Haloalkaliphilic sulfur-oxidizing bacteria in soda lakes

Revealing cellular (poly)sulphide storage in electrochemically active sulphide oxidising bacteria using rotating disc electrodes

Sulphide oxidising bacteria (SOB) have the potential to be used for bioelectrochemical removal, i.e. oxidation, of sulphide from waste streams. In anaerobic conditions, SOB are able to spatially separate sulphide removal and terminal electron transfer to an electrode and act as a sulphide shuttle. However, it is not fully understood how SOB anaerobically remove sulphide and store charge equivalents, and where in this process sulphur is formed. Therefore, the redox behaviour of sulphide shuttling SOB was investigated at haloalkaline conditions using a glassy carbon rotating disc electrode (RDE) and cyclic voltammetry. Voltammograms of SOB in the absence and presence of sulphide were compared to voltammograms of abiotic sulphur species solutions. Polysulphide and sulphide showed different redox behaviour, with distinct potentials for oxidation of > -0.3 V (vs. Ag/AgCl) for polysulphide and > -0.1 V for sulphide. Comparing biotic to abiotic experiments lead to the hypothesis that SOB formed polysulphides during anaerobic sulphide removal, which stayed sorbed to the cells. With this study, further steps were taken in elucidating the mechanisms of sulphide shuttling by SOB.

Undisclosed contribution of microbial assemblages selectively enriched by microplastics to the sulfur cycle in the large deep-water reservoir

The accumulation of microplastics in reservoirs due to river damming has drawn considerable attention due to their potential impacts on elemental biogeochemical cycling at the watershed scale. However, the effects of plastisphere communities on the sulfur cycle in the large deep-water reservoir remain poorly understood. Here, we collected microplastics and their surrounding environmental samples in the water and sediment ecosystems of Xiaowan Reservoir and found a significant spatiotemporal pattern of microplastics and sulfur distribution in this Reservoir. Based on the microbial analysis, plastic-degrading taxa (e.g., Ralstonia, Rhodococcus) involved in the sulfur cycle were enriched in the plastisphere of water and sediment, respectively. Typical thiosulfate oxidizing bacteria Limnobacter acted as keystone species in the plastisphere microbial network. Sulfate, oxidation reduction potential and organic matter drove the variations of the plastisphere. Environmental filtration significantly affected the plastisphere communities, and the deterministic process dominated the community assembly. Furthermore, predicted functional profiles related to sulfur cycling, compound degradation and membrane transport were significantly enriched in the plastisphere. Overall, our results suggest microplastics as a new microbial niche exert different effects in water and sediment environments, and provide insights into the potential impacts of the plastisphere on the sulfur biogeochemical cycle in the reservoir ecosystem.

Utilization of gene manipulation system for advancing the biotechnological potential of halophiles: A review

Halophiles are salt-loving microorganisms known to have their natural resistance against media contamination even when cultivated in nonsterile and continuous bioprocess system, thus acting as promising cell factories for Next Generation of Industrial Biotechnology (NGIB). NGIB - a successor to the traditional industrial biotechnology, is a more sustainable and efficient bioprocess technology while saving energy and water in a more convenient way as well as reducing the investment cost and skilled workforce requirement. Numerous studies have achieved intriguing outcomes during synthesis of different metabolite using halophiles such as polyhydroxyalkanoates (PHA), ectoine, biosurfactants, and carotenoids. Present-day development in genetic maneuverings have shown optimistic effects on the industrial applications of halophiles. However, viable and competent genetic manipulation system and gene editing tools are critical to accelerate the process of halophile engineering. With the aid of such powerful gene manipulation systems, exclusive microbial chassis are being crafted with desirable features to breed another innovative area of research such as synthetic biology. This review provides an aerial perspective on how the expansion of adaptable gene manipulation toolkits in halophiles are contributing towards biotechnological advancement, and also focusses on their subsequent application for production improvement. This current methodical and comprehensive review will definitely help the scientific fraternity to bridge the gap between challenges and opportunities in halophile engineering.

Elemental Sulfur and Organic Matter Amendment Drive Alkaline pH Neutralization and Mineral Weathering in Iron Ore Tailings Through Inducing Sulfur Oxidizing Bacteria

Mineral weathering and alkaline pH neutralization are prerequisites to the ecoengineering of alkaline Fe-ore tailings into soil-like growth media (i.e., Technosols). These processes can be accelerated by the growth and physiological functions of tolerant sulfur oxidizing bacteria (SOB) in tailings. The present study characterized an indigenous SOB community enriched in the tailings, in response to the addition of elemental sulfur (S0) and organic matter (OM), as well as resultant S0oxidation, pH neutralization, and mineral weathering in a glasshouse experiment. The addition of S0 was found to have stimulated the growth of indigenous SOB, such as acidophilic Alicyclobacillaceae, Bacillaceae, and Hydrogenophilaceae in tailings. The OM amendment favored the growth of heterotrophic/mixotrophic SOB (e.g., class Alphaproteobacteria and Gammaproteobacteria). The resultant S0 oxidation neutralized the alkaline pH and enhanced the weathering of biotite-like minerals and formation of secondary minerals, such as ferrihydrite- and jarosite-like minerals. The improved physicochemical properties and secondary mineral formation facilitated organo-mineral associations that are critical to soil aggregate formation. From these findings, co-amendments of S0 and plant biomass (OM) can be applied to enhance the abundance of the indigenous SOB community in tailings and accelerate mineral weathering and geochemical changes for eco-engineered soil formation, as a sustainable option for rehabilitation of Fe ore tailings.

Diversity, Taxonomic Novelty, and Encoded Functions of Salar de Ascotán Microbiota, as Revealed by Metagenome-Assembled Genomes

Salar de Ascotán is a high-altitude arsenic-rich salt flat exposed to high ultraviolet radiation in the Atacama Desert, Chile. It hosts unique endemic flora and fauna and is an essential habitat for migratory birds, making it an important site for conservation and protection. However, there is limited information on the resident microbiota's diversity, genomic features, metabolic potential, and molecular mechanisms that enable it to thrive in this extreme environment. We used long- and short-read metagenomics to investigate the microbial communities in Ascotán's water, sediment, and soil. Bacteria predominated, mainly Pseudomonadota, Acidobacteriota, and Bacteroidota, with a remarkable diversity of archaea in the soil. Following hybrid assembly, we recovered high-quality bacterial (101) and archaeal (6) metagenome-assembled genomes (MAGs), including representatives of two putative novel families of Patescibacteria and Pseudomonadota and two novel orders from the archaeal classes Halobacteriota and Thermoplasmata. We found different metabolic capabilities across distinct lineages and a widespread presence of genes related to stress response, DNA repair, and resistance to arsenic and other metals. These results highlight the remarkable diversity and taxonomic novelty of the Salar de Ascotán microbiota and its rich functional repertoire, making it able to resist different harsh conditions. The highly complete MAGs described here could serve future studies and bioprospection efforts focused on salt flat extremophiles, and contribute to enriching databases with microbial genome data from underrepresented regions of our planet.

Cold Sulfur Springs-Neglected Niche for Autotrophic Sulfur-Oxidizing Bacteria

Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. This metabolically and phylogenetically diverse group of microorganisms inhabits a variety of environments, including extreme environments. Although they have been of interest to microbiologists for more than 150 years, meso- and psychrophilic chemolithoautotrophic sulfur-oxidizing microbiota are less studied compared to the microbiota of hot springs. Several recent studies suggested that cold sulfur waters harbor unique, yet not described, bacterial taxa.

Prokaryotic Community Structure, Abundances, and Potential Ecological Functions in a Mars Analog Salt Lake

Barkol Lake, situated northeast of the Tianshan Mountains, Xinjiang, is a hypersaline lake with abundant sulfate and chloride minerals, which can be a potential analog for microbial saline paleolakes on Mars. The lake water, sediments, and surrounding soils of Barkol Lake were sampled for geochemical analysis and 16S rRNA gene sequencing to investigate the prokaryotic community structure, abundances, interactions, and ecological functions. Results show that (1) prokaryotic community structure differs significantly between biotopes (water, sediment, and soil), with the highest abundances of archaea occurring in water samples and highest prokaryotic diversities in soil samples; (2) archaeal communities are dominated by Halobacterota, Nanoarchaeota, Thermoplasmatota, and Crenarchaeota, while bacterial communities are mainly Proteobacteria, Bacteroidetes, Actinobacteria, Desulfobacterota, Chloroflexi, Gemmatimonadetes, Firmicutes, and Cyanobacteria; (3) the prokaryotic community network for soil is far more complicated and stable than those for water and sediment; (4) soil prokaryotic communities could be significantly affected by environmental factors such as salinity, pH, total sulfur, and Ca²⁺; (5) archaeal communities may play an important role in the nitrogen cycle, while bacterial communities may mainly participate in the sulfur cycle. This study extends the data set of prokaryotic communities for hypersaline environments, which will provide perspectives into identification of the counterparts and help to understand potential microbial interactions and biogeochemical cycles occurring on Mars.

Bacterial Community Structure of Two Cold Sulfur Springs in Slovakia (Central Europe)

Sulfur-oxidizing bacteria, especially those from hot springs, have attracted the attention of microbiologists for more than 150 years. In contrast, the microbial diversity of cold sulfur springs remains largely unrecognized. Culture-dependent and culture-independent approaches were used to study the diversity of sulfur-oxidizing bacterial communities in two cold sulfur springs in Slovakia. Geological conditions and resulting spring water chemistry appear to be major factors influencing the composition of the sulfur-oxidizing bacterial community. Bacterial communities in both springs were found to be dominated by Proteobacteria with Epsilonproteobacteria being prevalent in the high-salinity Stankovany spring and Alpha- and Gammaproteobacteria in the low-salinity Jovsa spring. Limited overlap was found between culture-dependent and culture-independent approaches with multiple taxa of cultivated sulfur-oxidizing bacteria not being detected by the culture-independent metagenomics approach. Moreover, four cultivated bacterial isolates could represent novel taxa based on the low similarity of their 16S rRNA gene sequence (similarity lower than 98%) to sequences of known bacteria. Our study supports the current view that multiple approaches are required to assess the bacterial diversity in natural habitats and indicates that sulfur springs in Slovakia harbor unique, yet-undescribed microorganisms.

Potential of biological sulphur recovery from thiosulphate by haloalkaliphilic Thioalkalivibrio denitrificans

The aim of this study was to investigate the potential for elemental sulphur recovery from sulphurous solutions under aerobic and anoxic conditions by haloalkalophilic Thioalkalivibrio denitrificans at 0.8-19.6 g S₂O₃^2--S L^-1 and 0.2-0.58 g NO₂ L^-1, respectively. The experiments were conducted as batch assays with haloalkaline (pH 10 and ≥ 14 g Na⁺ L^-1) thiosulphate solution. Aerobically, the highest biotransformation rate of thiosulphate obtained was 0.03 h^-1 at 8.5 g L S₂O₃^2--S. Based on Monod model, the maximum substrate utilisation rate (q_m) was 0.024 h^-1 with half saturation constant (K_s) 0.42 g S₂O₃^2--S L^-1 at initial [S₂O₃^2--S] of 14 g L^-1. S⁰ accumulated at [S₂O₃^2--S] ≥ 1.5 g L^-1 (10% yield at initial 9.5 g S₂O₃^2--S L^-1) and the highest S⁰ yield estimated with the model was 61% with initial [S₂O₃^2--S] of 16.5 g L^-1. Anoxically, the maximum nitrite removal rate based on Monod modelling was 0.011 h^-1 with K_s= 0.84 g NO₂^- L^-1. Aerobically and anoxically the maximum specific growth rates (µ_m) were 0.046 and 0.022 h^-1, respectively. In summary, high-rate aerobic biotransformation kinetics of thiosulphate were demonstrated, whereas the rates were slower and no S⁰ accumulated under anoxic conditions. Thus, future developments of biotechnical applications for the recovery of S⁰ from haloalkaline streams from the process industry should focus on aerobic treatment.HighlightsHaloalkaline S₂O₃^2- biotransformations kinetics by Thioalkalivibrio denitrificansAerobic thiosulphate-S bioconversion up to 0.024 h^-1 with K_s = 0.42 g S₂O₃^2--S L^-110% S⁰ yield with initial 9.5 g S₂O₃^2--S L^-1 in aerobic conditionAnoxic NO₂ removal up to 0.01 h^-1 with K_s = 0.84 g NO₂^- L^-1.

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.

Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations

Lake Hillier is a hypersaline lake known for its distinctive bright pink color. The cause of this phenomenon in other hypersaline sites has been attributed to halophiles, Dunaliella, and Salinibacter, however, a systematic analysis of the microbial communities, their functional features, and the prevalence of pigment-producing-metabolisms has not been previously studied. Through metagenomic sequencing and culture-based approaches, our results evidence that Lake Hillier is composed of a diverse set of microorganisms including archaea, bacteria, algae, and viruses. Our data indicate that the microbiome in Lake Hillier is composed of multiple pigment-producer microbes, including Dunaliella, Salinibacter, Halobacillus, Psychroflexus, Halorubrum, many of which are cataloged as polyextremophiles. Additionally, we estimated the diversity of metabolic pathways in the lake and determined that many of these are related to pigment production. We reconstructed complete or partial genomes for 21 discrete bacteria (N = 14) and archaea (N = 7), only 2 of which could be taxonomically annotated to previously observed species. Our findings provide the first metagenomic study to decipher the source of the pink color of Australia's Lake Hillier. The study of this pink hypersaline environment is evidence of a microbial consortium of pigment producers, a repertoire of polyextremophiles, a core microbiome and potentially novel species.

Composition and key-influencing factors of bacterial communities active in sulfur cycling of soda lake sediments

Bacteria are important participants in sulfur cycle of the extremely haloalkaline environment, e.g. soda lake. The effects of physicochemical factors on the composition of sulfide-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) in soda lake have remained elusive. Here, we surveyed the community structure of total bacteria, SOB and SRB based on 16S rRNA, soxB and dsrB gene sequencing, respectively, in five soda lakes with different physicochemical factors. The results showed that the dominant bacteria belonged to the phyla Proteobacteria, Bacteroidetes, Halanaerobiaeota, Firmicutes and Actinobacteria. SOB and SRB were widely distributed in lakes with different physicochemical characteristics, and the community composition were different. In general, salinity and inorganic nitrogen sources (NH₄⁺-N, NO₃^--N) were the most significant factors. Specifically, the communities of SOB, mainly including Thioalkalivibrio, Burkholderia, Paracoccus, Bradyrhizobium, and Hydrogenophaga genera, were remarkably influenced by the levels of NH₄⁺-N and salinity. Yet, for SRB communities, including Desulfurivibrio, Candidatus Electrothrix, Desulfonatronospira, Desulfonatronum, Desulfonatronovibrio, Desulfonatronobacter and so on, the most significant determinants were salinity and NO₃^--N. Besides, Rhodoplanes played a significant role in the interaction between SOB and SRB. From our results, the knowledge regarding the community structures of SOB and SRB in extremely haloalkaline environment was extended.

Revealing sulfate role in empowering the sulfur-oxidizing capacity of Thioalkalivibrio versutus D301 for an enhanced desulfurization process

Haloalkaliphilic Thioalkalivibrio, a dominant genus for sulfide removal, has attracted growing interest. However, the bacterial biological response to this process's final product, sulfate, has not been well-studied. Here, thiosulfate oxidation and sulfur formation by T. versutus D301 were being enhanced with increasing sulfate supply. With the addition of 0.73 M sulfate, the thiosulfate utilization rate and sulfur production were improved by 68.1% and 120.1% compared with carbonate-grown control at the same salinity (1.8 M). For sulfate-grown cells, based on metabolic analysis, the downregulation of central carbon metabolism indicated that sulfate triggered a decrease in energy conservation efficiency. Additionally, the gene expression analysis further revealed that sulfate induced the inhibition of sulfur to sulfate oxidation, causing the upregulation of thiosulfate to sulfur oxidation for providing cells with additional energy. This study enhances researchers' understanding regarding the sulfate effect on the bio-desulfurization process and presents a new perspective of optimizing the biotechniques.

Recent advances in microbial capture of hydrogen sulfide from sour gas via sulfur-oxidizing bacteria

Biological desulfurization offers several remarkably environmental advantages of operation at ambient temperature and atmospheric pressure, no demand of toxic chemicals as well as the formation of biologically re-usable sulfur (S0), which has attracted increasing attention compared to conventionally physicochemical approaches in removing hydrogen sulfide from sour gas. However, the low biomass of SOB, the acidification of process solution, the recovery of SOB, and the selectivity of bio-S0 limit its industrial application. Therefore, more efforts should be made in the improvement of the BDS process for its industrial application via different research perspectives. This review summarized the recent research advances in the microbial capture of hydrogen sulfide from sour gas based on strain modification, absorption enhancement, and bioreactor modification. Several efficient solutions to limitations for the BDS process were proposed, which paved the way for the future development of BDS industrialization.

Highly integrated adaptive mechanisms in Spiribacter halalkaliphilus, a bacterium abundant in Chinese soda-saline lakes

Soda-saline lakes are polyextreme environments inhabited by many haloalkaliphiles, including one of the most abundant Spiribacter species. However, its mechanisms of adaptation are not ecophysiologically characterized. Based on a large-scale cultivation strategy, we obtained a representative isolate of this Spiribacter species whose relative abundance was the highest (up to 15.63%) in a wide range of salinities in the soda-saline lakes in Inner Mongolia, China. This species is a chemoorganoheterotrophic haloalkaliphile. It has a small and streamlined genome and utilizes a wide variety of compatible solutes to resist osmotic pressure and multiple monovalent cation/proton antiporters for pH homeostasis. In addition to growth enhancement by light under microaerobic conditions, cell growth, organic substrate consumption and polyhydroxybutyrate biosynthesis were also improved by inorganic sulfide. Both quantitative RT-PCR and enzymatic assays verified that sulfide:quinone oxidoreductase was upregulated during this process. Metatranscriptomic analysis indicated that all genes related to environmental adaptation were transcribed in natural environments. Overall, this study has identified a novel abundant haloalkaliphile with multiple and highly integrated adaptive strategies and found that inorganic sulfide was able to improve the adaptation of a heterotroph to polyextreme environments.

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.

Catalytic Properties of Flavocytochrome c Sulfide Dehydrogenase from Haloalkaliphilic Bacterium Thioalkalivibrio paradoxus

Flavocytochrome c sulfide dehydrogenase (FCC) is one of the central enzymes of the respiratory chain in sulfur-oxidizing bacteria. FCC catalyzes oxidation of sulfide and polysulfide ions to elemental sulfur accompanied by electron transfer to cytochrome c. The catalytically active form of the enzyme is a non-covalently linked heterodimer composed of flavin- and heme-binding subunits. The Thioalkalivibrio paradoxus ARh1 genome contains five copies of genes encoding homologous FCCs with an amino acid sequence identity from 36 to 54%. When growing on thiocyanate or thiosulfate as the main energy source, the bacterium synthesizes products of different copies of FCC genes. In this work, we isolated and characterized FCC synthesized during the growth of Tv. paradoxus on thiocyanate. FCC was shown to oxidize exclusively sulfide but not other reduced sulfur compounds, such as thiosulfate, sulfite, tetrathionate, and sulfur, and it also does not catalyze the reverse reaction of sulfur reduction to sulfide. Kinetic parameters of the sulfide oxidation reaction are characterized.

Long Chain Fatty Acid Degradation Coupled to Biological Sulfidogenesis: A Prospect for Enhanced Metal Recovery

This research assessed the microbiological suitability of oleate degradation coupled to sulfidogenesis by enriching communities from anaerobic sludge treating dairy products with S⁰, SO 3 2 - , SO 4 2 - , and S₂ O 3 2 - as electron acceptors. The limiting factor hampering highly efficient oleate degradation was investigated in batch reactors. The best sulfidogenic performance coupled to specialization of the enriched bacterial community was obtained for S⁰- and S₂ O 3 2 - -reducing enrichments, with 15.6 (± 0.2) and 9.0 (± 0.0) mM of sulfide production, respectively. Microbial community analyses revealed predominance of Enterobacteraceae (50.6 ± 5.7%), Sulfurospirillum (23.1 ± 0.1%), Bacteroides (7.5 ± 1.5%) and Seleniivibrio (6.9 ± 1.1%) in S⁰-reducing cultures. In S₂ O 3 2 - -reducing enrichments, the genus Desulfurella predominated (49.2 ± 1.2%), followed by the Enterobacterales order (20.9 ± 2.3%). S⁰-reducing cultures were not affected by oleate concentrations up to 5 mM, while S₂ O 3 2 - -reducing cultures could degrade oleate in concentrations up to 10 mM, with no significant impact on sulfidogenesis. In sequencing batch reactors operated with sulfide stripping, the S⁰-reducing enrichment produced 145.8 mM sulfide, precipitating Zn as ZnS in a separate tank. The S₂ O 3 2 - fed bioreactor only produced 23.4 mM of sulfide precipitated as ZnS. The lower sulfide production likely happened due to sulfite toxicity, an intermediate of thiosulfate reduction. Therefore, elemental sulfur reduction represents an excellent alternative to the currently adopted approaches for LCFA degradation. To the best of our knowledge, this is the first report of oleate degradation with the flux of electrons totally diverted toward sulfide production for metal precipitation, showing great efficiency of LCFA degradation coupled to high levels of metals precipitated as metal sulfide.

Remediation of nitrogen polluted water using Fe-C microelectrolysis and biofiltration under mixotrophic conditions

A hybrid biofilter was established on Fe-C supported carriers aimed to enhance nitrogen removal from polluted water of low Carbon/Nitrogen (C/N) ratio. Effects of organic loadings, hydraulic retention time (HRT), additional electron donor (Fe²⁺) supplementation and operation mode on the performance of the biofilter were investigated. Results showed that up-flow operation mode was better than down-flow mode in terms of nitrate and total nitrogen (TN) removal at low COD/N. The average removal of NO₃^--N, NH₄⁺ -N and TN attained 83.1%, 84.7% and 81.2%, respectively, under the conditions of influent COD/NO₃^--N = 1.5-3.6, HRT = 10 h and up-flow operation. When the biofilter was operated under autotrophic conditions without organic compounds in influent as electron donors, the biofilter achieved a NO₃^--N removal of 46% and TN removal of 56% depending on the innate electron donors provided by the Fe-C carriers. Supplementation of Fe²⁺ in influent further promoted autotrophic denitrifying process, and the removal of NO₃^--N and TN increased to 96.3% and 84.7%, respectively, at the mol ratio of Fe²⁺/NO₃^- = 10 and HRT = 10 h. The microbial community was analyzed for the biofilm samples enriched under heterotrophic and autotrophic conditions. The Fe-C biofilter boosted the growth of a large population of mixotrophic denitrifying bacteria including Gallionella, heterotrophic denitrifying bacteria Denitratisoma, and autotrophic denitrifying bacteria Thiobacillus and Thioalkalispira. On the whole, the biofilter coupled with Fe-C micro-electrolysis provides a novel strategy to treat polluted water of low C/N under both heterotrophic and autotrophic conditions.

Simultaneous H2S mitigation and methanization enhancement of chicken manure through the introduction of the micro-aeration approach

The impact on H₂S alleviation and methane yield enhancement after submitting the anaerobic digestion of chicken manure to a finite amount of air was investigated. The largest reduction in the H₂S biogas content (58% lower) occurred when air intensity of 30 ml/g VS_in was injected into the reactors. Consequently, a maximum methane yield (335 mL-g VS_in^-1), which was 77% higher than the control, was concurrently achieved. Slight sulfate accumulation (<330 mg L^-1) was observed inside the micro-aerated digesters with higher air intensities, suggesting a suppression of sulfide inhibition. Bacterial diversity/richness was enhanced in these digesters while the relative abundance of Methanocelleus increased by 36%. The most important contributing factor to enhancement was the synergistic effect resulting from increments in the hydrolysis rate and the suppression of sulfide inhibition. The results highlighted the potential of in situ H₂S mitigation with the added benefit of methane yield enhancement.

Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia

Soda-saline lakes are a special type of alkaline lake in which the chloride concentration is greater than the carbonate/bicarbonate concentration. Due to the high pH and a usually higher osmotic pressure than that of a normal soda lake, the microbes may need more energy to thrive in such a double-extreme environment. In this study, we systematically investigated the microbiome of the brine and sediment samples of nine artificially separated ponds (salinities from 5.5% to saturation) within two soda-saline lakes in Inner Mongolia of China, assisted by deep metagenomic sequencing. The main inorganic ions shaped the microbial community in both the brines and sediments, and the chloride concentration exhibited the most significant effect. A total of 385 metagenome-assembled genomes (MAGs) were generated, in which 38 MAGs were revealed as the abundant species in at least one of the eighteen different samples. Interestingly, these abundant species also represented the most branches of the microbiome of the soda-saline lakes at the phylum level. These abundant taxa were close relatives of microorganisms from classic soda lakes and neutral saline environments, but forming a combination of both habitats. Notably, approximately half of the abundant MAGs had the potential to drive dissimilatory sulfur cycling. These MAGs included four autotrophic Ectothiorhodospiraceae MAGs, one Cyanobacteria MAG and nine heterotrophic MAGs with the potential to oxidize sulfur, as well as four abundant MAGs containing genes for elemental sulfur respiration. The possible reason is that reductive sulfur compounds could provide additional energy for the related species, and reductions of oxidative sulfur compounds are more prone to occur under alkaline conditions which support the sulfur cycling. In addition, a unique 1,4-alpha-glucan phosphorylation pathway, but not a normal hydrolysis one, was found in the abundant Candidatus Nanohaloarchaeota MAG NHA-1, which would produce more energy in polysaccharide degradation. In summary, this work has revealed the abundant taxa and favorable pathways in the soda-saline lakes, indicating that efficient energy regeneration pathway may increase the capacity for environmental adaptation in such saline-alkaline environments. These findings may help to elucidate the relationship between microbial metabolism and adaptation to extreme environments.

Ceramsite Facilitated Microbial Degradation of Pollutants in Domestic Wastewater

Although constructed wetlands (CWs) are widely used around the world with various substrates, the mechanisms of how these modified substrates affect wastewater treatment are still unknown. In this study, CW microcosms were established with and without ceramsite as a substrate, and the wastewater treatment efficiencies were evaluated during 71 days of incubation. Using the 16S rRNA high-through sequencing, the mechanisms of how CW substrate changed the microbial community was quantified. The results showed that compared to soil as substrate, the use of ceramsite as substrate material enhanced the removal of pollutants from CW systems, particularly under a short retention time (1.5-day) condition. There were more beneficial microorganism groups (nitrogen, sulfur, phosphate) in the ceramsite CW system than the non-ceramsite CW system, particularly in the bottom layers. Moreover, the CW with ceramsite substrate had more nitrification function. All of these results suggested that the ceramsite CW system enhanced the removal of pollutants because it increased the concentration of key microbes that are necessarily for nutrient cycles.

Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India

Anthropogenic activities mediated antibiotic resistance genes (ARGs) in the pristine aquatic bodies (lakes) is raising concern worldwide. Long read shotgun sequencing was used to assess taxonomic diversity, distribution of ARGs and metal resistance genes (MRGs) and mobile genetic elements (MGEs) in six sites within hypersaline Lonar soda lake (India) prone to various anthropogenic activities. Proteobacteria and Euryarchaeota were dominant phyla under domain Bacteria and Archaea respectively. Higher abundance of Bacteroidetes was pragmatic at sites 18LN5 and 18LN6. Functional analysis indicated 26 broad-spectrum ARGs types, not reported earlier in this ecosystem. Abundant ARG types identified were multidrug efflux, glycopepetide, bacitracin, tetracycline and aminogylcoside resistance. Sites 18LN1 and 18LN5 depicted 167 and 160 different ARGs subtypes respectively and rpoB2, bcrA, tetA(48), mupA, ompR, patA, vanR and multidrug ABC transporter genes were present in all samples. The rpoB2 gene was dominant in 18LN1, whereas bcrA gene in 18LN2-18LN6 sites. Around 24 MRGs types were detected with higher abundance of arsenic in 18LN1 and copper in 18LN2-18LN6, signifying metal contamination linked to MRGs. The bacterial taxa Pseudomonas, Thioalkalivibrio, Burkholderia, Clostridium, Paenibacillus, Bacillus and Streptomyces were significantly associated with ARGs. This study highlights the resistomic hotspots in the lake for deploying policies for conservation efforts.

Effect of dimethyl disulfide on the sulfur formation and microbial community composition during the biological H2S removal from sour gas streams

Removal of organic and inorganic sulfur compounds from sour gases is required because of their toxicity and atmospheric pollution. The most common are hydrogen sulfide (H₂S) and methanethiol (MT). Under oxygen-limiting conditions about 92 mol% of sulfide is oxidized to sulfur by haloalkaliphilic sulfur-oxidizing bacteria (SOB), whilst the remainder is oxidized either biologically to sulfate or chemically to thiosulfate. MT is spontaneously oxidized to dimethyl disulfide (DMDS), which was found to inhibit the oxidation of sulfide to sulfate. Hence, we assessed the effect of DMDS on product formation in a lab-scale biodesulfurization setup. DMDS was quantified using a newly, in-house developed analytical method. Subsequently, a chemical reaction mechanism was proposed for the formation of methanethiol and dimethyl trisulfide from the reaction between sulfide and DMDS. Addition of DMDS resulted in significant inhibition of sulfate formation, leading to 96 mol% of sulfur formation. In addition, a reduction in the dominating haloalkaliphilic SOB species, Thioalkalivibrio sulfidiphilus, was observed in favor of Thioalkaibacter halophilus as a more DMDS-tolerant with the 50 % inhibition coefficient at 2.37 mM DMDS.

Long Chain Fatty Acid Degradation Coupled to Biological Sulfidogenesis: A Prospect for Enhanced Metal Recovery

This research assessed the microbiological suitability of oleate degradation coupled to sulfidogenesis by enriching communities from anaerobic sludge treating dairy products with S⁰, SO 3 2 - , SO 4 2 - , and S₂ O 3 2 - as electron acceptors. The limiting factor hampering highly efficient oleate degradation was investigated in batch reactors. The best sulfidogenic performance coupled to specialization of the enriched bacterial community was obtained for S⁰- and S₂ O 3 2 - -reducing enrichments, with 15.6 (± 0.2) and 9.0 (± 0.0) mM of sulfide production, respectively. Microbial community analyses revealed predominance of Enterobacteraceae (50.6 ± 5.7%), Sulfurospirillum (23.1 ± 0.1%), Bacteroides (7.5 ± 1.5%) and Seleniivibrio (6.9 ± 1.1%) in S⁰-reducing cultures. In S₂ O 3 2 - -reducing enrichments, the genus Desulfurella predominated (49.2 ± 1.2%), followed by the Enterobacterales order (20.9 ± 2.3%). S⁰-reducing cultures were not affected by oleate concentrations up to 5 mM, while S₂ O 3 2 - -reducing cultures could degrade oleate in concentrations up to 10 mM, with no significant impact on sulfidogenesis. In sequencing batch reactors operated with sulfide stripping, the S⁰-reducing enrichment produced 145.8 mM sulfide, precipitating Zn as ZnS in a separate tank. The S₂ O 3 2 - fed bioreactor only produced 23.4 mM of sulfide precipitated as ZnS. The lower sulfide production likely happened due to sulfite toxicity, an intermediate of thiosulfate reduction. Therefore, elemental sulfur reduction represents an excellent alternative to the currently adopted approaches for LCFA degradation. To the best of our knowledge, this is the first report of oleate degradation with the flux of electrons totally diverted toward sulfide production for metal precipitation, showing great efficiency of LCFA degradation coupled to high levels of metals precipitated as metal sulfide.

A shared core microbiome in soda lakes separated by large distances

In alkaline soda lakes, concentrated dissolved carbonates establish productive phototrophic microbial mats. Here we show how microbial phototrophs and autotrophs contribute to this exceptional productivity. Amplicon and shotgun DNA sequencing data of microbial mats from four Canadian soda lakes indicate the presence of > 2,000 species of Bacteria and Eukaryotes. We recover metagenome-assembled-genomes for a core microbiome of < 100 abundant bacteria, present in all four lakes. Most of these are related to microbes previously detected in sediments of Asian alkaline lakes, showing that common selection principles drive community assembly from a globally distributed reservoir of alkaliphile biodiversity. Detection of > 7,000 proteins show how phototrophic populations allocate resources to specific processes and occupy complementary niches. Carbon fixation proceeds by the Calvin-Benson-Bassham cycle, in Cyanobacteria, Gammaproteobacteria, and, surprisingly, Gemmatimonadetes. Our study provides insight into soda lake ecology, as well as a template to guide efforts to engineer biotechnology for carbon dioxide conversion.

Microbial Ecology of Biofiltration Units Used for the Desulfurization of Biogas

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

Development and validation of a physiologically based kinetic model for starting up and operation of the biological gas desulfurization process under haloalkaline conditions

Hydrogen sulfide is a toxic and corrosive gas that must be removed from gaseous hydrocarbon streams prior to combustion. This paper describes a gas biodesulfurization process where sulfur-oxidizing bacteria (SOB) facilitate sulfide conversion to both sulfur and sulfate. In order to optimize the formation of sulfur, it is crucial to understand the relations between the SOB microbial composition, kinetics of biological and abiotic sulfide oxidation and the effects on the biodesulfurization process efficiency. Hence, a physiologically based kinetic model was developed for four different inocula. The resulting model can be used as a tool to evaluate biodesulfurization process performance. The model relies on a ratio of two key enzymes involved in the sulfide oxidation process, i.e., flavocytochrome c and sulfide-quinone oxidoreductase (FCC and SQR). The model was calibrated by measuring biological sulfide oxidation rates for different inocula obtained from four full-scale biodesulfurization installations fed with gases from various industries. Experimentally obtained biological sulfide oxidation rates showed dissimilarities between the tested biomasses which could be explained by assuming distinctions in the key-enzyme ratios. Hence, we introduce a new model parameter α to whereby α describes the ratio between the relative expression levels of FCC and SQR enzymes. Our experiments show that sulfur production is the highest at low α values.

Development of quantitative PCR for the detection of Alkalilimnicola ehrlichii, Thioalkalivibrio sulfidiphilus and Thioalkalibacter halophilus in gas biodesulfurization processes

Chemolithoautotrophic sulfur-oxidizing bacteria (SOB) are crucial key players in biotechnological processes to remove hydrogen sulfide from sour gas streams. Several different haloalkaliphilic SOB have been detected and isolated from lab- and full-scale facilities, which all performed differently considering end product yields (sulfur and sulfate) and conversion rates. Understanding and regulating bacterial community dynamics in biodesulfurization processes will enable optimization of the process operation. We developed quantitative PCR (qPCR) assays to quantify haloalkaliphilic sulfur-oxidizing gammaproteobacterial species Alkalilimnicola ehrlichii, Thioalkalivibrio sulfidiphilus, and Thioalkalibacter halophilus that dominate bacterial communities of biodesulfurization lab- and full-scale installations at haloalkaline conditions. The specificity and PCR efficiency of novel primer sets were evaluated using pure cultures of these target species. We further validated the qPCR assays by quantification of target organisms in five globally distributed full-scale biodesulfurization installations. The qPCR assays perform a sensitive and accurate quantification of Alkalilimnicola ehrlichii, Thioalkalivibrio sulfidiphilus and Thioalkalibacter halophilus, thus providing rapid and valuable insights into process performance and SOB growth dynamics in gas biodesulfurization systems.

Characterization of plant growth promoting feature of a neutromesophilic, facultatively chemolithoautotrophic, sulphur oxidizing bacterium Delftia sp. strain SR4 isolated from coal mine spoil

A new facultative chemolithoautotrophic heavy metal resistant sulfur-oxidizing bacterium was isolated from spoil sample of an open cast coal mine. FESEM demonstrated that the bacterium from Delftia genus was rod-shaped mucoid and motile. It autotrophically oxidized 20 mM thiosulfate and 1 g l^-1 elemental sulfur to 220 mg l^-1 and 203 mg l^-1 of sulfate, respectively in 7 days under oxic condition and was also able to grow heterotrophically. The strain showed many plant growth promoting properties like production of IAA (23 ug ml^-1), ammonia (6 umol ml^-1), siderophore (55% siderophore unit), and HCN (30 ppm) upon 48 hours of incubation. In Pikovskaya's agar, the strain showed phosphate solubilization index of 2.0 and solubilized tri-calcium phosphate (232 ug ml^-1) and lowered pH from 8.0 to 4.5 within 18 days. The strain yielded promising results on Brassica juncea growth and sulfur, phosphorus, and lead uptake. Where sulfur and phosphorous accumulation was 52 and 116% higher in whole treated plants (derived from microbe-coated seeds), lead accumulation were 81 and 50% higher in shoot and root of the treated plants than control plants (derived from untreated seeds) . These results point that this multifunctional strain can be proposed for phytorestoration of heavy metal contaminated sites.

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

BACKGROUND

Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.

RESULTS

We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L^-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.

CONCLUSIONS

Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.

Investigation of transient forms of sulfur during biological treatment of spent caustic

In the present study, the production of various transient forms of sulfur during biological oxidation of sulfidic spent caustics under haloalkaline conditions in a stirred tank bioreactor is investigated. Also, the effects of abiotic aeration (chemical oxidation), dissolved oxygen (DO) concentration and sodium concentration on forms of sulfur during biological treatment are demonstrated. Thioalkalivibrio versutus strain was used for sulfide oxidation in spent caustic (SC). The aeration had an important effect on sulfide oxidation and its final products. At DO concentrations above 2 mg l^-1, majority of sulfide was oxidized to sulfate. Maximum sulfide removal efficiency (%R) and yield of sulfate production [Formula: see text] was obtained in Na⁺ concentration ranging from 0.6 to 2 M. Abiotic aeration, which is the most important factor of production of thiosulfate, resulted in the formation of an undesired product-polysulfide. However, abiotic aeration can be used as a pretreatment to biological treatment. In the bioreactor the removal efficiency was obtained as 82.7% and various forms of sulfur such as polysulfide, biosulfur, thiosulfate and sulfate was observed during biological treatment of SC.

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2T Using Transcriptomics

Thiocyanate is a moderately toxic and chemically stable sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation.

Thiocyanate (N=C−S⁻) is a moderately toxic, inorganic sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolate-containing plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide pathway and the cyanate pathway, of which only the former has been fully characterized. Use of the cyanate pathway has been shown in only 10 strains of Thioalkalivibrio, a genus of obligately haloalkaliphilic sulfur-oxidizing Gammaproteobacteria found in soda lakes. So far, only the key enzyme in this reaction, thiocyanate dehydrogenase (TcDH), has been purified and studied. To gain a better understanding of the other genes involved in the cyanate pathway, we conducted a transcriptomics experiment comparing gene expression during the growth of Thioalkalivibrio thiocyanoxidans ARh 2^T with thiosulfate with that during its growth with thiocyanate. Triplicate cultures were grown in continuous substrate-limited mode, followed by transcriptome sequencing (RNA-Seq) of the total mRNA. Differential expression analysis showed that a cluster of genes surrounding the gene for TcDH were strongly upregulated during growth with thiocyanate. This cluster includes genes for putative copper uptake systems (copCD, ABC-type transporters), a putative electron acceptor (fccAB), and a two-component regulatory system (histidine kinase and a σ⁵⁴-responsive Fis family transcriptional regulator). Additionally, we observed the increased expression of RuBisCO and some carboxysome shell genes involved in inorganic carbon fixation, as well as of aprAB, genes involved in sulfite oxidation through the reverse sulfidogenesis pathway.

IMPORTANCE Thiocyanate is a moderately toxic and chemically stable sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation.

Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio

Thioalkalivibrio is a genus of obligate chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria. Their habitat are soda lakes which are dual extreme environments with a pH range from 9.5 to 11 and salt concentrations up to saturation. More than 100 strains of this genus have been isolated from various soda lakes all over the world, but only ten species have been effectively described yet. Therefore, the assignment of the remaining strains to either existing or novel species is important and will further elucidate their genomic diversity as well as give a better general understanding of this genus. Recently, the genomes of 76 Thioalkalivibrio strains were sequenced. On these, we applied different methods including (i) 16S rRNA gene sequence analysis, (ii) Multilocus Sequence Analysis (MLSA) based on eight housekeeping genes, (iii) Average Nucleotide Identity based on BLAST (ANIb) and MUMmer (ANIm), (iv) Tetranucleotide frequency correlation coefficients (TETRA), (v) digital DNA:DNA hybridization (dDDH) as well as (vi) nucleotide- and amino acid-based Genome BLAST Distance Phylogeny (GBDP) analyses. We detected a high genomic diversity by revealing 15 new "genomic" species and 16 new "genomic" subspecies in addition to the ten already described species. Phylogenetic and phylogenomic analyses showed that the genus is not monophyletic, because four strains were clearly separated from the other Thioalkalivibrio by type strains from other genera. Therefore, it is recommended to classify the latter group as a novel genus. The biogeographic distribution of Thioalkalivibrio suggested that the different "genomic" species can be classified as candidate disjunct or candidate endemic species. This study is a detailed genome-based classification and identification of members within the genus Thioalkalivibrio. However, future phenotypical and chemotaxonomical studies will be needed for a full species description of this genus.

A Sulfur Oxygenase from the Haloalkaliphilic Bacterium Thioalkalivibrio paradoxus with Atypically Low Reductase Activity

Sequence comparisons showed that the sulfur oxygenase reductase (SOR) of the haloalkaliphilic bacterium Thioalkalivibrio paradoxus Arh 1 (TpSOR) is branching deeply within dendrograms of these proteins (29 to 34% identity). A synthetic gene encoding TpSOR expressed in Escherichia coli resulted in a protein 14.7 ± 0.9 nm in diameter and an apparent molecular mass of 556 kDa. Sulfite and thiosulfate were formed from elemental sulfur in a temperature range of 10 to 98°C (optimum temperature ≈ 80°C) and a pH range of 6 to 11.5 (optimum pH ≈ 9; 308 ± 78 U/mg of protein). Sulfide formation had a maximum specific activity of 0.03 U/mg, or <1% of the corresponding activity of other SORs. Hence, reductase activity seems not to be an integral part of the reaction mechanism. TpSOR was most active at NaCl or glycine betaine concentrations of 0 to 1 M, although 0.2% of the maximal activity was detected even at 5 M NaCl and 4 M betaine. The melting point of TpSOR was close to 80°C, when monitored by circular dichroism spectroscopy or differential scanning fluorimetry; however, the denaturation kinetics were slow: 55% of the residual activity remained after 25 min of incubation at 80°C. Site-directed mutagenesis showed that the active-site residue Cys₄₄ is essential for activity, whereas alanine mutants of the two other conserved cysteines retained about 0.5% residual activity. A model of the sulfur metabolism in T. paradoxus is discussed.

IMPORTANCE

Sulfur oxygenase reductases (SORs) are the only enzymes catalyzing an oxygen-dependent disproportionation of elemental sulfur and/or polysulfides to sulfite, thiosulfate, and hydrogen sulfide. SORs are known from mesophilic and extremophilic archaea and bacteria. All SORs seem to form highly thermostable 24-subunit hollow spheres. They carry a low-potential mononuclear nonheme iron in the active site and an indispensable cysteine; however, their exact reaction mechanisms are unknown. Typically, the reductase activity of SORs is in the range of 5 to 50% of the oxygenase activity, but mutagenesis studies had so far failed to identify residues crucial for the reductase reaction. We describe here the first SOR, which is almost devoid of the reductase reaction and which comes from a haloalkaliphilic bacterium.

Three novel bacteriophages isolated from the East African Rift Valley soda lakes

Background

Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and consequently few bacteriophages that infect bacteria from haloalkaline environments have been described.

Methods

Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on two different Bacillus species and one Paracoccus species using agar overlays. The growth characteristics of each phage in its host was investigated and the genome sequences determined and analysed by comparison with known phages.

Results

Phage Shbh1 belongs to the family Myoviridae while Mgbh1 and Shpa belong to the Siphoviridae family. Tetranucleotide usage frequencies and G + C content suggests that Shbh1 and Mgbh1 do not regularly infect, and have therefore not evolved with, the hosts they were isolated on here. Shbh1 was shown capable of infecting two different Bacillus species from the two different lakes demonstrating its potential broad-host range. Comparative analysis of their genome sequence with known phages revealed that, although novel, Shbh1 does share substantial amino acid similarity with previously described Bacillus infecting phages (Grass, phiNIT1 and phiAGATE) and belongs to the Bastille group, while Mgbh1 and Shpa are highly novel.

Conclusion

The addition of these phages to current databases should help with metagenome/metavirome annotation efforts. We describe a highly novel Paracoccus infecting virus (Shpa) which together with NgoΦ6 and vB_PmaS_IMEP1 is one of only three phages known to infect Paracoccus species but does not show similarity to these phages.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-016-0656-6) contains supplementary material, which is available to authorized users.

Study on Haloalkaliphilic Sulfur-Oxidizing Bacterium for Thiosulfate Removal in Treatment of Sulfidic Spent Caustic

Due to the disadvantages of physiochemical methods for sulfidic spent caustic treatment, attentions are drawn to the environmental-friendly biotreatments including sulfur-oxidizing halo-alkaliphiles. Thioalkalivibrio versutus DSM 13738 was grown at alkaline (pH10) autotrophic medium with sodium carbonate/bicarbonate as the sole source of carbon and amended with sodium thiosulfate as the electron and energy source. The effect of various parameters including temperature (25-40 °C), pH (8-11), NaCl concentration (0.5-5 % w/v) and sodium thiosulfate concentrations (100-750 mM) was evaluated on bacterial growth and thiosulfate removal. This strain could eliminate sodium thiosulfate at very high concentrations up to 750 mM. The results showed that the highest specific growth rate was pH 9.5 and thiosulfate removal of Thioalkalivibrio versutus occurred at pH 10.5. The optimum salt concentration for thiosulfate removal was 2.5 % w/v and 5 % NaCl and specific growth rate elevated 2.5% w/v. It was also specified that this strain thrives occurred in 37 °C and at 35 and 37 °C higher removal of thiosulfate. Following chemical oxidation of sulfide to thiosulfate, application of Thioalkalivibrio versutus could be promising for spent caustic treatment. Since thiosulfate is utilized as an energy source, highest removal efficiency occurred at marginally different conditions compared to optimal growth.

Biocathodes reducing oxygen at high potential select biofilms dominated by Ectothiorhodospiraceae populations harboring a specific association of genes

Biocathodes polarized at high potential are promising for enhancing Microbial Fuel Cell performances but the microbes and genes involved remain poorly documented. Here, two sets of five oxygen-reducing biocathodes were formed at two potentials (-0.4V and +0.1V vs. saturated calomel electrode) and analyzed combining electrochemical and metagenomic approaches. Slower start-up but higher current densities were observed at high potential and a distinctive peak increasing over time was recorded on cyclic voltamogramms, suggesting the growth of oxygen reducing microbes. 16S pyrotag sequencing showed the enrichment of two operational taxonomic units (OTUs) affiliated to Ectothiorodospiraceae on high potential electrodes with the best performances. Shotgun metagenome sequencing and a newly developed method for the identification of Taxon Specific Gene Annotations (TSGA) revealed Ectothiorhodospiraceae specific genes possibly involved in electron transfer and in autotrophic growth. These results give interesting insights into the genetic features underlying the selection of efficient oxygen reducing microbes on biocathodes.

Study on Haloalkaliphilic Sulfur-Oxidizing Bacterium for Thiosulfate Removal in Treatment of Sulfidic Spent Caustic

Due to the disadvantages of physiochemical methods for sulfidic spent caustic treatment, attentions are drawn to the environmental-friendly biotreatments including sulfur-oxidizing halo-alkaliphiles.Thioalkalivibrio versutusDSM 13738 was grown at alkaline (pH10) autotrophic medium with sodium carbonate/bicarbonate as the sole source of carbon and amended with sodium thiosulfate as the electron and energy source. The effect of various parameters including temperature (25-40 °C), pH (8-11), NaCl concentration (0.5-5 % w/v) and sodium thiosulfate concentrations (100-750 mM) was evaluated on bacterial growth and thiosulfate removal. This strain could eliminate sodium thiosulfate at very high concentrations up to 750 mM. The results showed that the highest specific growth rate was pH 9.5 and thiosulfate removal ofThioalkalivibrio versutusoccurred at pH 10.5. The optimum salt concentration for thiosulfate removal was 2.5 % w/v and 5 % NaCl and specific growth rate elevated 2.5% w/v. It was also specified that this strain thrives occurred in 37 °C and at 35 and 37 °C higher removal of thiosulfate. Following chemical oxidation of sulfide to thiosulfate, application ofThioalkalivibrio versutuscould be promising for spent caustic treatment. Since thiosulfate is utilized as an energy source, highest removal efficiency occurred at marginally different conditions compared to optimal growth.

Haloalkaline Bioconversions for Methane Production from Microalgae Grown on Sunlight

Microalgal biomass can be converted to biofuels to replace nonsustainable fossil fuels, but the widespread use of microalgal biofuels remains hampered by the high energetic and monetary costs related to carbon dioxide supply and downstream processing. Growing microalgae in mixed culture biofilms reduces energy demands for mixing, maintaining axenic conditions, and biomass concentration. Furthermore, maintaining a high pH improves carbon dioxide absorption rates and inorganic carbon solubility, thus overcoming the carbon limitation and increasing the volumetric productivity of the microalgal biomass. Digesting the microalgal biomass anaerobically at high pH results in biogas that is enriched in methane, while the dissolved carbon dioxide is recycled to the phototrophic reactor. All of the required haloalkaline conversions are known in nature.

Prokaryotic Community Diversity Along an Increasing Salt Gradient in a Soda Ash Concentration Pond

The effect of salinity on prokaryotic community diversity in Abijata-Shalla Soda Ash Concentration Pond system was investigated by using high-throughput 16S rRNA gene 454 pyrosequencing. Surface water and brine samples from five sites spanning a salinity range of 3.4 % (Lake Abijata) to 32 % (SP230F, crystallizer pond) were analyzed. Overall, 33 prokaryotic phyla were detected, and the dominant prokaryotic phyla accounted for more than 95 % of the reads consisting of Planctomycetes, Bacteroidetes, candidate division TM7, Deinococcus-Thermus, Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota. Diversity indices indicated that operational taxonomic unit (OTU) richness decreases drastically with increasing salinity in the pond system. A total of 471 OTUs were found at 3.4 % salinity whereas 49 OTUs were detected in pond SP211 (25 % salinity), and only 19 OTUs in the crystallization pond at 32 % salinity (SP230F). Along the salinity gradient, archaeal community gradually replaced bacterial community. Thus, archaeal community accounted for 0.4 % in Lake Abijata while 99.0 % in pond SP230F. This study demonstrates that salinity appears to be the key environmental parameter in structuring the prokaryotic communities of haloalkaline environments. Further, it confirmed that the prokaryotic diversity in Lake Abijata is high and it harbors taxa with low or no phylogenetic similarities to existing prokaryotic taxa and thus represents novel microorganisms.

Influence of methanethiol on biological sulphide oxidation in gas treatment system

Inorganic and organic sulphur compounds such as hydrogen sulphide (H2S) and thiols (RSH) are unwanted components in sour gas streams (e.g. biogas and refinery gases) because of their toxicity, corrosivity and bad smell. Biological treatment processes are often used to remove H2S at small and medium scales (<50 tons per day of H2S). Preliminarily research by our group focused on achieving maximum sulphur production from biological H2S oxidation in the presence of methanethiol. In this paper the underlying principles have been further studied by assessing the effect of methanethiol on the biological conversion of H2S under a wide range of redox conditions covering not only sulphur but also sulphate-producing conditions. Furthermore, our experiments were performed in an integrated system consisting of a gas absorber and a bioreactor in order to assess the effect of methanethiol on the overall gas treatment efficiency. This study shows that methanethiol inhibits the biological oxidation of H2S to sulphate by way of direct suppression of the cytochrome c oxidase activity in biomass, whereas the oxidation of H2S to sulphur was hardly affected. We estimated the kinetic parameters of biological H2S oxidation that can be used to develop a mathematical model to quantitatively describe the biodesulphurization process. Finally, it was found that methanethiol acts as a competitive inhibitor; therefore, its negative effect can be minimized by increasing the enzyme (biomass) concentration and the substrate (sulphide) concentration, which in practice means operating the biodesulphurization systems under low redox conditions.

Microbially-driven strategies for bioremediation of bauxite residue

Globally, 3 Gt of bauxite residue is currently in storage, with an additional 120 Mt generated every year. Bauxite residue is an alkaline, saline, sodic, massive, and fine grained material with little organic carbon or plant nutrients. To date, remediation of bauxite residue has focused on the use of chemical and physical amendments to address high pH, high salinity, and poor drainage and aeration. No studies to date have evaluated the potential for microbial communities to contribute to remediation as part of a combined approach integrating chemical, physical, and biological amendments. This review considers natural alkaline, saline environments that present similar challenges for microbial survival and evaluates candidate microorganisms that are both adapted for survival in these environments and have the capacity to carry out beneficial metabolisms in bauxite residue. Fermentation, sulfur oxidation, and extracellular polymeric substance production emerge as promising pathways for bioremediation whether employed individually or in combination. A combination of bioaugmentation (addition of inocula from other alkaline, saline environments) and biostimulation (addition of nutrients to promote microbial growth and activity) of the native community in bauxite residue is recommended as the approach most likely to be successful in promoting bioremediation of bauxite residue.

Effect of Methanethiol Concentration on Sulfur Production in Biological Desulfurization Systems under Haloalkaline Conditions

Bioremoval of H2S from gas streams became popular in recent years because of high process efficiency and low operational costs. To expand the scope of these processes to gas streams containing volatile organic sulfur compounds, like thiols, it is necessary to provide new insights into their impact on overall biodesulfurization process. Published data on the effect of thiols on biodesulfurization processes are scarce. In this study, we investigated the effect of methanethiol on the selectivity for sulfur production in a bioreactor integrated with a gas absorber. This is the first time that the inhibition of biological sulfur formation by methanethiol is investigated. In our reactor system, inhibition of sulfur production started to occur at a methanethiol loading rate of 0.3 mmol L(-1) d(-1). The experimental results were also described by a mathematical model that includes recent findings on the mode of biomass inhibition by methanethiol. We also found that the negative effect of methanethiol can be mitigated by lowering the salinity of the bioreactor medium. Furthermore, we developed a novel approach to measure the biological activity by sulfide measurements using UV-spectrophotometry. On the basis of this measurement method, it is possible to accurately estimate the unknown kinetic parameters in the mathematical model.

Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome

A haloalkaline anaerobic microbial community obtained from soda lake sediments was used to inoculate anaerobic reactors for the production of methane rich biogas. The microalga Spirulina was successfully digested by the haloalkaline microbial consortium at alkaline conditions (pH 10, 2.0 M Na⁺). Continuous biogas production was observed and the obtained biogas was rich in methane, up to 96%. Alkaline medium acted as a CO₂ scrubber which resulted in low amounts of CO₂ and no traces of H₂S in the produced biogas. A hydraulic retention time (HRT) of 15 days and 0.25 g Spirulina L⁻¹ day⁻¹ organic loading rate (OLR) were identified as the optimal operational parameters. Metagenomic and metatranscriptomic analysis showed that the hydrolysis of the supplied substrate was mainly carried out by Bacteroidetes of the “ML635J-40 aquatic group” while the hydrogenotrophic pathway was the main producer of methane in a methanogenic community dominated by Methanocalculus.