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Cysteamine dioxygenase (ADO) plays a vital role in regulating thiol metabolism and preserving oxygen homeostasis in humans by oxidizing the sulfur of cysteamine and N-terminal cysteine-containing proteins to their corresponding sulfinic acids using O2 as a cosubstrate. However, as the only thiol dioxygenase that processes both small-molecule and protein substrates, how ADO handles diverse substrates of disparate sizes to achieve various reactions is not understood. The knowledge gap is mainly due to the three-dimensional structure not being solved, as ADO cannot be directly compared with other known thiol dioxygenases. Herein, we report the first crystal structure of human ADO at a resolution of 1.78 A with a nickel-bound metal center. Crystallization was achieved through both metal substitution and C18S/C239S double mutations. The metal center resides in a tunnel close to an entry site flanked by loops. While ADO appears to use extensive flexibility to handle substrates of different sizes, it also employs proline and proline pairs to maintain the core protein structure and to retain the residues critical for catalysis in place. This feature distinguishes ADO from thiol dioxygenases that only oxidize small-molecule substrates, possibly explaining its divergent substrate specificity. Our findings also elucidate the structural basis for ADO functioning as an oxygen sensor by modifying N-degron substrates to transduce responses to hypoxia. Thus, this work fills a gap in structure–function relationships of the thiol dioxygenase family and provides a platform for further mechanistic investigation and therapeutic intervention targeting impaired oxygen sensing.

Profound biogeochemical responses of anoxic sediments to the fluctuation of dissolved oxygen (DO) concentration in overlaying water are often observed, despite oxygen having a limited permeability in sediments. This contradiction is indicative of previously unrecognized mechanism that bridges the oxic and anoxic sediment layers. Using sediments from an urban river suffering from long-term polycyclic aromatic hydrocarbons (PAHs) contamination, we analyzed the physicochemical and microbial responses to artificially elevated DO (eDO) in the overlying water over 9 weeks of incubation. Significant changes in key environmental parameters and microbial diversity were detected over the 0-6 cm sediment depth, along with accelerated degradation of PAHs, despite that eDO only increased the porewater DO in the millimeter subfacial layer. The dynamics of physicochemical and microbial properties coincided well with significantly increased presence of centimeter-long sulfide-oxidizing cable bacteria filaments under eDO, and were predominantly driven by cable bacteria metabolic activities. Phylogenetic ecological network analyses further revealed that eDO reinforced cable bacteria associated interspecific interactions with functional microorganisms such as sulfate reducers, PAHs degraders, and electroactive microbes, suggesting enhanced microbial syntrophy taking advantage of cable bacteria metabolism for the regeneration of SO42- and long-distance electron transfer. Together, our results suggest cable bacteria may mediate the impacts of eDO in anaerobic sediments by altering sediment physiochemical properties and by reinforcing community interactions. Our findings highlight the ecological importance of cable bacteria in sediments.

Bacteria of the genus Sulfurimonas within the class Campylobacteria are predominant in global deep-sea hydrothermal environments and widespread in global oceans. However, only few bacteria of this group have been isolated, and their adaptations for these extreme environments remain poorly understood. Here, we report a novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, strain NW10T, isolated from a deep-sea sulfide chimney of Northwest Indian Ocean.16S rRNA gene sequence analysis showed that strain NW10T was most closely related to the vent species Sulfurimonas paralvinellae GO25T with 95.8% similarity, but ANI and DDH values between two strains were only 19.20 and 24.70%, respectively, indicating that strain NW10 represents a novel species. Phenotypic characterization showed strain NW10T is an obligate chemolithoautotroph utilizing thiosulfate, sulfide, elemental sulfur, or molecular hydrogen as energy sources, and molecular oxygen, nitrate, or elemental sulfur as electron acceptors. Moreover, hydrogen supported a better growth than reduced sulfur compounds. During thiosulfate oxidation, the strain can produce extracellular sulfur of elemental α-S8 with an unknown mechanism. Polyphasic taxonomy results support that strain NW10T represents a novel species of the genus Sulfurimonas, and named as Sulfurimonas hydrogeniphila sp. nov. Genome analyses revealed its diverse energy metabolisms driving carbon fixation via rTCA cycling, including pathways of sulfur/hydrogen oxidation, coupled oxygen/sulfur respiration and denitrification. Comparative analysis of the 11 available genomes from Sulfurimonas species revealed that vent bacteria, compared to marine non-vent strains, possess unique genes encoding Type V Sqr, Group II, and Coo hydrogenase, and are selectively enriched in genes related to signal transduction and inorganic ion transporters. These phenotypic and genotypic features of vent Sulfurimonas may explain their thriving in hydrothermal environments and help to understand the ecological role of Sulfurimonas bacteria in hydrothermal ecosystems.

Strain MG, isolated from an acidic pond sediment on the island of Milos (Greece), is proposed as a novel species of ferrous iron- and sulfur-oxidizing Acidithiobacillus. Currently, four of the eight validated species of this genus oxidize ferrous iron, and strain MG shares many key characteristics with these four, including the capacities for catalyzing the oxidative dissolution of pyrite and for anaerobic growth via ferric iron respiration. Strain MG also grows aerobically on hydrogen and anaerobically on hydrogen coupled to ferric iron reduction. While the 16S rRNA genes of the iron-oxidizing Acidi-thiobacillus species (and strain MG) are located in a distinct phylogenetic clade and are closely related (98–99% 16S rRNA gene identity), genomic relatedness indexes (ANI/dDDH) revealed strong genomic divergence between strain MG and all sequenced type strains of the taxon, and placed MG as the first cultured representative of an ancestral phylotype of iron oxidizing acidithiobacilli. Strain MG is proposed as a novel species, Acidithiobacillus ferrianus sp. nov. The type strain is MGT (= DSM 107098T = JCM 33084T). Similar strains have been found as isolates or indicated by cloned 16S rRNA genes from several mineral sulfide mine sites.

Here, we experimentally expand understanding of the reactions and enzymes involved in Acidithiobacillus thiooxidans ATCC 19377 S0 and S 2 ⁢ O 3 2 - metabolism by developing models that integrate gene expression analyzed by RNA-Seq, solution sulfur speciation, electron microscopy and spectroscopy. The A. thiooxidans S 2 ⁢ O 3 2 - metabolism model involves the conversion of S 2 ⁢ O 3 2 - to SO 4 2 - , S0 and S 4 ⁢ O 6 2 - , mediated by the sulfur oxidase complex (Sox), tetrathionate hydrolase (TetH), sulfide quinone reductase (Sqr), and heterodisulfate reductase (Hdr) proteins. These same proteins, with the addition of rhodanese (Rhd), were identified to convert S0 to SO 3 2 - , S 2 ⁢ O 3 2 - and polythionates in the A. thiooxidans S0 metabolism model. Our combined results shed light onto the important role specifically of TetH in S 2 ⁢ O 3 2 - metabolism. Also, we show that activity of Hdr proteins rather than Sdo are likely associated with S0 oxidation. Finally, our data suggest that formation of intracellular S 2 ⁢ O 3 2 - is a critical step in S0 metabolism, and that recycling of internally generated SO 3 2 - occurs, through comproportionating reactions that result in S 2 ⁢ O 3 2 - . Electron microscopy and spectroscopy confirmed intracellular production and storage of S0 during growth on both S0 and S 2 ⁢ O 3 2 - substrates.

This genus contains both phototrophs and nonphototrophic members. Here, we present a high-quality complete genome of the strain CHu59-6-5T, isolated from a freshwater sediment. The circular chromosome (4.39 Mbp) of the strain CHu59-6-5T has 64.4% G+C content and contains 4240 genes, of which a total of 3918 genes (92.4%) were functionally assigned to the COG (clusters of orthologous groups) database. Functional genes for denitrification (narGHJI, nirK and qnor) were identified on the genomes of the strain CHu59-6-5T, except for N2O reductase (nos) genes for the final step of denitrification. Genes (soxBXAZY) for encoding sulfur oxidation proteins were identified, and the FSD and soxF genes encoding the monomeric flavoproteins which have sulfide dehydrogenase activities were also detected. Lastly, genes for the assembly of two different RND (resistance-nodulation division) type efflux systems and one ABC (ATP-binding cassette) type efflux system were identified in the Rhodoferax sediminis CHu59-6-5T. Phylogenetic analysis based on 16S rRNA sequences and Average Nucleotide Identities (ANI) support the idea that the strain CHu59-6-5T has a close relationship to the genus Rhodoferax. A polyphasic study was done to establish the taxonomic status of the strain CHu59-6-5T. Based on these data, we proposed that the isolate be classified to the genus Rhodoferax as Rhodoferax sediminis sp. nov. with isolate CHu59-6-5T.

The diversity of microbially mediated redox processes that occur in marine sediments is likely underestimated, especially with respect to the metabolisms that involve solid substrate electron donors or acceptors. Though electrochemical studies that utilize poised potential electrodes as a surrogate for solid substrate or mineral interactions have shed some much needed light on these areas, these studies have traditionally been limited to one redox potential or metabolic condition. This work seeks to uncover the diversity of microbes capable of accepting cathodic electrons from a marine sediment utilizing a range of redox potentials, by coupling electrochemical enrichment approaches to microbial cultivation and isolation techniques. Five lab-scale three-electrode electrochemical systems were constructed, using electrodes that were initially incubated in marine sediment at cathodic or electron-donating voltages (five redox potentials between −400 and −750 mV versus Ag/AgCl) as energy sources for enrichment. Electron uptake was monitored in the laboratory bioreactors and linked to the reduction of supplied terminal electron acceptors (nitrate or sulfate). Enriched communities exhibited differences in community structure dependent on poised redox potential and terminal electron acceptor used. Further cultivation of microbes was conducted using media with reduced iron (Fe0, FeCl2) and sulfur (S0) compounds as electron donors, resulting in the isolation of six electrochemically active strains. The isolates belong to the genera Vallitalea of the Clostridia, Arcobacter of the Epsilonproteobacteria, Desulfovibrio of the Deltaproteobacteria, and Vibrio and Marinobacter of the Gammaproteobacteria. Electrochemical characterization of the isolates with cyclic voltammetry yielded a wide range of midpoint potentials (99.20 to −389.1 mV versus Ag/AgCl), indicating diverse metabolic pathways likely support the observed electron uptake. Our work demonstrates culturing under various electrochemical and geochemical regimes allows for enhanced cultivation of diverse cathode-oxidizing microbes from one environmental system. Understanding the mechanisms of solid substrate oxidation from environmental microbes will further elucidation of the ecological relevance of these electron transfer interactions with implications for microbe-electrode technologies.

Soda lakes are saline alkaline lakes characterized by high concentrations of sodium carbonate/bicarbonate which lead to a stable elevated pH (>9), and moderate to extremely high salinity. Despite this combination of extreme conditions, biodiversity in soda lakes is high, and the presence of diverse microbial communities provides a driving force for highly active biogeochemical cycles. The sulfur cycle is one of the most important of these and bacterial sulfur oxidation is dominated by members of the obligately chemolithoautotrophic genus Thioalkalivibrio. Currently, 10 species have been described in this genus, but over one hundred isolates have been obtained from soda lake samples. The genomes of 75 strains were sequenced and annotated previously, and used in this study to provide a comprehensive picture of the diversity and distribution of genes related to dissimilatory sulfur metabolism in Thioalkalivibrio. Initially, all annotated genes in 75 Thioalkalivibrio genomes were placed in ortholog groups and filtered by bi-directional best BLAST analysis. Investigation of the ortholog groups containing genes related to sulfur oxidation showed that flavocytochrome c (fcc), the truncated sox system, and sulfite:quinone oxidoreductase (soe) are present in all strains, whereas dissimilatory sulfite reductase (dsr; which catalyzes the oxidation of elemental sulfur) was found in only six strains. The heterodisulfide reductase system (hdr), which is proposed to oxidize sulfur to sulfite in strains lacking both dsr and soxCD, was detected in 73 genomes. Hierarchical clustering of strains based on sulfur gene repertoire correlated closely with previous phylogenomic analysis. The phylogenetic analysis of several sulfur oxidation genes showed a complex evolutionary history. All in all, this study presents a comprehensive investigation of sulfur metabolism-related genes in cultivated Thioalkalivibrio strains and provides several avenues for future research.

Sulfur oxidation is an essential component of the earth's sulfur cycle. Acidithiobacillus spp. can oxidize various reduced inorganic sulfur compounds (RISCs) with high efficiency to obtain electrons for their autotrophic growth. Strains in this genus have been widely applied in bioleaching and biological desulfurization. Diverse sulfur-metabolic pathways and corresponding regulatory systems have been discovered in these acidophilic sulfur-oxidizing bacteria. The sulfur-metabolic enzymes in Acidithiobacillus spp. can be categorized as elemental sulfur oxidation enzymes (sulfur dioxygenase, sulfur oxygenase reductase, and Hdr-like complex), enzymes in thiosulfate oxidation pathways (tetrathionate intermediate thiosulfate oxidation (S4I) pathway, the sulfur oxidizing enzyme (Sox) system and thiosulfate dehydrogenase), sulfide oxidation enzymes (sulfide:quinone oxidoreductase) and sulfite oxidation pathways/enzymes. The two-component systems (TCSs) are the typical regulation elements for periplasmic thiosulfate metabolism in these autotrophic sulfur-oxidizing bacteria. Examples are RsrS/RsrR responsible for S4I pathway regulation and TspS/TspR for Sox system regulation. The proposal of sulfur metabolic and regulatory models provide new insights and overall understanding of the sulfur-metabolic processes in Acidithiobacillus spp. The future research directions and existing barriers in the bacterial sulfur metabolism are also emphasized here and the breakthroughs in these areas will accelerate the research on the sulfur oxidation in Acidithiobacillus spp. and other sulfur oxidizers.

Aplysina aerophoba is an emerging model marine sponge, with a well-characterized microbial community in terms of diversity and structure. However, little is known about the expressed functional capabilities of its associated microbes. Here, we present the first metaproteomics-based study of the microbiome of A. aerophoba. We found that transport and degradation of halogenated and chloroaromatic compounds are common active processes in the sponge microbiomes. Our data further reveal that the highest number of proteins were affiliated to a sponge-associated Tectomicrobium, presumably from the family Entotheonellaceae, as well as to the well-known symbiont “Candidatus Synechococcus spongiarium”, suggesting a high metabolic activity of these two microorganisms in situ. Evidence for nitric oxide (NO) conversion to nitrous oxide was consistently observed for Tectomicrobia across replicates, by production of the NorQ protein. Moreover, we found a potential energy-yielding pathway through CO oxidation by putative Chloroflexi bacteria. Finally, we observed expression of enzymes that may be involved in the transformation of chitin, glycoproteins, glycolipids and glucans into smaller molecules, consistent with glycosyl hydrolases predicted from analyses of the genomes of Poribacteria sponge symbionts. Thus, this study provides crucial links between expressed proteins and specific members of the A. aerophoba microbiome.

Under paddy field conditions, biological sulfur oxidation occurs in the oxidized surface soil layer and rhizosphere, in which oxygen leaks from the aerenchyma system of rice plants. In the present study, we examined community shifts in sulfur-oxidizing bacteria associated with the oxidized surface soil layer and rice roots under different sulfur fertilization conditions based on the 16S ribosomal RNA (rRNA) gene in order to explore the existence of oligotrophic sulfur-oxidizing bacteria in the paddy rice ecosystem. Rice plants were grown in pots with no fertilization (control) or CaCO3 or CaSO4 fertilization. A principal-coordinates analysis (PCoA) showed that CaSO4 fertilization markedly affected bacterial communities associated with rice roots and soil, whereas no significant differences were observed in plant growth among the fertilizer treatments examined. In rice roots, the relative abundance of Acidobacteria, Alphaproteobacteria, Gammaproteobacteria, and TM7 was significantly higher in CaSO4-fertilized pots than in control pots. Alphaproteobacteria, Bradyrhizobiaceae, and Methylocystaceae members were significantly more abundant in CaSO4-fertilized roots than in control roots. On the other hand, the abundance of Actinobacteria and Proteobacteria was lower in CaSO4-fertilized soil than in control soil. These results indicate that the bacteria associated with rice roots and soil responded to the sulfur amendment, suggesting that more diverse bacteria are involved in sulfur oxidation in the rice paddy ecosystem than previously considered.

Cable bacteria are long, multicellular, filamentous bacteria that can conduct electrons over centimeter distances in marine and freshwater sediments. Recent studies indicate that cable bacteria are widely present in many coastal environments, where they exert a major influence on the biogeochemistry of the sediment. Their energy metabolism can be based on the aerobic oxidation of sulfide, and hence to better understand their natural occurrence and distribution, we examined the growth and activity of cable bacteria in relation to bottom water oxygenation. To this end, we conducted laboratory sediment incubations at four different O2 levels in the overlying water (10%, 20%, 40%, and 100% air saturation). The abundance of cable bacteria was determined by fluorescence in situ hybridization, while their activity was assessed via microsensor profiling and geochemical pore‐water analysis. Cable bacteria did not develop in the 10% air saturation O2 incubation but were present and active at all higher O2 levels. These data show that microbial long‐distance electron transport can occur under a wide range of bottom water O2 concentrations. However, the growth rate was notably slower at lower oxygen concentrations, suggesting a reduced metabolic activity of the population when the O2 supply becomes restricted. Finally, in response to lower O2 levels, cable bacteria filaments appear to partially emerge out of the sediment and extend into the overlying water, thus likely enhancing their oxygen supply.

Little is known about large sulfur bacteria that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of large sulfur bacteria. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoacaeae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H2-based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoacaeae contained genes for sulfur oxidation via the rDsr pathway, H2 oxidation via Ni-Fe hydrogenases, and the use of O2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction (sat, apr, and dsr) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel large sulfur bacteria, associated heterotrophic and sulfate-reducing bacteria, and enigmatic archaea.

Acidification by oxidation of elemental sulfur (ES) can solubilize ZnO, providing slow release of both sulfur (S) and zinc (Zn) in soil. For this study, a new granular fertilizer with ES and ZnO was produced and evaluated. The effect of incorporating microorganisms or a carbon source in the granule was also evaluated. Four granulated ES−Zn fertilizers with and without S-oxidizing microorganisms, a commercial ES pastille, ZnSO 4 , and ZnO were applied to the center of Petri dishes containing two contrasting pH soils. Soil pH, CaCl 2 -extractable S and Zn, and remaining ES were evaluated at 30 and 60 days in two soil sections (0−5 and 5−9 mm from the fertilizer application site). A visualization test was performed to evaluate Zn diffusion over time. A significant pH decrease was observed in the acidic soil for all ES−Zn fertilizer treatments and in the alkaline soil for the Acidithiobacillus thiooxidans-inoculated treatment only. In agreement with Zn visualization tests, extractable-Zn concentrations were higher from the point of application in the acidic (62.9 mg dm −3 ) compared to the alkaline soil (5.5 mg dm −3 ). Elemental S oxidation was greater in the acidic soil (20.9%) than slightly alkaline soil (12%). The ES−Zn granular fertilizers increased S and Zn concentrations in soil and can provide a strategically slow release of nutrients to the soil.

Thiobacillus thioparus DSM 505T is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture CT (=DSM 505T = ATCC 8158T) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth. The strain has a genome size of 3,201,518bp. Here we report the genome sequence, annotation and characteristics. The genome contains 3,135 protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant of the Calvin-Benson-Bassham cycle were also identified and an operon encoding carboxysomes, along with Smith's biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partial sox operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302 gene previously noted in the sox operon of other members of the 'Proteobacteria' that can use trithionate as an energy source. In spite of apparently not growing anaerobically with denitrification, the nar, nir, nor and nos operons encoding enzymes of denitrification are found in the T. thioparus genome, in the same arrangements as in the true denitrifier T. denitrificans.

Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyzes these reoxidation reactions is rarely studied. Here, we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions. Combined 16S rRNA gene amplicon sequencing and analysis of phospholipid-derived fatty acids indicated a major temporal shift in community structure. Aerobic sulfur-oxidizing Gammaproteobacteria ( Thiotrichales ) and Epsilonproteobacteria ( Campylobacterales ) were prevalent during spring, whereas Deltaproteobacteria ( Desulfobacterales ) related to sulfate-reducing bacteria prevailed during summer hypoxia. Chemolithoautotrophy rates in the surface sediment were three times higher in spring than in summer. The depth distribution of chemolithoautotrophy was linked to the distinct sulfur oxidation mechanisms identified through microsensor profiling, i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae . The metabolic diversity of the sulfur-oxidizing bacterial community suggests a complex niche partitioning within the sediment, probably driven by the availability of reduced sulfur compounds (H 2 S, S 0 , and S 2 O 3 2− ) and electron acceptors (O 2 and NO 3 − ) regulated by seasonal hypoxia. IMPORTANCE Chemolithoautotrophic microbes in the seafloor are dependent on electron acceptors, like oxygen and nitrate, that diffuse from the overlying water. Seasonal hypoxia, however, drastically changes the availability of these electron acceptors in the bottom water; hence, one expects a strong impact of seasonal hypoxia on sedimentary chemolithoautotrophy. A multidisciplinary investigation of the sediments in a seasonally hypoxic coastal basin confirms this hypothesis. Our data show that bacterial community structure and chemolithoautotrophic activity varied with the seasonal depletion of oxygen. Unexpectedly, the dark carbon fixation was also dependent on the dominant microbial pathway of sulfur oxidation occurring in the sediment (i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae ). These results suggest that a complex niche partitioning within the sulfur-oxidizing bacterial community additionally affects the chemolithoautotrophic community of seasonally hypoxic sediments.

At deep sea hydrothermal fields, a mixing gradient between hot reduced fluids and cold oxygenated sea water creates a number of micro-environments with different physico-chemical conditions in direct proximity to each other. Although many of the key microorganisms in these environments have been identified and described, a systematic understanding of their distribution across the mixing gradient and their niche partitioning is still missing. In my doctoral thesis, I investigated the interplay of geochemical settings, microbial community structures, and diversification of microorganisms in three collaborative studies of hydrothermal vent fields in the Atlantic and Pacific Oceans. Taken together, this thesis provides a detailed overview of the microbial community structures in hydrothermal vents. It deepens our understanding of niche differentiation of major marine sulfur oxidizers, and offers valuable insights into microbial diversification.

Roux, Simon ... et al.-- 5 pages, 3 figures, supporting information https://dx.doi.org/10.1038/nature19366, Ocean microbes drive biogeochemical cycling on a global scale1. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories2, 3. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known4. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions5, 6, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups7, 8). This roughly triples the number of known ocean viral populations4 and doubles the number of candidate bacterial and archaeal virus genera8, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks, This viral research was funded by a National Science Foundation grant (1536989) and Gordon and Betty Moore Foundation grants (3790, 2631) to M.B.S., and the French Ministry of Research and Government through the ‘Investissements d’Avenir’ program OCEANOMICS (ANR-11-BTBR-0008) and France Genomique (ANR-10-INBS-09-08). Virus researchers were partially supported by the Water, Environmental and Energy Solutions Initiative and the Ecosystem Genomics Institute (S.R.), the Netherlands Organization for Scientific Research Vidi grant 864.14.004 and CAPES/BRASIL (B.E.D.), and the Austrian Science Fund (project P25111-B22, A.L.)

An anaerobic, nitrate-reducing, sulfur- and thiosulfate-oxidizing bacterium, designated strain 1812E(T), was isolated from the vent polychaete Riftia pachyptila, which was collected from a deep-sea hydrothermal vent on the East Pacific Rise. Cells were Gram-stain-negative rods, measuring approximately 1.05 +/- 0.11 mu m by 0.40 +/- 0.05 mu m. Strain 1812E(T) grew at 25 - - 45 degrees C (optimum 35 degrees C), with 1.5-4.0% (w/v) NaCI (optimum 3.0%) and at pH 5.0-8.0 (optimum pH 6.0). The generation time under optimal conditions was 3 h. Strain 1812E(T) was an anaerobic chemolithotroph that grew with either sulfur or thiosulfate as the energy source and carbon dioxide as the sole carbon source. Nitrate was used as a sole terminal electron acceptor. The predominant fatty acids were C-16:1 omega 7c(1) C-18:1 omega 7c and C-16:0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was menaquinone MK-6 and the G+C content of the genomic DNA was 47.4 mol%. Phylogenetic analysis of the 16S rRNA gene of strain 1812E(T) showed that the isolate belonged to the Epsilon proteobacteria, and its closest relatives were Sulfurovum lithotrophicum 42BK(T) and Sulfurovum aggregans Monchim 33(T) (98.3 and 95.7% sequence similarity, respectively). DNA DNA relatedness between strain 1812E(T) and the type strain of S. lithotrophicum was 29.7%, demonstrating that the two strains are not members of the same species. Based on the phylogenetic, molecular, chemotaxonomic and physiological evidence, strain 1812E(T) represents a novel species within the genus Sulfurovum, for which the name Sulfurovum riftiae sp. nov. is proposed. The type strain is 1812E(T) (=DSM 101780(T)=JCM 30810(T))

The central protein of the sulfur-oxidizing enzyme system of Paracoccus pantotrophus, SoxYZ, reacts with three different Sox proteins. Its active site Cys110Y is on the carboxy-terminus of the SoxY subunit. SoxYZ “as isolated” consisted mainly of the catalytically inactive SoxY-Y(Z)2 heterotetramer linked by a Cys110Y-Cys110Y interprotein disulfide. Sulfide activated SoxYZ “as isolated” 456-fold, reduced the disulfide, and yielded an active SoxYZ heterodimer. The reductant tris(2-carboxyethyl)phosphine (TCEP) inactivated SoxYZ. This form was not re-activated by sulfide, which identified it as a different inactive form. In analytical gel filtration, the elution of “TCEP-treated” SoxYZ was retarded compared to active SoxYZ, indicating a conformational change. The possible enzymes involved in the re-activation of each inactive form of SoxYZ are discussed.

Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces at sites throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cultured or sequenced using environmental genomics approaches to date. We utilized single-cell genomic sequencing to obtain one incomplete and two nearly complete draft genomes for Achromatium collected at Warm Mineral Springs (WMS), FL. Based on 16S rRNA gene sequences, the three cells represent distinct and relatively distant Achromatium populations (91-92% identity). The draft genomes encode key genes involved in sulfur and hydrogen oxidation; oxygen, nitrogen and polysulfide respiration; carbon and nitrogen fixation; organic carbon assimilation and storage; chemotaxis; twitching motility; antibiotic resistance; and membrane transport. Known genes for iron and manganese energy metabolism were not detected. The presence of pyrophosphatase and vacuolar (V)-type ATPases, which are generally rare in bacterial genomes, suggests a role for these enzymes in calcium transport, proton pumping, and/or energy generation in the membranes of calcite-containing inclusions.

Microbial communities play central roles in ocean biogeochemical cycles, and are particularly important in in oceanic oxygen minimum zones (OMZs). However, the key carbon, nitrogen, and sulfur (S) cycling processes catalyzed by OMZ microbial communities are poorly constrained spatially, temporally, and with regard to the different microbial groups involved. Here we sample across dissolved oxygen gradients in the oceans’ largest OMZ by volume—the eastern tropical North Pacific ocean, or ETNP—and quantify 16S rRNA and functional gene transcripts to detect and constrain the activity of different S-cycling groups. Based on gene expression profiles, putative dissimilatory sulfite reductase (dsrA) genes are actively expressed within the ETNP OMZ. dsrA expression was limited almost entirely to samples with elevated nitrite concentrations, consistent with previous observations in the eastern tropical South Pacific (ETSP) OMZ. dsrA and ‘reverse’ dissimilatory sulfite reductase (rdsrA) genes are related and the associated enzymes are known to operate in either direction, reducing or oxidizing different S compounds. We found that rdsrA genes and soxB genes were expressed in the same samples, suggestive of active S cycling in the ETNP OMZ. These data provide potential thresholds for S cycling in OMZs that closely mimic recent predictions, and indicate that S cycling may be broadly relevant in OMZs.

Seasonal oxygen depletion (hypoxia) in coastal bottom waters can lead to the release and persistence of free sulfide (euxinia), which is highly detrimental to marine life. Although coastal hypoxia is relatively common, reports of euxinia are less frequent, which suggests that certain environmental controls can delay the onset of euxinia. However, these controls and their prevalence are poorly understood. Here we present field observations from a seasonally hypoxic marine basin (Grevelingen, The Netherlands), which suggest that the activity of cable bacteria, a recently discovered group of sulfur-oxidizing microorganisms inducing long-distance electron transport, can delay the onset of euxinia in coastal waters. Our results reveal a remarkable seasonal succession of sulfur cycling pathways, which was observed over multiple years. Cable bacteria dominate the sediment geochemistry in winter, whereas, after the summer hypoxia, Beggiatoaceae mats colonize the sediment. The specific electrogenic metabolism of cable bacteria generates a large buffer of sedimentary iron oxides before the onset of summer hypoxia, which captures free sulfide in the surface sediment, thus likely preventing the development of bottom water euxinia. As cable bacteria are present in many seasonally hypoxic systems, this euxinia-preventing firewall mechanism could be widely active, and may explain why euxinia is relatively infrequently observed in the coastal ocean.

The bioleaching of a nickel concentrate and an acid-consuming nickel ore was studied using a co-culture of Acidithiobacillus ferrooxidans and A. thiooxidans, as well as a thermophilic enrichment culture, VS2. The VS2 was dominated by a Sulfolobus species related to Sulfolobus metallicus. Nickel concentrate was readily solubilized with A. ferrooxidans and the VS2, resulting in nickel yields of 56% and 100%, respectively. Low-grade nickel ore required 350 g H2SO4 kg-1 ore for maintaining the pH of the leaching solution below 3. To overcome the high acid demand, biological elemental sulfur oxidation was combined with the ore leaching. Leaching of a 2% (wt/vol) nickel ore with a co-culture of A. thiooxidans and A. ferrooxidans resulted in nickel yield of up to 86% with acid supplementation of 290 g H2SO4 kg-1 ore. When coupled with biological sulfur oxidation, an 86% nickel recovery was achieved with 0.5% (wt/vol) ore concentration without further sulfuric acid addition. The VS2 oxidized sulfur at a rate of 0.063 g L-1 d-1 and the simultaneous nickel ore leaching resulted in 100% nickel yield. In summary, the potential of using elemental sulfur addition and subsequent biological acid generation to maintain the low pH during bioleaching of an acid-consuming nickel ore was demonstrated.

Diverse microbial assemblages inhabit subglacial aquatic environments. While few of these environments have been sampled, data reveal that subglacial organisms gain energy for growth from reduced minerals containing nitrogen, iron, and sulfur. Here we investigate the role of microbially mediated sulfur transformations in sediments from Subglacial Lake Whillans (SLW), Antarctica, by examining key genes involved in dissimilatory sulfur oxidation and reduction. The presence of sulfur transformation genes throughout the top 34 cm of SLW sediments changes with depth. SLW surficial sediments were dominated by genes related to known sulfur-oxidizing chemoautotrophs. Sequences encoding the adenosine-5'-phosphosulfate (APS) reductase gene, involved in both dissimilatory sulfate reduction and sulfur oxidation, were present in all samples and clustered into 16 distinct operational taxonomic units. The majority of APS reductase sequences (74%) clustered with known sulfur oxidizers including those within the "Sideroxydans" and Thiobacillus genera. Reverse-acting dissimilatory sulfite reductase (rDSR) and 16S rRNA gene sequences further support dominance of "Sideroxydans" and Thiobacillus phylotypes in the top 2 cm of SLW sediments. The SLW microbial community has the genetic potential for sulfate reduction which is supported by experimentally measured low rates (1.4 pmol cm(-3)d(-1)) of biologically mediated sulfate reduction and the presence of APS reductase and DSR gene sequences related to Desulfobacteraceae and Desulfotomaculum. Our results also infer the presence of sulfur oxidation, which can be a significant energetic pathway for chemosynthetic biosynthesis in SLW sediments. The water in SLW ultimately flows into the Ross Sea where intermediates from subglacial sulfur transformations can influence the flux of solutes to the Southern Ocean.

Background Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. Results Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. Conclusions The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle., National Science Foundation (U.S.) (Grant 0412205), United States. Dept. of Energy. Office of Science (Contract DE-AC02-05CH11231), United States. Dept. of Energy. Joint Genome Institute

Acidianus copahuensis is a recently characterized thermoacidophilic archaeon isolated from the Copahue volcanic area in Argentina. Here, we present its draft genome sequence, in which we found genes involved in key metabolic pathways for developing under Copahue's extreme environmental conditions, such as sulfur and iron oxidation, carbon fixation, and metal tolerance., Centro de Investigación y Desarrollo en Fermentaciones Industriales

International audience; Salt marshes are highly productive ecosystems hosting an intense sulfur (S) cycle, yet little is known about S-oxidizing microorganisms in these ecosystems. Here, we studied the diversity and transcriptional activity of S-oxidizers in salt marsh sediments colonized by the plant Spartina alterniflora, and assessed variations with sediment depth and small-scale compartments within the rhizosphere. We combined next-generation amplicon sequencing of 16S rDNA and rRNA libraries with phylogenetic analyses of marker genes for two S-oxidation pathways (soxB and rdsrAB). Gene and transcript numbers of soxB and rdsrAB phylotypes were quantified simultaneously, using newly designed (RT)-qPCR assays. We identified a diverse assemblage of S-oxidizers, with Chromatiales and Thiotrichales being dominant. The detection of transcripts from S-oxidizers was mostly confined to the upper 5 cm sediments, following the expected distribution of root biomass. A common pool of species dominated by Gammaproteobacteria transcribed S-oxidation genes across roots, rhizosphere, and surrounding sediment compartments, with rdsrAB transcripts prevailing over soxB. However, the root environment fine-tuned the abundance and transcriptional activity of the S-oxidizing community. In particular, the global transcription of soxB was higher on the roots compared to mix and rhizosphere samples. Furthermore, the contribution of Epsilonproteobacteria-related S-oxidizers tended to increase on Spartina roots compared to surrounding sediments. These data shed light on the under-studied oxidative part of the sulfur cycle in salt marsh sediments and indicate small-scale heterogeneities are important factors shaping abundance and potential activity of S-oxidizers in the rhizosphere.

Four proteins of Paracoccus pantotrophus are required for hydrogen sulfide-, sulfur-, thiosulfate- and sulfite-dependent horse heart cytochrome c reduction. The lack of free intermediates suggested a protein-bound sulfur oxidation mechanism. The SoxY protein has a novel motif containing a cysteine residue. Electrospray ionization and matrix-assisted laser desorption ionization mass spectrometry of the SoxYZ protein revealed one mass for SoxZ and different masses for SoxY, indicating native SoxY (10 977 Da) and SoxY with additional masses of +32, +80, +112 and +144 Da, suggesting addition of sulfur, sulfite, thiosulfate and thioperoxomonosulfate. Reduction of SoxY removed the additional masses, indicating a thioether or thioester bond. N-Ethylmaleimide inhibited thiosulfate-oxidation and the kinetics suggested a turn-over-dependent mode of action. These data were evidence that the sulfur atom to be oxidized was covalently linked to the thiol moiety of the cysteine residue of SoxY and the active site of sulfur oxidation.

International audience; Litoreibacter arenae Kim et al. 2012 is a member of the genomically well-characterized Rhodobacteraceae clade within the Roseobacter clade. Representatives of this clade are known to be metabolically versatile and involved in marine carbon-producing and biogeochemical processes. They form a physiologically heterogeneous group of Alphaproteobacteria and were mostly found in coastal or polar waters, especially in symbiosis with algae, in microbial mats, in sediments or together with invertebrates and vertebrates. Here we describe the features of L. arenae DSM 19593T, including novel aspects of its phenotype, together with the draft genome sequence and annotation. The 3,690,113 bp long genome consists of 17 scaffolds with 3,601 protein-coding and 56 RNA genes. This genome was sequenced as part of the activities of the Transregional Collaborative Research Centre 51 funded by the German Research Foundation (DFG).

Microorganisms throughout the dark ocean use reduced sulfur compounds for chemolithoautotrophy. In many deep-sea hydrothermal vents, sulfide oxidation is quantitatively the most important chemical energy source for microbial metabolism both at and beneath the seafloor. In this study, the presence and activity of vent endemic Epsilonproteobacteria was examined in six low-temperature diffuse vents over a range of geochemical gradients from Axial Seamount, a deep-sea volcano in the Northeast Pacific. PCR primers were developed and applied to target the sulfur oxidation soxB gene of Epsilonproteobacteria. soxB genes belonging to the genera Sulfurimonas and Sulfurovum are both present and expressed at most diffuse vent sites, but not in background seawater. Although Sulfurovum-like soxB genes were detected in all fluid samples, the RNA profiles were nearly identical among the vents and suggest that Sulfurimonas-like species are the primary Epsilonproteobacteria responsible for actively oxidizing sulfur via the Sox pathway at each vent. Community patterns of subseafloor Epsilonproteobacteria 16S rRNA genes were best matched to methane concentrations in vent fluids, as well as individual vent locations, indicating that both geochemistry and geographical isolation play a role in structuring subseafloor microbial populations. The data show that in the subseafloor at Axial Seamount, Epsilonproteobacteria are expressing the soxB gene and that microbial patterns in community distribution are linked to both vent location and chemistry.

During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria.

The World s oceans host a variety of sulfidic habitats. Yet, microorganisms oxidizing reduced inorganic sulfur compounds have mostly been studied at hydrothermal vents, in anoxic basins, conspicuous microbial mats and symbioses but rarely in coastal sediments. In this thesis sulfur-oxidizing prokaryotes (SOP) of a eutrophic intertidal sand flat in the German Wadden Sea were investigated by molecular techniques. The diversity, abundance and activity of SOP were analyzed in particular among the Gammaproteobacteria. Comparative sequence analysis of the 16S rRNA and three genes involved in sulfur oxidation revealed a high diversity of mainly gammaproteobacterial SOP. Most of them were closely related to thiotrophic symbionts, including those of the tubeworm genus Oligobrachia. A group of free-living relatives accounted for up to 4% of all cells (~1.3 × 108 cells ml-1). Consistent with a presumed chemolithoautotrophic utilization of inorganic sulfur compounds, these and numerous other members of the Gammaproteobacteria incorporated 14CO2 as revealed by microautoradiography (MAR). The findings demonstrate that non-filamentous Gammaproteobacteria are important catalysts of sedimentary sulfur oxidation and contribute to CO2-fixation in coastal surface sediments. Similarly, Roseobacter clade bacteria (RCB) accounted for unexpectedly high abundances of up to 10% of all cells in surface sediments (~2.5 × 108 cells ml-1). A RCB-related genome fragment of 35 kb was recovered from a metagenomic fosmid library. It encoded genes of the SOX multienzyme system including the sulfur dehydogenase SoxCD, but also the complete rDSR pathway, a gene arrangement that is unique among SOP. Gene-targeted FISH confirmed the presence of the gene dsrA in sedimentary RCB enriched in anaerobic sulfidic medium. In addition, a novel gene, which encodes a putative dioxygenase, designated as dsrU, was identified in the rDSR pathway. Protocols were developed for application of MAR and nano-scale secondary ion mass spectroscopy (nanoSIMS) to marine sediment samples to follow assimilation of acetate in single cells. Members of the Gammaproteobacteria appeared to assimilate slightly more acetate than RCB, whereas sulfate-reducing bacteria showed no significant incorporation. Particularly the combination of flow cytometry and nanoSIMS proved to be powerful for up-scaling of the analysis of substrate uptake by sediment bacteria enabling an efficient, high-resolution profiling of single cells from complex microbial communities.

Magnetotactic bacteria (MTB) mineralize nanosized magnetite or greigite crystals within cells and thus play an important role in the biogeochemical process. Despite decades of research, knowledge of MTB distribution and ecology, notably in areas subjected to oil industry activities, is still limited. In the present study, we investigated the presence of MTB in the Gulf of Fos, French Mediterranean coast, which is subjected to intensive oil industry activities. Microcosms containing sediments/water (1:2, v/v) from several sampling sites were monitored over several weeks. The presence of MTB was revealed in five of eight sites. Diverse and numerous MTB were revealed particularly from one site (named CAR), whilst temporal variations of a homogenous magnetotactic cocci population was shown within the LAV site microcosm over a 4-month period. Phylogenetic analysis revealed that they belonged to Alphaproteobacteria, and a novel genus from the LAV site was evidenced. Among the physicochemical parameters measured, a correlation was shown between the variation of MTB abundance in microcosms and the redox state of sulphur compounds.

Marin gutless oligochaete worms (Annelida, Phallodrilinae) live in an obligate association with bacterial endosymbionts. Each host, belonging to one of the two genera Olavius or Inanidrilus, harbours a specific, but morphologically, phylogenetically and metabolically diverse symbiont community. The primary symbionts of gutless oligochaetes, called Gamma 1, are large chemoautotrophic sulfur-storing bacteria that form a monophyletic clade within the Gammaproteobacteria and had been found in all host species studied so far. Secondary symbionts of gutless oligochaetes belong to the Alpha-, Gamma- and Deltaproteobacteria and to the Spirochaetes. In this PhD thesis the diversity and function of gutless oligochaete symbiont communities was investigated.In a first part, the phylogenetic and metabolic diversity of I. exumae was studied. The symbiont community of this host differed markedly from that of other gutless oligochaetes. Sulfate-reducing deltaproteobacterial symbionts co-occurred with alpha-proteobacterial symbionts in this host, showing that these do not mutually exclude each other as previously assumed. Furthermore, a large novel gammaproteobacterial symbiont only distantly related to the Gamma 1 symbionts, but morphologically similar, dominated the symbiont community, while no indication was found for a Gamma 1 symbiont. The presence of sulfur and genes diagnostic for autotrophy and sulfur oxidation indicate that this new symbiont is a sulfur-storing chemoautotroph. Thus, the novel symbiont seems to share its morphology and its function with the Gamma 1 symbionts and may have replaced the Gamma 1 symbiont in I. exumae.To learn more about the ecophysiology of gutless oligochaete symbioses, the autotrophic activity was investigated in a second project with tracer incubation experiments. Analyses of radiolabelled inorganic carbon uptake and sulfur content of individual Olavius algarvensis worms showed that in the presence of oxygen, internally stored sulfur was used as an energy source for the incorporation of inorganic carbon into biomass. In the absence of oxygen, inorganic carbon was taken up at lower rates. The electron donors and electron acceptors used under anoxic conditions could not be unambiguously identified. However, increased carbon fixation occurred in the presence of nitrate, sulfide and thiosulfate in a few worms.Identification of the autotrophic symbionts in the O. algarvensis symbiont community was achieved in a third project by applying in situ hybridization combined with microautoradiography (MARFISH) or high resolution mass spectrometry (nanoSIMS-HISH). The Gamma 1 symbionts immediately incorporated inorganic carbon into biomass under oxic conditions in the absence of external energy sources suggesting the usage of internally stored sulfur as electron donor. Uptake rates of individual cells varied, but were on average in the range of those found for free-living sulfur bacteria and chemoautotrophic symbionts. For the first time, the autotrophic symbiont could be directly identified and the inorganic carbon uptake analyzed for individual symbionts within the gutless oligochaete symbiosis.

Thiobacillus ferrooxidans is a Gram-negative chemolithotrophic bacterium able to oxidize ferrous iron, elemental sulfur and inorganic sulfur compounds. The oxidation of sulfur by T. ferrooxidans resulted in an expression of some outer membrane proteins (OMPs) at a level higher than that observed during ferrous iron oxidation. Among these OMPs, a protein with a molecular mass of 54 kDa was purified and 18 amino acids of the N-terminal sequence determined. Using a 54 bp PCR generated DNA product as a probe for the protein, we isolated a 4.5 kb Pst I DNA chromosomal fragment containing the corresponding gene. Sequencing 2169 bp of this fragment revealed the open reading frame codifying for the protein, consisting of 467 amino acids and a molecular mass of 49 674 Da. The mature protein was produced by the removal of a 32 amino acid signal peptide-like sequence from the N-terminus of a 499 amino acid peptide. Although no significant homology with any known protein has been found and its physiological role remains unclear, its high expression on sulfur substrates suggests a role in sulfide mineral oxidation.

Made available in DSpace on 2022-04-28T19:54:30Z (GMT). No. of bitstreams: 0 Previous issue date: 1997-01-01 The acid leaching of a pyrite-rich black shale concentrate (7% S) was tested in this study. The experiments were performed at 5-30% pulp densities and with inoculations of Fe- and S-oxidizing thiobacilli (Thiobacillus ferrooxidans and Thiobacillus thiooxidans). Cultures supplemented with S0 showed strong acid production, with final pH values of 0.9 in T. ferrooxidans cultures and 0.4-0.5 in the presence of T. thiooxidans. Fe dissolution was pronounced in the T. ferrooxidans culture whereas T. thiooxidans did not dissolve Fe from the black shale. Total dissolved Fe concentrations were 3 to 50 times higher in the cultures inoculated with T. ferrooxidans when compared to T. thiooxidans and sterile controls. The dissolution of Mo was enhanced in the inoculated cultures as compared with the chemical controls. With V, Si, and Al this effect was not as pronounced but was still discernible in solutions acidified by bacterial oxidation of S0. The leaching experiments suggested that the black shale was inhibitory to the inocula. The inhibition was related to the pulp density and was associated with the leach solution. The inhibition could be completely alleviated by replacing the leach solution. Department of Microbiology Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292 Department of Geology, P.O. Box 11, FIN-00014 Helsinki Inst. of Molecular and Cell Biology Tartu University, Riia 23, Tartu EE2400 Department of Biochemistry Institute of Chemistry São Paulo State University, P.O. Box 355, Araraquara, SP 14.800 Department of Biochemistry Institute of Chemistry São Paulo State University, P.O. Box 355, Araraquara, SP 14.800

Here, we report a type strain AST-10 representing a novel species Sulfurimonas hongkongensis within Epsilonproteobacteria, which is involved in marine sedimentary sulfur oxidation and denitrification. Strain AST-10(T) (= DSM 22096(T) = JCM 18418(T)) was isolated from the coastal sediment at the Kai Tak Approach Channel connected to Victoria Harbour in Hong Kong. It grew chemolithoautotrophically using thiosulfate, sulfide or hydrogen as the sole electron donor and nitrate as the electron acceptor under anoxic conditions. It was rod-shaped and grew at 15-35°C (optimum at 30°C), pH 6.5-8.5 (optimum at 7.0-7.5), and 10-60 g L(-1) NaCl (optimum at 30 g L(-1)). Genome sequencing and annotation of strain AST-10(T) showed a 2,302,023 bp genome size, with 34.9% GC content, 2,290 protein-coding genes, and 42 RNA genes, including 3 rRNA genes.

We studied the regulation mechanism of electron donations from menaquinol:cytochrome c oxidoreductase and cytochrome c -554 to the type I homodimeric photosynthetic reaction center complex of the green sulfur bacterium Chlorobium tepidum . We measured flash-induced absorption changes of multiple cytochromes in the membranes prepared from a mutant devoid of cytochrome c -554 or in the reconstituted membranes by exogenously adding cytochrome c -555 purified from Chlorobium limicola . The results indicated that the photo-oxidized cytochrome c z bound to the reaction center was rereduced rapidly by cytochrome c -555 as well as by the menaquinol:cytochrome c oxidoreductase and that cytochrome c -555 did not function as a shuttle-like electron carrier between the menaquinol:cytochrome c oxidoreductase and cytochrome c z . It was also shown that the rereduction rate of cytochrome c z by cytochrome c -555 was as high as that by the menaquinol:cytochrome c oxidoreductase. The two electron-transfer pathways linked to sulfur metabolisms seem to function independently to donate electrons to the reaction center.

Environmental fluctuations require rapid adjustment of the physiology of bacteria. Anoxygenic phototrophic purple sulfur bacteria, like Allochromatium vinosum, thrive in environments that are characterized by steep gradients of important nutrients for these organisms, i.e., reduced sulfur compounds, light, oxygen and carbon sources. Changing conditions necessitate changes on every level of the underlying cellular and molecular network. Thus far, two global analyses of A. vinosum responses to changes of nutritional conditions have been performed and these focused on gene expression and protein levels. Here, we provide a study on metabolite composition and relate it with transcriptional and proteomic profiling data to provide a more comprehensive insight on the systems level adjustment to available nutrients. We identified 131 individual metabolites and compared availability and concentration under four different growth conditions (sulfide, thiosulfate, elemental sulfur, and malate) and on sulfide for a ΔdsrJ mutant strain. During growth on malate, cysteine was identified to be the least abundant amino acid. Concentrations of the metabolite classes “amino acids” and “organic acids” (i.e., pyruvate and its derivatives) were higher on malate than on reduced sulfur compounds by at least 20 and 50 %, respectively. Similar observations were made for metabolites assigned to anabolism of glucose. Growth on sulfur compounds led to enhanced concentrations of sulfur containing metabolites, while other cell constituents remained unaffected or decreased. Incapability of sulfur globule oxidation of the mutant strain was reflected by a low energy level of the cell and consequently reduced levels of amino acids (40 %) and sugars (65 %). Electronic supplementary material The online version of this article (doi:10.1007/s11306-014-0649-7) contains supplementary material, which is available to authorized users.