Recent developments in the thermophilic microbiology of deep-sea hydrothermal vents

Two-dimensional (P/T) studies of secondary/tertiary conformational dynamics in nucleic acids: pressure induced melting and Maxwell relations at the single molecule level

A predictive understanding of conformational folding of nucleic acids depends crucially on the underlying competition between enthalpic and entropic contributions to overall free energy changes. In extreme environments (e.g. deep ocean vents), such free energy changes are in turn impacted by both pressure and temperature as strongly coupled intensive variables, emphasizing the importance of a detailed molecular level understanding of the underlying thermodynamics. In this work, single-molecule fluorescence energy resonance transfer (smFRET) microscopy methods are implemented for quantitative kinetic study of secondary structure (i.e., DNA hybridization) and tertiary structure (i.e., RNA Mn2+ riboswitch folding) equilibria as a function of both pressure (P = 1 to 1000 bar) and temperature (T = 21 to 27 °C). Temperature dependent studies at a series of fixed pressures reveal the single molecule DNA and RNA constructs to be stabilized and destabilized, respectively, with increasing T. Interestingly, results for the Mn2+ riboswitch indicate a positive entropy change (ΔS > 0) for achieving the native tertiary conformation at all external pressures. This is contrary to more common physical expectations of increased order and thus an entropically penalty for tertiary folding of the RNA. On the other hand, pressure dependent scans for a series of constant temperature conditions confirm that both the DNA hairpin and RNA riboswitch constructs destabilize ("melt") under increasing pressure, which by van't Hoff analysis implies a positive volume change (ΔV0 > 0) for both secondary and tertiary folding into the native state. Furthermore, slices through these two-dimensional free energy surfaces permit parameters for isobaric thermal expansion in both secondary and tertiary conformational folding coordinates to be extracted. Finally, experimental control of multiple variables allows determination of the folding free energies as a two-dimensional function of pressure and temperature (ΔG(P, T)). To the best of our knowledge, this facilitates a first experimental confirmation of the underlying Maxwell relation (∂ΔS/∂P)T = -(∂ΔV/∂T)P for the exact free energy differential dG(P, V, S, T) at the single molecule level.

The co-occurrence patterns and assembly mechanisms of microeukaryotic communities in geothermal ecosystems of the Qinghai-Tibet Plateau

Geothermal spring ecosystems, as extreme habitats, exert significant environmental pressure on their microeukaryotic communities. However, existing studies on the stability of microeukaryotic communities in geothermal ecosystems across different habitats and temperature gradients are still limited. In this study, we used high-throughput 18S rDNA sequencing in combination with environmental factor analysis to investigate the co-occurrence patterns, assembly mechanisms, and responses to environmental changes of microeukaryotic communities in sediment and water samples from 36 geothermal springs across different temperature gradients in southern Tibet. The results show that with increasing temperature, the network stability of microeukaryotic communities in sediments significantly improved, while the stability in water communities decreased. The assembly mechanisms of microeukaryotic communities in both sediment and water were primarily driven by undominant processes within stochastic processes. Latitude and longitude were the key factors influencing changes in sediment community composition, while water temperature and electrical conductivity were the major environmental factors affecting water community composition. Additionally, the stability of the geothermal community network was closely related to its response to external disturbances: sediment communities, being in relatively stable environments, demonstrated higher resistance to disturbances, whereas water communities, influenced by environmental changes such as water flow and precipitation, exhibited greater dynamic variability. These findings not only enhance our understanding of the ecological adaptability of microeukaryotic communities in geothermal springs but also provide valuable insights into how microorganisms in extreme environments respond to external disturbances. This is especially significant for understanding how microeukaryotic communities maintain ecological stability under highly dynamic and stressful environmental conditions.

Potential functions and applications of diverse microbial exopolysaccharides in marine environments

Exopolysaccharides (EPSs) from microorganisms are essential harmless natural biopolymers used in applications including medications, nutraceuticals and functional foods, cosmetics, and insecticides. Several microbes can synthesize and excrete EPSs with chemical properties and structures that make them suitable for several important applications. Microbes secrete EPSs outside their cell walls, as slime or as a "jelly" into the extracellular medium. These EPS-producing microbes are ubiquitous and can be isolated from aquatic and terrestrial environments, such as freshwater, marine water, wastewater, and soils. They have also been isolated from extreme niches like hot springs, cold waters, halophilic environments, and salt marshes. Recently, microbial EPSs have attracted interest for their applications such as environmental bio-flocculants because they are degradable and nontoxic. However, further efforts are required for the cost-effective and industrial-scale commercial production of microbial EPSs. This review focuses on the exopolysaccharides obtained from several extremophilic microorganisms, their synthesis, and manufacturing optimization for better cost and productivity. We also explored their role and applications in interactions between several organisms.

Pan-genome study of Thermococcales reveals extensive genetic diversity and genetic evidence of thermophilic adaption

Thermococcales has a strong adaptability to extreme environments, which is of profound interest in explaining how complex life forms emerge on earth. However, their gene composition, thermal stability and evolution in hyperthermal environments are still little known. Here, we characterized the pan-genome architecture of 30 Thermococcales species to gain insight into their genetic properties, evolutionary patterns and specific metabolisms adapted to niches. We revealed an open pan-genome of Thermococcales comprising 6070 gene families that tend to increase with the availability of additional genomes. The genome contents of Thermococcales were flexible, with a series of genes experienced gene duplication, progressive divergence, or gene gain and loss events exhibiting distinct functional features. These archaea had concise types of heat shock proteins, such as HSP20, HSP60 and prefoldin, which were constrained by strong purifying selection that governed their conservative evolution. Furthermore, purifying selection forced genes involved in enzyme, motility, secretion system, defence system and chaperones to differ in functional constraints and their disparity in the rate of evolution may be related to adaptation to specific niche. These results deepened our understanding of genetic diversity and adaptation patterns of Thermococcales, and provided valuable research models for studying the metabolic traits of early life forms.

Microbially Mediated Ore-Forming Processes and Cell Mineralization

Sedimentary black shale-hosted manganese carbonate and oxide ores were studied by high-resolution in situ detailed optical and cathodoluminescence microscopy, Raman spectroscopy, and FTIR spectroscopy to determine microbial contribution in metallogenesis. This study of the Urucum Mn deposit in Brazil is included as a case study for microbially mediated ore-forming processes. The results were compared and interpreted in a comparative way, and the data were elaborated by a complex, structural hierarchical method. The first syngenetic products of microbial enzymatic oxidation were ferrihydrite and lepidocrocite on the Fe side, and vernadite, todorokite, birnessite, and manganite on the Mn side, formed under obligatory oxic (Mn) and suboxic (Fe) conditions and close to neutral pH. Fe- and Mn-oxidizing bacteria played a basic role in metallogenesis based on microtextural features, bioindicator minerals, and embedded variable organic matter. Trace element content is determined by source of elements and microbial activity. The present Urucum (Brazil), Datangpo (China), and Úrkút (Hungary) deposits are the result of complex diagenetic processes, which include the decomposition and mineralization of cell and extracellular polymeric substance (EPS) of Fe and Mn bacteria and cyanobacteria. Heterotrophic cell colonies activated randomly in the microbialite sediment after burial in suboxic neutral/alkaline conditions, forming Mn carbonates and variable cation-bearing oxides side by side with lithification and stabilization of minerals. Deposits of variable geological ages and geographical occurrences show strong similarities and indicate two-step microbial metallogenesis: a primary chemolithoautotrophic, and a diagenetic heterotrophic microbial cycle, influenced strongly by mineralization of cells and EPSs. These processes perform a basic role in controlling major and trace element distribution in sedimentary environments on a global level and place biogeochemical constraints on the element content of natural waters, precipitation of minerals, and water contaminants.

Identification and characterization of a hyperthermophilic GH9 cellulase from the Arctic Mid-Ocean Ridge vent field

A novel GH9 cellulase (AMOR_GH9A) was discovered by sequence-based mining of a unique metagenomic dataset collected at the Jan Mayen hydrothermal vent field. AMOR_GH9A comprises a signal peptide, a catalytic domain and a CBM3 cellulose-binding module. AMOR_GH9A is an exceptionally stable enzyme with a temperature optimum around 100°C and an apparent melting temperature of 105°C. The novel cellulase retains 64% of its activity after 4 hours of incubation at 95°C. The closest characterized homolog of AMOR_GH9A is TfCel9A, a processive endocellulase from the model thermophilic bacterium Thermobifida fusca (64.2% sequence identity). Direct comparison of AMOR_GH9A and TfCel9A revealed that AMOR_GH9A possesses higher activity on soluble and amorphous substrates (phosphoric acid swollen cellulose, konjac glucomannan) and has an ability to hydrolyse xylan that is lacking in TfCel9A.

Discovery of a Thermostable GH10 Xylanase with Broad Substrate Specificity from the Arctic Mid-Ocean Ridge Vent System

A two-domain GH10 xylanase-encoding gene (amor_gh10a) was discovered from a metagenomic data set, generated after in situ incubation of a lignocellulosic substrate in hot sediments on the sea floor of the Arctic Mid-Ocean Ridge (AMOR). AMOR_GH10A comprises a signal peptide, a carbohydrate-binding module belonging to a previously uncharacterized family, and a catalytic glycosyl hydrolase (GH10) domain. The enzyme shares the highest sequence identity (42%) with a hypothetical protein from a Verrucomicrobia bacterium, and its GH10 domain shares low identity (24 to 28%) with functionally characterized xylanases. Purified AMOR_GH10A showed thermophilic and halophilic properties and was active toward various xylans. Uniquely, the enzyme showed high activity toward amorphous cellulose, glucomannan, and xyloglucan and was more active toward cellopentaose than toward xylopentaose. Binding assays showed that the N-terminal domain of this broad-specificity GH10 binds strongly to amorphous cellulose, as well as to microcrystalline cellulose, birchwood glucuronoxylan, barley β-glucan, and konjac glucomannan, confirming its classification as a novel CBM (CBM85).IMPORTANCE Hot springs at the sea bottom harbor unique biodiversity and are a promising source of enzymes with interesting properties. We describe the functional characterization of a thermophilic and halophilic multidomain xylanase originating from the Arctic Mid-Ocean Ridge vent system, belonging to the well-studied family 10 of glycosyl hydrolases (GH10). This xylanase, AMOR_GH10A, has a surprisingly wide substrate range and is more active toward cellopentaose than toward xylopentaose. This substrate promiscuity is unique for the GH10 family and could prove useful in industrial applications. Emphasizing the versatility of AMOR_GH10A, its N-terminal domain binds to both xylans and glycans, while not showing significant sequence similarities to any known carbohydrate-binding module (CBM) in the CAZy database. Thus, this N-terminal domain lays the foundation for the new CBM85 family.

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.

Energy Landscapes in Hydrothermal Chimneys Shape Distributions of Primary Producers

Hydrothermal systems are excellent natural laboratories for the study of how chemical energy landscapes shape microbial communities. Yet, only a few attempts have been made to quantify relationships between energy availability and microbial community structure in these systems. Here, we have investigated how microbial communities and chemical energy availabilities vary along cross-sections of two hydrothermal chimneys from the Soria Moria Vent Field and the Bruse Vent Field. Both vent fields are located on the Arctic Mid-Ocean Ridge, north of the Jan Mayen Island and the investigated chimneys were venting fluids with markedly different H2S:CH4 ratios. Energy landscapes were inferred from a stepwise in silico mixing of hydrothermal fluids (HFs) with seawater, where Gibbs energies of relevant redox-reactions were calculated at each step. These calculations formed the basis for simulations of relative abundances of primary producers in microbial communities. The simulations were compared with an analysis of 24 samples from chimney wall transects by sequencing of 16S rRNA gene amplicons using 454 sequencing. Patterns in relative abundances of sulfide oxidizing Epsilonproteobacteria and methane oxidizing Methylococcales and ANME-1, were consistent with simulations. However, even though H2 was present in HFs from both chimneys, the observed abundances of putative hydrogen oxidizing anaerobic sulfate reducers (Archaeoglobales) and methanogens (Methanococcales) in the inner parts of the Soria Moria Chimney were considerably higher than predicted by simulations. This indicates biogenic production of H2 in the chimney wall by fermentation, and suggests that biological activity inside the chimneys may modulate energy landscapes significantly. Our results are consistent with the notion that energy landscapes largely shape the distribution of primary producers in hydrothermal systems. Our study demonstrates how a combination of modeling and field observations can be useful in deciphering connections between chemical energy landscapes and metabolic networks within microbial communities.

Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits

To assess the risk that mining of seafloor massive sulfides (SMS) from extinct hydrothermal vent environments has for changing the ecosystem irreversibly, we sampled SMS analogous habitats from the Kairei and the Pelagia vent fields along the Indian Ridge. In total 19.8 million 16S rRNA tags from 14 different sites were analyzed and the microbial communities were compared with each other and with publicly available data sets from other marine environments. The chimneys appear to provide habitats for microorganisms that are not found or only detectable in very low numbers in other marine habitats. The chimneys also host rare organisms and may function as a vital part of the ocean’s seed bank. Many of the reads from active and inactive chimney samples were clustered into OTUs, with low or no resemblance to known species. Since we are unaware of the chemical reactions catalyzed by these unknown organisms, the impact of this diversity loss and bio-geo-coupling is hard to predict. Given that chimney structures can be considered SMS analogues, removal of sulfide deposits from the seafloor in the Kairei and Pelagia fields will most likely alter microbial compositions and affect element cycling in the benthic regions and probably beyond.

Specific enrichment of hyperthermophilic electroactive Archaea from deep-sea hydrothermal vent on electrically conductive support

While more and more investigations are done to study hyperthermophilic exoelectrogenic communities from environments, none have been performed yet on deep-sea hydrothermal vent. Samples of black smoker chimney from Rainbow site on the Atlantic mid-oceanic ridge have been harvested for enriching exoelectrogens in microbial electrolysis cells under hyperthermophilic (80 °C) condition. Two enrichments were performed in a BioElectrochemical System specially designed: one from direct inoculation of crushed chimney and the other one from inoculation of a pre-cultivation on iron (III) oxide. In both experiments, a current production was observed from 2.4 A/m² to 5.8 A/m² with a set anode potential of -0.110 V vs Ag/AgCl. Taxonomic affiliation of the exoelectrogen communities obtained on the electrode exhibited a specific enrichment of Archaea belonging to Thermococcales and Archeoglobales orders, even when both inocula were dominated by Bacteria.

Biodiversity of the microbial mat of the Garga hot spring

BACKGROUND

Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area.

RESULTS

In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA.

CONCLUSIONS

High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that the three studied points sampled at 70 °C, 55 °C, and 45 °C had similar species composition. Cyanobacteria of the genus Leptolyngbya dominated in the upper layer of the microbial mat. Chloroflexi and Chlorobi were less abundant and were mostly observed in the middle part of the microbial mat. We detected domains of heterotrophic organisms in high abundance (Proteobacteria, Firmicutes, Verrucomicrobia, Planctomicetes, Bacteroidetes, Actinobacteria, Thermi), according to metabolic properties of known relatives, which can form complete cycles of carbon, sulphur, and nitrogen in the microbial mat. The studied microbial mats evolved in early stages of biosphere formation. They can live autonomously, providing full cycles of substances and preventing live activity products poisoning.

Desulfurobacterium indicum sp. nov., a thermophilic sulfur-reducing bacterium from the Indian Ocean

A novel sulfur-reducing bacterium, strain K6013T, was isolated from a sulfide sample collected at a depth of 2771 m from a high-temperature hydrothermal vent in the Indian Ocean. Cells were Gram-stain-negative, anaerobic, motile rods (0.9-2.2×0.4-0.6 µm). The strain grew at NaCl concentrations ranging from 1 to 4.5 % (w/v) (optimum 2.5 %), at pH 5 to 8 (optimum pH 6), and at temperatures between 40 and 75 °C (optimum 65 °C). K6013T was an obligate chemolithoautotroph, using thiosulfate, sulfur and nitrate as terminal electron acceptors in the presence of H2 but not sulfate, sulfite nor nitrite. The major cellular fatty acids were C16 : 0 (17.4 %), C18 : 1ω7c/C18 : 1ω6c (ummed feature 8, 37.91 %), C18 : 0 (18.29 %) and C14 : 0 3-OH/iso-C16: 1I (summed feature 2, 8.56 %). The DNA G+C content was 38.2 mol%. The results of phylogenetic 16S rRNA gene sequence analyses indicated that K6013T represents a member of the genus Desulfurobacterium within the class Aquificae, with highest sequence similarity of 96.93 % to Desulfurobacterium atlanticum SL22T. On the basis of genotypic and phenotypic data, K6013T is considered to represent a novel species of the genus Desulfurobacterium, for which the name Desulfurobacterium indicum sp. nov. is proposed, with the type strain K6013T (=DSM 101677T=MCCC 1A01868T).

Bacterial Dormancy Is More Prevalent in Freshwater than Hypersaline Lakes

Bacteria employ a diverse array of strategies to survive under extreme environmental conditions but maintaining these adaptations comes at an energetic cost. If energy reserves drop too low, extremophiles may enter a dormant state to persist. We estimated bacterial dormancy and identified the environmental variables influencing our activity proxy in 10 hypersaline and freshwater lakes across the Western United States. Using ribosomal RNA:DNA ratios as an indicator for bacterial activity, we found that the proportion of the community exhibiting dormancy was 16% lower in hypersaline than freshwater lakes. Based on our indicator variable multiple regression results, saltier conditions in both freshwater and hypersaline lakes increased activity, suggesting that salinity was a robust environmental filter structuring bacterial activity in lake ecosystems. To a lesser degree, higher total phosphorus concentrations reduced dormancy in all lakes. Thus, even under extreme conditions, the competition for resources exerted pressure on activity. Within the compositionally distinct and less diverse hypersaline communities, abundant taxa were disproportionately active and localized in families Microbacteriaceae (Actinobacteria), Nitriliruptoraceae (Actinobacteria), and Rhodobacteraceae (Alphaproteobacteria). Our results are consistent with the view that hypersaline communities are able to capitalize on a seemingly more extreme, yet highly selective, set of conditions and finds that extremophiles may need dormancy less often to thrive and survive.

Handling temperature bursts reaching 464°C: different microbial strategies in the sisters peak hydrothermal chimney

The active venting Sisters Peak (SP) chimney on the Mid-Atlantic Ridge holds the current temperature record for the hottest ever measured hydrothermal fluids (400°C, accompanied by sudden temperature bursts reaching 464°C). Given the unprecedented temperature regime, we investigated the biome of this chimney with a focus on special microbial adaptations for thermal tolerance. The SP metagenome reveals considerable differences in the taxonomic composition from those of other hydrothermal vent and subsurface samples; these could be better explained by temperature than by other available abiotic parameters. The most common species to which SP genes were assigned were thermophilic Aciduliprofundum sp. strain MAR08-339 (11.8%), Hippea maritima (3.8%), Caldisericum exile (1.5%), and Caminibacter mediatlanticus (1.4%) as well as to the mesophilic Niastella koreensis (2.8%). A statistical analysis of associations between taxonomic and functional gene assignments revealed specific overrepresented functional categories: for Aciduliprofundum, protein biosynthesis, nucleotide metabolism, and energy metabolism genes; for Hippea and Caminibacter, cell motility and/or DNA replication and repair system genes; and for Niastella, cell wall and membrane biogenesis genes. Cultured representatives of these organisms inhabit different thermal niches; i.e., Aciduliprofundum has an optimal growth temperature of 70°C, Hippea and Caminibacter have optimal growth temperatures around 55°C, and Niastella grows between 10 and 37°C. Therefore, we posit that the different enrichment profiles of functional categories reflect distinct microbial strategies to deal with the different impacts of the local sudden temperature bursts in disparate regions of the chimney.

Diversity of the Epsilonproteobacteria Dsb (disulfide bond) systems

The bacterial proteins of the Dsb family-important components of the post-translational protein modification system-catalyze the formation of disulfide bridges, a process that is crucial for protein structure stabilization and activity. Dsb systems play an essential role in the assembly of many virulence factors. Recent rapid advances in global analysis of bacteria have thrown light on the enormous diversity among bacterial Dsb systems. While the Escherichia coli disulfide bond-forming system is quite well understood, the mechanisms of action of Dsb systems in other bacteria, including members of class Epsilonproteobacteria that contain pathogenic and non-pathogenic bacteria colonizing extremely diverse ecological niches, are poorly characterized. Here we present a review of current knowledge on Epsilonproteobacteria Dsb systems. We have focused on the Dsb systems of Campylobacter spp. and Helicobacter spp. because our knowledge about Dsb proteins of Wolinella and Arcobacter spp. is still scarce and comes mainly from bioinformatic studies. Helicobacter pylori is a common human pathogen that colonizes the gastric epithelium of humans with severe consequences. Campylobacter spp. is a leading cause of zoonotic enteric bacterial infections in most developed and developing nations. We focus on various aspects of the diversity of the Dsb systems and their influence on pathogenicity, particularly because Dsb proteins are considered as potential targets for a new class of anti-virulence drugs to treat human infections by Campylobacter or Helicobacter spp.

Anoxybacter fermentans gen. nov., sp. nov., a piezophilic, thermophilic, anaerobic, fermentative bacterium isolated from a deep-sea hydrothermal vent

A novel piezophilic, thermophilic, anaerobic, fermentative bacterial strain, designated strain DY22613(T), was isolated from a deep-sea hydrothermal sulfide deposit at the East Pacific Rise (GPS position: 102.6° W 3.1° S). Cells of strain DY22613(T) were long, motile rods (10 to 20 µm in length and 0.5 µm in width) with peritrichous flagella and were Gram-stain-negative. Growth was recorded at 44-72 °C (optimum 60-62 °C) and at hydrostatic pressures of 0.1-55 MPa (optimum 20 MPa). The pH range for growth was from pH 5.0 to 9.0 with an optimum at pH 7.0. Growth was observed in the presence of 1 to 8 % (w/v) sea salts and 0.65 to 5.2 % (w/v) NaCl, with optimum salt concentrations at 3.5 % for sea salts and at 2.3 % for NaCl. Under optimal growth conditions, the shortest generation time observed was 27 min (60 °C, 20 MPa). Strain DY22613(T) was heterotrophic, able to utilize complex organic compounds, amino acids, sugars and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamine, methionine, phenylalanine, serine, threonine, fructose, fucose, galactose, gentiobiose, glucose, mannose, melibiose, palatinose, rhamnose, turanose, pyruvate, lactic acid, methyl ester, erythritol, galacturonic acid and glucosaminic acid. Strain DY22613(T) was able to reduce Fe(III) compounds, including Fe(III) oxyhydroxide (pH 7.0), amorphous iron(III) oxide (pH 9.0), goethite (α-FeOOH, pH 12.0), Fe(III) citrate and elementary sulfur. Products of fermentation were butyrate, acetate and hydrogen. Main cellular fatty acids were iso-C15 : 0, iso-C14 : 0 3-OH and C14 : 0. The genomic DNA G+C content of strain DY22613(T) was 36.7 mol%. Based on 16S rRNA gene sequence analysis, the strain forms a novel lineage within the class Clostridia and clusters with the order Haloanaerobiales (86.92 % 16S rRNA gene sequence similarity). The phylogenetic data suggest that the lineage represents at least a novel genus and species, for which the name Anoxybacter fermentans gen. nov., sp. nov. is proposed. The type strain is DY22613(T) ( = JCM 19466(T) = DSM 28033(T) = MCCC 1A06456(T)).

Antibacterial gene transfer across the tree of life

Though horizontal gene transfer (HGT) is widespread, genes and taxa experience biased rates of transferability. Curiously, independent transmission of homologous DNA to archaea, bacteria, eukaryotes, and viruses is extremely rare and often defies ecological and functional explanations. Here, we demonstrate that a bacterial lysozyme family integrated independently in all domains of life across diverse environments, generating the only glycosyl hydrolase 25 muramidases in plants and archaea. During coculture of a hydrothermal vent archaeon with a bacterial competitor, muramidase transcription is upregulated. Moreover, recombinant lysozyme exhibits broad-spectrum antibacterial action in a dose-dependent manner. Similar to bacterial transfer of antibiotic resistance genes, transfer of a potent antibacterial gene across the universal tree seemingly bestows a niche-transcending adaptation that trumps the barriers against parallel HGT to all domains. The discoveries also comprise the first characterization of an antibacterial gene in archaea and support the pursuit of antibiotics in this underexplored group.

DOI:http://dx.doi.org/10.7554/eLife.04266.001

Living things inherit most of their genetic material from their parents, so genes tend to be passed on from one generation to the next—from ancestors to descendants. Sometimes, however, DNA is transferred from one organism to another by other means. These events, collectively called horizontal gene transfer, are fairly common in nature; genes have been passed between different species as well as between different groups of organisms. For example, genes that confer resistance to antibacterial drugs have transferred from one species of bacteria to another, and other genes have also ‘jumped’ from bacteria to plants or animals.

Now Metcalf et al. have studied a gene that first arose in bacteria and that encodes an enzyme called a lysozyme. This enzyme breaks down the outer casing of a bacterial cell: a step that is required for a bacterium to reproduce and divide in two. When Metcalf et al. searched for relatives of the lysozyme gene, they found copies in many other species of bacteria and revealed that this gene has been repeatedly transferred between different bacteria. Members of the lysozyme gene family have also ‘jumped out’ of bacteria and into other organisms at least four times. Metcalf et al. found related lysozyme genes in a plant, an insect, many species of fungi, and a single-celled microbe (called an archaeon) that lives at hot, deep-sea vents.

A gene family being spread this widely across the tree of life has not been seen before. Nevertheless, as DNA is a common biological language to all living things, it is likely that all the different species that have received a lysozyme gene might use it for similar purposes.

Metcalf et al. reveal that the lysozyme could be being used as an antibacterial molecule. The archaeon lysozyme can kill a broad range of bacteria; and when the gene was transferred into Escherichia coli bacteria, only the bacteria that mutated the lysozyme gene to render it useless were able to survive. Metcalf et al. also revealed that the archaeon microbe produces more of the enzyme if bacteria are present, which allows it to outcompete these bacteria.

These findings suggest that there may be a number of horizontally transferred genes that have antibacterial activity against a wide range of bacteria. Searching for these genes—particularly in the largely underexplored group of archaea—might reveal new sources for antibiotic drugs to treat bacterial infections.

DOI:http://dx.doi.org/10.7554/eLife.04266.002

Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering

We recently introduced ENCoM, an elastic network atomic contact model, as the first coarse-grained normal mode analysis method that accounts for the nature of amino acids and can predict the effect of mutations on thermostability based on changes vibrational entropy. In this proof-of-concept article, we use pairs of mesophile and thermophile homolog proteins with identical structures to determine if a measure of vibrational entropy based on normal mode analysis can discriminate thermophile from mesophile proteins. We observe that in around 60% of cases, thermophile proteins are more rigid at equivalent temperatures than their mesophile counterpart and this difference can guide the design of proteins to increase their thermostability through series of mutations. We observe that mutations separating thermophile proteins from their mesophile orthologs contribute independently to a decrease in vibrational entropy and discuss the application and implications of this methodology to protein engineering.

Exopolysaccharides produced by marine bacteria and their applications as glycosaminoglycan-like molecules

Although polysaccharides are ubiquitous and the most abundant renewable bio-components, their studies, covered by the glycochemistry and glycobiology fields, remain a challenge due to their high molecular diversity and complexity. Polysaccharides are industrially used in food products; human therapeutics fall into a more recent research field and pharmaceutical industry is looking for more and more molecules with enhanced activities. Glycosaminoglycans (GAGs) found in animal tissues play a critical role in cellular physiological and pathological processes as they bind many cellular components. Therefore, they present a great potential for the design and preparation of therapeutic drugs. On the other hand, microorganisms producing exopolysaccharides (EPS) are renewable resources meeting well the actual industrial demand. In particular, the diversity of marine microorganisms is still largely unexplored offering great opportunities to discover high value products such as new molecules and biocatalysts. EPS-producing bacteria from the marine environment will be reviewed with a focus on marine-derived EPS from bacteria isolated from deep-sea hydrothermal vents. Information on chemical and structural features, putative pathways of biosynthesis, novel strategies for chemical and enzymatic modifications and potentialities in the biomedical field will be provided. An integrated approach should be used to increase the basic knowledge on these compounds and their applications; new clean environmentally friendly processes for the production of carbohydrate bioactive compounds should also be proposed for a sustainable industry.

A novel hydrogen oxidizer amidst the sulfur-oxidizing Thiomicrospira lineage

Thiomicrospira species are ubiquitously found in various marine environments and appear particularly common in hydrothermal vent systems. Members of this lineage are commonly classified as sulfur-oxidizing chemolithoautotrophs. Although sequencing of Thiomicrospira crunogena's genome has revealed genes that encode enzymes for hydrogen uptake activity and for hydrogenase maturation and assembly, hydrogen uptake ability has so far not been reported for any Thiomicrospira species. We isolated a Thiomicrospira species (SP-41) from a deep sea hydrothermal vent and demonstrated that it can oxidize hydrogen. We show in vivo hydrogen consumption, hydrogen uptake activity in partially purified protein extracts and transcript abundance of hydrogenases during different growth stages. The ability of this strain to oxidize hydrogen opens up new perspectives with respect to the physiology of Thiomicrospira species that have been detected in hydrothermal vents and that have so far been exclusively associated with sulfur oxidation.

Bacterial diversity assessment in soil of an active Brazilian copper mine using high-throughput sequencing of 16S rDNA amplicons

Mining activities pose severe environmental risks worldwide, generating extreme pH conditions and high concentrations of heavy metals, which can have major impacts on the survival of organisms. In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. For the analysis, soil samples were collected from the slopes (geotechnical structures) and the surrounding drainage of the Sossego mine (comprising the Sossego and Sequeirinho deposits). The results revealed complex bacterial diversity, and there was no influence of deposit geographic location on the composition of the communities. However, the environment type played an important role in bacterial community divergence; the composition and frequency of OTUs in the slope samples were different from those of the surrounding drainage samples, and Acidobacteria, Chloroflexi, Firmicutes, and Gammaproteobacteria were responsible for the observed difference. Chemical analysis indicated that both types of sample presented a high metal content, while the amounts of organic matter and water were higher in the surrounding drainage samples. Non-metric multidimensional scaling (N-MDS) analysis identified organic matter and water as important distinguishing factors between the bacterial communities from the two types of mine environment. Although habitat-specific OTUs were found in both environments, they were more abundant in the surrounding drainage samples (around 50 %), and contributed to the higher bacterial diversity found in this habitat. The slope samples were dominated by a smaller number of phyla, especially Firmicutes. The bacterial communities from the slope and surrounding drainage samples were different in structure and composition, and the organic matter and water present in these environments contributed to the observed differences.

Increased growth and germination success in plants following hydrogen sulfide administration

This study presents a novel way of enhancing plant growth through the use of a non-petroleum based product. We report here that exposing either roots or seeds of multicellular plants to extremely low concentrations of dissolved hydrogen sulfide at any stage of life causes statistically significant increases in biomass including higher fruit yield. Individual cells in treated plants were smaller (~13%) than those of controls. Germination success and seedling size increased in, bean, corn, wheat, and pea seeds while time to germination decreases. These findings indicated an important role of H2S as a signaling molecule that can increase the growth rate of all species yet tested. The increased crop yields reported here has the potential to effect the world's agricultural output.

The hyperthermophilic bacterium Aquifex aeolicus: from respiratory pathways to extremely resistant enzymes and biotechnological applications

Aquifex aeolicus isolated from a shallow submarine hydrothermal system belongs to the order Aquificales which constitute an important component of the microbial communities at elevated temperatures. This hyperthermophilic chemolithoautotrophic bacterium, which utilizes molecular hydrogen, molecular oxygen, and inorganic sulfur compounds to flourish, uses the reductive TCA cycle for CO(2) fixation. In this review, the intricate energy metabolism of A. aeolicus is described. As the chemistry of sulfur is complex and multiple sulfur species can be generated, A. aeolicus possesses a multitude of different enzymes related to the energy sulfur metabolism. It contains also membrane-embedded [NiFe] hydrogenases as well as oxidases enzymes involved in hydrogen and oxygen utilization. We have focused on some of these proteins that have been extensively studied and characterized as super-resistant enzymes with outstanding properties. We discuss the potential use of hydrogenases in an attractive H(2)/O(2) biofuel cell in replacement of chemical catalysts. Using complete genomic sequence and biochemical data, we present here a global view of the energy-generating mechanisms of A. aeolicus including sulfur compounds reduction and oxidation pathways as well as hydrogen and oxygen utilization.

Phorcysia thermohydrogeniphila gen. nov., sp. nov., a thermophilic, chemolithoautotrophic, nitrate-ammonifying bacterium from a deep-sea hydrothermal vent

A novel hyperthermophilic, anaerobic, chemolithoautotrophic bacterium, designated strain HB-8T, was isolated from the tube of Alvinella pompejana tubeworms collected from the wall of an actively venting sulfide structure on the East Pacific Rise at 13° N. The cells were Gram-negative rods, approximately 1.0–1.5 µm long and 0.5 µm wide. Strain HB-8T grew between 65 and 80 °C (optimum 75 °C), 15 and 35 g NaCl l−1 (optimum 30 g l−1) and pH 4.5 and 8.5 (optimum pH 6.0). Generation time under optimal conditions was 26 min. Growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Nitrate and sulfur were used as electron acceptors, with concomitant formation of ammonium or hydrogen sulfide, respectively. The presence of lactate, formate, acetate or tryptone in the culture medium inhibited growth. The G+C content of the genomic DNA was 47.8 mol%. Phylogenetic analysis of the 16S rRNA gene and of the alpha subunit of the ATP citrate lyase of strain HB-8T indicated that this organism formed a novel lineage within the class Aquificae , equally distant from the type strains of the type species of the three genera that represent the family Desulfurobacteriaceae : Thermovibrio ruber ED11/3LLK8T, Balnearium lithotrophicum 17ST and Desulfurobacterium thermolithotrophum BSAT. The polar lipids of strain HB-8T differed substantially from those of other members of the Desulfurobacteriaceae , and this bacterium produced novel quinones. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, it is proposed that the organism represents a novel genus and species within the family Desulfurobacteriaceae , Phorcysia thermohydrogeniphila gen. nov., sp. nov. The type strain of Phorcysia thermohydrogeniphila is HB-8T ( = DSM 24425T  = JCM 17384T).

Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases

Four hyperthermophilic members of the bacterial genus Thermotoga (T. maritima, T. neapolitana, T. petrophila, and Thermotoga sp. strain RQ2) share a core genome of 1,470 open reading frames (ORFs), or about 75% of their genomes. Nonetheless, each species exhibited certain distinguishing features during growth on simple and complex carbohydrates that correlated with genomic inventories of specific ABC sugar transporters and glycoside hydrolases. These differences were consistent with transcriptomic analysis based on a multispecies cDNA microarray. Growth on a mixture of six pentoses and hexoses showed no significant utilization of galactose or mannose by any of the four species. T. maritima and T. neapolitana exhibited similar monosaccharide utilization profiles, with a strong preference for glucose and xylose over fructose and arabinose. Thermotoga sp. strain RQ2 also used glucose and xylose, but was the only species to utilize fructose to any extent, consistent with a phosphotransferase system (PTS) specific for this sugar encoded in its genome. T. petrophila used glucose to a significantly lesser extent than the other species. In fact, the XylR regulon was triggered by growth on glucose for T. petrophila, which was attributed to the absence of a glucose transporter (XylE2F2K2), otherwise present in the other Thermotoga species. This suggested that T. petrophila acquires glucose through the XylE1F1K1 transporter, which primarily serves to transport xylose in the other three Thermotoga species. The results here show that subtle differences exist among the hyperthermophilic Thermotogales with respect to carbohydrate utilization, which supports their designation as separate species.

Heparin-like entities from marine organisms

Polysaccharides are ubiquitous in animals and plant cells where they play a significant role in a number of physiological situations e.g. hydration, mechanical properties of cell walls and ionic regulation. This review concentrates on heparin-like entities from marine procaryotes and eukaryotes. Carbohydrates from marine prokaryotes offer a significant structural chemodiversity with novel material and biological properties. Cyanobacteria are Gram-negative photosynthetic prokaryotes considered as a rich source of novel molecules, and marine bacteria are a rich source of polysaccharides with novel structures, which may be a good starting point from which to synthesise heparinoid molecules. For example, some sulphated polysaccharides have been isolated from gamma-proteobacteria such as Alteromonas and Pseudoalteromonas sp. In contrast to marine bacteria, all marine algae contain sulphated wall polysaccharides, whereas such polymers are not found in terrestrial plants. In their native form, or after chemical modifications, a range of polysaccharides isolated from marine organisms have been described that have anticoagulant, anti-thrombotic, anti-tumour, anti-proliferative, anti-viral or anti-inflammatory activities.In spite of the enormous potential of sulphated oligosaccharides from marine sources, their technical and pharmaceutical usage is still limited because of the high complexity of these molecules. Thus, the production of tailor-made oligo- and polysaccharidic structures by biocatalysis is also a growing field of interest in biotechnology.

Comparison of microbial communities associated with three Atlantic ultramafic hydrothermal systems

The distribution of Archaea and methanogenic, methanotrophic and sulfate-reducing communities in three Atlantic ultramafic-hosted hydrothermal systems (Rainbow, Ashadze, Lost City) was compared using 16S rRNA gene and functional gene (mcrA, pmoA and dsrA) clone libraries. The overall archaeal community was diverse and heterogeneously distributed between the hydrothermal sites and the types of samples analyzed (seawater, hydrothermal fluid, chimney and sediment). The Lost City hydrothermal field, characterized by high alkaline warm fluids (pH>11; T<95 °C), harbored a singular archaeal diversity mostly composed of unaffiliated Methanosarcinales. The archaeal communities associated with the recently discovered Ashadze 1 site, one of the deepest active hydrothermal fields known (4100 m depth), showed significant differences between the two different vents analyzed and were characterized by putative extreme halophiles. Sequences related to the rarely detected Nanoarchaeota phylum and Methanopyrales order were also retrieved from the Rainbow and Ashadze hydrothermal fluids. However, the methanogenic Methanococcales was the most widely distributed hyper/thermophilic archaeal group among the hot and acidic ultramafic-hosted hydrothermal system environments. Most of the lineages detected are linked to methane and hydrogen cycling, suggesting that in ultramafic-hosted hydrothermal systems, large methanogenic and methanotrophic communities could be fuelled by hydrothermal fluids highly enriched in methane and hydrogen.

Activity and distribution of thermophilic prokaryotes in hydrothermal fluid, sulfidic structures, and sheaths of alvinellids (East Pacific Rise, 13°N)

Processes of inorganic carbon assimilation, methanogenesis, sulfate reduction, and acetate oxidation to CO(2) occurring in samples from the East Pacific Rise at 13°N were traced, using radioisotopically labeled substrates, at temperatures ranging from 65 to 100°C. Molecular hydrogen stimulated lithotrophic methanogenesis and sulfate reduction but inhibited inorganic carbon assimilation. Active mineralization of acetate was observed in an organic-rich Alvinella-associated system at 80°C. Members of the Thermococcales were the most numerous hyperthermophilic archaea in these samples, their density achieving 10(8) cells per cm(3), while the numbers of cultured hydrogen-utilizing thermophilic lithotrophs were several orders of magnitude lower.

Geochemical constraints on the diversity and activity of H2 -oxidizing microorganisms in diffuse hydrothermal fluids from a basalt- and an ultramafic-hosted vent

Mixing processes of reduced hydrothermal fluids with oxygenated seawater and fluid-rock reactions contribute to the chemical signatures of diffuse venting and likely determine the geochemical constraints on microbial life. We examined the influence of fluid chemistry on microbial diversity and activity by sampling diffuse fluids emanating through mussel beds at two contrasting hydrothermal vents. The H(2) concentration was very low at the basalt-hosted Clueless site, and mixing models suggest O(2) availability throughout much of the habitat. In contrast, effluents from the ultramafic-hosted Quest site were considerably enriched in H(2) , while O(2) is likely limited to the mussel layer. Only two different hydrogenase genes were identified in clone libraries from the H(2) -poor Clueless fluids, but these fluids exhibited the highest H(2) uptake rates in H(2) -spiked incubations (oxic conditions, at 18 °C). In contrast, a phylogenetically diverse H(2) -oxidizing potential was associated with distinct thermal conditions in the H(2) -rich Quest fluids, but under oxic conditions, H(2) uptake rates were extremely low. Significant stimulation of CO(2) fixation rates by H(2) addition was solely illustrated in Quest incubations (P-value <0.02), but only in conjunction with anoxic conditions (at 18 °C). We conclude that the factors contributing toward differences in the diversity and activity of H(2) oxidizers at these sites include H(2) and O(2) availability.

A molecular and physiological survey of a diverse collection of hydrothermal vent Thermococcus and Pyrococcus isolates

Strains of hyperthermophilic anaerobic hydrothermal vent archaea maintained in the culture collection assembled by Holger Jannasch at the Woods Hole Oceanographic Institution between 1984 and 1998 were identified and partially characterized by Denaturing Gradient Gel Electrophoresis, 16S rRNA gene sequencing, and by growth tests at different temperatures and on different organic carbon and nitrogen sources. All strains were members of the genera Thermococcus and Pyrococcus. The greatest phylogenetic diversity was found in strains from a single Guaymas Basin core isolated by serial dilution from four different depth horizons of heated sediment incubated at the corresponding in situ temperatures. In contrast, geographically distinct vent locations and sample materials yielded a lower diversity of isolates when enriched under uniform temperature regimes and without prior dilution of the source material.

Bhargavaea cecembensis gen. nov., sp. nov., isolated from the Chagos-Laccadive ridge system in the Indian Ocean

A novel Gram-positive, rod-shaped, non-motile, non-spore-forming bacterium, strain DSE10(T), was isolated from a deep-sea sediment sample collected at a depth of 5904 m from the Chagos-Laccadive ridge system in the Indian Ocean. Cells of strain DSE10(T) were positive for catalase, oxidase, urease and lipase activities and contained iso-C(14 : 0), iso-C(15 : 0), iso-C(16 : 0) and anteiso-C(15 : 0) as the major fatty acids. The major respiratory quinones were MK-6 and MK-8 and the major lipids were phosphatidylglycerol and diphosphatidylglycerol. The cell-wall peptidoglycan contained diaminopimelic acid as the diagnostic diamino acid. A blast sequence similarity search based on 16S rRNA gene sequences indicated that the genera Planococcus, Planomicrobium, Bacillus and Geobacillus were the nearest phylogenetic neighbours to the novel isolate with gene sequence similarities ranging from 94.9 to 95.2 %. Phylogenetic analyses using neighbour-joining, minimum-evolution and maximum-parsimony methods indicated that strain DSE10(T) formed a deeply rooted lineage distinct from the clades represented by the genera Planococcus, Planomicrobium, Bacillus and Geobacillus. Further, strain DSE10(T) could be distinguished from the above-mentioned genera based on the presence of signature nucleotides G, A, C, T, C, A, G, C and T at positions 182, 444, 480, 492, 563, 931, 1253, 1300 and 1391, respectively, in the 16S rRNA gene sequence. Based on the phenotypic and phylogenetic characteristics determined in this study, strain DSE10(T) was assigned as the type species of a new genus, Bhargavaea gen. nov., as Bhargavaea cecembensis sp. nov. The type strain of Bhargavaea cecembensis gen. nov., sp. nov. is DSE10(T) (=LMG 24411(T)=JCM 14375(T)). The genomic DNA G+C content of strain DSE10(T) is 59.5+/-2.5 mol%.

Short-term microbial and physico-chemical variability in low-temperature hydrothermal fluids near 5 degrees S on the Mid-Atlantic Ridge

This study examines the representativeness of low-temperature hydrothermal fluid samples with respect to their chemical and microbiological characteristics. Within this scope, we investigated short-term temporal chemical and microbial variability of the hydrothermal fluids. For this purpose we collected three fluid samples consecutively from the same spot at the Clueless field near 5 degrees S on the southern Mid-Atlantic Ridge over a period of 50 min. During sampling, the temperature was monitored online. We measured fluid chemical parameters, characterized microbial community compositions and used statistical analyses to determine significant differences between the samples. Overall, the three fluid samples are more closely related to each other than to any other tested habitat. Therefore, on a broad scale, the three collected fluid samples can be regarded as habitat representatives. However, small differences are apparent between all samples. One of the Clueless samples even displayed significant differences (P-value < 0.01) to the other two Clueless samples. Our data suggest that the observed variations in fluid chemical and microbial compositions are not reflecting sampling artefacts but are related to short-term fluid variability due to dynamic subseafloor fluid mixing. Recorded temporal changes in fact reflect spatial heterogeneity found in the subsurface as the fluid flows through distinctive pathways. While conservative elements (Cl, Si, Na and K) indicate variable degrees of fluid-seawater mixing, reactive components, including Fe(II), O(2) and H(2)S, show that chemical and microbial reactions within the mixing zone further modify the emanating fluids on short-time scales. Fluids entrain microorganisms, which modify the chemical microenvironment within the subsurface biotopes. This is the first study focusing on short-term microbial variability linked to chemical changes in hydrothermal fluids.

The Fur iron regulator-like protein is cryptic in the hyperthermophilic archaeon Thermococcus kodakaraensis

Archaea, which regroup organisms with extreme living conditions, possess many predicted iron-containing proteins that may be metabolically critical; however, their need for iron remains poorly documented. In this report, iron acquisition mechanisms were investigated in the hyperthermophilic archaeon Thermococcus kodakaraensis. Thermococcus kodakaraensis requires iron for its growth and possesses many putative iron uptake systems, including several ATP-binding cassette-like transporters and two FeoAB-like receptors, showing that this organism shares similar features with bacteria. One homolog of the major bacterial iron regulator, ferric uptake regulator (Fur), with about 50% similarity to Escherichia coli Fur was also identified. Thermococcus kodakaraensis Fur was found to be able to specifically bind to a Fur-binding site consensus-like sequence of its own gene promoter. However, its expression has been hindered by a -1 frameshift mutation and the chromosomal repair of this mutation did not affect T. kodakaraensis in vivo phenotypes. Microarrays analyses helped to further characterize T. kodakaraensis iron-dependent growth and revealed no role for the Fur homolog in the global regulatory response of the cells to iron. In contrast, additional evidences indicated that the T. kodakaraensis diphtheria toxin regulator (DtxR) homolog may control the expression of the major iron acquisition effectors, while its inactivation enabled higher resistance to iron deficiency.

SurR: a transcriptional activator and repressor controlling hydrogen and elemental sulphur metabolism in Pyrococcus furiosus

This work describes the identification and characterization of SurR, Pyrococcus furiosus sulphur (S(0)) response regulator. SurR was captured from cell extract using promoter DNA of a hydrogenase operon that is downregulated in the primary response of P. furiosus to S(0), as revealed by DNA microarray experiments. SurR was validated as a sequence-specific DNA binding protein, and characterization of the SurR DNA binding motif GTTn(3)AAC led to the identification of several target genes that contain an extended motif in their promoters. A number of these were validated to contain upstream SurR binding sites. These SurR targets strongly correspond with open reading frames and operons both up- and downregulated in the primary response to S(0). In vitro transcription revealed that SurR is an activator for its own gene as well as for two hydrogenase operons whose expression is downregulated during the primary S(0) response; it is also a repressor for two genes upregulated during the primary S(0) response, one of which encodes the primary S(0)-reducing enzyme NAD(P)H sulphur reductase. Herein we give evidence for the role of SurR in both mediating the primary response to S(0) and controlling hydrogen production in P. furiosus.

Comparison of the cecal microbiota of domestic and wild turkeys

The extent to which production methods alter intestinal microbial communities of livestock is currently unknown. As the intestinal microbiota may affect animal health, nutrition, and food safety, a baseline comparison of the cecal communities of domestic and wild turkeys was performed. Oligonucleotide fingerprinting of ribosomal RNA (rRNA) genes (OFRG) of 2,990 16S rRNA clones and dot blot quantification of dominant populations were used to identify the dominant bacterial taxa. Seventy-three percent of all the clones belonged to as yet uncultured genera. However, at a higher phylogenetic level, the OFRG library was composed of 54% Bacteroidetes clones (52% of the domestic library clones, 56% of the wild library clones), 30% Firmicutes clones (33% of the domestic library clones, 32% of the wild library clones), 3% Proteobacteria clones (5% domestic, 2% wild), and 3% Deferribacteres clones (4% domestic, 1% wild). Seven percent of the clones were unidentifiable (6% domestic, 9% wild). Bacteroidetes clones included the genera Alistipes, Prevotella, Megamonas, and Bacteroides. Of the Clostridiales clones, groups IV, IX, and XIV including genera Faecalibacterium, Megasphaera, Phascolarctobacterium, and Papillibacter were predominant. Lactobacillus, Enterococcus, and Streptococcus bacilli were also identified. beta- delta- and gamma-proteobacterial genera included Acinetobacter, Sutterella, and Escherichia. Deferribacteres clones showed high similarity to Mucispirillum schaedleri. Statistical comparison of the domestic and wild turkey clone libraries indicated similar levels of community richness and evenness despite the fact that the two libraries shared only 30% of the total clone operational taxonomic units. Together these results indicate that although high level taxonomic community structure is similar, high-density turkey production causes considerable divergence of the genera found in the ceca of commercial birds from those of their wild counterparts.

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.

Community analysis of hydrogen-producing extreme thermophilic anaerobic microflora enriched from cow manure with five substrates

The present study analyzed the community structures of anaerobic microflora producing hydrogen under extreme thermophilic conditions by two culture-independent methods: denaturing gradient gel electrophoresis (DGGE) and clone library analyses. Extreme thermophilic microflora (ETM) was enriched from cow manure by repeated batch cultures at 75 degrees C, using a substrate of xylose, glucose, lactose, cellobiose, or soluble starch, and produced hydrogen at yields of 0.56, 2.65, 2.17, 2.68, and 1.73 mol/mol-monosaccharide degraded, respectively. The results from the DGGE and clone library analyses were consistent and demonstrated that the community structures of ETM enriched with the four hexose-based substrates (glucose, lactose, cellobiose, and soluble starch) consisted of a single species, closely related to a hydrogen-producing extreme thermophile, Caldoanaerobacter subterraneus, with diversity at subspecies levels. The ETM enriched with xylose was more diverse than those enriched with the other substrates, and contained the bacterium related to C. subterraneus and an unclassified bacterium, distantly related to a xylan-degrading and hydrogen-producing extreme thermophile, Caloramator fervidus.