Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge

To evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted Lucky Strike (37°17'N, 32°16.3'W, depth 1600-1750 m) and the ultramafic-hosted Rainbow (36°13'N, 33°54.1'W, depth 2270-2330 m) vent fields along the Mid-Atlantic Ridge (MAR). Using multiplexed barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA genes, we show statistically significant differences between the archaeal and bacterial communities associated with the different vent fields. Quantitative polymerase chain reaction (qPCR) assays of the functional gene diagnostic for methanogenesis (mcrA), as well as geochemical modelling to predict pore fluid chemistries within the deposits, support the pyrosequencing observations. Collectively, these results show that the less reduced, hydrogen-poor fluids at Lucky Strike limit colonization by strict anaerobes such as methanogens, and allow for hyperthermophilic microaerophiles, like Aeropyrum. In contrast, the hydrogen-rich reducing vent fluids at the ultramafic-influenced Rainbow vent field support the prevalence of methanogens and other hydrogen-oxidizing thermophiles at this site. These results demonstrate that biogeographical patterns of hydrothermal vent microorganisms are shaped in part by large scale geological and geochemical processes.     

Diversity of Bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge

Two sediment cores were collected in an inactive area of the deep-sea hydrothermal vent field Rainbow (36 degrees N on the Mid-Atlantic Ridge). Metals and carbonates were abundant throughout the cores; calcite (CaCO3) was found throughout the cores while dolomite [CaMg(CO3)2] and siderite (FeCO3) were only found in deeper layers. Using polymerase chain reaction (PCR)-amplified 16S rRNA gene sequence analysis, we examined the bacterial and archaeal diversity in a sediment layer that contained the three carbonates. The retrieved bacterial and archaeal sequences were new and less than 4% of the sequences exhibited 94% or more identity with that of cultured organisms. The analysis of the composition of the bacterial library revealed a high diversity of sequences. Half of the bacterial clones was affiliated to the gamma-Proteobacteria. Most of them had environmental sequences retrieved from deep-sea sediments as closest relatives, some of which being distantly related to free-living and symbiotic sulfur-oxidizers. Other sequences clustered in the alpha-, delta- and epsilon-Proteobacteria, the 'Bacteroidetes', the 'Planctomycetes', the 'Nitrospirae', the 'Actinobacteria', the 'Chlorobi ' and the 'Verrumicrobia'. Based on clonal abundance and sequence comparisons, phylotype groups putatively involved in the oxydation of sulfur compounds appeared to dominate in the studied sample. The majority of the archaeal sequences clustered in an euryarchaeotic lineage recently identified in the walls of black smokers suggesting a possible thermophilic way of life of these uncultured microorganisms. Oxygen isotopic composition of siderite and dolomite indicated that they were formed at 67 degrees C and 94 degrees C respectively. Together with chemical and microbiological data, this suggested that hydrothermal fluids may have circulated through this sediment.     

Dual symbiosis of the vent shrimp Rimicaris exoculata with filamentous gamma- and epsilonproteobacteria at four Mid-Atlantic Ridge hydrothermal vent fields

The shrimp Rimicaris exoculata from hydrothermal vents on the Mid-Atlantic Ridge (MAR) harbours bacterial epibionts on specialized appendages and the inner surfaces of its gill chamber. Using comparative 16S rRNA sequence analysis and fluorescence in situ hybridization (FISH), we examined the R. exoculata epibiosis from four vents sites along the known distribution range of the shrimp on the MAR. Our results show that R. exoculata lives in symbiosis with two types of filamentous epibionts. One belongs to the Epsilonproteobacteria, and was previously identified as the dominant symbiont of R. exoculata. The second is a novel gammaproteobacterial symbiont that belongs to a clade consisting exclusively of sequences from epibiotic bacteria of hydrothermal vent animals, with the filamentous sulfur oxidizer Leucothrix mucor as the closest free-living relative. Both the epsilon- and the gammaproteobacterial symbionts dominated the R. exoculata epibiosis at all four MAR vent sites despite striking differences between vent fluid chemistry and distances between sites of up to 8500 km, indicating that the symbiosis is highly stable and specific. Phylogenetic analyses of two mitochondrial host genes showed little to no differences between hosts from the four vent sites. In contrast, there was significant spatial structuring of both the gamma- and the epsilonproteobacterial symbiont populations based on their 16S rRNA gene sequences that was correlated with geographic distance along the MAR. We hypothesize that biogeography and host-symbiont selectivity play a role in structuring the epibiosis of R. exoculata.     

A hybrid zone between hydrothermal vent mussels (Bivalvia: Mytilidae) from the Mid-Atlantic Ridge

This study provides the first example of a hybrid zone between animal taxa distributed along the mid-ocean ridge system. We examined the distribution and genetic structure of deep-sea hydrothermal vent mussels (Bivalvia: Mytilidae) along a 2888-km portion of the Mid-Atlantic Ridge between 37 degrees 50' N and 14 degrees 45' N latitude. Mitochondrial DNA (mtDNA), allozymes and multivariate-morphometric evidence discriminated between individuals of a northern species, Bathymodiolus azoricus, and a southern species, B. puteoserpentis, that were separated by an intermediate ridge segment almost devoid of mussels. A small sample of mussels from Broken Spur, a vent locality along this intermediate zone, revealed a mixed population with gene frequencies and morphology that were broadly intermediate to those of the northern and southern species. Multilocus clines in mtDNA and allozyme frequencies were centred over the intermediate zone. We consider intrinsic and extrinsic processes that might limit genetic exchange across this hybrid zone.     

Anaerobic respiration on tellurate and other metalloids in bacteria from hydrothermal vent fields in the eastern Pacific Ocean

This paper reports the discovery of anaerobic respiration on tellurate by bacteria isolated from deep ocean (1,543 to 1,791 m) hydrothermal vent worms. The first evidence for selenite- and vanadate-respiring bacteria from deep ocean hydrothermal vents is also presented. Enumeration of the anaerobic metal(loid)-resistant microbial community associated with hydrothermal vent animals indicates that a greater proportion of the bacterial community associated with certain vent fauna resists and reduces metal(loid)s anaerobically than aerobically, suggesting that anaerobic metal(loid) respiration might be an important process in bacteria that are symbiotic with vent fauna. Isolates from Axial Volcano and Explorer Ridge were tested for their ability to reduce tellurate, selenite, metavanadate, or orthovanadate in the absence of alternate electron acceptors. In the presence of metal(loid)s, strains showed an ability to grow and produce ATP, whereas in the absence of metal(loid)s, no growth or ATP production was observed. The protonophore carbonyl cyanide m-chlorophenylhydrazone depressed metal(loid) reduction. Anaerobic tellurate respiration will be a significant component in describing biogeochemical cycling of Te at hydrothermal vents.     

Comparison of intact polar lipid with microbial community composition of vent deposits of the Rainbow and Lucky Strike hydrothermal fields

The intact polar lipid (IPL) composition of twelve hydrothermal vent deposits from the Rainbow (RHF) and Lucky Strike hydrothermal fields (LSHF) has been investigated in order to assess its utility as a proxy for microbial community composition associated with deep‐sea hydrothermal locations. Gene‐based culture‐independent surveys of the microbial populations of the same vent deposits have shown that microbial populations are different in the two locations and appear to be controlled by the geochemical and geological processes that drive hydrothermal circulation. Large differences in the IPL composition between these two sites are evident. In the ultramafic‐hosted RHF, mainly archaeal‐IPLs were identified, including those known to be produced by hyperthermophilic Euryarchaeota. More specifically, polyglycosyl derivatives of archaeol and macrocyclic archaeol indicate the presence of hyperthermophilic methanogenic archaea in the vent deposits, which are related to members of the Methanocaldococcaceae or Methanococcaceae. In contrast, bacterial IPLs dominate IPL distributions from LSHF, suggesting that bacteria are more predominant at LSHF than at RHF. Bacterial Diacyl glycerol (DAG) IPLs containing phosphocholine, phosphoethanolamine or phosphoglycerol head groups were identified at both vent fields. In some vent deposits from LSHF ornithine lipids and IPLs containing phosphoaminopentanetetrol head groups were also observed. By comparison with previously characterized bacterial communities at the sites, it is likely the DAG‐IPLs observed derive from Epsilon‐ and Gammaproteobacteria. Variation in the relative amounts of archaeal versus bacterial IPLs appears to indicate differences in the microbial community between vent sites. Overall, IPL distributions appear to be consistent with gene‐based surveys.     

Spatial patterns of Aquificales in deep-sea vents along the Eastern Lau Spreading Center (SW Pacific)

The microbial diversity associated with actively venting deep-sea hydrothermal deposits is tightly connected to the geochemistry of the hydrothermal fluids. Although the dominant members of these deposits drive the structure of the microbial communities, it is less well understood whether the lower abundance groups are as closely connected to the geochemical milieu, or driven perhaps by biotic factors such as microbial community interactions. We used the natural geochemical gradients that exist in the back-arc basin, Eastern Lau Spreading Center and Valu-Fa Ridge (ELSC/VFR) in the Southwestern Pacific, to explore whether the chemolithotrophic Aquificales are influenced by geographical location, host-rock of the vent field or deposit type. Using a combination of cloning, DNA fingerprinting (DGGE) and enrichment culturing approaches, all genera of this order previously described at marine vents were detected, i.e., Desulfurobacterium, Thermovibrio, Aquifex, Hydrogenivirga, Persephonella and Hydrogenothermus. The comparison between clone libraries and DGGE showed similar patterns of distribution of different Aquificales whereas results differed for the enrichment cultures that were retrieved. However, the use of cultivation-based and -independent methods did provide complementary phylogenetic diversity overview of the Aquificales in these systems. Together, this survey revealed that the ELSC/VFR contains some of the largest diversity of Aquificales ever reported at a deep-sea vent area, that the diversity patterns are tied to the geography and geochemistry of the system, and that this geochemical diverse back-arc basin may harbor new members of the Aquificales.     

Host-symbiont relationships in hydrothermal vent gastropods of the genus Alviniconcha from the Southwest Pacific

Hydrothermal vent gastropods of the genus Alviniconcha are unique among metazoans in their ability to derive their nutrition from chemoautotrophic gamma- and epsilon-proteobacterial endosymbionts. Although host-symbiont relationships in Alviniconcha gastropods from the Central Indian Ridge in the Indian Ocean and the Mariana Trough in the Western Pacific have been studied extensively, host-symbiont relationships in Alviniconcha gastropods from the Southwest Pacific remain largely unknown. Phylogenetic analysis using mitochondrial cytochrome c oxidase subunit I gene sequences of host gastropods from the Manus, North Fiji, and Lau Back-Arc Basins in the Southwest Pacific has revealed a new host lineage in a Alviniconcha gastropod from the Lau Basin and the occurrence of the host lineage Alviniconcha sp. type 2 in the Manus Basin. Based on 16S rRNA gene sequences of bacterial endosymbionts, two gamma-proteobacterial lineages and one epsilon-proteobacterial lineage were identified in the present study. The carbon isotopic compositions of the biomass and fatty acids of the gastropod tissues suggest that the gamma- and epsilon-proteobacterial endosymbionts mediate the Calvin-Benson cycle and the reductive tricarboxylic acid cycle, respectively, for their chemoautotrophic growth. Coupling of the host and symbiont lineages from the three Southwest Pacific basins revealed that each of the Alviniconcha lineages harbors different bacterial endosymbionts belonging to either the gamma- or epsilon-Proteobacteria. The host specificity exhibited in symbiont selection provides support for the recognition of each of the host lineages as a distinct species. The results from the present study also suggest the possibility that Alviniconcha sp. types 1 and 2 separately inhabit hydrothermal vent sites approximately 120 m apart in the North Fiji Basin and 500 m apart in the Manus Basin.     

Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin

Diverse microbial communities thrive on and in deep-sea hydrothermal vent mineral deposits. However, our understanding of the inter-field variability in these communities is poor, as limited sampling and sequencing efforts have hampered most previous studies. To explore the inter-field variability in these communities, we used barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA gene to characterize the archaeal and bacterial communities of over 30 hydrothermal deposit samples from six vent fields located along the Eastern Lau Spreading Center. Overall, the bacterial and archaeal communities of the Eastern Lau Spreading Center are similar to other active vent deposits, with a high diversity of Epsilonproteobacteria and thermophilic Archaea. However, the archaeal and bacterial communities from the southernmost vent field, Mariner, were significantly different from the other vent fields. At Mariner, the epsilonproteobacterial genus Nautilia and the archaeal family Thermococcaceae were prevalent in most samples, while Lebetimonas and Thermofilaceae were more abundant at the other vent fields. These differences appear to be influenced in part by the unique geochemistry of the Mariner fluids resulting from active degassing of a subsurface magma chamber. These results show that microbial communities associated with hydrothermal vent deposits in back-arc basins are taxonomically similar to those from mid-ocean ridge systems, but differences in geologic processes between vent fields in a back-arc basin can influence microbial community structure.     

A review of the distribution of hydrothermal vent communities along the northern Mid-Atlantic Ridge: dispersal vs. environmental controls

Hydrobiologia - Until 1985, seven vent fields were described from the Mid-Atlantic Ridge (MAR). An eighth field, Mount Saldanha (36° N), discovered in 1998, showed unusual geological and...     

Diversity of dissimilatory bisulfite reductase genes of bacteria associated with the deep-sea hydrothermal vent polychaete annelid Alvinella pompejana

A unique community of bacteria colonizes the dorsal integument of the polychaete annelid Alvinella pompejana, which inhabits the high-temperature environments of active deep-sea hydrothermal vents along the East Pacific Rise. The composition of this bacterial community was characterized in previous studies by using a 16S rRNA gene clone library and in situ hybridization with oligonucleotide probes. In the present study, a pair of PCR primers (P94-F and P93-R) were used to amplify a segment of the dissimilatory bisulfite reductase gene from DNA isolated from the community of bacteria associated with A. pompejana. The goal was to assess the presence and diversity of bacteria with the capacity to use sulfate as a terminal electron acceptor. A clone library of bisulfite reductase gene PCR products was constructed and characterized by restriction fragment and sequence analysis. Eleven clone families were identified. Two of the 11 clone families, SR1 and SR6, contained 82% of the clones. DNA sequence analysis of a clone from each family indicated that they are dissimilatory bisulfite reductase genes most similar to the dissimilatory bisulfite reductase genes of Desulfovibrio vulgaris, Desulfovibrio gigas, Desulfobacterium autotrophicum, and Desulfobacter latus. Similarities to the dissimilatory bisulfite reductases of Thermodesulfovibrio yellowstonii, the sulfide oxidizer Chromatium vinosum, the sulfur reducer Pyrobaculum islandicum, and the archaeal sulfate reducer Archaeoglobus fulgidus were lower. Phylogenetic analysis separated the clone families into groups that probably represent two genera of previously uncharacterized sulfate-reducing bacteria. The presence of dissimilatory bisulfite reductase genes is consistent with recent temperature and chemical measurements that documented a lack of dissolved oxygen in dwelling tubes of the worm. The diversity of dissimilatory bisulfite reductase genes in the bacterial community on the back of the worm suggests a prominent role for anaerobic sulfate-reducing bacteria in the ecology of A. pompejana.     

Analysis of lipids from a hydrothermal vent methanogen and associated vent sediment by supercritical fluid chromatography

Lipids from a thermophilic methanogen and the associated hydrothermal vent sediment (Guaymas Basin, Gulf of California) were analyzed by gas chrmotography-mass spectrometry (GC-MS) and supercritical fluid chromatography (SFC). The neutral lipids of the thermophilic methagonen consisted of straight chain alkanes (nC₂₂ to nC₃₆), with nC₂₄, nC₂₈, nC₃₂ and nC₃₆ predominating and C₂₅, C₃₀ and C₃₅-isoprenoids and hydroisoprenoids. The squalene (C₃₀) series was the most abundant (95.6%). The backbone structure of the novel C₃₅-isoprenouds was tentatively identified as 2,6,10,14,19,23,27-heptamethyloctacosane. Polar lipids of the thermophilic methanogen were analyzed by SFC and consisted fo diphytanyl glyceril diether (61.6%), macrocyclic glycerol diether (15.3%), dibiphytanyl diglycerol tetraether (11.8%) and an unidentified component (11.4%).Biomarker analysis of the Guaymas Basin sediment revealed the presence of small amounts of polyunsaturated C₃₀-isoprenoids, with a distribution similar to the C₃₀-isoprenoids of the thermophilic methanogen. In addition, the sediment contained ‘free’ diphytanyl glycerol diether as predominant ether lipid. Low levels of polar ether lipids, indicative of ‘active’ archaebacteria, were also detected. Results suggest that Guaymas Basin sediment recently contained active microbial populations with a lipid profile similar to the isolated thermophilic methanogen.     

Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca Ridge

The subseafloor microbial habitat associated with typical unsedimented mid-ocean-ridge hydrothermal vent ecosystems may be limited by the availability of fixed nitrogen, inferred by the low ammonium and nitrate concentrations measured in diffuse hydrothermal fluid. Dissolved N2 gas, the largest reservoir of nitrogen in the ocean, is abundant in deep-sea and hydrothermal vent fluid. In order to test the hypothesis that biological nitrogen fixation plays an important role in nitrogen cycling in the subseafloor associated with unsedimented hydrothermal vents, degenerate PCR primers were designed to amplify the nitrogenase iron protein gene nifH from hydrothermal vent fluid. A total of 120 nifH sequences were obtained from four samples: a nitrogen-poor diffuse vent named marker 33 on Axial Volcano, sampled twice over a period of 1 year as its temperature decreased; a nitrogen-rich diffuse vent near Puffer on Endeavour Segment; and deep seawater with no detectable hydrothermal plume signal. Subseafloor nifH genes from marker 33 and Puffer are related to anaerobic clostridia and sulfate reducers. Other nifH genes unique to the vent samples include proteobacteria and divergent ARCHAEA: All of the nifH genes from the deep-seawater sample are most closely related to the thermophilic, anaerobic archaeon Methanococcus thermolithotrophicus (77 to 83% amino acid similarity). These results provide the first genetic evidence of potential nitrogen fixers in hydrothermal vent environments and indicate that at least two sources contribute to the diverse assemblage of nifH genes detected in hydrothermal vent fluid: nifH genes from an anaerobic, hot subseafloor and nifH genes from cold, oxygenated deep seawater.     

Comparative phylogeography among hydrothermal vent species along the East Pacific Rise reveals vicariant processes and population expansion in the South

The use of sequence polymorphism from individual mitochondrial genes to infer past demography has recently proved controversial because of the recurrence of selective sweeps acting over genes and the need for unlinked multilocus data sets. However, comparative analyses using several species for one gene and/or multiple genes for one species can serve as a test for potential selective effects and clarify our understanding of historical demographic effects. This study compares nucleotide polymorphisms in mitochondrial cytochrome oxidase I across seven deep-sea hydrothermal vent species that live along the volcanically active East Pacific Rise. Approximate Bayesian Computation (ABC) method, developed to trace shared vicariant events across species pairs, indicates the occurrence of two across species divergence times, and suggests that the present geographical patterns of genetic differentiation may be explained by two periods of significant population isolation. The oldest period dates back 11.6 Ma and is associated with the vent limpet Lepetodrilus elevatus , while the most recent period of isolation is 1.3 Ma, which apparently affected all species examined and coincides with a transition zone across the equator. Moreover, significant negative Tajima's D and star-like networks were observed for all southern lineages, suggesting that these lineages experienced a concomitant demographic and geographical expansion about 100 000–300 000 generations ago. This expansion may have initiated from a wave of range expansions during the secondary colonization of new sites along the Southern East Pacific Rise (founder effects below the equator) or recurrent bottleneck events because of the increase of eruptive phases associated with the higher spreading rates of the ridge in this region.     

New species of Stygiopontius (Copepoda, Siphonostomatoida) from a deep–sea hydrothermal vent at the East Pacific Rise

Three dirivultid copepods, Stygiopontius puxillifer sp.n . and S. appositus sp.n., unusual in having pegs along the ventral edges of the cephalosome, and S. lurniger sp.n., distinguiahcd from congeners by the modificd thorn-like seta on the second segment of the maxilliped, arc dcscrihcd from a depth of 2616 m at 21°N in the eastern Pacific.     

Bacterial and archaeal phylotypes associated with distinct mineralogical layers of a white smoker spire from a deep-sea hydrothermal vent site (9 degrees N, East Pacific Rise)

A diffusely venting chimney spire from the East Pacific Rise (9 degrees N) was analysed by petrographic thin sectioning and 16S rRNA gene cloning and sequencing in parallel, to correlate microbial community composition with mineralogy and inferred in situ conditions within the chimney mineral matrix. Both approaches indicated a zonation of the chimney spire into distinct microhabitats for different bacteria and archaea. The thermal gradient inferred from the mineral composition and porosity of the chimney was consistent with the distribution of bacterial and archaeal phylotypes in the chimney matrix. A novel phylogenetic lineage of euryarchaeota was found that co-occurred with clones related to cultured hyperthermophilic archaea. A few phylotypes related to mesophilic bacteria were found in the hot core of the chimney, indicating that seawater influx during retrieval and cooling of these highly porous structures can entrain microorganisms into chimney layers that are not their native habitat.     

Calispadella alata n. gen., n. sp., the first chaetognath recorded from a hydrothermal vent site (Mid-Atlantic Ridge)

Calispadella alata n. gen., n. sp., is the first chaetognathdescribed from a hydrothermal vent field (Mid-Atlantic Ridge,depth 1600 m). It belongs to the family Spadellidae (presenceof transverse muscles in trunk and long tail segment). Thereis a pair of lateral fins making no contact with the body posteriorly;these free wing-like extensions end in festoons provided distallywith patches of adhesive cells. This unique feature in a deepbentho-planktonic species can be seen as an adaptation to adhereat times to the substrate to resist local turbulences producedby the hydrothermal fluids. This may also indicate that thisnew genus is phylogenetically close to the neritic genus Paraspadella,which has adhesive finger-like processes. Calispadella alatais sexually precocious as reported for other deep chaetognaths,contrary to most deep living organisms which exhibit delayedsexual maturity. This feature might be a means to increase thepossibility of mating in scarce populations.