Aerobic carboxydotrophy under extremely haloalkaline conditions in Alkalispirillum/Alkalilimnicola strains isolated from soda lakes

Metagenomics and metatranscriptomics insights into microbial enhancement of H2S removal and CO2 assimilation

This study focuses on the coupled process of bio-enhanced absorption and biodesulfurization for the toxic gas H2S and the greenhouse gas CO2. The results show that on the basis of stabilized absorption of H2S and CO2 by alkaline solution (Stage I), the addition of air-lift bioreactor process solution in the absorption column enhanced their absorption (Stage II). Specifically, at constant inlet concentrations of H₂S and CO₂ of 3% (30,000 ppmv) and 30% (300,000 ppmv), respectively, the outlet gases were primarily H₂S, CO₂, and N₂. And the outlet H2S and CO2 concentrations decreased from 10,038 ± 1166 ppmv and 49,897 ± 2545 ppmv in Stage I to 940 ± 163 ppmv and 21,000 ± 2165 ppmv in Stage II. S0-producing performance (348 ± 20-503 ± 23 mg S/L) and biomass concentration (467 ± 13-677 ± 55 mg/L) in the subsequent bioreactor also increased in response to the enhanced absorption of H2S and CO2. Biologically enhanced H2S and CO2 absorption differs from physicochemical factors in that it depends on several physiological parameters such as microbial community composition and gene expression levels. In this study, the sulfur autotrophic denitrifying bacteria Thioalkalivibrio and Arenimonas had high abundance and activity (abundance: 69.5% and 21.1%, expression: 82.4% and 13.9%), and they were the main contributors to the bio-enhanced absorption of H2S and CO2 in this system. In addition, the main factor for enhanced H2S absorption could be the high expression of sulfide:quinone oxidoreductase (SQR, encoding gene sqr) (45 ± 9 to 821 ± 102 transcripts per million). Enhanced CO2 absorption could have been achieved by the oxidation of more H2S generating more energy to increase the carboxylation activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, encoding genes rbcLS). Enhanced H2S absorption enhances CO2 absorption and facilitates microbial growth, which in turn benefits the metabolism of H2S, creating a complementary biologically enhanced absorption. This study provides a novel strategy, demonstrating the potential of autotrophic sulfide-oxidizing microorganisms in the simultaneous removal of H₂S and assimilation of CO₂, and offers a deeper understanding of the underlying mechanisms.

Process conditions affect microbial diversity and activity in a haloalkaline biodesulfurization system

Biodesulfurization (BD) systems that treat sour gas employ mixtures of haloalkaliphilic sulfur-oxidizing bacteria to convert sulfide to elemental sulfur. In the past years, these systems have seen major technical innovations that have led to changes in microbial community composition. Different studies have identified and discussed the microbial communities in both traditional and improved systems. However, these studies do not identify metabolically active community members and merely focus on members' presence/absence. Therefore, their results cannot confirm the activity and role of certain bacteria in the BD system. To investigate the active community members, we determined the microbial communities of six different runs of a pilot-scale BD system. 16S rRNA gene-based amplicon sequencing was performed using both DNA and RNA. A comparison of the DNA- and RNA-based sequencing results identified the active microbes in the BD system. Statistical analyses indicated that not all the existing microbes were actively involved in the system and that microbial communities continuously evolved during the operation. At the end of the run, strains affiliated with Alkalilimnicola ehrlichii and Thioalkalivibrio sulfidiphilus were confirmed as the most active key bacteria in the BD system. This study determined that microbial communities were shaped predominantly by the combination of hydraulic retention time (HRT) and sulfide concentration in the anoxic reactor and, to a lesser extent, by other operational parameters.IMPORTANCEHaloalkaliphilic sulfur-oxidizing bacteria are integral to biodesulfurization (BD) systems and are responsible for converting sulfide to sulfur. To understand the cause of conversions occurring in the BD systems, knowing which bacteria are present and active in the systems is essential. So far, only a few studies have investigated the BD system's microbial composition, but none have identified the active microbial community. Here, we reveal the metabolically active community, their succession, and their influence on product formation.

Anaerobic sulphide removal by haloalkaline sulphide oxidising bacteria

Sulphide is a toxic and corrosive compound and requires removal from waste streams. Recent discoveries show that sulphide oxidising bacteria (SOB) from modern desulphurisation plants are able to spatially separate sulphide removal and oxygen reduction when exposed to intermittent anaerobic and aerobic environments. Here, SOB act as electron shuttles between electron donor and acceptor. The underlying mechanisms for electron shuttling are of yet unknown. To investigate the anaerobic sulphide removal of SOB, batch experiments and mathematical models were applied. The sulphide removal capacity decreased at increasing biomass concentrations. At 0.6 mgN/L SOB could remove up to 8 mgS/mgN in 30 min. It was found that biological activity determines sulphide removal, alongside chemical processes. Anaerobic oxidation of electron carriers was determined to only explain 0.1% of charge storage, where irreversible cleavage of long chain polysulphides could explain full sulphide storage. Different sulphide removal and intracellular storage processes are postulated.

Anaerobic carboxydotrophy in sulfur-respiring haloarchaea from hypersaline lakes

Anaerobic carboxydotrophy is a widespread catabolic trait in bacteria, with two dominant pathways: hydrogenogenic and acetogenic. The marginal mode by direct oxidation to CO₂ using an external e-acceptor has only a few examples. Use of sulfidic sediments from two types of hypersaline lakes in anaerobic enrichments with CO as an e-donor and elemental sulfur as an e-acceptor led to isolation of two pure cultures of anaerobic carboxydotrophs belonging to two genera of sulfur-reducing haloarchaea: Halanaeroarchaeum sp. HSR-CO from salt lakes and Halalkaliarchaeum sp. AArc-CO from soda lakes. Anaerobic growth of extremely halophilic archaea with CO was obligatory depended on the presence of elemental sulfur as the electron acceptor and yeast extract as the carbon source. CO served as a direct electron donor and H₂ was not generated from CO when cells were incubated with or without sulfur. The genomes of the isolates encode a catalytic Ni,Fe-CODH subunit CooS (distantly related to bacterial homologs) and its Ni-incorporating chaperone CooC (related to methanogenic homologs) within a single genomic locus. Similar loci were also present in a genome of the type species of Halalkaliarchaeum closely related to AArc-CO, and the ability for anaerobic sulfur-dependent carboxydotrophy was confirmed for three different strains of this genus. Moreover, similar proteins are encoded in three of the four genomes of recently described carbohydrate-utilizing sulfur-reducing haloarchaea belonging to the genus Halapricum and in two yet undescribed haloarchaeal species. Overall, this work demonstrated for the first time the potential for anaerobic sulfur-dependent carboxydotrophy in extremely halophilic archaea.

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.

Biologically enhanced hydrogen sulfide absorption from sour gas under haloalkaline conditions

We studied a biotechnological desulfurization process for removal of toxic hydrogen sulfide (H₂S) from sour gas. The process consists of two steps: i) Selective absorption of H₂S into a (bi)carbonate solution in the absorber column and ii) conversion of sulfide to sulfur by sulfide oxidizing bacteria (SOB) in the aerated bioreactor. In previous studies, several physico-chemical factors were assessed to explain the observed enhancement of H₂S absorption in the absorber, but a full explanation was not provided. We investigated the relation between the metabolic activity of SOB and the enhancement factor. Two continuous experiments on pilot-scale were performed to determine H₂S absorption efficiencies at different temperatures and biomass concentrations. The absorption efficiency improved at increasing temperatures, i.e. H₂S concentration in the treated gas decreased from 715 ± 265 ppmv at 25.4 °C to 69 ± 25 ppmv at 39.4 °C. The opposite trend is expected when H₂S absorption is solely determined by physico-chemical factors. Furthermore, increasing biomass concentrations to the absorber also resulted in decreased H₂S concentrations in the treated gas, from approximately 6000 ppmv without biomass to 1664 ± 126 ppmv at 44 mg N/L. From our studies it can be concluded that SOB activity enhances H₂S absorption and leads to increased H₂S removal efficiencies in biotechnological gas desulfurization.

Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival

Carbon monoxide (CO) is a ubiquitous atmospheric trace gas produced by natural and anthropogenic sources. Some aerobic bacteria can oxidize atmospheric CO and, collectively, they account for the net loss of ~250 teragrams of CO from the atmosphere each year. However, the physiological role, genetic basis, and ecological distribution of this process remain incompletely resolved. In this work, we addressed these knowledge gaps through culture-based and culture-independent work. We confirmed through shotgun proteomic and transcriptional analysis that the genetically tractable aerobic soil actinobacterium Mycobacterium smegmatis upregulates expression of a form I molydenum-copper carbon monoxide dehydrogenase by 50-fold when exhausted for organic carbon substrates. Whole-cell biochemical assays in wild-type and mutant backgrounds confirmed that this organism aerobically respires CO, including at sub-atmospheric concentrations, using the enzyme. Contrary to current paradigms on CO oxidation, the enzyme did not support chemolithoautotrophic growth and was dispensable for CO detoxification. However, it significantly enhanced long-term survival, suggesting that atmospheric CO serves a supplemental energy source during organic carbon starvation. Phylogenetic analysis indicated that atmospheric CO oxidation is widespread and an ancestral trait of CO dehydrogenases. Homologous enzymes are encoded by 685 sequenced species of bacteria and archaea, including from seven dominant soil phyla, and we confirmed genes encoding this enzyme are abundant and expressed in terrestrial and marine environments. On this basis, we propose a new survival-centric model for the evolution of aerobic CO oxidation and conclude that, like atmospheric H₂, atmospheric CO is a major energy source supporting persistence of aerobic heterotrophic bacteria in deprived or changeable environments.

Increasing the Selectivity for Sulfur Formation in Biological Gas Desulfurization

In the biotechnological desulfurization process under haloalkaline conditions, dihydrogen sulfide (H₂S) is removed from sour gas and oxidized to elemental sulfur (S₈) by sulfide-oxidizing bacteria. Besides S₈, the byproducts sulfate (SO₄^2-) and thiosulfate (S₂O₃^2-) are formed, which consume caustic and form a waste stream. The aim of this study was to increase selectivity toward S₈ by a new process line-up for biological gas desulfurization, applying two bioreactors with different substrate conditions (i.e., sulfidic and microaerophilic), instead of one (i.e., microaerophilic). A 111-day continuous test, mimicking full scale operation, demonstrated that S₈ formation was 96.6% on a molar H₂S supply basis; selectivity for SO₄^2- and S₂O₃^2- were 1.4 and 2.0% respectively. The selectivity for S₈ formation in a control experiment with the conventional 1-bioreactor line-up was 75.6 mol %. At start-up, the new process line-up immediately achieved lower SO₄^2- and S₂O₃^2- formations compared to the 1-bioreactor line-up. When the microbial community adapted over time, it was observed that SO₄^2- formation further decreased. In addition, chemical formation of S₂O₃^2- was reduced due to biologically mediated removal of sulfide from the process solution in the anaerobic bioreactor. The increased selectivity for S₈ formation will result in 90% reduction in caustic consumption and waste stream formation compared to the 1-bioreactor line-up.

Variations in Soil Bacterial Composition and Diversity in Newly Formed Coastal Wetlands

Coastal ecosystems experience some of the most active land–ocean interactions in the world, and they are characterized by high primary productivity and biological diversity in the sediment. Given the roles of microorganisms in soil biogeochemical cycling and their multifaceted influence on soil ecosystems, it is critical to understand the variations and drivers of soil microbial communities across coastal ecosystems. Here, we studied soil bacterial community dynamics at different sites (from seawater to freshwater) in the Yellow River Delta, China. Bacterial community composition and diversity over four seasons were analyzed through 16S rRNA genes. Notably, the bacterial community near the ocean had the lowest alpha-diversity when compared with the other sites. No significant differences in bacterial communities among seasons were found, indicating that seasonal variation in temperature had little influence on bacterial community in the newly formed wetlands in the Yellow River Delta. Bacterial community structure changed substantially along the salinity gradient, revealing a clear ecological replacement along the gradual transformation gradient from freshwater to seawater environment. Redundancy analysis revealed that salinity was the main driver of variations in bacterial community structure and explained 17.5% of the variability. Our study provides a better understanding of spatiotemporally determined bacterial community dynamics in coastal ecosystems.

Bacteria as an Electron Shuttle for Sulfide Oxidation

Biological desulfurization under haloalkaliphilic conditions is a widely applied process, in which haloalkalophilic sulfide-oxidizing bacteria (SOB) oxidize dissolved sulfide with oxygen as the final electron acceptor. We show that these SOB can shuttle electrons from sulfide to an electrode, producing electricity. Reactor solutions from two different biodesulfurization installations were used, containing different SOB communities; 0.2 mM sulfide was added to the reactor solutions with SOB in absence of oxygen, and sulfide was removed from the solution. Subsequently, the reactor solutions with SOB, and the centrifuged reactor solutions without SOB, were transferred to an electrochemical cell, where they were contacted with an anode. Charge recovery was studied at different anode potentials. At an anode potential of +0.1 V versus Ag/AgCl, average current densities of 0.48 and 0.24 A/m² were measured for the two reactor solutions with SOB. Current was negligible for reactor solutions without SOB. We postulate that these differences in current are related to differences in microbial community composition. Potential mechanisms for charge storage in SOB are proposed. The ability of SOB to shuttle electrons from sulfide to an electrode offers new opportunities for developing a more sustainable desulfurization process.

Functional microbiology of soda lakes

Soda lakes represent unique permanently haloalkaline system. Despite the harsh conditions, they are inhabited by abundant, mostly prokaryotic, microbial communities. This review summarizes results of studies of main functional groups of the soda lake prokaryotes responsible for carbon, nitrogen and sulfur cycling, including oxygenic and anoxygenic phototrophs, aerobic chemolithotrophs, fermenting and respiring anaerobes. The main conclusion from this work is that the soda lakes are very different from other high-salt systems in respect to microbial richness and activity. The reason for this difference is determined by the major physico-chemical features of two dominant salts - NaCl in neutral saline systems and sodium carbonates in soda lakes, that are influencing the amount of energy required for osmotic adaptation.

Arhodomonas sp. strain Seminole and its genetic potential to degrade aromatic compounds under high-salinity conditions

Arhodomonas sp. strain Seminole was isolated from a crude oil-impacted brine soil and shown to degrade benzene, toluene, phenol, 4-hydroxybenzoic acid (4-HBA), protocatechuic acid (PCA), and phenylacetic acid (PAA) as the sole sources of carbon at high salinity. Seminole is a member of the genus Arhodomonas in the class Gammaproteobacteria, sharing 96% 16S rRNA gene sequence similarity with Arhodomonas aquaeolei HA-1. Analysis of the genome predicted a number of catabolic genes for the metabolism of benzene, toluene, 4-HBA, and PAA. The predicted pathways were corroborated by identification of enzymes present in the cytosolic proteomes of cells grown on aromatic compounds using liquid chromatography-mass spectrometry. Genome analysis predicted a cluster of 19 genes necessary for the breakdown of benzene or toluene to acetyl coenzyme A (acetyl-CoA) and pyruvate. Of these, 12 enzymes were identified in the proteome of toluene-grown cells compared to lactate-grown cells. Genomic analysis predicted 11 genes required for 4-HBA degradation to form the tricarboxylic acid (TCA) cycle intermediates. Of these, proteomic analysis of 4-HBA-grown cells identified 6 key enzymes involved in the 4-HBA degradation pathway. Similarly, 15 genes needed for the degradation of PAA to the TCA cycle intermediates were predicted. Of these, 9 enzymes of the PAA degradation pathway were identified only in PAA-grown cells and not in lactate-grown cells. Overall, we were able to reconstruct catabolic steps for the breakdown of a variety of aromatic compounds in an extreme halophile, strain Seminole. Such knowledge is important for understanding the role of Arhodomonas spp. in the natural attenuation of hydrocarbon-impacted hypersaline environments.

Physiological and metabolic effects of carbon monoxide oxidation in the model marine bacterioplankton Ruegeria pomeroyi DSS-3

Ruegeria pomeroyi expresses carbon monoxide (CO) dehydrogenase and oxidizes CO; however, CO has no effect on growth. Nuclear magnetic resonance (NMR) spectra showed that CO has no effect on cellular metabolite profiles. These data support ecosystem models proposing that, even though bacterioplankton CO oxidation is biogeochemically significant, it has an insignificant effect on bacterioplankton productivity.

One carbon metabolism in SAR11 pelagic marine bacteria

The SAR11 Alphaproteobacteria are the most abundant heterotrophs in the oceans and are believed to play a major role in mineralizing marine dissolved organic carbon. Their genomes are among the smallest known for free-living heterotrophic cells, raising questions about how they successfully utilize complex organic matter with a limited metabolic repertoire. Here we show that conserved genes in SAR11 subgroup Ia (Candidatus Pelagibacter ubique) genomes encode pathways for the oxidation of a variety of one-carbon compounds and methyl functional groups from methylated compounds. These pathways were predicted to produce energy by tetrahydrofolate (THF)-mediated oxidation, but not to support the net assimilation of biomass from C1 compounds. Measurements of cellular ATP content and the oxidation of ¹⁴C-labeled compounds to ¹⁴CO₂ indicated that methanol, formaldehyde, methylamine, and methyl groups from glycine betaine (GBT), trimethylamine (TMA), trimethylamine N-oxide (TMAO), and dimethylsulfoniopropionate (DMSP) were oxidized by axenic cultures of the SAR11 strain Ca. P. ubique HTCC1062. Analyses of metagenomic data showed that genes for C1 metabolism occur at a high frequency in natural SAR11 populations. In short term incubations, natural communities of Sargasso Sea microbial plankton expressed a potential for the oxidation of ¹⁴C-labeled formate, formaldehyde, methanol and TMAO that was similar to cultured SAR11 cells and, like cultured SAR11 cells, incorporated a much larger percentage of pyruvate and glucose (27–35%) than of C1 compounds (2–6%) into biomass. Collectively, these genomic, cellular and environmental data show a surprising capacity for demethylation and C1 oxidation in SAR11 cultures and in natural microbial communities dominated by SAR11, and support the conclusion that C1 oxidation might be a significant conduit by which dissolved organic carbon is recycled to CO₂ in the upper ocean.

Analysis of ammonia-oxidizing bacteria dominating in lab-scale bioreactors with high ammonium bicarbonate loading

The ammonia-oxidizing bacterial community (AOB) was investigated in two types of laboratory-scale bioreactors performing partial oxidation of ammonia to nitrite or nitrate at high (80 mM) to extremely high (428 mM) concentrations of ammonium bicarbonate. At all conditions, the dominant AOB was affiliated to the Nitrosomonas europaea lineage as was determined by fluorescence in situ hybridization and polymerase chain reaction in combination with denaturing gradient gel electrophoresis. Molecular analysis of the mixed populations, based on the 16S rRNA and cbbL genes, demonstrated the presence of two different phylotypes of Nitrosomonas, while microbiological analysis produced a single phylotype, represented by three different morphotypes. One of the most striking features of the AOB populations encountered in the bioreactors was the domination of highly aggregated obligate microaerophilic Nitrosomonas, with unusual cellular and colony morphology, commonly observed in nitrifying bioreactors but rarely investigated by cultural methods. The latter is probably not an adaptation to stressful conditions created by high ammonia or nitrite concentrations, but oxygen seems to be a stressful factor in these bioreactors.

Diversity of RuBisCO and ATP citrate lyase genes in soda lake sediments

Sediments from six soda lakes of the Kulunda Steppe (Altai, Russia) and from hypersaline alkaline lakes of Wadi Natrun (Egypt) were analyzed for the presence of cbb and aclB genes encoding key enzymes Ci assimilation (RuBisCO in Calvin-Benson and ATP citrate lyase in rTCA cycles, respectively). The cbbL gene (RuBisCO form I) was found in all samples and was most diverse, while the cbbM (RuBisCO form II) and aclB were detected only in few samples and with a much lower diversity. The cbbL libraries from hypersaline lakes were dominated by members of the extremely haloalkaliphilic sulfur-oxidizing Ectothiorhodospiraceae, i.e. the chemolithotrophic Thioalkalivibrio and the phototrophic Halorhodospira. In the less saline soda lakes from the Kulunda Steppe, the cbbL gene comprised up to ten phylotypes with a domination of members of a novel phototrophic Chromatiales lineage. The cbbM clone libraries consisted of two major unidentified lineages probably belonging to chemotrophic sulfur-oxidizing Gammaproteobacteria. One of them, dominating in the haloalkaline lakes from Wadi Natrun, was related to a cbbM phylotype detected previously in a hypersaline lake with a neutral pH, and another, dominating in lakes from the Kulunda Steppe, was only distantly related to the Thiomicrospira cluster. The aclB sequences detected in two samples from the Kulunda Steppe formed a single, deep branch in the Epsilonproteobacteria, distantly related to Arcobacter sulfidicus.