[Show abstract][Hide abstract] ABSTRACT: 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.
Frontiers in Microbiology 02/2015; 6:157. DOI:10.3389/fmicb.2015.00157 · 3.94 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: 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
[Show abstract][Hide abstract] ABSTRACT: The microbial diversity associated with actively venting deep-sea hydrothermal deposits is tightly connected to the geochemistry of the hydrothermal fluids. Although the dominant members of these deposits drive the structure of the microbial communities, it is less well understood whether the lower abundance groups are as closely connected to the geochemical milieu, or driven perhaps by biotic factors such as microbial community interactions. We used the natural geochemical gradients that exist in the back-arc basin, Eastern Lau Spreading Center and Valu-Fa Ridge (ELSC/VFR) in the Southwestern Pacific, to explore whether the chemolithotrophic Aquificales are influenced by geographical location, host-rock of the vent field or deposit type. Using a combination of cloning, DNA fingerprinting (DGGE) and enrichment culturing approaches, all genera of this order previously described at marine vents were detected, i.e., Desulfurobacterium, Thermovibrio, Aquifex, Hydrogenivirga, Persephonella and Hydrogenothermus. The comparison between clone libraries and DGGE showed similar patterns of distribution of different Aquificales whereas results differed for the enrichment cultures that were retrieved. However, the use of cultivation-based and -independent methods did provide complementary phylogenetic diversity overview of the Aquificales in these systems. Together, this survey revealed that the ELSC/VFR contains some of the largest diversity of Aquificales ever reported at a deep-sea vent area, that the diversity patterns are tied to the geography and geochemistry of the system, and that this geochemical diverse back-arc basin may harbor new members of the Aquificales.
[Show abstract][Hide abstract] ABSTRACT: Summary A novel moderately thermophilic, heterotrophic bacterium was isolated from a deep-sea hydrothermal vent deposit from the Mariner field along the Eastern Lau Spreading Center, Southwestern Pacific. Cells were short motile rods (about 0.4 μm-0.8 μm) that occurred singly or in pairs and were surrounded by a sheath-like membrane or 'toga'. The cells grew between 45 and 65°C (optimum 57-60°C), pH 4.1-6.0 (optimum pH 5.5-5.7) and optimally at 3% (w/v) NaCl. The isolate grew on a range of carbon and proteinaceous substrates and reduced sulfur. The G + C content of the DNA was about 45 mol%. Phylogenetic analysis of the 16S rRNA gene placed the new isolate as a deeply diverging lineage within the Thermotogales. Based on the physiological, morphological and phylogenetic data, the isolate is a novel species of a new genus with the proposed name Mesoaciditoga lauensis gen. nov. sp. nov. The type strain is cd-1655RT (DSM 25116, OCM 1212).
International Journal of Systematic and Evolutionary Microbiology 08/2013; 63(Pt 12). DOI:10.1099/ijs.0.050518-0 · 2.80 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal "filamentous streamer" communities (∼40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae) populations, whereas the circum-neutral pH (6.5-7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circum-neutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse-TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl). The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl-CoA synthetase (Ccs), and citryl-CoA lyase (Ccl). All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I) involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2) have resulted in niche specialization among members of the Aquificales.
Frontiers in Microbiology 05/2013; 4:84. DOI:10.3389/fmicb.2013.00084 · 3.94 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Background
A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.
The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales.
Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships.
This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia
Biology Direct 04/2013; 8(1):9. DOI:10.1186/1745-6150-8-9 · 4.04 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Members of Sulfurihydrogenibium are often observed as visible filamentous biomass in circumneutral hot springs and play roles in sulfur-cycling, hydrogen oxidation and iron mineralization. To gain insight into the ecophysiology of Sulfurihydrogenibium populations, we conducted preliminary metatranscriptomic analysis of three distinct thermal springs; Calcite Springs (YNP-CS) and Mammoth Springs (YNP-MHS) in Yellowstone National Park, USA, and Furnas Springs (AZ) in Azores, Portugal. Genes to which transcripts were assigned revealed commonly expressed functions among the sites, while several differences were also observed. All three sites, Sulfurihydrogenibium spp. dominate and are obtaining energy via metabolism of sulfur compounds under microaerophilic conditions. Cell motility was one of the expressed functions in two sites (YNP-CS and AZ) with slower stream flow rates and thicker well-formed biofilms. The transcripts from YNP-CS and -MHS exhibited varying levels of sequence divergence from the reference genomes and corresponding metagenomes, suggesting the presence of microdiversity among Sulfurihydrogenibium populations in situ. Conversely, the majority of the AZ transcripts were identical to the S. azorense genome. Our initial results show that the metatranscriptomes in these similar Aquificales-dominated communities can reveal community-level gene function in geochemically distinct thermal environments.
[Show abstract][Hide abstract] ABSTRACT: Cultivation-independent studies have shown that taxa belonging to the "deep-sea hydrothermal vent euryarchaeota 2" (DHVE2) lineage are widespread at deep-sea hydrothermal vents. While this lineage appears to be a common and important member of the microbial community at vent environments, relatively little is known about their overall distribution and phylogenetic diversity. In this study, we examined the distribution, relative abundance, co-occurrence patterns, and phylogenetic diversity of cultivable thermoacidophilic DHVE2 in deposits from globally distributed vent fields. Results of quantitative polymerase chain reaction assays with primers specific for the DHVE2 and Archaea demonstrate the ubiquity of the DHVE2 at deep-sea vents and suggest that they are significant members of the archaeal communities of established vent deposit communities. Local similarity analysis of pyrosequencing data revealed that the distribution of the DHVE2 was positively correlated with 10 other Euryarchaeota phylotypes and negatively correlated with mostly Crenarchaeota phylotypes. Targeted cultivation efforts resulted in the isolation of 12 axenic strains from six different vent fields, expanding the cultivable diversity of this lineage to vents along the East Pacific Rise and Mid-Atlantic Ridge. Eleven of these isolates shared greater than 97% 16S rRNA gene sequence similarity with one another and the only described isolate of the DHVE2, Aciduliprofundum boonei T469(T). Sequencing and phylogenetic analysis of five protein-coding loci, atpA, EF-2, radA, rpoB, and secY, revealed clustering of isolates according to geographic region of isolation. Overall, this study increases our understanding of the distribution, abundance, and phylogenetic diversity of the DHVE2.
Frontiers in Microbiology 02/2012; 3:47. DOI:10.3389/fmicb.2012.00047 · 3.94 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain S95T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Center, Pacific Ocean at a depth of 1910 m. Cells of strain S95T were oval to short Gram-negative rods, 0.5 to 0.6 µm in diameter and 1.0 to 1.5 µm in length, growing singly or in pairs. Cells were motile with a single polar flagellum. The temperature range for growth was 50-92°C, with an optimum at 74°C. The pH range for growth was 5.5-8.0, with an optimum at 7.0. Growth of strain S95T was observed at NaCl concentrations ranging from 1.5 to 3.5% (w/v). Strain S95T grew anaerobically with elemental sulfur as an energy source and bicarbonate/CO2 as a carbon source. Elemental sulfur was disproportionated to sulfide and sulfate. The growth was enhanced in the presence of poorly crystalline Fe(III) oxide (ferrihydrite) as a sulfide-scavenging agent. Strain S95T was also able to grow by disproportionation of thiosulfate and sulfite. Sulfate was not used as an electron acceptor. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to the phylum Thermodesulfobacteria. On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the new isolate represents the sole species of a novel genus, Thermosulfurimonas dismutans gen. nov., sp. nov. with the type strain S95T (=DSM 24515T =VKM B-2683T). Thermosulfurimonas dismutans is a first described thermophilic microorganism that disproportionates elemental sulfur.
International Journal of Systematic and Evolutionary Microbiology 12/2011; 62(Pt 11). DOI:10.1099/ijs.0.034397-0 · 2.80 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The pace of species discovery and documentation remains too slow on a human-altered planet in the midst of a massive extinction event. Increasing this pace requires altering conventional workflows. In this review, we propose that systematics needs to shift to a model of quantum contributions whereby species hypotheses are published as they are formulated and data as they are collected in web-based repositories and content-management systems. If our recommendation is followed, many species will make their first appearance on the Internet as candidate new species before documentation is complete. Acknowledging the changes that we describe may be controversial, we discuss problems that may be encountered along with possible solutions.
[Show abstract][Hide abstract] ABSTRACT: Subduction of oceanic crust and the formation of volcanic arcs above the subduction zone are important components in Earth’s geological and geochemical cycles. Subduction consumes and recycles material from the oceanic plates, releasing fluids and gases that enhance magmatic activity, feed hydrothermal systems, generate ore deposits and nurture chemosynthetic biological communities. Among the first lavas to erupt at the surface from a nascent subduction zone are a type classified as boninites. These lavas contain information about the early stages of subduction, yet because most subduction systems on Earth are old and well-established, boninite lavas have previously only been observed in the ancient geological record. Here we observe and sample an active boninite eruption occurring at 1,200 m depth at the West Mata submarine volcano in the northeast Lau Basin, southwest Pacific Ocean. We find that large volumes of H2O, CO2 and sulphur are emitted, which we suggest are derived from the subducting slab. These volatiles drive explosive eruptions that fragment rocks and generate abundant incandescent magma-skinned bubbles and pillow lavas. The eruption has been ongoing for at least 2.5 years and we conclude that this boninite eruption is a multi-year, low-mass-transfer-rate eruption. Thus the Lau Basin may provide an important site for the long-term study of submarine volcanic eruptions related to the early stages of subduction.
[Show abstract][Hide abstract] ABSTRACT: Thirteen novel, obligately anaerobic, thermoacidophilic bacteria were isolated from deep-sea hydrothermal vent sites. Four of the strains, designated EP5-r(T), KM1, Mar08-272r(T) and Mar08-368r, were selected for metabolic and physiological characterization. With the exception of strain EP5-r(T), all strains were short rods that grew between 40 and 72 °C, with optimal growth at 60-65 °C. Strain EP5-r(T) was more ovoid in shape and grew between 45 and 75 °C, with optimum growth at 60 °C. The pH range for growth of all the isolates was between pH 3.5 and 5.5 (optimum pH 4.5 to 5.0). Strain Mar08-272r(T) could only grow up to pH 5.0. Elemental sulfur was required for heterotrophic growth on acetate, succinate, Casamino acids and yeast extract. Strains EP5-r(T), Mar08-272r(T) and Mar08-368r could also use fumarate, while strains EP5-r(T), KM1 and Mar08-272r(T) could also use propionate. All isolates were able to grow chemolithotrophically on H(2), CO(2), sulfur and vitamins. Phylogenetic analysis of 16S rRNA gene sequences placed all isolates within the family Desulfurellaceae of the class Deltaproteobacteria, with the closest cultured relative being Hippea maritima MH(2)(T) (~95-98 % gene sequence similarity). Phylogenetic analysis also identified several isolates with at least one intervening sequence within the 16S rRNA gene. The genomic DNA G+C contents of strains EP5-r(T), KM1, Mar08-272r(T) and Mar08-368r were 37.1, 42.0, 35.6 and 37.9 mol%, respectively. The new isolates differed most significantly from H. maritima MH(2)(T) in their phylogenetic placement and in that they were obligate thermoacidophiles. Based on these phylogenetic and phenotypic properties, the following two novel species are proposed: Hippea jasoniae sp. nov. (type strain Mar08-272r(T) = DSM 24585(T) = OCM 985(T)) and Hippea alviniae sp. nov. (type strain EP5-r(T) = DSM 24586(T) = OCM 986(T)).
International Journal of Systematic and Evolutionary Microbiology 07/2011; 62(Pt 6):1252-8. DOI:10.1099/ijs.0.033001-0 · 2.80 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted Lucky Strike (37°17'N, 32°16.3'W, depth 1600-1750 m) and the ultramafic-hosted Rainbow (36°13'N, 33°54.1'W, depth 2270-2330 m) vent fields along the Mid-Atlantic Ridge (MAR). Using multiplexed barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA genes, we show statistically significant differences between the archaeal and bacterial communities associated with the different vent fields. Quantitative polymerase chain reaction (qPCR) assays of the functional gene diagnostic for methanogenesis (mcrA), as well as geochemical modelling to predict pore fluid chemistries within the deposits, support the pyrosequencing observations. Collectively, these results show that the less reduced, hydrogen-poor fluids at Lucky Strike limit colonization by strict anaerobes such as methanogens, and allow for hyperthermophilic microaerophiles, like Aeropyrum. In contrast, the hydrogen-rich reducing vent fluids at the ultramafic-influenced Rainbow vent field support the prevalence of methanogens and other hydrogen-oxidizing thermophiles at this site. These results demonstrate that biogeographical patterns of hydrothermal vent microorganisms are shaped in part by large scale geological and geochemical processes.
[Show abstract][Hide abstract] ABSTRACT: The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site) was obtained for five high-temperature (>65 degrees C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs.
PLoS ONE 03/2010; 5(3):e9773. DOI:10.1371/journal.pone.0009773 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A thermophilic bacterium, designated strain CR11(T), was isolated from a filamentous sample collected from a terrestrial hot spring on the south-western foothills of the Rincón volcano in Costa Rica. The Gram-negative cells are approximately 2.4-3.9 microm long and 0.5-0.6 microm wide and are motile rods with polar flagella. Strain CR11(T) grows between 65 and 85 degrees C (optimum 75 degrees C, doubling time 4.5 h) and between pH 4.8 and 7.8 (optimum pH 5.9-6.5). The isolate grows chemolithotrophically with S(0), S(2)O(2)(3)(-) or H(2) as the electron donor and with O(2) (up to 16 %, v/v) as the sole electron acceptor. The isolate can grow on mannose, glucose, maltose, succinate, peptone, Casamino acids, starch, citrate and yeast extract in the presence of oxygen (4 %) and S(0). Growth occurs only at NaCl concentrations below 0.4 % (w/v). The G+C content of strain CR11(T) is 40.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence places the strain as a close relative of Thermocrinis ruber OC 1/4(T) (95.7 % sequence similarity). Based on phylogenetic and physiological characteristics, we propose the name Thermocrinis minervae sp. nov., with CR11(T) (=DSM 19557(T) =ATCC BAA-1533(T)) as the type strain.
International Journal of Systematic and Evolutionary Microbiology 09/2009; 60(Pt 2):338-43. DOI:10.1099/ijs.0.010496-0 · 2.80 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Aquificales are widespread in marine and terrestrial hydrothermal environments. Here, we report the complete and draft genome sequences of six new members of the Aquificales: two marine species, Persephonella marina strain EX-H1 and Hydrogenivirga strain 128-5-R1 (from the East Pacific Rise, 9 degrees 50.3'N, 104 degrees 17.5'W, and the Eastern Lau Spreading Center, 176 degrees 11.5'W, 20 degrees 45.8'S, respectively), and four terrestrial isolates, Sulfurihydrogenibium azorense strain Az-Fu1, Sulfurihydrogenibium yellowstonense strain SS-5, and Sulfurihydrogenibium strain Y03AOP1 (from Furnas, Azores, Portugal, and Calcite Springs and Obsidian Pool in Yellowstone National Park, United States, respectively), and the only thermoacidophilic isolate, Hydrogenobaculum strain Y04AAS1 (from a stream adjacent to Obsidian Pool). Significant differences among the different species exist that include nitrogen metabolism, hydrogen utilization, chemotaxis, and signal transduction, providing insights into their ecological niche adaptations.
Journal of bacteriology 02/2009; 191(6):1992-3. DOI:10.1128/JB.01645-08 · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: It has been suggested that the distribution of microorganisms should be cosmopolitan because of their enormous capacity for dispersal. However, recent studies have revealed that geographically isolated microbial populations do exist. Geographic distance as a barrier to dispersal is most often invoked to explain these distributions. Here we show that unique and diverse sequences of the bacterial genus Sulfurihydrogenibium exist in Yellowstone thermal springs, indicating that these sites are geographically isolated. Although there was no correlation with geographic distance or the associated geochemistry of the springs, there was a strong historical signal. We found that the Yellowstone calderas, remnants of prehistoric volcanic eruptions, delineate biogeographical provinces for the Sulfurihydrogenibium within Yellowstone (chi(2): 9.7, P = 0.002). The pattern of distribution that we have detected suggests that major geological events in the past 2 million years explain more of the variation in sequence diversity in this system than do contemporary factors such as habitat or geographic distance. These findings highlight the importance of historical legacies in determining contemporary microbial distributions and suggest that the same factors that determine the biogeography of macroorganisms are also evident among bacteria.