and Guaymas Basin vent sites. Using molecular and phylogenetic analysis of the 16S rDNA, we show here that at high temperatures, early colonization of a natural chimney is dominated by members of the archaeal genus Ignicoccus and its symbiont, Nanoarchaeum. We have identified 19 unique sequences closely related to the nanoarchaeal group, and five archaeal sequences that group closely with Ignicoccus. These organisms were found to colonize a natural, high temperature protochimney and vent-like mineral assemblages deployed over high temperature outflows within 92 h. When compared phylogenetically, several of these colonizing organisms form a unique clade independent of those found in mature chimneys and low-temperature mineral chamber samples. As a model ecosystem, the identification of pioneering consortia in deep-sea hydrothermal vents may help advance the understanding of how early microbial life forms gained a foothold in hydrothermal systems on early Earth and potentially on other planetary bodies.     

Comparative composition, diversity and trophic ecology of sediment macrofauna at vents, seeps and organic falls

Sediments associated with hydrothermal venting, methane seepage and large organic falls such as whale, wood and plant detritus create deep-sea networks of soft-sediment habitats fueled, at least in part, by the oxidation of reduced chemicals. Biological studies at deep-sea vents, seeps and organic falls have looked at macrofaunal taxa, but there has yet to be a systematic comparison of the community-level attributes of sediment macrobenthos in various reducing ecosystems. Here we review key similarities and differences in the sediment-dwelling assemblages of each system with the goals of (1) generating a predictive framework for the exploration and study of newly identified reducing habitats, and (2) identifying taxa and communities that overlap across ecosystems. We show that deep-sea seep, vent and organic-fall sediments are highly heterogeneous. They sustain different geochemical and microbial processes that are reflected in a complex mosaic of habitats inhabited by a mixture of specialist (heterotrophic and symbiont-associated) and background fauna. Community-level comparisons reveal that vent, seep and organic-fall macrofauna are very distinct in terms of composition at the family level, although they share many dominant taxa among these highly sulphidic habitats. Stress gradients are good predictors of macrofaunal diversity at some sites, but habitat heterogeneity and facilitation often modify community structure. The biogeochemical differences across ecosystems and within habitats result in wide differences in organic utilization (i.e., food sources) and in the prevalence of chemosynthesis-derived nutrition. In the Pacific, vents, seeps and organic-falls exhibit distinct macrofaunal assemblages at broad-scales contributing to ß diversity. This has important implications for the conservation of reducing ecosystems, which face growing threats from human activities.     

Decades of dietary data demonstrate regional food web structures in the Southern Ocean

Understanding regional‐scale food web structure in the Southern Ocean is critical to informing fisheries management and assessments of climate change impacts on Southern Ocean ecosystems and ecosystem services. Historically, a large component of Southern Ocean ecosystem research has focused on Antarctic krill, which provide a short, highly efficient food chain, linking primary producers to higher trophic levels. Over the last 15 years, the presence of alternative energy pathways has been identified and hypotheses on their relative importance in different regions raised. Using the largest circumpolar dietary database ever compiled, we tested these hypotheses using an empirical circumpolar comparison of food webs across the four major regions/sectors of the Southern Ocean (defined as south of 40°S) within the austral summer period. We used network analyses and generalizations of taxonomic food web structure to confirm that while Antarctic krill are dominant as the mid‐trophic level for the Atlantic and East Pacific food webs (including the Scotia Arc and Western Antarctic Peninsula), mesopelagic fish and other krill species are dominant contributors to predator diets in the Indian and West Pacific regions (East Antarctica and the Ross Sea). We also highlight how tracking data and habitat modeling for mobile top predators in the Southern Ocean show that these species integrate food webs over large regional scales. Our study provides a quantitative assessment, based on field observations, of the degree of regional differentiation in Southern Ocean food webs and the relative importance of alternative energy pathways between regions.     

Diversity of Meiofauna from the 9°50′N East Pacific Rise across a Gradient of Hydrothermal Fluid Emissions

Background

We studied the meiofauna community at deep-sea hydrothermal vents along a gradient of vent fluid emissions in the axial summit trought (AST) of the East Pacific Rise 9°50′N region. The gradient ranged from extreme high temperatures, high sulfide concentrations, and low pH at sulfide chimneys to ambient deep-sea water conditions on bare basalt. We explore meiofauna diversity and abundance, and discuss its possible underlying ecological and evolutionary processes.

Methodology/Principal Findings

After sampling in five physico-chemically different habitats, the meiofauna was sorted, counted and classified. Abundances were low at all sites. A total of 52 species were identified at vent habitats. The vent community was dominated by hard substrate generalists that also lived on bare basalt at ambient deep-sea temperature in the axial summit trough (AST generalists). Some vent species were restricted to a specific vent habitat (vent specialists), but others occurred over a wide range of physico-chemical conditions (vent generalists). Additionally, 35 species were only found on cold bare basalt (basalt specialists). At vent sites, species richness and diversity clearly increased with decreasing influence of vent fluid emissions from extreme flow sulfide chimney (no fauna), high flow pompei worm (S: 4–7, H''_loge: 0.11–0.45), vigorous flow tubeworm (S: 8–23; H''_loge: 0.44–2.00) to low flow mussel habitats (S: 28–31; H''_loge: 2.34–2.60).

Conclusions/Significance

Our data suggest that with increasing temperature and toxic hydrogen sulfide concentrations and increasing amplitude of variation of these factors, fewer species are able to cope with these extreme conditions. This results in less diverse communities in more extreme habitats. The finding of many species being present at sites with and without vent fluid emissions points to a non endemic deep-sea hydrothermal vent meiofaunal community. This is in contrast to a mostly endemic macrofauna but similar to what is known for meiofauna from shallow-water vents.     

Comparative analysis between protist communities from the deep‐sea pelagic ecosystem and specific deep hydrothermal habitats

Protist communities associated with deep seawater and bivalves from six hydrothermal sites in the Pacific Ocean were characterized by microscopy and molecular rRNA gene surveys (18S rRNA) and compared with planktonic communities from Pacific deep‐pelagic seawater (from 500 to 3000 m in depth). Genetic libraries from larger size fractions (> 3 µm) of deep‐pelagic water were mainly dominated by Dinophyceae, whereas small size fractions (< 3 µm) mainly revealed radiolarians and Syndiniales. In contrast, more specific opportunistic detritivores and grazers, mostly belonging to Stramenopiles and Cercozoa, were detected from water surrounding vent chimneys. Protist communities were different in the pallial cavity of the giant hydrothermal bivalves Bathymodiolus thermophilus and Calyptogena magnifica, dominated by Ciliophora (primarily belonging to Phyllopharyngea, Oligohymenophorea and Oligotrichea) and Cercozoa. Interestingly, protist communities retrieved from the pallial cavity liquid of hydrothermal bivalves were remarkably homogeneous along the Southern East Pacific Rise, in contrast to bivalves collected on the Mid‐Atlantic Ridge hydrothermal vents and cold seeps from the Gulf of Mexico. Hence, complex protist communities seem to occur inside hydrothermal bivalves, and these metazoa may constitute a stable micro‐niche for micro‐eukaryotes, including grazers, detritivores, symbionts and potential parasites. From these communities, new lineages within the ciliates may emerge.