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Anoxic biotrickling filters (BTFs) represent a technology with high H2S elimination capacity and removal efficiencies widely studied for biogas desulfurization. Three changes in the final electron acceptors were made using nitrate and nitrite during an operating period of 520 days. The stability and performance of the anoxic BTF were maintained when a significant perturbation was applied to the system that involved the progressive change of nitrate to nitrite and vice versa. Here the impact of electron acceptor changes on the microbial community was characterized by denaturing gel gradient electrophoresis (DGGE) and next generation sequencing (NGS). Both platforms revealed that the community underwent changes during the perturbations but was resilient because the removal capacity did not significantly change. Proteobacteria and Bacteroidetes were the main Phyla and Sulfurimonas and Thiobacillus the main nitrate-reducing sulfide-oxidizing bacteria (NR-SOB) genera involved in the biodesulfurization process.

The Sansha Yongle Blue Hole is the world’s deepest (301 m) underwater cave and has a sharp redox gradient, with oligotrophic, anoxic, and sulfidic bottom seawater. In order to discover the microbial communities and their special biogeochemical pathways in the blue hole, we analyzed the 16S ribosomal RNA amplicons and metagenomes of microbials from seawater depths with prominent physical, chemical, and biological features. Redundancy analysis showed that dissolved oxygen was the most important factor affecting the microbial assemblages of the blue hole and surrounding open sea waters, and significantly explained 44.7% of the total variation, followed by silicate, temperature, sulfide, ammonium, methane, nitrous oxide, nitrate, dissolved organic carbon, salinity, particulate organic carbon, and chlorophyll a. We identified a bloom of Alteromonas (34.9%) at the primary nitrite maximum occurring in close proximity to the chlorophyll a peak in the blue hole. Genomic potential for nitrate reduction of Alteromonas might contribute to this maximum under oxygen decrease. Genes that would allow for aerobic ammonium oxidation, complete denitrification, and sulfur-oxidization were enriched at nitrate/nitrite-sulfide transition zone (90 and 100 m) of the blue hole, but not anammox pathways. Moreover, γ-Proteobacterial clade SUP05, ε-Proteobacterial genera Sulfurimonas and Arcobacter, and Chlorobi harbored genes for sulfur-driven denitrification process that mediated nitrogen loss and sulfide removal. In the anoxic bottom seawater (100-300 m), high levels of sulfate reducers and dissimilatory sulfite reductase gene (dsrA) potentially created a sulfidic zone of ~200 m thickness. Our findings suggest that in the oligotrophic Sansha Yongle Blue Hole, O2 deficiency promotes nitrogen- and sulfur-cycling processes mediated by metabolically versatile microbials.

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 .

The deep terrestrial subsurface remains an environment where there is limited understanding of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is under construction for the final storage of spent nuclear fuel. It is therefore critical to evaluate the potential impact microbial metabolism, including sulfide generation, could have upon the safety of the repository. We investigated a deep groundwater where sulfate is present, but groundwater geochemistry suggests limited microbial sulfate-reducing activity. Examination of the microbial community at the genome-level revealed microorganisms with the metabolic capacity for both oxidative and reductive sulfur transformations. Deltaproteobacteria are shown to have the genetic capacity for sulfate reduction and possibly sulfur disproportionation, while Rhizobiaceae, Rhodocyclaceae, Sideroxydans, and Sulfurimonas oxidize reduced sulfur compounds. Further examination of the proteome confirmed an active sulfur cycle, serving for microbial energy generation and growth. Our results reveal that this sulfide-poor groundwater harbors an active microbial community of sulfate-reducing and sulfide-oxidizing bacteria, together mediating a sulfur cycle that remained undetected by geochemical monitoring alone. The ability of sulfide-oxidizing bacteria to limit the accumulation of sulfide was further demonstrated in groundwater incubations and highlights a potential sink for sulfide that could be beneficial for geological repository safety.

A novel mesophilic facultative anaerobic bacterium, strain SN118T, 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 SN118T 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 C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. 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 1251T (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 SN118T (=DSM 109248T=VKM B-3378T).

Methane is a powerful greenhouse gas but the microbial diversity mediating methylotrophic methanogenesis is not well-characterized. One overlooked route to methane is via the degradation of dimethylsulfide (DMS), an abundant organosulfur compound in the environment. Methanogens and sulfate-reducing bacteria (SRB) can degrade DMS in anoxic sediments depending on sulfate availability. However, we know little about the underlying microbial community and how sulfate availability affects DMS degradation in anoxic sediments. We studied DMS-dependent methane production along the salinity gradient of the Medway Estuary (UK) and characterized, for the first time, the DMS-degrading methanogens and SRB using cultivation-independent tools. DMS metabolism resulted in high methane yield (39%-42% of the theoretical methane yield) in anoxic sediments regardless of their sulfate content. Methanomethylovorans, Methanolobus and Methanococcoides were dominant methanogens in freshwater, brackish and marine incubations respectively, suggesting niche-partitioning of the methanogens likely driven by DMS amendment and sulfate concentrations. Adding DMS also led to significant changes in SRB composition and abundance in the sediments. Increases in the abundance of Sulfurimonas and SRB suggest cryptic sulfur cycling coupled to DMS degradation. Our study highlights a potentially important pathway to methane production in sediments with contrasting sulfate content and sheds light on the diversity of DMS degraders.

Dysoxic marine waters (DMW, SIAM Gravitation grant 024.002.002 to AJMS and JSSD of the Netherlands Ministry of Education, Culture and Science and the Netherlands Organisation for Scientific Research (NWO). BED and FABvM were supported by the NWO Vidi grant 864.14.004. BED was supported by the European Research Council (ERC) Consolidator grant 865694: DiversiPHI, info:eu-repo/semantics/publishedVersion

The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique inland salt marsh environment.

This study aims to explore an alternative way to accelerate the start-up of sulfide-oxidizing autotrophic denitrification (SOAD) in moving-bed biofilm reactors (MBBRs). Two approaches were tested: i) cultivating sulfide-based autotrophic denitrifiers with sulfide and nitrate (MBBR1); and ii) cultivating facultative denitrifiers by switching the feed from organic carbon/nitrate to sulfide/nitrate (MBBR2). The mechanisms behind these two approaches are discussed. The results showed that both MBBRs could achieve stable nitrate removal (≥90%) after 20 days, while the SOAD microbial communities cultivated in MBBR2 performed better than those cultivated in MBBR1 in terms of the sulfur oxidation activity (0.47 ± 0.03 vs. 0.21 ± 0.07 kg SO42--Sgenerated/(m3·d)), biomass activity and immobilization (540 mg attached volatile solids (AVS)/L vs. 390 mg AVS/L, respectively). Moreover, the proportion of sulfur-oxidizing bacteria (SOB) enriched was higher in MBBR2 (35.0% Paracoccus) than in MBBR1 (9.7% Sulfurimonas and 5.2% Thauera), further legitimizing the hybridized approach for significant SOB enrichment. The findings of this study provide important clues for accelerating and optimizing the development of the MBBR-based SOAD bioprocess.

The deep sea hydrothermal vent ecosystem was first discovered in 1977 at East Pacific Rise (EPR) near the Galapagos Islands. In the past decades, over 640 hydrothermal vent sites have been found in oceans, a majority of which have been found on the mid-ocean ridges. Chinese scientists have contributed significantly to the discovery of new sites on the Southwest Indian Ridge and South Mid-Atlantic Ridge. Due to worldwide oceanic expeditions, significant advances have been made in the observation of hydrothermal vent ecosystems, regarding the diversity and geographical distribution of vent fauna and microbial communities. The vent chemolithoautotrophs and their symbiosis with vent clams, mussels, tube worms and shrimps, in particular, gained more attention. In this paper, recent advances in diversity and versatile metabolisms of prokaryotic chemoautotrophs are reviewed. The vent chemolithoautotrophs are pivotal in the cross-connected interactions of abiotic and biotic processes. They act as the primary producer in the unique ecosystem driven by the deep dark energy derived from water-rock reaction around the magma chamber. Correspondingly, various chemoautotrophic bacteria are capable of utilizing the reduced compounds generated by water-rock reaction, via sulfur oxidization, methane oxidization, hydrogen oxidization, iron oxidization and ammonia oxidization; in contrast, chemoautotrophic vent archaea tend to harness energy from hydrogen in the inner part of the hydrothermal chimney coupling with sulfur reduction. In addition, heterotrophic archaea of Thermococcales also frequently occurs in high temperature chimneys; while some archaea can oxidize ammonia and methane in the vent surroundings. These diverse prokaryotes selectively distribute in a variety of vent niches along the steep environmental gradients of temperature, pH, Eh and concentrations of the reduced compounds. In the case of a black smoke ecosystem, where the hydrogen sulfide in hydrothermal fluids is effluent, sulfur oxidation is recognized as a major process driving carbon fixation for primary production; while in the mixing zones, the partially oxidized inorganic sulfur compounds like thiosulfate and polysulfide can be further oxidized by sulfur-oxidizing bacteria (SOB). Among them, Epsilonproteobacteria such as Sulfurimonas, Sulfurovum, Arcobacter , Hydrogenovibrio and Thiomicrospira are predominant genera of SOBs in plume-mixed seawater close to the vent, while bacteria of Gammaproteobacteria SUP05 clade are relatively abundant in the cold oxidized seawater farther away from the vent. In the case of the white chimney, methane-metabolizing archaea of Methanosarcinales and hydrogen- oxidizing Thiomicrospira dominate the prokaryotic community in microbial mat. In addition, another group of chemolithoautotrophs function as endo- and epi-symbionts of vent animals that are essential to the health of vent ecosystem; these symbionts mostly belong to sulfur, hydrogen and methane oxidizers. However, all these processes need quantification to evaluate the efflux of energy and synthesized organic compounds. Considering the global distribution and the immense influence in respect to continuous efflux of energy and substances, hydrothermal vents play an important role in life evolution. Both geological records and computational analysis reveal that early life on Earth is likely originated from the deep hydrothermal system, with features of anaerobic, thermophilic, hydrogen-oxidizing, coupled with carbon and nitrogen fixation, represented by the Last Universal Common Ancestor (LUCA). Because of our limited knowledge about the deep biosphere along with deep time evolution, more efforts are needed to investigate the dark ecosystem with integrated approaches, to project the nature of life in dark with unique mechanisms, and to finally elucidate the origin and evolution of life on earth.

This initial microbial analysis of the Piñones lagoon shows a high representation of sulfur-oxidizing Sulfurimonas and sulfur-reducing Sulfurospirillum bacteria. These species are likely responsible for maintaining sulfur homeostasis and prevent the buildup of toxic sulfur components, but may contribute to nitrogen buildup, in the mangrove ecosystem., This initial microbial analysis of the Piñones Lagoon shows a high representation of sulfur-oxidizing Sulfurimonas and sulfur-reducing Sulfurospirillum bacteria. These species are likely responsible for maintaining sulfur homeostasis and prevent the buildup of toxic sulfur components, but may contribute to nitrogen buildup, in the mangrove ecosystem.

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 (C16:1ω7c and/or C16:1ω6c), C16:0 and summed feature 8 (C18:1ω7c and/or C18:1ω6c). 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 GO25T (96.8% sequence identity) and Sulfurimonas autotrophica OK10T (95.8% sequence identity). The average nucleotide identity and DNA-DNA hybridization values between strain S2-6 T and S. paralvinellae GO25T and S. autotrophica OK10T 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 1A14513T = KCTC 15854 T).

The present study attempts to investigate the microbial communities and their potential to oxidize ammonia and sulfur at different sites of Arctic Fjord by targeted metagenomics. The high throughput sequencing revealed archaeal Thaumarchaeota (79.3%), Crenarchaeota (10.9%), Euryarchaeota (5.4%), and Woesearchaeota (2.9%) across different depths. In contrast, the bacterial communities depict predominance of Proteobacteria (52.6%), which comprises of dominant genera viz. Sulfurovum (11.2%) and Sulfurimonas (6.3%). Characterizing the metabolic potential of microbial communities with prime focus on the ammonia and sulfur cycling revealed the presence of amoABC and narGHYZ/ nxrAB genes encoding key enzymes. The ammonia cycling coupled with an augmentation of members of Nitrosopumilus belonging to the phylum Thaumarcheaota suggests the vital role of archaeal communities. Similarly, the persistence of chemolithoautotrophic members of Sulfurovum and Sulfurimonas along with the anaerobic genera Desulfocapsa and Desulfobulbus harboring SOX (sulfur-oxidation) system indicates the modulatory role of bacterial communities in sulfur cycling.

Sulfurimonas species (class Campylobacteria, phylum Campylobacterota) were globally distributed and especially predominant in deep-sea hydrothermal environments. They were previously identified as chemolithoautotrophic sulfur-oxidizing bacteria (SOB), whereas little is known about their potential in sulfur reduction. In this report, we found that the elemental sulfur reduction is quite common in different species of genus Sulfurimonas. To gain insights into the sulfur reduction mechanism, growth tests, morphology observation, as well as genomic and transcriptomic analyses were performed on a deep-sea hydrothermal vent bacterium Sulfurimonas sp. NW10. Scanning electron micrographs and dialysis tubing tests confirmed that elemental sulfur reduction occurred without direct contact of cells with sulfur particles while direct access strongly promoted bacterial growth. Furthermore, we demonstrated that most species of Sulfurimonas probably employ both periplasmic and cytoplasmic polysulfide reductases, encoded by genes psrA1 B1 CDE and psrA2 B2 , respectively, to accomplish cyclooctasulfur reduction. This is the first report showing two different sulfur reduction pathways coupled to different energy conservations could coexist in one sulfur-reducing microorganism, and demonstrates that most bacteria of Sulfurimonas could employ both periplasmic and cytoplasmic polysulfide reductases to perform cyclooctasulfur reduction. The capability of sulfur reduction coupling with hydrogen oxidation may partially explain the prevalenceof Sulfurimonas in deep-sea hydrothermal vent environments.

Oil souring occurs when H2S is generated in oil reservoirs. This not only leads to operational risks and health hazards but also increases the cost of refining crude oil. Sulfate-reducing microorganisms are considered to be the main source of the H2S that leads to oil souring. Substrate competition between nitrate-reducing and sulfate-reducing microorganisms makes biosouring mitigation via the addition of nitrate salts a viable strategy. This study explores the shift in microbial community across different phases of biosouring and mitigation. Anaerobic sand-filled columns wetted with seawater and/or oil were used to initiate the processes of sulfidogenesis, followed by mitigation with nitrate, rebound sulfidogenesis, and rebound control phases (via nitrate and low salinity treatment). Shifts in microbial community structure and function were observed across different phases of seawater and oil setups. Marine bacterial taxa (Marinobacter, Marinobacterium, Thalassolituus, Alteromonas, and Cycloclasticus) were found to be the initial responders to the application of nitrate during mitigation of sulfidogenesis in both seawater- and oil- wetted columns. Autotrophic groups (Sulfurimonas and Desulfatibacillum) were found to be higher in seawater-wetted columns compared to oil-wetted columns, suggesting the potential for autotrophic volatile fatty acid (VFA) production in oil-field aquifers when seawater is introduced. Results indicate that fermentative (such as Bacteroidetes) and oil-degrading bacteria (such as Desulfobacula toluolica) play an important role in generating electron donors in the system, which may sustain biosouring and nitrate reduction. Persistence of certain microorganisms (Desulfobacula) across different phases was observed, which may be due to a shift in metabolic lifestyle of the microorganisms across phases, or zonation based on nutrient availability in the columns. Overall results suggest mitigation strategies for biosouring can be improved by monitoring VFA concentrations and microbial community dynamics in the oil reservoirs during secondary recovery of oil.

The central Baltic Sea is characterized by a pelagic redox zone exhibiting high dark CO(2) 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.

Intraterrestrial waters harbor microbial communities being extensively studied to understand microbial processes underlying subsurface ecosystem functioning. This paper provides the results of an investigation on the microbiomes of unique, subsurface sulfidic waters associated with Upper Jurassic, Cretaceous, and Miocene sediments. We used high-throughput 16S rDNA amplicon sequencing to reveal the structure of bacterial and archaeal communities in water samples differing in sulfide content (20–960 mg/dm3), salinity (1.3–3.2%), and depth of extraction (60–660 m below ground level). Composition of the bacterial communities strongly varied across the samples; however, the bacteria participating in the sulfur cycle were common in all sulfidic waters. The shallowest borehole water (60 m bgl) was dominated by sulfur-oxidizing Epsilonproteobacteria (Sulfurimonas, Sulfurovum). In the waters collected from greater depths (148–300 m bgl), the prevalence of Betaproteobacteria (Comamonadaceae) and sulfate/sulfur-reducing Deltaproteobacteria (Desulfopila, Desulfomicrobium, MSBL7) was observed. Sulfate reducers (members of Clostridia: Candidatus Desulforudis) were the most abundant bacteria in the deepest borehole water (660 m bgl). Out of 850 bacterial OTUs, only one, affiliated with the Comamonadaceae family, was found abundant (> 1% of total bacterial sequences) in all samples. Contribution of Archaea to the whole microbial communities was lower than 0.5%. Archaeal communities did not differ across the samples and they consisted of Halobacteriaceae. Out of 372 archaeal OTUs, five, belonging to the four genera Natronomonas, Halorubrum, Halobellus, and Halorhabdus, were the most numerous. Electronic supplementary material The online version of this article (10.1007/s00248-018-1270-5) contains supplementary material, which is available to authorized users.

Two bioreactors were investigated as an alternative to post-treatment of effluent from an upflow anaerobic sludge blanket (UASB) reactor treating domestic sewage, with an aim of oxidizing sulfide into elemental sulfur, and removal of solid and organic material. The bioreactors were operated at different hydraulic retention times (HRTs) (6, 4, and 2 h) and in the presence or absence (control) of packing material (polypropylene rings). Greater sulfide removal efficiencies – 75% (control reactor) and 92% (packed reactor) – were achieved in both reactors for an HRT of 6 h. Higher organic matter (COD) and solid (TSS) removal levels were observed in the packed reactor, which produced effluent with low COD (100 mg CODL−1) and TSS concentrations (30 mg TSSL−1). Denaturing gradient gel electrophoresis results revealed that a metabolically diverse bacterial community was present in both bioreactors, with sequences related to heterotrophic bacteria, sulfur bacteria (Thiocapsa, Sulfurimonas sp., Chlorobaculum sp., Chromatiales and Sulfuricellales), phototrophic purple non-sulfur bacteria (Rhodopseudomonas, Rhodocyclus sp.) and cyanobacteria. The packed reactor presented higher extracellular sulfur formation and potential for elemental sulfur recovery was seen. Higher efficiencies related to the packed reactor were attributed to the presence of packing material and higher cell retention time. The studied bioreactors seemed to be a simple and low-cost alternative for the post-treatment of anaerobic effluent.

This study investigated temperature-induced changes in a microbial community performing autotrophic denitrification with HS− for S0 recovery. The study was performed over 120 days in an expanded granular sludge bed (EGSB) reactor at invariable feeding conditions (0.4 kg S/m3 d loading rate and 0.35 N/S molar ratio). NO3− and HS− were simultaneously removed at 25–10 °C range. Average HS−-S removal was 98 and 89% at 25 and 10 °C, respectively. While NO3− was completely removed in studied temperature range. High-throughput sequencing indicated that the transition from methanogenic conditions (inoculum sludge) to the imposed experimental conditions led to development of a Proteobacteria dominated phylum. β-Proteobacteria (mainly Thauera sp. and Alicycliphilus sp.) predominated at 25 °C (64%), when the S0 accumulation was the highest (45%). Decreasing temperature to 10 °C, reduced both the abundance of β-Proteobacteria (2.3 times to 28%) and the accumulation of S0 (2.5 times to 18%). At 10 °C, chemolithoautotrophic sulfide-oxidizing bacteria belonging to Sulfurimonas sp. and Thiobacillus sp. were present in the biomass (over 34% of all sequences) while S0ss and SO42− production increased slightly. These results indicate that temperature-induced changes in the microbial community influenced reactor performance and effluent characteristics, especially S0 accumulation.

Geochemical, biogeochemical, and molecular genetic investigation of the upper (0–5 cm) bottom sediments of the Yamal sector of the Kara Sea was carried out. The Yamal sector is well-protected from the massive inflow of river water. The sediments were oxidized at the surface and weakly reduced in the 3−5-cm layer. Corg content varied from 0.1 to 1.3%, while the level of dissolved СН4 was 1.9 to 20.3 μmol L–1. The isotopic composition of organic matter (OM) carbon, δ13Corg, varied from–27.5 to–22.2‰ (–25.4‰ on average). The share of terrigenous OM was 13.3 to 72.2% (48.9% on average). The rate of methane production, methane oxidation, and sulfate reduction varied from 0.8 to 9.0 (2.7 on average) nmol СН4 dm–3 day–1, from 9.9 to 103 (31.6 on average) nmol СН4 dm–3 day–1, and from 0.49 to 2.2 (1.1 on average) μmol S dm–3 day–1, respectively. High-throughput sequencing of the amplicons of the 16S rRNA genes was used to reveal the physiological groups of microorganisms responsible for the processes of methane production and oxidation, sulfate reduction, and oxidation of reduced sulfur compounds. Members of the phylum Woesearchaeota were predominant among archaea. Methanogenic archaea belonged to the families Methanobacteriaceae, Methanococcaceae, and Methanosarcinaceae (Euryarchaeota). Methanotrophs of the family Methylococcaceae were revealed among the Gammaproteobacteria, with their share in the sediments ~1%. In the class Deltaproteobacteria (15.4%), three orders of sulfate reducers were predominant: Desulfobacterales, Desulfovibrionales, and Desulfuromonadales. Oxidation of reduced sulfur compounds was carried out by chemolithoautotrophic bacteria of the genera Sulfurovum, Sulfurimonas, and Arcobacter of the class Epsilonproteobacteria (1.1% of the total microbial number).

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface., Analysis of a CO2-driven geyser over a complete eruption cycle showed temporal changes in microbial community composition and function, associated with eruption phase and aquifer water depth, and revealed a putative archaeal symbiosis.

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.

Spatial distribution (horizonal and vertical) of groundwater microbial communities and the hydrogeochemistry in confined aquifers were studied approximately along the groundwater flow path from coteau to plain in the Nomhon area, Qinghai-Tibet plateau, China. The confined groundwater samples at different depths and locations were collected in three boreholes through a hydrogeological section in this arid and semi-arid area. The phylogenetic analysis of 16S rRNA genes and multivariate statistical analysis were used to elucidate similarities and differences between groundwater microbial communities and hydrogeochemical properties. The integrated isotopic geochemical measurements were applied to estimate the source and recharge characteristics of groundwater. The results showed that groundwater varied from fresh to saline water, and modern water to ancient water following the flowpath. The recharge characteristics of the saline water was distinct with that of fresh water. Cell abundance did not vary greatly along the hydrogeochemical zonality; however, dissimilarities in habitat-based microbial community structures were evident, changing from Betaproteobacteria in the apex of alluvial fan to Gammaproteobacteria and then to Epsilonproteobacteria in the core of the basin (alluvial-lacustrine plain). Rhodoferax, Hydrogenophaga, Pseudomonas, and bacterium isolated from similar habitats unevenly thrived in the spatially distinct fresh water environments, while Sulfurimonas dominanted in the saline water environment. The microbial communities presented likely reflected to the hydrogeochemical similarities and zonalities along groundwater flowpath.

Summary 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 34S0, 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.

Potential threats exist where groundwater is polluted by high concentrations of oil compounds (980.20 mg L−1 the highest TPHs). An abandoned petrochemical plant in Lanzhou City, where long-term petrochemical products leakage contaminated the groundwater, was used as a field site in this study. To determine the extent of pollution and find an effective solution, chemical techniques combined with molecular biological techniques were used to survey the migration and decomposition of pollutants. Moreover, Illumina Sequencing was employed to reveal the microbial changes of different sites. Light-chain alkanes (mostly C6–C9), most benzene compounds, and some polycyclic aromatic hydrocarbons (naphthalene, 2-methylnaphthalene) mainly polluted the source. C29 to C36 and chlorobenzenes (hexachlorocyclohexane) polluted the secondary polluted sites. Moreover, chloralkane (trichloroethane and dichloroethane), benzene derivatives (trimethylbenzene and butylbenzene), and PAHs (fluorene and phenanthrene) were present in the other longtime-contaminated water. The bacterial genera are closely related with the chemical matters, and different groups of microorganisms gather in the sample sites that are polluted with different kinds of oil. The biodiversity and abundance of observed species change with pollution conditions. The dominant phyla (81%) of the bacterial community structure are Proteobacteria (62.2% of the total microbes), Bacteroidetes (8.85%), Actinobacteria (6.70%), and Choloroflexi (3.03%). Pseudomonadaceae is significant in the oil-polluted source and Comamonadaceae is significant in the secondary polluted (migrated oil) sample; these two genera are natural decomposers of refractory matters. Amycolatopsis, Rhodocyclaceae, Sulfurimonas, and Sulfuricurvum are the dominant genera in the long-migrated oil-polluted samples. Bioavailability of the oil-contaminated place differs with levels of pollution and cleaning the worse-polluted sites by microbes is more difficult.

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

Nitrate-driven sulfide oxidation has been proved a cost-effective way to control sediments odor which has long been a universal problem for urban rivers in south China areas. In this work, sediments treatment experiments under a dynamic variation of temperature from 5 °C to 35 °C with 3% of calcium nitrate added were conducted to reveal the influence of temperature variation on this process. The results showed that microbial community was remarkably restructured by temperature variation. Pseudomonas (15.56–29.31%), Sulfurimonas (26.81%) and Thiobacillus (37.99%) were dominant genus at temperature of ≤15 °C, 25 °C and 35 °C, respectively. It seemed that species enrichment occurring at different temperature gradient resulted in the distinct variation of microbial community structure and diversity. Moreover, nitrate-driven sulfide and ferrous oxidation were proportionally promoted only when temperature increased above 15 °C. The dominant bacteria at high temperature stage were those genus that closely related to autotrophic nitrate-driven sulfide and ferrous oxidizing bacteria (e.g.Thiobacillus, Sulfurimonas and Thermomonas), revealing that promotion of sulfide/ferrous oxidation could be attributed to the change of dominant bacteria determined by temperature variation. Thus, a higher treatment efficiency by calcium nitrate addition for odor control would be achieved in summer than any other seasons in south China areas.

Shallow-water hydrothermal vents (HTVs) are an ecologically important habitat with a geographic origin similar to that of deep-sea HTVs. Studies on shallow-water HTVs have not only facilitated understanding of the influences of vents on local ecosystems but also helped to extend the knowledge on deep-sea vents. In this study, the diversity of bacterial communities in the sediments of shallow-water HTVs off Kueishan Island, Taiwan, was investigated by examining the 16S ribosomal RNA gene as well as key functional genes involved in chemoautotrophic carbon fixation (aclB, cbbL and cbbM). In the vent area, Sulfurovum and Sulfurimonas of Epsilonproteobacteria appeared to dominate the benthic bacterial community. Results of aclB gene analysis also suggested involvement of these bacteria in carbon fixation using the reductive tricarboxylic acid (rTCA) cycle. Analysis of the cbbM gene showed that Alphaproteobacterial members such as the purple non-sulfur bacteria were the major chemoautotrophic bacteria involving in carbon fixation via the Calvin-Benson-Bassham (CBB) cycle. However, they only accounted for

Sulfur-oxidizing Sulfurimonas spp. are widespread in sediments, hydrothermal vent fields, aquifers and subsurface environments such as oil reservoirs where they play an important role in the sulfur cycle. We determined the genome sequence of the oil field isolate Sulfurimonas sp. strain CVO and compared its gene expression during nitrate-dependent sulfide oxidation to the coastal sediment isolate Sulfurimonas denitrificans. Formation of elemental sulfur (S0 ) and high expression of sulfide quinone oxidoreductase (SQR) genes indicates that sulfide oxidation in both strains is mediated by SQR. Subsequent oxidation of S0 was achieved by the sulfur oxidation enzyme complex (SOX). In the coastal S. denitrificans, the genes are arranged and expressed as two clusters: soxXY1 Z1 AB and soxCDY2 Z2 H, and sulfate was the sole metabolic end product. By contrast, the oil field strain CVO has only the soxCDY2 Z2 H cluster and not soxXY1 Z1 AB. Despite the absence of the soxXY1 Z1 AB cluster, strain CVO oxidized S0 to thiosulfate and sulfate, demonstrating that soxCDY2 Z2 H genes alone are sufficient for S0 oxidation in Sulfurimonas spp. and that thiosulfate is an additional metabolic end product. Screening of publicly available metagenomes revealed that Sulfurimonas spp. with only the soxCDY2 Z2 H cluster are widespread suggesting this mechanism of thiosulfate formation is environmentally significant.

Ambiguous reports of corrosion problems associated with the injection of nitrate for souring control necessitate a deeper understanding of this frequently applied bioengineering strategy. Sulfide-oxidizing, nitrate-reducing bacteria have been proposed as key culprits, despite the underlying microbial corrosion mechanisms remaining insufficiently understood. This study provides a comprehensive characterization of how individual metabolic intermediates of the microbial nitrogen and sulfur cycles can impact the integrity of carbon steel infrastructure. The results help explain the dramatic increases seen at times in corrosion rates observed during nitrate injection in field and laboratory trials and point to strategies for reducing adverse integrity-related side effects of nitrate-based souring mitigation.

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 S2-), elemental sulfur (S0) and thiosulfate (S2O32-) 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 GD1T 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 nutrient and oxygen gradient present in marine sediments promotes high levels of microbial diversity. We applied metagenomics and biogeochemical tools to analyze microbial communities in different sediment depths (0–4 m below sea floor, mbsf) from Guanabara Bay, Brazil, a brackish tropical ecosystem with a history of massive anthropogenic impacts, and a largely unknown sediment microbial diversity. Methanogens (e.g. Methanosarcinales, Methanomicrobiales) were more abundant at 1 mbsf, while sulphate-reducing microbes (Desulfurococcales, Thermoprotales, and Sulfolobales) were more abundant at deeper layers (4 mbsf; corresponding to 3 K Radiocarbon years before present, Holocene Epoch). Taxonomic analyzes and functional gene identification associated with anaerobic methane oxidation (e.g. monomethylamine methyltransferase (mtmB), trimethylamine methyltransferase (mttB) and CO dehydrogenase/acetyl-CoA synthase delta subunit) and sulfate reduction indicated the dominance of Campylobacteria (Sulfurimonas) at deeper sediment layers. Gene sequences related to assimilation of inorganic sulfur increased with depth, while organic sulfur related sequences decrease, accompanying the clear reduction in the concentration of sulfur, organic carbon and chla torwards deeper layers. Analyzes of metagenome assembled genomes also led to the discovery of a novel order within the phylum Acidobacteriota, named Guanabacteria. This novel order had several in silico phenotyping features that differentiate it from closely related phylogenetic neighbors (e.g. Acidobacteria, Aminicenantes, and Thermoanaerobaculum), including several genes (carbon monoxide dehydrogenase, CO dehydrogenase/CO-methylating acetyl-CoA synthase complex subunit beta, heterodisulfide reductase, sulfite exporter TauE/SafE family protein, sulfurtransferase) that relevant for the S and C cycles. Furthermore, the recovered Bathyarchaeota genome SS9 illustrates the methanogenic potential in deeper sediment layer.

Nitrate-driven sulfide/ferrous oxidation has been proved a cost-effective approach for river sediments in-situ odor control. However, calcium nitrate addition would sharply increase ammonium concentration in interstitial water and the mechanism was not yet clear. In this work, though sulfide and ferrous iron were efficiently oxidized, about 102% of NH4+ concentration increased in interstitial water on the first day of calcium nitrate injection (30 mg kg dwt−1), and about 31% more NH4+ increase at the 21st days was observed. To discover the mechanism of ammonium sharp release, desorption kinetics experiment was conducted and the results suggested that the short-time sharp releases of ammonium when calcium nitrate was added could be attributed to the chemical extraction of exchangeable ammonium by calcium ion. Furthermore, at the end of treatment, many genus such as Thiobacillus, Sulfurimonas, Thermomonas, and Clostridium, which were closely related to sulfide and ferrous-driven denitrification and dissimilatory nitrate reduction to ammonium (DNRA), were identified by 16S rRNA Illumina sequencing method. These findings indicated the long-time increase of ammonium might be determined by the biochemical processes (e.g. DNRA) driven by nitrate reduction. Therefore, to avoid the impact of ammonium release, an alternative subsurface injection method was introduced in this work, and the results showed that ammonium releases could be well controlled when the injection position was beneath 10 cm of the sediment surface.

The characterization of bacterial community compositions and the change in perfluoroalkyl acids (PFAAs) along a natural river distribution system were explored in the present study. Illumina high-throughput sequencing was used to explore bacterial community diversity and structure in sediment polluted by PFAAs from the Xiaoqing River, the area with concentrated fluorochemical facilities in China. The concentration of PFAAs was in the range of 8.44-465.60 ng/g dry weight (dw) in sediment. Perfluorooctanoic acid (PFOA) was the dominant PFAA in all samples, which accounted for 94.2 % of total PFAAs. High-level PFOA could lead to an obvious increase in relative abundance of Proteobacteria, ε-Proteobacteria, Thiobacillus, and Sulfurimonas and the decrease in relative abundance of other bacteria. Redundancy analysis revealed that PFOA played an important role in the formation of bacterial community, and PFOA at higher concentration could reduce the diversity of bacterial community. When the concentration of PFOA was below 100 ng/g dw in sediment, no significant effect on microbial community structure was observed. Thiobacillus and Sulfurimonas were positively correlated with the concentration of PFOA, suggesting that both genera were resistant to PFOA contamination.

Here we present the results from a shotgun sequencing effort on foot tissues from a deep-sea hydrothermal vent endemic limpet. We present the complete mitochondrial genome of the hydrothermal vent endemic gastropod Peltospira smaragdina (Gastropoda, Peltospiridae) for the first time. This species is characteristic of circa-Azores hydrothermal vent ecoregion and provides a candidate environmental DNA (eDNA) indicator of active hydrothermal vent sites. The results also suggest that the epilithic biofilm on the newly discovered Moytirra hydrothermal vents is dominated by Sulfurimonas –like microbes and corresponds with similar studies on hydrothermal hosted microbial communities. The association between Peltospira and Sulfurimonas is presented as potentially a holobiontic relationship, with both the snail and the microbial biofilm. We highlight the efficacy of using non-traditional sampling to develop a broader ecosystem understanding.

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 Aquarium9s Ocean Voyager, the largest indoor closed-system seawater exhibit in the United States. The exhibit9s 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 Sedimenticolathiotaurini 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.

A sulfur-dominated supraglacial spring system found at Borup Fiord Pass (BFP), Ellesmere Island, Nunavut, Canada, is a unique sulfur-on-ice system expressed along the toe of a glacier. BFP has an intermittent flowing, subsurface-derived, glacial spring that creates a large white-yellow icing (aufeis) that extends down-valley. Over field campaigns in 2014, 2016, and 2017, numerous samples were collected and analyzed for both microbial community composition and aqueous geochemistry. Samples were collected from multiple site types: spring discharge fluid, aufeis (spring-derived ice), melt pools with sedimented cryoconite material, and mineral precipitate scrapings, to probe how microbial communities differed between site types in a dynamic freeze/thaw sulfur-rich system. Dissolved sulfate varied between 0.07 and 11.6 mM and was correlated with chloride concentrations, where the fluids were saltiest among spring fluids. The highest sulfate samples exhibited high dissolved sulfide values between 0.22 and 2.25 mM. 16S rRNA gene sequencing from melt pool and aufeis samples from the 2014 campaign were highly abundant in operational taxonomic units (OTUs) closely related to sulfur-oxidizing microorganisms (SOM; Sulfurimonas, Sulfurovum, and Sulfuricurvum). Subsequent sampling 2 weeks later had fewer SOMs and showed an increased abundance of the genus Flavobacterium. Desulfocapsa, an organism that specializes in the disproportionation of inorganic sulfur compounds was also found. Samples from 2016 and 2017 revealed that microorganisms present were highly similar in community composition to 2014 samples, primarily echoed by the continued presence of Flavobacterium sp. Results suggest that while there may be acute events where sulfur cycling organisms dominate, a basal community structure appears to dominate over time and site type. These results further enhance our knowledge of low-temperature sulfur systems on Earth, and help to guide the search for potential life on extraterrestrial worlds, such as Europa, where similar low-temperature sulfur-rich conditions may exist.

Chemoautotrophic bacteria belonging to the genus Sulfurimonas in the class Campylobacteria are widespread in many marine environments characterized by redox interfaces, yet little is known about their physiological adaptations to different environmental conditions. Here, we used liquid chromatography coupled with tandem mass spectrometry (LC‐MS/MS) in a targeted metabolomics approach to study the adaptations of Sulfurimonas denitrificans to varying salt concentrations that are found in its natural habitat of tidal mudflats. Proline was identified as one of the most abundant internal metabolites and its concentration showed a strong positive correlation with ionic strength, suggesting that it acts as an important osmolyte in S. denitrificans. 2,3‐dihydroxypropane‐1‐sulfonate was also positively correlated with ionic strength, indicating it might play a previously unrecognized role in osmoregulation. Furthermore, the detection of metabolites from the reductive tricarboxylic acid cycle at high internal concentrations reinforces the importance of this pathway for carbon fixation in Campylobacteria and as a hub for biosynthesis. As the first report of metabolomic data for an campylobacterial chemolithoautotroph, this study provides data that will be useful to understand the adaptations of Campylobacteria to their natural habitat at redox interfaces.

In estuarine and coastal ecosystems, the majority of previous studies have considered coupled nitrification-denitrification (CND) processes to be exclusively sediment based, with little focus on suspended particulate matter (SPM) in the water column. Here, we present evidence of CND processes in the water column of Hangzhou Bay, one of the largest macrotidal embayments in the world. Spearman’s correlation analysis showed that SPM was negatively correlated with nitrate (rho = −0.372, P = 0.018) and marker genes for nitrification and denitrification in the water column were detected by quantitative PCR analysis. The results showed that amoA and nir gene abundances strongly correlated with SPM (all P amoA/nir strongly correlated with nitrate (rho = −0.454, P = 0.003). Furthermore, aggregates consisting of nitrifiers and denitrifiers on SPM were also detected by fluorescence in situ hybridization. Illumina MiSeq sequencing further showed that ammonia oxidizers mainly belonged to the genus Nitrosomonas, while the potential denitrifying genera Bradyrhizobium, Comamonas, Thauera, Stenotrophomonas, Acinetobacter, Anaeromyxobacter, Sulfurimonas, Paenibacillus and Sphingobacterium showed significant correlations with SPM (all P

Seagrass roots host a diverse microbiome that is critical for plant growth and health. Composition of microbial communities can be regulated in part by root exudates, but the specifics of these interactions in seagrass rhizospheres are still largely unknown. As light availability controls primary productivity, reduced light may impact root exudation and consequently the composition of the root microbiome. Hence, we analyzed the influence of light availability on root exudation and community structure of the root microbiome of three co-occurring seagrass species, Halophila ovalis, Halodule uninervis and Cymodocea serrulata. Plants were grown under four light treatments in mesocosms for two weeks; control (100 % surface irradiance (SI), medium (40 % SI), low (20 % SI) and fluctuating light (10 days 20 % and 4 days 100%). 16S rDNA amplicon sequencing revealed that microbial diversity, composition and predicted function were strongly influenced by the presence of seagrass roots, such that root microbiomes were unique to each seagrass species. Reduced light availability altered seagrass root exudation, as characterized using fluorescence spectroscopy, and altered the composition of seagrass root microbiomes with a reduction in abundance of potentially beneficial microorganisms. Overall, this study highlights the potential for above-ground light reduction to invoke a cascade of changes from alterations in root exudation to a reduction in putative beneficial microorganisms and, ultimately, confirms the importance of the seagrass root environment – a critical, but often overlooked space. ISSN:1664-302X

Fjords and continental shelves represent distinct marine ecosystems in the pan-arctic region. Kongsfjorden is a glacial fjord that is located on the west coast of Svalbard, and is influenced by both Atlantic and Arctic water masses. The Bering Sea consists of a huge continental shelf in the northeast and a deep ocean basin in the southwest, and is influenced by Pacific water. Microbial community compositions of Arctic sediment samples BJ4 from outer basin and BJ36 from inner basin of Kongsfjorden and sub-Arctic samples NEC5 from shallow shelf and DBS1 from deep basin region of the northern Bering Sea were investigated using 454 pyrosequencing of archaeal and bacterial 16S rRNA genes. Most archaeal sequences in the sediments were related to Thaumarchaeota, though Euryarchaeota were more abundant in the Arctic glacier-influencing inner basin sediment BJ36. Thaumarchaeota Group C3 was the dominant archaeal population in all samples. Proteobacteria and Bacteroidetes dominated the sediment bacterial communities. Acidobacteria and Actinobacteria were also dominant in the northern Bering Sea samples. Alphaproteobacteria and Epsilonproteobacteria were the two main classes in Kongsfjorden sediment bacterial communities while Deltaproteobacteria and Gammaproteobacteria were dominant in the northern Bering Sea sediments. Differences in the presence and abundance of other dominant archaeal and bacterial populations were observed among sediment samples. In contrast to archaeal community differences that the Arctic BJ36 archaeal community was distinct from the sub-Arctic sediments and the Arctic outer basin sediment BJ4, cluster analysis based on bacterial OTU (operational taxonomic unit) distributions indicated that the Arctic and sub-Arctic bacterial communities segregated from one another. These results suggest that the sediment archaeal and bacterial community compositions can be driven by different environmental factors. Differences in the presence and abundance of particular archaeal species (e.g., Candidatus Nitrosopumilus and Methanococcoides) or bacterial species (e.g., Sulfurimonas, Sulfurovum, and Desulfobulbaceae) involved in biogeochemical cycles were also observed among sediment samples. At the same time, despite the community variation, some phylotypes (e.g., Marinicella) were dominant in all sediments. This study indicates diverse microbial communities inhabiting pan-arctic marine sediments, and highlights potential roles for Archaea and Bacteria in global biogeochemical cycles in these environments.

International audience; Active hydrothermal chimneys host diverse microbial communities exhibiting various metabolisms including those involved in various biogeochemical cycles. To investigate microbe-mineral-fluid interactions in hydrothermal chimney and the driver of microbial diversity, a cultural approach using a gas-lift bioreactor was chosen. An enrichment culture was performed using crushed active chimney sample as inoculum and diluted hydrothermal fluid from the same vent as culture medium. Daily sampling provided time-series access to active microbial diversity and medium composition. Active archaeal and bacterial communities consisted mainly of sulfur, sulfate and iron reducers and hydrogen oxidizers with the detection of Thermococcus, Archaeoglobus, Geoglobus, Sulfurimonas and Thermotoga sequences. The simultaneous presence of active Geoglobus sp. and Archaeoglobus sp. argues against competition for available carbon sources and electron donors between sulfate and iron reducers at high temperature. This approach allowed the cultivation of microbial populations that were under-represented in the initial environmental sample. The microbial communities are heterogeneously distributed within the gas-lift bioreactor; it is unlikely that bulk mineralogy or fluid chemistry is the drivers of microbial community structure. Instead, we propose that micro-environmental niche characteristics, created by the interaction between the mineral grains and the fluid chemistry, are the main drivers of microbial diversity in natural systems.

In deep-sea cold seeps, microbial communities are shaped by geochemical components in seepage solutions. In the present study, we report the composition of microbial communities and potential metabolic activities in the surface sediment of Jiaolong cold seep at the northern South China Sea. Pyrosequencing of 16S rRNA gene amplicons revealed that a majority of the microbial inhabitants of the surface layers (0–6 cm) were sulfur oxidizer bacteria Sulfurimonas and archaeal methane consumer ANME-1, while sulfate reducer bacteria SEEP-SRB1, ANME-1 and ANME-2 dominated the bottom layers (8–14 cm). The potential ecological roles of the microorganisms were further supported by the presence of functional genes for methane oxidation, sulfur oxidation, sulfur reduction and nitrate reduction in the metagenomes. Metagenomic analysis revealed a significant correlation between coverage of 16S rRNA gene of sulfur oxidizer bacteria, functional genes involved in sulfur oxidation and nitrate reduction in different layers, indicating that sulfur oxidizing may be coupled to nitrate reducing at the surface layers of Jiaolong seeping site. This is probably related to the sulfur oxidizers of Sulfurimonas and Sulfurovum, which may be the capacity of nitrate reduction or associated with unidentified syntrophic nitrate-reducing microbes in the surface of the cold seep.

In this study, we categorize the microbial community in mangrove sediment samples from four different locations within a vast mangrove system in Kerala, India. We compared this data to other samples taken from the other known mangrove data, a tropical rainforest, and ocean sediment. An examination of the microbial communities from a large mangrove forest that stretches across southwestern India showed strong similarities across the higher taxonomic levels. When ocean sediment and a single isolate from a tropical rain forest were included in the analysis, a strong pattern emerged with Bacteria from the phylum Proteobacteria being the prominent taxon among the forest samples. The ocean samples were predominantly Archaea, with Euryarchaeota as the dominant phylum. Principal component and functional analyses grouped the samples isolated from forests, including those from disparate mangrove forests and the tropical rain forest, from the ocean. Our findings show similar patterns in samples were isolated from forests, and these were distinct from the ocean sediment isolates. The taxonomic structure was maintained to the level of class, and functional analysis of the genes present also displayed these similarities. Our report for the first time shows the richness of microbial diversity in the Kerala coast and its differences with tropical rain forest and ocean microbiome. DST-SERB; UGC-BSR; twas-cnpq The authors would like to acknowledge the gracious access to research datasets made publicly available by Andreote, Jimenez et al. 2012; DeAngelis, Gladden et al. 2010; Chen, Yang et al. 2013 and to the MG-RAST team for the free availability of the pipeline and server resources. RK thanks to DST-SERB (Young Scientist Award & EEQ project) and also UGC-BSR startup grants for partial financial assistance and the research facilities supported by Central University of Kerala. DB would like to thank twas-cnpq for the PDF fellowship.

To obtain new insights into community compositions of hyperthermophilic microorganisms, defined as having optimal growth temperatures of 80 degrees C and above, sediment and water samples were taken from two shallow marine hydrothermal vents (I and II) with temperatures of 100 degrees C at Vulcano Island, Italy. A combinatorial approach of denaturant gradient gel electrophoresis (DGGE) and metagenomic sequencing was used for microbial community analyses of the samples. In addition, enrichment cultures, growing anaerobically on selected polysaccharides such as starch and cellulose, were also analyzed by the combinatorial approach. Our results showed a high abundance of hyperthermophilic archaea, especially in sample II, and a comparable diverse archaeal community composition in both samples. In particular, the strains of the hyperthermophilic anaerobic genera Staphylothermus and Thermococcus, and strains of the aerobic hyperthermophilic genus Aeropyrum, were abundant. Regarding the bacterial community, e-Proteobacteria, especially the genera Sulfurimonas and Sulfurovum, were highly abundant. The microbial diversity of the enrichment cultures changed significantly by showing a high dominance of archaea, particularly the genera Thermococcus and Palaeococcus, depending on the carbon source and the selected temperature.

Rich animal and microbial communities have been found at deep-sea hydrothermal vents. Although the biogeography of vent macrofauna is well understood, the corresponding knowledge about vent microbial biogeography is lacking. Here, we apply the multilocus sequence analysis (MLSA) to assess the genetic variation of 109 Sulfurimonas strains with greater than or equal to98% 16S rRNA gene sequence similarity, which were isolated from four different geographical regions (Okinawa Trough (OT), Mariana Volcanic Arc and Trough (MVAT), Central Indian Ridge (CIR) and Mid-Atlantic Ridge (MAR)). Sequence typing based on 11 protein-coding genes revealed high genetic variation, including some allele types that are widespread within regions, resulting in 102 nucleotide sequence types (STs). This genetic variation was predominantly due to mutation rather than recombination. Phylogenetic analysis of the 11 concatenated genes showed a clear geographical isolation corresponding to the hydrothermal regions they originated from, suggesting limited dispersal. Genetic differentiation among Sulfurimonas populations was primarily influenced by geographical distance rather than gas composition of vent fluid or habitat, although in situ environmental conditions of each microhabitat could not be examined. Nevertheless, Sulfurimonas may possess a higher dispersal capability compared with deep-sea hydrothermal vent thermophiles. This is the first report on MLSA of deep-sea hydrothermal vent Epsilonproteobacteria, which is indicative of allopatric speciation.

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.

There are still notable gaps regarding the detailed distribution of microorganisms between and within insular habitats such as deep-sea hydrothermal vents. This study investigates the community composition of black smoker vent microorganisms in the Southern Hemisphere, and changes thereof along a spatial and chemical gradient ranging from the vent plume to surrounding waters. We sampled two hydrothermal vent fields, one at the South West Indian Ridge (SWIR), the other at the East Scotia Ridge (ESR). Samples were collected across vent fields at varying vertical distances from the origin of the plumes. The microbial data were sequenced on an Illumina MiSeq platform for the 16SrRNA gene. A substantial amount of vent-specific putative chemosynthetic microorganisms were found, particularly in samples from focused hydrothermal venting. Common vent-specific organisms from both vent fields were the generaArcobacter,CaminibacterandSulfurimonasfrom the Epsilonproteobacteria and the SUP05 group from the Gammaproteobacteria. There were no major differences in microbial composition between SWIR and ESR for focused plume samples. However, within the ESR the diffuse flow and focused samples differed significantly in microbial community composition and relative abundance. For Epsilonproteobacteria, we found evidence of niche-specificity to hydrothermal vent environments. This taxon decreased in abundance by three orders of magnitude from the vent orifice to background water. Epsilonproteobacteria distribution followed a distance–decay relationship as vent-effluents mixed with the surrounding seawater. This study demonstrates strong habitat affinity of vent microorganisms on a metre scale with distinct environmental selection.

International audience; The bacterial diversity of a naturally seeping bitumen source was investigated by 16S rRNA gene cloning and sequencing. Epsilonproteobacteria were shown to dominate the bacterial diversity in the underground water and within the bitumen, representing ca. 75% of the total bacterial diversity. These Epsilonproteobacteria were dominated by Sulfurimonas OTUs, while Sulfurovum and Arcobacter OTUs completed the remaining diversity. Epsilonproteobacteria are sulfur-oxidizer, nitrate-reducing chemo-lithoautotrophic bacteria, unable to use most organics for growth but capable of CO2 fixation. Thus, reduced sulfur species, but not the complex organic matter of the tar, are utilized for growth by bacterial communities at the Puy-de-la-Poix. The large prevalence of populations of Epsilonproteobacteria is a clear indication that crude oil offers a competitive ecological niche for these organisms.

The dynamics of the bacterial community associated with the denitrification process in a fixed bed column reactor (FBCR) were investigated using 454-pyrosequencing methodology. A FBCR filled with elemental sulfur and limestone was operated for about 94 days under autotrophic and mixotrophic (autotrophic + heterotrophic) conditions at 30 °C. Efficient simultaneous bromate and nitrate removal was achieved at feed concentrations of 500 µg/L bromate and 45 mg/L nitrate under autotrophic and mixotrophic conditions. Operational taxonomic units-based analysis (97% similarity cut-off) of bioreactor samples (three periods) revealed that the microbial diversity changed regardless of operational conditions. Sulfurimonas spp. was dominant in the reactor at the adaptation stage. Thiobacillus denitrificans is a chemolithoautotrophic bacterium that is capable of the oxidation of inorganic sulfur compounds. After the adaptation period, the microbial profile changed such that Spirochaetacea spp. and Denitratisoma spp. were major species in the column reactor. After 60 d of operation, Hyphomicrobium vulgare became dominant due to the mixotrophic denitrification conditions.