The complete genome sequence for putative H2- and S-oxidizerCandidatusSulfuricurvum sp., assembledde novofrom an aquifer-derived metagenome

pH and thiosulfate dependent microbial sulfur oxidation strategies across diverse environments

Sulfur oxidizing bacteria (SOB) play a key role in sulfur cycling in mine tailings impoundment (TI) waters, where sulfur concentrations are typically high. However, our understanding of SOB sulfur cycling via potential S oxidation pathways (sox, rdsr, and S4I) in these globally ubiquitous contexts, remains limited. Here, we identified TI water column SOB community composition, metagenomics derived metabolic repertoires, physicochemistry, and aqueous sulfur concentration and speciation in four Canadian base metal mine, circumneutral-alkaline TIs over four years (2016 - 2019). Identification and examination of genomes from nine SOB genera occurring in these TI waters revealed two pH partitioned, metabolically distinct groups, which differentially influenced acid generation and sulfur speciation. Complete sox (csox) dominant SOB (e.g., Halothiobacillus spp., Thiomonas spp.) drove acidity generation and S2O3 2- consumption via the csox pathway at lower pH (pH ~5 to ~6.5). At circumneutral pH conditions (pH ~6.5 to ~8.5), the presence of non-csox dominant SOB (hosting the incomplete sox, rdsr, and/or other S oxidation reactions; e.g. Thiobacillus spp., Sulfuriferula spp.) were associated with higher [S2O3 2-] and limited acidity generation. The S4I pathway part 1 (tsdA; S2O3 2- to S4O6 2-), was not constrained by pH, while S4I pathway part 2 (S4O6 2- disproportionation via tetH) was limited to Thiobacillus spp. and thus circumneutral pH values. Comparative analysis of low, natural (e.g., hydrothermal vents and sulfur hot springs) and high (e.g., Zn, Cu, Pb/Zn, and Ni tailings) sulfur systems literature data with these TI results, reveals a distinct TI SOB mining microbiome, characterized by elevated abundances of csox dominant SOB, likely sustained by continuous replenishment of sulfur species through tailings or mining impacted water additions. Our results indicate that under the primarily oxic conditions in these systems, S2O3 2- availability plays a key role in determining the dominant sulfur oxidation pathways and associated geochemical and physicochemical outcomes, highlighting the potential for biological management of mining impacted waters via pH and [S2O3 2-] manipulation.

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

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

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

BACKGROUND

Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling.

RESULTS

Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix. Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems.

CONCLUSIONS

Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract.

Arsenic Contamination of Groundwater Is Determined by Complex Interactions between Various Chemical and Biological Processes

At a great many locations worldwide, the safety of drinking water is not assured due to pollution with arsenic. Arsenic toxicity is a matter of both systems chemistry and systems biology: it is determined by complex and intertwined networks of chemical reactions in the inanimate environment, in microbes in that environment, and in the human body. We here review what is known about these networks and their interconnections. We then discuss how consideration of the systems aspects of arsenic levels in groundwater may open up new avenues towards the realization of safer drinking water. Along such avenues, both geochemical and microbiological conditions can optimize groundwater microbial ecology vis-à-vis reduced arsenic toxicity.

Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat

Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.

Rapid Consumption of Dihydrogen Injected into a Shallow Aquifer by Ecophysiologically Different Microbes

The envisaged future dihydrogen (H2) economy requires a H2 gas grid as well as large deep underground stores. However, the consequences of an unintended spread of H2 through leaky pipes, wells, or subterranean gas migrations on groundwater resources and their ecosystems are poorly understood. Therefore, we emulated a short-term leakage incident by injecting gaseous H2 into a shallow aquifer at the TestUM test site and monitored the subsequent biogeochemical processes in the groundwater system. At elevated H2 concentrations, an increase in acetate concentrations and a decrease in microbial α-diversity with a concomitant change in microbial β-diversity were observed. Additionally, microbial H2 oxidation was indicated by temporally higher abundances of taxa known for aerobic or anaerobic H2 oxidation. After H2 concentrations diminished below the detection limit, α- and β-diversity approached baseline values. In summary, the emulated H2 leakage resulted in a temporally limited change of the groundwater microbiome and associated geochemical conditions due to the intermediate growth of H2 consumers. The results confirm the general assumption that H2, being an excellent energy and electron source for many microorganisms, is quickly microbiologically consumed in the environment after a leakage.

Implications for nitrogen and sulphur cycles: phylogeny and niche-range of Nitrospirota in terrestrial aquifers

Increasing evidence suggests Nitrospirota are important contributors to aquatic and subsurface nitrogen and sulphur cycles. We determined the phylogenetic and ecological niche associations of Nitrospirota colonizing terrestrial aquifers. Nitrospirota compositions were determined across 59 groundwater wells. Distributions were strongly influenced by oxygen availability in groundwater, marked by a trade-off between aerobic (Nitrospira, Leptospirillum) and anaerobic (Thermodesulfovibrionia, unclassified) lineages. Seven Nitrospirota metagenome-assembled genomes (MAGs), or populations, were recovered from a subset of wells, including three from the recently designated class 9FT-COMBO-42-15. Most were relatively more abundant and transcriptionally active in dysoxic groundwater. These MAGs were analysed with 743 other Nitrospirota genomes. Results illustrate the predominance of certain lineages in aquifers (e.g. non-nitrifying Nitrospiria, classes 9FT-COMBO-42-15 and UBA9217, and Thermodesulfovibrionales family UBA1546). These lineages are characterized by mechanisms for nitrate reduction and sulphur cycling, and, excluding Nitrospiria, the Wood-Ljungdahl pathway, consistent with carbon-limited, low-oxygen, and sulphur-rich aquifer conditions. Class 9FT-COMBO-42-15 is a sister clade of Nitrospiria and comprises two families spanning a transition in carbon fixation approaches: f_HDB-SIOIB13 encodes rTCA (like Nitrospiria) and f_9FT-COMBO-42-15 encodes Wood-Ljungdahl CO dehydrogenase (like Thermodesulfovibrionia and UBA9217). The 9FT-COMBO-42-15 family is further differentiated by its capacity for sulphur oxidation (via DsrABEFH and SoxXAYZB) and dissimilatory nitrate reduction to ammonium, and gene transcription indicated active coupling of nitrogen and sulphur cycles by f_9FT-COMBO-42-15 in dysoxic groundwater. Overall, results indicate that Nitrospirota are widely distributed in groundwater and that oxygen availability drives the spatial differentiation of lineages with ecologically distinct roles related to nitrogen and sulphur metabolism.

Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses

BACKGROUND

Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes.

METHODS

Seawater samples were collected from Labrador Sea Water (LSW, ~ 2000 m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1 µM thiosulfate, or with 1 µM thiosulfate plus 10 µM glucose and 10 µM acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1 h and 72 h of incubation.

RESULTS

Amendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.).

CONCLUSIONS

The gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean. Video Abstract.

Ecological landscape explains aquifers microbial structure

Aquifers have significant social, economic, and ecological importance. They supply 30 % of the freshwater for human consumption worldwide, including agricultural and industrial use. Despite aquifers' importance, the relationships between aquifer categories and their inhabiting microbial communities are still unknown. Characterizing variations within microbial communities' function and taxonomy structure at different aquifers could give a panoramic view of patterns that may enable the detection and prediction of environmental impact caused by multiple sources. Using publicly available shotgun metagenomic datasets, we examined whether soil properties, land use, and climate variables would have a more significant influence on the taxonomy and functional structure of the microbial communities than the ecological landscapes of the aquifer (i.e., Karst, Porous, Saline, Geyser, and Porous Contaminated). We found that these categories are stronger predictors of microbial communities' structure than geographical localization. In addition, our results show that microbial richness and dominance patterns are the opposite of those found in multicellular life, where extreme habitats harbour richer functional and taxonomic microbial communities. We found that low-abundant and recently described candidate taxa, such as the chemolithoautotrophic genus Candidatus Altiarcheum and the Candidate phylum Parcubacteria, are the main contributors to aquifer microbial communities' dissimilarities. Genes related to gram-negative bacteria proteins, cell wall structures, and phage activity were the primary contributors to aquifer microbial communities' dissimilarities among the aquifers' ecological landscapes. The results reported in the present study highlight the utility of using ecological landscapes for investigating aquifer microbial communities. In addition, we suggest that functions played by recently described and low abundant bacterial groups need further investigation once they might affect water quality, geochemical cycles, and the effects of anthropogenic disturbances such as pollution and climatic events on aquifers.

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.

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

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

Nitrogen cycling and microbial cooperation in the terrestrial subsurface

The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding N₂O reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.

Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater

Current understanding of organic carbon inputs into ecosystems lacking photosynthetic primary production is predicated on data and inferences derived almost entirely from metagenomic analyses. The elevated abundances of putative chemolithoautotrophs in groundwaters suggest that dark CO₂ fixation is an integral component of subsurface trophic webs. To understand the impact of autotrophically fixed carbon, the flux of CO₂-derived carbon through various populations of subsurface microbiota must first be resolved, both quantitatively and temporally. Here we implement novel Stable Isotope Cluster Analysis to render a time-resolved and quantitative evaluation of ¹³CO₂-derived carbon flow through a groundwater community in microcosms stimulated with reduced sulfur compounds. We demonstrate that mixotrophs, not strict autotrophs, were the most abundant active organisms in groundwater microcosms. Species of Hydrogenophaga, Polaromonas, Dechloromonas, and other metabolically versatile mixotrophs drove the production and remineralization of organic carbon. Their activity facilitated the replacement of 43% and 80% of total microbial carbon stores in the groundwater microcosms with ¹³C in just 21 and 70 days, respectively. The mixotrophs employed different strategies for satisfying their carbon requirements by balancing CO₂ fixation and uptake of available organic compounds. These different strategies might provide fitness under nutrient-limited conditions, explaining the great abundances of mixotrophs in other oligotrophic habitats, such as the upper ocean and boreal lakes.

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.

Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O2 Cyanobacterial Mat Community

Cyanobacterial mats profoundly influenced Earth's biological and geochemical evolution and still play important ecological roles in the modern world. However, the biogeochemical functioning of cyanobacterial mats under persistent low-O2 conditions, which dominated their evolutionary history, is not well understood. To investigate how different metabolic and biogeochemical functions are partitioned among community members, we conducted metagenomics and metatranscriptomics on cyanobacterial mats in the low-O2, sulfidic Middle Island sinkhole (MIS) in Lake Huron. Metagenomic assembly and binning yielded 144 draft metagenome assembled genomes, including 61 of medium quality or better, and the dominant cyanobacteria and numerous Proteobacteria involved in sulfur cycling. Strains of a Phormidium autumnale-like cyanobacterium dominated the metagenome and metatranscriptome. Transcripts for the photosynthetic reaction core genes psaA and psbA were abundant in both day and night. Multiple types of psbA genes were expressed from each cyanobacterium, and the dominant psbA transcripts were from an atypical microaerobic type of D1 protein from Phormidium. Further, cyanobacterial transcripts for photosystem I genes were more abundant than those for photosystem II, and two types of Phormidium sulfide quinone reductase were recovered, consistent with anoxygenic photosynthesis via photosystem I in the presence of sulfide. Transcripts indicate active sulfur oxidation and reduction within the cyanobacterial mat, predominately by Gammaproteobacteria and Deltaproteobacteria, respectively. Overall, these genomic and transcriptomic results link specific microbial groups to metabolic processes that underpin primary production and biogeochemical cycling in a low-O2 cyanobacterial mat and suggest mechanisms for tightly coupled cycling of oxygen and sulfur compounds in the mat ecosystem. IMPORTANCE Cyanobacterial mats are dense communities of microorganisms that contain photosynthetic cyanobacteria along with a host of other bacterial species that play important yet still poorly understood roles in this ecosystem. Although such cyanobacterial mats were critical agents of Earth's biological and chemical evolution through geological time, little is known about how they function under the low-oxygen conditions that characterized most of their natural history. Here, we performed sequencing of the DNA and RNA of modern cyanobacterial mat communities under low-oxygen and sulfur-rich conditions from the Middle Island sinkhole in Lake Huron. The results reveal the organisms and metabolic pathways that are responsible for both oxygen-producing and non-oxygen-producing photosynthesis as well as interconversions of sulfur that likely shape how much O2 is produced in such ecosystems. These findings indicate tight metabolic reactions between community members that help to explain the limited the amount of O2 produced in cyanobacterial mat ecosystems.

Genome-resolved metagenomics using environmental and clinical samples

Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.

Candidatus Thiovulum sp. strain imperiosus: the largest free-living Epsilonproteobacteraeota Thiovulum strain lives in a marine mangrove environment

A large (47.75 ± 3.56 µm in diameter) Thiovulum bacterial strain forming white veils is described from a marine mangrove ecosystem. High sulfide concentrations (up to 8 mM of H2S) were measured on sunken organic matter (wood/bone debris) under laboratory conditions. This sulfur-oxidizing bacterium colonized the organic matter, forming a white veil. According to conventional scanning electron microscope (SEM) observations, bacterial cells are ovoid and slightly motile by numerous small flagella present on the cell surface. Large intracytoplasmic internal sulfur granules were observed, suggesting a sulfidic-based metabolism. Observations were confirmed by elemental sulfur distribution detected by energy-dispersive X-ray spectroscopy (EDXS) analysis using an environmental scanning electron microscope (ESEM) on non-dehydrated samples. Phylogenetic analysis of the partial sequence of 16S rDNA obtained from purified fractions of this Epsilonproteobacteraeota strain indicates that this bacterium belongs to the Thiovulaceae cluster and could be one of the largest Thiovulum ever described. We propose to name this species Candidatus Thiovulum sp. strain imperiosus.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Red Clover Isoflavones Influence Estradiol Concentration, Exercise Performance, and Gut Microbiota in Female Mice

In red clover (Trifolium pratense L.; RC) the main compound is isoflavones, which are selective estrogen receptor modulators for maintaining female health. Isoflavones exert antifatigue effects during exercise in high-temperature environments. This study aimed to investigate the effect of RC supplementation on gut microbiota composition to determine whether it improves intestinal barrier function and exercise performance. Female ICR mice were divided into four groups (n = 8 per group) and orally administered RC once daily for 6 weeks at 0 (vehicle), 308 (RC-1X), 615 (RC-2X), and 1,538 (RC-5X) mg/kg. RC supplementation decreased the fat mass and increased exhaustive swimming time, grip strength, and muscle glycogen in female mice. In the RC supplementation group, serum levels of lactate, ammonia, and creatine kinase decreased after swimming. The estradiol and progesterone levels were higher in the RC group than in the vehicle group. Regarding gut microbiota composition, the RC-2X group may increase intestinal health related to the microorganisms Pseudobutyrivibrio and Parabacteroide. Thus, the use of RC supplements as nutraceuticals could have positive effects on athletes' gut and overall health.

Anaerobic biodegradation of fluoxetine using a high-performance bacterial community

Fluoxetine (FLX), an antidepressant extensively used worldwide is considered an emerging pollutant. The present work intends to investigate for the first time the capacity of a bacterial community containing sulphate-reducing bacteria (SRB) enriched from an anaerobic sludge to biodegrade and use FLX as sole carbon source, since current literature suggests that this drug is poorly biodegraded being mainly removed by adsorption to sediments, where it persists. FLX was biodegraded under sulphate reducing conditions until reaching its lowest and reliably detectable concentration, when 20 mg/L of the drug was used as sole carbon source, while 66 ± 9% of 50 mg/L FLX was removed, after 31 days. The initial bacterial population was mainly constituted by Desulfomicrobium and Desulfovibrio whereas during the experiments using FLX as unique carbon source a clear shift occurred with the increase of vadinBC27 wastewater-sludge group, Macellibacteroidetes, Dethiosulfovibrio, Bacteroides, Tolumonas, Sulfuricurvum, f_Enterobacteriaceae_OTU_18 that are assumed for the first time as FLX degrading bacteria. Although the main mechanism of FLX removal described in literature is by adsorption, in the results herein presented anaerobic biodegradation appears to play the main role in the removal of the FLX, thus demonstrating the potentialities that the anaerobic processes can play in wastewater treatment aiming the removal of new emerging compounds.

Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions

The anaerobic digestion of wastes is globally important in the production of methane (CH4) as a biofuel. When sulfate is present, sulfate-reducing bacteria (SRB) are stimulated, competing with methanogens for common substrates, which decreases CH4 production and results in the formation of corrosive, odorous hydrogen sulfide gas (H2S). Here, we show that a population of SRB within a methanogenic bioreactor fed only butyrate for years immediately (within hours) responded to sulfate availability and shifted the microbial community dynamics within the bioreactor. By mapping shotgun metatranscriptomes to metagenome-assembled genomes, we shed light on the transcriptomic responses of key community members in response to increased sulfate provision. We link these short-term transcriptional responses to long-term niche partitioning using comparative metagenomic analyses. Our results suggest that sulfate provision supports a syntrophic butyrate oxidation community that disfavors poly-β-hydroxyalkanoate storage and that hydrogenotrophic SRB populations effectively exclude obligately hydrogenotrophic, but not aceticlastic, methanogens when sulfate is readily available. These findings elucidate key ecological dynamics between SRB, methanogens and syntrophic butyrate-oxidizing bacteria, which can be applied to a variety of engineered and natural systems.

Accurate and complete genomes from metagenomes

Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.

Identification of a Chlorodibenzo-p-dioxin Dechlorinating Dehalococcoides mccartyi by Stable Isotope Probing

Polychlorinated dibenzo-p-dioxins (PCDDs) are released into the environment from a variety of both anthropogenic and natural sources. While highly chlorinated dibenzo-p-dioxins are persistent under oxic conditions, in anoxic environments, these organohalogens can be reductively dechlorinated to less chlorinated compounds that are then more amenable to subsequent aerobic degradation. Identifying the microorganisms responsible for dechlorination is an important step in developing bioremediation approaches. In this study, we demonstrated the use of a DNA-stable isotope probing (SIP) approach to identify the bacteria active in dechlorination of PCDDs in river sediments, with 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD) as a model. In addition, pyrosequencing of reverse transcribed 16S rRNA of TeCDD dechlorinating enrichment cultures was used to reveal active members of the bacterial community. A set of operational taxonomic units (OTUs) responded positively to the addition of 1,2,3,4-TeCDD in SIP microcosms assimilating ¹³C-acetate as the carbon source. Analysis of bacterial community profiles of the ¹³C labeled heavy DNA fraction revealed that an OTU corresponding to Dehalococcoides mccartyi accounted for a significantly greater abundance in cultures amended with 1,2,3,4-TeCDD than in cultures without 1,2,3,4-TeCDD. This implies the involvement of this Dehalococcoides mccartyi strain in the reductive dechlorination of 1,2,3,4-TeCDD and suggests the applicability of SIP for a robust assessment of the bioremediation potential of organohalogen contaminated sites.

Elemental Sulfur Formation by Sulfuricurvum kujiense Is Mediated by Extracellular Organic Compounds

Elemental sulfur [S(0)] is a central and ecologically important intermediate in the sulfur cycle, which can be used by a wide diversity of microorganisms that gain energy from its oxidation, reduction, or disproportionation. S(0) is formed by oxidation of reduced sulfur species, which can be chemically or microbially mediated. A variety of sulfur-oxidizing bacteria can biomineralize S(0), either intracellularly or extracellularly. The details and mechanisms of extracellular S(0) formation by bacteria have been in particular understudied so far. An important question in this respect is how extracellular S(0) minerals can be formed and remain stable in the environment outside of their thermodynamic stability domain. It was recently discovered that S(0) minerals could be formed and stabilized by oxidizing sulfide in the presence of dissolved organic compounds, a process called S(0) organomineralization. S(0) particles formed through this mechanism possess specific signatures such as morphologies that differ from that of their inorganically precipitated counterparts, encapsulation within an organic envelope, and metastable crystal structures (presence of the monoclinic β- and γ-S₈ allotropes). Here, we investigated S(0) formation by the chemolithoautotrophic sulfur-oxidizing and nitrate-reducing bacterium Sulfuricurvum kujiense (Epsilonproteobacteria). We performed a thorough characterization of the S(0) minerals produced extracellularly in cultures of this microorganism, and showed that they present all the specific signatures (morphology, association with organics, and crystal structures) of organomineralized S(0). Using "spent medium" experiments, we furthermore demonstrated that soluble extracellular compounds produced by S. kujiense are necessary to form and stabilize S(0) minerals outside of the cells. This study provides the first experimental evidence of the importance of organomineralization in microbial S(0) formation. The prevalence of organomineralization in extracellular S(0) precipitation by other sulfur bacteria remains to be investigated, and the biological role of this mechanism is still unclear. However, we propose that sulfur-oxidizing bacteria could use soluble organics to stabilize stores of bioavailable S(0) outside the cells.

Metagenome-Assembled Genome Sequence of Sulfuricurvum sp. Strain IAE1, Isolated from a 4-Chlorophenol-Degrading Consortium

The draft genome sequence of Sulfuricurvum sp. strain IAE1 was assembled and annotated from the metagenome of an anaerobically grown 4-chlorophenol-degrading consortium. The draft genome size is 2,338,235 bp with a G+C content of 52.6%.

Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer

Determining the carbon sources for active microbial populations in the subsurface is a challenging but highly informative component of subsurface microbial ecology. This work developed a method to provide ecological insights into groundwater microbial communities by characterizing community RNA through its radiocarbon and ribosomal RNA (rRNA) signatures. RNA was chosen as the biomolecule of interest because rRNA constitutes the majority of RNA in prokaryotes, represents recently active organisms, and yields detailed taxonomic information. The method was applied to a groundwater filter collected from a shallow alluvial aquifer in Colorado. RNA was extracted, radiometrically dated, and the 16S rRNA was analyzed by RNA-Seq. The RNA had a radiocarbon signature (Δ14C) of -193.4 ± 5.6‰. Comparison of the RNA radiocarbon signature to those of potential carbon pools in the aquifer indicated that at least 51% of the RNA was derived from autotrophy, in close agreement with the RNA-Seq data, which documented the prevalence of autotrophic taxa, such as Thiobacillus and Gallionellaceae. Overall, this hybrid method for RNA analysis provided cultivation-independent information on the in-situ carbon sources of active subsurface microbes and reinforced the importance of autotrophy and the preferential utilization of dissolved over sedimentary organic matter in alluvial aquifers.

Exploring Biodiversity and Arsenic Metabolism of Microbiota Inhabiting Arsenic-Rich Groundwaters in Northern Italy

Arsenic contamination of groundwater aquifers is an issue of global concern. Among the affected sites, in several Italian groundwater aquifers arsenic levels above the WHO limits for drinking water are present, with consequent issues of public concern. In this study, for the first time, the role of microbial communities in metalloid cycling in groundwater samples from Northern Italy lying on Pleistocene sediments deriving from Alps mountains has been investigated combining environmental genomics and cultivation approaches. 16S rRNA gene libraries revealed a high number of yet uncultured species, which in some of the study sites accounted for more of the 50% of the total community. Sequences related to arsenic-resistant bacteria (arsenate-reducing and arsenite-oxidizing) were abundant in most of the sites, while arsenate-respiring bacteria were negligible. In some of the sites, sulfur-oxidizing bacteria of the genus Sulfuricurvum accounted for more than 50% of the microbial community, whereas iron-cycling bacteria were less represented. In some aquifers, arsenotrophy, growth coupled to autotrophic arsenite oxidation, was suggested by detection of arsenite monooxygenase (aioA) and 1,5-ribulose bisphosphate carboxylase (RuBisCO) cbbL genes of microorganisms belonging to Rhizobiales and Burkholderiales. Enrichment cultures established from sampled groundwaters in laboratory conditions with 1.5 mmol L^-1 of arsenite as sole electron donor were able to oxidize up to 100% of arsenite, suggesting that this metabolism is active in groundwaters. The presence of heterotrophic arsenic resistant bacteria was confirmed by enrichment cultures in most of the sites. The overall results provided a first overview of the microorganisms inhabiting arsenic-contaminated aquifers in Northern Italy and suggested the importance of sulfur-cycling bacteria in the biogeochemistry of arsenic in these ecosystems. The presence of active arsenite-oxidizing bacteria indicates that biological oxidation of arsenite, in combination with arsenate-adsorbing materials, could be employed for metalloid removal.

Determining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom Barriers

Microorganisms can have a profound and varying effect on the chemical character of environments and, thereby, ecological health. Their capacity to consume or transform contaminants leads to contrasting outcomes, such as the dissipation of nutrient pollution via denitrification, the breakdown of spilled oil, or eutrophication via primary producer overgrowth.

Microorganisms can have a profound and varying effect on the chemical character of environments and, thereby, ecological health. Their capacity to consume or transform contaminants leads to contrasting outcomes, such as the dissipation of nutrient pollution via denitrification, the breakdown of spilled oil, or eutrophication via primary producer overgrowth. Recovering the genomes of organisms directly from the environment is useful to gain insights into resource usage, interspecies collaborations (producers and consumers), and trait acquisition. Microbial data can also be considered alongside the broader biological character of an environment through the co-recovery of eukaryotic DNA. The contributions of individual microorganisms (bacteria, archaea, and protists) to snapshots of ecosystem processes can be determined by integrating genomics with functional methods. This combined approach enables a detailed understanding of how microbial communities drive biogeochemical cycles, and although currently limited by scale, key attributes can be effectively extrapolated with lower-resolution methods to determine wider ecological relevance.

Insights into microbial community structure and function from a shallow, simulated CO2 -leakage aquifer demonstrate microbial selection and adaptation

Geological carbon storage is likely to be a part of a comprehensive strategy to minimize the atmospheric release of carbon dioxide (CO₂ ), raising concerns that injected CO₂ will leak into overlying freshwater aquifers. CO_2(aq) leakage may impact the dominant microbial community responsible for important ecosystem functions such as nutrient cycling, metal cycling and carbon conversion. Here, we examined the impact of an experimental in situ CO₂ -leakage on a freshwater aquifer microbial community. High-throughput 16S rRNA gene sequencing demonstrated lower microbial diversity in freshwater wells with CO₂ concentrations above 1.15 g l^-1 . Metagenomic sequencing and population genome binning were used to evaluate the metabolic potential of microbial populations across four CO₂ exposed samples and one control sample. Population genome binning resulted in the recovery and annotation of three metagenome assembled genomes (MAGs). Two of the MAGs, most closely related to Curvibacter and Sulfuricurvum, had the functional capacity for CO₂ utilization via carbon fixation coupled to sulfur and iron oxidation. The third draft genome was an Archaea, most closely related to Methanoregula, characterized by the metabolic potential for methanogenesis. Together, these findings show that CO₂ leakage in a freshwater aquifer poses a strong selection, driving both microbial community structure and metabolic function.

Bioremediation of contaminated urban river sediment with methanol stimulation: Metabolic processes accompanied with microbial community changes

The intense pollution of urban river sediments with rapid urbanization has attracted considerable attention. Complex contaminated sediments urgently need to be remediated to conserve the ecological functions of impacted rivers. This study investigated the effect of using methanol as a co-substrate on the stimulation of the indigenous microbial consortium to enhance the bioremediation of petroleum hydrocarbons (PHs) and polycyclic aromatic hydrocarbons (PAHs) in an urban river sediment. After 65 days of treatment, the PAHs degradation efficiencies in the sediment adding methanol were 4.87%-40.3% higher than the control. The removal rate constant of C31 was 0.0749 d^-1 with 100 mM of supplied methanol, while the corresponding rate was 0.0399 d^-1 in the control. Four-ring PAHs were effectively removed at a degradation efficiency of 65%-69.8%, increased by 43.3% compared with the control. Sulfate reduction and methanogenesis activity were detected, and methane-producing archaea (such as Methanomethylovorans, with a relative abundance of 25.87%-58.53%) and the sulfate-reducing bacteria (SRB, such as Desulfobulbus and Desulfobacca) were enriched. In addition, the chemolithoautotrophic sulfur-oxidizing bacteria (SOB, such as Sulfuricurvum, with a relative abundance of 34%-39.2%) were predominant after the depletion of total organic carbon (TOC), and markedly positively correlated with the PHs and PAHs degradation efficiencies (P < 0.01). The SRB and SOB populations participated in the sulfur cycle, which was associated with PHs and PAHs degradation. Other potential functional bacteria (such as Dechloromonas) were also obviously enriched and significantly positively correlated with the TOC concentration after methanol injection (P < 0.001). This study provides a new insight into the succession of the indigenous microbial community with methanol as a co-substrate for the enhanced bioremediation of complexly contaminated urban river sediments.

Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria

Hydrogen-producing bacteria are of environmental importance, since hydrogen is a major electron donor for prokaryotes in anoxic ecosystems. Epsilonproteobacteria are currently considered to be hydrogen-oxidizing bacteria exclusively. Here, we report hydrogen production upon pyruvate fermentation for free-living Epsilonproteobacteria, Sulfurospirillum spp. The amount of hydrogen produced is different in two subgroups of Sulfurospirillum spp., represented by S. cavolei and S. multivorans. The former produces more hydrogen and excretes acetate as sole organic acid, while the latter additionally produces lactate and succinate. Hydrogen production can be assigned by differential proteomics to a hydrogenase (similar to hydrogenase 4 from E. coli) that is more abundant during fermentation. A syntrophic interaction is established between Sulfurospirillum multivorans and Methanococcus voltae when cocultured with lactate as sole substrate, as the former cannot grow fermentatively on lactate alone and the latter relies on hydrogen for growth. This might hint to a yet unrecognized role of Epsilonproteobacteria as hydrogen producers in anoxic microbial communities.

Epsilonproteobacteria, such as Sulfurospirillum, can use molecular hydrogen as an electron donor for respiration. Here, the authors show that Sulfurospirillum can, in addition, release hydrogen during fermentation, allowing metabolic interactions with other hydrogen-consuming microorganisms.

Effects of mercury addition on microbial community composition and nitrate removal inside permeable reactive barriers

Permeable reactive barriers (PRBs) remove nitrogen from groundwater by enhancing microbial denitrification. The PRBs consist of woodchips that provide carbon for denitrifiers, but these woodchips also support other anaerobic microbes, including sulfate-reducing bacteria. Some of these anaerobes have the ability to methylate inorganic mercury present in groundwater. Methylmercury is hazardous to human health, so it is essential to understand whether PRBs promote mercury methylation. We examined microbial communities and geochemistry in fresh water and sulfate-enriched PRB flow-through columns by spiking replicates of both treatments with mercuric chloride. We hypothesized that mercury addition could alter bacterial community composition to favor higher abundances of genera containing known methylating taxa and that the sulfate-rich columns would produce more methylmercury after mercury addition, due mainly to an increase in abundance of sulfate reducing bacteria (SRB). However, methylmercury output at the end of the experiment was not different from output at the beginning, due in part to coupled Hg methylation and demethylation. There was a transient reduction in nitrate removal after mercury addition in the sulfate enriched columns, but nitrate removal returned to initial rates after two weeks, demonstrating resilience of the denitrifying community. Since methylmercury output did not increase and nitrate removal was not permanently affected, PRBs could be a low cost approach to combat eutrophication.

Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences

The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.

Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages

Despite the abundance, ubiquity and impact of environmental viruses, their inherent genomic plasticity and extreme diversity pose significant challenges for the examination of bacteriophages on Earth. Viral metagenomic studies have offered insight into broader aspects of phage ecology and repeatedly uncover genes to which we are currently unable to assign function. A combined effort of phage isolation and metagenomic survey of Chicago&rsquo;s nearshore waters of Lake Michigan revealed the presence of Pbunaviruses, relatives of the Pseudomonas phage PB1. This prompted our expansive investigation of PB1-like phages. Genomic signatures of PB1-like phages and Pbunaviruses were identified, permitting the unambiguous distinction between the presence/absence of these phages in soils, freshwater and wastewater samples, as well as publicly available viral metagenomic datasets. This bioinformatic analysis led to the de novo assembly of nine novel PB1-like phage genomes from a metagenomic survey of samples collected from Lake Michigan. While this study finds that Pbunaviruses are abundant in various environments of Northern Illinois, genomic variation also exists to a considerable extent within individual communities.

Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead

The role of microbial communities in the degradation of trace organic contaminants in the environment is little understood. In this study, the biotransformation potential of 27 pharmaceuticals and endocrine-disrupting compounds was examined in parallel with a characterization of the native microbial community in water samples from four sites variously impacted by urban run-off and wastewater discharge in Lake Mead, Nevada and Arizona, USA. Samples included relatively pristine Colorado River water at the upper end of the lake, nearly pure tertiary-treated municipal wastewater entering via the Las Vegas Wash, and waters of mixed influence (Las Vegas Bay and Boulder Basin), which represented a gradient of treated wastewater effluent impact. Microbial diversity analysis based on 16S rRNA gene censuses revealed the community at this site to be distinct from the less urban-impacted locations, although all sites were similar in overall diversity and richness. Similarly, Biolog EcoPlate assays demonstrated that the microbial community at Las Vegas Wash was the most metabolically versatile and active. Organic contaminants added as a mixture to laboratory microcosms were more rapidly and completely degraded in the most wastewater-impacted sites (Las Vegas Wash and Las Vegas Bay), with the majority exhibiting shorter half-lives than at the other sites or in a bacteriostatic control. Although the reasons for enhanced degradation capacity in the wastewater-impacted sites remain to be established, these data are consistent with the acclimatization of native microorganisms (either through changes in community structure or metabolic regulation) to effluent-derived trace contaminants. This study suggests that in urban, wastewater-impacted watersheds, prior exposure to organic contaminants fundamentally alters the structure and function of microbial communities, which in turn translates into greater potential for the natural attenuation of these compounds compared to more pristine sites.

A seasonal study of a passive abandoned coalmine drainage remediation system reveals three distinct zones of contaminant levels and microbial communities

A passive remediation system that treats coalmine drainage was sampled to determine the impact seasonal changes had on water quality and microbial diversity. Every quarter for 1 year, water-soil slurries were collected at the influent of the 5 settling ponds and the wetlands, and the effluent of the system. The concentration of 12 metals and sulfate, as well as sequences from the V4 region of the bacterial 16S rrn genes were determined. The water quality analysis revealed high levels of iron and sulfate, and measurable levels of Al, Ba, Cu, Pb, Mn, Sr, and Zn. Iron increased 25-fold in the summer and spikes in metal concentrations were observed during several seasons in pond 3 and the wetlands. These spikes cannot be explained by abiotic chemical reactions in the neutral pH found in the pond. Based on contaminant levels and microbial community composition, our results indicate that there were 3 unique environments in the system (ponds 1 and 2; pond 3; pond 4 through the end) and that changes in contaminant levels and bacterial composition in these environments correlated with seasonal variation. Iron and sulfate are the most prevalent contaminants in the system. An examination of sequences from known iron- and sulfur-cycling bacteria demonstrated that there were more iron-reducing (IRB) bacterial sequences than iron-oxidizing (IOB) (137,912 IRB vs. 98,138 IOB), the two groups of bacteria were found mainly in the fall and winter samples, and were prevalent in different ponds. There were more sulfur/sulfide-oxidizing (SOB) bacterial sequences than sulfur/sulfate-reducing (SRB) bacterial sequences (72,978 SOB vs 30,504 SRB), they were found mainly in the fall and winter samples, and the sequences were mixed in ponds 4, 5 and the wetlands effluent. Iron is remediated in this system but sulfate is not.

Elucidating the stimulatory and inhibitory effects of dissolved sulfide on sulfur-oxidizing bacteria (SOB) driven autotrophic denitrification

Autotrophic denitrification has been widely studied for odor mitigation, corrosion control and nitrogen removal in recent years. This paper examines the response of sulfur-oxidizing bacteria (SOB) driven autotrophic denitrification under short-term stress of dissolved sulfide. A series of batch tests were conducted to investigate the effect of different sulfide concentrations (0-1600 mg-total dissolved sulfide (TDS)/L) on autotrophic denitrification and sulfide oxidation by SOB-enriched sludge. Our results show that autotrophic denitrification (NO₃^- to N₂) was stimulated up to 200 mg-TDS/L with a maximum denitrification rate of 9.4 mg-N/g-volatile suspended solids (VSS)/h, and the nitrite reduction was a rate limiting step. When sulfide concentration was higher than 200 mg-TDS/L, it inhibited nitrate reductase, and nitrate reduction became the rate limiting step according to Edwards and Aiba inhibition models. Sulfide oxidation, however, was not inhibited and the maximum rate of 100.3 mg-TDS/g-VSS/h was obtained at sulfide concentration of 1000 mg-TDS/L. It is important to point out that the transient inhibition on autotrophic denitrification caused by high sulfide stress was resilient and non-lethal with no significant changes in cell viability even under sulfide concentration of 1000 mg-TDS/L. This study reveals the stimulatory and inhibitory effects of dissolved sulfide on SOB driven autotrophic denitrification and its possible underlying mechanism with discussion on engineering implications.

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China

The release of toxic organic pollutants and heavy metals by primitive electronic waste (e-waste) processing to waterways has raised significant concerns, but little is known about their potential ecological effects on aquatic biota especially microorganisms. We characterized the microbial community composition and diversity in sediments sampled along two rivers consistently polluted by e-waste, and explored how community functions may respond to the complex combined pollution. High-throughput 16S rRNA gene sequencing showed that Proteobacteria (particularly Deltaproteobacteria) dominated the sediment microbial assemblages followed by Bacteroidetes, Acidobacteria, Chloroflexi and Firmicutes. PICRUSt metagenome inference provided an initial insight into the metabolic potentials of these e-waste affected communities, speculating that organic pollutants degradation in the sediment might be mainly performed by some of the dominant genera (such as Sulfuricurvum, Thiobacillus and Burkholderia) detected in situ. Statistical analyses revealed that toxic organic compounds contributed more to the observed variations in sediment microbial community structure and predicted functions (24.68% and 8.89%, respectively) than heavy metals (12.18% and 4.68%), and Benzo(a)pyrene, bioavailable lead and electrical conductivity were the key contributors. These results have shed light on the microbial assemblages in e-waste contaminated river sediments, indicating a potential influence of e-waste pollution on the microbial community structure and function in aquatic ecosystems.

Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome-resolved metagenomics

BACKGROUND

Methanogenic biodegradation of aromatic compounds depends on syntrophic metabolism. However, metabolic enzymes and pathways of uncultured microorganisms and their ecological interactions with methanogenic consortia are unknown because of their resistance to isolation and limited genomic information.

RESULTS

Genome-resolved metagenomics approaches were used to reconstruct and dissect 23 prokaryotic genomes from 37 and 20 °C methanogenic phenol-degrading reactors. Comparative genomic evidence suggests that temperature difference leads to the colonization of two distinct cooperative sub-communities that can respire sulfate/sulfite/sulfur or nitrate/nitrite compounds and compete for uptake of methanogenic substrates (e.g., acetate and hydrogen). This competition may differentiate methanogenesis. The uncultured ε-Proteobacterium G1, whose close relatives have broad ecological niches including the deep-sea vents, aquifers, sediment, limestone caves, spring, and anaerobic digesters, is implicated as a Sulfurovum-like facultative anaerobic diazotroph with metabolic versatility and remarkable environmental adaptability. We provide first genomic evidence for butyrate, alcohol, and carbohydrate utilization by a Chloroflexi T78 clade bacterium, and phenol carboxylation and assimilatory sulfite reduction in a Cryptanaerobacter bacterium.

CONCLUSION

Genome-resolved metagenomics enriches our view on the differentiation of microbial community composition, metabolic pathways, and ecological interactions in temperature-differentiated methanogenic phenol-degrading bioreactors. These findings suggest optimization strategies for methanogenesis on phenol, such as temperature control, protection from light, feed desulfurization, and hydrogen sulfide removal from bioreactors. Moreover, decoding genome-borne properties (e.g., antibiotic, arsenic, and heavy metal resistance) of uncultured bacteria help to bring up alternative schemes to isolate them.

Novel arsenic-transforming bacteria and the diversity of their arsenic-related genes and enzymes arising from arsenic-polluted freshwater sediment

Bacteria are essential in arsenic cycling. However, few studies have addressed 16S rRNA and arsenic-related functional gene diversity in long-term arsenic-contaminated tropical sediment. Here, using culture-based, metagenomic and computational approaches, we describe the diversity of bacteria, genes and enzymes involved in AsIII and AsV transformation in freshwater sediment and in anaerobic AsIII- and AsV-enrichment cultures (ECs). The taxonomic profile reveals significant differences among the communities. Arcobacter, Dechloromonas, Sedimentibacter and Clostridium thermopalmarium were exclusively found in ECs, whereas Anaerobacillus was restricted to AsV-EC. Novel taxa that are both AsV-reducers and AsIII-oxidizers were identified: Dechloromonas, Acidovorax facilis, A. delafieldii, Aquabacterium, Shewanella, C. thermopalmarium and Macellibacteroides fermentans. Phylogenic discrepancies were revealed among the aioA, arsC and arrA genes and those of other species, indicating horizontal gene transfer. ArsC and AioA have sets of amino acids that can be used to assess their functional and structural integrity and familial subgroups. The positions required for AsV reduction are conserved, suggesting strong selective pressure for maintaining the functionality of ArsC. Altogether, these findings highlight the role of freshwater sediment bacteria in arsenic mobility, and the untapped diversity of dissimilatory arsenate-reducing and arsenate-resistant bacteria, which might contribute to arsenic toxicity in aquatic environments.

Treatment of high-strength sulfate wastewater using an autotrophic biocathode in view of elemental sulfur recovery

Treatment of high-strength sulfate wastewaters is becoming a research issue not only for its optimal management but also for the possibility of recovering elemental sulfur. Moreover, sulfate-rich wastewater production is expected to grow due to the increased SO₂ emission contained in flue gases which are treated by chemical absorption in water. Bioelectrochemical systems (BESs) are a promising alternative for sulfate reduction with a lack of electron donor, since hydrogen can be generated in situ from electricity. However, complete sulfate reduction leads to hydrogen sulfide as final sulfur compound. This work is the first to demonstrate that, in addition to an efficient sulfate-rich wastewater treatment, elemental sulfur could be recovered in a biocathode of a BES under oxygen limiting conditions. The key of the process is the biological oxidation of sulfide to elemental sulfur simultaneously to the sulfate reduction in the cathode using the oxygen produced in the anode that diffuses through the membrane. High sulfate reduction rates (up to 388 mg S-SO₄^2- L^-1 d^-1) were observed linked to a low production of sulfide. Accumulation of elemental sulfur over graphite fibers of the biocathode was demonstrated by energy dispersive spectrometry, discarding the presence of metal sulfides. Microbial community analysis of the cathode biofilm demonstrated the presence of sulfate-reducing bacteria (mainly Desulfovibrio sp.) and sulfide-oxidizing bacteria (mainly Sulfuricurvum sp.). Hence, this biocathode allows simultaneous biological sulfate reduction and biological sulfide oxidation to elemental sulfur, opening up a novel process for recovering sulfur from sulfate-rich wastewaters.

Recovering complete and draft population genomes from metagenome datasets

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.

Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer

Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated by heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment to a perennially suboxic aquifer in Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive and diverse chemolithoautotrophic bacterial activity relevant to C, S, N and Fe cycling. Before nitrate injection, anaerobic ammonia-oxidizing (anammox) bacteria accounted for 16% of overall microbial community gene expression, whereas during the nitrate injection, two other groups of chemolithoautotrophic bacteria collectively accounted for 80% of the metatranscriptome: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Notably, the proportion of the metatranscriptome accounted for by these three groups was considerably greater than the proportion of the metagenome coverage that they represented. Transcriptional analysis revealed some unexpected metabolic couplings, in particular, putative nitrate-dependent Fe(II) and S oxidation among nominally microaerophilic Gallionellaceae strains, including expression of periplasmic (NapAB) and membrane-bound (NarGHI) nitrate reductases. The three most active groups of chemolithoautotrophic bacteria in this study had overlapping metabolisms that allowed them to occupy different yet related metabolic niches throughout the study. Overall, these results highlight the important role that chemolithoautotrophy can have in aquifer biogeochemical cycling, a finding that has broad implications for understanding terrestrial carbon cycling and is supported by recent studies of geochemically diverse aquifers.

Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation

BACKGROUND

The Anaerolineae lineage of Chloroflexi had been identified as one of the core microbial populations in anaerobic digesters; however, the ecological role of the Anaerolineae remains uncertain due to the scarcity of isolates and annotated genome sequences. Our previous metatranscriptional analysis revealed this prevalent population that showed minimum involvement in the main pathways of cellulose hydrolysis and subsequent methanogenesis in the thermophilic cellulose fermentative consortium (TCF).

RESULTS

In further pursuit, five high-quality curated draft genomes (>98 % completeness) of this population, including two affiliated with the inaccessible lineage of SBR1031, were retrieved by sequence-based multi-dimensional coverage binning. Comparative genomic analyses revealed versatile genetic capabilities for carbohydrate-based fermentative lifestyle including key genes catalyzing cellulose hydrolysis in Anaerolinea phylotypes. However, the low transcriptional activities of carbohydrate-active genes (CAGs) excluded cellulolytic capability as the selective advantage for their prevalence in the community. Instead, a substantially active type VI pili (Tfp) assembly was observed. Expression of the tight adherence protein on the Tfp indicated its function for cellular attachment which was further testified to be more likely related to cell aggregation other than cellulose surface adhesion. Meanwhile, this Tfp structure was found not contributing to syntrophic methanogenesis. Members of the SBR1031 encoded key genes for acetogenic dehydrogenation that may allow ethanol to be used as a carbon source.

CONCLUSION

The common prevalence of Anaerolineae in anaerobic digesters should be originated from advantageous cellular adhesiveness enabled by Tfp assembly other than its potential as cellulose degrader or anaerobic syntrophs.

Metagenome-Based Metabolic Reconstruction Reveals the Ecophysiological Function of Epsilonproteobacteria in a Hydrocarbon-Contaminated Sulfidic Aquifer

The population genome of an uncultured bacterium assigned to the Campylobacterales (Epsilonproteobacteria) was reconstructed from a metagenome dataset obtained by whole-genome shotgun pyrosequencing. Genomic DNA was extracted from a sulfate-reducing, m-xylene-mineralizing enrichment culture isolated from groundwater of a benzene-contaminated sulfidic aquifer. The identical epsilonproteobacterial phylotype has previously been detected in toluene- or benzene-mineralizing, sulfate-reducing consortia enriched from the same site. Previous stable isotope probing (SIP) experiments with ¹³C₆-labeled benzene suggested that this phylotype assimilates benzene-derived carbon in a syntrophic benzene-mineralizing consortium that uses sulfate as terminal electron acceptor. However, the type of energy metabolism and the ecophysiological function of this epsilonproteobacterium within aromatic hydrocarbon-degrading consortia and in the sulfidic aquifer are poorly understood. Annotation of the epsilonproteobacterial population genome suggests that the bacterium plays a key role in sulfur cycling as indicated by the presence of an sqr gene encoding a sulfide quinone oxidoreductase and psr genes encoding a polysulfide reductase. It may gain energy by using sulfide or hydrogen/formate as electron donors. Polysulfide, fumarate, as well as oxygen are potential electron acceptors. Auto- or mixotrophic carbon metabolism seems plausible since a complete reductive citric acid cycle was detected. Thus the bacterium can thrive in pristine groundwater as well as in hydrocarbon-contaminated aquifers. In hydrocarbon-contaminated sulfidic habitats, the epsilonproteobacterium may generate energy by coupling the oxidation of hydrogen or formate and highly abundant sulfide with the reduction of fumarate and/or polysulfide, accompanied by efficient assimilation of acetate produced during fermentation or incomplete oxidation of hydrocarbons. The highly efficient assimilation of acetate was recently demonstrated by a pulsed ¹³C₂-acetate protein SIP experiment. The capability of nitrogen fixation as indicated by the presence of nif genes may provide a selective advantage in nitrogen-depleted habitats. Based on this metabolic reconstruction, we propose acetate capture and sulfur cycling as key functions of Epsilonproteobacteria within the intermediary ecosystem metabolism of hydrocarbon-rich sulfidic sediments.

Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms

We investigated the N-utilizing bacterial community in anoxic brackish groundwater of the low and intermediate level nuclear waste repository cave in Olkiluoto, Finland, at 100 m depth using ¹⁵N-based stable isotope probing (SIP) and enrichment with ^14∕15N-ammonium or ^14∕15N-nitrate complemented with methane. Twenty-eight days of incubation at 12°C increased the concentration of bacterial 16S rRNA and nitrate reductase (narG) gene copies in the substrate amended microcosms simultaneously with a radical drop in the overall bacterial diversity and OTU richness. Hydrogenophaga/Malikia were enriched in all substrate amended microcosms and Methylobacter in the ammonium and ammonium+methane supplemented microcosms. Sulfuricurvum was especially abundant in the nitrate+methane treatment and the unamended incubation control. Membrane-bound nitrate reductase genes (narG) from Polarimonas sp. were detected in the original groundwater, while Burkholderia, Methylibium, and Pseudomonas narG genes were enriched due to substrate supplements. Identified amoA genes belonged to Nitrosomonas sp. ¹⁵N-SIP revealed that Burkholderiales and Rhizobiales clades belonging to the minority groups in the original groundwater used ¹⁵N from ammonium and nitrate as N source indicating an important ecological function of these bacteria, despite their low number, in the groundwater N cycle in Olkiluoto bedrock system.