Thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the TOTO caldera, Mariana Arc, Western Pacific

Recent Advances in Biotechnologies for the Treatment of Environmental Pollutants Based on Reactive Sulfur Species

The definition of reactive sulfur species (RSS) is inspired by the reactivity and variable chemical valence of sulfur. Sulfur is an essential element for life and is a part of global geochemical cycles. Wastewater treatment bioreactors can be divided into two major categories: sulfur reduction and sulfur oxidation. We review the origins of the definition of RSS and related biotechnological processes in environmental management. Sulfate reduction, sulfide oxidation, and sulfur-based redox reactions are key to driving the coupled global carbon, nitrogen, and sulfur co-cycles. This shows the coupling of the sulfur cycle with the carbon and nitrogen cycles and provides insights into the global material-chemical cycle. We also review the biological classification and RSS metabolic mechanisms of functional microorganisms involved in the biological processes, such as sulfate-reducing and sulfur-oxidizing bacteria. Developments in molecular biology and genomic technologies have allowed us to obtain detailed information on these bacteria. The importance of RSS in environmental technologies requires further consideration.

Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field

The genus Alcanivorax is common in various marine environments, including in hydrothermal fields. They were previously recognized as obligate hydrocarbonoclastic bacteria, but their potential for autotrophic carbon fixation and Fe(II)-oxidation remains largely elusive. In this study, an in situ enrichment experiment was performed using a hydrothermal massive sulfide slab deployed 300 m away from the Wocan hydrothermal vent. Furthermore, the biofilms on the surface of the slab were used as an inoculum, with hydrothermal massive sulfide powder from the same vent as an energy source, to enrich the potential iron oxidizer in the laboratory. Three dominant bacterial families, Alcanivoraceae, Pseudomonadaceae, and Rhizobiaceae, were enriched in the medium with hydrothermal massive sulfides. Subsequently, strain Alcanivorax sp. MM125-6 was isolated from the enrichment culture. It belongs to the genus Alcanivorax and is closely related to Alcanivorax profundimaris ST75FaO-1 T (98.9% sequence similarity) indicated by a phylogenetic analysis based on 16S rRNA gene sequences. Autotrophic growth experiments on strain MM125-6 revealed that the cell concentrations were increased from an initial 7.5 × 105 cells/ml to 3.13 × 108 cells/ml after 10 days, and that the δ13C VPDB in the cell biomass was also increased from 234.25‰ on day 2 to gradually 345.66 ‰ on day 10. The gradient tube incubation showed that bands of iron oxides and cells formed approximately 1 and 1.5 cm, respectively, below the air-agarose medium interface. In addition, the SEM-EDS data demonstrated that it can also secrete acidic exopolysaccharides and adhere to the surface of sulfide minerals to oxidize Fe(II) with NaHCO3 as the sole carbon source, which accelerates hydrothermal massive sulfide dissolution. These results support the conclusion that strain MM125-6 is capable of autotrophic carbon fixation and Fe(II) oxidization chemoautotrophically. This study expands our understanding of the metabolic versatility of the Alcanivorax genus as well as their important role(s) in coupling hydrothermal massive sulfide weathering and iron and carbon cycles in hydrothermal fields.

Thiomicrorhabdus heinhorstiae sp. nov. and Thiomicrorhabdus cannonii sp. nov.: novel sulphur-oxidizing chemolithoautotrophs isolated from the chemocline of Hospital Hole, an anchialine sinkhole in Spring Hill, Florida, USA

Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phylogenetic analysis of the 16S rRNA gene and predicted amino acid sequences of ribosomal proteins, average nucleotide identities, and alignment fractions suggest the strains HH1^T and HH3^T represent novel species belonging to the genus Thiomicrorhabdus. The genome G+C fraction of HH1^T is 47.8 mol% with a genome length of 2.61 Mb, whereas HH3^T has a G+C fraction of 52.4 mol% and 2.49 Mb genome length. Major fatty acids of the two strains included C_16 : 1, C_18 : 1 and C_16 : 0, with the addition of C_10:0 3-OH in HH1^T and C_12 : 0 in HH3^T. Chemolithoautotrophic growth of both strains was supported by elemental sulphur, sulphide, tetrathionate, and thiosulphate, and HH1^T was also able to use molecular hydrogen. Neither strain was capable of heterotrophic growth or use of nitrate as a terminal electron acceptor. Strain HH1^T grew from pH 6.5 to 8.5, with an optimum of pH 7.4, whereas strain HH3^T grew from pH 6 to 8 with an optimum of pH 7.5. Growth was observed between 15-35 °C with optima of 32.8 °C for HH1^T and 32 °C for HH3^T. HH1^T grew in media with [NaCl] 80-689 mM, with an optimum of 400 mM, while HH3^T grew at 80-517 mM, with an optimum of 80 mM. The name Thiomicrorhabdus heinhorstiae sp. nov. is proposed, and the type strain is HH1^T (=DSM 111584^T=ATCC TSD-240^T). The name Thiomicrorhabdus cannonii sp. nov is proposed, and the type strain is HH3^T (=DSM 111593^T=ATCC TSD-241^T).

Microorganisms from deep-sea hydrothermal vents

With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00086-4.

Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases

In the present study we investigate the microbial community inhabiting As Burgas geothermal spring, located in Ourense (Galicia, Spain). The approximately 23 Gbp of Illumina sequences generated for each replicate revealed a complex microbial community dominated by Bacteria in which Proteobacteria and Aquificae were the two prevalent phyla. An association between the two most prevalent genera, Thermus and Hydrogenobacter, was suggested by the relationship of their metabolism. The high relative abundance of sequences involved in the Calvin-Benson cycle and the reductive TCA cycle unveils the dominance of an autotrophic population. Important pathways from the nitrogen and sulfur cycle are potentially taking place in As Burgas hot spring. In the assembled reads, two complete ORFs matching GH2 beta-galactosidases were found. To assess their functional characterization, the two ORFs were cloned and overexpressed in E. coli. The pTsbg enzyme had activity towards o-Nitrophenyl-β-D-galactopyranoside (ONPG) and p-Nitrophenyl-β-D-fucopyranoside, with high thermal stability and showing maximal activity at 85 °C and pH 6, nevertheless the enzyme failed to hydrolyze lactose. The other enzyme, Tsbg, was unable to hydrolyze even ONPG or lactose. This finding highlights the challenge of finding novel active enzymes based only on their sequence.

A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index

In recent decades, the taxonomy of Bacteria and Archaea, and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of Bacteria and Archaea that are identified in this study will help assign genera with higher taxonomic resolution.

Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and Archaea.

Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments

The microbial community composition and its functionality was assessed for hydrothermal fluids and volcanic ash sediments from Haungaroa and hydrothermal fluids from the Brothers volcano in the Kermadec island arc (New Zealand). The Haungaroa volcanic ash sediments were dominated by epsilonproteobacterial Sulfurovum sp. Ratios of electron donor consumption to CO₂ fixation from respective sediment incubations indicated that sulfide oxidation appeared to fuel autotrophic CO₂ fixation, coinciding with thermodynamic estimates predicting sulfide oxidation as the major energy source in the environment. Transcript analyses with the sulfide-supplemented sediment slurries demonstrated that Sulfurovum prevailed in the experiments as well. Hence, our sediment incubations appeared to simulate environmental conditions well suggesting that sulfide oxidation catalyzed by Sulfurovum members drive biomass synthesis in the volcanic ash sediments. For the Haungaroa fluids no inorganic electron donor and responsible microorganisms could be identified that clearly stimulated autotrophic CO₂ fixation. In the Brothers hydrothermal fluids Sulfurimonas (49%) and Hydrogenovibrio/Thiomicrospira (15%) species prevailed. Respective fluid incubations exhibited highest autotrophic CO₂ fixation if supplemented with iron(II) or hydrogen. Likewise catabolic energy calculations predicted primarily iron(II) but also hydrogen oxidation as major energy sources in the natural fluids. According to transcript analyses with material from the incubation experiments Thiomicrospira/Hydrogenovibrio species dominated, outcompeting Sulfurimonas. Given that experimental conditions likely only simulated environmental conditions that cause Thiomicrospira/Hydrogenovibrio but not Sulfurimonas to thrive, it remains unclear which environmental parameters determine Sulfurimonas’ dominance in the Brothers natural hydrothermal fluids.

The effect of O2 and pressure on thiosulfate oxidation by Thiomicrospira thermophila

Microbial sulfur cycling in marine sediments often occurs in environments characterized by transient chemical gradients that affect both the availability of nutrients and the activity of microbes. High turnover rates of intermediate valence sulfur compounds and the intermittent availability of oxygen in these systems greatly impact the activity of sulfur-oxidizing micro-organisms in particular. In this study, the thiosulfate-oxidizing hydrothermal vent bacterium Thiomicrospira thermophila strain EPR85 was grown in continuous culture at a range of dissolved oxygen concentrations (0.04-1.9 mM) and high pressure (5-10 MPa) in medium buffered at pH 8. Thiosulfate oxidation under these conditions produced tetrathionate, sulfate, and elemental sulfur, in contrast to previous closed-system experiments at ambient pressure during which thiosulfate was quantitatively oxidized to sulfate. The maximum observed specific growth rate at 5 MPa pressure under unlimited O₂ was 0.25 hr^-1 . This is comparable to the μ_max (0.28 hr^-1 ) observed at low pH (<6) at ambient pressure when T. thermophila produces the same mix of sulfur species. The half-saturation constant for O₂ ( KO2 ) estimated from this study was 0.2 mM (at a cell density of 10⁵ cells/ml) and was robust at all pressures tested (0.4-10 MPa), consistent with piezotolerant behavior of this strain. The cell-specific KO2 was determined to be 1.5 pmol O₂ /cell. The concentrations of products formed were correlated with oxygen availability, with tetrathionate production in excess of sulfate production at all pressure conditions tested. This study provides evidence for transient sulfur storage during times when substrate concentration exceeds cell-specific KO2 and subsequent consumption when oxygen dropped below that threshold. These results may be common among sulfur oxidizers in a variety of environments (e.g., deep marine sediments to photosynthetic microbial mats).

Study of sulfate-reducing ammonium oxidation process and its microbial community composition

In this study, the simultaneous removal of ammonium and sulfate was detected in a self-designed circulating flow reactor, in which ammonium oxidization was combined with sulfate reduction. The highest removal efficiencies of NH₄ ⁺-N and SO₄ ^2-S were 92% and 59.2%. NO₂ ^- and NO₃ ^- appeared in the effluent, and experimental studies showed that increasing the proportion of N/S in the influent would increase the NO₂ ^- concentration in the effluent. However, N/S [n(NH₄ ⁺-N)/n(SO₄ ^2-S)] conversion rates during the experiment were between 2.1 and 12.9, which may have been caused by the experiment's complex process. The microbial community in the sludge reactor included Proteobacteria, Chloroflexi, Bacteroidetes, Chlorobi, Acidobacteria and Planctomycetes after 187 days of operation. Proteobacteria bacteria had a more versatile metabolism. The sulfate-reducing ammonium oxidation (SRAO) was mainly due to the high performance of Proteobacteria. Nitrospirae has been identified as the dominant functional bacteria in several anammox reactors used for nitrogen removal. Approximately 12.4% of denitrifying bacteria were found in the sludge. These results show that a portion of the nitrogen was converted by nitrification-denitrification, and that traditional anammox proceeds simultaneously with SRAO.

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.

Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments

Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb₃ cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba₃ -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO₂ concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.

Sulfur Metabolism of Hydrogenovibrio thermophilus Strain S5 and Its Adaptations to Deep-Sea Hydrothermal Vent Environment

Hydrogenovibrio bacteria are ubiquitous in global deep-sea hydrothermal vents. However, their adaptations enabling survival in these harsh environments are not well understood. In this study, we characterized the physiology and metabolic mechanisms of Hydrogenovibrio thermophilus strain S5, which was first isolated from an active hydrothermal vent chimney on the Southwest Indian Ridge. Physiological characterizations showed that it is a microaerobic chemolithomixotroph that can utilize sulfide, thiosulfate, elemental sulfur, tetrathionate, thiocyanate or hydrogen as energy sources and molecular oxygen as the sole electron acceptor. During thiosulfate oxidation, the strain produced extracellular sulfur globules 0.7–6.0 μm in diameter that were mainly composed of elemental sulfur and carbon. Some organic substrates including amino acids, tryptone, yeast extract, casamino acids, casein, acetate, formate, citrate, propionate, tartrate, succinate, glucose and fructose can also serve as carbon sources, but growth is weaker than under CO₂ conditions, indicating that strain S5 prefers to be chemolithoautotrophic. None of the tested organic carbons could function as energy sources. Growth tests under various conditions confirmed its adaption to a mesophilic mixing zone of hydrothermal vents in which vent fluid was mixed with cold seawater, preferring moderate temperatures (optimal 37°C), alkaline pH (optimal pH 8.0), microaerobic conditions (optimal 4% O₂), and reduced sulfur compounds (e.g., sulfide, optimal 100 μM). Comparative genomics showed that strain S5 possesses more complex sulfur metabolism systems than other members of genus Hydrogenovibrio. The genes encoding the intracellular sulfur oxidation protein (DsrEF) and assimilatory sulfate reduction were first reported in the genus Hydrogenovibrio. In summary, the versatility in energy and carbon sources, and unique physiological properties of this bacterium have facilitated its adaptation to deep-sea hydrothermal vent environments.

Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs

Petroleum is produced by thermal decay of buried organic material over millions of years. Petroleum oilfield ecosystems represent resource of reduced carbon which favours microbial growth. Therefore, it is obvious that many microorganisms have adapted to harsh environmental conditions of these ecosystems specifically temperature, oxygen availability and pressure. Knowledge of microorganisms present in ecosystems of petroleum oil reservoirs; their physiological and biological properties help in successful exploration of petroleum. Understanding microbiology of petroleum oilfield(s) can be used to enhance oil recovery, as microorganisms in oil reservoirs produce various metabolites viz. gases, acids, solvents, biopolymers and biosurfactants. The aim of this review is to discuss characteristics of petroleum oil reservoirs. This review also provides an updated literature on microbial ecology of these extreme ecosystems including microbial origin as well as various types of microorganisms such as methanogens; iron, nitrate and sulphate reducing bacteria, and fermentative microbes present in petroleum oilfield ecosystems.

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents

At deep-sea hydrothermal vents, primary production is carried out by chemolithoautotrophic microorganisms, with the oxidation of reduced sulfur compounds being a major driver for microbial carbon fixation. Dense and highly diverse assemblies of sulfur-oxidizing bacteria (SOB) are observed, yet the principles of niche differentiation between the different SOB across geochemical gradients remain poorly understood. In this study niche differentiation of the key SOB was addressed by extensive sampling of active sulfidic vents at six different hydrothermal venting sites in the Manus Basin, off Papua New Guinea. We subjected 33 diffuse fluid and water column samples and 23 samples from surfaces of chimneys, rocks and fauna to a combined analysis of 16S rRNA gene sequences, metagenomes and real-time in situ measured geochemical parameters. We found Sulfurovum Epsilonproteobacteria mainly attached to surfaces exposed to diffuse venting, while the SUP05-clade dominated the bacterioplankton in highly diluted mixtures of vent fluids and seawater. We propose that the high diversity within Sulfurimonas- and Sulfurovum-related Epsilonproteobacteria observed in this study derives from the high variation of environmental parameters such as oxygen and sulfide concentrations across small spatial and temporal scales.

Thiosulfate oxidation by Thiomicrospira thermophila: metabolic flexibility in response to ambient geochemistry

Previous studies of the stoichiometry of thiosulfate oxidation by colorless sulfur bacteria have failed to demonstrate mass balance of sulfur, indicating that unidentified oxidized products must be present. Here the reaction stoichiometry and kinetics under variable pH conditions during the growth of Thiomicrospira thermophila strain EPR85, isolated from diffuse hydrothermal fluids at the East Pacific Rise, is presented. At pH 8.0, thiosulfate was stoichiometrically converted to sulfate. At lower pH, the products of thiosulfate oxidation were extracellular elemental sulfur and sulfate. We were able to replicate previous experiments and identify the missing sulfur as tetrathionate, consistent with previous reports of the activity of thiosulfate dehydrogenase. Tetrathionate was formed under slightly acidic conditions. Genomic DNA from T. thermophila strain EPR85 contains genes homologous to those in the Sox pathway (soxAXYZBCDL), as well as rhodanese and thiosulfate dehydrogenase. No other sulfur oxidizing bacteria containing sox(CD)2 genes have been reported to produce extracellular elemental sulfur. If the apparent modified Sox pathway we observed in T. thermophila is present in marine Thiobacillus and Thiomicrospira species, production of extracellular elemental sulfur may be biogeochemically important in marine sulfur cycling.

Draft Genome Sequences of Two Thiomicrospira Strains Isolated from the Brine-Seawater Interface of Kebrit Deep in the Red Sea

Two Thiomicrospira strains, WB1 and XS5, were isolated from the Kebrit Deep brine-seawater interface in the Red Sea, Saudi Arabia. Here, we present the draft genome sequences of these gammaproteobacteria, which both produce sulfuric acid from thiosulfate in culture.

Hydrogenase Gene Distribution and H2 Consumption Ability within the Thiomicrospira Lineage

Thiomicrospira were originally characterized as sulfur-oxidizing chemolithoautotrophs. Attempts to grow them on hydrogen failed for many years. Only recently we demonstrated hydrogen consumption among two of three tested Thiomicrospira and posited that hydrogen consumption may be more widespread among Thiomicrospira than previously assumed. Here, we investigate and compare the hydrogen consumption ability and the presence of group 1 [NiFe]-hydrogenase genes (enzyme catalyzes H₂↔2H⁺ + 2e^-) for sixteen different Thiomicrospira species. Seven of these Thiomicrospira species encoded group 1 [NiFe]-hydrogenase genes and five of these species could also consume hydrogen. All Thiomicrospira species exhibiting hydrogen consumption were from hydrothermal vents along the Mid-Atlantic ridge or Eastern Pacific ridges. The tested Thiomicrospira from Mediterranean and Western Pacific vents could not consume hydrogen. The [NiFe]-hydrogenase genes were categorized into two clusters: those resembling the hydrogenase from Hydrogenovibrio are in cluster I and are related to those from Alpha- and other Gammaproteobacteria. In cluster II, hydrogenases found exclusively in Thiomicrospira crunogena strains are combined and form a monophyletic group with those from Epsilonproteobacteria suggesting they were acquired through horizontal gene transfer. Hydrogen consumption appears to be common among some Thiomicrospira, given that five of the tested sixteen strains carried this trait. The hydrogen consumption ability expands their competitiveness within an environment.

Reasons for Thiomicrospira crunogena's recalcitrance towards previous attempts to detect its hydrogen consumption ability

The first Thiomicrospira species was isolated in 1972 and was described as a sulfur-oxidizing chemolithoautotroph. Since then, several other Thiomicrospira species have been recovered from around the globe and have been classified as common sulfur oxidizers. In the past, attempts to demonstrate hydrogen consumption of a Thiomicrospira species have failed. However, recently, we showed that some Thiomicrospira strains can indeed consume hydrogen. Here, we discuss why Thiomicrospira species have likely resisted efforts to consume hydrogen under the offered conditions. It appears that their hydrogen consumption ability is closely tied to the concentration of nickel in the medium. Investigated carbonate and thiosulfate concentrations did not appear to be critical for hydrogen utilization under the tested conditions.

Novel Barite Chimneys at the Loki's Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems

In order to fully understand the cycling of elements in hydrothermal systems it is critical to understand intra-field variations in geochemical and microbiological processes in both focused, high-temperature and diffuse, low-temperature areas. To reveal important causes and effects of this variation, we performed an extensive chemical and microbiological characterization of a low-temperature venting area in the Loki's Castle Vent Field (LCVF). This area, located at the flank of the large sulfide mound, is characterized by numerous chimney-like barite (BaSO₄) structures (≤ 1 m high) covered with white cotton-like microbial mats. Results from geochemical analyses, microscopy (FISH, SEM), 16S rRNA gene amplicon-sequencing and metatranscriptomics were compared to results from previous analyses of biofilms growing on black smoker chimneys at LCVF. Based on our results, we constructed a conceptual model involving the geochemistry and microbiology in the LCVF. The model suggests that CH₄ and H₂S are important electron donors for microorganisms in both high-temperature and low-temperature areas, whereas the utilization of H₂ seems restricted to high-temperature areas. This further implies that sub-seafloor processes can affect energy-landscapes, elemental cycling, and the metabolic activity of primary producers on the seafloor. In the cotton-like microbial mats on top of the active barite chimneys, a unique network of single cells of Epsilonproteobacteria interconnected by threads of extracellular polymeric substances (EPS) was seen, differing significantly from the long filamentous Sulfurovum filaments observed in biofilms on the black smokers. This network also induced nucleation of barite crystals and is suggested to play an essential role in the formation of the microbial mats and the chimneys. Furthermore, it illustrates variations in how different genera of Epsilonproteobacteria colonize and position cells in different vent fluid mixing zones within a vent field. This may be related to niche-specific physical characteristics. Altogether, the model provides a reference for future studies and illustrates the importance of systematic comparative studies of spatially closely connected niches in order to fully understand the geomicrobiology of hydrothermal systems.

Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria

In this study we characterized and sequenced the genome of Arcobacter anaerophilus strain IR-1 isolated from enrichment cultures used in nitrate-amended corrosion experiments. A. anaerophilus IR-1 could grow lithoautotrophically on hydrogen and hydrogen sulfide and lithoheterothrophically on thiosulfate and elemental sulfur. In addition, the strain grew organoheterotrophically on yeast extract, peptone, and various organic acids. We show for the first time that Arcobacter could grow on the complex organic substrate tryptone and oxidize acetate with elemental sulfur as electron acceptor. Electron acceptors utilized by most Epsilonproteobacteria, such as oxygen, nitrate, and sulfur, were also used by A. anaerophilus IR-1. Strain IR-1 was also uniquely able to use iron citrate as electron acceptor. Comparative genomics of the Arcobacter strains A. butzleri RM4018, A. nitrofigilis CI and A. anaerophilus IR-1 revealed that the free-living strains had a wider metabolic range and more genes in common compared to the pathogen strain. The presence of genes for NAD(+)-reducing hydrogenase (hox) and dissimilatory iron reduction (fre) were unique for A. anaerophilus IR-1 among Epsilonproteobacteria. Finally, the new strain had an incomplete denitrification pathway where the end product was nitrite, which is different from other Arcobacter strains where the end product is ammonia. Altogether, our study shows that traditional characterization in combination with a modern genomics approach can expand our knowledge on free-living Arcobacter, and that this complementary approach could also provide invaluable knowledge about the physiology and metabolic pathways in other Epsilonproteobacteria from various environments.

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.

Physiological and genomic features of a novel sulfur-oxidizing gammaproteobacterium belonging to a previously uncultivated symbiotic lineage isolated from a hydrothermal vent

Strain Hiromi 1, a sulfur-oxidizing gammaproteobacterium was isolated from a hydrothermal vent chimney in the Okinawa Trough and represents a novel genus that may include a phylogenetic group found as endosymbionts of deep-sea gastropods. The SSU rRNA gene sequence similarity between strain Hiromi 1 and the gastropod endosymbionts was approximately 97%. The strain was shown to grow both chemolithoautotrophically and chemolithoheterotrophically with an energy metabolism of sulfur oxidation and O₂ or nitrate reduction. Under chemolithoheterotrophic growth conditions, the strain utilized organic acids and proteinaceous compounds as the carbon and/or nitrogen sources but not the energy source. Various sugars did not support growth as a sole carbon source. The observation of chemolithoheterotrophy in this strain is in line with metagenomic analyses of endosymbionts suggesting the occurrence of chemolithoheterotrophy in gammaproteobacterial symbionts. Chemolithoheterotrophy and the presence of homologous genes for virulence- and quorum sensing-related functions suggest that the sulfur-oxidizing chomolithotrophic microbes seek animal bodies and microbial biofilm formation to obtain supplemental organic carbons in hydrothermal ecosystems.

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1–V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.

Galenea microaerophila gen. nov., sp. nov., a mesophilic, microaerophilic, chemosynthetic, thiosulfate-oxidizing bacterium isolated from a shallow-water hydrothermal vent

A mesophilic, strictly microaerophilic, chemosynthetic bacterium, designated strain P2DT, was isolated from the sediment of an active shallow-water hydrothermal vent in Paleochori Bay, on the Greek island of Milos. The cells were Gram-staining-negative rods that measured approximately 0.8–1.3 µm in length and 0.4–0.5 µm in width. Strain P2DT grew at 20–50 °C (optimum 35 °C), with 1.0–5.0 % (w/v) NaCl (optimum 3.0 %), and at pH 4.5–8.0 (optimum pH 5.5). The generation time under optimal conditions was 1.1 h. Growth occurred under chemolithoautotrophic conditions with S 2 O 3 2 - and CO2 as the energy and carbon sources, respectively. Oxygen (5 %) was used as sole terminal electron acceptor. No growth was observed in the presence of acetate, formate, lactate, tryptone or peptone. Chemolithoheterotrophic growth occurred when d-glucose or sucrose were present as carbon sources. None of the organic compounds tested was used as an electron donor. The genomic DNA G+C content of the novel strain was 44.9 mol%. In a phylogenetic analysis based on 16S rRNA gene sequences, strain P2DT was found to be most closely related to Thiomicrospira psychrophila DSM 13453T (92.8% sequence similarity). Based on the phylogenetic, physiological and chemotaxonomic evidence, strain P2DT represents a novel species of a new genus within the class Gammaproteobacteria of the family Piscirickettsiaceae , for which the name Galenea microaerophila gen. nov., sp. nov. is proposed. The type strain of the type species is P2DT ( = DSM 24963T = JCM 17795T).

Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin

Diverse microbial communities thrive on and in deep-sea hydrothermal vent mineral deposits. However, our understanding of the inter-field variability in these communities is poor, as limited sampling and sequencing efforts have hampered most previous studies. To explore the inter-field variability in these communities, we used barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA gene to characterize the archaeal and bacterial communities of over 30 hydrothermal deposit samples from six vent fields located along the Eastern Lau Spreading Center. Overall, the bacterial and archaeal communities of the Eastern Lau Spreading Center are similar to other active vent deposits, with a high diversity of Epsilonproteobacteria and thermophilic Archaea. However, the archaeal and bacterial communities from the southernmost vent field, Mariner, were significantly different from the other vent fields. At Mariner, the epsilonproteobacterial genus Nautilia and the archaeal family Thermococcaceae were prevalent in most samples, while Lebetimonas and Thermofilaceae were more abundant at the other vent fields. These differences appear to be influenced in part by the unique geochemistry of the Mariner fluids resulting from active degassing of a subsurface magma chamber. These results show that microbial communities associated with hydrothermal vent deposits in back-arc basins are taxonomically similar to those from mid-ocean ridge systems, but differences in geologic processes between vent fields in a back-arc basin can influence microbial community structure.

Thioprofundum hispidum sp. nov., an obligately chemolithoautotrophic sulfur-oxidizing gammaproteobacterium isolated from the hydrothermal field on Suiyo Seamount, and proposal of Thioalkalispiraceae fam. nov. in the order Chromatiales

A novel mesophilic, facultatively anaerobic, sulfur-oxidizing bacterial strain, designated gps61T, was isolated from a surface rock sample collected from the hydrothermal field of Suiyo Seamount on the Izu-Bonin Arc in the Western Pacific Ocean. Cells of the isolate were rod-shaped with a single sheathed polar flagellum. Neither extensive internal membranes nor storage materials were present in the cells. In a 20 % CO2 atmosphere, strain gps61T grew using thiosulfate, sulfur or tetrathionate as electron donors and oxygen or nitrate as electron acceptors. Other substrates, including organic acids and sugars, did not support growth, indicating that strain gps61T was an obligate chemolithoautotroph. 16S rRNA gene sequence analysis revealed that strain gps61T was closely related to Thioprofundum lithotrophicum 106T (98.5 % sequence similarity) in the order Chromatiales. Phylogenetic trees grouped strain gps61T and Thioprofundum lithotrophicum in the same cluster along with Thioalkalispira microaerophila and Thiohalophilus thiocyanoxidans, but it was apparent from the analysis that the novel strain had definitely departed from the family lineage. On the basis of its phylogenetic position along with its morphological and physiological characteristics, strain gps61T ( = NBRC 101261T  = DSM 18546T) represents a novel species of the genus Thioprofundum, for which the name Thioprofundum hispidum sp. nov. is proposed. In addition, we propose a novel family name, Thioalkalispiraceae, in the order Chromatiales, to accommodate the genera Thioalkalispira, Thiohalophilus and Thioprofundum.

Microbial ecology of the dark ocean above, at, and below the seafloor

The majority of life on Earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.

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.

Abundance of Zetaproteobacteria within crustal fluids in back-arc hydrothermal fields of the Southern Mariana Trough

To extend knowledge of subseafloor microbial communities within the oceanic crust, the abundance, diversity and composition of microbial communities in crustal fluids at back-arc hydrothermal fields of the Southern Mariana Trough (SMT) were investigated using culture-independent molecular techniques based on 16S rRNA gene sequences. Seafloor drilling was carried out at two hydrothermal fields, on- and off-ridge of the back-arc spreading centre of the SMT. 16S rRNA gene clone libraries for bacterial and archaeal communities were constructed from the fluid samples collected from the boreholes. Phylotypes related to Thiomicrospira in the Gammaproteobacteria (putative sulfide-oxidizers) and Mariprofundus in the Zetaproteobacteria (putative iron-oxidizers) were recovered from the fluid samples. A number of unique archaeal phylotypes were also recovered. Fluorescence in situ hybridization (FISH) analysis indicated the presence of active bacterial and archaeal populations in the fluids. The Zetaproteobacteria accounted for up to 32% of the total prokaryotic cell number as shown by FISH analysis using a specific probe designed in this study. Our results lead to the hypothesis that the Zetaproteobacteria play a role in iron oxidation within the oceanic crust.

Salinisphaera hydrothermalis sp. nov., a mesophilic, halotolerant, facultatively autotrophic, thiosulfate-oxidizing gammaproteobacterium from deep-sea hydrothermal vents, and emended description of the genus Salinisphaera

A mesophilic, aerobic, facultatively chemolithoautotrophic bacterium, designated strain EPR70(T), was isolated from hydrothermal fluids from diffuse-flow vents on the East Pacific Rise at degrees 50' N 10 degrees 17' W. Cells were Gram-negative rods, approximately 0.8-1.0 microm long and 0.3-0.5 microm wide. Strain EPR70(T) grew at 20-40 degrees C (optimum 30-35 degrees C), 1-25 % NaCl (optimum 2.5 %) and pH 5.0-7.5 (optimum pH 5.5). The shortest generation time observed for strain EPR70(T) was 42 min. Growth occurred under aerobic chemolithoautotrophic conditions in the presence of thiosulfate and CO(2). Strain EPR70(T) grew heterotrophically with acetate or n-alkanes as sole carbon and energy sources, and in complex artificial seawater medium. Nitrate was not used as an electron acceptor. The G+C content of the genomic DNA was 64 mol%. Phylogenetic analysis of the 16S rRNA gene indicated that this organism is a member of the class Gammaproteobacteria, with Salinisphaera shabanensis E1L3A(T) as its closest relative (94 % sequence similarity). On the basis of phylogenetic analyses based on 16S rRNA, rbcL and alkB genes and physiological analysis, it is proposed that the organism represents a novel species within the genus Salinisphaera, for which the name Salinisphaera hydrothermalis sp. nov. is proposed. The type strain is EPR70(T) (=DSM 21483(T) =JCM 15514(T)).

Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough

The abundance, diversity and composition of bacterial and archaeal communities in the microbial mats at deep-sea hydrothermal fields were investigated, using culture-independent 16S rRNA and functional gene analyses combined with mineralogical analysis. Microbial mats were collected at two hydrothermal areas on the ridge of the back-arc spreading centre in the Southern Mariana Trough. Scanning electron microscope and energy dispersive X-ray spectroscopic (SEM-EDS) analyses revealed that the mats were mainly composed of amorphous silica and contained numerous filamentous structures of iron hydroxides. Direct cell counting with SYBR Green I staining showed that the prokaryotic cell densities were more than 10(8) cells g(-1). Quantitative polymerase chain reaction (Q-PCR) analysis revealed that Bacteria are more abundant than Archaea in the microbial communities. Furthermore, zetaproteobacterial cells accounted for 6% and 22% of the prokaryotic cells in each mat estimated by Q-PCR with newly designed primers and TaqMan probe. Phylotypes related to iron-oxidizers, methanotrophs/methylotrophs, ammonia-oxidizers and sulfate-reducers were found in the 16S rRNA gene clone libraries constructed from each mat sample. A variety of unique archaeal 16S rRNA gene phylotypes, several pmoA, dsrAB and archaeal amoA gene phylotypes were also recovered from the microbial mats. Our results provide insights into the diversity and abundance of microbial communities within microbial mats in deep-sea hydrothermal fields.

Thiofaba tepidiphila gen. nov., sp. nov., a novel obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the Gammaproteobacteria isolated from a hot spring

A novel obligately chemolithoautotrophic, sulfur-oxidizing bacterium designated strain BDA453T was isolated from a hot spring in Fukushima prefecture, Japan. The cells were short-rod-shaped and possessed an inclusion, a Gram-negative type cell wall and a single polar flagellum. Strain BDA453T grew by sulfur-oxidizing respiration with thiosulfate, elemental sulfur, sulfide and tetrathionate as electron donors and used only carbon dioxide as a carbon source. The optimum growth conditions were 45 degrees C, pH 6.5 and the absence of NaCl. Analysis of the 16S rRNA gene revealed that the isolate was a member of the Gammaproteobacteria and related to the genera Halothiobacillus and Thiovirga in the family Halothiobacillaceae. However, the phylogenetic tree constructed using 16S rRNA gene sequences showed that strain BDA453T was distant from any other known bacteria with sequence similarities of less than 90 %. On the basis of phenotypic features and phylogenetic analysis, strain BDA453T is considered to represent a novel species of a new genus within the family Halothiobacillaceae, for which the name Thiofaba tepidiphila gen. nov., sp. nov. is proposed. The type strain of Thiofaba tepidiphila is BDA453T (=NBRC 103218T=DSM 19618T).

Application of anaerobic ammonium-oxidizing consortium to achieve completely autotrophic ammonium and sulfate removal

The simultaneous ammonium and sulfate removal was detected in an anammox reactor, consisted of ammonium oxidization with sulfate deoxidization, and subsequently traditional anammox process, in via of middle medium nitrite with solid sulfur and N2 as the terminal products. The pure anammox bacteria offered a great biotechnological potential for the completely autotrophic reaction indicated by batch tests. Denaturing gradient gel electrophoresis (DGGE) analysis further revealed that a new organism belonging to Planctomycetales was strongly enriched in the defined niche: the redox of ammonium and sulfate. The new species "Anammoxoglobussulfate" was so considered as holding a critical role in the ammonium oxidization with sulfate deoxidization to nitrite. Afterwards, the Planctomyces existing in the bacteria community performed the anammox process together to achieve the complete nitrogen and sulfate removal. The potential use of sulfate as electron acceptor for ammonium oxidizing widens the usage of anammox bacteria.

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.

Quantifying microbial utilization of petroleum hydrocarbons in salt marsh sediments by using the 13C content of bacterial rRNA

Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we took a whole-community approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon isotopic abundance between a salt marsh ecosystem supported by the 13C-enriched C4 grass Spartina alterniflora and 13C-depleted petroleum to monitor changes in the 13C content of biomass. Magnetic bead capture methods for selective recovery of bacterial RNA were used to monitor the 13C content of bacterial biomass during a 2-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass was derived from consumption of the freshly spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of Gamma- and Deltaproteobacteria and Firmicutes in the remineralization of hydrocarbons. The magnetic bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in situ. Although employed here at the domain level, RNA capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the 13C content of biomarker lipids.

The influence of ultramafic rocks on microbial communities at the Logatchev hydrothermal field, located 15°N on the Mid-Atlantic Ridge

The ultramafic-hosted Logatchev hydrothermal field (LHF) on the Mid-Atlantic Ridge is characterized by high hydrogen and methane contents in the subseafloor, which support a specialized microbial community of phylogenetically diverse, hydrogen-oxidizing chemolithoautotrophs. We compared the prokaryotic communities of three sites located in the LHF and encountered a predominance of archaeal sequences affiliated with methanogenic Methanococcales at all three. However, the bacterial composition varied in accordance with differences in fluid chemistry between the three sites investigated. An increase in hydrogen seemed to coincide with the diversification of hydrogen-oxidizing bacteria. This might indicate that the host rock indirectly selects this specific group of bacteria. However, next to hydrogen availability further factors are evident (e.g. mixing of hot reduced hydrothermal fluids with cold oxygenated seawater), which have a significant impact on the distribution of microorganisms.

Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas

A novel mesophilic bacterium, strain GO25(T), was isolated from a nest of hydrothermal vent polychaetes, Paralvinella sp., at the Iheya North field in the Mid-Okinawa Trough. Cells were motile short rods with a single polar flagellum. Growth was observed between 4 and 35 degrees C (optimum 30 degrees C; 13-16 h doubling time) and between pH 5.4 and 8.6 (optimum pH 6.1). The isolate was a facultatively anaerobic chemolithoautotroph capable of growth using molecular hydrogen, elemental sulfur or thiosulfate as the sole energy source, carbon dioxide as the sole carbon source, ammonium or nitrate as the sole nitrogen source and elemental sulfur, thiosulfate or yeast extract as the sole sulfur source. Strain GO25(T) represents the first deep-sea epsilonproteobacterium capable of growth by both hydrogen and sulfur oxidation. Nitrate or molecular oxygen (up to 10 % partial pressure) could serve as the sole electron acceptor to support growth. Metabolic products of nitrate reduction shifted in response to the electron donor provided. The G+C content of genomic DNA was 37.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas autotrophica OK10(T) (96.3 % sequence similarity). DNA-DNA hybridization demonstrated that the novel isolate could be differentiated genotypically from Sulfurimonas autotrophica OK10(T). On the basis of the physiological and molecular properties of the novel isolate, the name Sulfurimonas paralvinellae sp. nov. is proposed, with strain GO25(T) (=JCM 13212(T)=DSM 17229(T)) as the type strain. Thiomicrospira denitrificans DSM 1251(T) (=ATCC 33889(T)) is phylogenetically associated with Sulfurimonas autotrophica OK10(T) and Sulfurimonas paralvinellae GO25(T). Based on the phylogenetic relationship between Thiomicrospira denitrificans DSM 1251(T), Sulfurimonas autotrophica OK10(T) and Sulfurimonas paralvinellae GO25(T), we propose the reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. (type strain DSM 1251(T)=ATCC 33889(T)). In addition, an emended description of the genus Sulfurimonas is proposed.

Sulfurivirga caldicuralii gen. nov., sp. nov., a novel microaerobic, thermophilic, thiosulfate-oxidizing chemolithoautotroph, isolated from a shallow marine hydrothermal system occurring in a coral reef, Japan

Novel thermophilic bacteria, designated strains VW1 and MM1(T), were isolated from hydrothermal fluid and microbial mat samples, respectively, collected from a shallow marine hydrothermal system (water depth 22 m) occurring in coral reefs off Taketomi Island, Okinawa, Japan. Cells of the two novel strains were motile rods with a single polar flagellum in the exponential growth phase. In a medium that included elemental sulfur, cells of the two strains became non-motile with oval to spherical cell shapes. For both strains, growth occurred at between 30 and 60 degrees C (optimum temperature of 50-55 degrees C; 60-80 min doubling time) and between pH 5.5 and 7.1 (optimum pH 6.0). The isolates were microaerobic chemolithoautotrophs capable of using thiosulfate or tetrathionate as the sole energy source, O(2) as the sole electron acceptor and CO(2) as the sole carbon source. Organic substrates, such as yeast extract and tryptone, inhibited growth of both strains. The G+C contents of genomic DNA were 51.3 and 49.5 mol% for strains VW1 and MM1(T), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains were closely related to each other (99.9 % sequence similarity) and were distantly related to other previously described genera within the Gammaproteobacteria. The novel isolates could also be differentiated from other gammaproteobacterial genera on the basis of their physiological properties. It is suggested that the novel isolates represent the type species of a new genus, for which the name Sulfurivirga caldicuralii gen. nov., sp. nov. (type strain MM1(T)=JCM 13439(T)=DSM 17737(T)) is proposed.

Dominant microbial populations in limestone-corroding stream biofilms, Frasassi cave system, Italy

Waters from an extensive sulfide-rich aquifer emerge in the Frasassi cave system, where they mix with oxygen-rich percolating water and cave air over a large surface area. The actively forming cave complex hosts a microbial community, including conspicuous white biofilms coating surfaces in cave streams, that is isolated from surface sources of C and N. Two distinct biofilm morphologies were observed in the streams over a 4-year period. Bacterial 16S rDNA libraries were constructed from samples of each biofilm type collected from Grotta Sulfurea in 2002. beta-, gamma-, delta-, and epsilon-proteobacteria in sulfur-cycling clades accounted for > or = 75% of clones in both biofilms. Sulfate-reducing and sulfur-disproportionating delta-proteobacterial sequences in the clone libraries were abundant and diverse (34% of phylotypes). Biofilm samples of both types were later collected at the same location and at an additional sample site in Ramo Sulfureo and examined, using fluorescence in situ hybridization (FISH). The biomass of all six stream biofilms was dominated by filamentous gamma-proteobacteria with Beggiatoa-like and/or Thiothrix-like cells containing abundant sulfur inclusions. The biomass of epsilon-proteobacteria detected using FISH was consistently small, ranging from 0 to less than 15% of the total biomass. Our results suggest that S cycling within the stream biofilms is an important feature of the cave biogeochemistry. Such cycling represents positive biological feedback to sulfuric acid speleogenesis and related processes that create subsurface porosity in carbonate rocks.

Thiomicrospira halophila sp. nov., a moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium from hypersaline lakes

Enrichments at 2 M NaCl and pH 7.5–8, with thiosulfate or sulfide as electron donor, inoculated with sediments from hypersaline chloride–sulfate lakes of the Kulunda Steppe (Altai, Russia) resulted in the domination of two different groups of moderately halophilic, chemolithoautotrophic, sulfur-oxidizing bacteria. Under fully aerobic conditions with thiosulfate, bacteria belonging to the genus Halothiobacillus dominated while, under microaerophilic conditions, a highly motile, short vibrio-shaped phenotype outcompeted the halothiobacilli. Three genetically and phenotypically highly similar vibrio-shaped isolates were obtained in pure culture and one of them, strain HL 5T, was identified as a member of the Thiomicrospira crunogena cluster by 16S rRNA gene sequencing. The new isolates were able to grow with thiosulfate as electron donor within a broad salinity range from 0.5 to 3.5 M NaCl with an optimum at 1.5 M and within a pH range from 6.5 to 8.5 with an optimum at pH 7.5–7.8. Comparative analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) gene sequences demonstrated that strain HL 5T possessed two genes, cbbL-1 and cbbL-2, of the form I RuBisCO and a cbbM gene of the form II RuBisCO, similar to the other members of the Thiomicrospira crunogena cluster. On the basis of phenotypic and genetic comparison, the new halophilic isolates are proposed to be placed into a novel species, Thiomicrospira halophila sp. nov. (type strain HL 5T=DSM 15072T=UNIQEM U 221T).

Geomicrobiological exploration and characterization of a novel deep-sea hydrothermal system at the TOTO caldera in the Mariana Volcanic Arc

Novel hydrothermal activities accompanying effluent white smokers and elemental sulfur chimney structures at the north-east lava dome of the TOTO caldera depression in the Mariana Volcanic Arc have been explored and characterized by geochemical and microbiological surveys. White smoker hydrothermal fluids were observed in the potential hydrothermal activity centre of the field and represented the maximal temperature of 170 degrees C and the lowest pH of 1.6. The chimney structures, all consisting of elemental sulfur (sulfur chimney), were also unique to the TOTO caldera hydrothermal field. Microbial community structures in a sulfur chimney and its formation hydrothermal fluid with a high concentration of hydrogen sulfide (15 mM) have been investigated by culture-dependent and -independent analyses. 16S rRNA gene clone analysis and fluorescence in situ hybridization (FISH) analysis revealed that epsilon-Proteobacteria dominated the microbial communities in the sulfur chimney structure and formed a dense microbial mat covering the sulfur chimney surface. Archaeal phylotypes were consistently minor components in the communities and related to the genera Thermococcus, Pyrodictium, Aeropyrum, and the uncultivated archaeal group of 'deep-sea hydrothermal vent euryarchaeotal group'. Cultivation analysis suggested that the chemolithoautotrophs might play a significant ecological role as primary producers utilizing gas and sulfur compounds provided from hydrothermal fluids.