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The success of Next generation sequencing (NGS) technology over the past decades has led to a better understanding of complex microbial communities in such environment. Here, we employed NGS to monitor sulfur oxidizing bacteria (SOB) community from cassava starch industry (BPT), which can oxidize H2S into sulfate or elemental sulfur under aerobic conditions. Microbial sludge was collected from two sampling points comprising starting sludge (BPT1) and recirculating sludge (BPT2) of the biotrickling filter. gDNA was extracted from BPT1 and BPT2 samples and removed other contaminations by using the GenepHarM Gel/PCR Kit (Geneaid). DNA concentrations and DNA purity were analyzed by using gel electrophoresis and NanoDrop™ 1000 Spectrophotometer, respectively. Analysis of SOB species using NGS technique was based on the hypervariable regions V4 on the 16S rRNA gene. The comparative genomic hybridization (CGH) microarray probes for detection and identification of SOB species-strain that high expression of soxAXBYZ and fccAB genes in the cassava starch industry. For the recirculating sludge (BPT2), the bacterial communities were dominated by Sulfurimonas (13.7%) followed by Synechococcus (9.4%), Hydrogenophaga (6.5%), Methanosaeta (2.4%), and Acidithiobacillus (2.1%), the same dominant genera were also found in the starting sludge (BPT1), but with slightly different abundancy. The heatmap revealed that Acidithiobacillus caldus species (33.9%–49.9%) could play a vital role in eliminating H2S in biogas from the cassava starch industry. The CGH microarray indicated that Thiothrix, Paracoccus, Sulfurimonas, Hydrogenophaga, Magnetospirillum, Rhodoplanes, Syntrophomonas, Pseudomonas, Sulfuricurvum, and Arcobacter were dominant genus, that has a high expression of sulfur oxidation genes in biotrickling filter.

Subterranean estuaries (STEs), the zones in which seawater and subsurface groundwater mix, are recognized as hotspots for biogeochemical reactions; however, little is known of the microbial communities that control many of those reactions. This study investigated the potential functions of microbes inhabiting a cenote and an offshore submarine spring (Pargos) in the near-coastal waters of the Yucatan Peninsula, Mexico. The inland cenote (Cenote Siete Bocas; C7B) is characterized by a chemocline that is host to an array of physicochemical gradients associated with microbial activities. The chemocline includes an increasing gradient in sulfide concentrations with depth and a decreasing gradient in nitrate concentrations. The microbial community within the chemocline was dominated by Sulfurimonas and Sulfurovum of the Campylobacteria, which are likely responsible for sulfide oxidation coupled with nitrate reduction. Although C7B has not been directly connected with Pargos Spring, water discharging from the spring has physicochemical characteristics and microbial community structures similar to C7B, strongly suggesting biogeochemical processing in the STE impacts groundwater composition prior to discharge. This work yields insight into the microbial communities and biogeochemical reactions in STEs in karstic aquifers and provides evidence for the importance of Campylobacteria in controlling nitrate concentrations exported to marine springs.

The work was aimed at detection of potential degraders of polyethylene terephthalate (PET), polystyrene (PS), and steel 20 based on comparison of the taxonomic composition of the biofilm communities formed on these materials immersed in aqueous environments of diverse origin (marine, natural freshwater, and industrial) in different climatic regions. The libraries obtained by high-throughput sequencing of the 16S rRNA gene V3–V4 region were mainly grouped according to the media types. The composition and relative abundance of the taxa (both at the phylum/class and the genus levels) differed significantly between the groups of libraries; within the groups, these parameters varied depending mainly on the incubation time and on antimicrobial treatment (for industrial samples), while the material of the samples had less effect. Our results indicated that industrial recirculated water was more aggressive against polymer materials, with potential degraders of the polymers (PET and PS) belonging to the genera Pseudomonas, Acidovorax, and Arenimonas. Iron- and sulfur-oxidizing bacteria of the genera Sulfurimonas and Mariprofundus are probably involved in steel biocorrosion in seawater.

Although denitrification-dependent chemolithotrophic sulfur oxidizers proliferated in tsunami-deposited marine sediment with nitrate amendment, their ecophysiological roles in biogeochemical carbon transfer are not addressed. We employed time-resolved high-sensitivity 13C-bicarbonate probing of rRNA to unveil the carbon fixation and resulting trophic relationship of the nitrate-amended sediment microorganisms. Nitrate reduction and sulfur oxidation co-occurred along with significant decreases in the 13CO2 and dissolved bicarbonate concentrations for the first 4 days of the incubation, during which the denitrification-dependent sulfur-oxidizing chemolithotrophs, i.e., the Sulfurimonas sp. HDS01 and Thioalkalispira sp. HDS22 relatives, and the sulfate-reducing heterotrophs, i.e., the Desulfobulbus spp. and Desulfofustis glycolicus relatives, actively incorporated 13C. These indicated that the sulfur oxidizers and sulfate reducers were tightly associated with each other through the direct carbon transfer. Relatives of the fermentative Thalassomonas sediminis and the hydrolytic Pararheinheimera aquatica, in addition to various sulfur-cycling microorganisms, significantly assimilated 13C at day 14. Although the incorporation of 13C was not detected, a syntrophic volatile-fatty-acid oxidizer and hydrogenotrophic methanogens significantly expressed their 16S rRNA molecules at day 21, indicating the metabolic activation of these final decomposers under the latter nutrient-limited conditions. The results demonstrated the nitrate-driven trophic association of sulfur-cycling microorganisms and the subsequent microbial activation and diversification, triggering the restoration of the marine ecosystem function.

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).

Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (previously Epsilonproteobacteria) often dominate the microbial community and that three genera, Arcobacter, Sulfurimonas, and Sulfurovum, frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate activity of each genus under three experimental conditions. To quantify genus-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for Arcobacter, Sulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three genera actively fixed CO2 in short-term (similar to 20 h) incubations, but responded differently to the additions of nitrate and oxygen. Oxygen additions had the largest effect on community composition, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation. The effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. The presented results support the hypothesis that these chemoautotrophic genera possess functionally redundant core metabolic capabilities, but also reveal finer-scale differences in growth likely reflecting adaptation of physiologically-distinct phylotypes to varying oxygen concentrations in situ. Overall, our study provides new insights into how oxygen controls community composition and total chemoautotrophic activity, and underscores how quickly deep-sea vent microbial communities respond to disturbances. IMPORTANCE Sulfidic environments worldwide are often dominated by sulfur-oxidizing, carbon-fixing Campylobacteria. Environmental factors associated with this group's dominance are now understood, but far less is known about the ecology and physiology of members of subgroups of chemoautotrophic Campylobacteria. In this study, we used a novel method to differentiate the genus-specific chemoautotrophic activity of three subtypes of Campylobacteria. In combination with evidence from microscopic counts, chemical consumption/production during incubations, and DNA-based measurements, our data show that oxygen concentration affects both community composition and chemoautotrophic function in situ. These results help us better understand factors controlling microbial diversity at deep-sea hydrothermal vents, and provide first-order insights into the ecophysiological differences between these distinct microbial taxa.

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

International audience; This study investigated the performance and microbiome of cyclic denitrification filters (CDFs) for wood and sulfur heterotrophic-autotrophic denitrification (WSHAD) of saline wastewater. Wood-sulfur CDFs integrated into two pilot-scale marine recirculating aquaculture systems achieved high denitrification rates (103 ± 8.5 g N/(m3·d)). The combined use of pine wood and sulfur resulted in lower SO42− accumulation compared with prior saline wastewater denitrification studies with sulfur alone. Although fish tank water quality parameters, including ammonia, nitrite, nitrate and sulfide, were below the inhibitory levels for marine fish production, lower survival rates of Poecilia sphenops were observed compared with prior studies. Heterotrophic denitrification was the dominant removal mechanism during the early operational stages, while sulfur autotrophic denitrification increased as readily biodegradable organic carbon released from wood chips decreased over time. 16S rRNA-based analysis of the CDF microbiome revealed that Sulfurimonas, Thioalbus, Defluviimonas, and Ornatilinea as notable genera that contributed to denitrification performance.

Siderite (FeCO3) is one kind of abundant and cheap carbonate minerals, but it has never been used as inorganic carbon sources and pH buffer in the sulfur autotrophic denitrification before. In this study, sulfur-siderite autotrophic denitrification (SSAD) system was formed. Batch, column and pilot experiments of the SSAD system showed that siderite could provide inorganic sources and pH buffer for sulfur autotrophic denitrification. The optimal volume ratio of sulfur and siderite was 1:3 for the SSAD system. Siderite could not be used as an electron donor by the sulfur autotrophic denitrifiers. The SSAD column removed 28 mg/L NO3−-N and 3.1 mg/L PO43--P completely at 12 h HRT. The SSAD pilot biofilter during treating secondary effluent obtained stable NO3− and PO43− removal, and controlled effluent NO3−-N and PO43--P around 4 and 0.2 mg/L, respectively, at 4 h HRT, and no blocking occurred in operation of 401 days. In the SSAD system, the main bacteria were Thiobacillus (67.8%), Sulfurimonas (20.0%), and Simplicispira (3.5%); and Sulfurimonas (29.4%), Ferritrophicum (15.2%), and Thiobacillus (10.3%) during treating synthetic wastewater and secondary effluent, respectively. PO43− was removed through iron phosphate precipitate. The SSAD system was a promising way to remove NO3− and PO43− simultaneously from wastewater lack of organic carbon sources.

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 integrated sulfur- and Fe0-based autotrophic denitrification process in an anoxic fluidized-bed membrane bioreactor (AnFB-MBR) was developed for the nitrate-contaminated water treatment in order to control sulfate generation and avoid alkalinity supplement. The nitrate removal rate of the AnFB-MBR reached 1.22 g NO3−-N L−1d−1 with NO3−–N ranging 40–200 mg L−1 at hydraulic retention times of 1.0–5.0 h. The denitrification in the integrated system was simultaneously carried out by sulfur- and Fe0-oxidizing autotrophic denitrifiers. The effluent sulfate generation was decreased by 29.3–70.3% and 31.2–50.9% due to the functional role of Fe0-based denitrification in the integrated system. Alkalinity produced by Fe0-oxidizing autotrophic denitrification could compensate for the alkalinity consumption by sulfur-based autotrophic denitrification. The sulfur- and Fe0-oxidizing autotrophic denitrifying bacterial consortium was composed mainly of bacteria from Thiobacillus, Sulfurimonas, and Geothrix genera. The integrated modes leads to a harmonious co-existence of sulfur- and Fe0-oxidizing denitrifying microbes, which may make a difference to the functional performance of the bioreactor. Overall, the integrated sulfur- and Fe0-based autotrophic denitrification could overcome the shortcomings of excess sulfate generation and external alkalinity supplementation compared to the sole sulfur-based autotrophic denitrification, indicating further potential for the technology in practice.

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.

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.

Compacted bentonites are one of the best sealing and backfilling clays considered for use in Deep Geological Repositories of radioactive wastes. However, an in-depth understanding of their behavior after placement in the repository is required, including if the activity of indigenous microorganisms affects safety conditions. Here we provide an optimized phenol:chloroform based protocol that facilitates higher DNA-yields when other methods failed. To demonstrate the efficiency of this method, DNA was extracted from acetate-treated bentonites compacted at 1.5 and 1.7 g/cm3 densities after 24 months anoxic incubation. Among the 16S rRNA gene sequences identified, those most similar to taxa mediating biogeochemical sulfur cycling included sulfur oxidizing (e.g., Thiobacillus, and Sulfurimonas) and sulfate reducing (e.g., Desulfuromonas and Desulfosporosinus) bacteria. In addition, iron-cycling populations included iron oxidizing (e.g., Thiobacillus and Rhodobacter) plus reducing taxa (e.g., Geobacillus). Genera described for their capacity to utilize acetate as a carbon source were also detected such as Delftia and Stenotrophomonas. Lastly, microscopic analyses revealed pores and cracks that could host nanobacteria or spores. This study highlights the potential role of microbial driven biogeochemical processes in compacted bentonites and the effect of high compaction on microbial diversity in Deep Geological Repositories.

A novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, designated strain NW8NT, 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 NW8NT 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 NW8NT were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 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 GO25T (97.4 % sequence identity). The average nucleotide identity and DNA–DNAhybridization values between strain NW8NT and S. paralvinellae GO25T was 77.8 and 21.1 %, respectively. Based on the phylogenetic, genomic and phenotypic data presented here, strain NW8NT represents a novel species of the genus Sulfurimonas , for which the name Sulfurimonas indica sp. nov. is proposed, with the type strain NW8NT (=MCCC 1A13988T=KTCC 15780T).

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).

Municipal landfills are hot spots of dynamic bioprocesses facilitated by complex interactions of a multifaceted microbiome, whose functioning in municipal landfills at different maturing stages is poorly understood. This study determined bacterial community composition, interaction conetworks, metabolic functions, and controlling physicochemical properties in two landfills aged 14 and 36 years. High throughput sequencing revealed a similar distribution of bacterial diversity, evenness, and richness in the 14‐ and 36‐year‐old landfills in the 0–90 cm depth. At deeper layers (120–150 cm), the 14‐year‐old landfill had significantly greater bacterial diversity and richness indicating that it is a more active microcosm than the 36‐year‐old landfill, where phylum Epsilonbacteraeota was overwhelmingly dominant. The taxonomic and functional diversity in the 14‐year‐old landfill was further reflected by the abundant presence of indicator genera Pseudomonas,Lutispora,Hydrogenspora, and Sulfurimonas coupled with the presence of biomarker enzymes associated with carbon (C), nitrogen (N), and sulfur (S) metabolism. Furthermore, canonical correspondence analysis revealed that bacteria in the 14‐year‐old landfill were positively correlated with high C, N, S, and phosphorus resulting in positive cooccurrence interactions. In the 36‐year‐old landfill, negative coexclusion interactions populated by members of N fixing Rhizobiales were dominant, with metabolic functions and biomarker enzymes predicting significant N fixation that, as indicated by interaction network, potentially inhibited ammonia‐intolerant bacteria. Overall, our findings show that diverse bacterial community in the 14‐year‐old landfill was dominated by copiotrophs associated with positive conetworks, whereas the 36‐year‐old landfill was dominated by lithotrophs linked to coexclusion interactions that greatly reduced bacterial diversity and richness., Greater bacterial diversity, richness, and evenness were observed in a new landfill site (NS) than an old landfill site (OS) at 90–150 cm depth. Bacteria positively correlated with K, Ca, and Mn in OS and with TC, TN, and moisture content in NS. Negative coexclusion interactions dominated in OS while positive cooccurrence interactions were found in NS.

Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (prev. Epsilonproteobacteria) often dominate the microbial community and that three subgroups - Arcobacter, Sulfurimonas and Sulfurovum - frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate the activities of each group under three distinct incubation conditions. In order to quantify group-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for Arcobacter, Sulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in-situ hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three groups actively fixed CO2 in short-term (~ 20 h) incubations with either nitrate, oxygen, or no additions (control) at similar per-cell carbon fixation rates. Oxygen additions had the largest effect on community composition and overall cell numbers, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation for all three groups. Interestingly, the effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. Higher carbon fixation rates in oxygen-amended treatments were noted for all three taxa after an unintended disturbance to the sample site that may have selected for more oxygen-tolerant phylotypes. When viewed from a coarse taxonomic level, our data support assertions that these chemoautotrophic groups are functionally redundant in terms of their core metabolic capabilities since they were simultaneously active under all incubation conditions. In contrast, the higher resolution of amplicon sequencing allowed us to reveal finer-scale differences in growth that likely reflect adaptation of physiologically-distinct subtypes to varying oxygen concentrations in situ. Despite this progress, we still know remarkably little about the factors that maintain genomic diversity and allow for stable co-existence among these three campylobacterial groups. Moving forward, we suggest that more subtle biological factors such as enzyme substrate specificity, motility, cell morphology, and tolerance to environmental stress should be more thoroughly investigated to better understand ecological niche differentiation at deep-sea hydrothermal vents.

The distribution and succession of microbial communities along the dispersion path of hydrothermal plumes has not been well investigated. In this study, we collected several types of samples from the Longqi hydrothermal field located on the Southwest Indian Ridge, including hydrothermal plumes at different stages of formation, a suite of water column samples across the non-buoyant hydrothermal plumes above this field, and a background seawater column approximately 350 km away from the hydrothermal field. Using CH4 concentration anomalies, three non-buoyant plume samples between 2,535 m and 2,735 m were identified within the water column. Microbial community compositions within these plumes and background seawater samples were examined based on the 16S rRNA genes and revealed significant variations and successions in community composition between different portions of the hydrothermal plumes. Near the vent orifice, representing the initial stage of plume formation, microbial populations were characterized by abundant and diverse putative vent-associated communities including (hyper)thermophiles such as Aquificaceae and Hydrogenothermaceae within the phylum Aquificae, and some epsilonproteobacterial chemolithoautotrophs such as Sulfurovum, Sulfurimonas, and Caminibacter. By contrast, in the rising buoyant plumes and adjacent seawaters, most vent-associated microbial taxa were still present but made only minor contributions to community composition. Some microbial taxa that are common in seawater columns such as alphaproteobacterial Sphingomonadaceae and SAR11 clade, deltaproteobacterial SAR324 clade, and gammaproteobacterial Pseudomonas, together with Sulfurimonas and SUP05 clade, became predominant. Members within the Sulfurimonas and SUP05 clade flourished with considerable abundance in the non-buoyant plumes, although these plumes were mainly composed of alphaproteobacterial Rhodobacteraceae, gammaproteobacterial Alteromonadaceae and Saccharospirillaceae putatively derived from the surrounding ambient seawater. We also analyzed archaeal components in the initial discharge and rising buoyant plume stages, with both primarily consisting of thaumarchaeal Nitrosopumilales and euryarchaeal Marine Group II. Our results indicated that being characteristic microbial lineages within the hydrothermal plumes of the Southwest Indian Ridge, both Sulfurimonas and SUP05 clade display a common and abundant distribution across the plume path. However, out of these clades, Sulfurimonas is more abundant and widespread.

This study was carried out to determine the effect of influent nitrate loading on nitrite accumulation during elemental-sulfur based denitrification process, and proposed to enhance the nitrogen removal efficiency by mitigating nitrite accumulation with thiosulfate as external electron donor. Along with increasing the nitrate influent loading (from 0.09 kg N/m3/d to 1.73 kg N/m3/d) by shortening the empty bed contact time (EBCT) (from 5 h to 0.25 h), the nitrate removal loading increased from 0.08 to 0.83 kg N/m3/d. Meanwhile, the raise of the nitrate influent loading obviously aggravated the nitrite accumulation. Herein, nitrite began to accumulate since the nitrate influent loading was over 0.86 kg N/m3/d, and a maximum nitrite accumulation of 2.39 mg/L was observed under the 0.25 h of EBCT and 15 mg/L of nitrate influent concentration condition. Thiosulfate was used as the external electron donor to accelerate the nitrite reduction rate in order to mitigate the nitrite accumulation. As a result, the nitrite accumulation significantly decreased from 2.39 mg/L to 0.17 mg/L with the thiosulfate dosage of 13.36 mg/L. However, the nitrite accumulation bounced with the on-going increase of the thiosulfate dosage, indicating that the nitrate reduction rate and nitrite reduction rate were accelerated alternatively. After dosing thiosulfate, the relative abundances of sulfurimonas and ferritrophicum grew up significantly.

Nitrate has been widely used in sewer systems for sulfide control. However, significant chemical consumption and the loss of carbon source were observed in previous studies. To find a feasible and cost-effective control strategy of the sulfide control, the effect of nitrate combined with sodium nitroprusside (SNP) dosage strategy was tested in lab-scale sewer biofilm reactors. Results showed that nitrate and SNP were strongly synergistic, with 30 mg N/L nitrate and 20 mg/L SNP being sufficient for sulfide control in this study. While large amount of nitrate alone (100 mg N/L) is required to achieve the same sulfide control effectiveness. Meanwhile, the nitrate combined with SNP could reduce the organic carbon source loss by 80%. Additionally, the high-throughput sequencing results showed that the relative abundance of autotrophic, nitrate reducing-sulfide oxidizing bacteria genera (a-NR-SOB) such as Arcobacter and Sulfurimonas was increased by around 18%, while the heterotrophic, nitrate-reducing bacteria (hNRB) such as Thauera was substantially reduced. It demonstrated that the sulfide control was mainly due to the a-NR-SOB activity under the nitrate and SNP dosing strategy. The microbial functional prediction further revealed that nitrate and SNP promoted the dissimilatory nitrate reduction process which utilizes sulfide as an effective electron donor. Moreover, economic assessment indicated that using the combination of nitrate and SNP for sulfide control in sewers would lower the chemical costs by approximately 35% compared with only nitrate addition.