Phylum Aquificae Research Articles

Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community.

Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.

Genome-Resolved Metagenomics and Metatranscriptomics Reveal that Aquificae Dominates Arsenate Reduction in Tengchong Geothermal Springs.

Elevated arsenic (As) is common in geothermal springs, shaping the evolution of As metabolism genes and As transforming microbes. Herein, genome-level microbial metabolisms and As cycling strategies in Tengchong geothermal springs were demonstrated for the first time based on metagenomic and metatranscriptomic analyses. Sulfur cycling was dominated by Aquificae oxidizing thiosulfate via the sox system, fueling the respiration and carbon dioxide fixation processes. Arsenate reduction via arsC [488.63 ± 271.60 transcripts per million (TPM)] and arsenite efflux via arsB (442.98 ± 284.81 TPM) were the primary detoxification pathway, with most genes and transcripts contributed by the members in phylum Aquificae. A complete arsenotrophic cycle was also transcriptionally active as evidenced by the detection of aioA transcripts and arrA transcript reads mapped onto metagenome-assembled genomes (MAGs) affiliated with Crenarchaeota. MAGs affiliated with Aquificae had great potential of reducing arsenate via arsC and fixing nitrogen and carbon dioxide via nifDHK and reductive tricarboxylic acid (rTCA) cycle, respectively. Aquificae's arsenate reduction potential via arsC was observed for the first time at the transcriptional level. This study expands the diversity of the arsC-based arsenate-reducing community and highlights the importance of Aquificae to As biogeochemistry.

Sulfur cycling and host-virus interactions in Aquificales-dominated biofilms from Yellowstone's hottest ecosystems.

Modern linkages among magmatic, geochemical, and geobiological processes provide clues about the importance of thermophiles in the origin of biogeochemical cycles. The aim of this study was to identify the primary chemoautotrophs and host-virus interactions involved in microbial colonization and biogeochemical cycling at sublacustrine, vapor-dominated vents that represent the hottest measured ecosystems in Yellowstone National Park (~140 °C). Filamentous microbial communities exposed to extreme thermal and geochemical gradients were sampled using a remotely operated vehicle and subjected to random metagenome sequencing and microscopic analyses. Sulfurihydrogenibium (phylum Aquificae) was the predominant lineage (up to 84% relative abundance) detected at vents that discharged high levels of dissolved H2, H2S, and CO2. Metabolic analyses indicated carbon fixation by Sulfurihydrogenibium spp. was powered by the oxidation of reduced sulfur and H2, which provides organic carbon for heterotrophic community members. Highly variable Sulfurihydrogenibium genomes suggested the importance of intra-population diversity under extreme environmental and viral pressures. Numerous lytic viruses (primarily unclassified taxa) were associated with diverse archaea and bacteria in the vent community. Five circular dsDNA uncultivated virus genomes (UViGs) of ~40 kbp length were linked to the Sulfurihydrogenibium metagenome-assembled genome (MAG) by CRISPR spacer matches. Four UViGs contained consistent genome architecture and formed a monophyletic cluster with the recently proposed Pyrovirus genus within the Caudovirales. Sulfurihydrogenibium spp. also contained CRISPR arrays linked to plasmid DNA with genes for a novel type IV filament system and a highly expressed β-barrel porin. A diverse suite of transcribed secretion systems was consistent with direct microscopic analyses, which revealed an extensive extracellular matrix likely critical to community structure and function. We hypothesize these attributes are fundamental to the establishment and survival of microbial communities in highly turbulent, extreme-gradient environments.

Metagenomic Analysis of the Microbial Community in the Underground Coal Fire Area (Kemerovo Region, Russia) Revealed Predominance of Thermophilic Members of the Phyla Deinococcus-Thermus, Aquificae, and Firmicutes

Underground burning of coal seams accompanied by release of gases leads to development of local thermal ecosystems. We investigated the microbial community of the ground heated to 72°C in the release area of hot gases resulting from underground combustion of coal mining waste at the Bungurskiy-Severny coal deposit in the Kemerovo region of Russia. Analysis of the composition of the microbial community by 16S rRNA gene profiling revealed predominance of thermophilic bacteria of the phyla Deinococcus-Thermus, Aquificae, and Firmicutes. As a result of metagenomic analysis, 18 genomes of the main members of the microbial community were assembled, including the complete genomes of Hydrogenobacter thermophiles, a member of the candidate genus UBA11096 of the phylum Aquificae (RBS10-58), Thermoflexus hugenholtzii, and Thermus antranikianii. Analysis of the RBS10-58 genome indicates that this bacterium can autotrophically fix carbon in the reductive tricarboxylic acid cycle and obtain energy via oxidation of hydrogen and sulfur compounds with oxygen or nitrate as electron acceptors. Genome analysis of the two dominant Firmicutes species, Hydrogenibacillus schlegelii and an uncultured member of the class Thermaerobacteria, showed that these bacteria could grow aerobically by oxidizing hydrogen and carbon monoxide. Overall, the community was dominated by aerobic bacteria capable of growing autotrophically and obtaining energy via oxidation of the main components of coal gases, hydrogen and carbon monoxide. Thermus antranikianii, which makes up about a half of the microbial community, probably uses organic matter produced by autotrophic members of Firmicutes and Aquificae.

Characterization of a Non‐Classic Type Phosphoserine Phosphatase Homolog in Thermodesulfidibacter takaii , a Thermophilic, Autotrophic Bacterium in the Phylum Aquificae

Phosphoserine phosphatase (PSP) catalyzes the dephosphorylation of phosphoserine to serine, and is found in all three domains of life. Classic, metal-dependent PSPs (dPSPs) belong to the haloacid dehalogenase-like hydrolase superfamily. Some organisms, however, lack a known PSP even though they exhibit a functional phosphoserine synthetic pathway, and should then possess a genetically new type of PSP. Hydrogenobacter thermophilus, a thermophilic, obligate chemolithoautotroph in the phylum Aquificae, possesses two novel-type, metal-independent PSP (iPSP). These proteins, named HtPspA and HtPspB, belong to the histidine phosphatase superfamily. Despite their high primary structure similarity and the conservation of residues essential for phosphatase activity, HtPspA and HtPspB present notable differences. In H. thermophilus they are expressed as homodimers (A-A) or heterodimers (A-B). However, only HtPspA shows significant PSP activity, and is therefore the catalytic subunit as a PSP. HtPspB does not have substantial PSP activity and is only soluble in the presence of HtPspA, at least when it is expressed in E. coli. Crystal structure analysis revealed that His85 and the C-terminal region, which exist in HtPspA but not in HtPspB, are necessary for PSP activity in this organism. Thermosulfidibacter takaii, which belongs to a distinct family in the phylum Aquificae, possesses only one homolog of iPSP which lacks His85 and the C-terminal region, showing higher identity to HtPspB than to HtPspA. To examine whether this homolog can serve as a serine synthetic enzyme in T. takaii - which should have a serine synthetic pathway - while lacking the structural units of HtPspA essential for PSP activity, we characterized its enzymatic properties. In contrast to HtPspB, TtPsp was expressed in the soluble fraction in E. coli. It is thermostable at 70°C, the optimal growth temperature of T. takaii, and is likely to form a homodimer as suggested by gel chromatography. Enzymatic activity assays revealed that TtPsp possesses only about 1% of the PSP activity (per mole of protein) exhibited by HtPspA, and displays higher activity towards L-phosphothreonine than L-phosphoserine. The phylogenetic characterization of TtPspB showed that this protein forms a clade with PspB homologs of distinct families within the phylum Aquificae. Our study revealed that an ancestor of Aquificae already possessed PspA and PspB, and that the lack of a PspA homolog in T. takaii was caused by gene loss. Whether the common ancestor of PspA and PspB was a functional PSP or not, and the physiological function of PspB, is still unknown.

Microbe Profile: Aquifex aeolicus: an extreme heat-loving bacterium that feeds on gases and inorganic chemicals.

The bacterium 'Aquifex aeolicus' is the model organism for the deeply rooted phylum Aquificae. This 'water-maker' is an H2-oxidizing microaerophile that flourishes in extremely hot marine habitats, and it also thrives on the sulphur compounds commonly found in volcanic environments. 'A. aeolicus' has hyper-stable proteins and a fully sequenced genome, with some of its essential metabolic pathways deciphered (including energy conservation). Many of its proteins have also been characterized (especially structurally), including many of the enzymes involved in replication, transcription, RNA processing and cell envelope biosynthesis. Enzymes that are of promise for biotechnological applications have been widely investigated in this species. 'A. aeolicus' has also added to our understanding of the origins of life and evolution.

Distribution and Succession of Microbial Communities Along the Dispersal Pathway of Hydrothermal Plumes on the Southwest Indian Ridge

The distribution and succession of microbial communities along the dispersion path of hydrothermal plumes has not been well investigated. In this study, we collected several types of samples from the Longqi hydrothermal field located on the Southwest Indian Ridge, including hydrothermal plumes at different stages of formation, a suite of water column samples across the non-buoyant hydrothermal plumes above this field, and a background seawater column approximately 350 km away from the hydrothermal field. Using CH4 concentration anomalies, three non-buoyant plume samples between 2,535 m and 2,735 m were identified within the water column. Microbial community compositions within these plumes and background seawater samples were examined based on the 16S rRNA genes and revealed significant variations and successions in community composition between different portions of the hydrothermal plumes. Near the vent orifice, representing the initial stage of plume formation, microbial populations were characterized by abundant and diverse putative vent-associated communities including (hyper)thermophiles such as Aquificaceae and Hydrogenothermaceae within the phylum Aquificae, and some epsilonproteobacterial chemolithoautotrophs such as Sulfurovum, Sulfurimonas, and Caminibacter. By contrast, in the rising buoyant plumes and adjacent seawaters, most vent-associated microbial taxa were still present but made only minor contributions to community composition. Some microbial taxa that are common in seawater columns such as alphaproteobacterial Sphingomonadaceae and SAR11 clade, deltaproteobacterial SAR324 clade, and gammaproteobacterial Pseudomonas, together with Sulfurimonas and SUP05 clade, became predominant. Members within the Sulfurimonas and SUP05 clade flourished with considerable abundance in the non-buoyant plumes, although these plumes were mainly composed of alphaproteobacterial Rhodobacteraceae, gammaproteobacterial Alteromonadaceae and Saccharospirillaceae putatively derived from the surrounding ambient seawater. We also analyzed archaeal components in the initial discharge and rising buoyant plume stages, with both primarily consisting of thaumarchaeal Nitrosopumilales and euryarchaeal Marine Group II. Our results indicated that being characteristic microbial lineages within the hydrothermal plumes of the Southwest Indian Ridge, both Sulfurimonas and SUP05 clade display a common and abundant distribution across the plume path. However, out of these clades, Sulfurimonas is more abundant and widespread.

The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan.

Diverse microorganisms specifically inhabit extreme environments, such as hot springs and deep-sea hydrothermal vents. To test the hypothesis that the microbial community structure is predictable based on environmental factors characteristic of such extreme environments, we conducted correlation analyses of microbial taxa/functions and environmental factors using metagenomic and 61 types of physicochemical data of water samples from nine hot springs in the Kirishima area (Kyusyu, Japan), where hot springs with diverse chemical properties are distributed in a relatively narrow area. Our metagenomic analysis revealed that the samples can be classified into two major types dominated by either phylum Crenarchaeota or phylum Aquificae. The correlation analysis showed that Crenarchaeota dominated in nutrient-rich environments with high concentrations of ions and total carbons, whereas Aquificae dominated in nutrient-poor environments with low ion concentrations. These environmental factors were also important explanatory variables in the generalized linear models constructed to predict the abundances of Crenarchaeota or Aquificae. Functional enrichment analysis of genes also revealed that the separation of the two major types is primarily attributable to genes involved in autotrophic carbon fixation, sulfate metabolism and nitrate reduction. Our results suggested that Aquificae and Crenarchaeota play a vital role in the Kirishima hot spring water ecosystem through their metabolic pathways adapted to each environment. Our findings provide a basis to predict microbial community structures in hot springs from environmental parameters, and also provide clues for the exploration of biological resources in extreme environments.

Phylogenetic Diversity of Nitrogenase Reductase Genes and Possible Nitrogen-Fixing Bacteria in Thermophilic Chemosynthetic Microbial Communities in Nakabusa Hot Springs.

Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70–86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation, we examined the diversities of 16S rRNA and nitrogenase reductase (NifH) gene sequences in four types of chemosynthetic communities with visually different colors and thicknesses. The results of a 16S rRNA gene analysis indicated that all four microbial communities had similar bacterial constituents; the phylum Aquificae was the dominant member, followed in abundance by Thermodesulfobacteria, Firmicutes, and Thermotogae. Most of the NifH sequences were related to sequences reported in hydrothermal vents and terrestrial hot springs. The results of a phylogenetic analysis of NifH sequences revealed diversity in this gene among the communities collected, distributed within 7 phylogenetic groups. NifH sequences affiliated with Aquificae (Hydrogenobacter/Thermocrinis) and Firmicutes (Caldicellulosiruptor) were abundant. At least two different energy metabolic pathways appeared to be related to nitrogen fixation in the communities analyzed; aerobic sulfur/hydrogen-oxidizing bacteria in Aquificae and fermentative bacteria in Firmicutes. The metabolic characteristics of these two dominant phyla differed from those previously inferred from nitrogenase activity assays on chemosynthetic communities, which were associated with hydrogen-dependent autotrophic sulfate reduction. These assays may correspond to the observed NifH sequences that are distantly related to the known species of Thermodesulfovibrio sp. (Nitrospirae) detected in the present study. The activities of nitrogen-fixing organisms in communities may depend on redox states as well as the availability of electron donors, acceptors, and carbon sources.

Nitrogenase Activity in Thermophilic Chemolithoautotrophic Bacteria in the Phylum Aquificae Isolated under Nitrogen-Fixing Conditions from Nakabusa Hot Springs.

The phylum Aquificae comprises chemolithoautotrophic thermophilic to hyperthermophilic bacteria, in which the nitrogenase reductase gene (nifH) has been reported. However, nitrogen-fixing activity has not yet been demonstrated in members of this deeply branching bacterial phylum. We isolated two thermophilic diazotrophic strains from chemosynthetic microbial communities in slightly alkaline hot springs (≥70°C) in Nakabusa, Nagano Prefecture, Japan. A phylogenetic analysis based on 16S rRNA genes identified these strains as members of the genus Hydrogenobacter within Aquificae. Their NifH sequences showed 96.5 and 97.4% amino acid sequence identities to that from Hydrogenobacter thermophilus TK-6. Nitrogenase activity, measured by acetylene reduction, was confirmed in both strains at 70°C. These novel strains grew under semi-aerobic conditions by using CO2 as the sole carbon source and N2 as the sole nitrogen source in media containing hydrogen and/or thiosulfate. To the best of our knowledge, this is the first demonstration of active nitrogen fixation in thermophilic bacteria at 70°C and in the phylum Aquificae.

Phosphoserine Phosphatase Is Required for Serine and One-Carbon Unit Synthesis in Hydrogenobacter thermophilus.

Hydrogenobacter thermophilus is an obligate chemolithoautotrophic bacterium of the phylum Aquificae and is capable of fixing carbon dioxide through the reductive tricarboxylic acid (TCA) cycle. The recent discovery of two novel-type phosphoserine phosphatases (PSPs) in H. thermophilus suggests the presence of a phosphorylated serine biosynthesis pathway; however, the physiological role of these novel-type metal-independent PSPs (iPSPs) in H. thermophilus has not been confirmed. In the present study, a mutant strain with a deletion of pspA, the catalytic subunit of iPSPs, was constructed and characterized. The generated mutant was a serine auxotroph, suggesting that the novel-type PSPs and phosphorylated serine synthesis pathway are essential for serine anabolism in H. thermophilus. As an autotrophic medium supplemented with glycine did not support the growth of the mutant, the reversible enzyme serine hydroxymethyltransferase does not appear to synthesize serine from glycine and may therefore generate glycine and 5,10-CH2-tetrahydrofolate (5,10-CH2-THF) from serine. This speculation is supported by the lack of glycine cleavage activity, which is needed to generate 5,10-CH2-THF, in H. thermophilus Determining the mechanism of 5,10-CH2-THF synthesis is important for understanding the fundamental anabolic pathways of organisms, because 5,10-CH2-THF is a major one-carbon donor that is used for the synthesis of various essential compounds, including nucleic and amino acids. The findings from the present experiments using a pspA deletion mutant have confirmed the physiological role of iPSPs as serine producers and show that serine is a major donor of one-carbon units in H. thermophilusIMPORTANCE Serine biosynthesis and catabolism pathways are intimately related to the metabolism of 5,10-CH2-THF, a one-carbon donor that is utilized for the biosynthesis of various essential compounds. For this reason, determining the mechanism of serine synthesis is important for understanding the fundamental anabolic pathways of microorganisms. In the present study, we experimentally confirmed that a novel phosphoserine phosphatase in the obligate chemolithoautotrophic bacterium Hydrogenobacter thermophilus is essential for serine biosynthesis. This finding indicates that serine is synthesized from an intermediate of gluconeogenesis in H. thermophilus In addition, because glycine cleavage system activity and genes encoding an enzyme capable of producing 5,10-CH2-THF were not detected, serine appears to be the major one-carbon donor to tetrahydrofolate (THF) in H. thermophilus.

Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka.

Microbial communities of four acidic thermal pools in the Uzon Caldera, Kamchatka, Russia, were studied using amplification and pyrosequencing of 16S rRNA gene fragments. The sites differed in temperature and pH: 1805 (60°C, pH 3.7), 1810 (90°C, pH 4.1), 1818 (80°C, pH 3.5), and 1807 (86°C, pH 5.6). Archaea of the order Sulfolobales were present among the dominant groups in all four pools. Acidilobales dominated in pool 1818 but were a minor fraction at the higher temperature in pool 1810. Uncultivated Archaea of the Hot Thaumarchaeota-related clade were present in significant quantities in pools 1805 and 1807, but they were not abundant in pools 1810 and 1818, where high temperatures were combined with low pH. Nanoarchaeota were present in all pools, but were more abundant in pools 1810 and 1818. A similar abundance pattern was observed for Halobacteriales. Thermophilic Bacteria were less diverse and were mostly represented by aerobic hydrogen- and sulfur-oxidizers of the phylum Aquificae and sulfur-oxidising Proteobacteria of the genus Acidithiobacillus. Thus we showed that extremely acidic hot pools contain diverse microbial communities comprising different metabolic groups of prokaryotes, including putative lithoautotrophs using energy sources of volcanic origin, and various facultative and obligate heterotrophs.

Microbial diversity and autotrophic activity in Kamchatka hot springs.

Microbial communities of Kamchatka Peninsula terrestrial hot springs were studied using molecular, radioisotopic and cultural approaches. Analysis of 16S rRNA gene fragments performed by means of high-throughput sequencing revealed that aerobic autotrophic sulfur-oxidizing bacteria of the genus Sulfurihydrogenibium (phylum Aquificae) dominated in a majority of streamers. Another widely distributed and abundant group was that of anaerobic bacteria of the genus Caldimicrobium (phylum Thermodesulfobacteria). Archaea of the genus Vulcanisaeta were abundant in a high-temperature, slightly acidic hot spring, where they were accompanied by numerous Nanoarchaeota, while the domination of uncultured Thermoplasmataceae A10 was characteristic for moderately thermophilic acidic habitats. The highest rates of inorganic carbon assimilation determined by the in situ incubation of samples in the presence of 14C-labeled bicarbonate were found in oxygen-dependent streamers; in two sediment samples taken from the hottest springs this process, though much weaker, was found to be not dependent on oxygen. The isolation of anaerobic lithoautotrophic prokaryotes from Kamchatka hot springs revealed a wide distribution of the ability for sulfur disproportionation, a new lithoautotrophic process capable to fuel autonomous anaerobic ecosystems.

Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China.

The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 45.2–83.3°C and pH 2.6–9.1) in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the strains belong to the genera Hydrogenobacter, Hydrogenobaculum, and Sulfurihydrogenibium, including strains distant enough to likely justify new species of Hydrogenobacter and Hydrogenobaculum. The additional strain may represent a new genus in the Hydrogenothermaceae. All strains were capable of aerobic respiration under microaerophilic conditions; however, they had variable capacity for chemolithotrophic oxidation of hydrogen and sulfur compounds and nitrate reduction.

Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacteriaceae

We report here detailed phylogenetic and comparative analyses on 11 sequenced genomes from the phylum Aquificae to identify molecular markers that are specific for the species from this phylum or its different families (viz. Aquificaceae, Hydrogenothermaceae and Desulfurobacteriaceae). In phylogenetic trees based on 16S rRNA gene or concatenated sequences for 32 conserved proteins, species from the three Aquificae families formed distinct clades. These trees also supported a strong relationship between the Aquificaceae and Hydrogenothermaceae families. In parallel, comparative analyses on protein sequences from Aquificae genomes have identified 46 conserved signature indels (CSIs) in broadly distributed proteins that are either exclusively or mainly found in members of the phylum Aquificae or its different families and subclades. Four of these CSIs, which are found in all sequenced Aquificae species, provide potential molecular markers for this phylum. Twelve, six and thirteen other CSIs that respectively are specific for the sequenced Aquificaceae, Hydrogenothermaceae and Desulfurobacteriaceae species provide molecular markers and novel tools for the identification of members of these families and for genetic and biochemical studies on them. Lastly, these studies have identified 11 CSIs in divergent proteins that are uniquely shared by members of the Aquificaceae and Hydrogenothermaceae families providing strong evidence that these two groups of bacteria shared a common ancestor exclusive of all other Aquificae (bacteria). The species from these two families are also very similar in their metabolic and physiological properties and they consist of aerobic or microaerophilic bacteria, which generally obtain energy by oxidation of hydrogen or reduced sulfur compounds by molecular oxygen. Based upon their strong association in phylogenetic trees, unique shared presence of large numbers of CSIs in different proteins, and similarities in their metabolic and physiological properties, it is proposed that the order Aquificales should be emended to include only the members of the families Aquificaceae and Hydrogenothermaceae. The members of the family Desulfurobacteriaceae, which are obligate anaerobes that strictly use hydrogen as electron donor, are now transferred to a new order Desulfurobacteriales ord. nov. The emended descriptions of the phylum Aquificae and its three families incorporating information for different molecular signatures are also provided.

Lateral Gene Transfer of Family A DNA Polymerases between Thermophilic Viruses, Aquificae, and Apicomplexa

Bioinformatics and functional screens identified a group of Family A-type DNA Polymerase (polA) genes encoded by viruses inhabiting circumneutral and alkaline hot springs in Yellowstone National Park and the US Great Basin. The proteins encoded by these viral polA genes (PolAs) shared no significant sequence similarity with any known viral proteins but were remarkably similar to PolAs encoded by two of three families of the bacterial phylum Aquificae and by several apicoplast-targeted PolA-like proteins found in the eukaryotic phylum Apicomplexa, which includes the obligate parasites Plasmodium, Babesia, and Toxoplasma. The viral gene products share signature elements previously associated only with Aquificae and Apicomplexa PolA-like proteins and were similar to proteins encoded by prophage elements of a variety of otherwise unrelated Bacteria, each of which additionally encoded a prototypical bacterial PolA. Unique among known viral DNA polymerases, the viral PolA proteins of this study share with the Apicomplexa proteins large amino-terminal domains with putative helicase/primase elements but low primary sequence similarity. The genomic context and distribution, phylogeny, and biochemistry of these PolA proteins suggest that thermophilic viruses transferred polA genes to the Apicomplexa, likely through secondary endosymbiosis of a virus-infected proto-apicoplast, and to the common ancestor of two of three Aquificae families, where they displaced the orthologous cellular polA gene. On the basis of biochemical activity, gene structure, and sequence similarity, we speculate that the xenologous viral-type polA genes may have functions associated with diversity-generating recombination in both Bacteria and Apicomplexa.

A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

The Rehai and Ruidian geothermal fields, located in Tengchong County, Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report a comprehensive, cultivation-independent census of microbial communities in 37 samples collected from these geothermal fields, encompassing sites ranging in temperature from 55.1 to 93.6°C, in pH from 2.5 to 9.4, and in mineralogy from silicates in Rehai to carbonates in Ruidian. Richness was low in all samples, with 21–123 species-level OTUs detected. The bacterial phylum Aquificae or archaeal phylum Crenarchaeota were dominant in Rehai samples, yet the dominant taxa within those phyla depended on temperature, pH, and geochemistry. Rehai springs with low pH (2.5–2.6), high temperature (85.1–89.1°C), and high sulfur contents favored the crenarchaeal order Sulfolobales, whereas those with low pH (2.6–4.8) and cooler temperature (55.1–64.5°C) favored the Aquificae genus Hydrogenobaculum. Rehai springs with neutral-alkaline pH (7.2–9.4) and high temperature (>80°C) with high concentrations of silica and salt ions (Na, K, and Cl) favored the Aquificae genus Hydrogenobacter and crenarchaeal orders Desulfurococcales and Thermoproteales. Desulfurococcales and Thermoproteales became predominant in springs with pH much higher than the optimum and even the maximum pH known for these orders. Ruidian water samples harbored a single Aquificae genus Hydrogenobacter, whereas microbial communities in Ruidian sediment samples were more diverse at the phylum level and distinctly different from those in Rehai and Ruidian water samples, with a higher abundance of uncultivated lineages, close relatives of the ammonia-oxidizing archaeon “Candidatus Nitrosocaldus yellowstonii”, and candidate division O1aA90 and OP1. These differences between Ruidian sediments and Rehai samples were likely caused by temperature, pH, and sediment mineralogy. The results of this study significantly expand the current understanding of the microbiology in Tengchong hot springs and provide a basis for comparison with other geothermal systems around the world.

Complete genome sequence of Thermovibrio ammonificans HB-1T, a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent

Thermovibrio ammonificans type strain HB-1T is a thermophilic (Topt: 75°C), strictly anaerobic, chemolithoautotrophic bacterium that was isolated from an active, high temperature deep-sea hydrothermal vent on the East Pacific Rise. This organism grows on mineral salts medium in the presence of CO2/H2, using NO3- or S0 as electron acceptors, which are reduced to ammonium or hydrogen sulfide, respectively. T. ammonificans is one of only three species within the genus Thermovibrio, a member of the family Desulfurobacteriaceae, and it forms a deep branch within the phylum Aquificae. Here we report the main features of the genome of T. ammonificans strain HB-1T (DSM 15698T).

Polyamine analysis of thermophilic, acidophilic, alkaliphilic and radio-tolerant bacteria belonging to the domain Bacteria and methanogens, thermophiles and extreme halophiles belonging to the domain Archaea-Polyamine catalogues of bacterial (eubacterial) and archaeal (archaebacterial) extremophiles IV-

Cellular polyamines of 25 newly validated thermophilic, acidophilic, alkaliphilic or radio-resistant bacteria (eubacteria) and 35 methanogenic, thermophilic or extremely halophilic archaea (archaebacteria) were analyzed by HPLC and GC. In the domain Bacteria, quaternary branched penta-amines, N4-bis(aminopropyl) norspermidine and/or N4-bis (aminopropyl)spermidine, were detected in the extreme thermophiles, Hydrogenovirga and Thermodesulfidibacter of the phylum Aquificae and Thermus of the phylum Thermus-Deinococcus. A liner penta-amine, homocaldopentamine, was found in moderately thermophilic Thermodesulfovibrio. Spermine, a tetra-amine, was found in the moderate thermophiles, Meiothermus, Exilispira, Desulfurispora, Desulfotomaculum, Caloramator and Calditerrivibrio but not in slightly thermophilc Thiofava and mesophilic radio-resistant Deinococcus. An acidophilic slight thermophile, Acidimicrobium, contained only cadaverine as a novel polyamine profile. The occurrence of spermine in mesophilic Acanthopleuribacter belonging to the phylum Acidobacteria was a unique profile. Alkaliphilic Alkalibacterium species were devoid of cellular polyamines. In the phylum Euryarchaeota of the domain Archaea, the branched penta-amines were distributed in the extremely thermophilic genera, Methanocaldococcus, Archaeoglobus and Thermococcus but not in hyperthermophilic Methanopyrus as well as in the mesophilic genera, Methanobacterium, Methanosaeta, Methanolobus, Methanocella and Methanofollis. Some methanogenic mesophiles contained spermine. Long and branched polyamines were not found in 23 extreme halophiles and halalkaliphiles belonging to the order Halobacteriales.

Thermosulfidibacter takaii gen. nov., sp. nov., a thermophilic, hydrogen-oxidizing, sulfur-reducing chemolithoautotroph isolated from a deep-sea hydrothermal field in the Southern Okinawa Trough

A novel thermophilic, sulfur-reducing chemolithoautotroph, strain ABI70S6(T), was isolated from a deep-sea hydrothermal field at the Yonaguni Knoll IV, Southern Okinawa Trough. Cells of strain ABI70S6(T) were motile rods, 0.9-2.0 microm in length and 0.4-0.8 microm in width. Strain ABI70S6(T) was an obligately anaerobic chemolithotroph, exhibiting hydrogen oxidation coupled with sulfur reduction. Growth was observed at 55-78 degrees C (optimum, 70 degrees C), pH 5.0-7.5 (optimum, pH 5.5-6.0) and 0.5-4.5 % NaCl (optimum, 3.0 % NaCl). H(2) and elemental sulfur were utilized as electron donor and acceptor, respectively. The major fatty acids were C(16 : 0) (40.0 %) and C(20 : 1) (60.0 %). The G+C content of genomic DNA was 44.2 mol%. The physiological attributes of strain ABI70S6(T) are similar to those of species of genera within the family Desulfurobacteriaceae, most of which are thermophilic and chemolithoautotrophic sulfur reducers. However, 16S rRNA gene sequence similarities between the novel isolate and type strains of all species within the family Desulfurobacteriaceae were <87 %, which is close to the similarities found between the novel isolate and members of the family Thermodesulfobacteriaceae (<85 %). Based on physiological and phylogenetic features of the novel isolate, it is proposed that it represents a novel species in a novel genus, Thermosulfidibacter takaii gen. nov., sp. nov., within the phylum Aquificae. The type strain of T. takaii is ABI70S6(T) (=JCM 13301(T)=DSM 17441(T)).