Cyanobacteria and chloroflexi-dominated hypolithic colonization of quartz at the hyper-arid core of the Atacama Desert,Chile

Quartz stones are ubiquitous in deserts and are a substrate for hypoliths, microbial colonists of the underside of such stones. These hypoliths thrive where extreme temperature and moisture stress limit the occurrence of higher plant and animal life. Several studies have reported the occurrence of green hypolithic colonization dominated by cyanobacteria. Here, we describe a novel red hypolithic colonization from Yungay, at the hyper-arid core of the Atacama Desert in Chile. Comparative analysis of green and red hypoliths from this site revealed markedly different microbial community structure as revealed by 16S rRNA gene clone libraries. Green hypoliths were dominated by cyanobacteria (Chroococcidiopsis and Nostocales phylotypes), whilst the red hypolith was dominated by a taxonomically diverse group of chloroflexi. Heterotrophic phylotypes common to all hypoliths were affiliated largely to desiccation-tolerant taxa within the Actinobacteria and Deinococci. Alphaproteobacterial phylotypes that affiliated with nitrogen-fixing taxa were unique to green hypoliths, whilst Gemmatimonadetes phylotypes occurred only on red hypolithon. Other heterotrophic phyla recovered with very low frequency were assumed to represent functionally relatively unimportant taxa.     

深海热液生物共附生可培养硫氧化细菌的多样性及硫氧化特性

[背景]深海热液环境中存在大量H2S及含硫化合物,许多微生物与大型生物形成了紧密的共生体系,例如硫氧化细菌,它们利用其独特的代谢体系协助宿主更好地适应极端环境,但目前尚未对热液底栖生物共附生的硫氧化细菌进行培养鉴定和功能分析.[目的]了解深海热液生物共附生硫氧化细菌的种群特征和功能特征,筛选出深海热液生物共附生微生物中...     

Biodiversity and monitoring of colorless filamentous bacteitrtn sulfide aquatic systems of North Caucasus region

Bacterial mats in sulfide aquatic systems of North Caucasus are basically composed by the species of genera Thiothrix and Sphaerotilus. Additionally, several non-filamentous sulfur-oxidizing bacteria were isolated from the mats and several minor 16S rRNA phylotypes were found in clone libraries from these mats. The minor components were affiliated with Proteobacteria, Chlorobia, Cyanobacteria and Firmicutes. Even in an individual mat population heterogeneity of Thiothrix spp. was revealed by analysis of 16S rRNA gene and RAPD-PCR. Five Thiothrix isolates were described as new species Thiothrix caldifontis sp. nov. and Thiothrix lacustris sp. nov. In the Thiothrix-Sphaerotilus type of bacterial mat the proportion of dominant organisms might be influenced by sulfide concentration in the spring water. The higher sulfide concentration (more than 10 mg/1) in the spring water is more favorable for the development of bacterial mats with dominant Thiothrix organisms than for Thiothrix-Sphaerotilus type of sulfur mat.     

Microbial diversity of a sulphide spire located in the Edmond deep-sea hydrothermal vent field on the Central Indian Ridge

A culture‐independent molecular phylogenetic survey was carried out for a bacterial and archaeal community of a mineralized crust coating a sulphide spire, which was collected from the Edmond vent field (23° S, 69° E, 3300 m depth) on the Central Indian Ridge. Small‐subunit rRNA genes (16S rDNA) were amplified from environmental DNA by PCR utilizing Bacteria‐specific, and Archaea‐specific 16S rDNA primers. PCR products were cloned and 26 bacterial and nine archaeal unique sequence types (phylotypes) were identified from 150 clones analysed by restriction fragment length polymorphism, representing eight and four distinct lineages, respectively. The majority (>90%) of the bacterial phylotypes group with the ?‐Proteobacteria and confirms the global prevalence of ?‐Proteobacteria in deep‐sea hydrothermal environments. Among the ?‐Proteobacteria, >40% of the phylotypes were closely related to the recently isolated deep‐sea vent thermophilic chemolithoautotrophic sulphur‐reducer, Nautilia lithotrophica. A single bacterial sequence was nearly identical (99% similarity) to the thermophilic hydrogen‐oxidizing Hydrogenobacter thermolithotrophum, and is the first report of Hydrogenobacter at deep‐sea hydrothermal vents. A majority (97%) of the archaeal phylotypes grouped with the ‘Deep‐sea Hydrothermal Vent Euryarchaeotal Group’, a phylogenetic lineage of uncultured Archaea that have only been reported from other deep‐sea hydrothermal vents on the Mid‐Atlantic Ridge, East Pacific Rise, Juan de Fuca Ridge, Isu–Ogasawara Arc, Okinawa Trough and the Manus Basin. A single sequence was closely related to the hyperthermophilic sulphur‐reducing Thermococcales frequently found in diverse deep‐sea vent environments. Scanning electron micrographs of the mineralized crust reveal abundant filamentous, rod and coccoidal forms encased in sulphur and sulphide mineral precipitate, suggesting that the thermophilic chemolithoautorophs and sulphide‐producing heterotrophs may influence the architecture and sulphur cycling of the sulphide spire.     

Analysis of dissimilatory sulfite reductase and 16S rRNA gene fragments from deep-sea hydrothermal sites of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific

This study describes the occurrence of unique dissimilatory sulfite reductase (DSR) genes at a depth of 1,380 m from the deep-sea hydrothermal vent field at the Suiyo Seamount, Izu-Bonin Arc, Western Pacific, Japan. The DSR genes were obtained from microbes that grew in a catheter-type in situ growth chamber deployed for 3 days on a vent and from the effluent water of drilled holes at 5 degrees C and natural vent fluids at 7 degrees C. DSR clones SUIYOdsr-A and SUIYOdsr-B were not closely related to cultivated species or environmental clones. Moreover, samples of microbial communities were examined by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA gene. The sequence analysis of 16S rRNA gene fragments obtained from the vent catheter after a 3-day incubation revealed the occurrence of bacterial DGGE bands affiliated with the Aquificae and gamma- and epsilon-Proteobacteria as well as the occurrence of archaeal phylotypes affiliated with the Thermococcales and of a unique archaeon sequence that clustered with "Nanoarchaeota." The DGGE bands obtained from drilled holes and natural vent fluids from 7 to 300 degrees C were affiliated with the delta-Proteobacteria, genus Thiomicrospira, and Pelodictyon. The dominant DGGE bands retrieved from the effluent water of casing pipes at 3 and 4 degrees C were closely related to phylotypes obtained from the Arctic Ocean. Our results suggest the presence of microorganisms corresponding to a unique DSR lineage not detected previously from other geothermal environments.     

Phylogenetic relationships ofThiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments

Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments was used to explore the genetic diversity of hydrothermal vent microbial communities, specifically to determine the importance of sulfur-oxidizing bacteria therein. DGGE analysis of two different hydrothermal vent samples revealed one PCR band for one sample and three PCR bands for the other sample, which probably correspond to the dominant bacterial populations in these communities. Three of the four 16S rDNA fragments were sequenced. By comparison with 16S rRNA sequences of the Ribosomal Database Project, two of the DGGE-separated fragments were assigned to the genusThiomicrospira. To identify these ‘phylotypes’ in more detail, a phylogenetic framework was created by determining the nearly complete 16S rRNA gene sequence (approx. 1500 nucleotides) from three describedThiomicrospira species, viz.,Tms. crunogena, Tms. pelophila, Tms. denitrificans, and from a new isolate,Thiomicrospira sp. strain MA2-6. AllThiomicrospira species exceptTms. denitrificans formed a monophyletic group within the gamma subdivision of the Proteobacteria.Tms. denitrificans was assigned as a member of the epsilon subdivision and was distantly affiliated withThiovulum, another sulfur-oxidizing bacterium. Sequences of two dominant 16S rDNA fragments obtained by DGGE analysis fell into the gamma subdivisionThiomicrospira. The sequence of one fragment was in all comparable positions identical to the 16S rRNA sequence ofTms. crunogena. Identifying a dominant molecular isolate asTms. crunogena indicates that this species is a dominant community member of hydrothermal vent sites. Another ‘phylotype’ represented a newThiomicrospira species, phylogenetically in an intermediate position betweenTms. crunogena andTms. pelophila. The third ‘phylotype’ was identified as aDesulfovibrio, indicating that sulfate-reducing bacteria, as sources of sulfide, may complement sulfur- and sulfide-oxidizing bacteria ecologically in these sulfide-producing hydrothermal vents.     

Microbial diversity of a sulfide black smoker in main endeavour hydrothermal vent field,Juan de Fuca Ridge

Submarine hydrothermal vents are among the least-understood habitats on Earth but have been the intense focus of research in the past 30 years. An active hydrothermal sulfide chimney collected from the Dudley site in the Main Endeavour vent Field (MEF) of Juan de Fuca Ridge was investigated using mineralogical and molecular approaches. Mineral analysis indicated that the chimney was composed mainly of Fe-, Zn-and Cu-rich sulfides. According to phylogenetic analysis, within the Crenarchaeota, clones of the order Desulfurococcales predominated, comprising nearly 50% of archaeal clones. Euryarchaeota were composed mainly of clones belonging to Thermococcales and deep-sea hydrothermal vent Euryarchaeota (DHVE), each of which accounted for about 20% of all clones. Thermophilic or hyperthermophilic physiologies were common to the predominant archaeal groups. More than half of bacterial clones belonged to ɛ-Proteobacteria, which confirmed their prevalence in hydrothermal vent environments. Clones of Proteobacteria (γ-, δ-, β-), Cytophaga-Flavobacterium-Bacteroides (CFB) and Deinococcus-Thermus occurred as well. It was remarkable that methanogens and methanotrophs were not detected in our 16S rRNA gene library. Our results indicated that sulfur-related metabolism, which included sulfur-reducing activity carried out by thermophilic archaea and sulfur-oxidizing by mesophilic bacteria, was common and crucial to the vent ecosystem in Dudley hydrothermal site.     

Submarine Hydrothermal Vents of the Aeolian Islands: Relationship Between Microbial Communities and Thermal Fluids

The relationship between fluid geochemistry and microbial communities was investigated for shallow (< 25 m) submarine hydrothermal vents in the Aeolian Islands (Southern Italy). Thermal waters, gases, and deposits of white filamentous material were collected from 11 sites. The geochemical analyses showed a magmatic component was present in all sampled fluids. The total microbial abundances, evaluated as direct counts of picoplanktonic cells (ranging from 0.2 to 2 mu m in diameter), were between 1.55 107 and 4.18 108 cells per liter. Picophytoplankton (total autofluorescent cells) ranged from 9.6 105 to 7.88 106 cells per liter. Yellow-orange autofluorescent prokaryotes belonging to the cyanobacteria were more abundant than red autofluorescent eukaryotic cells. Chemolithoautotrophic, sulfur-oxidizing, rod-shaped Bacteria were isolated from venting water samples and identified as Thiobacillus -like. Microscopic examination of the white mat deposits showed the presence of filamentous microorganisms.     

Analysis of Dissimilatory Sulfite Reductase and 16S rRNA Gene Fragments from Deep-Sea Hydrothermal Sites of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific

This study describes the occurrence of unique dissimilatory sulfite reductase (DSR) genes at a depth of 1,380 m from the deep-sea hydrothermal vent field at the Suiyo Seamount, Izu-Bonin Arc, Western Pacific, Japan. The DSR genes were obtained from microbes that grew in a catheter-type in situ growth chamber deployed for 3 days on a vent and from the effluent water of drilled holes at 5°C and natural vent fluids at 7°C. DSR clones SUIYOdsr-A and SUIYOdsr-B were not closely related to cultivated species or environmental clones. Moreover, samples of microbial communities were examined by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA gene. The sequence analysis of 16S rRNA gene fragments obtained from the vent catheter after a 3-day incubation revealed the occurrence of bacterial DGGE bands affiliated with the Aquificae and γ- and -Proteobacteria as well as the occurrence of archaeal phylotypes affiliated with the Thermococcales and of a unique archaeon sequence that clustered with “Nanoarchaeota.” The DGGE bands obtained from drilled holes and natural vent fluids from 7 to 300°C were affiliated with the δ-Proteobacteria, genus Thiomicrospira, and Pelodictyon. The dominant DGGE bands retrieved from the effluent water of casing pipes at 3 and 4°C were closely related to phylotypes obtained from the Arctic Ocean. Our results suggest the presence of microorganisms corresponding to a unique DSR lineage not detected previously from other geothermal environments.     

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.     

Individual hydrothermal vents at Axial Seamount harbor distinct subseafloor microbial communities

The microbial community structure of five geographically distinct hydrothermal vents located within the Axial Seamount caldera, Juan de Fuca Ridge, was examined over 6 years following the 1998 diking eruptive event. Terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene sequence analyses were used to determine the bacterial and archaeal diversity, and the statistical software primer v6 was used to compare vent microbiology, temperature and fluid chemistry. Statistical analysis of vent fluid temperature and composition shows that there are significant differences between vents in any year, but that the fluid composition changes over time such that no vent maintains a chemical composition completely distinct from the others. In contrast, the subseafloor microbial communities associated with individual vents changed from year to year, but each location maintained a distinct community structure (based on TRFLP and 16S rRNA gene sequence analyses) that was significantly different from all other vents included in this study. Epsilonproteobacterial microdiversity is shown to be important in distinguishing vent communities, while archaeal microdiversity is less variable between sites. We propose that persistent venting at diffuse flow vents over time creates the potential to isolate and stabilize diverse microbial community structures between vents.     

Detection of Putatively Thermophilic Anaerobic Methanotrophs in Diffuse Hydrothermal Vent Fluids

The anaerobic oxidation of methane (AOM) is carried out by a globally distributed group of uncultivated Euryarchaeota, the anaerobic methanotrophic arachaea (ANME). In this work, we used G+C analysis of 16S rRNA genes to identify a putatively thermophilic ANME group and applied newly designed primers to study its distribution in low-temperature diffuse vent fluids from deep-sea hydrothermal vents. We found that the G+C content of the 16S rRNA genes (P_GC) is significantly higher in the ANME-1GBa group than in other ANME groups. Based on the positive correlation between the P_GC and optimal growth temperatures (T_opt) of archaea, we hypothesize that the ANME-1GBa group is adapted to thrive at high temperatures. We designed specific 16S rRNA gene-targeted primers for the ANME-1 cluster to detect all phylogenetic groups within this cluster, including the deeply branching ANME-1GBa group. The primers were successfully tested both in silico and in experiments with sediment samples where ANME-1 phylotypes had previously been detected. The primers were further used to screen for the ANME-1 microorganisms in diffuse vent fluid samples from deep-sea hydrothermal vents in the Pacific Ocean, and sequences belonging to the ANME-1 cluster were detected in four individual vents. Phylotypes belonging to the ANME-1GBa group dominated in clone libraries from three of these vents. Our findings provide evidence of existence of a putatively extremely thermophilic group of methanotrophic archaea that occur in geographically and geologically distinct marine hydrothermal habitats.     

Diversity of bacterial community in freshwater of Woopo wetland

Diversity of bacterial community in water layer of Woopo wetland was investigated. Cultivable bacterial strains were isolated by the standard dilution plating technique and culture-independent 16S rRNA gene clones were obtained directly from DNA extracts of a water sample. Amplified rDNA restriction analysis (ARDRA) was applied onto both of the isolates and 16S rRNA gene clones. Rarefaction curves, coverage rate and diversity indices of ARDRA patterns were calculated. Representative isolates and clones of all the single isolate/clone phylotype were partially sequenced and analyzed phylogenetically. Sixty-four and 125 phylotypes were obtained from 203 bacterial isolates and 235 culture-independent 16S rRNA gene clones, respectively. Bacterial isolates were composed of 4 phyla, of which Firmicutes (49.8%) and Actinobacteria (32.0%) were predominant. Isolates were affiliated with 58 species. Culture-independent 16S rRNA gene clones were composed of 8 phyla, of which Proteobacteria (62.2%), Actinobacteria (15.5%), and Bacteroidetes (13.7%) were predominant. Diversity of 16S rRNA gene clones originated from cultivation-independent DNA extracts was higher than that of isolated bacteria.     

Multifaceted approach for the analysis of the phototrophic microbial community in a freshwater recreational area of Xochimilco,México

The freshwater microbial community in a recreational area of Xochimilco, México was investigated and compared based on spatial (three different sites) and temporal (dry and rainy seasons) environmental variables. Many of the 16S- and 18S rRNA gene sequences recovered by DGGE fingerprinting analysis were related to phototrophic microbial phylotypes of known identity. Our genetic and morphological analysis indicated the ubiquitous presence of the microeukaryotic green algae Desmodesmus-Scenedesmus spp. and of the unicellular cyanobacteria Cyanobium spp. as the most representative populations in the samples. While 18S rRNA-DGGE fingerprinting analysis revealed a homogeneous community composition across sites and seasons, the 16S rRNA showed significant differences between localities and seasons. None of the cyanobacteria species with potential to produce toxins were identified across the investigated samples. Correlations between biotic and abiotic variables evidenced an important difference between the dry and the rainy season, with a greater consistency in data from the rainy season. According to Principal Component Analysis (PCA), a strong relation between inorganic nitrogen, species richness, and subaquatic irradiance determines environmental variability in Xochimilco. Complementary and relevant data in results obtained from microscopy, fingerprinting, and statistical analysis applied in ecology indicate that a multifaceted approach to the study of microbial communities is necessary to accomplish a comprehensive scientific framework and to generate proper management strategies.     

南大西洋深海热液区可培养硫氧化微生物多样性及其硫氧化特性

【目的】探索南大西洋热液环境中的硫氧化细菌多样性并研究其硫氧化特性。【方法】通过富集培养和分离纯化获得硫氧化细菌,利用变性梯度凝胶电泳(DGGE)分析富集菌群组成结构,采用离子色谱法对获得的硫氧化细菌硫氧化特性进行检测。【结果】从南大西洋深海环境样品中共分离到48株菌,分属于alpha-Proteobacteria(28株,58.3%)、Actinobacteria(11株,22.9%)和gama-Proteobacteria(9株,18.8%)共3个门,其中Thalassospira、Martelella和Microbacterium为优势属。DGGE结果表明深海热液环境样品中微生物多样性丰富且不同站位存在差异。硫氧化特性研究结果表明,约60%的分离菌株具有硫氧化能力,可以氧化S_2O_3~(2–)生成SO_4~(2–)。获得一株硫氧化能力较强的潜在新种L6M1-5,在实验条件下可高效氧化S_2O_3~(2–),最大氧化速率可达0.56 mmol/(L·h)。【结论】南大西洋深海热液环境中可培养硫氧化细菌多样性丰富,为研究热液环境中的硫循环过程提供了实验材料和理论参考;同时高效硫氧化菌的获得,为工业化含硫废水的处理提供了良好的菌种资源。     

A dual symbiosis shared by two mussel species, Bathymodiolus azoricus and Bathymodiolus puteoserpentis (Bivalvia: Mytilidae), from hydrothermal vents along the northern Mid-Atlantic Ridge

Bathymodiolus azoricus and Bathymodiolus puteoserpentis are symbiont-bearing mussels that dominate hydrothermal vent sites along the northern Mid-Atlantic Ridge (MAR). Both species live in symbiosis with two physiologically and phylogenetically distinct Gammaproteobacteria: a sulfur-oxidizing chemoautotroph and a methane-oxidizer. A detailed analysis of mussels collected from four MAR vent sites (Menez Gwen, Lucky Strike, Rainbow, and Logatchev) using comparative 16S rRNA sequence analysis and fluorescence in situ hybridization (FISH) showed that the two mussel species share highly similar to identical symbiont phylotypes. FISH observations of symbiont distribution and relative abundances showed no obvious differences between the two host species. In contrast, distinct differences in relative symbiont abundances were observed between mussels from different sites, indicating that vent chemistry may influence the relative abundance of thiotrophs and methanotrophs in these dual symbioses.     

Abundance and Diversity of Picocyanobacteria in Shallow Hydrothermal Vents of Panarea Island (Italy)

The abundance and diversity of cyanobacteria living in sediments collected from six vents (temperature range 37–130°C) close to the Panarea Island (Italy) were studied. The diversity of cyanobacteria was analyzed by using a PCR-DGGE approach with group-specific primers. The greatest number and diversity of cyanobacteria were registered at the coldest vent. Sequencing of DGGE fragments revealed that most sequences matched with uncultured cyanobacteria deposited in databases and some were distantly affiliated with different species of Synechococcus. New, genetically distant ribotypes of cyanobacteria are the dominant oxygenic phototrophs in shallow hydrothermal system of Panarea Island.     

Phylotype diversity in a benthic cyanobacterial mat community on King George Island, maritime Antarctica

Cyanobacterial 16S ribosomal RNA gene diversity was examined in a benthic mat on Fildes Peninsula of King George Island (62o09′54.4′′S, 58o57′20.9′′W), maritime Antarctica. Environmental DNA was isolated from the mat, a clone library of PCR-amplified 16S rRNA gene fragments was prepared, and amplified ribosomal DNA restriction analysis (ARDRA) was done to assign clones to seven groups. Low cyanobacterial diversity in the mat was suggested in that 83% of the clones were represented by one ARDRA group. DNA sequences from this group had high similarity with 16S rRNA genes of Tychonema bourrellyi and T. bornetii isolates, whose geographic origins were southern Norway and Northern Ireland. Cyanobacterial morphotypes corresponding to Tychonema have not been reported in Antarctica, however, this morphotype was previously found at Ward Hunt Lake (83oN), and in western Europe (52oN). DNA sequences of three of the ARDRA groups had highest similarity with 16S rDNA sequences of the Tychonema group accounting for 9.4% of the clones. Sequences of the remaining three groups (7.6%) had highest similarity with 16S rRNA genes of uncultured cyanobacteria clones from benthic mats of Lake Fryxell and fresh meltwater on the McMurdo Ice Shelf.     

SSU‐rRNA Gene Sequencing Survey of Benthic Microbial Eukaryotes from Guaymas Basin Hydrothermal Vent

Microbial eukaryotes have important roles in marine food webs, but their diversity and activities in hydrothermal vent ecosystems are poorly characterized. In this study, we analyzed microbial eukaryotic communities associated with bacterial (Beggiatoa) mats in the 2,000 m deep‐sea Guaymas Basin hydrothermal vent system using 18S rRNA gene high‐throughput sequencing of the V4 region. We detected 6,954 distinct Operational Taxonomic Units (OTUs) across various mat systems. Of the sequences that aligned with known protistan phylotypes, most were affiliated with alveolates (especially dinoflagellates and ciliates) and cercozoans. OTU richness and community structure differed among sediment habitats (e.g. different mat types and cold sediments away from mats). Additionally, full‐length 18S rRNA genes amplified and cloned from single cells revealed the identities of some of the most commonly encountered, active ciliates in this hydrothermal vent ecosystem. Observations and experiments were also conducted to demonstrate that ciliates were trophically active and ingesting fluorescent bacteria or Beggiatoa trichomes. Our work suggests that the active and diverse protistan community at the Guaymas Basin hydrothermal vent ecosystem likely consumes substantial amounts of bacterial biomass, and that the different habitats, often defined by distances of just a few 10s of cm, select for particular assemblages and levels of diversity.     

Culture dependent and independent analyses of 16S rRNA and ATP citrate lyase genes: a comparison of microbial communities from different black smoker chimneys on the Mid-Atlantic Ridge

The bacterial and archaeal communities of three deep-sea hydrothermal vent systems located on the Mid-Atlantic Ridge (MAR; Rainbow, Logatchev and Broken Spur) were investigated using an integrated culture-dependent and independent approach. Comparative molecular phylogenetic analyses, using the 16S rRNA gene and the deduced amino acid sequences of the alpha and beta subunits of the ATP citrate lyase encoding genes were carried out on natural microbial communities, on an enrichment culture obtained from the Broken Spur chimney, and on novel chemolithoautotrophic bacteria and reference strains originally isolated from several different deep-sea vents. Our data showed that the three MAR hydrothermal vent chimneys investigated in this study host very different microbial assemblages. The microbial community of the Rainbow chimney was dominated by thermophilic, autotrophic, hydrogen-oxidizing, sulfur- and nitrate-reducing Epsilonproteobacteria related to the genus Caminibacter. The detection of sequences related to sulfur-reducing bacteria and archaea (Archaeoglobus) indicated that thermophilic sulfate reduction might also be occurring at this site. The Logatchev bacterial community included several sequences related to mesophilic sulfur-oxidizing bacteria, while the archaeal component of this chimney was dominated by sequences related to the ANME-2 lineage, suggesting that anaerobic oxidation of methane may be occurring at this site. Comparative analyses of the ATP citrate lyase encoding genes from natural microbial communities suggested that Epsilonproteobacteria were the dominant primary producers using the reverse TCA cycle (rTCA) at Rainbow, while Aquificales of the genera Desulfurobacterium and Persephonella were prevalent in the Broken Spur chimney.