Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

DsrC is involved in fermentative growth and interacts directly with the FlxABCD-HdrABC complex in Desulfovibrio vulgaris Hildenborough

DsrC is a key protein in dissimilatory sulfur metabolism, where it works as co-substrate of the dissimilatory sulfite reductase DsrAB. DsrC has two conserved cysteines in a C-terminal arm that are converted to a trisulfide upon reduction of sulfite. In sulfate-reducing bacteria, DsrC is essential and previous works suggested additional functions beyond sulfite reduction. Here, we studied whether DsrC also plays a role during fermentative growth of Desulfovibrio vulgaris Hildenborough, by studying two strains where the functionality of DsrC is impaired by a lower level of expression (IPFG07) and additionally by the absence of one conserved Cys (IPFG09). Growth studies coupled with metabolite and proteomic analyses reveal that fermentation leads to lower levels of DsrC, but impairment of its function results in reduced growth by fermentation and a shift towards more fermentative metabolism during sulfate respiration. In both respiratory and fermentative conditions, there is increased abundance of the FlxABCD-HdrABC complex and Adh alcohol dehydrogenase in IPFG09 versus the wild type, which is reflected in higher production of ethanol. Pull-down experiments confirmed a direct interaction between DsrC and the FlxABCD-HdrABC complex, through the HdrB subunit. Dissimilatory sulfur metabolism, where sulfur compounds are used for energy generation, is a key process in the ecology of anoxic environments, and is more widespread among bacteria than previously believed. Two central proteins for this type of metabolism are DsrAB dissimilatory sulfite reductase and its co-substrate DsrC. Using physiological, proteomic and biochemical studies of Desulfovibrio vulgaris Hildenborough and mutants affected in DsrC functionality, we show that DsrC is also relevant for fermentative growth of this model organism and that it interacts directly with the soluble FlxABCD-HdrABC complex that links the NAD(H) pool with dissimilatory sulfite reduction.

Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings

Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties. Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers. Genome-resolved metagenomics retrieved 406 intermediate or high-quality genomes spanning 26 phyla, including major new groups (e.g., Patescibacteria and DPANN). Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds. These results have implications for in situ AMD bioremediation.

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

Cold seeps, where cold hydrocarbon-rich fluid escapes from the seafloor, show strong enrichment of toxic metalloid arsenic (As). The toxicity and mobility of As can be greatly altered by microbial processes that play an important role in global As biogeochemical cycling. However, a global overview of genes and microbes involved in As transformation at seeps remains to be fully unveiled. Using 87 sediment metagenomes and 33 metatranscriptomes derived from 13 globally distributed cold seeps, we show that As detoxification genes (arsM, arsP, arsC1/arsC2, acr3) were prevalent at seeps and more phylogenetically diverse than previously expected. Asgardarchaeota and a variety of unidentified bacterial phyla (e.g. 4484-113, AABM5-125-24 and RBG-13-66-14) may also function as the key players in As transformation. The abundances of As cycling genes and the compositions of As-associated microbiome shifted across different sediment depths or types of cold seep. The energy-conserving arsenate reduction or arsenite oxidation could impact biogeochemical cycling of carbon and nitrogen, via supporting carbon fixation, hydrocarbon degradation and nitrogen fixation. Overall, this study provides a comprehensive overview of As cycling genes and microbes at As-enriched cold seeps, laying a solid foundation for further studies of As cycling in deep sea microbiome at the enzymatic and processual levels.

Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria

Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.

Crystal lattice defects in nanocrystalline metacinnabar in contaminated streambank soils suggest a role for biogenic sulfides in the formation of mercury sulfide phases

At mercury (Hg)-contaminated sites, streambank erosion can act as a main mobilizer of Hg into nearby waterbodies. Once deposited into the waters, mercury from these soils can be transformed to MeHg by microorganisms. It is therefore important to understand the solid-phase speciation of Hg in streambanks as differences in Hg speciation will have implications for Hg transport and bioavailability. In this study, we characterized Hg solid phases in Hg-contaminated soils (100-1100 mg per kg Hg) collected from the incised bank of the East Fork Poplar Creek (EFPC) in Oak Ridge, TN (USA). The analysis of the soil samples by scanning electron microscopy-energy dispersive spectroscopy indicated numerous microenvironments where Hg and sulfur (S) are co-located. According to bulk soil analyses by extended X-ray absorption fine structure spectroscopy (EXAFS), the near-neighbor Hg molecular coordination in the soils closely resembled freshly precipitated Hg sulfide (metacinnabar, HgS); however, EXAFS fits indicated the Hg in the HgS structure was undercoordinated with respect to crystalline metacinnabar. This undercoordination of Hg-S observed by spectroscopy is consistent with transmission electron microspy images showing the presence of nanocrystallites with structural defects (twinning, stacking faults, dislocations) in individual HgS-bearing particles. Although the soils were collected from exposed parts of the stream bank (i.e., open to the atmosphere), the presence of reduced forms of S and sulfate-reducing microbes suggests that biogenic sulfides promote the formation of HgS nanoparticles in these soils. Altogether, these data demonstrate the predominance of nanoparticulate HgS with crystal lattice defects in the bank soils of an industrially impacted stream. Efforts to predict the mobilization and bioavailability of Hg associated with nano-HgS forms should consider the impact of nanocrystalline lattice defects on particle surface reactivity, including Hg dissolution rates and bioavailability on Hg fate and transformations.

Recent Advances in Biotechnologies for the Treatment of Environmental Pollutants Based on Reactive Sulfur Species

The definition of reactive sulfur species (RSS) is inspired by the reactivity and variable chemical valence of sulfur. Sulfur is an essential element for life and is a part of global geochemical cycles. Wastewater treatment bioreactors can be divided into two major categories: sulfur reduction and sulfur oxidation. We review the origins of the definition of RSS and related biotechnological processes in environmental management. Sulfate reduction, sulfide oxidation, and sulfur-based redox reactions are key to driving the coupled global carbon, nitrogen, and sulfur co-cycles. This shows the coupling of the sulfur cycle with the carbon and nitrogen cycles and provides insights into the global material-chemical cycle. We also review the biological classification and RSS metabolic mechanisms of functional microorganisms involved in the biological processes, such as sulfate-reducing and sulfur-oxidizing bacteria. Developments in molecular biology and genomic technologies have allowed us to obtain detailed information on these bacteria. The importance of RSS in environmental technologies requires further consideration.

What Controls the Sulfur Isotope Fractionation during Dissimilatory Sulfate Reduction?

Sulfate often behaves conservatively in the oxygenated environments but serves as an electron acceptor for microbial respiration in a wide range of natural and engineered systems where oxygen is depleted. As a ubiquitous anaerobic dissimilatory pathway, therefore, microbial reduction of sulfate to sulfide has been of continuing interest in the field of microbiology, ecology, biochemistry, and geochemistry. Stable isotopes of sulfur are an effective tool for tracking this catabolic process as microorganisms discriminate strongly against heavy isotopes when cleaving the sulfur-oxygen bond. Along with its high preservation potential in environmental archives, a wide variation in the sulfur isotope effects can provide insights into the physiology of sulfate reducing microorganisms across temporal and spatial barriers. A vast array of parameters, including phylogeny, temperature, respiration rate, and availability of sulfate, electron donor, and other essential nutrients, has been explored as a possible determinant of the magnitude of isotope fractionation, and there is now a broad consensus that the relative availability of sulfate and electron donors primarily controls the magnitude of fractionation. As the ratio shifts toward sulfate, the sulfur isotope fractionation increases. The results of conceptual models, centered on the reversibility of each enzymatic step in the dissimilatory sulfate reduction pathway, are in qualitative agreement with the observations, although the underlying intracellular mechanisms that translate the external stimuli into the isotopic phenotype remain largely unexplored experimentally. This minireview offers a snapshot of our current understanding of the sulfur isotope effects during dissimilatory sulfate reduction as well as their potential quantitative applications. It emphasizes the importance of sulfate respiration as a model system for the isotopic investigation of other respiratory pathways that utilize oxyanions as terminal electron acceptors.

Does inorganic carbon species alter chromium reduction mechanism in sulfur-based autotrophic biosystem?

Sulfur-based autotrophic bioremediation is recognized as an environmentally-friendly and effective method for the treatment of Cr(VI) in groundwater. However, inorganic carbon (IC), especially IC-rich solid kitchen waste, has rarely been reported as an important factor in the autotrophic process. In China, kitchen waste containing IC is generated in large quantities, and in combination with Cr(VI) autotrophic treatment technology in groundwater can achieve a win-win situation. Herein, the efficiency of Cr(VI)-bioreduction coupling solid inorganic carbon (SIC) (e.g. marble, egg shell, oyster shell, and NSAD synthetic material) and liquid inorganic carbon (LIC) was compared for the first time. After 18 d incubation, there were significant differences in Cr(VI) reduction efficiency and microbial community between SIC-bioreactors and LIC-bioreactors. Higher electron transfer activity, greater bioavailability of organics, and multiple Cr(VI) reductases were detected in SIC-biosystems, which effectively promoted Cr(VI) energy metabolism and enzyme-mediated biological reduction. High-throughput 16S rRNA gene sequencing reveled multiple cooperative mechanism in different substrate biosystems. This study not only advances the understanding of SIC coupled with Cr(VI) autotrophic bioreduction, but also provides new insights for the treatment of solid kitchen waste and groundwater bioremediation.

Microbial Contributions to Iodide Enrichment in Deep Groundwater in the North China Plain

Microorganisms play crucial roles in the global iodine cycling through iodine oxidation, reduction, volatilization, and deiodination. In contrast to iodate formation in radionuclide-contaminated groundwater by the iodine-oxidizing bacteria, microbial contribution to the formation of high level of iodide in geogenic high iodine groundwater is poorly understood. In this study, our results of comparative metagenomic analyses of deep groundwater with typical high iodide concentrations in the North China Plain revealed the existence of putative dissimilatory iodate-reducing idrABP1P2 gene clusters in groundwater. Heterologous expression and characterization of an identified idrABP1P2 gene cluster confirmed its functional role in iodate reduction. Thus, microbial dissimilatory iodate reduction could contribute to iodide formation in geogenic high iodine groundwater. In addition, the identified iron-reducing, sulfur-reducing, sulfur-oxidizing, and dehalogenating bacteria in the groundwater could contribute to the release and production of iodide through the reductive dissolution of iron minerals, abiotic iodate reduction of derived ferrous iron and sulfide, and dehalogenation of organic iodine, respectively. These microbially mediated iodate reduction and organic iodine dehalogenation processes may also result in the transformation among iodine species and iodide enrichment in other geogenic iodine-rich groundwater systems worldwide.

Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms

The iron-oxidizing Gallionellaceae drive a wide variety of biogeochemical cycles through their metabolisms and biominerals. To better understand the environmental impacts of Gallionellaceae, we need to improve our knowledge of their diversity and metabolisms, especially any novel iron oxidation mechanisms. Here, we used a pangenomic analysis of 103 genomes to resolve Gallionellaceae phylogeny and explore the range of genomic potential. Using a concatenated ribosomal protein tree and key gene patterns, we determined Gallionellaceae has four genera, divided into two groups-iron-oxidizing bacteria (FeOB) Gallionella, Sideroxydans, and Ferriphaselus with known iron oxidases (Cyc2, MtoA) and nitrite-oxidizing bacteria (NOB) Candidatus Nitrotoga with nitrite oxidase (Nxr). The FeOB and NOB have similar electron transport chains, including genes for reverse electron transport and carbon fixation. Auxiliary energy metabolisms including S oxidation, denitrification, and organotrophy were scattered throughout the Gallionellaceae FeOB. Within FeOB, we found genes that may represent adaptations for iron oxidation, including a variety of extracellular electron uptake (EEU) mechanisms. FeOB genomes encoded more predicted c-type cytochromes overall, notably more multiheme c-type cytochromes (MHCs) with >10 CXXCH motifs. These include homologs of several predicted outer membrane porin-MHC complexes, including MtoAB and Uet. MHCs are known to efficiently conduct electrons across longer distances and function across a wide range of redox potentials that overlap with mineral redox potentials, which can help expand the range of usable iron substrates. Overall, the results of pangenome analyses suggest that the Gallionellaceae genera Gallionella, Sideroxydans, and Ferriphaselus are primarily iron oxidizers, capable of oxidizing dissolved Fe2+ as well as a range of solid iron or other mineral substrates.

Cupriavidus pinatubonensis JMP134 Alleviates Sulfane Sulfur Toxicity after the Loss of Sulfane Dehydrogenase through Oxidation by Persulfide Dioxygenase and Hydrogen Sulfide Release

An incomplete Sox system lacking sulfane dehydrogenase SoxCD may produce and accumulate sulfane sulfur when oxidizing thiosulfate. However, how bacteria alleviate the pressure of sulfane sulfur accumulation remains largely unclear. In this study, we focused on the bacterium Cupriavidus pinatubonensis JMP134, which contains a complete Sox system. When soxCD was deleted, this bacterium temporarily produced sulfane sulfur when oxidizing thiosulfate. Persulfide dioxygenase (PDO) in concert with glutathione oxidizes sulfane sulfur to sulfite. Sulfite can spontaneously react with extra persulfide glutathione (GSSH) to produce thiosulfate, which can feed into the incomplete Sox system again and be oxidized to sulfate. Furthermore, the deletion strain lacking PDO and SoxCD produced volatile H₂S gas when oxidizing thiosulfate. By comparing the oxidized glutathione (GSSG) between the wild-type and deletion strains, we speculated that H₂S is generated during the interaction between sulfane sulfur and the glutathione/oxidized glutathione (GSH/GSSG) redox couple, which may reduce the oxidative stress caused by the accumulation of sulfane sulfur in bacteria. Thus, PDO and H₂S release play a critical role in alleviating sulfane sulfur toxicity after the loss of soxCD in C. pinatubonensis JMP134.

Implications of a short carbon pulse on biofilm formation on mica schist in microcosms with deep crystalline bedrock groundwater

Microbial life in the deep subsurface occupies rock surfaces as attached communities and biofilms. Previously, epilithic Fennoscandian deep subsurface bacterial communities were shown to host genetic potential, especially for heterotrophy and sulfur cycling. Acetate, methane, and methanol link multiple biogeochemical pathways and thus represent an important carbon and energy source for microorganisms in the deep subsurface. In this study, we examined further how a short pulse of low-molecular-weight carbon compounds impacts the formation and structure of sessile microbial communities on mica schist surfaces over an incubation period of ∼3.5 years in microcosms containing deep subsurface groundwater from the depth of 500 m, from Outokumpu, Finland. The marker gene copy counts in the water and rock phases were estimated with qPCR, which showed that bacteria dominated the mica schist communities with a relatively high proportion of epilithic sulfate-reducing bacteria in all microcosms. The dominant bacterial phyla in the microcosms were Proteobacteria, Firmicutes, and Actinobacteria, whereas most fungal genera belonged to Ascomycota and Basidiomycota. Dissimilarities between planktic and sessile rock surface microbial communities were observed, and the supplied carbon substrates led to variations in the bacterial community composition.

Quantifying sulfidization and non-sulfidization in long-term in-situ microbial colonized As(V)-ferrihydrite coated sand columns: Insights into As mobility

Sulfide-induced reduction (sulfidization) of arsenic (As)-bearing Fe(III) (oxyhydro)oxides may lead to As mobilization in aquifer systems. However, little is known about the relative contributions of sulfidization and non-sulfidization of Fe(III) (oxyhydro)oxides reduction to As mobilization. To address this issue, high As groundwater with low sulfide (LS) and high sulfide (HS) concentrations were pumped through As(V)-bearing ferrihydrite-coated sand columns (LS-column and HS-column, respectively) being settled within wells in the western Hetao Basin, China. Sulfidization of As(V)-bearing ferrihydrite was evidenced by the increase in dissolved Fe(II) and the presence of solid Fe(II) and elemental sulfur (S⁰) in both the columns. A conceptual model was built using accumulated S⁰ and Fe(II) produced in the columns to calculate the proportions of sulfidization-induced Fe(III) (oxyhydro)oxide reduction and non-sulfidization-induced Fe(III) (oxyhydro)oxide reduction. Fe(III) reduction via sulfidization occurred preferentially in the inlet ends (LS-column, 31 %; HS-column, 86 %), while Fe(III) reduction via non-sulfidization processes predominated in the outlet ends (LS-column, 96 %; HS-column, 86 %), and was attributed to the metabolism of genera associated with Fe(III) reduction (including Shewanella, Ferribacterium, and Desulfuromonas). Arsenic was mobilized in the columns via sulfidization and non-sulfidization processes. More As was released from the solid of the HS-column than that of the LS-column due to the higher intensity of sulfidization in the presence of higher concentrations of dissolved S(-II). Overall, this study highlights the sulfidization of As-bearing Fe(III) (oxyhydro)oxides as an important As-mobilizing pathway in complex As-Fe-S bio-hydrogeochemical networks.

Implications of hydrogen sulfide in colorectal cancer: Mechanistic insights and diagnostic and therapeutic strategies

Hydrogen sulfide (H2S) is an important signaling molecule in colorectal cancer (CRC). It is produced in the colon by the catalytic synthesis of the colonocytes' enzymatic systems and the release of intestinal microbes, and is oxidatively metabolized in the colonocytes' mitochondria. Both endogenous H2S in colonic epithelial cells and exogenous H2S in intestinal lumen contribute to the onset and progression of CRC. The up-regulation of endogenous synthetases is thought to be the cause of the elevated H2S levels in CRC cells. Different diagnostic probes and combination therapies, as well as tumor treatment approaches through H2S modulation, have been developed in recent years and have become active area of investigation for the diagnosis and treatment of CRC. In this review, we focus on the specific mechanisms of H2S production and oxidative metabolism as well as the function of H2S in the occurrence, progression, diagnosis, and treatment of CRC. We also discuss the present challenges and provide insights into the future research of this burgeoning field.

Unravelling microbial drivers of the sulfate-reduction process inside landfill using metagenomics

Hydrogen sulfide (H₂S) is one of the common landfill odor. This research demonstrates that the sulfate transformation behavior is significantly enhanced during the landfill process, accompanied by a shift in microbial structure. The relative abundance of dissimilatory sulfate reduction (DSR) and thiosulfate oxidation by SOX (sulfur-oxidation) complex gradually decreases through the landfill processes while the assimilatory sulfate reduction (ASR) demonstrates the opposite behavior. The major module for landfill sulfate reduction is ASR, accounting for 31.72% ± 2.84% of sulfate metabolism. Based on the functional genes for the sulfate pathway, the drivers for sulfate biotransformation in landfills were determined and further identified their contribution in the sulfate metabolism during landfill processes. Pseudomonas, Methylocaldum, Bacillus, Methylocystis and Hyphomicrobium were the top 5 contributors for ASR pathway, and only one genus Pseudomonas was found for DSR pathway. Among the 26 high-quality metagenome-assembled genomes of sulfate functional species, 24 were considered novel species for sulfuric metabolism. Overall, this study provides unique insight into the sulfate transformation process related to the H₂S odor control in landfill management.

Integration of Microbial Transformation Mechanism of Polyphosphate Accumulation and Sulfur Cycle in Subtropical Marine Mangrove Ecosystems with Spartina alterniflora Invasion

Excessive phosphorus can lead to eutrophication in marine and coastal ecosystems. Sulfur metabolism-associated microorganisms stimulate biological phosphorous removal. However, the integrating co-biotransformation mechanism of phosphorus and sulfur in subtropical marine mangrove ecosystems with Spartina alterniflora invasion is poorly understood. In this study, an ecological model of the coupling biotransformation of sulfur and phosphorus is constructed using metagenomic analysis and quantitative polymerase chain reaction strategies. Phylogenetic analysis profiling, a distinctive microbiome with high frequencies of Gammaproteobacteria and Deltaproteobacteria, appears to be an adaptive characteristic of microbial structures in subtropical mangrove ecosystems. Functional analysis reveals that the levels of sulfate reduction, sulfur oxidation, and poly-phosphate (Poly-P) aggregation decrease with increasing depth. However, at depths of 25-50 cm in the mangrove ecosystems with S. alterniflora invasion, the abundance of sulfate reduction genes, sulfur oxidation genes, and polyphosphate kinase (ppk) significantly increased. A strong positive correlation was found among ppk, sulfate reduction, sulfur oxidation, and sulfur metabolizing microorganisms, and the content of sulfide was significantly and positively correlated with the abundance of ppk. Further microbial identification suggested that Desulfobacterales, Anaerolineales, and Chromatiales potentially drove the coupling biotransformation of phosphorus and sulfur cycling. In particular, Desulfobacterales exhibited dominance in the microbial community structure. Our findings provided insights into the simultaneous co-biotransformation of phosphorus and sulfur bioconversions in subtropical marine mangrove ecosystems with S. alterniflora invasion.

Estimation of sulfur fate and contribution to VSC emissions from lakes during algae decay

Algae decay is an important process influencing environmental variables and emissions of volatile sulfur compounds (VSCs) in eutrophic lakes. However, effects of algae decay on VSC emissions from eutrophic lakes as well as fate of algae-derived sulfur remain poorly understood. In this study, simulated algae-sediment systems were used to explore the flow and distribution of sulfur during algae decay. VSCs including hydrogen sulfide (H₂S), methanethiol (CH₃SH), carbon disulfide (CS₂) and dimethyl sulfide ((CH₃)₂S) were detected during algae decay, which increased with algae biomass and eutrophic levels in lakes. During algae decay, the highest H₂S, CH₃SH and (CH₃)₂S emission rates of 10.45, 21.82 and 43.26 μg d^-1 occurred in the first 1-2 days, respectively, while the highest CS₂ emission rates were observed between days 8 and 11. The maximum emissions of H₂S and CS₂ from algae decay were estimated at 0.51 and 0.35 mg m^-2 d^-1 in Lake Taihu, accounting for 1.57% and 0.69% of the total H₂S and CS₂ emissions of in situ, respectively. Algae decay could significantly increase the contents of total sulfur and total carbon in sediments by 2.90%-21.11% and 4.23%-45.05%, respectively. The VSC emissions during algae decay could be predicted using the multiple regression models with the contents of total carbon, total nitrogen and sulfur-containing compounds in sediments. Partial least squares path modelling demonstrated that algae decay had a low direct effect on VSC emissions with a strength of 0.06, while it had a significant influence on environmental variables with a strength of 0.63, which could affect VSC emissions with a strength of 0.85, indicating VSC emissions from eutrophic lakes were affected by the environmental variables rather than the direct influence of algae decay. These findings illustrated the mechanisms of VSC emissions during algae decay and provided insights into VSC control and mitigation for eutrophic lakes.

Treatment of acid rock drainage using a sulphate-reducing bioreactor with a limestone precolumn

Sulphate reducing bacteria (SRB) offer promise for the treatment of mine waste due to their effectiveness removing toxic heavy metals as highly insoluble metal sulphides and their ability to generate alkalinity. The main objective of this study was to develop a treatment composed of a sulphate-reducing bioreactor with a limestone precolumn for the removal of Cu(II) from a synthetic ARD. The purpose of the limestone column was to increase the pH values and decrease the level of Cu in the effluent to prevent SRB inhibition. The system was fed with a pH-2.7 synthetic ARD containing Cu(II) (10-40 mg/L), sulphate (2000 mg/L) and acetate (2.5 g COD/L) for 150 days. Copper removal efficiencies in the two-stage system were very high (95-99%), with a final concentration of 0.53 mg/L Cu, and almost complete removal occurred in the limestone precolumn. In the same manner, the acidity of the synthetic ARD was effectively reduced in the limestone precolumn to 7.3 and the pH was raised in the bioreactor (7.3-8.0). COD consumption by methanogens was predominant from day 0-118, but SRB dominated at the end of the experiment (day 150) when the average COD removal and sulphide production were 74.8% and 61.7%, respectively. Study of the microbial taxonomic composition in the bioreactor revealed that Methanosarcina and Methanosaeta were the most prevalent methanogens while the genera Desulfotomaculum and Syntrophobacter were the dominant SRB. Among the SRB identified Desulfotomaculum intricatum (99% identity) and Desulfotomaculum acetoxidans (96%) were the most abundant sequences of bacteria capable of using acetate.

Microbial communities and metabolic pathways involved in reductive decolorization of an azo dye in a two-stage AD system

Multiple stage anaerobic system was found to be an effective strategy for reductive decolorization of azo dyes in the presence of sulfate. Bulk color removal (56-90%) was achieved concomitant with acidogenic activity in the 1st-stage reactor (R1), while organic matter removal (≤100%) and sulfate reduction (≤100%) occurred predominantly in the 2nd-stage reactor (R2). However, azo dye reduction mechanism and metabolic routes involved remain unclear. The involved microbial communities and conditions affecting the azo dye removal in a two-stage anaerobic digestion (AD) system were elucidated using amplicon sequencing (16S rRNA, fhs, dsrB and mcrA) and correlation analysis. Reductive decolorization was found to be co-metabolic and mainly associated with hydrogen-producing pathways. We also found evidence of the involvement of an azoreductase from Lactococcus lactis. Bacterial community in R1 was sensitive and shifted in the presence of the azo dye, while microorganisms in R2 were more protected. Higher diversity of syntrophic-acetate oxidizers, sulfate reducers and methanogens in R2 highlights the role of the 2nd-stage in organic matter and sulfate removals, and these communities might be involved in further transformations of the azo dye reduction products. The results improve our understanding on the role of different microbial communities in anaerobic treatment of azo dyes and can help in the design of better solutions for the treatment of textile effluents.

Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge

The Southwest Indian Ridge (SWIR) is one of the typical representatives of deep-sea ultraslow-spreading ridges, and has increasingly become a hot spot of studying subsurface geological activities and deep-sea mining management. However, the understanding of microbial activities is still limited on active hydrothermal vent chimneys in SWIR. In this study, samples from an active black smoker and a diffuse vent located in the Longqi hydrothermal region were collected for deep metagenomic sequencing, which yielded approximately 290 GB clean data and 295 mid-to-high-quality metagenome-assembled genomes (MAGs). Sulfur oxidation conducted by a variety of Gammaproteobacteria, Alphaproteobacteria, and Campylobacterota was presumed to be the major energy source for chemosynthesis in Longqi hydrothermal vents. Diverse iron-related microorganisms were recovered, including iron-oxidizing Zetaproteobacteria, iron-reducing Deferrisoma, and magnetotactic bacterium. Twenty-two bacterial MAGs from 12 uncultured phyla harbored iron oxidase Cyc2 homologs and enzymes for organic carbon degradation, indicated novel chemolithoheterotrophic iron-oxidizing bacteria that affected iron biogeochemistry in hydrothermal vents. Meanwhile, potential interactions between microbial communities and chimney minerals were emphasized as enriched metabolic potential of siderophore transportation, and extracellular electron transfer functioned by multi-heme proteins was discovered. Composition of chimney minerals probably affected microbial iron metabolic potential, as pyrrhotite might provide more available iron for microbial communities. Collectively, this study provides novel insights into microbial activities and potential mineral-microorganism interactions in hydrothermal vents. IMPORTANCE Microbial activities and interactions with minerals and venting fluid in active hydrothermal vents remain unclear in the ultraslow-spreading SWIR (Southwest Indian Ridge). Understanding about how minerals influence microbial metabolism is currently limited given the obstacles in cultivating microorganisms with sulfur or iron oxidoreduction functions. Here, comprehensive descriptions on microbial composition and metabolic profile on 2 hydrothermal vents in SWIR were obtained based on cultivation-free metagenome sequencing. In particular, autotrophic sulfur oxidation supported by minerals was presumed, emphasizing the role of chimney minerals in supporting chemosynthesis. Presence of novel heterotrophic iron-oxidizing bacteria was also indicated, suggesting overlooked biogeochemical pathways directed by microorganisms that connected sulfide mineral dissolution and organic carbon degradation in hydrothermal vents. Our findings offer novel insights into microbial function and biotic interactions on minerals in ultraslow-spreading ridges.

Generation and Physiology of Hydrogen Sulfide and Reactive Sulfur Species in Bacteria

Sulfur is not only one of the most abundant elements on the Earth, but it is also essential to all living organisms. As life likely began and evolved in a hydrogen sulfide (H₂S)-rich environment, sulfur metabolism represents an early form of energy generation via various reactions in prokaryotes and has driven the sulfur biogeochemical cycle since. It has long been known that H₂S is toxic to cells at high concentrations, but now this gaseous molecule, at the physiological level, is recognized as a signaling molecule and a regulator of critical biological processes. Recently, many metabolites of H₂S, collectively called reactive sulfur species (RSS), have been gradually appreciated as having similar or divergent regulatory roles compared with H₂S in living organisms, especially mammals. In prokaryotes, even in bacteria, investigations into generation and physiology of RSS remain preliminary and an understanding of the relevant biological processes is still in its infancy. Despite this, recent and exciting advances in the fields are many. Here, we discuss abiotic and biotic generation of H₂S/RSS, sulfur-transforming enzymes and their functioning mechanisms, and their physiological roles as well as the sensing and regulation of H₂S/RSS.

Unexpected diversity found within benthic microbial mats at hydrothermal springs in Crater Lake, Oregon

Crater Lake, Oregon is an oligotrophic freshwater caldera lake fed by thermally and chemically enriched hydrothermal springs. These vents distinguish Crater Lake from other freshwater systems and provide a unique ecosystem for study. This study examines the community structure of benthic microbial mats occurring with Crater Lake hydrothermal springs. Small subunit rRNA gene amplicon sequencing from eight bacterial mats was used to assess community structure. These revealed a relatively homogeneous, yet diverse bacterial community. High alpha diversity and low beta diversity indicate that these communities are likely fueled by homogeneous hydrothermal fluids. An examination of autotrophic taxa abundance indicates the potential importance of iron and sulfur inputs to the primary productivity of these mats. Chemoautotrophic potential within the mats was dominated by iron oxidation from Gallionella and Mariprofundus and by sulfur oxidation from Sulfuricurvum and Thiobacillus with an additional contribution of nitrite oxidation from Nitrospira. Metagenomic analysis showed that cbbM genes were identified as Gallionella and that aclB genes were identified as Nitrospira, further supporting these taxa as autotrophic drivers of the community. The detection of several taxa containing arsC and nirK genes suggests that arsenic detoxification and denitrification processes are likely co-occurring in addition to at least two modes of carbon fixation. These data link the importance of the detected autotrophic metabolisms driven by fluids derived from benthic hydrothermal springs to Crater Lake’s entire lentic ecosystem.

Metagenomic and metatranscriptomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland

The widespread occurrence of sulfate-reducing microorganisms (SRMs) in temporarily oxic/hypoxic aquatic environments indicates an intriguing possibility that SRMs can prevail in constantly oxic/hypoxic terrestrial sulfate-rich environments. However, little attention has been given to this possibility, leading to an incomplete understanding of microorganisms driving the terrestrial part of the global sulfur (S) cycle. In this study, genome-centric metagenomics and metatranscriptomics were employed to explore the diversity, metabolic potential, and gene expression profile of SRMs in a revegetated acidic mine wasteland under constantly oxic/hypoxic conditions. We recovered 16 medium- to high-quality metagenome-assembled genomes (MAGs) containing reductive dsrAB. Among them, 12 and four MAGs belonged to Acidobacteria and Deltaproteobacteria, respectively, harboring three new SRM genera. Comparative genomic analysis based on seven high-quality MAGs (completeness >90% and contamination <10%; including six acidobacterial and one deltaproteobacterial) and genomes of three additional cultured model species showed that Acidobacteria-related SRMs had more genes encoding glycoside hydrolases, oxygen-tolerant hydrogenases, and cytochrome c oxidases than Deltaproteobacteria-related SRMs. The opposite pattern was observed for genes encoding superoxide reductases and thioredoxin peroxidases. Using VirSorter, viral genome sequences were found in five of the 16 MAGs and in all three cultured model species. These prophages encoded enzymes involved in glycoside hydrolysis and antioxidation in their hosts. Moreover, metatranscriptomic analysis revealed that 15 of the 16 SRMs reported here were active in situ. An acidobacterial MAG containing a prophage dominated the SRM transcripts, expressing a large number of genes involved in its response to oxidative stress and competition for organic matter.

Microbial behaviours inside alternating anaerobic-anoxic environment of a sulfur cycle-driven EBPR system: A metagenomic investigation

Denitrifying sulfur conversion-assisted enhanced biological phosphorus removal (DS-EBPR) was recently developed for saline wastewater treatment. However, the main functional bacteria and the interrelationship of functional bacteria of the DS-EBPR have not been defined and identified so far. This study used metagenomics and multivariate statistics to deduce the functional microbial community and distribution of functional genes associated with the critical metabolic pathways of carbon (C), nitrogen (N), phosphorus (P) and sulfur (S), particularly regarding how they would behave under the alternating anaerobic-anoxic conditions inside a long-term DS-EBPR system. An analysis of the metagenomics and metabolic functions identified 11 major microbial species which were classifiable into four groups: sulfate reducing bacteria (SRB, 0.8-2.2%), sulfur oxidizing bacteria (SOB, 31.9-37.7%), denitrifying phosphate accumulating organisms (DPAOs, 10.0-15.8%) and glycogen accumulating organisms (GAOs, 3.7-7.7%). The four groups of microorganisms performed their respective metabolisms synergistically. In terms of distribution of functional genes, SRB (Desulfococcus and Desulfobacter) and SOB (Chromatiaceae and Thiobacillus) are not only encoded by the related sulfur conversion genes (sqr, dsrAB, aprAB and sat), but also encoded by the necessary ppx and ppk1 gene for P removal that they can be considered as the potential S-related PAOs. Between the anaerobic and anoxic conditions, the metagenome-based microbial community remained structurally similar, but the functional genes, which encode various key enzymes for the P, N, and S pathways, changed in abundance. This study contributes to our understanding on the interactions and competition between the SRB, SOB, DPAOs, and GAOs in a DS-EBPR system.

Novel Microorganisms Contribute to Biosulfidogenesis in the Deep Layer of an Acidic Pit Lake

Cueva de la Mora is a permanently stratified acidic pit lake with extremely high concentrations of heavy metals at depth. In order to evaluate the potential for in situ sulfide production, we characterized the microbial community in the deep layer using metagenomics and metatranscriptomics. We retrieved 18 high quality metagenome-assembled genomes (MAGs) representing the most abundant populations. None of the MAGs were closely related to either cultured or non-cultured organisms from the Genome Taxonomy or NCBI databases (none with average nucleotide identity >95%). Despite oxygen concentrations that are consistently below detection in the deep layer, some archaeal and bacterial MAGs mapped transcripts of genes for sulfide oxidation coupled with oxygen reduction. Among these microaerophilic sulfide oxidizers, mixotrophic Thermoplasmatales archaea were the most numerous and represented 24% of the total community. Populations associated with the highest predicted in situ activity for sulfate reduction were affiliated with Actinobacteria, Chloroflexi, and Nitrospirae phyla, and together represented about 9% of the total community. These MAGs, in addition to a less abundant Proteobacteria MAG in the genus Desulfomonile, contained transcripts of genes in the Wood-Ljungdahl pathway. All MAGs had significant genetic potential for organic carbon oxidation. Our results indicate that novel acidophiles are contributing to biosulfidogenesis in the deep layer of Cueva de la Mora, and that in situ sulfide production is limited by organic carbon availability and sulfur oxidation.

Microbially promoted calcite precipitation in the pelagic redoxcline: Elucidating the formation of the turbid layer

Large bell-shaped calcite formations called "Hells Bells" were discovered underwater in the stratified cenote El Zapote on the Yucatán Peninsula, Mexico. Together with these extraordinary speleothems, divers found a white, cloudy turbid layer into which some Hells Bells partially extend. Here, we address the central question if the formation of the turbid layer could be based on microbial activity, more specifically, on microbially induced calcite precipitation. Metagenomic and metatranscriptomic profiling of the microbial community in the turbid layer, which overlaps with the pelagic redoxcline in the cenote, revealed chemolithoautotrophic Hydrogenophilales and unclassified β-Proteobacteria as the metabolic key players. Bioinformatic and hydrogeochemical data suggest chemolithoautotrophic oxidation of sulfide to zero-valent sulfur catalyzed by denitrifying organisms due to oxygen deficiency. Incomplete sulfide oxidation via nitrate reduction and chemolithoautotrophy are both proton-consuming processes, which increase the pH in the redoxcline favoring authigenic calcite precipitation and may contribute to Hells Bells growth. The observed mechanism of microbially induced calcite precipitation is potentially applicable to many other stagnant sulfate-rich water bodies.

Structural evolution of the ancient enzyme, dissimilatory sulfite reductase

Dissimilatory sulfite reductase is an ancient enzyme that has linked the global sulfur and carbon biogeochemical cycles since at least 3.47 Gya. While much has been learned about the phylogenetic distribution and diversity of DsrAB across environmental gradients, far less is known about the structural changes that occurred to maintain DsrAB function as the enzyme accompanied diversification of sulfate/sulfite reducing organisms (SRO) into new environments. Analyses of available crystal structures of DsrAB from Archaeoglobus fulgidus and Desulfovibrio vulgaris, representing early and late evolving lineages, respectively, show that certain features of DsrAB are structurally conserved, including active siro-heme binding motifs. Whether such structural features are conserved among DsrAB recovered from varied environments, including hot spring environments that host representatives of the earliest evolving SRO lineage (e.g., MV2-Eury), is not known. To begin to overcome these gaps in our understanding of the evolution of DsrAB, structural models from MV2.Eury were generated and evolutionary sequence co-variance analyses were conducted on a curated DsrAB database. Phylogenetically diverse DsrAB harbor many conserved functional residues including those that ligate active siro-heme(s). However, evolutionary co-variance analysis of monomeric DsrAB subunits revealed several False Positive Evolutionary Couplings (FPEC) that correspond to residues that have co-evolved despite being too spatially distant in the monomeric structure to allow for direct contact. One set of FPECs corresponds to residues that form a structural path between the two active siro-heme moieties across the interface between heterodimers, suggesting the potential for allostery or electron transfer within the enzyme complex. Other FPECs correspond to structural loops and gaps that may have been selected to stabilize enzyme function in different environments. These structural bioinformatics results suggest that DsrAB has maintained allosteric communication pathways between subunits as SRO diversified into new environments. The observations outlined here provide a framework for future biochemical and structural analyses of DsrAB to examine potential allosteric control of this enzyme.

Assessing Microbial Monitoring Methods for Challenging Environmental Strains and Cultures

This paper focuses on the comparison of microbial biomass increase (cell culture growth) using field-relevant testing methods and moving away from colony counts. Challenges exist in exploring the antimicrobial growth of fastidious strains, poorly culturable bacteria and bacterial communities of environmental interest. Thus, various approaches have been explored to follow bacterial growth that can be efficient surrogates for classical optical density or colony-forming unit measurements. Here, six species grown in pure culture were monitored using optical density, ATP assays, DNA concentrations and 16S rRNA qPCR. Each of these methods have different advantages and disadvantages concerning the measurement of growth and activity in complex field samples. The species used as model systems for monitoring were: Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica. All four techniques were found to successfully measure and detect cell biomass/activity differences, though the shape and accuracy of each technique varied between species. DNA concentrations were found to correlate the best with the other three assays (ATP, DNA concentrations and 16S rRNA-targeted qPCR) and provide the advantages of rapid extraction, consistency between replicates and the potential for downstream analysis. DNA concentrations were determined to be the best universal monitoring method for complex environmental samples.

Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India

Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.

Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer

BACKGROUND

Recent evidence implicates microbial sulfidogenesis as a potential trigger of colorectal cancer (CRC), highlighting the need for comprehensive knowledge of sulfur metabolism within the human gut. Microbial sulfidogenesis produces genotoxic hydrogen sulfide (H₂S) in the human colon using inorganic (sulfate) and organic (taurine/cysteine/methionine) substrates; however, the majority of studies have focused on sulfate reduction using dissimilatory sulfite reductases (Dsr).

RESULTS

Here, we show that genes for microbial sulfur metabolism are more abundant and diverse than previously observed and are statistically associated with CRC. Using ~ 17,000 bacterial genomes from publicly available stool metagenomes, we studied the diversity of sulfur metabolic genes in 667 participants across different health statuses: healthy, adenoma, and carcinoma. Sulfidogenic genes were harbored by 142 bacterial genera and both organic and inorganic sulfidogenic genes were associated with carcinoma. Significantly, the anaerobic sulfite reductase (asr) genes were twice as abundant as dsr, demonstrating that Asr is likely a more important contributor to sulfate reduction in the human gut than Dsr. We identified twelve potential pathways for reductive taurine metabolism and discovered novel genera harboring these pathways. Finally, the prevalence of metabolic genes for organic sulfur indicates that these understudied substrates may be the most abundant source of microbially derived H₂S.

CONCLUSIONS

Our findings significantly expand knowledge of microbial sulfur metabolism in the human gut. We show that genes for microbial sulfur metabolism in the human gut are more prevalent than previously known, irrespective of health status (i.e., in both healthy and diseased states). Our results significantly increase the diversity of pathways and bacteria that are associated with microbial sulfur metabolism in the human gut. Overall, our results have implications for understanding the role of the human gut microbiome and its potential contributions to the pathogenesis of CRC. Video abstract.

Abundant and persistent sulfur-oxidizing microbial populations are responsive to hypoxia in the Chesapeake Bay

The number, size and severity of aquatic low‐oxygen dead zones are increasing worldwide. Microbial processes in low‐oxygen environments have important ecosystem‐level consequences, such as denitrification, greenhouse gas production and acidification. To identify key microbial processes occurring in low‐oxygen bottom waters of the Chesapeake Bay, we sequenced both 16S rRNA genes and shotgun metagenomic libraries to determine the identity, functional potential and spatiotemporal distribution of microbial populations in the water column. Unsupervised clustering algorithms grouped samples into three clusters using water chemistry or microbial communities, with extensive overlap of cluster composition between methods. Clusters were strongly differentiated by temperature, salinity and oxygen. Sulfur‐oxidizing microorganisms were found to be enriched in the low‐oxygen bottom water and predictive of hypoxic conditions. Metagenome‐assembled genomes demonstrate that some of these sulfur‐oxidizing populations are capable of partial denitrification and transcriptionally active in a prior study. These results suggest that microorganisms capable of oxidizing reduced sulfur compounds are a previously unidentified microbial indicator of low oxygen in the Chesapeake Bay and reveal ties between the sulfur, nitrogen and oxygen cycles that could be important to capture when predicting the ecosystem response to remediation efforts or climate change.

Sulfate-reducing and methanogenic microbial community responses during anaerobic digestion of tannery effluent

Microbial communities were monitored in terms of structure, function and response to physicochemical variables during anaerobic digestion of tannery and associated slaughterhouse effluent in: (i) 2 L biochemical methane potential batch reactors at different inoculum to substrate ratios (2-5) and initial sulfate concentrations (665-2000 mg/L), and (ii) 20 L anaerobic sequencing batch reactors with different mixing regimes (continuous vs. intermittent). Methanogenic and sulfidogenic community compositions in the 2 L reactors evolved initially, but stabilised after the start of biogas generation, although significant (ANOSIM p < 0.05) changes in the physicochemical parameters indicated continued metabolic activity. Both hydrogenotrophic and acetoclastic archaeal genera were present in high relative abundances. Continuous stirring preferentially selected the metabolically versatile genus Methanosarcina, suggesting that higher specific methane generation in the continuously stirred system (168 vs. 19.5 mL methane per gram volatile solids per week) was related to the metabolic activities of members of this genus.

Characterization of the biofilm structure and microbial diversity of sulfate-reducing bacteria from petroleum produced water supplemented by different carbon sources

Colonization by sulfate-reducing bacteria (SRB) in environments associated with oil is mainly dependent on the availability of sulfate and carbon sources. The formation of biofilms by SRB increases the corrosion of pipelines and oil storage tanks, representing great occupational and operational risks and respective economic losses for the oil industry. The aim of this study was to evaluate the influence of the addition of acetate, butyrate, lactate, propionate and oil on the structure of biofilm formed in carbon steel coupons, as well as on the diversity of total bacteria and SRB in the planktonic and sessile communities from petroleum produced water. The biofilm morphology, chemical composition, average roughness and the microbial diversity was analyzed. In all carbon sources, formation of dense biofilm without morphological and/or microbial density differences was detected, with the most of cells observed in the form of individual rods. The diversity and richness indices of bacterial species in the planktonic community was greater than in the biofilm. Geotoga was the most abundant genus, and more than 85% of SRB species were common to all treatments. The functional predicted profile shown that the observed genres in planktonic communities were related to the reduction of sulfate, sulfite, elementary sulfur and other sulfur compounds, but the abundance varied between treatments. For the biofilm, the functions predicted profile for the oil treatment was the one that most varied in relation to the control, while for the planktonic community, the addition of all carbon sources interfered in the predicted functional profile. Thus, although it does not cause changes in the structure and morphology biofilm, the supplementation of produced water with different carbon sources is associated with changes in the SRB taxonomic composition and functional profiles of the biofilm and the planktonic bacterial communities.

Optimal start-up conditions for the efficient treatment of acid mine drainage using sulfate-reducing bioreactors based on physicochemical and microbiome analyses

Typically, sulfate-reducing bioreactors used to treat acid mine drainage (AMD) undergo an initial incubation period of a few weeks to acclimatize sulfate-reducing bacteria (SRB), although necessity of this preincubation has rarely been evaluated. To reduce time and economic cost, we developed an SRB acclimatization method using the continuous flow of AMD into bioreactors fed with rice bran, and compared with the conventional acclimatization method. We found that the SRB sufficiently acclimatized without the preincubation phase. Furthermore, we examined the performance and SRB communities in bioreactors operated for >200 days under seven different conditions, in which the amount of rice bran added and hydraulic retention times (HRTs) were varied. A comparison of the various bioreactor conditions revealed that the lowest rice bran amount (50 g) and the shortest HRT (6 h) caused a deterioration in reactor performance after day 144 and 229, respectively. In both cases, relatively aerobic environments developed due to the lack of organic matter seemed to inhibit sulfate reduction. Of the conditions tested, operation of the bioreactors with 200 g of rice bran and an HRT of 12.5 h was the most effective in treating AMD, showing a sulfate reduction rate of 20.7-77.9% during days 54-242. DATA AND MATERIALS AVAILABILITY: All data needed to evaluate the conclusions of this study are presented in the paper and/or the appendix.

Dynamics of Microbial Communities during the Removal of Copper and Zinc in a Sulfate-Reducing Bioreactor with a Limestone Pre-Column System

Biological treatment using sulfate-reducing bacteria (SRB) is a promising approach to remediate acid rock drainage (ARD). Our purpose was to assess the performance of a sequential system consisting of a limestone bed filter followed by a sulfate-reducing bioreactor treating synthetic ARD for 375 days and to evaluate changes in microbial composition. The treatment system was effective in increasing the pH of the ARD from 2.7 to 7.5 and removed total Cu(II) and Zn(II) concentrations by up to 99.8% and 99.9%, respectively. The presence of sulfate in ARD promoted sulfidogenesis and changed the diversity and structure of the microbial communities. Methansarcina spp. was the most abundant amplicon sequence variant (ASV); however, methane production was not detected. Biodiversity indexes decreased over time with the bioreactor operation, whereas SRB abundance remained stable. Desulfobacteraceae, Desulfocurvus, Desulfobulbaceae and Desulfovibrio became more abundant, while Desulfuromonadales, Desulfotomaculum and Desulfobacca decreased. Geobacter and Syntrophobacter were enriched with bioreactor operation time. At the beginning, ASVs with relative abundance <2% represented 65% of the microbial community and 21% at the end of the study period. Thus, the results show that the microbial community gradually lost diversity while the treatment system was highly efficient in remediating ARD.

The DsrD functional marker protein is an allosteric activator of the DsrAB dissimilatory sulfite reductase

Metagenomic data have recently transformed our view of the role played by sulfur metabolism in anoxic environments by showing that this trait is much more widespread than previously believed. A key enzyme in sulfur metabolism is the dissimilatory sulfite reductase DsrAB that is ubiquitous in organisms with a reductive, oxidative, or disproportionating activity. However, the function of some dsr genes, such as dsrD, has so far been unknown despite its use as a functional marker to genomically assign the type of sulfur energy metabolism, sometimes with unclear results. Here, we disclose the function of DsrD as an activator of DsrAB that significantly increases its activity, providing important insights into the mechanism of this enzyme in different types of sulfur metabolism.

Dissimilatory sulfur metabolism was recently shown to be much more widespread among bacteria and archaea than previously believed. One of the key pathways involved is the dsr pathway that is responsible for sulfite reduction in sulfate-, sulfur-, thiosulfate-, and sulfite-reducing organisms, sulfur disproportionators and organosulfonate degraders, or for the production of sulfite in many photo- and chemotrophic sulfur-oxidizing prokaryotes. The key enzyme is DsrAB, the dissimilatory sulfite reductase, but a range of other Dsr proteins is involved, with different gene sets being present in organisms with a reductive or oxidative metabolism. The dsrD gene codes for a small protein of unknown function and has been widely used as a functional marker for reductive or disproportionating sulfur metabolism, although in some cases this has been disputed. Here, we present in vivo and in vitro studies showing that DsrD is a physiological partner of DsrAB and acts as an activator of its sulfite reduction activity. DsrD is expressed in respiratory but not in fermentative conditions and a ΔdsrD deletion strain could be obtained, indicating that its function is not essential. This strain grew less efficiently during sulfate and sulfite reduction. Organisms with the earliest forms of dsrAB lack the dsrD gene, revealing that its activating role arose later in evolution relative to dsrAB.

Microbial communities in petroleum-contaminated sites: Structure and metabolisms

Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.

Microbial communities in full-scale woodchip bioreactors treating aquaculture effluents

Woodchip bioreactors are being successfully applied to remove nitrate from commercial land-based recirculating aquaculture system (RAS) effluents. In order to understand and optimize the overall function of these bioreactors, knowledge on the microbial communities, especially on the microbes with potential for production or mitigation of harmful substances (e.g. hydrogen sulfide; H₂S) is needed. In this study, we quantified and characterized bacterial and fungal communities, including potential H₂S producers and consumers, using qPCR and high throughput sequencing of 16S rRNA gene. We took water samples from bioreactors and their inlet and outlet, and sampled biofilms growing on woodchips and on the outlet of the three full-scale woodchip bioreactors treating effluents of three individual RAS. We found that bioreactors hosted a high biomass of both bacteria and fungi. Although the composition of microbial communities of the inlet varied between the bioreactors, the conditions in the bioreactors selected for the same core microbial taxa. The H₂S producing sulfate reducing bacteria (SRB) were mainly found in the nitrate-limited outlets of the bioreactors, the main groups being deltaproteobacterial Desulfobulbus and Desulfovibrio. The abundance of H₂S consuming sulfate oxidizing bacteria (SOB) was 5-10 times higher than that of SRB, and SOB communities were dominated by Arcobacter and other genera from phylum Epsilonbacteraeota, which are also capable of autotrophic denitrification. Indeed, the relative abundance of potential autotrophic denitrifiers of all denitrifier sequences was even 54% in outlet water samples and 56% in the outlet biofilm samples. Altogether, our results show that the highly abundant bacterial and fungal communities in woodchip bioreactors are shaped through the conditions prevailing within the bioreactor, indicating that the bioreactors with similar design and operational settings should provide similar function even when conditions in the preceding RAS would differ. Furthermore, autotrophic denitrifiers can have a significant role in woodchip biofilters, consuming potentially produced H₂S and removing nitrate, lengthening the operational age and thus further improving the overall environmental benefit of these bioreactors.

Addition of organic acids to acid mine drainage polluted wetland sediment leads to microbial community structure and functional changes and improved water quality

Acid mine drainage (AMD) is a serious environmental problem worldwide that requires efficient and sustainable remediation technologies including the use of biological mechanisms. A key challenge for AMD bioremediation is to provide optimal conditions for microbial-mediated immobilisation of trace metals. Although organic carbon and oxygen can enhance treatment efficiency, the effect on microbial communities is unclear. In this study, surface sediments from a natural wetland with proven efficiency for AMD bioremediation were artificially exposed to oxygen (by aeration) and/or organic carbon (in the form of mixed organic acids) and incubated under laboratory conditions. In addition to measuring changes in water chemistry, a metagenomics approach was used to determine changes in sediment bacterial, archaeal and fungal community structure, and functional gene abundance. The addition of organic carbon produced major changes in the abundance of microorganisms related to iron and sulfur metabolism (including Geobacter and Pelobacter) and increased levels of particulate metals via sulfate reduction. Aeration resulted in an increase in Sideroxydans abundance but no significant changes in metal chemistry were observed. The study concludes that the utilisation of organic carbon by microorganisms is more important for achieving efficient AMD treatment than the availability of oxygen, yet the combination of oxygen with organic carbon addition did not inhibit the improvements to water quality.

Understanding Microbial Arsenic-Mobilization in Multiple Aquifers: Insight from DNA and RNA Analyses

Biogeochemical processes critically control the groundwater arsenic (As) enrichment; however, the key active As-mobilizing biogeochemical processes and associated microbes in high dissolved As and sulfate aquifers are poorly understood. To address this issue, the groundwater-sediment geochemistry, total and active microbial communities, and their potential functions in the groundwater-sediment microbiota from the western Hetao basin were determined using 16S rRNA gene (rDNA) and associated 16S rRNA (rRNA) sequencing. The relative abundances of either sediment or groundwater total and active microbial communities were positively correlated. Interestingly, groundwater active microbial communities were mainly associated with ammonium and sulfide, while sediment active communities were highly related to water-extractable nitrate. Both sediment-sourced and groundwater-sourced active microorganisms (rRNA/rDNA ratios > 1) noted Fe(III)-reducers (induced by ammonium oxidation) and As(V)-reducers, emphasizing the As mobilization via Fe(III) and/or As(V) reduction. Moreover, active cryptic sulfur cycling between groundwater and sediments was implicated in affecting As mobilization. Sediment-sourced active microorganisms were potentially involved in anaerobic pyrite oxidation (driven by denitrification), while groundwater-sourced organisms were associated with sulfur disproportionation and sulfate reduction. This study provides an extended whole-picture concept model of active As-N-S-Fe biogeochemical processes affecting As mobilization in high dissolved As and sulfate aquifers.

The Capacity to Produce Hydrogen Sulfide (H2S) via Cysteine Degradation Is Ubiquitous in the Human Gut Microbiome

As one of the three mammalian gasotransmitters, hydrogen sulfide (H₂S) plays a major role in maintaining physiological homeostasis. Endogenously produced H₂S plays numerous beneficial roles including mediating vasodilation and conferring neuroprotection. Due to its high membrane permeability, exogenously produced H₂S originating from the gut microbiota can also influence human physiology and is implicated in reducing intestinal mucosal integrity and potentiating genotoxicity and is therefore a potential target for therapeutic interventions. Gut microbial H₂S production is often attributed to dissimilatory sulfate reducers such as Desulfovibrio and Bilophila species. However, an alternative source for H₂S production, cysteine degradation, is present in some gut microbes, but the genes responsible for cysteine degradation have not been systematically annotated in all known gut microbes. We classify mechanisms of cysteine degradation into primary, secondary, and erroneous levels of H₂S production and perform a comprehensive search for primary, secondary, and erroneous cysteine-degrading enzymes in 4,644 non-redundant bacterial genomes from the Unified Human Gastrointestinal Genome (UHGG) catalog. Of the 4,644 genomes we have putatively identified 2,046 primary, 1,951 secondary, and 5 erroneous cysteine-degrading species. We identified the presence of at least one putative cysteine-degrading bacteria in metagenomic data of 100% of 6,623 healthy subjects and the expression of cysteine-degrading genes in metatranscriptomic data of 100% of 736 samples taken from 318 individuals. Additionally, putative cysteine-degrading bacteria are more abundant than sulfate-reducing bacteria across healthy controls, IBD patients and CRC patients (p < 2.2e-16, Wilcoxon rank sum test). Although we have linked many taxa with the potential for cysteine degradation, experimental validation is required to establish the H₂S production potential of the gut microbiome. Overall, this study improves our understanding of the capacity for H₂S production by the human gut microbiome and may help to inform interventions to therapeutically modulate gut microbial H₂S production.

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling

Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

Biostimulation of sulfate-reducing bacteria used for treatment of hydrometallurgical waste by secondary metabolites of urea decomposition by Ochrobactrum sp. POC9: From genome to microbiome analysis

Sulfate-reducing bacteria (SRB) are key players in many passive and active systems dedicated to the treatment of hydrometallurgical leachates. One of the main factors reducing the efficiency and activity of SRB is the low pH and poor nutrients in leachates. We propose an innovative solution utilizing biogenic ammonia (B-NH₃), produced by urea degrading bacteria, as a pretreatment agent for increasing the pH of the leachate and spontaneously stimulating SRB activity via bacterial secondary metabolites. The selected strain, Ochrobactrum sp. POC9, generated 984.7 mg/L of ammonia in 24 h and promotes an effective neutralization of B-NH₃. The inferred metabolic traits indicated that the Ochrobactrum sp. POC9 can synthesize a group of vitamins B, and the production of various organic metabolites was confirmed by GC-MS analysis. These metabolites comprise alcohols, organic acids, and unsaturated hydrocarbons that may stimulate biological sulfate reduction. With the pretreatment of B-NH₃, sulfate removal efficiency reached ~92.3% after 14 days of incubation, whereas SRB cell count and abundance were boosted (~10⁷ cell counts and 88 OTUs of SRB) compared to synthetic ammonia (S-NH₃) (~10³ cell counts and 40 OTUs of SRB). The dominant SRB is Desulfovibrio in both S-NH₃ and B-NH₃ pretreated leachate, however, it belonged to two different clades. By reconstructing the ecological network, we found that B-NH₃ not only directly increases SRB performance but also promotes other strains with positive correlations with SRB.

Microbial ecology of sulfur cycling near the sulfate-methane transition of deep-sea cold seep sediments

Microbial sulfate reduction is largely associated with anaerobic methane oxidation and alkane degradation in sulfate-methane transition zone (SMTZ) of deep-sea cold seeps. How the sulfur cycling is mediated by microbes near SMTZ has not been fully understood. In this study, we detected a shallow SMTZ in three of eight sediment cores sampled from two cold seep areas in the South China Sea. One hundred ten genomes representing sulfur-oxidizing bacteria (SOB) and sulfur-reducing bacteria (SRB) strains were identified from three SMTZ-bearing cores. In the layers above SMTZ, SOB were mostly constituted by Campylobacterota, Gammaproteobacteria and Alphaproteobacteria that probably depended on nitrogen oxides and/or oxygen for oxidation of sulfide and thiosulfate in near-surface sediment layers. In the layers below the SMTZ, the deltaproteobacterial SRB genomes and metatranscriptomes revealed CO₂ fixation by Wood-Ljungdahl pathway, sulfate reduction and nitrogen fixation for syntrophic or fermentative lifestyle. A total of 68% of the metagenome assembled genomes were not adjacent to known species in a phylogenomic tree, indicating a high diversity of bacteria involved in sulfur cycling. With the large number of genomes for SOB and SRB, our study uncovers the microbial populations that potentially mediate sulfur metabolism and associated carbon and nitrogen cycles, which sheds light on complex biogeochemical processes in deep-sea environments.

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.

Rhizosphere bacterial community composition affects cadmium and arsenic accumulation in rice (Oryza sativa L.)

Cadmium (Cd) and arsenic (As) contamination in paddy soils poses serious health risks to humans. The accumulation of Cd and As in rice (Oryza sativa L.) depends on their bioavailability, which is affected by soil physicochemical properties and soil microbial activities. However, little is known about the intricate interplay between rice plants and their rhizosphere microbes during the uptake of Cd and As. In this study, different bacterial communities were established by sterilizing paddy soils with γ-radiation. A pot experiment using two paddy soils with different levels of contamination was conducted to explore how the bacterial community composition affects Cd and As accumulation in rice plants. The results showed that the sterilization treatment substantially changed the bacterial composition in the rhizosphere, and significantly increased the grain yield (by 33.5-38.3%). The sterilization treatment resulted in significantly decreased concentrations of Cd (by 18.2-38.7%) and As (by 20.3-36.7%) in the grain, straw, and root of rice plants. The accumulation of Cd and As in rice plants was negatively correlated with the relative abundance of sulfate-reducing bacteria and iron-oxidizing bacteria in the rhizosphere. Other specific taxa associated with the accumulation of Cd and As in rice plants were also identified. Our results suggest that regulating the composition of the rhizosphere bacterial community could simultaneously reduce Cd and As accumulation in rice grain and increase the grain yield. These results would be useful for developing strategies to cultivate safe rice crops in areas contaminated with Cd and As.

Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria

Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood-Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b-3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H2-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.

Diversity and Activity of Sulfate-Reducing Prokaryotes in Kamchatka Hot Springs

Microbial communities of the Kamchatka Peninsula terrestrial hot springs were studied using radioisotopic and cultural approaches, as well as by the amplification and sequencing of dsrB and 16S rRNA genes fragments. Radioisotopic experiments with 35S-labeled sulfate showed that microbial communities of the Kamchatka hot springs are actively reducing sulfate. Both the cultivation experiments and the results of dsrB and 16S rRNA genes fragments analyses indicated the presence of microorganisms participating in the reductive part of the sulfur cycle. It was found that sulfate-reducing prokaryotes (SRP) belonging to Desulfobacterota, Nitrospirota and Firmicutes phyla inhabited neutral and slightly acidic hot springs, while bacteria of phylum Thermodesulofobiota preferred moderately acidic hot springs. In high-temperature acidic springs sulfate reduction was mediated by archaea of the phylum Crenarchaeota, chemoorganoheterotrophic representatives of genus Vulcanisaeta being the most probable candidates. The 16S rRNA taxonomic profiling showed that in most of the studied communities SRP was present only as a minor component. Only in one microbial community, the representatives of genus Vulcanisaeta comprised a significant group. Thus, in spite of comparatively low sulfate concentrations in terrestrial hot springs of the Kamchatka, phylogenetically and metabolically diverse groups of sulfate-reducing prokaryotes are operating there coupling carbon and sulfur cycles in these habitats.

Microbial Community Diversity Dynamics in Acid Mine Drainage and Acid Mine Drainage-Polluted Soils: Implication on Mining Water Irrigation Agricultural Sustainability

Environmental degradation related to mining-generated acid mine drainage (AMD) is a major global concern, contaminating surface and groundwater sources, including agricultural land. In the last two decades, many developing countries are expanding agricultural productivity in mine-impacted soils to meet food demand for their rapidly growing population. Further, the practice of AMD water (treated or untreated) irrigated agriculture is on the increase, particularly in water-stressed nations around the world. For sustainable agricultural production systems, optimal microbial diversity, and functioning is critical for soil health and plant productivity. Thus, this review presents up-to-date knowledge on the microbial structure and functional dynamics of AMD habitats and AMD-impacted agricultural soils. The long-term effects of AMD water such as soil acidification, heavy metals (HM), iron and sulfate pollution, greatly reduces microbial biomass, richness, and diversity, impairing soil health plant growth and productivity, and impacts food safety negatively. Despite these drawbacks, AMD-impacted habitats are unique ecological niches for novel acidophilic, HM, and sulfate-adapted microbial phylotypes that might be beneficial to optimal plant growth and productivity and bioremediation of polluted agricultural soils. This review has also highlighted the impact active and passive treatment technologies on AMD microbial diversity, further extending the discussion on the interrelated microbial diversity, and beneficial functions such as metal bioremediation, acidity neutralization, symbiotic rhizomicrobiome assembly, and plant growth promotion, sulfates/iron reduction, and biogeochemical N and C recycling under AMD-impacted environment. The significance of sulfur-reducing bacteria (SRB), iron-oxidizing bacteria (FeOB), and plant growth promoting rhizobacteria (PGPRs) as key players in many passive and active systems dedicated to bioremediation and microbe-assisted phytoremediation is also elucidated and discussed. Finally, new perspectives on the need for future studies, integrating meta-omics and process engineering on AMD-impacted microbiomes, key to designing and optimizing of robust active and passive bioremediation of AMD-water before application to agricultural production is proposed.

Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria) Expands the Metabolic Capacities of the Phylum and Highlights Adaptations to Terrestrial Habitats

Approaches for recovering and analyzing genomes belonging to novel, hitherto-unexplored bacterial lineages have provided invaluable insights into the metabolic capabilities and ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent and ecologically successful lineages on Earth, yet currently, multiple lineages within this phylum remain unexplored. Here, we utilize genomes recovered from Zodletone Spring, an anaerobic sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil and nonsoil habitats, to examine the metabolic capabilities and ecological role of members of family UBA6911 (group 18) Acidobacteria. The analyzed genomes clustered into five distinct genera, with genera Gp18_AA60 and QHZH01 recovered from soils, genus Ga0209509 from anaerobic digestors, and genera Ga0212092 and UBA6911 from freshwater habitats. All genomes analyzed suggested that members of Acidobacteria group 18 are metabolically versatile heterotrophs capable of utilizing a wide range of proteins, amino acids, and sugars as carbon sources, possess respiratory and fermentative capacities, and display few auxotrophies. Soil-dwelling genera were characterized by larger genome sizes, higher numbers of CRISPR loci, an expanded carbohydrate active enzyme (CAZyme) machinery enabling debranching of specific sugars from polymers, possession of a C1 (methanol and methylamine) degradation machinery, and a sole dependence on aerobic respiration. In contrast, nonsoil genomes encoded a more versatile respiratory capacity for oxygen, nitrite, sulfate, and trimethylamine N-oxide (TMAO) respiration, as well as the potential for utilizing the Wood-Ljungdahl (WL) pathway as an electron sink during heterotrophic growth. Our results not only expand our knowledge of the metabolism of a yet-uncultured bacterial lineage but also provide interesting clues on how terrestrialization and niche adaptation drive metabolic specialization within the Acidobacteria. IMPORTANCE Members of the Acidobacteria are important players in global biogeochemical cycles, especially in soils. A wide range of acidobacterial lineages remain currently unexplored. We present a detailed genomic characterization of genomes belonging to family UBA6911 (also known as group 18) within the phylum Acidobacteria. The genomes belong to different genera and were obtained from soil (genera Gp18_AA60 and QHZH01), freshwater habitats (genera Ga0212092 and UBA6911), and an anaerobic digestor (genus Ga0209509). While all members of the family shared common metabolic features, e.g., heterotrophic respiratory abilities, broad substrate utilization capacities, and few auxotrophies, distinct differences between soil and nonsoil genera were observed. Soil genera were characterized by expanded genomes, higher numbers of CRISPR loci, a larger carbohydrate active enzyme (CAZyme) repertoire enabling monomer extractions from polymer side chains, and methylotrophic (methanol and methylamine) degradation capacities. In contrast, nonsoil genera encoded more versatile respiratory capacities for utilizing nitrite, sulfate, TMAO, and the WL pathway, in addition to oxygen as electron acceptors. Our results not only broaden our understanding of the metabolic capacities within the Acidobacteria but also provide interesting clues on how terrestrialization shaped Acidobacteria evolution and niche adaptation.