Alkalilimnicola ehrlichii sp. nov., a novel, arsenite-oxidizing haloalkaliphilic gammaproteobacterium capable of chemoautotrophic or heterotrophic growth with nitrate or oxygen as the electron acceptor

Various microbial taxa couple arsenic transformation to nitrogen and carbon cycling in paddy soils

BACKGROUND

Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies.

RESULTS

Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination.

CONCLUSIONS

Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. Video Abstract.

Comparative analysis of the intestinal flora of BmNPV-resistant and BmNPV-sensitive silkworm varieties

Bombyx mori nucleopolyhedrovirus (BmNPV) is a very common and infectious virus that affects silkworms and hinders silk production. To investigate the intestinal flora of BmNPV-resistant and BmNPV-sensitive silkworm varieties, 16 S rDNA high-throughput sequencing was performed. The results of the cluster analysis showed that the intestinal flora of the resistant silkworm variety was more abundant than that of the sensitive silkworm variety. This was found even when infection with BmNPV caused a sharp decline in the number of intestinal floral species in both resistant and sensitive silkworm varieties. The abundances of the intestinal flora, including Aureimonas, Ileibacterium, Peptostreptococcus, Pseudomonas, Enterococcus, and Halomonas, in the resistant variety were considerably greater after infection with BmNPV than those in the sensitive variety. After infection with BmNPV, four kinds of important intestinal bacteria, namely, f_Saccharimonadaceae, Peptostreptococcus, Aureirmonas, and f_Rhizobiaceae, were found in the resistant silkworm variety. In the sensitive silkworm variety, only Faecalibaculum was an important intestinal bacterium. The differential or important bacteria mentioned above might be involved in immunoreaction or antiviral activities, especially in the intestines of BmNPV-resistant silkworms. By conducting a functional enrichment analysis, we found that BmNPV infection did not change the abundance of important functional components of the intestinal flora in resistant or sensitive silkworm varieties. However, some functional factors, such as the biosynthesis, transport, and catabolism of secondary metabolites (e.g., terpenoids and polyketides) and lipid transport and metabolism, were more important in the resistant silkworm variety than in the sensitive variety; thus, these factors may increase the resistance of the host to BmNPV. To summarize, we found significant differences in the composition, abundance, and function of the intestinal flora between resistant and sensitive silkworm varieties, especially after infection with BmNPV, which might be closely related to the resistance of resistant silkworm varieties to BmNPV.

Can Sb(III)-oxidizing prokaryote also oxidize As(III) under aerobic and anaerobic conditions, and vice versa?

Sb(III) and As(III) share similar chemical features and coexist in the environment. However, their oxidase enzymes have completely different sequences and structures. This raises an intriguing question: Could Sb(III)-oxidizing prokaryotes (SOPs) also oxidize As(III), and vice versa? Regarding this issue, previous investigations have yielded unclear, incorrect and even conflicting data. This work aims to address this matter. First, we prepared an enriched population of SOPs that comprises 55 different AnoA genes, lacking AioAB and ArxAB genes. We found that these SOPs can oxidize both Sb(III) and As(III) with comparable capabilities. To further confirm this finding, we isolated three cultivable SOP strains that have AnoA gene, but lack AioAB and ArxAB genes. We observed that they also oxidize both Sb(III) and As(III) under both anaerobic and aerobic conditions. Secondly, we obtained an enriched population of As(III)-oxidizing prokaryotes (AOPs) from As-contaminated soils, which comprises 69 different AioA genes, lacking AnoA gene. We observed that the AOP population has significant As(III)-oxidizing activities, but lack detectable Sb(III)-oxidizing activities under both aerobic and anaerobic conditions. Therefore, we convincingly show that SOPs can oxidize As(III), but AOPs cannot oxidize Sb(III). These findings clarify the previous ambiguities, confusion, errors or contradictions regarding how SOPs and AOPs oxidize each other's substrate.

Functional features of a novel Sb(III)- and As(III)-oxidizing bacterium: Implications for the interactions between bacterial Sb(III) and As(III) oxidation pathways

Antimony (Sb) and arsenic (As) share similar chemical characteristics and commonly coexist in contaminated environments. It has been reported that the biogeochemical cycles of antimony and arsenic affect each other. However, there is limited understanding regarding microbial coupling between the biogeochemical processes of antimony and arsenic. Here, we aimed to solve this issue. We successfully isolated a novel bacterium, Shinella sp. SbAsOP1, which possesses both Sb(III) and As(III) oxidase, and can effectively oxidize both Sb(III) and As(III) under aerobic and anaerobic conditions. SbAsOP1 exhibits greater aerobic oxidation activity for the oxidation of As(III) or Sb(III) compared to its anaerobic activity. SbAsOP1 also significantly catalyzes the oxidative mobilization of solid-phase Sb(III) under aerobic conditions. The activity of SbAsOP1 in oxidizing solid Sb(III) is 3 times lower than its activity in oxidizing soluble form. It is noteworthy that, in the presence of both Sb(III) and As(III) under aerobic conditions, either As(III) or Sb(III) significantly inhibits the oxidation of Sb(III) or As(III), respectively. In comparison, under anaerobic conditions and in the coexistence of Sb(III) and As(III), As(III) significantly inhibits Sb(III) oxidation, whereas Sb(III) almost completely inhibits As(III) oxidation. These findings suggest that under both aerobic and anaerobic conditions, SbAsOP1 demonstrates a partial preference for Sb(III) oxidation. Additionally, bacterial oxidations of Sb(III) and As(III) mutually inhibit each other to varying degrees. These observations gain a novel understanding of the interplay between the biogeochemical processes of antimony and arsenic.

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.

Genome sequence and characterisation of a freshwater photoarsenotroph, Cereibacter azotoformans strain ORIO, isolated from sediments capable of cyclic light-dark arsenic oxidation and reduction

A freshwater photosynthetic arsenite-oxidizing bacterium, Cereibacter azotoformans strain ORIO, was isolated from Owens River, CA, USA. The waters from Owens River are elevated in arsenic and serve as the headwaters to the Los Angeles Aqueduct. The complete genome sequence of strain ORIO is 4.8 Mb genome (68% G + C content) and comprises two chromosomes and six plasmids. Taxonomic analysis placed ORIO within the Cereibacter genus (formerly Rhodobacter). The ORIO genome contains arxB2 AB1 CD (encoding an arsenite oxidase), arxXSR (regulators) and several ars arsenic resistance genes all co-localised on a 136 kb plasmid, named pORIO3. Phylogenetic analysis of ArxA, the molybdenum-containing arsenite oxidase catalytic subunit, demonstrated photoarsenotrophy is likely to occur within members of the Alphaproteobacteria. ORIO is a mixotroph, oxidises arsenite to arsenate (As(V)) photoheterotrophically, and expresses arxA in cultures grown with arsenite. Further ecophysiology studies with Owens River sediment demonstrated the interconversion of arsenite and As(V) was dependent on light-dark cycling. arxA and arrA (As(V) respiratory reductase) genes were detected in the light-dark cycled sediment metagenomes suggesting syntrophic interactions among arsenotrophs. This work establishes C. azotoformans str. ORIO as a new model organism for studying photoarsenotrophy and light-dark arsenic biogeochemical cycling.

Blue light promotes zero-valent sulfur production in a deep-sea bacterium

Increasing evidence has shown that light exists in a diverse range of deep-sea environments. We unexpectedly found that blue light is necessary to produce excess zero-valent sulfur (ZVS) in Erythrobacter flavus 21-3, a bacterium that has been recently isolated from a deep-sea cold seep. E. flavus 21-3 is able to convert thiosulfate to ZVS using a novel thiosulfate oxidation pathway comprising a thiosulfate dehydrogenase (TsdA) and a thiosulfohydrolase (SoxB). Using proteomic, bacterial two-hybrid and heterologous expression assays, we found that the light-oxygen-voltage histidine kinase LOV-1477 responds to blue light and activates the diguanylate cyclase DGC-2902 to produce c-di-GMP. Subsequently, the PilZ domain-containing protein mPilZ-1753 binds to c-di-GMP and activates TsdA through direct interaction. Finally, Raman spectroscopy and gene knockout results verified that TsdA and two SoxB homologs cooperate to regulate ZVS production. As ZVS is an energy source for E. flavus 21-3, we propose that deep-sea blue light provides E. flavus 21-3 with a selective advantage in the cold seep, suggesting a previously unappreciated relationship between light-sensing pathways and sulfur metabolism in a deep-sea microorganism.

Microbial conversion of carbon dioxide and hydrogen into the fine chemicals hydroxyectoine and ectoine

This study explores a novel conversion of CO₂ into the chemicals hydroxyectoine and ectoine, which are compounds with high retail values in the pharmaceutical industry. Firstly, 11 species of microbes able to use CO₂ and H₂ and that have the genes for ectoines synthesis (ectABCD) were identified through literature search and genomic mining. Laboratory tests were then conducted to ascertain the capacity of these microbes to produce ectoines from CO₂. Results showed that the most promising bacteria for CO₂ to ectoines bioconversion areHydrogenovibrio marinus, Rhodococcus opacus, and Hydrogenibacillus schlegelii.Upon salinity and H₂/CO₂/O₂ ratio optimization,H. marinus accumulated 85 mg of ectoine g biomass^-1. Interestingly, R.opacusand H. schlegelii mainly produced hydroxyectoine (53 and 62 mg g biomass^-1), which has a higher commercial value. Overall, these results constitute the first proof of a novel valorization platform of CO₂ and lay the foundation for a new economic niche aimed at CO₂ recircularization into pharmaceuticals.

Distinct arsenic uptake feature in rice reveals the importance of N fertilization strategies

The environmental behavior of arsenic (As) is commonly affected by the biogeochemical processes of iron (Fe) and nitrogen (N). In this study, field experiments were conducted to explore As uptake in rice and As translation and distribution in As-contaminated iron-rich paddy soils after applying different forms of N fertilizers, including urea (CO(NH2)2), ammonium bicarbonate (NH4HCO3), nitrate of potash (KNO3), and ammonium bicarbonate + nitrate of potash (NH4HCO3 + KNO3). The results indicated that applying nitrate N fertilizer inhibited the reduction and dissolution of As-bearing iron minerals and promoted microbial-mediated As(III) oxidation in flooded soil, thus reducing the soil As bioavailability. The concentrations of total As and inorganic As ratio (iAs/TAs) in rice grain decreased by 32.4 % and 15.4 %, respectively. However, the application of ammonium nitrogen promoted the reductive dissolution of As-bearing iron minerals and stimulated microbial As(V) reduction in flooded soil, leading to the release of As from soil to porewater. The total As concentration and inorganic As uptake ratio in rice grain increased by 20.1 % and 6.2 %, respectively, when urea was applied, and by 29.6 % and 10.5 %, respectively, when ammonium bicarbonate was applied. However, the simultaneous application of NH4+ and NO3- had no significant effect on As concentration in rice grain and its transformation in paddy soils. Ammonium nitrogen enhanced the organic As concentration in rice grain because the increased As(III) promoted As methylation in soil. In contrast, nitrate decreased the organic As uptake by rice grain because the decreased As(III) diminished As methylation in soil. The results provide reasonable N fertilization strategies for regulating the As biogeochemical process and reducing the risk of As contamination in rice.

Single Strain-Triggered Biogeochemical Cycle of Arsenic

The microbial metabolism of arsenic plays a prominent role in governing the biogeochemical cycle of arsenic. Although diverse microbes are known to be involved in the redox transformation of inorganic arsenic, the underlying mechanisms about the arsenic redox cycle mediated by a single microbial strain remain unclear yet. Herein, we discover that Shewanella putrefaciens CN32, a well-known arsenate-respiring and dissimilatory metal-reducing bacterium, could mediate the reversible arsenic redox transformation under aerobic conditions. Genetic analysis shows that S. putrefaciens CN32 contains both ars and arr operon but lacks an As(III) oxidase encoding gene. Arsenic(V) reduction tests demonstrate that the ars operon is advantageous but not essential for As(V) respiration in S. putrefaciens CN32. The Arr complex encoded by the arr operon not only plays a crucial role in arsenate respiration under anaerobic conditions but also participates in the sequential process of As(V) reduction and As(III) oxidation under aerobic conditions. The Arr enzyme also contributes to the microbial As(III) resistance. The expression and catalysis directionality of Arr in S. putrefaciens CN32 are regulated by the carbon source types. Our results highlight the complexity of arsenic redox biotransformation in environments and provide new insights into the important contribution of Arr to the As biogeochemical cycle in nature.

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.

Different Regulatory Strategies of Arsenite Oxidation by Two Isolated Thermus tengchongensis Strains From Hot Springs

Arsenic is a ubiquitous constituent in geothermal fluids. Thermophiles represented by Thermus play vital roles in its transformation in geothermal fluids. In this study, two Thermus tengchongensis strains, named as 15Y and 15W, were isolated from arsenic-rich geothermal springs and found different arsenite oxidation behaviors with different oxidation strategies. Arsenite oxidation of both strains occurred at different growth stages, and two enzyme-catalyzed reaction kinetic models were observed. The arsenite oxidase of Thermus strain 15W performed better oxidation activity, exhibiting typical Michaelis–Menten kinetics. The kinetic parameter of arsenite oxidation in whole cell showed a V_max of 18.48 μM min^–1 and K_M of 343 μM. Both of them possessed the arsenite oxidase-coding genes aioB and aioA. However, the expression of gene aioBA was constitutive in strain 15W, whereas it was induced by arsenite in strain 15Y. Furthermore, strain 15Y harbored an intact aio operon including the regulatory gene of the ArsR family, whereas a genetic inversion of an around 128-kbp fragment produced the inactivation of this regulator in strain 15W, leading to the constitutive expression of aioBA genes. This study provides a valuable insight into the adaption of thermophiles to extreme environments.

Continuous electron shuttling by sulfide oxidizing bacteria as a novel strategy to produce electric current

Sulfide oxidizing bacteria (SOB) are widely applied in industry to convert toxic H₂S into elemental sulfur. Haloalkaliphilic planktonic SOB can remove sulfide from solution under anaerobic conditions (SOB are 'charged'), and release electrons at an electrode (discharge of SOB). The effect of this electron shuttling on product formation and biomass growth is not known. Here, we study and demonstrate a continuous process in which SOB remove sulfide from solution in an anaerobic 'uptake chamber', and shuttle these electrons to the anode of an electrochemical cell, in the absence of dissolved sulfide. Two experiments over 31 and 41 days were performed. At a sulfide loading rate of 1.1 mmolS/day, electricity was produced continuously (3 A/m²) without dissolved sulfide in the anolyte. The main end product was sulfate (56% in experiment 1% and 78% in experiment 2), and 87% and 77% of the electrons in sulfide were recovered as electricity. It was found that the current density was dependent on the sulfide loading rate and not on the anode potential. Biological growth occurred, mainly at the anode as biofilm, in which the deltaproteobacterial genus Desulfurivibrio was dominating. Our results demonstrate a novel strategy to produce electricity from sulfide in an electrochemical system.

Comparative analysis of microbial communities from different full-scale haloalkaline biodesulfurization systems

Abstract

In biodesulfurization (BD) at haloalkaline and dO₂-limited conditions, sulfide-oxidizing bacteria (SOB) effectively convert sulfide into elemental sulfur that can be used in agriculture as a fertilizer and fungicide. Here we show which bacteria are present in this biotechnological process. 16S rRNA gene amplicon sequencing of biomass from ten reactors sampled in 2018 indicated the presence of 444 bacterial Amplicon Sequence Variants (ASVs). A core microbiome represented by 30 ASVs was found in all ten reactors, with Thioalkalivibrio sulfidiphilus as the most dominant species. The majority of these ASVs are phylogenetically related to bacteria previously identified in haloalkaline BD processes and in natural haloalkaline ecosystems. The source and composition of the feed gas had a great impact on the microbial community composition followed by alkalinity, sulfate, and thiosulfate concentrations. The halophilic SOB of the genus Guyparkeria (formerly known as Halothiobacillus) and heterotrophic SOB of the genus Halomonas were identified as potential indicator organisms of sulfate and thiosulfate accumulation in the BD process.

Key points

• Biodesulfurization (BD) reactors share a core microbiome

• The source and composition of the feed gas affects the microbial composition in the BD reactors

• Guyparkeria and Halomonas indicate high concentrations of sulfate and thiosulfate in the BD process

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-11771-y.

Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation

Owing to their roles in the arsenic (As) biogeochemical cycle, microorganisms and plants offer significant potential for developing innovative biotechnological applications able to remediate As pollutions. This possible use in bioremediation processes and phytomanagement is based on their ability to catalyse various biotransformation reactions leading to, e.g. the precipitation, dissolution, and sequestration of As, stabilisation in the root zone and shoot As removal. On the one hand, genomic studies of microorganisms and their communities are useful in understanding their metabolic activities and their interaction with As. On the other hand, our knowledge of molecular mechanisms and fate of As in plants has been improved by laboratory and field experiments. Such studies pave new avenues for developing environmentally friendly bioprocessing options targeting As, which worldwide represents a major risk to many ecosystems and human health.

Draft Genome Sequence of the Anaerobic Arsenite-Oxidizing Halomonas sp. Strain ANAO-440, Isolated from an Alkaline Saline Lake in Khovsgol, Mongolia

The draft genome sequence of Halomonas sp. strain ANAO-440 contains 3,866 predicted protein-coding sequences. This strain is capable of anaerobic arsenite oxidation and encodes an arxA-type arsenite oxidase within the arxB2AB1CD gene island. This genome sequence provides valuable information regarding the physiological diversity of Arx-dependent arsenite-oxidizing microorganisms.

The Microbiology of Metal Mine Waste: Bioremediation Applications and Implications for Planetary Health

Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long-term field studies of metal-impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field-scale. Further demonstration of this technology at full field-scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health.

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.

Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module

In prokaryotes, the proton or sodium motive force required for ATP synthesis is produced by respiratory complexes that present an ion-pumping mechanism or are involved in redox loops performed by membrane proteins that usually have substrate and quinone-binding sites on opposite sides of the membrane. Some respiratory complexes include a dimeric redox module composed of a quinone-interacting membrane protein of the NrfD family and an iron‑sulfur protein of the NrfC family. The QrcABCD complex of sulfate reducers, which includes the QrcCD module homologous to NrfCD, was recently shown to perform electrogenic quinone reduction providing the first conclusive evidence for energy conservation among this family. Similar redox modules are present in multiple respiratory complexes, which can be associated with electroneutral, energy-driven or electrogenic reactions. This work discusses the presence of the NrfCD/PsrBC dimeric redox module in different bioenergetics contexts and its role in prokaryotic energy conservation mechanisms.

Divergent Patterns of Bacterial Community Structure and Function in Response to Estuarine Output in the Middle of the Bohai Sea

Understanding environment-community relationships under shifting environmental conditions helps uncover mechanisms by which environmental microbial communities manage to improve ecosystem functioning. This study investigated the microbial community and structure near the Yellow Sea River estuary in 12 stations across the middle of the Bohai Sea for over two seasons to elucidate the influence of estuarine output on them. We found that the dominant phyla in all stations were Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, and Planctomycetes. Alpha-diversity increased near the estuary and bacterial community structure differed with variation of spatiotemporal gradients. Among all the environmental factors surveyed, temperature, salinity, phosphate, silicon, nitrate, and total virioplankton abundance played crucial roles in controlling the bacterial community composition. Some inferred that community functions such as carbohydrate, lipid, amino acid metabolism, xenobiotics biodegradation, membrane transport, and environmental adaptation were much higher in winter; energy and nucleotide metabolism were lower in winter. Our results suggested that estuarine output had a great influence on the Bohai Sea environment and changes in the water environmental conditions caused by estuarine output developed distinctive microbial communities in the middle of the Bohai Sea. The distinctive microbial communities in winter demonstrated that the shifting water environment may stimulate changes in the diversity and then strengthen the predicted functions.

Autotrophic denitrification in constructed wetlands: Achievements and challenges

The use of constructed wetlands for wastewater treatment is rapidly increasing worldwide due to their advantages of low operating and maintenance costs. Denitrification in constructed wetlands is dependent on the presence of organic carbon sources, and the shortage of organic carbon is the primary hurdle for nitrate removal. Therefore, the use of inorganic electronic donors has emerged as an alternative. This paper provides a comprehensive review of nitrate removal pathways using various inorganic electron donors and the performance and development of autotrophic denitrification in constructed wetlands. The main environmental parameters and operating conditions for nitrate removal in wetlands are discussed, and the challenges currently faced in the application of enhanced autotrophic denitrification wetlands are emphasized. Overall, this review illustrates the need for a deep understanding of the complex interrelationships among environmental and operational parameters and wetland substrates for improving the wastewater treatment performance of constructed wetlands.

The controversy on the ancestral arsenite oxidizing enzyme; deducing evolutionary histories with phylogeny and thermodynamics

The three presently known enzymes responsible for arsenic-using bioenergetic processes are arsenite oxidase (Aio), arsenate reductase (Arr) and alternative arsenite oxidase (Arx), all of which are molybdoenzymes from the vast group referred to as the Mo/W-bisPGD enzyme superfamily. Since arsenite is present in substantial amounts in hydrothermal environments, frequently considered as vestiges of primordial biochemistry, arsenite-based bioenergetics has long been predicted to be ancient. Conflicting scenarios, however, have been put forward proposing either Arr/Arx or Aio as operating in the ancestral metabolism. Phylogenetic data argue in favor of Aio whereas biochemical and physiological data led several authors to propose Arx/Arr as the most ancient anaerobic arsenite metabolizing enzymes. Here we combine phylogenetic approaches with physiological and biochemical experiments to demonstrate that the Arx/Arr enzymes could not have been functional in the Archaean geological eon. We propose that Arr reacts with menaquinones to reduce arsenate whereas Arx reacts with ubiquinone to oxidize arsenite, in line with thermodynamic considerations. The distribution of the quinone biosynthesis pathways, however, clearly indicates that the ubiquinone pathway is recent. An updated phylogeny of Arx furthermore reinforces the hypothesis of a recent emergence of this enzyme. We therefore conclude that anaerobic arsenite redox conversion in the Archaean must have been performed in a metabolism involving Aio.

Natranaerofaba carboxydovora gen. nov., sp. nov., an extremely haloalkaliphilic CO-utilizing acetogen from a hypersaline soda lake representing a novel deep phylogenetic lineage in the class 'Natranaerobiia'

An anaerobic enrichment with CO from sediments of hypersaline soda lakes resulted in a methane‐forming binary culture, whereby CO was utilized by a bacterium and not the methanogenic partner. The bacterial isolate ANCO1 forms a deep‐branching phylogenetic lineage at the level of a new family within the class ‘Natranaerobiia’. It is an extreme haloalkaliphilic and moderate thermophilic acetogen utilizing CO, formate, pyruvate and lactate as electron donors and thiosulfate, nitrate (reduced to ammonia) and fumarate as electron acceptors. The genome of ANCO1 encodes a full Wood–Ljungdahl pathway allowing for CO oxidation and acetogenic conversion of pyruvate. A locus encoding Nap nitrate reductase/NrfA ammonifying nitrite reductase is also present. Thiosulfate respiration is encoded by a Phs/Psr‐like operon. The organism obviously relies on Na‐based bioenergetics, since the genome encodes for the Na⁺‐Rnf complex, Na⁺‐F1F0 ATPase and Na⁺‐translocating decarboxylase. Glycine betaine serves as a compatible solute. ANCO1 has an unusual membrane polar lipid composition dominated by diethers, more common among archaea, probably a result of adaptation to multiple extremophilic conditions. Overall, ANCO1 represents a unique example of a triple extremophilic CO‐oxidizing anaerobe and is classified as a novel genus and species Natranaerofaba carboxydovora in a novel family Natranaerofabacea.

Performance and mechanism of carbon dioxide fixation by a newly isolated chemoautotrophic strain Paracoccus denitrificans PJ-1

CO₂ is regarded as a major contributor to the global warming. CO₂ utilization is promising to reduce the CO₂ emissions. Currently, the biofixation of CO₂ using chemoautotrophs has markedly gain interest in CO₂ utilization. In this study, a newly isolated chemoautotroph, Paracoccus denitrificans PJ-1, was used for the biofixation of CO₂ under anaerobic condition. Experimental results revealed that Paracoccus denitrificans PJ-1 achieved a high carbon fixation rate (13.25 mg·L^-1·h^-1) which was ∼10 times faster than the previous reported chemotrophic bacteria using thiosulfate as electron donor. The best CO₂ fixation activity of Paracoccus denitrificans PJ-1 was achieved at the pH value of 9.0 and CO₂ concentration of 20 vol%. Meanwhile, a high CO₂ fixation yield of 106.03 mg·L^-1 was reached. The presence of oxygen was adverse to the biofixation, indicating that strain PJ-1 was more suitable for CO₂ fixation in anaerobic environments. Carbon mass balance analysis revealed that the carbon from CO₂ was mainly fixed into the extracellular organic carbon rather than the biomass. GC-MS analysis and cbbL gene test revealed that Paracoccus denitrificans PJ-1 fixed CO₂ through the Calvin-Benson-Bassham cycle and mainly converted CO₂ to oxalic acid and succinic acid. Overall, the excellent CO₂ fixation capacity of Paracoccus denitrificans PJ-1 suggests that it had potential for CO₂ utilization.

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling

The rise of oxygen on the early Earth about 2.4 billion years ago reorganized the redox cycle of harmful metal(loids), including that of arsenic, which doubtlessly imposed substantial barriers to the physiology and diversification of life. Evaluating the adaptive biological responses to these environmental challenges is inherently difficult because of the paucity of fossil records. Here we applied molecular clock analyses to 13 gene families participating in principal pathways of arsenic resistance and cycling, to explore the nature of early arsenic biogeocycles and decipher feedbacks associated with planetary oxygenation. Our results reveal the advent of nascent arsenic resistance systems under the anoxic environment predating the Great Oxidation Event (GOE), with the primary function of detoxifying reduced arsenic compounds that were abundant in Archean environments. To cope with the increased toxicity of oxidized arsenic species that occurred as oxygen built up in Earth's atmosphere, we found that parts of preexisting detoxification systems for trivalent arsenicals were merged with newly emerged pathways that originated via convergent evolution. Further expansion of arsenic resistance systems was made feasible by incorporation of oxygen-dependent enzymatic pathways into the detoxification network. These genetic innovations, together with adaptive responses to other redox-sensitive metals, provided organisms with novel mechanisms for adaption to changes in global biogeocycles that emerged as a consequence of the GOE.

Metagenomic analysis reveals enhanced nutrients removal from low C/N municipal wastewater in a pilot-scale modified AAO system coupling electrolysis

The conventional biological nutrients removal process is challenged by insufficient organic carbon in influent. To cross such an organic-dependent barrier, a pilot-scale electrolysis-integrated anaerobic/anoxic/oxic (AAO) process was developed for enhanced removal of nitrogen (N) and phosphorus (P) from low carbon/nitrogen (C/N) municipal wastewater. Average removal efficiencies of total nitrogen (TN) and total phosphorus (TP) in the electrolysis-AAO reached to 77.24% and 95.08% respectively, showing increases of 13.88% and 21.87%, as compared to the control reactor. Spatial variations of N and P showed that NH₄⁺-N removal rate was promoted in aerobic zone of electrolysis-AAO. The intensified TN elimination, which was mostly reflected by abatement of NO₃^--N with the concomitant slight accumulation of NH₄⁺-N and NO₂^--N, mainly occurred in anoxic2 compartment as the electrons supplied by electrolysis. Furthermore, minor P contents were measured and remained almost unchanged along the reaction units, indicating that chemical precipitation should be the dominant mechanism of P-removal in electrolysis-AAO. From the metagenomic-based taxonomy, phylum Actinobacteria was dramatically inhibited, and phylum Proteobacteria dominated the electrolysis-AAO. Particularly, nitrifying bacteria and multifarious autotrophic denitrifiers were enriched, meanwhile, a significant evolution of heterotrophic denitrifiers was found in electrolysis-AAO compared to control, which was mostly reflected by the inhibition of genus Candidatus Microthrix. Batch tests further confirmed that autotrophic denitrifiers using H₂ and Fe²⁺ as essential electron sinks were mainly responsible for the electrolysis-induced denitrification. Differential metabolic capacities were revealed from the perspectives of functional enzymes and genes, and network analysis allowed insight of microbial taxa-functional genes associations and shed light on stronger relevance between autotrophic denitrifiers and denitrification-associated genes in the electrolysis-AAO system.

Arsenic and the gastrointestinal tract microbiome

Arsenic is a toxin, ranking first on the Agency for Toxic Substances and Disease Registry and the Environmental Protection Agency Priority List of Hazardous Substances. Chronic exposure increases the risk of a broad range of human illnesses, most notably cancer; however, there is significant variability in arsenic-induced disease among exposed individuals. Human genetics is a known component, but it alone cannot account for the large inter-individual variability in the presentation of arsenicosis symptoms. Each part of the gastrointestinal tract (GIT) may be considered as a unique environment with characteristic pH, oxygen concentration, and microbiome. Given the well-established arsenic redox transformation activities of microorganisms, it is reasonable to imagine how the GIT microbiome composition variability among individuals could play a significant role in determining the fate, mobility and toxicity of arsenic, whether inhaled or ingested. This is a relatively new field of research that would benefit from early dialogue aimed at summarizing what is known and identifying reasonable research targets and concepts. Herein, we strive to initiate this dialogue by reviewing known aspects of microbe-arsenic interactions and placing it in the context of potential for influencing host exposure and health risks. We finish by considering future experimental approaches that might be of value.

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.

Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation

Background:

Amidases are ubiquitous enzymes and biological functions of these enzymes vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals synthesis, pharmaceuticals agrochemicals and wastewater treatments.

Methods:

They hydrolyse a wide variety of amides (short-chain aliphatic amides, mid-chain amides, arylamides, α-aminoamides and α-hydroxyamides) and can be grouped on the basis of their catalytic site and preferred substrate. Despite their economic importance, we lack knowledge as to how these amidases withstand elevated pH and temperature whereas others cannot.

Results:

The present study focuses on the statistical comparison between the acid-tolerant, alkali tolerant and neutrophilic organisms. In silico analysis of amidases of acid-tolerant, alkali tolerant and neutrophilic organisms revealed some striking trends as to how amino acid composition varies significantly. Statistical analysis of primary and secondary structure revealed amino acid trends in amidases of these three groups of bacteria. The abundance of isoleucine (Ile, I) in acid-tolerant and leucine (Leu, L) in alkali tolerant showed the aliphatic amino acid dominance in extreme conditions of pH in acidtolerant and alkali tolerant amidases.

Conclusion:

The present investigation insights physiochemical properties and dominance of some crucial amino acid residues in the primary and secondary structure of some amidases from acid-tolerant, alkali tolerant and neutrophilic microorganisms.

Arsenic-resistance mechanisms in bacterium Leclercia adecarboxylata strain As3-1: Biochemical and genomic analyses

Microbial arsenic transformation is important in As biogeochemical cycles in the environment. In this study, a new As-resistant bacterial strain Leclercia adecarboxylata As3-1 was isolated and its associated mechanisms in As resistance and detoxification were evaluated based on genome sequencing and gene annotations. After subjecting strain As3-1 to medium containing arsenate (AsV), AsV reduction occurred and an AsV-enhanced bacterial growth was observed. Strain As3-1 lacked arsenite (AsIII) oxidation ability and displayed lower AsIII resistance than AsV, probably due to its higher AsIII accumulation. Polymerase chain reaction and phylogenetic analysis showed that strain As3-1 harbored a typical AsV reductase gene (arsC) on the plasmids. Genome sequencing and gene annotations identified four operons phoUpstBACS, arsHRBC, arsCRDABC and ttrRSBCA, with 8 additional genes outside the operons that might have involved in As resistance and detoxification in strain As3-1. These included 5 arsC genes explaining why strain As3-1 tolerated high AsV concentrations. Besides ArsC, TtrB, TtrC and TtrA proteins could also be involved in AsV reduction and consequent energy acquisition for bacterial growth. Our data provided a new example of diverse As-regulating systems and AsV-enhanced growth without ArrA in bacteria. The information helps to understand the role of As in selecting microbial systems that can transform and utilize As.

Significance of Fe(II) and environmental factors on carbon-fixing bacterial community in two paddy soils

The seasonal flooding and drainage process affect the paddy soils, the existence of the iron state either Fe(III) or Fe(II) is the main redox system of paddy soil. Its morphological transformation affects the redox nature of paddy soils, which also affects the distribution of bacterial community diversity. This study based on molecular biological methods (qPCR, Illumina MiSeq sequencing technique) to investigate the effect of Fe(II) and environmental factors on cbbM genes containing carbon fixing microbes. Both Eh5 and pH were reduced with Fe(II) concentrations. The Fe(II) addition significantly affects the cbbM gene copy number in both texture soils. In loamy soil, cbbM gene copy number increased with high addition of Fe(II), while both low and high concentrations significantly reduced the cbbM gene copy number in sandy soil. Chemotrophic bacterial abundance significantly increased by 79.7% and 54.8% with high and low Fe(II) addition in loamy soil while in sandy soil its abundance decreased by 53% and 54% with the low and high Fe(II) accumulation. The phototrophic microbial community increased by 37.8% with low Fe(II) concentration and decreased by 16.2% with a high concentration in loamy soil, while in sandy soil increased by 21% and 14.3% in sandy soil with low and high Fe(II) addition. Chemoheterotrophic carbon fixing bacterial abundance decreased with the Fe(II) accumulation in both soil textures in loamy soil its abundance decreased by 5.8% and 24.8%, while in sand soil 15.7% and 12.8% with low and high Fe(II) concentrations. The Fe(II) concentration and soil textures maybe two of the major factors to shape the bacterial community structure in paddy soils. These results provide a scientific basis for management of paddy soil fertility and it can be beneficial to take measures to ease the greenhouse gases effect.

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.

Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway

The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern California, which is found there in concentrations up to 3000 μM. Arsenic is a widespread element that can be an environmental issue, as it is highly toxic to most organisms. However, resistance mechanisms in the form of detoxification are widespread and some prokaryotes can even use arsenic as an energy source. We first screened the genomes of 76 Thioalkalivibrio strains for the presence of known arsenic oxidoreductases and found 15 putative ArxA (arsenite oxidase) and two putative ArrA (arsenate reductase). Subsequently, we studied the resistance to arsenite in detail in Thioalkalivibrio jannaschii ALM2^T, and Thioalkalivibrio thiocyanoxidans ARh2^T by comparative genomics and by growing them at different arsenite concentrations followed by arsenic species and transcriptomic analysis. Tv. jannaschii ALM2^T, which has been isolated from Mono Lake, an arsenic-rich soda lake, could resist up to 5 mM arsenite, whereas Tv. thiocyanoxidans ARh2^T, which was isolated from a Kenyan soda lake, could only grow up to 0.1 mM arsenite. Interestingly, both species oxidized arsenite to arsenate under aerobic conditions, although Tv. thiocyanoxidans ARh2^T does not contain any known arsenite oxidases, and in Tv. jannaschii ALM2^T, only arxB2 was clearly upregulated. However, we found the expression of a SoeABC-like gene, which we assume might have been involved in arsenite oxidation. Other arsenite stress responses for both strains were the upregulation of the vitamin B₁₂ synthesis pathway, which can be linked to antioxidant activity, and the up- and downregulation of different DsrE/F-like genes whose roles are still unclear. Moreover, Tv. jannaschii ALM2^T induced the ars gene operon and the Pst system, and Tv. thiocanoxidans ARh2^T upregulated the sox and apr genes as well as different heat shock proteins. Our findings for Thioalkalivibrio confirm previously observed adaptations to arsenic, but also provide new insights into the arsenic stress response and the connection between the arsenic and the sulfur cycle.

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.

Genomics of Alkaliphiles

Alkalinicity presents a challenge for life due to a "reversed" proton gradient that is unfavourable to many bioenergetic processes across the membranes of microorganisms. Despite this, many bacteria, archaea, and eukaryotes, collectively termed alkaliphiles, are adapted to life in alkaline ecosystems and are of great scientific and biotechnological interest due to their niche specialization and ability to produce highly stable enzymes. Advances in next-generation sequencing technologies have propelled not only the genomic characterization of many alkaliphilic microorganisms that have been isolated from nature alkaline sources but also our understanding of the functional relationships between different taxa in microbial communities living in these ecosystems. In this review, we discuss the genetics and molecular biology of alkaliphiles from an "omics" point of view, focusing on how metagenomics and transcriptomics have contributed to our understanding of these extremophiles. Graphical Abstract.

Responses of soil fungal and archaeal communities to environmental factors in an ongoing antimony mine area

Microorganisms are vital to biogeochemical cycles. However, heavy metal contamination has been implicated in altering the microbial community. Antimony (Sb) and arsenic (As) in soils can alter soil bacterial community composition in previous studies and, therefore, may have effects on soil fungal and archaeal community composition. The aim of this study was to assess the microbial activity and fungal and archaeal community composition in long-term Sb and As contamination areas. We analyzed soil respiration rates from 247.91 μg C/kg SDW h to 1372.93 μg C/kg SDW h, which revealed a positive correlation with concentrations of antimony (r = 0.79). The microbial diversity indices (Shannon and Simpson indices) showed that the abundances of the fungal and archaeal communities were more sensitive to As. Redundancy analysis (RDA) revealed that soil properties and contamination are drivers controlling the fungal and archaeal community. All of these two microbial groups responded strongly to pH. However, the dominant drivers for fungal and archaeal community composition were very different. These differences were related to limiting conditions for different species, with fungal community composition affected strongly by pH, TC, TSb, RI and Sb_DGT, while archaeal community composition was mainly affected by the pH, As_DGT and TAs. Furthermore, soil respiration showed a very strong relationship with fungal community composition with r² = 0,60, p < 0.01. These results showed that microbial responses to contamination gradients of Sb and As were heterogeneous due to the limiting environmental conditions of different microbial taxa.

Biological As(III) oxidation in biofilters by using native groundwater microorganisms

Arsenic (As) contamination in drinking water represents a worldwide threat to human health. During last decades, the exploitation of microbial As-transformations has been proposed for bioremediation applications. Among biological methods for As-contaminated water treatment, microbial As(III)-oxidation is one of the most promising approaches since it can be coupled to commonly used adsorption removal technologies, without requiring the addition of chemicals and producing toxic by-products. Despite the As(III) oxidation capability has been described in several bacterial pure or enrichment cultures, very little is known about the real potentialities of this process when mixed microbial communities, naturally occurring in As contaminated waters, are used. This study highlighted the contribution of native groundwater bacteria to As(III)-oxidation in biofilters, under conditions suitable for a household-scale treatment system. This work elucidated the influence of a variety of experimental conditions (i.e., various filling materials, flow rates, As(III) inflow concentration, As(III):As(V) ratio, filter volumes) on the microbially-mediated As(III)-oxidation process in terms of oxidation efficiency and rate. The highest oxidation efficiencies (up to 90% in 3 h) were found on coarse sand biofilters treating total initial As concentration of 100 μg L^-1. The detailed microbial characterization of the As(III) oxidizing biofilms revealed the occurrence of several OTUs affiliated with families known to oxidize As(III) (e.g., Burkholderiaceae, Comamonadaceae, Rhodobacteraceae, Xanthomonadaceae). Furthermore, As-related functional genes increased in biofilter systems in line with the observed oxidative performances.

Autotrophic microbial arsenotrophy in arsenic-rich soda lakes

A number of prokaryotes are capable of employing arsenic oxy-anions as either electron acceptors [arsenate; As(V)] or electron donors [arsenite; As(III)] to sustain arsenic-dependent growth ('arsenotrophy'). A subset of these microorganisms function as either chemoautotrophs or photoautotrophs, whereby they gain sufficient energy from their redox metabolism of arsenic to completely satisfy their carbon needs for growth by autotrophy, that is the fixation of inorganic carbon (e.g. HCO3-) into their biomass. Here we review what has been learned of these processes by investigations we have undertaken in three soda lakes of the western USA and from the physiological characterizations of the relevant bacteria, which include the critical genes involved, such as respiratory arsenate reductase (arrA) and the discovery of its arsenite-oxidizing counterpart (arxA). When possible, we refer to instances of similar process occurring in other, less extreme ecosystems and by microbes other than haloalkaliphiles.

Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake

We compared the composition of microbial communities obtained by sequencing 16S rRNA gene amplicons with taxonomy derived from metatranscriptomes from the same samples. Samples were collected from alkaline, hypersaline Mono Lake, California, USA at five depths that captured the major redox zones of the lake during the onset of meromixis. The prokaryotic community was dominated by bacteria from the phyla Proteobacteria, Firmicutes, and Bacteroidetes, while the picoeukaryotic chlorophyte Picocystis dominated the eukaryotes. Most (80%) of the abundant (>1% relative abundance) OTUs recovered as amplicons of 16S rRNA genes have been reported in previous surveys, indicating that Mono Lake's microbial community has remained stable over 12 years that have included periods of regular, annual overturn interspersed by episodes of prolonged meromixis that result in extremely reducing conditions in bottom water. Metatranscriptomic sequences binned predominately to the Gammaproteobacteria genera Thioalkalivibrio (4–13%) and Thioalkalimicrobium (0–14%); and to the Firmicutes genera Dethiobacter (0–5%) and Clostridium (1–4%), which were also abundant in the 16S rRNA gene amplicon libraries. This study provides insight into the taxonomic affiliations of transcriptionally active communities of the lake's water column under different redox conditions.

Phylogenetic Structure and Metabolic Properties of Microbial Communities in Arsenic-Rich Waters of Geothermal Origin

Arsenic (As) is a toxic element released in aquatic environments by geogenic processes or anthropic activities. To counteract its toxicity, several microorganisms have developed mechanisms to tolerate and utilize it for respiratory metabolism. However, still little is known about identity and physiological properties of microorganisms exposed to natural high levels of As and the role they play in As transformation and mobilization processes. This work aims to explore the phylogenetic composition and functional properties of aquatic microbial communities in As-rich freshwater environments of geothermal origin and to elucidate the key microbial functional groups that directly or indirectly may influence As-transformations across a natural range of geogenic arsenic contamination. Distinct bacterial communities in terms of composition and metabolisms were found. Members of Proteobacteria, affiliated to Alpha- and Betaproteobacteria were mainly retrieved in groundwaters and surface waters, whereas Gammaproteobacteria were the main component in thermal waters. Most of the OTUs from thermal waters were only distantly related to 16S rRNA gene sequences of known taxa, indicating the occurrence of bacterial biodiversity so far unexplored. Nitrate and sulfate reduction and heterotrophic As(III)-oxidization were found as main metabolic traits of the microbial cultivable fraction in such environments. No growth of autotrophic As(III)-oxidizers, autotrophic and heterotrophic As(V)-reducers, Fe-reducers and oxidizers, Mn-reducers and sulfide oxidizers was observed. The ars genes, involved in As(V) detoxifying reduction, were found in all samples whereas aioA [As(III) oxidase] and arrA genes [As(V) respiratory reductase] were not found. Overall, we found that As detoxification processes prevailed over As metabolic processes, concomitantly with the intriguing occurrence of novel thermophiles able to tolerate high levels of As.

Acetylacetone as an efficient electron shuttle for concerted redox conversion of arsenite and nitrate in the opposite direction

The redox conversion of arsenite and nitrate has direct effects on their potential environment risks. Due to the similar reduction potentials, there are few technologies that can simultaneously oxidize arsenite and reduce nitrate in one process. Here, we demonstrate that a diketone-mediated photochemical process could efficiently do this. A combined experimental and theoretical investigation was conducted to elucidate the mechanisms behind the redox conversion in the UV/acetylacetone (AA) process. Our key finding is that UV irradiation significantly changed the redox potential of AA. The excited AA, ³(AA)*, acted as a semiquinone radical-like electron shuttle. For arsenite oxidation, the efficiency of ³(AA)* was 1-2 orders of magnitude higher than those of quinone-type electron shuttles, whereas the consumption of AA was 2-4 orders of magnitude less than those of benzonquinones. The oxidation of arsenite and reduction of nitrate could be both accelerated when they existed together in UV/AA process. The results indicate that small diketones are some neglected but potent electron shuttles of great application potential in regulating aquatic redox reactions with the combination of UV irradiation.

Effect of the environment on horizontal gene transfer between bacteria and archaea

Background

Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted).

Results

We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids.

Conclusions

Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria. In general, these transfers are from archaea that live in similar oxygen and temperature conditions as the bacteria that receive the genes. Potential hotspots of horizontal gene transfer between archaea and bacteria include hot springs, marine sediments, and oil wells. Cold spots for horizontal transfer included dilute, aerobic, mesophilic environments such as marine and freshwater surface waters.

Linking Genes to Microbial Biogeochemical Cycling: Lessons from Arsenic

The biotransformation of arsenic is highly relevant to the arsenic biogeochemical cycle. Identification of the molecular details of microbial pathways of arsenic biotransformation coupled with analyses of microbial communities by meta-omics can provide insights into detailed aspects of the complexities of this biocycle. Arsenic transformations couple to other biogeochemical cycles, and to the fate of both nutrients and other toxic environmental contaminants. Microbial redox metabolism of iron, carbon, sulfur, and nitrogen affects the redox and bioavailability of arsenic species. In this critical review we illustrate the biogeochemical processes and genes involved in arsenic biotransformations. We discuss how current and future metagenomic-, metatranscriptomic-, metaproteomic-, and metabolomic-based methods will help to decipher individual microbial arsenic transformation processes, and their connections to other biogeochemical cycle. These insights will allow future use of microbial metabolic capabilities for new biotechnological solutions to environmental problems. To understand the complex nature of inorganic and organic arsenic species and the fate of environmental arsenic will require integrating systematic approaches with biogeochemical modeling. Finally, from the lessons learned from these studies of arsenic biogeochemistry, we will be able to predict how the environment changes arsenic, and, in response, how arsenic biotransformations change the environment.

Flexible biological arsenite oxidation utilizing NOx and O2 as alternative electron acceptors

The feasibility of flexible microbial arsenite (As^III) oxidation coupled with the reduction of different electron acceptors was investigated. The results indicated the acclimated microorganisms could oxidize As^III with oxygen, nitrate and nitrite as the alternative electron acceptors. A series of batch tests were conducted to measure the kinetic parameters of As^III oxidation and to evaluate the effects of environmental conditions including pH and temperature on the activity of biological As^III oxidation dependent on different electron acceptors. Kinetic results showed that oxygen-dependent As^III oxidation had the highest oxidation rate (0.59 mg As g^-1 VSS min^-1), followed by nitrate- (0.40 mg As g^-1 VSS min^-1) and nitrite-dependent As^III oxidation (0.32 mg As g^-1 VSS min^-1). The kinetic data of aerobic As^III oxidation were fitted well with the Monod kinetic model, while the Haldane substrate inhibition model was better applicable to describe the inhibition of anoxic As^III oxidation. Both aerobic and anoxic As^III oxidation performed the optimal activity at the near neutral pH. Besides, the optimal temperature for oxygen-, nitrate- and nitrite-dependent As^III oxidation was 30 ± 1 °C, 40 ± 1 °C and 20 ± 1 °C, respectively.

Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA

This study evaluates the transcriptionally active, dissimilatory sulfur- and arsenic-cycling components of the microbial community in alkaline, hypersaline Mono Lake, CA, USA. We sampled five depths spanning the redox gradient (10, 15, 18, 25 and 31 m) during maximum thermal stratification. We used custom databases to identify transcripts of genes encoding complex iron-sulfur molybdoenzyme (CISM) proteins, with a focus on arsenic (arrA, aioA and arxA) and sulfur cycling (dsrA, aprA and soxB), and assigned them to taxonomic bins. We also report on the distribution of transcripts related to the ars arsenic detoxification pathway. Transcripts from detoxification pathways were not abundant in oxic surface waters (10 m). Arsenic cycling in the suboxic and microaerophilic zones of the water column (15 and 18 m) was dominated by arsenite-oxidizing members of the Gammaproteobacteria most closely affiliated with Thioalkalivibrio and Halomonas, transcribing arxA. We observed a transition to arsenate-reducing bacteria belonging to the Deltaproteobacteria and Firmicutes transcribing arsenate reductase (arrA) in anoxic bottom waters of the lake (25 and 31 m). Sulfur cycling at 15 and 18 m was dominated by Gammaproteobacteria (Thioalkalivibrio and Thioalkalimicrobium) oxidizing reduced S species, with a transition to sulfate-reducing Deltaproteobacteria at 25 and 31 m. Genes related to arsenic and sulfur oxidation from Thioalkalivibrio were more highly transcribed at 15 m relative to other depths. Our data highlight the importance of Thioalkalivibrio to arsenic and sulfur biogeochemistry in Mono Lake and identify new taxa that appear capable of transforming arsenic.