Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans

In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium

The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains. Sphingobium indicum UT26S exhibited the highest number of genomic islands, while Sphingopyxis alaskensis RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of lin genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the Sphingobium and Sphingomonas genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the czcABCD operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.

Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea

Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼106 cell ml-1) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L-1 d-1 ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.

Seasonal variation in metabolic profiles and microbial communities in a subarctic ore processing plant

The mining industry strives to reduce its water footprint by recycling water in ore processing. This leads to build-up of ions, flotation chemicals and microbial biomass, which may affect the process. The Boliden Kevitsa mine in Northern Finland is exposed to seasonal change and recycles up to 90% of the process water. We studied the variation in size, composition and putative functions of microbial communities in summer and winter in the ore processing plant. The raw water, Cu and Ni thickener overflow waters had statistically significantly higher bacterial numbers in winter compared to summer, and specific summer and winter communities were identified. Metagenomic analysis indicated that Cu and Hg resistance genes, sulphate/thiosulphate, molybdate, iron(III) and zinc ABC transporters, nitrate reduction, denitrification, thiosulphate oxidation and methylotrophy were more common in winter than in summer. Raw water drawn from the nearby river did not affect the microbial communities in the process samples, indicating that the microbial communities and metabolic capacities develop within the process over time in response to the conditions in the processing plant, water chemistry, used chemicals, ore properties and seasonal variation. We propose that the microbial community structures are unique to the Boliden Kevitsa mine and processing plant.

Coupling of the Feammox - Anammox pathways by using a sequential discontinuous bioreactor

Treating nitrogenous compounds in wastewater is a contemporary challenge, prompting novel approaches for ammonium (NH4+) conversion to molecular nitrogen (N2). This study explores the classic anaerobic ammonium oxidation process (Anammox) coupled to the iron-dependent anaerobic ammonium oxidation process (Feammox) in a sequential discontinuous bioreactor (SBR) for NH4+ removal. Feammox and Anammox cultures were individually enriched and combined, optimizing the coupling, and identifying key variables influencing the enrichment process. Adding sodium acetate as a carbon source significantly reduces Fe3+ to Fe2+, indicating Feammox activity. Both Anammox and Feammox processes were successfully operated in SBRs, achieving efficient NH4+ removal (Anammox: 64.6 %; Feammox: 43.4 %). Combining these pathways in a single SBR enhances the NH4+ removal capacity of 50.8 %, improving Feammox efficiency. The Feammox process coupled with Anammox may generate the nitrite (NO2-) needed for Anammox. This research contributes to biotechnological advancements for sustainable nitrogenous compound treatment in SBRs.

Genomic and morphological characterization of a new Thiothrix species from a sulfide hot spring of the Zmeinaya bay (Northern Baikal, Russia)

A survey for bacteria of the genus Thiothrix indicated that they inhabited the area where the water of the Zmeiny geothermal spring (northern basin of Lake Baikal, Russia) mixed with the lake water. In the coastal zone of the lake oxygen (8.25 g/L) and hydrogen sulfide (up to 1 mg/L) were simultaneously present at sites of massive growth of these particular Thiothrix bacteria. Based on the analysis of the morphological characteristics and sequence of individual genes (16S rRNA, rpoB and tilS), we could not attribute the Thiothrix from Lake Baikal to any of the known species of this genus. To determine metabolic capabilities and phylogenetic position of the Thiothrix sp. from Lake Baikal, we analyzed their whole genome. Like all members of this genus, the bacteria from Lake Baikal were capable of organo-heterotrophic, chemolithoheterotrophic, and chemolithoautotrophic growth and differed from its closest relatives in the spectrum of nitrogen and sulfur cycle genes as well as in the indices of average nucleotide identity (ANI < 75-94%), amino acid identity (AAI < 94%) and in silico DNA-DNA hybridization (dDDH < 17-57%), which were below the boundary of interspecies differences, allowing us to identify them as novel candidate species.

Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments

Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. So far chemolithoautotrophic bacteria are widely recognized as the principal diazotrophs in oligotrophic marine and terrestrial ecosystems. However, the contribution of chemolithoautotrophs to nitrogen fixation in organic-rich habitats remains unclear. Here, we utilized metagenomic and metatranscriptomic approaches integrated with cultivation assays to investigate the diversity, distribution, and activity of diazotrophs residing in Zhangzhou mangrove sediments. Physicochemical assays show that the studied mangrove sediments are typical carbon-rich, sulfur-rich, nitrogen-limited, and low-redox marine ecosystems. These sediments host a wide phylogenetic variety of nitrogenase genes, including groups I-III and VII-VIII. Unexpectedly diverse chemolithoautotrophic taxa including Campylobacteria, Gammaproteobacteria, Zetaproteobacteria, and Thermodesulfovibrionia are the predominant and active nitrogen fixers in the 0-18 cm sediment layer. In contrast, the 18-20 cm layer is dominated by active diazotrophs from the chemolithoautotrophic taxa Desulfobacterota and Halobacteriota. Further analysis of MAGs shows that the main chemolithoautotrophs can fix nitrogen by coupling the oxidation of hydrogen, reduced sulfur, and iron, with the reduction of oxygen, nitrate, and sulfur. Culture experiments further demonstrate that members of chemolithoautotrophic Campylobacteria have the nitrogen-fixing capacity driven by hydrogen and sulfur oxidation. Activity measurements confirm that the diazotrophs inhabiting mangrove sediments preferentially drain energy from diverse reduced inorganic compounds other than from organics. Overall, our results suggest that chemolithoautotrophs rather than heterotrophs are dominant nitrogen fixers in mangrove sediments. This study underscores the significance of chemolithoautotrophs in carbon-dominant ecosystems.

Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains

For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved in aliphatic and polycyclic hydrocarbon degradation. Comparative genomic analyses with 18 crude-oil degrading bacteria in addition to two C. oranimense strains not associated with oil were carried out. The data revealed important differences in terms of annotated genes involved in the hydrocarbon degradation process that may explain the molecular mechanisms of hydrocarbon and xenobiotic biotransformation. Notably, many gene families were expanded to explain COTT's competitive ability to manage habitat-specific stressors. Gene-based evidence of the metabolic potential of COTT supports the application of indigenous microbes for the remediation of polluted terrestrial environments and provides a genomic resource for improving our understanding of how to optimize these characteristics for more effective bioremediation.

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

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

Substrate Specificity of Biofilms Proximate to Historic Shipwrecks

The number of built structures on the seabed, such as shipwrecks, energy platforms, and pipelines, is increasing in coastal and offshore regions. These structures, typically composed of steel or wood, are substrates for microbial attachment and biofilm formation. The success of biofilm growth depends on substrate characteristics and local environmental conditions, though it is unclear which feature is dominant in shaping biofilm microbiomes. The goal of this study was to understand the substrate- and site-specific impacts of built structures on short-term biofilm composition and functional potential. Seafloor experiments were conducted wherein steel and wood surfaces were deployed for four months at distances extending up to 115 m away from three historic (>50 years old) shipwrecks in the Gulf of Mexico. DNA from biofilms on the steel and wood was extracted, and metagenomes were sequenced on an Illumina NextSeq. A bioinformatics analysis revealed that the taxonomic composition was significantly different between substrates and sites, with substrate being the primary determining factor. Regardless of site, the steel biofilms had a higher abundance of genes related to biofilm formation, and sulfur, iron, and nitrogen cycling, while the wood biofilms showed a higher abundance of manganese cycling and methanol oxidation genes. This study demonstrates how substrate composition shapes biofilm microbiomes and suggests that marine biofilms may contribute to nutrient cycling at depth. Analyzing the marine biofilm microbiome provides insight into the ecological impact of anthropogenic structures on the seabed.

Nanoplastics impacts on Thiobacillus denitrificans: Effects of size and dissolved organic matter

The widespread distribution of nanoplastics and dissolved organic matter (DOM) in sewage raises concerns about the potential impact of DOM on the bioavailability of nanoplastics. In this study, the effects of different sizes (100 nm and 350 nm) of polystyrene nanoplastics (PS-NPs, 50 mg/L) and combined with 10 mg/L or 50 mg/L DOMs (fulvic acid, humic acid and sodium alginate) on the growth and denitrification ability of Thiobacillus denitrificans were investigated. Results showed that 100 nm PS-NPs (50 mg/L) cause a longer delay in the nitrate reduction (3 days) of T. denitrificans than 350 nm PS-NPs (2 days). Furthermore, the presence of DOM exacerbated the adverse effect of 100 nm PS-NPs on denitrification, resulting in a delay of 1-4 days to complete denitrification. Fulvic acid (50 mg/L) and humic acid (50 mg/L) had the most significant adverse effect on increasing 100 nm PS-NPs (50 mg/L), causing a reduction of 20 mmol/L nitrate by T. denitrificans in nearly 7 days. It is noteworthy that the presence of DOM did not modify the adverse effect of 350 nm PS-NPs on denitrification. Further analysis of toxicity mechanism of PS-NPs revealed that they could induce reactive oxygen species (ROS) and suppressed denitrification gene expression. The results suggested that DOM may assist in the cellular internalization of PS-NPs by inhibiting PS-NPs aggregation, leading to the increased ROS levels and accelerated T. denitrificans death. This study highlights the potential risk of nanoplastics to autotrophic denitrifying bacteria in the presence of DOM and provides new insights for the treatment of nitrogen-containing wastewater by T. denitrificans.

Microbial mats as model to decipher climate change effect on microbial communities through a mesocosm study

Marine environments are expected to be one of the most affected ecosystems by climate change, notably with increasing ocean temperature and ocean acidification. In marine environments, microbial communities provide important ecosystem services ensuring biogeochemical cycles. They are threatened by the modification of environmental parameters induced by climate change that, in turn, affect their activities. Microbial mats, ensuring important ecosystem services in coastal areas, are well-organized communities of diverse microorganisms representing accurate microbial models. It is hypothesized that their microbial diversity and metabolic versatility will reveal various adaptation strategies in response to climate change. Thus, understanding how climate change affects microbial mats will provide valuable information on microbial behaviour and functioning in changed environment. Experimental ecology, based on mesocosm approaches, provides the opportunity to control physical-chemical parameters, as close as possible to those observed in the environment. The exposure of microbial mats to physical-chemical conditions mimicking the climate change predictions will help to decipher the modification of the microbial community structure and function in response to it. Here, we present how to expose microbial mats, following a mesocosm approach, to study the impact of climate change on microbial community.

Synergetic effects of pyrrhotite and biochar on simultaneous removal of nitrate and phosphate in autotrophic denitrification system

In the trend of upgrading wastewater treatment plants, developing advanced treatment technologies for more efficient nutrient removal is crucial. This study prepared a pyrrhotite-biochar composite (Fe_x S_y @BC) to investigate its potential for simultaneous removal of nitrate and phosphate under autotrophic denitrification conditions. X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS) were used to characterize the novel composite of Fe_x S_y @BC, which exhibited 9.2 mg N/(L·d) NO₃ ^- -N reduction rate, 97.3% N₂ production, and 81.8 mmol N/(kg·d) NO₃ ^- -N material load with small solid/liquid ratio (0.008). The NO₃ ^- -N removal with Fe_x S_y @BC was 1.2-2.2 times higher than that with pure iron sulfides or biochar or their mixtures, whereas the Δn(S)/Δn(N) of Fe_x S_y @BC was the lowest (1.80). Moreover, the PO₄ ^3- -P reduction rate of Fe_x S_y @BC reached 3.23 mg P/(L·d), as high as that of pure pyrite or pyrrhotite. Thiobacillus was the most dominant denitrifying bacterium. Fe_x S_y @BC exhibited great promise for enhancing nutrient removal from secondary effluent without additional carbon source. PRACTITIONER POINTS: FexSy@BC enhanced nitrate and phosphate removal simultaneously. First-order kinetics and Monod model were fitted for denitrification with FexSy@BC. FexSy@BC had smaller molar ratio of sulfate release to nitrate removal. Thiobacillus was the dominant bacterium in FexSy@BC autotrophic denitrification. Synergistic effects on nutrients removal existed between biochar and pyrrhotite.

Seasonal variation of microbial community and methane metabolism in coalbed water in the Erlian Basin, China

Coalbed water is a semi-open system connecting underground coalbeds with the external environment. Microorganisms in coalbed water play an important role in coal biogasification and the carbon cycle. The community assemblages of microorganisms in such a dynamic system are not well understood. Here, we used high-throughput sequencing and metagenomic analysis to investigate microbial community structure and identify the potential functional microorganisms involved in methane metabolism in coalbed water in the Erlian Basin, a preferred low-rank coal bed methane (CBM) exploration and research area in China. The results showed that there were differences in the responses of bacteria and archaea to seasonal variation. Bacterial community structure was affected by seasonal variation but archaea was not. Methane oxidation metabolism dominated by Methylomonas and methanogenesis metabolism dominated by Methanobacterium may exist simultaneously in coalbed water.

Iron mediated autotrophic denitrification for low C/N ratio wastewater: A review

In recent years, iron mediated autotrophic denitrification has been a concern because it overcomes the absence of organic carbon and has been successfully used in denitrification for low C/N ratio wastewater. However, there is currently a lack of a more systematic summary of iron-based materials that can be used for denitrification, and no detailed overview about the mechanism of iron mediated autotrophic denitrification has been reported. In this study, the iron materials with different valence states that can be used for denitrification were summarized, and emphasized, as well as the mechanism in different interaction systems were emphasize. In addition, the contribution of various microorganisms in nitrate reduction were analyzed and the effects of operating conditions and water quality were evaluated. Finally, the challenges and shortcomings of the denitrification process were discussed aiming to find better practical engineering applications of iron-based denitrification.

Metagenomic insights into the functions of microbial communities in sulfur-rich sediment of a shallow-water hydrothermal vent off Kueishan Island

Hydrothermal vent (HTV) systems are important habitats for understanding the biological processes of extremophiles on Earth and their relative contributions to material and energy cycles in the ocean. Current understanding on hydrothermal systems have been primarily focused on deep-sea HTVs, and little is known about the functions and metabolisms of microorganisms in shallow-water HTVs (SW-HTVs), which are distinguished from deep-sea HTVs by a depth limit of 200 m. In this study, we analyzed metagenomes of sulfur-rich sediment samples collected from a SW-HTV of Kueishan Island, located in a marginal sea of the western Pacific Ocean. Comparing with a previously published report of pelagic samples from the nearby sampling site, microbial communities in the SW-HTV sediments enriching with genes of both aerobic and anaerobic respiration inferred variable environments in the tested sediments. Abundant genes of energy metabolism encoding sulfur oxidation, H2 oxidation, and carbon fixation were detected from the sediment samples. Sixty-eight metagenome-assembled-genomes (MAGs) were reconstructed to further understand the metabolism and potential interactions between different microbial taxa in the SW-HTVs sediment. MAGs with the highest abundant were chemolithotrophic sulfur-oxidization bacteria, including Sulfurovum represented Campylobacteria involved sox multienzyme, sulfide oxidation genes and rTCA cycle, and Gammaproteobacteria involved dsr gene and CBB cycle. In addition, Desulfobacterota with the potential to participate in sulfur-disproportionating processes also had higher abundance than the sample’s overall mean value. The interaction of these bacterial groups allows the microbial communities to efficiently metabolize a large variety of sulfur compounds. In addition, the potential to use simple organic carbon, such as acetate, was found in chemolithotrophic Campylobacterial MAGs. Collectively, our results revealed the complexity of environmental conditions of the vent sediment and highlight the interactive relationships of the dominant microbial populations in driving sulfur cycles in the SW-HTV sediments off Kueishan Island.

The mixed/mixotrophic nitrogen removal for the effective and sustainable treatment of wastewater: From treatment process to microbial mechanism

Biological nitrogen removal (BNR) is one of the most important environmental concerns in the field of wastewater treatment. The conventional BNR process based on heterotrophic nitrogen removal (HeNR) is suffering from several limitations, including external carbon source dependence, excessive sludge production, and greenhouse gas emissions. Through the mediation of autotrophic nitrogen removal (AuNR), mixed/mixotrophic nitrogen removal (MixNR) offers a viable solution to the optimization of the BNR process. Here, the recent advance and characteristics of MixNR process guided by sulfur-driven autotrophic denitrification (SDAD) and anammox are summarized in this review. Additionally, we discuss the functional microorganisms in different MixNR systems, shedding light on metabolic mechanisms and microbial interactions. The significance of MixNR for carbon reduction in the BNR process has also been noted. The knowledge gaps and the future research directions that may facilitate the practical application of the MixNR process are highlighted. Overall, the prospect of the MixNR process is attractive, and this review will provide guidance for the future implementation of MixNR process as well as deciphering the microbially metabolic mechanisms.

Genome-centric insight into metabolically active microbial population in shallow-sea hydrothermal vents

BACKGROUND

Geothermal systems have contributed greatly to both our understanding of the functions of extreme life and the evolutionary history of life itself. Shallow-sea hydrothermal systems are ecological intermediates of deep-sea systems and terrestrial springs, harboring unique and complexed ecosystems, which are well-lit and present physicochemical gradients. The microbial communities of deep-sea and terrestrial geothermal systems have been well-studied at the population genome level, yet little is known about the communities inhabiting the shallow-sea hydrothermal systems and how they compare to those inhabiting other geothermal systems.

RESULTS

Here, we used genome-resolved metagenomic and metaproteomic approaches to probe into the genetic potential and protein expression of microorganisms from the shallow-sea vent fluids off Kueishantao Island. The families Nautiliaceae and Campylobacteraceae within the Epsilonbacteraeota and the Thiomicrospiraceae within the Gammaproteobacteria were prevalent in vent fluids over a 3-year sampling period. We successfully reconstructed the in situ metabolic modules of the predominant populations within the Epsilonbacteraeota and Gammaproteobacteria by mapping the metaproteomic data back to metagenome-assembled genomes. Those active bacteria could use the reductive tricarboxylic acid cycle or Calvin-Benson-Bassham cycle for autotrophic carbon fixation, with the ability to use reduced sulfur species, hydrogen or formate as electron donors, and oxygen as a terminal electron acceptor via cytochrome bd oxidase or cytochrome bb3 oxidase. Comparative metagenomic and genomic analyses revealed dramatic differences between submarine and terrestrial geothermal systems, including microbial functional potentials for carbon fixation and energy conversion. Furthermore, shallow-sea hydrothermal systems shared many of the major microbial genera that were first isolated from deep-sea and terrestrial geothermal systems, while deep-sea and terrestrial geothermal systems shared few genera.

CONCLUSIONS

The metabolic machinery of the active populations within Epsilonbacteraeota and Gammaproteobacteria at shallow-sea vents can mirror those living at deep-sea vents. With respect to specific taxa and metabolic potentials, the microbial realm in the shallow-sea hydrothermal system presented ecological linkage to both deep-sea and terrestrial geothermal systems. Video Abstract.

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

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

Pyrite-Based Autotrophic Denitrifying Microorganisms Derived from Paddy Soils: Effects of Organic Co-Substrate Addition

The presence of organic co-substrate in groundwater and soils is inevitable, and much remains to be learned about the roles of organic co-substrates during pyrite-based denitrification. Herein, an organic co-substrate (acetate) was added to a pyrite-based denitrification system, and the impact of the organic co-substrate on the performance and bacterial community of pyrite-based denitrification processes was evaluated. The addition of organic co-substrate at concentrations higher than 48 mg L^-1 inhibited pyrite-based autotrophic denitrification, as no sulfate was produced in treatments with high organic co-substrate addition. In contrast, both competition and promotion effects on pyrite-based autotrophic denitrification occurred with organic co-substrate addition at concentrations of 24 and 48 mg L^-1. The subsequent validation experiments suggested that competition had a greater influence than promotion when organic co-substrate was added, even at a low concentration. Thiobacillus, a common chemolithoautotrophic sulfur-oxidizing denitrifier, dominated the system with a relative abundance of 13.04% when pyrite served as the sole electron donor. With the addition of organic co-substrate, Pseudomonas became the dominant genus, with 60.82%, 61.34%, 70.37%, 73.44%, and 35.46% abundance at organic matter concentrations of 24, 48, 120, 240, and 480 mg L^-1, respectively. These findings provide an important theoretical basis for the cultivation of pyrite-based autotrophic denitrifying microorganisms for nitrate removal in soils and groundwater.

Bacterial community response to chronic heavy metal contamination in marine sediments of the East China Sea

Marine sediments act as a sink for various heavy metals, which may have profound impact on sedimentary microbiota. However, our knowledge about the collaborative response of bacterial community to chronic heavy metal contamination remains little. In this study, concentrations of seven heavy metals (As, Cd, Cr, Cu, Hg, Pb, and Zn) in sediments collected from the East China Sea were analyzed and Illumina Miseq 16 S rRNA sequencing was applied to characterize the structure of bacterial community. Microbiota inhabiting sediments in the East China Sea polluted with heavy metals showed different community composition from relatively pristine sites. The response of bacterial community to heavy metal stress was further interrogated with weighted correlation network analysis (WGCNA). WGCNA revealed ten bacterial modules exhibiting distinct co-occurrence patterns and among them, five modules were related to heavy metal pollution. Three of them were positively correlated with an increase in at least one heavy metal concentration, hubs (more influential bacterial taxa) of which were previously reported to be involved in the geochemical cycling of heavy metals or possess tolerance to heavy metals, while another two modules showed opposite patterns. Our research suggested that ecological functional transition might have occurred in East China Sea sediments by shifts of community composition with sensitive modules majorly involved in the meaningful global biogeochemical cycling of carbon, sulfur, and nitrogen replaced by more tolerant groups of bacteria due to long-term exposure to low-concentration heavy metals. Hubs may serve as indicators of perturbations of benthic bacterial community caused by heavy metal pollution and support monitoring remediation of polluted sites in marine environments.

Effect of S2O32--S addition on Anammox coupling sulfur autotrophic denitrification and mechanism analysis using N and O dual isotope effects

Anaerobic ammonia oxidation (Anammox) coupling sulfur autotrophic denitrification is an effective method for the advanced nitrogen removal from the wastewater with limited carbon source. The influence of S₂O₃^2--S addition on Anammox coupling sulfur autotrophic denitrification was investigated by adding different concentrations of S₂O₃^2--S (0, 39, 78, 156 and 312 mg/L) to the Anammox system. The contribution of sulfur autotrophic denitrification and Anammox to nitrogen removal at S₂O₃^2--S concentrations of 156 mg/L was 75% ∼83% and 17%∼25%, respectively, and the mixed system achieved completely nitrogen removal. However, Anammox bioactivity was completely inhibited at S₂O₃^2--S concentrations up to 312 mg/L, and only sulfur autotrophic denitrification occurred. The isotopic effects of NO₂^--N (δ¹⁵N_NO2 and δ¹⁸O_NO2) and NO₃^--N (δ¹⁵N_NO3 and δ¹⁸O_NO3) during Anammox coupling sulfur autotrophic denitrification showed a gradual decrease trend with the increase of S₂O₃^2--S addition. The ratios of δ¹⁵N_NO2:δ¹⁸O_NO2 and δ¹⁵N_NO3:δ¹⁸O_NO3 was maintained at 1.30-2.41 and 1.36-2.52, respectively, which revealed that Anammox was dominant nitrogen removal pathway at S₂O₃^2--S concentrations less than 156 mg/L. Microbial diversity gradually decreased with the increase of S₂O₃^2--S. The S₂O₃^2--S addition enhanced the S₂O₃^2--driven autotrophic denitrification and weakened the Anammox, leading to a gradually decreasing trend of the proportion of Candidatus Brocadia as Anammox bacteria from the initial 27% to 4% (S₂O₃^2--S of 156 mg/L). Yet Norank-f-Hydrogenophilaceae (more than 50%) and Thiobacillus (54%) as functional bacteria of autotrophic denitrification obviously increased. The appropriate amount of S₂O₃^2--S addition promoted the performance of Anammox coupling sulfur autotrophic denitrification achieved completely nitrogen removal.

A new inoculation method of sulfur autotrophic denitrification reactor for accelerated start-up and better low-temperature adaption

Elemental sulfur (S⁰) autotrophic denitrification (SAD) has been proved feasible for nitrate removal from aquatic environments. The long start-up period up to weeks of the SAD reactor impedes its industrial application. To accelerate the start-up process, this study employed S⁰ powder packed sequencing batch reactor operated for 10 days to obtain a seed biofilm, which was inoculated into a regular S⁰ flake packed bed reactor afterwards. Merely two days after inoculation, the reactor inoculated with seed biofilm was well started up and outperformed the control reactor, which was inoculated with regular anaerobic sludge and operated for more than 10 days, delivering much increased denitrification rate of 126 ± 0.68 mg N/(L·d) and a high nitrate removal efficiency of 93.0%. Batch tests during the start-up period showed that the seed biofilm developed well on S⁰ flakes and delivered improved nitrate removal performance than the control. Extracellular polymeric substance (EPS) analysis revealed an abundant content of protein in tightly bound EPS in the biofilm developed from the seed biofilm, which was recognized as a major contributor to facilitate the biofilm's attachment and growth onto S⁰ flakes. After operating under moderate temperature, the reactors were tested at a reduced temperature of 15 °C. Results indicated that the reactor inoculated with seed biofilm showed stronger adaptation ability towards low temperature and sustained better denitrification performance than the control, which was attributed to increased protein content in tightly bound EPS produced by the microbes against low-temperature. Determination of the microbial communities in tested reactors when the whole experiment was closing found that sulfur-related genera were dominating in the packed-bed reactor inculcated with seed biofilm, which played an important role in the S⁰-based denitrification process.

Effects of organic carbon and sulfide on the anammox reaction in the anoxic column in the SRDAPN process for treating high-strength wastewater

Low energy consumption treatment of high-strength wastewater is crucial in controlling groundwater pollution and eutrophication in closed waterbodies. In this study, the sulfate reduction, denitrification/anammox, and partial nitrification (SRDAPN) process, which is an effective organic carbon and nitrogen removal process with low energy consumption for low strength wastewater, was applied to treat livestock wastewater with high COD and sulfate concentration, and microbial reaction and community were examined using an anaerobic-anoxic biological filter reactor that simulates circulation from an aerobic reactor. At a total organic carbon loading rate of 2.7-5.8 kgC/m³·day, sulfate reduction and methane production occurred simultaneously in the anaerobic column of the reactor. Specifically, sulfate reduction resulted in organic matter removal rates of 38 and 26% at ambient temperature and 25 °C, respectively. Furthermore, both heterotrophic and autotrophic denitrification occurred in the anoxic column, and when the organic loading rate in the anoxic reactor was below 0.2 kgC/m³·day, 33%-37% of ammonium and 33%-34% of nitrite were removed by the anammox reaction. Heterotrophic denitrification bacteria (Thauera, Comamonas, and Denitratisoma) and sulfur denitrification bacteria (Sulfurimonas denitrificans) grew in the lower and middle parts of the anoxic column, whereas anammox bacteria (2.5% of Candidatus Brocadia at ambient temperature and 9.4% of Candidatus Kuenenia at 25 °C) grew in the upper part of the anoxic column. These results indicate that the SRDAPN process based on sulfur cycle and anammox is useful for treatment of high strength wastewater with low energy consumption.

Recent Advances in Autotrophic Biological Nitrogen Removal for Low Carbon Wastewater: A Review

Due to carbon source dependence, conventional biological nitrogen removal (BNR) processes based on heterotrophic denitrification are suffering from great bottlenecks. The autotrophic BNR process represented by sulfur-driven autotrophic denitrification (SDAD) and anaerobic ammonium oxidation (anammox) provides a viable alternative for addressing low carbon wastewater. Whether for low carbon municipal wastewater or industrial wastewater with high nitrogen, the SDAD and anammox process can be suitably positioned accordingly. Herein, the recent advances and challenges to autotrophic BNR process guided by SDAD and anammox are systematically reviewed. Specifically, the present applications and crucial operation factors were discussed in detail. Besides, the microscopic interpretation of the process was deepened in the viewpoint of functional microbial species and their physiological characteristics. Furthermore, the current limitations and some future research priorities over the applications were identified and discussed from multiple perspectives. The obtained knowledge would provide insights into the application and optimization of the autotrophic BNR process, which will contribute to the establishment of a new generation of efficient and energy-saving wastewater nitrogen removal systems.

Hybrid zeolite-based ion-exchange and sulfur oxidizing denitrification for advanced slaughterhouse wastewater treatment

The discharge of slaughterhouse wastewater (SWW) is increasing and its wastewater has to be treated thoroughly to avoid the eutrophication. The hybrid zeolite-based ion-exchange and sulfur autotrophic denitrification (IX-AD) process was developed to advanced treat SWW after traditional secondary biological process. Compared with traditional sulfur oxidizing denitrification (SOD), this study found that IX-AD column showed: (1) stronger ability to resist NO₃^- pollution load, (2) lower SO₄^2- productivity, and (3) higher microbial diversity and richness. Liaoning zeolites addition guaranteed not only the standard discharge of NH₄⁺-N, but also the denitrification performance and effluent TN. Especially, when the ahead secondary biological treatment process run at the ultra-high load, NO₃^--N removal efficiency for IX-AD column was still ~100%, whereas only 64.2% for control SOD column. The corresponding average effluent TN concentrations for IX-AD and SOD columns were 5.89 and 65.55 mg/L, respectively. Therefore, IX-AD is a promising technology for advanced SWW treatment and should be widely researched and popularized.

Biological manganese-dependent sulfide oxidation impacts elemental gradients in redox-stratified systems: indications from the Black Sea water column

The reduction of manganese oxide with sulfide in aquatic redox-stratified systems was previously considered to be mainly chemical, but recent isolation of the Black Sea isolate Candidatus Sulfurimonas marisnigri strain SoZ1 suggests an important role for biological catalyzation. Here we provide evidence from laboratory experiments, field data, and modeling that the latter process has a strong impact on redox zonation in the Black Sea. High relative abundances of Sulfurimonas spp. across the redoxcline in the central western gyre of the Black Sea coincided with the high-level expression of both the sulfide:quinone oxidoreductase gene (sqr, up to 93% expressed by Sulfurimonas spp.) and other sulfur oxidation genes. The cell-specific rate of manganese-coupled sulfide oxidation by Ca. S. marisnigri SoZ1 determined experimentally was combined with the in situ abundance of Sulfurimonas spp. in a one-dimensional numerical model to calculate the vertical sulfide distribution. Abiotic sulfide oxidation was too slow to counterbalance the sulfide flux from euxinic water. We conclude that microbially catalyzed Mn-dependent sulfide oxidation influences the element cycles of Mn, S, C, and N and therefore the prevalence of other functional groups of prokaryotes (e.g., anammox bacteria) in a sulfide-free, anoxic redox zone.

Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in the phylum Chloroflexi

Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in this pathway. Here we present a previously unreported Nir domain architecture in members of phylum Chloroflexi. Phylogenetic analyses of protein domains within Nir indicate that an ancestral horizontal transfer and fusion event produced this chimeric domain architecture. We also identify an expanded genomic diversity of a rarely reported NOR subtype, eNOR. Together, these results suggest a greater diversity of denitrification enzyme arrangements exist than have been previously reported.

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

Metagenomics reveals functional species and microbial mechanisms of an enriched thiosulfate-driven denitratation consortia

In this study, thiosulfate-driven denitratation (TDD) system was successfully established under optimal S/N molar ratio of 1.00, with nitrite accumulation efficiency (NAE) of 82.24 ± 17.09%. This work highlighted that thiosulfate significantly preferred the reduction of nitrate than nitrite. However, after the depletion of thiosulfate, the in-situ formed intermediate product element sulfur (S⁰) served as the main electron donor, and significantly favored the reduction of nitrite than nitrate, which constrained nitrite accumulation and nitrate removal. In addition, metagenomic sequencing revealed that the functional denitratation species might be Thiobacillus_sp._65-29, but the occurrence of Nir-annotated species would decrease nitrite accumulation. Under S/N ratio of 1.00, the decreased abundant Nir-annotated species (e.g., Thiobacillus_sp.), as well as the down-regulated quorum sensing interactions between Nar- and Nir-annotated species were key microbial metabolisms of high NAE in the TDD system. Overall, this work provides new sight into the metagenome-base functional species and metabolic potential of thiosulfate-driven denitratation.

Substrate usage determines carbon flux via the citrate cycle in Helicobacter pylori

Helicobacter pylori displays a worldwide infection rate of about 50%. The Gram-negative bacterium is the main reason for gastric cancer and other severe diseases. Despite considerable knowledge about the metabolic inventory of H. pylori, carbon fluxes through the citrate cycle (TCA cycle) remained enigmatic. In this study, different ¹³ C-labeled substrates were supplied as carbon sources to H. pylori during microaerophilic growth in a complex medium. After growth, ¹³ C-excess and ¹³ C-distribution were determined in multiple metabolites using GC-MS analysis. [U-¹³ C₆ ]Glucose was efficiently converted into glyceraldehyde but only less into TCA cycle-related metabolites. In contrast, [U-¹³ C₅ ]glutamate, [U-¹³ C₄ ]succinate, and [U-¹³ C₄ ]aspartate were incorporated at high levels into intermediates of the TCA cycle. The comparative analysis of the ¹³ C-distributions indicated an adaptive TCA cycle fully operating in the closed oxidative direction with rapid equilibrium fluxes between oxaloacetate-succinate and α-ketoglutarate-citrate. ¹³ C-Profiles of the four-carbon intermediates in the TCA cycle, especially of malate, together with the observation of an isocitrate lyase activity by in vitro assays, suggested carbon fluxes via a glyoxylate bypass. In conjunction with the lack of enzymes for anaplerotic CO₂ fixation, the glyoxylate bypass could be relevant to fill up the TCA cycle with carbon atoms derived from acetyl-CoA.

Diversity of dimethylsulfide-degrading methanogens and sulfate-reducing bacteria in anoxic sediments along the Medway Estuary, UK

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.

Nitrate-Driven Trophic Association of Sulfur-Cycling Microorganisms in Tsunami-Deposited Marine Sediment Revealed by High-Sensitivity 13C-Bicarbonate Probing

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.

Transcriptional and Post-transcriptional Control of the Nitrate Respiration in Bacteria

In oxygen (O2) limiting environments, numerous aerobic bacteria have the ability to shift from aerobic to anaerobic respiration to release energy. This process requires alternative electron acceptor to replace O2 such as nitrate (NO3 -), which has the next best reduction potential after O2. Depending on the organism, nitrate respiration involves different enzymes to convert NO3 - to ammonium (NH4 +) or dinitrogen (N2). The expression of these enzymes is tightly controlled by transcription factors (TFs). More recently, bacterial small regulatory RNAs (sRNAs), which are important regulators of the rapid adaptation of microorganisms to extremely diverse environments, have also been shown to control the expression of genes encoding enzymes or TFs related to nitrate respiration. In turn, these TFs control the synthesis of multiple sRNAs. These results suggest that sRNAs play a central role in the control of these metabolic pathways. Here we review the complex interplay between the transcriptional and the post-transcriptional regulators to efficiently control the respiration on nitrate.

Characteristics of bacterial community structure and function associated with nutrients and heavy metals in coastal aquaculture area

Coastal aquaculture area has become one of the critical zones that are more susceptible to the influence of human activity. Many aquaculture operations invariably result in the accumulation of nutrients and heavy metals in the coastal ecosystem. Our study investigated sediment bacterial community structure and function across 23 sites under the influence of nutrients and heavy metals in the coastal aquaculture area. The habitat environment of the sediment was described by analyzing physicochemical characteristics. Sediment bacterial community structure and diversity were investigated by 16S rRNA sequencing. The sequencing data presented that Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria and Chloroflexi were predominant at phylum level. Variations in the bacterial community composition and diversity were significant (P < 0.01) among different groups (according to the distance from the bank side) which indicated that specific environmental conditions had shaped distinct bacterial community. Specifically, bacterial diversity and composition were significantly influenced by the temperature, salinity, pH, dissolved oxygen (DO), TOC, TON, nitrite, nitrate and heavy metals (P < 0.05). Results related to functional prediction demonstrated that carbon, nitrogen and sulfur metabolism were the dominant processes in the coastal aquaculture area. In the meantime, the potential pathogens such as Arcobacter was found in site S3, which indicated the possible threat to the cultured species in this area. Overall, variations in bacterial communities caused by nutrients and heavy metals can affect biogeochemical cycles, which may provide an indication for the protection of coastal aquaculture environments.

Classroom undergraduate research experiences are a "CURE" that increases engagement by students and teachers

It is widely acknowledged that having experience conducting research is invaluable for undergraduate science students. Most undergraduate research is undertaken by students in a mentor's laboratory, but this limits the number of opportunities for students, as each laboratory can only take on a certain number of undergraduate researchers each semester. Additionally, it is also widely acknowledged that it is difficult for teachers to meet research goals while providing the best possible coursework for undergraduate students. Both of these bottlenecks can be circumvented via Classroom Undergraduate Research Experiences (CUREs), which integrate research into the curricula of structured undergraduate classes. Students enrolled in classes that include CUREs conduct research to address open-ended questions as part of their coursework. In this commentary, I describe the many ways in which CUREs are helpful for students and teachers, as well as considerations for designing successful CUREs. I provide several examples of CUREs from Microbial Physiology laboratory classes and Genomics classes that I have taught. Results from these CUREs have been successfully integrated into many peer-reviewed publications in which the students are co-authors, which has been a boon both to students' post-baccalaureate opportunities, as well as my research agenda.

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

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

Achieving rapid thiosulfate-driven denitrification (TDD) in a granular sludge system

Sulfur-oxidizing bacteria (SOB) can drive a high level of autotrophic denitrification (AD) activity with thiosulfate (S₂O₃^2-) as the electron donor. However, the slow growth of SOB results in a low biomass concentration in the AD reactor and unsatisfactory biological nitrogen removal (BNR). In this study, our goal was to establish a high-rate thiosulfate-driven denitrification (TDD) system via sludge granulation. Granular sludge was successfully cultivated by increasing the nitrogen loading rate stepwise in thiosulfate-oxidizing/nitrate-reducing conditions in an upflow anaerobic blanket reactor. In the mature-granular-sludge reactor, a nitrate removal rate of 280 mg N/L/h was achieved with a nitrate removal efficiency of 97.7%±1.0% at a hydraulic retention time of only 15 minutes, with no nitrite detected in the effluent. Extracellular polymeric substance (EPS) analysis indicated that the proteins in loosely bound and tightly bound EPS were responsible for maintaining the compact structure of the TDD granular sludge. The dynamics of the microbial-community shift were identified by 16S rRNA high-throughput pyrosequencing analysis. The Sulfurimonas genus was found to be enriched at 74.1% of total community and may play the most critical role in the high-rate BNR. The batch assay results reveal that no nitrite accumulation occurred during nitrate reduction because the nitrate reduction rate (75.90±0.67 mg N/g MLVSS/h) was almost equal to the nitrite reduction rate (66.06±1.28 mg N/g MLVSS/h) in the thiosulfate-driven granular sludge reactor. The results of this study provide support for the establishment of a high-rate BNR system that maintains its stability with a low sludge yield.

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

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

Elemental sulfur reduction by a deep-sea hydrothermal vent Campylobacterium Sulfurimonas sp. NW10

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.

Pin-point denitrification for groundwater purification without direct chemical dosing: Demonstration of a two-chamber sulfide-driven denitrifying microbial electrochemical system

The nitrate concentration in groundwater has been increasing over time due to the intensive use of nitrogen fertilizer. Current nitrate removal technologies are restricted by the high operational cost or the inevitable secondary contaminations. This study proposed a two-chamber sulfide-driven denitrifying microbial electrochemical system to denitrify nitrate in its cathode chamber. Instead of conventional organic substrates, sulfide is oxidized in the anode chamber to generate electrons for cathodic denitrification. Long-term performance of this novel system was evaluated over 200 days (100 cycles) of batch-fed operation. With the assistance of anodic microorganisms, sulfide can be directly oxidized to sulfate thus avoiding passivating the anode. Catalyzed by the cathodic microorganisms, complete denitrification was realized with neither nitrite nor nitrous oxide accumulation. Benefiting from the electroautotrophic behavior of the functional microorganisms, high electron utilization efficiencies were achieved, 80% and 85% for the anode (sulfide oxidation) and the cathode (denitrification) respectively. Both observed electrode potentials and microbial analyses revealed that cytochrome c is the crucial electron transfer mediator in the cathodic electron transfer for denitrification. Based on the analysis of planktonic and biofilm microbial samples, anodic and cathodic extracellular electron transfer bioprocesses are proposed, both the direct and mediated electron transfers involved, as were revealed by immobilized and planktonic functional microorganisms, respectively. This study demonstrates the feasibility of purifying nitrate-contaminated groundwater without sacrificing its water quality in a separate mode of treatment. This concept can be extended to a broader field, in which the water requires bio-polishing without introducing unwanted secondary pollution like the post-denitrification of wastewater effluents.

Sulfur and Methane-Oxidizing Microbial Community in a Terrestrial Mud Volcano Revealed by Metagenomics

Mud volcanoes are prominent geological structures where fluids and gases from the deep subsurface are discharged along a fracture network in tectonically active regions. Microbial communities responsible for sulfur and methane cycling and organic transformation in terrestrial mud volcanoes remain poorly characterized. Using a metagenomics approach, we analyzed the microbial community of bubbling fluids retrieved from an active mud volcano in eastern Crimea. The microbial community was dominated by chemolithoautotrophic Campylobacterota and Gammaproteobacteria, which are capable of sulfur oxidation coupled to aerobic and anaerobic respiration. Methane oxidation could be enabled by aerobic Methylococcales bacteria and anaerobic methanotrophic archaea (ANME), while methanogens were nearly absent. The ANME community was dominated by a novel species of Ca. Methanoperedenaceae that lacked nitrate reductase and probably couple methane oxidation to the reduction of metal oxides. Analysis of two Ca. Bathyarchaeota genomes revealed the lack of mcr genes and predicted that they could grow on fatty acids, sugars, and proteinaceous substrates performing fermentation. Thermophilic sulfate reducers indigenous to the deep subsurface, Thermodesulfovibrionales (Nitrospirae) and Ca. Desulforudis (Firmicutes), were found in minor amounts. Overall, the results obtained suggest that reduced compounds delivered from the deep subsurface support the development of autotrophic microorganisms using various electron acceptors for respiration.

Characterization of eubacterial communities by Denaturing Gradient Gel Electrophoresis (DGGE) and Next Generation Sequencing (NGS) in a desulfurization biotrickling filter using progressive changes of nitrate and nitrite as final electron acceptors

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.

Iron sulphides mediated autotrophic denitrification: An emerging bioprocess for nitrate pollution mitigation and sustainable wastewater treatment

Iron sulphides, mainly in the form of mackinawite (FeS), pyrrhotite (Fe_1-xS, x = 0-0.125) and pyrite (FeS₂), are the most abundant sulphide minerals and can be oxidized under anoxic and circumneutral pH conditions by chemoautotrophic denitrifying bacteria to reduce nitrate to N₂. Iron sulphides mediated autotrophic denitrification (ISAD) represents an important natural attenuation process of nitrate pollution and plays a pivotal role in linking nitrogen, sulphur and iron cycles in a variety of anoxic environments. Recently, it has emerged as a promising bioprocess for nutrient removal from various organic-deficient water and wastewater, due to its specific advantages including high denitrification capacity, simultaneous nitrogen and phosphorus removal, self-buffering properties, and fewer by-products generation (sulphate, waste sludge, N₂O, NH₄⁺, etc.). This paper provides a critical overview of fundamental and engineering aspects of ISAD, including the theoretical knowledge (biochemistry, and microbial diversity), its natural occurrence and engineering applications. Its potential and limitations are elucidated by summarizing the key influencing factors including availability of iron sulphides, low denitrification rates, sulphate emission and leaching heavy metals. This review also put forward two key questions in the mechanism of anoxic iron sulphides oxidation, i.e. dissolution of iron sulphides and direct substrates for denitrifiers. Finally, its prospects for future sustainable wastewater treatment are highlighted. An iron sulphides-based biotechnology towards next-generation wastewater treatment (NEO-GREEN) is proposed, which can potentially harness bioenergy in wastewater, incorporate resources (P and Fe) recovery, achieve simultaneous nutrient and emerging contaminants removal, and minimize waste sludge production.

Integrative taxonomy revisits the ontogeny and trophic niches of Rimicaris vent shrimps

Among hydrothermal vent species, Rimicaris exoculata is one of the most emblematic, hosting abundant and diverse ectosymbioses that provide most of its nutrition. Rimicaris exoculata co-occurs in dense aggregates with the much less abundant Rimicaris chacei in many Mid-Atlantic Ridge vent fields. This second shrimp also houses ectosymbiotic microorganisms but has a mixotrophic diet. Recent observations have suggested potential misidentifications between these species at their juvenile stages, which could have led to misinterpretations of their early-life ecology. Here, we confirm erroneous identification of the earliest stages and propose a new set of morphological characters unambiguously identifying juveniles of each species. On the basis of this reassessment, combined use of C, N and S stable isotope ratios reveals distinct ontogenic trophic niche shifts in both species, from photosynthesis-based nutrition before settlement, towards a chemosynthetic diet afterwards. Furthermore, isotopic compositions in the earliest juvenile stages suggest differences in larval histories. Each species thus exhibits specific early-life strategies that would, without our re-examination, have been interpreted as ontogenetic variations. Overall, our results provide a good illustration of the identification issues persisting in deep-sea ecosystems and the importance of integrative taxonomy in providing an accurate view of fundamental aspects of the biology and ecology of species inhabiting these environments.

Biological and Bioinspired Inorganic N-N Bond-Forming Reactions

The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.

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

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

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

A novel mesophilic facultative anaerobic bacterium, strain SN118^T, was isolated from a terrestrial mud volcano in Taman Peninsula, Russia. The cells were Gram-negative, motile, short, straight or curved rods with a single polar flagellum. Growth was observed at 5-40 °C (optimum, 30 °C) and pH 5.5-9.5 (optimum, pH 8.0). Growth of strain SN118^T was observed in NaCl concentrations ranging from 0.5 to 8.0 % (w/v) with an optimum at 2.0-3.0 % (w/v). The isolate grew chemolithoautotrophically with sulfide, elemental sulfur or thiosulfate as electron donor, oxygen, nitrate or nitrite as an electron acceptor and CO₂/HCO₃ ^- as a carbon source. Molecular hydrogen or organic substances did not support growth. Nitrate was reduced to N₂. The dominant fatty acids were C_16 : 1ω7c, C_16 : 0 and C_{18  :  1}ω7c. The total size of the genome of the novel isolate was 2 209 279 bp and the genomic DNA G+C content was 38.8 mol%. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas denitrificans DSM 1251^T (96.74 %). Based on its physiological properties and results from phylogenetic analyses, including average nucleotide identity and in silico DNA-DNA hybridization values, the isolate is considered to represent a novel species of the genus Sulfurimonas, for which the name Sulfurimonas crateris sp. nov. is proposed. The type strain is SN118^T (=DSM 109248^T=VKM B-3378^T).

Active sulfur cycling in the terrestrial deep subsurface

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.

Recent advances in partial denitrification in biological nitrogen removal: From enrichment to application

To maximize energy recovery, carbon capture followed by shortcut nitrogen removal is becoming the most promising route in biological wastewater treatment. As the intermediate of microbial denitrification, nitrite could serve as a substrate for anammox bacteria, while N₂O is a combustion promoter that can increase 37% energy release from CH₄ than O₂. Therefore, the important advances in partial denitrification (PD) that produces nitrite or N₂O as the main product using inorganic or organic electron donors were critically reviewed. Specifically, the enrichment strategies of PD microorganisms were obtained by analyzing the selection pressures, metabolism, physiology, and microbiology of these microorganisms. Furthermore, some prospective and promising processes integrating PD microorganisms and the bottlenecks of current applications were discussed. The obtained knowledge would provide new insights into the upgrading of current WWTPs involving commitment to achieve nitrogen removal from wastewaters more economically and environmentally friendly.