Detection and phylogenetic analysis of the membrane-bound nitrate reductase (Nar) in pure cultures and microbial communities from deep-sea hydrothermal vents

The Genome of Varunaivibrio sulfuroxidans Strain TC8T, a Metabolically Versatile Alphaproteobacterium from the Tor Caldara Gas Vents in the Tyrrhenian Sea

Varunaivibrio sulfuroxidans type strain TC8^T is a mesophilic, facultatively anaerobic, facultatively chemolithoautotrophic alphaproteobacterium isolated from a sulfidic shallow-water marine gas vent located at Tor Caldara, Tyrrhenian Sea, Italy. V. sulfuroxidans belongs to the family Thalassospiraceae within the Alphaproteobacteria, with Magnetovibrio blakemorei as its closest relative. The genome of V. sulfuroxidans encodes the genes involved in sulfur, thiosulfate and sulfide oxidation, as well as nitrate and oxygen respiration. The genome encodes the genes involved in carbon fixation via the Calvin-Benson-Bassham cycle, in addition to genes involved in glycolysis and the TCA cycle, indicating a mixotrophic lifestyle. Genes involved in the detoxification of mercury and arsenate are also present. The genome also encodes a complete flagellar complex, one intact prophage and one CRISPR, as well as a putative DNA uptake mechanism mediated by the type IVc (aka Tad pilus) secretion system. Overall, the genome of Varunaivibrio sulfuroxidans highlights the organism's metabolic versatility, a characteristic that makes this strain well-adapted to the dynamic environmental conditions of sulfidic gas vents.

Physiological and metabolic responses of chemolithoautotrophic NO 3 - reducers to high hydrostatic pressure

We investigated the impact of pressure on thermophilic, chemolithoautotrophic NO 3 - reducing bacteria of the phyla Campylobacterota and Aquificota isolated from deep-sea hydrothermal vents. Batch incubations at 5 and 20 MPa resulted in decreased NO 3 - consumption, lower cell concentrations, and overall slower growth in Caminibacter mediatlanticus (Campylobacterota) and Thermovibrio ammonificans (Aquificota), relative to batch incubations near standard pressure (0.2 MPa) conditions. Nitrogen isotope fractionation effects from chemolithoautotrophic NO 3 - reduction by both microorganisms were, on the contrary, maintained under all pressure conditions. Comparable chemolithoautotrophic NO 3 - reducing activities between previously reported natural hydrothermal vent fluid microbial communities dominated by Campylobacterota at 25 MPa and Campylobacterota laboratory isolates at 0.2 MPa, suggest robust similarities in cell-specific NO 3 - reduction rates and doubling times between microbial populations and communities growing maximally under similar temperature conditions. Physiological and metabolic comparisons of our results with other studies of pressure effects on anaerobic chemolithoautotrophic processes (i.e., microbial S⁰ -oxidation coupled to Fe(III) reduction and hydrogenotrophic methanogenesis) suggest that anaerobic chemolithoautotrophs relying on oxidation-reduction (redox) reactions that yield higher Gibbs energies experience larger shifts in cell-specific respiration rates and doubling times at increased pressures. Overall, our results advance understanding of the role of pressure, its relationship with temperature and redox conditions, and their effects on seafloor chemolithoautotrophic NO 3 - reduction and other anaerobic chemolithoautotrophic processes.

Distinct oxygen isotope fractionations driven by different electron donors during microbial nitrate reduction in lake sediments

Microbial nitrate reduction can be driven by organic carbon oxidation, as well as by inorganic electron donors, such as reduced forms of sulfur and iron. An apparent inverse oxygen isotope fractionation effect was observed during nitrate reduction in sediment incubations from five sampling sites of a freshwater lake, Hongze Lake, China. Incubations with organic and inorganic electron donor additions were performed. Especially, the inverse oxygen isotope effect was intensified after glucose addition, whereas the incubations with sulfide and Fe²⁺ showed normal fractionation factors. Nitrate reductase encoding genes, napA and narG, were analysed with metagenomics. Higher napA/narG ratios were associated with higher oxygen fractionation factors. The most abundant clade (59%) of NapA in the incubation with glucose was affiliated with Rhodocyclales. In contrast, it only accounted for 8%-9% of NapA in the incubations with sulfide and Fe²⁺ . Differences in nitrate reductases might explain different oxygen isotope effects. Our findings also suggested that large variance of O-nitrate isotope fractionations might have to be considered in the interpretation of natural isotope records.

Metaproteogenomic Profiling of Chemosynthetic Microbial Biofilms Reveals Metabolic Flexibility During Colonization of a Shallow-Water Gas Vent

Tor Caldara is a shallow-water gas vent located in the Mediterranean Sea, with active venting of CO₂ and H₂S. At Tor Caldara, filamentous microbial biofilms, mainly composed of Epsilon- and Gammaproteobacteria, grow on substrates exposed to the gas venting. In this study, we took a metaproteogenomic approach to identify the metabolic potential and in situ expression of central metabolic pathways at two stages of biofilm maturation. Our findings indicate that inorganic reduced sulfur species are the main electron donors and CO₂ the main carbon source for the filamentous biofilms, which conserve energy by oxygen and nitrate respiration, fix dinitrogen gas and detoxify heavy metals. Three metagenome-assembled genomes (MAGs), representative of key members in the biofilm community, were also recovered. Metaproteomic data show that metabolically active chemoautotrophic sulfide-oxidizing members of the Epsilonproteobacteria dominated the young microbial biofilms, while Gammaproteobacteria become prevalent in the established community. The co-expression of different pathways for sulfide oxidation by these two classes of bacteria suggests exposure to different sulfide concentrations within the biofilms, as well as fine-tuned adaptations of the enzymatic complexes. Taken together, our findings demonstrate a shift in the taxonomic composition and associated metabolic activity of these biofilms in the course of the colonization process.

Temperature dependence of denitrification microbial communities and functional genes in an expanded granular sludge bed reactor treating nitrate-rich wastewater

The temperature dependence of denitrification was investigated for high nitrate nitrogen denitrification in an expanded granular sludge bed (EGSB) reactor. The optimal reaction temperatures were 15-35 °C in which nearly complete denitrification was achieved with the removal of COD maintained over 80%. Nitrite accumulation was observed at 10 °C indicating the incomplete denitrification at low temperature. However, almost complete denitrification was even accomplished as high as 52 °C. High-throughput sequencing detected a total of 84 bacterial genera and 7 phyla, and temperature variation resulted in the shift of microbial community structure and diversity. Proteobacteria thrived while Firmicutes and Bacteroidetes were inhibited by temperature stress. The predominance of Halomonas and the significant decrease of Azoarcus at low temperature indicated a more important role of these two genera in denitrification in an EGSB reactor. The results of qPCR indicated that temperature exerted effects on the abundance of denitrification function genes, nirK, nirS, narG, and nosZ, due to the shift of the bacterial community. This study provided a comprehensive understanding of temperature effects on the denitrification process in an EGSB reactor treating high concentration nitrate wastewater.

Co-registered Geochemistry and Metatranscriptomics Reveal Unexpected Distributions of Microbial Activity within a Hydrothermal Vent Field

Despite years of research into microbial activity at diffuse flow hydrothermal vents, the extent of microbial niche diversity in these settings is not known. To better understand the relationship between microbial activity and the associated physical and geochemical conditions, we obtained co-registered metatranscriptomic and geochemical data from a variety of different fluid regimes within the ASHES vent field on the Juan de Fuca Ridge. Microbial activity in the majority of the cool and warm fluids sampled was dominated by a population of Gammaproteobacteria (likely sulfur oxidizers) that appear to thrive in a variety of chemically distinct fluids. Only the warmest, most hydrothermally-influenced flows were dominated by active populations of canonically vent-endemic Epsilonproteobacteria. These data suggest that the Gammaproteobacteria collected during this study may be generalists, capable of thriving over a broader range of geochemical conditions than the Epsilonproteobacteria. Notably, the apparent metabolic activity of the Gammaproteobacteria—particularly carbon fixation—in the seawater found between discrete fluid flows (the intra-field water) suggests that this area within the Axial caldera is a highly productive, and previously overlooked, habitat. By extension, our findings suggest that analogous, diffuse flow fields may be similarly productive and thus constitute a very important and underappreciated aspect of deep-sea biogeochemical cycling that is occurring at the global scale.

Characteristics of the cultivable bacteria from sediments associated with two deep-sea hydrothermal vents in Okinawa Trough

In this study, different culture-dependent methods were used to examine the cultivable heterotrophic bacteria in the sediments associated with two deep-sea hydrothermal vents (named HV1 and HV2) located at Iheya Ridge and Iheya North in Okinawa Trough. The two vents differed in morphology, with HV1 exhibiting diffuse flows while HV2 being a black smoker with a chimney-like structure. A total of 213 isolates were identified by near full-length 16S rRNA gene sequence analysis. Of these isolates, 128 were from HV1 and 85 were from HV2. The bacterial community structures were, in large parts, similar between HV1 and HV2. Nevertheless, differences between HV1 and HV2 were observed in one phylum, one class, 4 orders, 10 families, and 20 genera. Bioactivity analysis revealed that 25 isolates belonging to 9 different genera exhibited extracellular protease activities, 21 isolates from 11 genera exhibited extracellular lipase activities, and 13 isolates of 8 genera displayed antimicrobial activities. This is the first observation of a large population of bacteria with extracellular bioactivities existing in deep-sea hydrothermal vents. Taken together, the results of this study provide new insights into the characteristics of the cultivable heterotrophic bacteria in deep-sea hydrothermal ecosystems.

Phylogenetic diversity of nitrogen-utilizing genes in hydrothermal chimneys from 3 middle ocean ridges

Nitrogen-metabolizing genes, including nitrogenase (nifH), periplasmic nitrate reductase (napA), and cytochrome cd 1-type nitrite reductase (nirS), were collected from hydrothermal chimney sulfides on 3 middle ocean ridges and compared for the first time. There was a clear phylogenetic distinction of these nifH genes between different hydrothermal ecosystems, which supported the colonization and potential adaptation by different nitrogen fixing microbes in those sulfides. In particular, in sulfides from low-temperature hydrothermal vents of the Southwest Indian Ocean Ridge, the prevalence of nifH genes appears to be attributed to sulfate-reducing bacteria, suggesting their ecological significance. Phylogenetic analysis of nitrate/nitrite reductase genes indicated that nitrate was a critical electron acceptor for sulfur- or metal-oxidizing bacteria in these hydrothermal ecosystems. Our results provided information about the compositions and diversity of the 3 important genes involved in nitrogen fixation and nitrate/nitrite reduction processes in hydrothermal ecosystems and is the first comprehensive genetic repertoire of genes related to potential nitrogen fixation and denitrification processes in various hydrothermal environments.

Biostimulation of biogas producing microcosm for enhancing oil recovery in low-permeability oil reservoir

Indigenous microbial enhanced oil recovery (IMEOR) has been successfully applied in conventional oil reservoirs, however the mechanism in low-permeability oil reservoirs is still misunderstood.

Deep-sea hydrothermal vent Epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (Nap)

Despite the frequent isolation of nitrate-respiring Epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. In this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing Epsilonproteobacteria from deep-sea hydrothermal vents. Furthermore, we have shown that the napA gene is expressed in pure cultures of vent Epsilonproteobacteria and it is highly conserved in microbial communities collected from deep-sea vents characterized by different temperature and redox regimes. The diversity of nitrate-reducing Epsilonproteobacteria was found to be higher in moderate temperature, diffuse flow vents than in high temperature black smokers or in low temperatures, substrate-associated communities. As NapA has a high affinity for nitrate compared with the membrane-bound enzyme, its occurrence in vent Epsilonproteobacteria may represent an adaptation of these organisms to the low nitrate concentrations typically found in vent fluids. Taken together, our findings indicate that nitrate reduction is widespread in vent Epsilonproteobacteria and provide insight on alternative energy metabolism in vent microorganisms. The occurrence of the nap cluster in vent, commensal and pathogenic Epsilonproteobacteria suggests that the ability of these bacteria to respire nitrate is important in habitats as different as the deep-sea vents and the human body.