Sulfurimonas gotlandica sp. nov., a chemoautotrophic and psychrotolerant epsilonproteobacterium isolated from a pelagic redoxcline, and an emended description of the genus Sulfurimonas

Naturalization of treated wastewater by a constructed wetland in a water-scarce Mediterranean region

The effluents from conventional wastewater treatment plants (WWTP), even if accomplishing quality regulations, substantially differ in their characteristics with those of waters in natural environments. Constructed wetlands (CWs) serve as transitional ecosystems within WWTPs, mitigating these differences and restoring natural features before water is poured into the natural environment. Our study focused on an experimental surface-flow CW naturalizing the WWTP effluent in a semiarid area in Eastern Spain. Despite relatively low pollutant concentrations entering the CW, it effectively further reduced settled organic matter and nitrogen. Dissolved organic matter (DOM) reaching the CW was mainly protein-like, yet optical property changes in the DOM indicated increased humification, aromaticity, and stabilization as it flowed through the CW. Flow cytometry analysis revealed that the CW released less abundant but more active bacterial populations than those received. MiSeq Illumina sequencing highlighted changes in the prokaryotic community composition, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria dominating the CW outflow. Functional prediction tools (FaproTax and PICRUSt2) demonstrated a shift towards microbial guilds aligned with those of the natural aquatic environments, increased aerobic chemoheterotrophs, photoautotrophs, and metabolic reactions at higher redox potentials. Enhanced capabilities for degrading plant material correlated well with changes in the DOM pool. Our findings emphasize the role of CWs in releasing biochemically stable DOM and functionally suited microbial populations for natural receiving environments. Consequently, we propose CWs as a naturalization nature-based solution (NBS) in water-scarce regions like the Mediterranean, where reclaimed discharged water can significantly contribute to ecosystem's water resources compared to natural flows.

Adaptive characteristics of indigenous microflora in an organically contaminated high salinity groundwater

Salinity, a critical factor, could directly or indirectly affect the microbial community structure and diversity. Changes in salinity levels act as environmental filters that influence the transformation of key microbial species. This study investigates the adaptive characteristics of indigenous microflora in groundwater in relation to external organic pollutants under high salinity stress. A highly mineralized shallow groundwater in Northwest China was conducted as the study area, and six representative sampling points were chosen to explore the response of groundwater hydrochemical parameters and microflora, as well as to identify the tolerance mechanisms of indigenous microflora to combined pollution. The results revealed that the dominant genera found in high salinity groundwater contaminated with organic pollutants possess the remarkable ability to degrade such pollutants even under challenging high salinity conditions, including Halomonas, Pseudomonas, Halothiobacillus, Sphingomonas, Lutibacter, Aquabacterium, Thiomicrospira, Aequorivita, etc. The hydrochemical factors, including total dissolved solids (TDS), sulfide, nitrite, nitrate, oxidation reduction potential (ORP), NH3-N, Na, Fe, benzene series, phenols, and halogenated hydrocarbons, demonstrated a significant influence on microflora. High levels of sulphate and sulfide in groundwater can exhibit dual effects on microflora. On one hand, these compounds can inhibit the growth and metabolism of microorganisms. On the other hand, they can also serve as effective electron donors/receptors during the microbial degradation of organic pollutants. Microorganisms exhibit resilience to the inhibitory effects of high salinity and organic pollutants via a series of tolerance mechanisms, such as strengthening the extracellular membrane barrier, enhancing the synthesis of relevant enzymes, initiating novel biochemical reactions, improving cellular self-healing capabilities, responding to unfavorable environmental conditions by migration, and enhancing the S cycle for the microbial metabolism of organic pollutants.

Rapid Consumption of Dihydrogen Injected into a Shallow Aquifer by Ecophysiologically Different Microbes

The envisaged future dihydrogen (H2) economy requires a H2 gas grid as well as large deep underground stores. However, the consequences of an unintended spread of H2 through leaky pipes, wells, or subterranean gas migrations on groundwater resources and their ecosystems are poorly understood. Therefore, we emulated a short-term leakage incident by injecting gaseous H2 into a shallow aquifer at the TestUM test site and monitored the subsequent biogeochemical processes in the groundwater system. At elevated H2 concentrations, an increase in acetate concentrations and a decrease in microbial α-diversity with a concomitant change in microbial β-diversity were observed. Additionally, microbial H2 oxidation was indicated by temporally higher abundances of taxa known for aerobic or anaerobic H2 oxidation. After H2 concentrations diminished below the detection limit, α- and β-diversity approached baseline values. In summary, the emulated H2 leakage resulted in a temporally limited change of the groundwater microbiome and associated geochemical conditions due to the intermediate growth of H2 consumers. The results confirm the general assumption that H2, being an excellent energy and electron source for many microorganisms, is quickly microbiologically consumed in the environment after a leakage.

Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses

BACKGROUND

Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes.

METHODS

Seawater samples were collected from Labrador Sea Water (LSW, ~ 2000 m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1 µM thiosulfate, or with 1 µM thiosulfate plus 10 µM glucose and 10 µM acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1 h and 72 h of incubation.

RESULTS

Amendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.).

CONCLUSIONS

The gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean. Video Abstract.

Elemental sulfur-driven autotrophic denitrification process for effective removal of nitrate in mariculture wastewater: Performance, kinetics and microbial community

To date, there is a lack of systematic investigation on the elemental sulfur-driven autotrophic denitrification (SDAD) process for removing nitrate (NO3--N) from mariculture wastewater deficient in organic carbon sources. Therefore, a packed-bed reactor was established and continuously operated for 230 days to investigate the operation performance, kinetic characteristics and microbial community of SDAD biofilm process. Results indicate that the NO3--N removal efficiencies and rates varied with the operational conditions including HRT (1-4 h), influent concentrations of NO3--N (25-100 mg L-1) and DO (0.2-7.0 mg L-1), and temperature (10oC-30 °C), in the ranges of 51.4%-98.6% and 0.054-0.546 g L-1 d-1, respectively. Limestone could partially neutralize the produced acidity. Small portions of NO3--N were converted to nitrite (<4.5%) and ammonia (<2.8%) in the reactor. Operational conditions also influenced the production of acidity, nitrite and ammonia as well as sulfate. Shortening HRT and increasing influent NO3--N concentration turned the optimal fitting model depicting the NO3--N removal along the reactor from half-order to zero-order. Furthermore, the NO3--N removal was accelerated by a higher temperature and influent NO3--N concentration and a lower HRT and influent DO concentration. Microbial richness, evenness and diversity gradually decreased during the autotrophic denitrifier enrichment cultivation and the reactor start-up and operation. Sulfurimonas constituted the predominate genus and the primary functional bacteria in the reactor. This study highlights the SDAD as a promising way to control the coastal eutrophication associated with mariculture wastewater discharge.

Nitrogen and sulfur cycling driven by Campylobacterota in the sediment-water interface of deep-sea cold seep: a case in the South China Sea

Chemoautotrophs within Campylobacterota, especially Sulfurovum and Sulfurimonas, are abundant in the seawater-sediment interface of the Formosa cold seep in the South China Sea. However, the in situ activity and function of Campylobacterota are unknown. In this study, the geochemical role of Campylobacterota in the Formosa cold seep was investigated with multiple means. Two members of Sulfurovum and Sulfurimonas were isolated for the first time from deep-sea cold seep. These isolates are new chemoautotrophic species that can use molecular hydrogen as an energy source and CO2 as a sole carbon source. Comparative genomics identified an important hydrogen-oxidizing cluster in Sulfurovum and Sulfurimonas. Metatranscriptomic analysis detected high expression of hydrogen-oxidizing gene in the RS, suggesting that H2 was likely an energy source in the cold seep. Genomic analysis indicated that the Sulfurovum and Sulfurimonas isolates possess a truncated sulfur-oxidizing system, and metatranscriptomic analysis revealed that Sulfurovum and Sulfurimonas with this genotype were active in the surface of RS and likely contributed to thiosulfate production. Furthermore, geochemical and in situ analyses revealed sharply decreased nitrate concentration in the sediment-water interface due to microbial consumption. Consistently, the denitrification genes of Sulfurimonas and Sulfurovum were highly expressed, suggesting an important contribution of these bacteria to nitrogen cycling. Overall, this study demonstrated that Campylobacterota played a significant role in the cycling of nitrogen and sulfur in a deep-sea cold seep. IMPORTANCE Chemoautotrophs within Campylobacterota, in particular Sulfurovum and Sulfurimonas, are ubiquitous in deep-sea cold seeps and hydrothermal vents. However, to date, no Sulfurovum or Sulfurimonas has been isolated from cold seeps, and the ecological roles of these bacteria in cold seeps remain to be investigated. In this study, we obtained two isolates of Sulfurovum and Sulfurimonas from Formosa cold seep, South China Sea. Comparative genomics, metatranscriptomics, geochemical analysis, and in situ experimental study indicated collectively that Campylobacterota played a significant part in nitrogen and sulfur cycling in cold seep and was the cause of thiosulfate accumulation and sharp reduction of nitrate level in the sediment-water interface. The findings of this study promoted our understanding of the in situ function and ecological role of deep-sea Campylobacterota.

In the Alphaproteobacterium Hyphomicrobium denitrificans SoxR Serves a Sulfane Sulfur-Responsive Repressor of Sulfur Oxidation

In organisms that use reduced sulfur compounds as alternative or additional electron donors to organic compounds, transcriptional regulation of genes for enzymes involved in sulfur oxidation is needed to adjust metabolic flux to environmental conditions. However, little is known about the sensing and response to inorganic sulfur compounds such as thiosulfate in sulfur-oxidizing bacteria. In the Alphaproteobacterium Hyphomicrobium denitrificans, one strategy is the use of the ArsR-SmtB-type transcriptional regulator SoxR. We show that this homodimeric repressor senses sulfane sulfur and that it is crucial for the expression not only of sox genes encoding the components of a truncated periplasmic thiosulfate-oxidizing enzyme system but also of several other sets of genes for enzymes of sulfur oxidation. DNA binding and transcriptional regulatory activity of SoxR are controlled by polysulfide-dependent cysteine modification. The repressor uses the formation of a sulfur bridge between two conserved cysteines as a trigger to bind and release DNA and can also form a vicinal disulfide bond to orchestrate a response to oxidizing conditions. The importance of the sulfur bridge forming cysteines was confirmed by site-directed mutagenesis, mass spectrometry, and gel shift assays. In vivo, SoxR interacts directly or indirectly with a second closely related repressor, sHdrR.

A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes

Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonas from the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, ^USulfurimonas pluma, was found to be globally abundant and active in cold (<0-4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes. Compared with other Sulfurimonas species, ^US. pluma has a reduced genome (>17%) and genomic signatures of an aerobic chemolithotrophic metabolism using hydrogen as an energy source, including acquisition of A2-type oxidase and loss of nitrate and nitrite reductases. The dominance and unique niche of ^US. pluma in hydrothermal plumes suggest an unappreciated biogeochemical role for Sulfurimonas in the deep ocean.

Investigating the effects of physical properties of sulphur-based carriers on autotrophic denitrification

In this study, four sulphur-based carriers (C1-C4) which have different mass ratio of sodium silicate to carrier from 30% to 50% (C1-C3) and the existence of water (C4) were prepared in order to evaluate the effect of the different physical properties on denitrification in sulphur-based autotrophic processes. While the apparent density and the compressive strength decreased as the proportion of sodium silicate increased and water was added in the carriers, the average pore size and the porosity increased from 0.43 to 3.13 µm and from 38% to 67%, respectively. The treatment system using the carrier C4 with the highest surface area was stabilized most rapidly and achieved the highest nitrogen removal efficiency of 85.6 ± 5.0% during a relatively short HRT of 3 h. The efficiency of nitrate removal was enhanced by 36.9% due to the increase of the ratio of sodium silicate in the carriers from C1 to C3, and more 4.8% point of removal rate increased in the carrier C4 by adding water to the carrier C3. The sum of Thiobacillus and Sulfurimonas was obtained up to 65.90% among the microbial community in the carrier C4 which has the highest distribution (38.35%) of pore size above 20 µm considered to be favourable for retaining autotrophic denitrifiers. From the above results, it is obvious that the physical properties of the sulphur-based carrier and its ability of denitrification can be influenced significantly by the composition of the carrier.

Changes in the membrane lipid composition of a Sulfurimonas species depend on the electron acceptor used for sulfur oxidation

Sulfurimonas species are among the most abundant sulfur-oxidizing bacteria in the marine environment. They are capable of using different electron acceptors, this metabolic flexibility is favorable for their niche adaptation in redoxclines. When oxygen is depleted, most Sulfurimonas spp. (e.g., Sulfurimonas gotlandica) use nitrate ([Formula: see text]) as an electron acceptor to oxidize sulfur, including sulfide (HS-), S0 and thiosulfate, for energy production. Candidatus Sulfurimonas marisnigri SoZ1 and Candidatus Sulfurimonas baltica GD2, recently isolated from the redoxclines of the Black Sea and Baltic Sea respectively, have been shown to use manganese dioxide (MnO2) rather than [Formula: see text] for sulfur oxidation. The use of different electron acceptors is also dependent on differences in the electron transport chains embedded in the cellular membrane, therefore changes in the membrane, including its lipid composition, are expected but are so far unexplored. Here, we used untargeted lipidomic analysis to reveal changes in the composition of the lipidomes of three representative Sulfurimonas species grown using either [Formula: see text] and MnO2. We found that all Sulfurimonas spp. produce a series of novel phosphatidyldiazoalkyl-diacylglycerol lipids. Ca. Sulfurimonas baltica GD2 adapts its membrane lipid composition depending on the electron acceptors it utilizes for growth and survival. When carrying out MnO2-dependent sulfur oxidation, the novel phosphatidyldiazoalkyl-diacylglycerol headgroup comprises shorter alkyl moieties than when sulfur oxidation is [Formula: see text]-dependent. This is the first report of membrane lipid adaptation when an organism is grown with different electron acceptors. We suggest novel diazoalkyl lipids have the potential to be used as a biomarker for different conditions in redox-stratified systems.

Sulfurimonas marina sp. nov., an obligately chemolithoautotrophic, sulphur-oxidizing bacterium isolated from a deep-sea sediment sample from the South China Sea

A novel marine bacterium, designated strain B2T, was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were observed to be Gram-stain negative, motile and rod shaped with a single polar flagellum. B2T could grow at 10–45 °C (optimum, 35 °C), pH 4.5–9.0 (optimum, pH 7.0) and in the presence of 1.0–8.0 % (w/v) NaCl (optimum, 3.0%). The isolate grew chemolithoautotrophically with sulphide, elemental sulphur and thiosulphate as electron donors, carbon dioxide as the sole carbon source, and molecular oxygen as the sole electron acceptor. Molecular hydrogen did not support growth. The predominant fatty acids of B2T were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that B2T represented a member of the genus Sulfurimonas , with the highest similarity to the 16S rRNA gene sequences of Sulfurimonas indica NW8NT (95.9 %), Sulfurimonas crateris SN118T (95.7 %), Sulfurimonas xiamenensis 1-1NT (95.6 %) and Sulfurimonas paralvinellae GO25T (95.4 %). Sequence similarities to other members of the genus Sulfurimonas were less than 95.0 %. In addition, the average nucleotide identity (ANI) value and digital DNA–DNA hybridization (dDDH) estimate between B2T and S. indica NW8NT were 73.0 and 23.7 %, respectively. The size of the complete genome of B2T is 22 61 034 bp, with a DNA G+C content of 36.0 mol %. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain B2T represent a novel species of the genus Sulfurimonas , for which the name Sulfurimonas marina sp. nov. is proposed, with the type strain B2T (=MCCC 1A14515T=KCTC 15852T).

Impact of sulfamethoxazole and organic supplementation on mixotrophic denitrification process: Nitrate removal efficiency and the response of functional microbiota

Recirculating aquaculture systems (RAS) effluent is characterized by low COD to total inorganic nitrogen ratio (C/N), excessive nitrate, and the presence of traces of antibiotics. Hence, it urgently needs to be treated before recycling or discharging. In this study, four denitrification bioreactors at increasing C/N ratios (0, 0.7, 2, and 5) were started up to treat mariculture wastewater under the sulfamethoxazole (SMX) stress, during which the bioreactors performance and the shift of mixotrophic microbial communities were explored. The result showed that during the SMX exposure, organic supplementation enhanced nitrate and thiosulfate removal, and eliminated nitrite accumulation. The denitrification rate was accelerated by increasing C/N from 0 to 2, while it declined at C/N of 5. The decline was ascribed to which SMX reduced the relative abundance of denitrifiers, but improved the capability of dissimilatory nitrogen reduction to ammonia (DNRA) and sulfide production. The direct evidence was the relative abundance of sulfidogenic populations, such as Desulfuromusa, Desulfurocapsa, and Desulfobacter increased under the SMX stress. Moreover, high SMX (1.5 mg L^-1) caused the obvious accumulation of ammonia at C/N of 5 due to the high concentration of sulfide (3.54 ± 1.08 mM) and the enhanced DNRA process. This study concluded that the mixotrophic denitrification process with the C/N of 0.7 presented the best performance in nitrate and sulfur removal and indicated the maximum resistance to SMX.

Coupling sulfur-based denitrification with anammox for effective and stable nitrogen removal: A review

Anoxic ammonium oxidation (anammox) is an energy-efficient nitrogen removal process for wastewater treatment. However, the unstable nitrite supply and residual nitrate in the anammox process have limited its wide application. Recent studies have proven coupling of sulfur-based denitrification with anammox (SDA) can achieve an effective nitrogen removal, owing to stable provision of substrate nitrite from the sulfur-based denitrification, thus making its process control more efficient in comparison with that of partial nitrification and anammox process. Meanwhile, the anammox-produced nitrate can be eliminated through sulfur-based denitrification, thereby enhancing SDA's overall nitrogen removal efficiency. Nonetheless, this process is governed by a complex microbial system that involves both complicated sulfur and nitrogen metabolisms as well as multiple interactions among sulfur-oxidising bacteria and anammox bacteria. A comprehensive understanding of the principles of the SDA process is the key to facilitating the development and application of this novel process. Hence, this review is conducted to systematically summarise various findings on the SDA process, including its associated biochemistry, biokinetic reactions, reactor performance, and application. The dominant functional bacteria and microbial interactions in the SDA process are further discussed. Finally, the advantages, challenges, and future research perspectives of SDA are outlined. Overall, this work gives an in-depth insight into the coupling mechanism of SDA and its potential application in biological nitrogen removal.

Sulfurimonas aquatica sp. nov., a sulfur-oxidizing bacterium isolated from water of a brackish lake

A novel chemolithoautotrophic bacterium, strain H1576^T, was isolated from water of a brackish lake. Strain H1576^T grew aerobically on inorganic sulfur compounds. Hydrogen gas did not support autotrophic growth, and heterotrophic growth was not observed. Cells were rod shaped, motile, 1.5-2.7 μm in length and 0.6-0.7 μm in width. Growth was observed at 3-22 °C with an optimum growth temperature of 13-15 °C. The pH range for growth was 6.0-7.4 with an optimum pH of 6.6-6.8. Major fatty acids were summed feature 3 (C_{16: 1}ω7c and/or C_{16: 1}ω6c). The complete genome of strain H1576^T consists of a circular chromosome and a plasmid, with total length of 2.8 Mbp and G+C content of 46.4 mol%. Phylogenetic analyses indicated that strain H1576^T belongs to the genus Sulfurimonas but distinct from representatives of existing species. On the basis of genomic and phenotypic characteristics, a new species named Sulfurimonas aquatica sp. nov. is proposed with the type strain of strain H1576^T (= BCRC 81254^T = JCM 35004^T).

Advances in elemental sulfur-driven bioprocesses for wastewater treatment: From metabolic study to application

Elemental sulfur (S0) is known to be an abundant, non-toxic material with a wide range of redox states (-2 to +6) and may serve as an excellent electron carrier in wastewater treatment. In turn, S0-driven bioprocesses, which employ S0 as electron donor or acceptor, have recently established themselves as cost-effective therefore attractive solutions for wastewater treatment. Numerous related processes have, to date, been developed from laboratory experiments into full-scale applications, including S0-driven autotrophic denitrification for nitrate removal and S0-reducing organic removal. Compared to the conventional activated sludge process, these bioprocesses require only a small amount of organic matter and produce very little sludge. There have been great efforts to characterize chemical and biogenic S0 and related functional microorganisms in order to identify the biochemical pathways, upgrade the bioprocesses, and assess the impact of the operating factors on process performance, ultimately aiming to better understand and to optimize the processes. This paper is therefore a comprehensive overview of emerging S0-driven biotechnologies, including the development of S0-driven autotrophic denitrification and S0-based sulfidogenesis, as well as the associated microbiology and biochemistry. Also reviewed here are the physicochemical characteristics of S0 and the effects that environmental factors such as pH, influent sulfur/nitrate ratio, temperature, S0 particle size and reactor configurations have on the process. Research gaps, challenges of process applications and potential areas for future research are further proposed and discussed.

Study on the Bacterial Communities of the Biofilms on Titanium, Aluminum, and Copper Alloys at 5,772 m Undersea in Yap Trench

Biofilms formed on metal surfaces strongly affect metallic instruments serving in marine environments. However, due to sampling difficulty, less has been known about the bacterial communities of the biofilm on metallic surfaces in hadal environments, so the failure process of these deep-sea metallic instruments influenced by microbial communities could be hardly predicted. In this research, seven alloys, including titanium, aluminum, and copper alloys, were exposed in Yap Trench hadal environment for 1 year. Thus, the communities of the biofilms formed on metallic surfaces at 5,772 m undersea in Yap Trench were initially reported in previous studies. Then, 16S rRNA gene sequencing was performed to visualize the in situ bacterial communities of the biofilms formed on titanium, aluminum, and copper alloys at 5,772 m undersea in Yap Trench. It was found that Proteobacteria was the dominant phylum in all samples, but distinct genera were discovered on various alloys. The titanium alloy provided a suitable substrate for a mutualistic symbiotic biofilm with abundant bacterial richness. Aluminum alloys without copper components showed the least bacterial richness and formed a cold-adapted and oligotrophic-adapted biofilm containing the genera Sulfurimonas and PS1 Clade, while copper-present alloys showed relatively high bacterial richness with copper-resistant or even copper-utilizing biofilms constituting the genera Stenotrophomonas, Burkholderia-Caballeronia-Paraburkholderia, and Achromobacter on the surfaces. Furthermore, among all the element components contained in alloys investigated in this research, copper element showed the strongest influences on the composition and function of microbial communities in the biofilms formed on various metallic surfaces.

The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters

Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.

Sulfurimonas sediminis sp. nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal vent at the Longqi system, southwestern Indian ocean

A novel marine hydrogen- and sulfur-oxidizing bacterium, designated strain S2-6 ^T, was isolated from the deep-sea sediment samples at the Longqi hydrothermal system, southwestern Indian Ocean. Cells were Gram-stain-negative, motile, short rods with a single polar flagellum. Growth was observed at 10-45 °C (optimum 33 °C), pH 5.0-8.0 (optimum pH 7.0) and 1.5 to 6.0% (w/v) NaCl with an optimum at 3.0% (w/v). The isolate was an obligate chemolithoautotroph capable of growth using thiosulfate, tetrathionate, elemental sulfur or sodium sulfide as the energy source, and oxygen or nitrate as the sole electron acceptor. When hydrogen was used as the energy source, strain S2-6 ^T could respire oxygen, nitrate or element sulfur. The major cellular fatty acids of strain S2-6 ^T were summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), C_16:0 and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). The total size of its genome was 2,320,257 bp and the genomic DNA G + C content was 37.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and core genes showed that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas paralvinellae GO25^T (96.8% sequence identity) and Sulfurimonas autotrophica OK10^T (95.8% sequence identity). The average nucleotide identity and DNA-DNA hybridization values between strain S2-6 ^T and S. paralvinellae GO25^T and S. autotrophica OK10^T were 74.6%-81.2% and 19.1%-24.6%, respectively. Based on the polyphase taxonomical data, strain S2-6 ^T represents a novel species of the genus Sulfurimonas, for which the name Sulfurimonas sediminis sp. nov. is proposed, with the type strain S2-6 ^T (= MCCC 1A14513^T = KCTC 15854 ^T).

Characterization of Sulfurimonas hydrogeniphila sp. nov., a Novel Bacterium Predominant in Deep-Sea Hydrothermal Vents and Comparative Genomic Analyses of the Genus Sulfurimonas

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.

Sulfurimonas indica sp. nov., a hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal sulfide chimney in the Northwest Indian Ocean

A novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, designated strain NW8N^T, was collected from a sulfide chimney at the deep-sea hydrothermal vent on the Carlsberg Ridge of the Northwest Indian Ocean. The cells were Gram-stain-negative, motile, short rods with a single polar flagellum. The temperature, pH and salinity ranges for growth of strain NW8N^T were 4-40 °C (optimum, 33 °C), pH 4.5-7.5 (optimum, pH 5.5) and 340-680 mM NaCl (optimum, 510 mM). The isolate was an obligate chemolithoautotroph capable of growth using hydrogen, thiosulfate, sulfide or elemental sulphur as the sole energy source, carbon dioxide as the sole carbon source and molecular oxygen as the sole electron acceptor. The major cellular fatty acids of strain NW8N^T were summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_16 : 0 and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). The total size of its genome was 2 093 492 bp and the genomic DNA G+C content was 36.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and core genes showed that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas paralvinellae GO25^T (97.4 % sequence identity). The average nucleotide identity and DNA-DNAhybridization values between strain NW8N^T and S. paralvinellae GO25^T was 77.8 and 21.1 %, respectively. Based on the phylogenetic, genomic and phenotypic data presented here, strain NW8N^T represents a novel species of the genus Sulfurimonas, for which the name Sulfurimonas indica sp. nov. is proposed, with the type strain NW8N^T (=MCCC 1A13988^T=KTCC 15780^T).

Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov., thiotrophic manganese oxide reducing chemolithoautotrophs of the class Campylobacteria isolated from the pelagic redoxclines of the Black Sea and the Baltic Sea

Species of the genus Sulfurimonas are reported and isolated from terrestrial habitats and marine sediments and water columns with steep redox gradients. Here we report on the isolation of strains SoZ1 and GD2 from the pelagic redoxcline of the Black Sea and the Baltic Sea, respectively. Both strains are gram-stain-negative and appear as short and slightly curved motile rods. The autecological preferences for growth of strain SoZ1 were 0-25°C (optimum 20°C), pH 6.5-9.0 (optimum pH 7.5-8.0) and salinity 10-40gL^-1 (optimum 25gL^-1). Preferences for growth of strain GD2 were 0-20°C (optimum 15°C), pH 7.0-8.0 (optimum pH 7.0-7.5) and salinity 5-40gL^-1 (optimum 21gL^-1). Strain SoZ1 grew chemolithoautotrophically, while strain GD2 also showed heterotrophic growth with short chained fatty acids as carbon source. Both species utilized hydrogen (H₂), sulfide (H₂S here taken as the sum of H₂S, HS^- and S^2-), elemental sulfur (S⁰) and thiosulfate (S₂O₃^2-) as electron donors and nitrate (NO₃^-), oxygen (O₂) and particulate manganese oxide (MnO₂) as electron acceptors. Based on 16S rRNA gene sequence similarity, both strains cluster within the genus Sulfurimonas with Sulfurimonas gotlandica GD1^T as the closest cultured relative species with a sequence similarity of 96.74% and 96.41% for strain SoZ1 and strain GD2, respectively. Strains SoZ1 and GD2 share a ribosomal 16S sequence similarity of 99.27% and were demarcated based on average nucleotide identity and average amino acid identity of the whole genome sequence. These calculations have been applied to the whole genus. We propose the names Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov. for the thiotrophic manganese reducing culture isolates from the Black Sea and Baltic Sea, respectively.

The oxidation of hydrocarbons by diverse heterotrophic and mixotrophic bacteria that inhabit deep-sea hydrothermal ecosystems

Hydrothermal activity can generate numerous and diverse hydrocarbon compounds. However, little is known about the influence of such hydrocarbons on deep-sea hydrothermal microbial ecology. We hypothesize that certain bacteria live on these hydrocarbons. Therefore, in this study, the distribution of hydrocarbons and their associated hydrocarbon-degrading bacteria were investigated at deep-sea hydrothermal vents at the Southern Mid-Atlantic Ridge, the Southwest Indian Ridge, and the East Pacific Rise. A variety of hydrocarbon-degrading consortia were obtained from hydrothermal samples collected at the aforementioned sites after low-temperature enrichment under high hydrostatic pressures, and the bacteria responsible for the degradation of hydrocarbons were investigated by DNA-based stable-isotope probing with uniformly ¹³C-labeled hydrocarbons. Unusually, we identified several previously recognized sulfur-oxidizing chemoautotrophs as hydrocarbon-degrading bacteria, e.g., the SAR324 group, the SUP05 clade, and Sulfurimonas, and for the first time confirmed their ability to degrade hydrocarbons. In addition, Erythrobacter, Pusillimonas, and SAR202 clade were shown to degrade polycyclic aromatic hydrocarbons for the first time. These results together with relatively high abundance in situ of most of the above-described bacteria highlight the potential influence of hydrocarbons in configuring the vent microbial community, and have made the importance of mixotrophs in hydrothermal vent ecosystems evident.

Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov., hydrogen- and sulfur-oxidizing chemolithoautotrophs within the Epsilonproteobacteria isolated from coastal sediments, and an emended description of the genus Sulfurimonas

Strains 1-1NT and GYSZ_1T were isolated from marine sediments collected from the coast of Xiamen, PR China. Cells of the two strains were Gram-stain-negative, rod-shaped or slightly curved. Strain 1-1NT was non-motile, whereas strain GYSZ_1T was motile by means of one polar flagellum. The temperature, pH and salinity concentration ranges for growth of 1-1NT were 10–45 °C (optimum 30 °C), pH 5.5–8.0 (optimum 7.0) and 0–90 g l−1 NaCl (optimum 50 g l−1), while the growth of GYSZ_1T occurred at 4–45 °C (optimum 33 °C), pH 5.0–8.5 (optimum 6.5) and 5–90 g l−1 NaCl (optimum 20 g l−1). The two novel isolates were obligate chemolithoautotrophs capable of growth using hydrogen, thiosulfate, sulfide or elemental sulfur as the sole energy source, and nitrate, elemental sulfur or molecular oxygen as an electron acceptor. The major fatty acids of 1-1NT were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C18 : 0, while the predominant fatty acids of strain GYSZ_1T were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C14 : 0 3-OH. The DNA G+C contents of 1-1NT and GYSZ_1T were 34.5 mol% and 33.2 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 1-1NT and GYSZ_1T represented members of the genus Sulfurimonas , with the highest sequence similarities to Sulfurimonas crateris SN118T (97.4 %) and Sulfurimonas denitrificans DSM 1251T (94.7 %), respectively. However, 1-1NT and GYSZ_1T shared 95.5 % similarity of 16S rRNA gene sequences, representing different species of the genus Sulfurimonas . On the basis of the physiological properties and the results of phylogenetic analyses, including average nucleotide identity and in silico DNA–DNA hybridization values, strains 1-1NT and GYSZ_1T represent two novel species within the genus Sulfurimonas , for which the names Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov. are proposed, with the type strains 1-1NT (=MCCC 1A14514T=KCTC 15851T) and GYSZ_1T (=MCCC 1A14739T=KCTC 15853T), respectively. Our results also justify an emended description of the genus Sulfurimonas .

Sulfurimonas crateris sp. nov., a facultative anaerobic sulfur-oxidizing chemolithoautotrophic bacterium isolated from a terrestrial mud volcano

A novel mesophilic facultative anaerobic bacterium, strain SN118^T, was isolated from a terrestrial mud volcano in Taman Peninsula, Russia. The cells were Gram-negative, motile, short, straight or curved rods with a single polar flagellum. Growth was observed at 5-40 °C (optimum, 30 °C) and pH 5.5-9.5 (optimum, pH 8.0). Growth of strain SN118^T was observed in NaCl concentrations ranging from 0.5 to 8.0 % (w/v) with an optimum at 2.0-3.0 % (w/v). The isolate grew chemolithoautotrophically with sulfide, elemental sulfur or thiosulfate as electron donor, oxygen, nitrate or nitrite as an electron acceptor and CO₂/HCO₃ ^- as a carbon source. Molecular hydrogen or organic substances did not support growth. Nitrate was reduced to N₂. The dominant fatty acids were C_16 : 1ω7c, C_16 : 0 and C_{18  :  1}ω7c. The total size of the genome of the novel isolate was 2 209 279 bp and the genomic DNA G+C content was 38.8 mol%. Results of 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 denitrificans DSM 1251^T (96.74 %). Based on its physiological properties and results from phylogenetic analyses, including average nucleotide identity and in silico DNA-DNA hybridization values, the isolate is considered to represent a novel species of the genus Sulfurimonas, for which the name Sulfurimonas crateris sp. nov. is proposed. The type strain is SN118^T (=DSM 109248^T=VKM B-3378^T).

Changes in Bacterial Communities in Seawater-Flooded Soil in the Four Years After the 2011 Tohoku Tsunami in Japan

The 2011 Tohoku tsunami had a serious impact, such as an increase in harmful substances and salinity over a large area. Herein, we evaluated transitions in bacterial communities in agricultural fields in the four years after the 2011 Tohoku tsunami. Bacterial communities were compared across four different types of soil—unflooded field (UF) soil, soil flooded for a short term (ST), soil flooded for the long term (LT), soil flooded long term and cultivated fields (LTC), and marine environmental materials (bay sediment, sea sand and sea water), using a polymerase chain reaction (PCR) and pyrosequencing of 16S ribosomal RNA genes. In the soil bacterial communities that were flooded by the 2011 Tohoku tsunami, these effects were not seen after 2013. Although the difference in bacterial communities between LT and UF became smaller during the four years, the bacterial communities in LT were different from those in UF in several ways, such as a higher tendency frequency of sulfur-oxidizing bacteria (SOB) and the presence of halotolerant SOB. Therefore, it is thought that the Tohoku tsunami affected the microbial communities in the soil for more than four years. Especially genus Halothiobacillus, which is Halotolerant SOB in flooded soils, was detected neither in unflooded soil nor in the marine environment. Therefore, it is thought that inundation by a tsunami produces a unique environment with bacterial communities to form in soil. Further, SOB structure, especially halotolerant, might serve as a good indicators of the impacts of inundation on bacterial communities in agricultural fields over the long term.

Microbial Ecology of Biofiltration Units Used for the Desulfurization of Biogas

Bacterial communities’ composition, activity and robustness determines the effectiveness of biofiltration units for the desulfurization of biogas. It is therefore important to get a better understanding of the bacterial communities that coexist in biofiltration units under different operational conditions for the removal of H2S, the main reduced sulfur compound to eliminate in biogas. This review presents the main characteristics of sulfur-oxidizing chemotrophic bacteria that are the base of the biological transformation of H2S to innocuous products in biofilters. A survey of the existing biofiltration technologies in relation to H2S elimination is then presented followed by a review of the microbial ecology studies performed to date on biotrickling filter units for the treatment of H2S in biogas under aerobic and anoxic conditions.

A bacterial isolate from the Black Sea oxidizes sulfide with manganese(IV) oxide

Mn is one of the most abundant redox-sensitive metals on earth. Some microorganisms are known to use Mn(IV) oxide (MnO₂) as electron acceptor for the oxidation of organic compounds or hydrogen (H₂), but so far the use of sulfide (H₂S) has been suggested but not proven. Here we report on a bacterial isolate which grows autotrophically and couples the reduction of MnO₂ to the oxidation of H₂S or thiosulfate (S₂O₃²⁻) for energy generation. The isolate, originating from the Black Sea, is a species within the genus Sulfurimonas, which typically occurs with high cell numbers in the vicinity of sulfidic environments [Y. Han, M. Perner, Front. Microbiol. 6, 989 (2015)]. H₂S and S₂O₃²⁻ are oxidized completely to sulfate (SO₄²⁻) without the accumulation of intermediates. In the culture, Mn(IV) reduction proceeds via Mn(III) and finally precipitation of Ca-rich Mn(II) carbonate [Mn(Ca)CO₃]. In contrast to Mn-reducing bacteria, which use organic electron donors or H₂, Fe oxides are not observed to support growth, which may either indicate an incomplete gene set or a different pathway for extracellular electron transfer.

Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure

Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO₂^- + NO₃^- in the sediment surface (0-1 cm) and iron in the underlying layer (1-2 cm). In addition, an increase in NO₂^- + NO₃^- was observed in the overlying benthic water in all amended and control incubations. The combination of NO₂^- + NO₃^- diffusion plus nitrification could not account for this increase. Based on 16S rRNA gene sequences, the addition of cyanobacterial biomass during autumn caused a large increase in ferrous iron-oxidizing archaea while diatom biomass amendment during spring caused minor changes in the microbial community. Considering that OTUs sharing lineages with acidophilic microorganisms had a high relative abundance during autumn, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling and early microbial community changes in the sediment due to sinking phytoplankton before potential hypoxia occurs.

Effect of large magnetotactic bacteria with polyphosphate inclusions on the phosphate profile of the suboxic zone in the Black Sea

The Black Sea is the world's largest anoxic basin and a model system for studying processes across redox gradients. In between the oxic surface and the deeper sulfidic waters there is an unusually broad layer of 10-40 m, where neither oxygen nor sulfide are detectable. In this suboxic zone, dissolved phosphate profiles display a pronounced minimum at the upper and a maximum at the lower boundary, with a peak of particulate phosphorus in between, which was suggested to be caused by the sorption of phosphate on sinking particles of metal oxides. Here we show that bacterial polyphosphate inclusions within large magnetotactic bacteria related to the genus Magnetococcus contribute substantially to the observed phosphorus peak, as they contain 26-34% phosphorus compared to only 1-5% in metal-rich particles. Furthermore, we found increased gene expression for polyphosphate kinases by several groups of bacteria including Magnetococcaceae at the phosphate maximum, indicating active bacterial polyphosphate degradation. We propose that large magnetotactic bacteria shuttle up and down within the suboxic zone, scavenging phosphate at the upper and releasing it at the lower boundary. In contrast to a passive transport via metal oxides, this bacterial transport can quantitatively explain the observed phosphate profiles.

Thermoplasmatales and sulfur-oxidizing bacteria dominate the microbial community at the surface water of a CO2-rich hydrothermal spring located in Tenorio Volcano National Park, Costa Rica

Here we report the chemical and microbial characterization of the surface water of a CO₂-rich hydrothermal vent known in Costa Rica as Borbollones, located at Tenorio Volcano National Park. The Borbollones showed a temperature surrounding 60 °C, a pH of 2.4 and the gas released has a composition of ~ 97% CO₂, ~ 0.07% H₂S, ~ 2.3% N₂ and ~ 0.12% CH₄. Other chemical species such as sulfate and iron were found at high levels with respect to typical fresh water bodies. Analysis by 16S rRNA gene metabarcoding revealed that in Borbollones predominates an archaeon from the order Thermoplasmatales and one bacterium from the genus Sulfurimonas. Other sulfur- (genera Thiomonas, Acidithiobacillus, Sulfuriferula, and Sulfuricurvum) and iron-oxidizing bacteria (genera Sideroxydans, Gallionella, and Ferrovum) were identified. Our results show that CO₂-influenced surface water of Borbollones contains microorganisms that are usually found in acid rock drainage environments or sulfur-rich hydrothermal vents. To our knowledge, this is the first microbiological characterization of a CO₂-dominated hydrothermal spring from Central America and expands our understanding of those extreme ecosystems.

Ecological Succession of Sulfur-Oxidizing Epsilon- and Gammaproteobacteria During Colonization of a Shallow-Water Gas Vent

In this study, we integrated geochemical measurements, microbial diversity surveys and physiological characterization of laboratory strains to investigate substrate-attached filamentous microbial biofilms at Tor Caldara, a shallow-water gas vent in the Tyrrhenian Sea. At this site, the venting gases are mainly composed of CO₂ and H₂S and the temperature at the emissions is the same as that of the surrounding water. To investigate the composition of the total and active fraction of the Tor Caldara biofilm communities, we collected established and newly formed filaments and we sequenced the 16S rRNA genes (DNA) and the 16S rRNA transcripts (cDNA). Chemoautotrophic sulfur-oxidizing members of the Gammaproteobacteria (predominantly Thiotrichales) dominate the active fraction of the established microbial filaments, while Epsilonproteobacteria (predominantly Sulfurovum spp.) are more prevalent in the young filaments. This indicates a succession of the two communities, possibly in response to age, sulfide and oxygen concentrations. Growth experiments with representative laboratory strains in sulfide gradient medium revealed that Sulfurovum riftiae (Epsilonproteobacteria) grew closer to the sulfide source than Thiomicrospira sp. (Gammaproteobacteria, Thiotrichales). Overall, our findings show that sulfur-oxidizing Epsilonproteobacteria are the dominant pioneer colonizers of the Tor Caldara biofilm communities and that Gammaproteobacteria become prevalent once the community is established. This succession pattern appears to be driven - among other factors - by the adaptation of Epsilon- and Gammaproteobacteria to different sulfide concentrations.

The influence of phosphorus on the autotrophic and mixotrophic denitrification

Autotrophic and mixotrophic denitrification, two approaches of biological denitrification, have drawn more and more attention among the techniques to remove nitrogen from the aquatic environment. This study investigated the influence of phosphorus on the denitrification performance and bacterial community structure in the autotrophic and mixotrophic denitrification reactors. The activity test was applied to evaluate the variation of denitrification activity of autotrophic and mixotrophic sludge before and after phosphorus addition. High-throughput sequencing was used to analyze the change of bacterial community structure. The results showed that NO₃^--N removal efficiency of autotrophic and mixotrophic denitrification process increased by 40 and 35%, respectively, after phosphorus addition. The sludge denitrification activity of autotrophic and mixotrophic sludge was enhanced significantly. And phosphorus addition could greatly improve the proportion of denitrifying bacteria in both autotrophic (from 11.83 to 64.31%) and mixotrophic denitrifying sludge (from 13.59 to 45.12%). Overall, phosphorus addition could greatly improve the autotrophic and mixotrophic denitrification ability in the phosphorus deficient surface water.

Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan

Nitrous oxide (N₂O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N₂O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N₂O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N₂O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N₂O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N₂O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N₂O only. Collectively, these results suggest that the N₂O-reducing microbiome in eelgrass meadows is largely responsible for coastal N₂O mitigation.

Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland

Crystalline bedrock has been chosen for deep geologic long-term storage of used nuclear fuel in Finland. The risks generated by the deep subsurface microbial communities in these disposal sites need to be well characterised in advance to ensure safety. Deep subsurface microbial communities in a steady state are unlikely to contribute to known risk factors, such as corrosion or gas production. However, the construction of the geological final-disposal facility, bedrock disturbances, and hydraulic gradients cause changes that affect the microbial steady-state. To study the induced metabolism of deep microbial communities in changing environmental conditions, the activating effect of different electron donors and acceptors were measured with redox sensing fluorescent dyes (5-Cyano-2,3-ditolyl tetrazolium chloride, CTC and RedoxSensor™ Green, RSG). Fluids originating from two different fracture zones of the Finnish disposal site in Olkiluoto were studied. These fracture fluids were very dissimilar both chemically and in terms of bacterial and archaeal diversity. However, the microbial communities of both fracture fluids were activated, especially with acetate, which indicates the important role of acetate as a preferred electron donor for Olkiluoto deep subsurface communities.

Decoupling between sulfate reduction and the anaerobic oxidation of methane in the shallow methane seep of the Black sea

Methane seepages are widespread in the Black Sea. However, microbiological research has been carried out only at the continental shelf seeps. The present work dealt with coastal gas seepages of the Kalamit Bay (Black Sea). High-throughput 16S rRNA gene sequencing and radiotracer analysis (14С and 35S) were used to determine the composition of the microbial community and the rates of microbial sulfate reduction and methane oxidation. The phylum Proteobacteria, represented mainly by sulfate reducers of the class Deltaproteobacteria, was the predominant in sequence dataset. Bacteroidetes and Planctomycetes were other numerous phyla. Among archaea, the phylum Woesearchaeota and Marine Benthic Group B were predominant in the upper horizons. Relative abundance of Euryarchaeota of the families Methanomicrobiaceae and Methanosarcinaceae (including ANME-3 archaea) increased in deeper sediment layers. Sulfate reduction rate (up to 2.9 mmol/L × day) was considerably higher than the rate of anaerobic methane oxidation (up to 43.4 μmol/L × day), which indicated insignificant contribution of anaerobic methane oxidation to the total sulfide production.

Sulfurimonas subgroup GD17 cells accumulate polyphosphate under fluctuating redox conditions in the Baltic Sea: possible implications for their ecology

The central Baltic Sea is characterized by a pelagic redox zone exhibiting high dark CO₂ fixation rates below the chemocline. These rates are mainly driven by chemolithoautotrophic and denitrifying Sulfurimonas GD17 subgroup cells which are motile and fast-reacting r-strategists. Baltic Sea redox zones are unstable and a measurable overlap of nitrate and reduced sulfur, essential for chemosynthesis, is often only available on small scales and short times due to local mixing events. This raises the question of how GD17 cells gain access to electron donors or acceptors over longer term periods and under substrate deficiency. One possible answer is that GD17 cells store high-energy-containing polyphosphate during favorable nutrient conditions to survive periods of nutrient starvation. We used scanning electron microscopy with energy-dispersive X-ray spectroscopy to investigate potential substrate enrichments in single GD17 cells collected from Baltic Sea redox zones. More specific substrate enrichment features were identified in experiments using Sulfurimonas gotlandica GD1^T, a GD17 representative. Sulfurimonas cells accumulated polyphosphate both in situ and in vitro. Combined genome and culture-dependent analyses suggest that polyphosphate serves as an energy reservoir to maintain cellular integrity at unfavorable substrate conditions. This redox-independent energy supply would be a precondition for sustaining the r-strategy lifestyle of GD17 and may represent a newly identified survival strategy for chemolithoautotrophic prokaryotes occupying eutrophic redox zones.

Broad Phylogenetic Diversity Associated with Nitrogen Loss through Sulfur Oxidation in a Large Public Marine Aquarium

Denitrification by sulfur-oxidizing bacteria is an effective nitrate removal strategy in engineered aquatic systems. However, the community taxonomic and metabolic diversity of sulfur-driven denitrification (SDN) systems, as well as the relationship between nitrate removal and SDN community structure, remains underexplored. This is particularly true for SDN reactors applied to marine aquaria, despite the increasing use of this technology to supplement filtration. We applied 16S rRNA gene, metagenomic, and metatranscriptomic analyses to explore the microbial basis of SDN reactors operating on Georgia Aquarium's Ocean Voyager, the largest indoor closed-system seawater exhibit in the United States. The exhibit's two SDN systems vary in water retention time and nitrate removal efficiency. The systems also support significantly different microbial communities. These communities contain canonical SDN bacteria, including a strain related to Thiobacillus thioparus that dominates the system with the higher water retention time and nitrate removal but is effectively absent from the other system. Both systems contain a wide diversity of other microbes whose metagenome-assembled genomes contain genes of SDN metabolism. These include hundreds of strains of the epsilonproteobacterium Sulfurimonas, as well as gammaproteobacterial sulfur oxidizers of the Thiotrichales and Chromatiales, and a relative of Sedimenticola thiotaurini with complete denitrification potential. The SDN genes are transcribed and the taxonomic richness of the transcript pool varies markedly among the enzymatic steps, with some steps dominated by transcripts from noncanonical SDN taxa. These results indicate complex and variable SDN communities that may involve chemical dependencies among taxa as well as the potential for altering community structure to optimize nitrate removal.IMPORTANCE Engineered aquatic systems such as aquaria and aquaculture facilities have large societal value. Ensuring the health of animals in these systems requires understanding how microorganisms contribute to chemical cycling and waste removal. Focusing on the largest seawater aquarium in the United States, we explore the microbial communities in specialized reactors designed to remove excess nitrogen through the metabolic activity of sulfur-consuming microbes. We show that the diversity of microbes in these reactors is both high and highly variable, with distinct community types associated with significant differences in nitrogen removal rate. We also show that the genes encoding the metabolic steps of nitrogen removal are distributed broadly throughout community members, suggesting that the chemical transformations in this system are likely a result of microbes relying on other microbes. These results provide a framework for future studies exploring the contributions of different community members, both in waste removal and in structuring microbial biodiversity.

Microbial community structure in deep natural gas-bearing aquifers subjected to sulfate-containing fluid injection

In the natural gas field located in central Japan, high concentrations of natural gases and iodide ions are dissolved in formation water and commercially produced in deep aquifers. In the iodine recovery process, the produced formation water is amended with sulfate, and this fluid is injected into gas-bearing aquifers, which may lead to infrastructure corrosion by hydrogen sulfide. In this study, we examined the microbial community in aquifers subjected to sulfate-containing fluid injection. Formation water samples were collected from production wells located at different distances from the injection wells. The chemical analysis showed that the injection fluid contained oxygen, nitrate, nitrite and sulfate, in contrast to the formation water, which had previously been shown to be depleted in these components. Sulfur isotopic analysis indicated that sulfate derived from the injection fluid was present in the sample collected from near the injection wells. Quantitative and sequencing analysis of dissimilatory sulfite reductase and 16S rRNA genes revealed that sulfate-reducing bacteria (SRB), sulfur-oxidizing bacteria, and anaerobic methanotrophic archaea (ANME) in the wells located near injection wells were more abundant than those in wells located far from the injection wells, suggesting that fluid injection stimulated these microorganisms through the addition of oxygen, nitrate, nitrite and sulfate to the methane-rich aquifers. The predominant taxa were assigned to the ANME-2 group, its sulfate-reducing partner SEEP-SRB1 cluster and sulfur-oxidizing Epsilonproteobacteria. These results provide important insights for future studies to support the development of natural gas and iodine resources in Japan.

Success of chemolithoautotrophic SUP05 and Sulfurimonas GD17 cells in pelagic Baltic Sea redox zones is facilitated by their lifestyles as K- and r-strategists

Chemolithoautotrophic sulfur-oxidizing and denitrifying Gamma- (particularly the SUP05 cluster) and Epsilonproteobacteria (predominantly Sulfurimonas subgroup GD17) are assumed to compete for substrates (electron donors and acceptors) in marine pelagic redox gradients. To elucidate their ecological niche separation we performed ³⁴ S⁰ , ¹⁵ NO3- and H¹³ CO3- stable-isotope incubations with water samples from Baltic Sea suboxic, chemocline and sulfidic zones followed by combined phylogenetic staining and high-resolution secondary ion mass spectrometry of single cells. SUP05 cells were small-sized (0.06-0.09 µm³ ) and most abundant in low-sulfidic to suboxic zones, whereas Sulfurimonas GD17 cells were significantly larger (0.26-0.61 µm³ ) and most abundant at the chemocline and below. Together, SUP05 and GD17 cells accumulated up to 48% of the labelled substrates but calculation of cell volume-specific rates revealed that GD17 cells incorporated labelled substrates significantly faster throughout the redox zone, thereby potentially outcompeting SUP05 especially at high substrate concentrations. Thus, in synopsis with earlier described features of SUP05/GD17 we conclude that their spatially overlapping association in stratified sulfidic zones is facilitated by their different lifestyles: whereas SUP05 cells are streamlined, non-motile K-strategists adapted to low substrate concentrations, GD17 cells are motile r-strategists well adapted to fluctuating substrate and redox conditions.

Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment

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 (H₂S, S⁰, and S₂O₃^2-) and electron acceptors (O₂ and NO₃^-) 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.

Role of Flagella in the Pathogenesis of Helicobacter pylori

This review aimed to investigate the role of Helicobacter pylori flagella on the pathogenicity of this bacterium in humans. Helicobacter pylori is a flagellated pathogen that colonizes the human gastroduodenal mucosa and produces inflammation, and is responsible for gastrointestinal disease. Its pathogenesis is attributed to colonization and virulence factors. The primary function of H. pylori flagella is to provide motility. We believe that H. pylori flagella play an important role in the colonization of the gastrointestinal mucosa. Therefore, we reviewed previous studies on flagellar morphology and motility in order to explore the relationship between H. pylori flagella and pathogenicity. Further investigation is required to confirm the association between flagella and pathogenicity in H. pylori.

Capturing Compositional Variation in Denitrifying Communities: a Multiple-Primer Approach That Includes Epsilonproteobacteria

Denitrifying Epsilonproteobacteria may dominate nitrogen loss processes in marine habitats with intense redox gradients, but assessment of their importance is limited by the currently available primers for nitrite reductase genes. Nine new primers targeting the nirS gene of denitrifying Epsilonproteobacteria were designed and tested for use in sequencing and quantitative PCR on two microbial mat samples (vent 2 and vent 4) from the Calypso hydrothermal vent field, Bay of Plenty, New Zealand. Commonly used nirS and nirK primer sets nirS1F/nirS6R, cd3aF/R3cd, nirK1F/nirK5R, and F1aCu/R3Cu were also tested to determine what may be missed by the common single-primer approach to assessing denitrifier diversity. The relative importance of Epsilonproteobacteria in these samples was evaluated by 16S rRNA gene sequencing. Epsilonproteobacteria represented up to 75.6% of 16S rRNA libraries, but nirS genes from this group were not found with commonly used primers. Pairing of the new primer EPSnirS511F with either EPSnirS1100R or EPSnirS1105R recovered nirS sequences from members of the genera Sulfurimonas, Sulfurovum, and Nitratifractor. The new quantitative PCR primers EPSnirS103F/EPSnirS530R showed dominance of denitrifying Epsilonproteobacteria in vent 4 compared to vent 2, which had greater representation by "standard" denitrifiers measured with the cd3aF/R3cd primers. Limited results from commonly used nirK primers suggest biased amplification between primers. Future application of multiple nirS and nirK primers, including the new epsilonproteobacterial nirS primers, will improve the detection of denitrifier diversity and the capability to identify changes in dominant denitrifying communities.IMPORTANCE Estimating the potential for increasing nitrogen limitation in the changing global ocean is reliant on understanding the microbial community that removes nitrogen through the process of denitrification. This process is favored under oxygen limitation, which is a growing global-ocean phenomenon. Current methods use the nitrite reductase genes nirS and nirK to assess denitrifier diversity and abundance using primers that target only a few known denitrifiers and systematically exclude denitrifying Epsilonproteobacteria, a group known to dominate in reducing environments, such as hydrothermal vents and anoxic basins. As oxygen depletion expands in the oceans, it is important to study denitrifier community dynamics within those areas to predict future global ocean changes. This study explores the design and testing of new primers that target epsilonproteobacterial nirS and reveals the varied success of existing primers, leading to the recommendation of a multiple-primer approach to assessing denitrifier diversity.

The role of microaerophilic Fe-oxidizing micro-organisms in producing banded iron formations

Despite the historical and economic significance of banded iron formations (BIFs), we have yet to resolve the formation mechanisms. On modern Earth, neutrophilic microaerophilic Fe-oxidizing micro-organisms (FeOM) produce copious amounts of Fe oxyhydroxides, leading us to wonder whether similar organisms played a role in producing BIFs. To evaluate this, we review the current knowledge of modern microaerophilic FeOM in the context of BIF paleoenvironmental studies. In modern environments wherever Fe(II) and O2 co-exist, microaerophilic FeOM proliferate. These organisms grow in a variety of environments, including the marine water column redoxcline, which is where BIF precursor minerals likely formed. FeOM can grow across a range of O2 concentrations, measured as low as 2 μm to date, although lower concentrations have not been tested. While some extant FeOM can tolerate high O2 concentrations, many FeOM appear to prefer and thrive at low O2 concentrations (~3-25 μm). These are similar to the estimated dissolved O2 concentrations in the few hundred million years prior to the 'Great Oxidation Event' (GOE). We compare biotic and abiotic Fe oxidation kinetics in the presence of varying levels of O2 and show that microaerophilic FeOM contribute substantially to Fe oxidation, at rates fast enough to account for BIF deposition. Based on this synthesis, we propose that microaerophilic FeOM were capable of playing a significant role in depositing the largest, most well-known BIFs associated with the GOE, as well as afterward when global O2 levels increased.

Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea)

Over the past century the spread of hypoxia in the Baltic Sea has been drastic, reaching its ‘arm’ into the easternmost sub-basin, the Gulf of Finland. The hydrographic and climatological properties of the gulf offer a broad suite of discrete niches for microbial communities. The current study explores spatiotemporal dynamics of bacterioplankton community in the Gulf of Finland using massively parallel sequencing of 16S rRNA fragments obtained by amplifying community DNA from spring to autumn period. The presence of redoxcline and drastic seasonal changes make spatiotemporal dynamics of bacterioplankton community composition (BCC) and abundances in such estuary remarkably complex. To the best of our knowledge, this is the first study that analyses spatiotemporal dynamics of BCC in relation to phytoplankton bloom throughout the water column (and redoxcline), not only at the surface layer. We conclude that capability to survive (or benefit from) shifts between oxic and hypoxic conditions is vital adaptation for bacteria to thrive in such environments. Our results contribute to the understanding of emerging patterns in BCCs that occupy hydrographically similar estuaries dispersed all over the world, and we suggest the presence of a global redox- and salinity-driven metacommunity. These results have important implications for understanding long-term ecological and biogeochemical impacts of hypoxia expansion in the Baltic Sea (and similar ecosystems), as well as global biogeography of bacteria specialized inhabiting similar ecosystems.

Sulfide Consumption in Sulfurimonas denitrificans and Heterologous Expression of Its Three Sulfide-Quinone Reductase Homologs

Sulfurimonas denitrificans is a sulfur-oxidizing epsilonproteobacterium. It has been reported to grow with sulfide and to harbor genes that encode sulfide-quinone reductases (SQRs) (catalyze sulfide oxidation). However, the actual sulfide concentrations at which S. denitrificans grows and whether its SQRs are functional remain enigmatic. Here, we illustrate the sulfide concentrations at which S. denitrificans exhibits good growth, namely, 0.18 mM to roughly 1.7 mM. Around 2.23 mM, sulfide appears to inhibit growth. S. denitrificans harbors three SQR homolog genes on its genome (Suden_2082 for type II SQR, Suden_1879 for type III SQR, and Suden_619 for type IV SQR). They are all transcribed in S. denitrificans. According to our experiments, they appear to be loosely bound to the membrane. Each individual S. denitrificans SQR was heterologously expressed in the Rhodobacter capsulatus SB1003 sqr deletion mutant, and all exhibited SQR activities individually. This suggests that all of these three genes encode functional SQRs. This study also provides the first experimental evidence of a functional bacterial type III SQR.

IMPORTANCE

Although the epsilonproteobacterium Sulfurimonas denitrificans has been described as using many reduced sulfur compounds as electron donors, there is little knowledge about its growth with sulfide. In many bacteria, the sulfide-quinone reductase (SQR) is responsible for catalyzing sulfide oxidation. S. denitrificans has an array of different types of sqr genes on its genome and so do several other sulfur-oxidizing Epsilonproteobacteria. However, whether these SQRs are functional has remained unknown. Here, we shed light on sulfide metabolism in S. denitrificans. Our study provides the first experimental evidence of active epsilonproteobacterial SQRs and also gives the first report of a functional bacterial type III SQR.

Sulfide-driven autotrophic denitrification significantly reduces N2O emissions

The Sulfate reduction-Autotrophic denitrification-Nitrification Integrated (SANI) process build on anaerobic carbon conversion through biological sulfate reduction and autotrophic denitrification by using the sulfide byproduct from the previous reaction. This study confirmed extra decreases in N2O emissions from the sulfide-driven autotrophic denitrification by investigating N2O reduction, accumulation, and emission in the presence of different sulfide/nitrate (S/N) mass ratios at pH 7 in a long-term laboratory-scale granular sludge autotrophic denitrification reactor. The N2O reduction rate was linearly proportional to the sulfide concentration, which confirmed that no sulfide inhibition of N2O reductase occurred. At S/N = 5.0 g-S/g-N, this rate resulted by sulfide-driven autotrophic denitrifying granular sludge (average granule size = 701 μm) was 27.7 mg-N/g-VSS/h (i.e., 2 and 4 times greater than those at 2.5 and 0.8 g-S/g-N, respectively). Sulfide actually stimulates rather than inhibits N2O reduction no matter what granule size of sulfide-driven autotrophic denitrifying sludge engaged. The accumulations of N2O, nitrite and free nitrous acid (FNA) with average granule size 701 μm of sulfide-driven autotrophic denitrifying granular sludge engaged at S/N = 5.0 g-S/g-N were 4.7%, 11.4% and 4.2% relative to those at 3.0 g-S/g-N, respectively. The accumulation of FNA can inhibit N2O reduction and increase N2O accumulation during sulfide-driven autotrophic denitrification. In addition, the N2O gas emission level from the reactor significantly increased from 14.1 ± 0.5 ppmv (0.002% of the N load) to 3707.4 ± 36.7 ppmv (0.405% of the N load) as the S/N mass ratio in the influent decreased from 2.1 to 1.4 g-S/g-N over the course of the 120-day continuous monitoring period. Sulfide-driven autotrophic denitrification may significantly reduce greenhouse gas emissions from biological nutrient removal when sulfur conversion processes are applied.