Deep-sea Hydrothermal Ecosystems Research Articles

Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

BackgroundWhen deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018 and document their potential implications in biogeochemical cycles.ResultsOur dataset represents 3635 metagenome-assembled genomes encompassing 511 novel and recently identified genera from deep-sea hydrothermal settings. Some of the novel bacterial (107) and archaeal genera (30) that were recently reported from the deep-sea Brothers volcano were also detected at the deep-sea hydrothermal vent fields, while 99 bacterial and 54 archaeal genera were endemic to the deep-sea Brothers volcano deposits. We report some of the first examples of medium- (≥ 50% complete, ≤ 10% contaminated) to high-quality (> 90% complete, < 5% contaminated) MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur, and hydrogen metabolic processes across all sites and illustrates sulfur and nitrogen metabolic “handoffs” in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment.ConclusionOur study of globally distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa.6aUVBDbDZ6m8Eohc79dCDgVideo

Competition-cooperation in the chemoautotrophic ecosystem of Movile Cave: first metagenomic approach on sediments

BackgroundMovile Cave (SE Romania) is a chemoautotrophically-based ecosystem fed by hydrogen sulfide-rich groundwater serving as a primary energy source analogous to the deep-sea hydrothermal ecosystems. Our current understanding of Movile Cave microbiology has been confined to the sulfidic water and its proximity, as most studies focused on the water-floating microbial mat and planktonic accumulations likely acting as the primary production powerhouse of this unique subterranean ecosystem. By employing comprehensive genomic-resolved metagenomics, we questioned the spatial variation, chemoautotrophic abilities, ecological interactions and trophic roles of Movile Cave’s microbiome thriving beyond the sulfidic-rich water.ResultsA customized bioinformatics pipeline led to the recovery of 106 high-quality metagenome-assembled genomes from 7 cave sediment metagenomes. Assemblies’ taxonomy spanned 19 bacterial and three archaeal phyla with Acidobacteriota, Chloroflexota, Proteobacteria, Planctomycetota, Ca. Patescibacteria, Thermoproteota, Methylomirabilota, and Ca. Zixibacteria as prevalent phyla. Functional gene analyses predicted the presence of CO2 fixation, methanotrophy, sulfur and ammonia oxidation in the explored sediments. Species Metabolic Coupling Analysis of metagenome-scale metabolic models revealed the highest competition-cooperation interactions in the sediments collected away from the water. Simulated metabolic interactions indicated autotrophs and methanotrophs as major donors of metabolites in the sediment communities. Cross-feeding dependencies were assumed only towards 'currency' molecules and inorganic compounds (O2, PO43−, H+, Fe2+, Cu2+) in the water proximity sediment, whereas hydrogen sulfide and methanol were assumedly traded exclusively among distant gallery communities.ConclusionsThese findings suggest that the primary production potential of Movile Cave expands way beyond its hydrothermal waters, enhancing our understanding of the functioning and ecological interactions within chemolithoautotrophically-based subterranean ecosystems.

Characterization and Diversity Analysis of the Extracellular Proteases of Thermophilic Anoxybacillus caldiproteolyticus 1A02591 From Deep-Sea Hydrothermal Vent Sediment.

Protease-producing bacteria play key roles in the degradation of marine organic nitrogen. Although some deep-sea bacteria are found to produce proteases, there has been no report on protease-secreting Anoxybacillus from marine hydrothermal vent regions. Here, we analyzed the diversity and functions of the proteases, especially the extracellular proteases, of Anoxybacillus caldiproteolyticus 1A02591, a protease-secreting strain isolated from a deep-sea hydrothermal vent sediment of the East Pacific Ocean. Strain 1A02591 is a thermophilic bacterium with a strong protease-secreting ability, which displayed the maximum growth rate (0.139 h–1) and extracellular protease production (307.99 U/mL) at 55°C. Strain 1A02591 contains 75 putative proteases, including 65 intracellular proteases and 10 extracellular proteases according to signal peptide prediction. When strain 1A02591 was cultured with casein, 12 proteases were identified in the secretome, in which metalloproteases (6/12) and serine proteases (4/12) accounted for the majority, and a thermolysin-like protease of the M4 family was the most abundant, suggesting that strain 1A02591 mainly secreted a thermophilic metalloprotease. Correspondingly, the secreted proteases of strain 1A02591 showed the highest activity at the temperature as high as 70°C, and was inhibited 70% by metalloprotease inhibitor o-phenanthroline and 50% by serine protease inhibitor phenylmethylsulfonyl fluoride. The secreted proteases could degrade different proteins, suggesting the role of strain 1A02591 in organic nitrogen degradation in deep-sea hydrothermal ecosystem. These results provide the first insight into the proteases of an Anoxybacillus strain from deep-sea hydrothermal ecosystem, which is helpful in understanding the function of Anoxybacillus in the marine biogeochemical cycle.

The oxidation of hydrocarbons by diverse heterotrophic and mixotrophic bacteria that inhabit deep-sea hydrothermal ecosystems

Hydrothermal activity can generate numerous and diverse hydrocarbon compounds. However, little is known about the influence of such hydrocarbons on deep-sea hydrothermal microbial ecology. We hypothesize that certain bacteria live on these hydrocarbons. Therefore, in this study, the distribution of hydrocarbons and their associated hydrocarbon-degrading bacteria were investigated at deep-sea hydrothermal vents at the Southern Mid-Atlantic Ridge, the Southwest Indian Ridge, and the East Pacific Rise. A variety of hydrocarbon-degrading consortia were obtained from hydrothermal samples collected at the aforementioned sites after low-temperature enrichment under high hydrostatic pressures, and the bacteria responsible for the degradation of hydrocarbons were investigated by DNA-based stable-isotope probing with uniformly 13C-labeled hydrocarbons. Unusually, we identified several previously recognized sulfur-oxidizing chemoautotrophs as hydrocarbon-degrading bacteria, e.g., the SAR324 group, the SUP05 clade, and Sulfurimonas, and for the first time confirmed their ability to degrade hydrocarbons. In addition, Erythrobacter, Pusillimonas, and SAR202 clade were shown to degrade polycyclic aromatic hydrocarbons for the first time. These results together with relatively high abundance in situ of most of the above-described bacteria highlight the potential influence of hydrocarbons in configuring the vent microbial community, and have made the importance of mixotrophs in hydrothermal vent ecosystems evident.

Microbially Mediated Hydrogen Cycling in Deep-Sea Hydrothermal Vents.

Deep-sea hydrothermal vents may provide one of the largest reservoirs on Earth for hydrogen-oxidizing microorganisms. Depending on the type of geological setting, hydrothermal environments can be considerably enriched in hydrogen (up to millimolar concentrations). As hot, reduced hydrothermal fluids ascend to the seafloor they mix with entrained cold, oxygenated seawater, forming thermal and chemical gradients along their fluid pathways. Consequently, in these thermally and chemically dynamic habitats biochemically distinct hydrogenases (adapted to various temperature regimes, oxygen and hydrogen concentrations) from physiologically and phylogenetically diverse Bacteria and Archaea can be expected. Hydrogen oxidation is one of the important inorganic energy sources in these habitats, capable of providing relatively large amounts of energy (237 kJ/mol H2) for driving ATP synthesis and autotrophic CO2 fixation. Therefore, hydrogen-oxidizing organisms play a key role in deep-sea hydrothermal vent ecosystems as they can be considerably involved in light-independent primary biomass production. So far, the specific role of hydrogen-utilizing microorganisms in deep-sea hydrothermal ecosystems has been investigated by isolating hydrogen-oxidizers, measuring hydrogen consumption (ex situ), studying hydrogenase gene distribution and more recently by analyzing metatranscriptomic and metaproteomic data. Here we summarize this available knowledge and discuss the advent of new techniques for the identification of novel hydrogen-uptake and -evolving enzymes from hydrothermal vent microorganisms.

Gill chamber and gut microbial communities of the hydrothermal shrimp Rimicaris chacei Williams and Rona 1986: A possible symbiosis.

Rimicaris chacei Williams and Rona 1986, formerly named as Chorocaris chacei, is a caridean shrimp living in deep-sea hydrothermal ecosystems. This shrimp is endemic to the Mid Atlantic Ridge (MAR) and lives at the periphery of aggregates of its well-known congeneric R. exoculata Williams and Rona 1986. Contrasting with the very dense and mobile clusters formed by R. exoculata, R. chacei lives in small groups of several individuals that are not very mobile. Although devoid of the characteristic hypertrophied cephalothorax of R. exoculata, which harbors the ectosymbionts, a microbial community has also been reported in the cephalothorax of R. chacei. Previous data on morphology, behavior and isotopic values indicate a diet based on a combination of feeding on its epibiotic bacteria and scavenging or occasional predation. In this study, our objective was to describe, for the first time, the distribution, morphology and phylogeny of the microbial communities associated with R. chacei. This species is significantly less studied than R. exoculata, but nevertheless represents the only other known example of symbiosis in crustaceans of MAR hydrothermal vent sites. Microbial communities have been observed at the same locations as in R. exoculata (mouthparts, branchiostegites and digestive tract). However, in R. chacei, the surfaces occupied by the bacteria are smaller. The main lineages are affiliated to Epsilon and Gammaproteobacteria in the cephalothorax and to Deferribacteres, Mollicutes, Epsilon and Gammaproteobacteria in the digestive tract. Comparison with the well-described bacterial communities of R. exoculata and hypotheses about the role of these communities in R. chacei are discussed.

Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields.

The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.

Biological and environmental rhythms in (dark) deep-sea hydrothermal ecosystems

Abstract. During 2011, two deep-sea observatories focusing on hydrothermal vent ecology were up and running in the Atlantic (Eiffel Tower, Lucky Strike vent field) and the Northeast Pacific Ocean (NEP) (Grotto, Main Endeavour Field). Both ecological modules recorded imagery and environmental variables jointly for a time span of 23 days (7–30 October 2011) and environmental variables for up to 9 months (October 2011–June 2012). Community dynamics were assessed based on imagery analysis and rhythms in temporal variation for both fauna and environment were revealed. Tidal rhythms were found to be at play in the two settings and were most visible in temperature and tubeworm appearances (at NEP). A ∼ 6 h lag in tidal rhythm occurrence was observed between Pacific and Atlantic hydrothermal vents, which corresponds to the geographical distance and time delay between the two sites.

Not-So-Large Charge: Deep-Sea Microbes Directly Consume Electricity

The bacterium Acidithiobacillus ferrooxidans can thrive on electrons obtained directly from an electrode when its usual energy source—iron—is unavailable. This switch from using an inorganic element to consuming electricity itself as a source of electrons “demonstrates a previously unknown bioenergetic versatility,” say Ryuhei Nakamura of the RIKEN Center for Sustainable Resource Science in Saitama, Japan, and his collaborators. Thus, electrons might be a primary energy source for these bacteria while dwelling within the deep-sea hydrothermal ecosystems in which they are found, they point out. Details appeared in the September 2015 Frontiers in Microbiology (doi:10.3389/fmicb.2015.00994).

Characteristics of the cultivable bacteria from sediments associated with two deep-sea hydrothermal vents in Okinawa Trough.

In this study, different culture-dependent methods were used to examine the cultivable heterotrophic bacteria in the sediments associated with two deep-sea hydrothermal vents (named HV1 and HV2) located at Iheya Ridge and Iheya North in Okinawa Trough. The two vents differed in morphology, with HV1 exhibiting diffuse flows while HV2 being a black smoker with a chimney-like structure. A total of 213 isolates were identified by near full-length 16S rRNA gene sequence analysis. Of these isolates, 128 were from HV1 and 85 were from HV2. The bacterial community structures were, in large parts, similar between HV1 and HV2. Nevertheless, differences between HV1 and HV2 were observed in one phylum, one class, 4 orders, 10 families, and 20 genera. Bioactivity analysis revealed that 25 isolates belonging to 9 different genera exhibited extracellular protease activities, 21 isolates from 11 genera exhibited extracellular lipase activities, and 13 isolates of 8 genera displayed antimicrobial activities. This is the first observation of a large population of bacteria with extracellular bioactivities existing in deep-sea hydrothermal vents. Taken together, the results of this study provide new insights into the characteristics of the cultivable heterotrophic bacteria in deep-sea hydrothermal ecosystems.

Microbial community structure and diversity in deep-sea hydrothermal vent sediments along the Eastern Lau Spreading Centre

The aim of this study is to investigate microbial structures and diversities in five active hydrothermal fields’ sediments along the Eastern Lau Spreading Centre (ELSC) in the Lau Basin (southwest Pacific). Microbial communities were surveyed by denatured gradient gel electrophoresis (DGGE) and clone library analysis of 16S rRNA genes. The differences in microbial community structures among sediment samples from the five deep-sea hydrothermal sites were revealed by DGGE profiles. Cluster analysis of DGGE profiles separated the five hydrothermal samples into two groups. Four different 16S rRNA gene clone libraries, representing two selected hydrothermal samples (19-4TVG8 and 19-4TVG11), were constructed. Twenty-three and 32 phylotypes were identified from166 and 160 bacterial clones respectively, including Proteobacteria, Bacteroidetes, Firmicutes, Nitrospirae and Planctomycetes. The phylum Proteobacteria is dominant in both bacterial libraries with a predominance of Gamma-Proteobacteria. A total of 31 and 25 phylotypes were obtained from 160 and 130 archaeal clones respectively, including Miscellaneous Crenarchaeotic Group, Marine Group I and III, Marine Benthic Group E, Terrestrial Hot Spring Crenarchaeota and Deep-sea Hydrothermal Vent Euryarchaeota. These results show a variety of clones related to those involved in sulfur cycling, suggesting that the cycling and utilization of sulfur compounds may extensively occur in the Lau Basin deep-sea hydrothermal ecosystem.

Biogeography of Persephonella in deep-sea hydrothermal vents of the Western Pacific

Deep-sea hydrothermal vent fields are areas on the seafloor with high biological productivity fueled by microbial chemosynthesis. Members of the Aquificales genus Persephonella are obligately chemosynthetic bacteria, and appear to be key players in carbon, sulfur, and nitrogen cycles in high temperature habitats at deep-sea vents. Although this group of bacteria has cosmopolitan distribution in deep-sea hydrothermal ecosystem around the world, little is known about their population structure such as intraspecific genomic diversity, distribution pattern, and phenotypic diversity. We developed the multi-locus sequence analysis (MLSA) scheme for their genomic characterization. Sequence variation was determined in five housekeeping genes and one functional gene of 36 Persephonella hydrogeniphila strains originated from the Okinawa Trough and the South Mariana Trough (SNT). Although the strains share >98.7% similarities in 16S rRNA gene sequences, MLSA revealed 35 different sequence types (ST), indicating their extensive genomic diversity. A phylogenetic tree inferred from all concatenated gene sequences revealed the clustering of isolates according to the geographic origin. In addition, the phenotypic clustering pattern inferred from whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) analysis can be correlated to their MLSA clustering pattern. This study represents the first MLSA combined with phenotypic analysis indicative of allopatric speciation of deep-sea hydrothermal vent bacteria.

Some features of the trace metal biogeochemistry in the deep-sea hydrothermal vent fields (Menez Gwen, Rainbow, Broken Spur at the MAR and 9°50′N at the EPR): A synthesis

Along with summarizing the published literature and our own data some new results on properties of the trace metal biogeochemistry in the deep-sea hydrothermal ecosystems at the Mid-Atlantic Ridge (MAR) and East Pacific Rise (EPR) are shown. Differences in mean concentrations of big group of trace metals (Fe, Mn, Zn, Cu, Ni, Cr, Co, As, Pb, Cd, Ag, Hg) between the biotope water of the low- and high-temperature hydrothermal vent fields were firstly revealed. The same trace metals were studied in different groups of organisms within different temperature zones at one and the same vent field (9°50′N EPR), as well as in fauna inhabiting geochemically different vent sites. Distribution patterns of Fe, Mn, Zn, Cu, Cd, Pb, Ag, Ni, Cr, Co, As, Se, Sb, and Hg in different taxa gave an evidence of the influence of environmental and biological parameters on their bioaccumulation in organisms. Among the animals a particular “champion” with respect to the trace metal content was found to be a polychaeta Alvinella pompejana that inhabits the hottest places of the vent sulfide chimneys of the 9°50′N field, EPR. New data on the trace metal distribution between soft tissues and carbonate shell let us estimate a role of biomineralization in the accumulation of metals in the Bathimodiolus mussels. Contrasting geochemical behavior was revealed for Cu that is enriched in soft tissues of mussels and depleted in shells, on the one hand, and Mn that is accumulated almost totally in mussel shells, on the other hand.Deep-sea hydrothermal biological communities demonstrate a strong concentration function, and bioconcentration factors (BCF) of trace metals estimated for Bathimodiolus mussels collected at the four hydrothermal fields vary within the limits of n102–n105 and are similar to that of the littoral mussels. Due to this and to the high values of biomasses per square meter, the hydrothermal fauna may be considered as a newly discovered biological filter of the oceans.

Proteomic Analysis of Interactions between a Deep-Sea Thermophilic Bacteriophage and Its Host at High Temperature

The virus-host interaction is essential to understanding the role that viruses play in ecological and geochemical processes in deep-sea vent ecosystems. Virus-induced changes in cellular gene expression and host physiology have been studied extensively. However, the molecular mechanism of interaction between a bacteriophage and its host at high temperature remains poorly understood. In the present study, the virus-induced gene expression profile of Geobacillus sp. E263, a thermophile isolated from a deep-sea hydrothermal ecosystem, was characterized. Based on proteomic analysis and random arbitrarily primed PCR (RAP-PCR) of Geobacillus sp. E263 cultured under non-bacteriophage GVE2 infection and GVE2 infection conditions, there were two types of protein/gene profiles in response to GVE2 infection. Twenty differentially expressed genes and proteins were revealed that could be grouped into 3 different categories based on cellular function, suggesting a coordinated response to infection. These differentially expressed genes and proteins were further confirmed by Northern blot analysis. To characterize the host proteins in response to virus infection, aspartate aminotransferase (AST) was inactivated to construct the AST mutant of Geobacillus sp. E263. The results showed that the AST protein was essential in virus infection. Thus, transcriptional and proteomic analyses and functional analysis revealed previously unknown host responses to deep-sea thermophilic virus infection.

海底熱水系の物理・化学的多様性と化学合成微生物生態系の存在様式

Deep-sea hydrothermal vents are among the habitats that host the most diverse microbial communities on the Earth. It is promised that hydrothermal vent microbial communities play a major role in the circulation of energy and materials in the global oceanic and suboceanic environments, and even provide important insights into the origin and early evolution of life on the Earth and extraterrestrial life on other planets and moons. Deep-sea hydrothermal vent ecosystems are strongly dependent on the primary production of symbiotic and free-living chemolithoautotrophic microorganisms that can obtain energy from inorganic substances such as H2S, CO2, H2, and CH4 derived from hydrothermal vent fluids. The diversity and abundance of these energy and carbon sources at hydrothermal vent fluids are, in turn, controlled by subseafloor physical and chemical processes such as fluid–rock interactions and phase-separation and -partition of fluids. Therefore, linkage between rock (magma), hydrothermal fluid, and ecosystem is a key to understanding how deep-sea hydrothermal ecosystems are generated and sustained. In this article, we approach this whole “Rock–Fluid–Ecosystem linkage” with the two separate sub-linkages of “Rock–Fluid linkage” and “Fluid–Ecosystem linkage”, which have not been addressed by the individual research fields of the Geochemistry of Hydrothermal Systems and Hydrothermal Vent Microbiology, respectively. Here, we overview the progress of understanding the “Rock–Fluid” and “Fluid–Ecosystem” linkages, both of which will establish the basis for an integrated “Rock–Fluid–Ecosystem linkage”. (View PDF for the rest of the abstract.)

Ultramafics-Hydrothermalism-Hydrogenesis-HyperSLiME (UltraH3) linkage: a key insight into early microbial ecosystem in the Archean deep-sea hydrothermal systems

Since their discovery in the late 1970s, deep-sea hydrothermal systems have been considered as likely candidates for the origin and early evolution of life on Earth. However, while subsequent investigations have revealed a great diversity of modern deep-sea hydrothermal ecosystems, they have done little to shed light on the issues of the origin and early evolution of life, metabolism, cells, or communities. Phylogenetic, biochemical and geochemical clues all seem to point to the early evolution of hydrogenotrophic chemolithoautotrophy such as methanogenesis and sulfurreduction, thus pinpointing the availability of hydrogen as one of the key elements needed for the early evolution of earthly life. Hydrogen-driven, photosynthesis-independent communities are very rare on the contemporary Earth, however, being unambiguously found only in subsurface environments of H2-dominated hydrothermal systems. Such systems have been termed hyperthermophilic subsurface lithoautotrophic microbial ecosystems (HyperSLiMEs) (Takai et al., 2004; Nealson et al., 2005). The supply of abundant hydrogen and available inorganic carbon sources to power such communities is most likely coupled to hydrothermal serpentinization of ultramafic rocks and input of magmatic volatiles, both of which are related to specific geological settings. We propose here, on the basis of findings in the modern Earth and implications for the deep-sea hydrothermal systems in the Archean Earth, that “Ultramafics-Hydrothermalism-Hydrogenesis-HyperSLiME”, a linkage we refer to as Ultra H3, provided a suitable habitat for the early microbial ecosystem on the Archean Earth.

Continuous Enrichment Culture and Molecular Monitoring to Investigate the Microbial Diversity of Thermophiles Inhabiting Deep-Sea Hydrothermal Ecosystems

The microflora developing during a continuous enrichment culture from a hydrothermal chimney sample was investigated by molecular methods. The culture was performed in a gas-lift bioreactor under anaerobic conditions, at 90 degrees C and pH 6.5, on a complex medium containing sulfur as the terminal electron acceptor. Archaeal and bacterial diversity was studied. Microorganisms affiliated with the genera Pyrococcus, Marinitoga, and Bacillus were detected through DGGE analysis of 16S rDNA. Additional sequences phylogenetically related to Thermococcus and epsilon-Proteobacteria were detected by cloning and sequencing of 16S rDNA from two samples of the enrichment culture. In comparison, the sequences retrieved from cloning analysis from an enrichment culture performed in a flask (batch condition) using the same culture medium showed that only members of the genus Thermococcus were cultivated. Therefore, continuous enrichment culture using the gas-lift bioreactor can be considered as an efficient and improved method for investigating microbial communities originating from deep-sea hydrothermal vents.

Genome sequence of the deep-sea γ-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy

We report the complete genome sequence of the deep-sea gamma-proteobacterium, Idiomarina loihiensis, isolated recently from a hydrothermal vent at 1,300-m depth on the Loihi submarine volcano, Hawaii. The I. loihiensis genome comprises a single chromosome of 2,839,318 base pairs, encoding 2,640 proteins, four rRNA operons, and 56 tRNA genes. A comparison of I. loihiensis to the genomes of other gamma-proteobacteria reveals abundance of amino acid transport and degradation enzymes, but a loss of sugar transport systems and certain enzymes of sugar metabolism. This finding suggests that I. loihiensis relies primarily on amino acid catabolism, rather than on sugar fermentation, for carbon and energy. Enzymes for biosynthesis of purines, pyrimidines, the majority of amino acids, and coenzymes are encoded in the genome, but biosynthetic pathways for Leu, Ile, Val, Thr, and Met are incomplete. Auxotrophy for Val and Thr was confirmed by in vivo experiments. The I. loihiensis genome contains a cluster of 32 genes encoding enzymes for exopolysaccharide and capsular polysaccharide synthesis. It also encodes diverse peptidases, a variety of peptide and amino acid uptake systems, and versatile signal transduction machinery. We propose that the source of amino acids for I. loihiensis growth are the proteinaceous particles present in the deep sea hydrothermal vent waters. I. loihiensis would colonize these particles by using the secreted exopolysaccharide, digest these proteins, and metabolize the resulting peptides and amino acids. In summary, the I. loihiensis genome reveals an integrated mechanism of metabolic adaptation to the constantly changing deep-sea hydrothermal ecosystem.

ϵ-Proteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge

The prokaryotic phylogenetic diversity was determined for a sample associated with an in situ growth chamber deployed for 5 days on a Mid-Atlantic Ridge hydrothermal vent (23°22′N, 44°57′W). The DNA was extracted from the sample and the 16S rDNA amplified by PCR. No Archaea were detected in the sample. Eighty-seven clones containing bacterial 16S rDNA inserts were selected. Based on restriction fragment length polymorphism analysis, 47 clones were unique, however, based on comparative sequence analysis some of these were very similar, and thus only 22 clones were selected for full sequence and phylogenetic analysis. The phylotypes were dominated by ϵ- Proteobacteria (66%). The remainder formed a novel lineage within the Proteobacteria (33%). One clone formed a distinct deeply branching lineage, and was a distant relative of the Aquificales. This report further expands the growing evidence that ϵ- Proteobacteria are important members in biogeochemical cycling at deep-sea hydrothermal ecosystems, participating as epibionts and free living bacteria.

Epsilon-proteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge.

The prokaryotic phylogenetic diversity was determined for a sample associated with an in situ growth chamber deployed for 5 days on a Mid-Atlantic Ridge hydrothermal vent (23 degrees 22'N, 44 degrees 57'W). The DNA was extracted from the sample and the 16S rDNA amplified by PCR. No Archaea were detected in the sample. Eighty-seven clones containing bacterial 16S rDNA inserts were selected. Based on restriction fragment length polymorphism analysis, 47 clones were unique, however, based on comparative sequence analysis some of these were very similar, and thus only 22 clones were selected for full sequence and phylogenetic analysis. The phylotypes were dominated by epsilon-Proteobacteria (66%). The remainder formed a novel lineage within the Proteobacteria (33%). One clone formed a distinct deeply branching lineage, and was a distant relative of the Aquificales. This report further expands the growing evidence that epsilon-Proteobacteria are important members in biogeochemical cycling at deep-sea hydrothermal ecosystems, participating as epibionts and free living bacteria.