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A strictly anaerobic, organohalide-respiring bacterium, designated strain GPT, was characterized using a polyphasic approach. GPT is Gram-stain-negative, non-spore-forming and non-motile. Cells are irregular cocci ranging between 0.6 and 0.9 µm in diameter. GPT couples growth with the reductive dechlorination of 1,2-dichloroethane, vinyl chloride and all polychlorinated ethenes, except tetrachloroethene, yielding ethene and inorganic chloride as dechlorination end products. H2 and formate serve as electron donors for organohalide respiration in the presence of acetate as carbon source. Major cellular fatty acids include C16 : 0, C18 : 1ω9c, C16 : 1, C14 : 0 and C18 : 0. On the basis of 16S rRNA gene phylogeny, GPT is most closely related to Dehalogenimonas formicexedens NSZ-14T and Dehalogenimonas alkenigignens IP3-3T with 99.8 and 97.4 % sequence identities, respectively. Genome-wide pairwise comparisons based on average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization do not support the inclusion of GPT in previously described species of the genus Dehalogenimonas with validly published names. On the basis of phylogenetic, physiological and phenotypic traits, GPT represents a novel species within the genus Dehalogenimonas , for which the name Dehalogenimonas etheniformans sp. nov. is proposed. The type strain is GPT (= JCM 39172T = CGMCC 1.17861T).

Anthropogenic activities and natural processes release dichloromethane (DCM, methylene chloride), a toxic chemical with substantial ozone-depleting capacity. Specialized anaerobic bacteria metabolize DCM; however, the genetic basis for this process has remained elusive. Comparative genomics of the three known anaerobic DCM-degrading bacterial species revealed a homologous gene cluster, designated the methylene chloride catabolism (mec) gene cassette, comprising 8-10 genes encoding proteins with 79.6%-99.7% amino acid identities. Functional annotation identified genes encoding a corrinoid-dependent methyltransferase system, and shotgun proteomics applied to two DCM-catabolizing cultures revealed high expression of proteins encoded on the mec gene cluster during anaerobic growth with DCM. In a DCM-contaminated groundwater plume, the abundance of mec genes strongly correlated with DCM concentrations (R

The nexus of food, energy, and water (FEW) systems is key to ensuring global sustainability in the face of climate change, population growth, and urbanization. To address FEW resources inequity among different regions and countries, transdisciplinary research networking becomes increasingly important for tackling this intractable, complex grand challenge. In contrast to interdisciplinary or multidisciplinary research, transdisciplinary research emphasizes the interactions of scientific, cognitive, and social factors from a top-down view. Intellectual and strategic integrations entail weaving scientific, socioeconomic, and political perspectives together into a new convergence model and fostering a shared vision and comparable assessment, though these goals might not be realistically achievable in the short term. This article summarizes major barriers to transdisciplinary research on FEW nexus grand challenges and possible solutions to be implemented at multiple levels of distinct social systems. Implementation of the solutions relies on not only top-down incentives of governments but also bottom-up initiatives of academic communities and individual researchers. The relevance of shared interests and visions between the research communities and the public is emphasized.

Two anaerobic, tetrachloroethene- (PCE-) respiring bacterial isolates, designated strain ACSDCE T and strain ACSTCE, were characterized using a polyphasic approach. Cells were Gram-stain-negative, motile, non-spore-forming and shared a vibrioid- to spirillum-shaped morphology. Optimum growth occurred at 30 °C and 0.1–0.4 % salinity. The pH range for growth was pH 5.5–7.5, with an optimum at pH 7.2. Hydrogen, formate, pyruvate and lactate as electron donors supported respiratory reductive dechlorination of PCE to cis-1,2-dichloroethene (cDCE) in strain ACSDCE T and of PCE to trichloroethene (TCE) in strain ACSTCE. Both strains were able to grow with pyruvate under microaerobic conditions. Nitrate, elemental sulphur, and thiosulphate were alternative electron acceptors. Autotrophic growth was not observed and acetate served as carbon source for both strains. The major cellular fatty acids were C16 : 1 ω7c, C16 : 0, C14 : 0 and C18 : 1 ω7c. Both genomes feature a circular plasmid. Strains ACSDCE T and ACSTCE were previously assigned to the candidate species 'Sulfurospirillum acididehalogenans'. Here, based on key genomic features and pairwise comparisons of whole-genome sequences, including average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity, strains ACSDCE T and ACSTCE, 'Ca. Sulfurospirillum diekertiae' strains SL2-1 and SL2-2, and the unclassified Sulfurospirillum sp. strain SPD-1 are grouped into one distinct species separate from previously described Sulfurospirillum species. Compared to Sulfurospirillum multivorans and Sulfurospirillum halorespirans , which dechlorinate PCE to cDCE without substantial TCE accumulation, these five strains produce TCE or cDCE as the end product. In addition, some cellular fatty acids (e.g., C16 : 0 3OH, C17 : 0 iso 3OH, C17 : 0 2OH) were detected in strains ACSDCE T and ACSTCE but not in other Sulfurospirillum species. On the basis of phylogenetic, physiological and phenotypic characteristics, 'Ca. Sulfurospirillum acididehalogenans' and 'Ca. Sulfurospirillum diekertiae' are proposed to be merged into one novel species within the genus Sulfurospirillum , for which the name Sulfurospirillum diekertiae sp. nov. is proposed. The type strain is ACSDCE T (=JCM 33349T= KCTC 15819T=CGMCC 1.5292T).

Quantitative measurement of process-specific biomarker genes of Dehalococcoides mccartyi (Dhc) supports monitoring at chlorinated ethene contaminated sites. In this study, we varied Dhc cell abunda...

DNA sequencing has led to an explosion in discovery of microbial phylogenetic novelty, especially that represented by uncultivated taxa, to which the traditional system of prokaryotic taxonomy has not adapted. A lack of expansion of the International Code of Nomenclature of Prokaryotes (ICNP, 'the Code') to effectively capture this information has created a 'wild west' situation where names are published or appear in popular reference databases without further verification or validation. The rapid propagation of variant and questionable naming methods has led to widespread confusion and undermines prior accomplishments. We exemplify inconsistencies that have arisen from this practice and endanger the interoperability of scientific findings. The immediate solution to this problem is to develop and adopt universal best practices that are accepted by expert researchers, major publishers, the International Committee on Systematics of Prokaryotes (ICSP), and international microbiological societies.

Remediation of toxic chlorinated ethenes via microbial reductive dechlorination can lead to ethene formation; however, the process stalls in acidic groundwater, leading to the accumulation of carcinogenic vinyl chloride (VC). This study explored the feasibility of cometabolic VC degradation by moderately acidophilic methanotrophs. Two novel isolates, Methylomonas sp. strain JS1 and Methylocystis sp. strain MJC1, were obtained from distinct alpine peat bogs located in South Korea. Both isolates cometabolized VC with CH4 as the primary substrate under oxic conditions at pH at or below 5.5. VC cometabolism in axenic cultures occurred in the presence (10 μM) or absence (

Many biotic and abiotic processes contribute to nitrous oxide (N2 O) production in the biosphere, but N2 O consumption in the environment has heretofore been attributed primarily to canonical denitrifying microorganisms. The nosZ genes encoding the N2 O reductase enzyme, NosZ, responsible for N2 O reduction to dinitrogen are now known to include two distinct groups: the well-studied Clade I which denitrifiers typically possess, and the novel Clade II possessed by diverse groups of microorganisms, most of which are non-denitrifiers. Clade II N2 O reducers could play an important, previously unrecognized role in controlling N2 O emissions for several reasons, including: (1) the consumption of N2 O produced by processes other than denitrification, (2) hypothesized non-respiratory functions of NosZ as an electron sink or for N2 O detoxification, (3) possible differing enzyme kinetics of Clade II NosZ compared to Clade I NosZ, and (4) greater nosZ gene abundance for Clade II compared to Clade I in soils of many ecosystems. Despite the potential ecological significance of Clade II NosZ, a census of 800 peer-reviewed original research articles discussing nosZ and published from 2013 to 2019 showed that the percentage of articles evaluating or mentioning Clade II nosZ increased from 5% in 2013 to only 22% in 2019. The census revealed that the slowly spreading awareness of Clade II nosZ may result in part from disciplinary silos, with the percentage of nosZ articles mentioning Clade II nosZ ranging from 0% in Agriculture and Agronomy journals to 32% in Multidisciplinary Sciences journals. In addition, inconsistent nomenclature for Clade I nosZ and Clade II nosZ, with 17 different terminologies used in the literature, may have created confusion about the two distinct groups of N2 O reducers. We provide recommendations to accelerate advances in understanding the role of the diversity of N2 O reducers in regulating soil N2 O emissions.

Bioremediation of chlorinated ethenes in anoxic aquifers hinges on organohalide-respiring Dehalococcoidia expressing vinyl chloride (VC) reductive dehalogenase (RDase). The tceA gene encoding the trichloroethene-dechlorinating RDase TceA is frequently detected in contaminated groundwater but not recognized as a biomarker for VC detoxification. We demonstrate that tceA-carrying Dehalococcoides mccartyi (Dhc) strains FL2 and 195 grow with VC as an electron acceptor when sufficient vitamin B12 (B12) is provided. Strain FL2 cultures that received 50 μg L-1 B12 completely dechlorinated VC to ethene at rates of 14.80 ± 1.30 μM day-1 and attained 1.64 ± 0.11 × 108 cells per μmol of VC consumed. Strain 195 attained similar growth yields of 1.80 ± 1.00 × 108 cells per μmol of VC consumed, and both strains could be consecutively transferred with VC as the electron acceptor. Proteomic analysis demonstrated TceA expression in VC-grown strain FL2 cultures. Resequencing of the strain FL2 and strain 195 tceA genes identified non-synonymous substitutions, although their consequences for TceA function are currently unknown. The finding that Dhc strains expressing TceA respire VC can explain ethene formation at chlorinated solvent sites, where quantitative polymerase chain reaction analysis indicates that tceA dominates the RDase gene pool.

Hydrology is a key factor influencing microbial degradation of emerging organic contaminants (EOCs) in soils, but the underlying mechanisms are not clear. In this study, biotic and abiotic column experiments were performed to investigate the removal and degradation of five EOCs in soils with different soil organic matter (SOM) contents under saturated and unsaturated flow conditions. In biotic experiments, 54-90% of bisphenol A (BPA) and 9-22% of ibuprofen (IBU) were removed from the aqueous phase of saturated columns due to adsorption and biodegradation. The biodegradation removed 26-65% of BPA and 1-22% of IBU. Decreasing soil pore water saturation from 100 to 80% increased BPA removal to 97-100% and IBU removal to 42-43% due to increased biodegradation (67-81% for BPA and 36-39% for IBU). No significant removal of BPA and IBU was observed in SOM-removed soils under saturated and unsaturated flow conditions. The desaturation did not influence sorptive losses of BPA (27%) and IBU (7%), suggesting their negligible adsorption at air-water interfaces but increased biodegradation of BPA and IBU sorbed at SOM-water interfaces. The study shows that soil drying and SOM can synergistically degrade BPA and IBU but have no effect on recalcitrant carbamazepine, tetracycline, and ciprofloxacin.

Dehalococcoides mccartyi strains harboring vinyl chloride (VC) reductive dehalogenase (RDase) genes are keystone bacteria for VC detoxification in groundwater aquifers, and bioremediation monitoring regimens focus on D. mccartyi biomarkers. We isolated a novel anaerobic bacterium, “Candidatus Dehalogenimonas etheniformans” strain GP, capable of respiratory dechlorination of VC to ethene. This bacterium couples formate and hydrogen (H(2)) oxidation to the reduction of trichloro-ethene (TCE), all dichloroethene (DCE) isomers, and VC with acetate as the carbon source. Cultures that received formate and H(2) consumed the two electron donors concomitantly at similar rates. A 16S rRNA gene-targeted quantitative PCR (qPCR) assay measured growth yields of (1.2 ± 0.2) × 10(8) and (1.9 ± 0.2) × 10(8) cells per μmol of VC dechlorinated in cultures with H(2) or formate as electron donor, respectively. About 1.5-fold higher cell numbers were measured with qPCR targeting cerA, a single-copy gene encoding a putative VC RDase. A VC dechlorination rate of 215 ± 40 μmol L(−1) day(−1) was measured at 30°C, with about 25% of this activity occurring at 15°C. Increasing NaCl concentrations progressively impacted VC dechlorination rates, and dechlorination ceased at 15 g NaCl L(−1). During growth with TCE, all DCE isomers were intermediates. Tetrachloroethene was not dechlorinated and inhibited dechlorination of other chlorinated ethenes. Carbon monoxide formed and accumulated as a metabolic by-product in dechlorinating cultures and impacted reductive dechlorination activity. The isolation of a new Dehalogenimonas species able to effectively dechlorinate toxic chlorinated ethenes to benign ethene expands our understanding of the reductive dechlorination process, with implications for bioremediation and environmental monitoring. IMPORTANCE Chlorinated ethenes are risk drivers at many contaminated sites, and current bioremediation efforts focus on organohalide-respiring Dehalococcoides mccartyi strains to achieve detoxification. We isolated and characterized the first non-Dehalococcoides bacterium, “Candidatus Dehalogenimonas etheniformans” strain GP, capable of metabolic reductive dechlorination of TCE, all DCE isomers, and VC to environmentally benign ethene. In addition to hydrogen, the new isolate utilizes formate as electron donor for reductive dechlorination, providing opportunities for more effective electron donor delivery to the contaminated subsurface. The discovery that a broader microbial diversity can achieve detoxification of toxic chlorinated ethenes in anoxic aquifers illustrates the potential of naturally occurring microbes for biotechnological applications.

Food, energy, and water (FEW) systems have been recognized as an issue of critical global importance. Understanding the mechanisms that govern the FEW nexus is essential to develop solutions and avoid humanitarian crises of displacement, famine, and disease. The U.S. and China are the world's leading economies. Although the two nations are shaped by fundamentally different political and economic systems, they share FEW trajectories in several complementary ways. These realities place the U.S. and China in unique positions to engage in problem definition, dialogue, actions, and transdisciplinary convergence of research to achieve productive solutions addressing FEW challenges. By comparing the nexus and functions of the FEW systems in the two nations, this perspective aims to facilitate collaborative innovations that reduce disciplinary silos, mitigate FEW challenges, and enhance environmental sustainability. The review of experiences and challenges facing the U.S. and China also offers valuable insights for other nations seeking to achieve sustainable development goals.

Fluorinated organic compounds have emerged as environmental constituents of concern. We demonstrate that the alkane degrader Pseudomonas sp. strain 273 utilizes terminally monofluorinated C7-C10 alkanes and 1,10-difluorodecane (DFD) as the sole carbon and energy sources in the presence of oxygen. Strain 273 degraded 1-fluorodecane (FD) (5.97 ± 0.22 mM, nominal) and DFD (5.62 ± 0.13 mM, nominal) within 7 days of incubation, and 92.7 ± 3.8 and 90.1 ± 1.9% of the theoretical maximum amounts of fluorine were recovered as inorganic fluoride, respectively. With n-decane, strain 273 attained (3.24 ± 0.14) × 107 cells per μmol of carbon consumed, while lower biomass yields of (2.48 ± 0.15) × 107 and (1.62 ± 0.23) × 107 cells were measured with FD or DFD as electron donors, respectively. The organism coupled decanol and decanoate oxidation to denitrification, but the utilization of (fluoro)alkanes was strictly oxygen-dependent, presumably because the initial attack on the terminal carbon requires oxygen. Fluorohexanoate was detected as an intermediate in cultures grown with FD or DFD, suggesting that the initial attack on the fluoroalkanes can occur on the terminal methyl or fluoromethyl groups. The findings indicate that specialized bacteria such as Pseudomonas sp. strain 273 can break carbon-fluorine bonds most likely with oxygenolytic enzyme systems and that terminally monofluorinated alkanes are susceptible to microbial degradation. The findings have implications for the fate of components associated with aqueous film-forming foam (AFFF) mixtures.

At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as Dehalococcoides mccartyi (Dhc). Metagenome sequencing of the commercial, Dhc-containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including pceA (two copies), vcrA, and tceA, and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with 13C-/15N-labeled peptides determined 1.8 × 103 TceA and 1.2 × 102 VcrA RDase molecules per Dhc cell. The MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant Dhc RDases and has potential utility in bioremediation monitoring regimes.

The SARS-CoV-2 pandemic has profoundly impacted communities across the globe, requiring accurate and accessible diagnostic technologies in support of public health mitigation efforts. As testing has evolved throughout the course of the pandemic, varying sample preparation methodologies have been employed. Herein we perform a comparison of three commercial sample preparation methods: two mechanical homogenization workflows and one enzymatic digestion approach for the detection of SARS-CoV-2 from biomarker genes in 20 human saliva pools. SARS-CoV-2 variants of concern were also identified on the University of Tennessee, Knoxville campus during the spring semester of 2021 utilizing the commercial PerkinElmer PKamp VariantDetect SARS-CoV-2 RT-PCR Assay kit. Two hundred and ten (210) human saliva pools were selected and analyzed for the presence of SARS-CoV-2 variants of concern providing insight into the utility of these various commercial workflows for integration into current public health SARS-CoV-2 surveillance measures.

Dehalococcoides mccartyi (Dhc) and Dehalogenimonas spp. (Dhgm) are members of the class Dehalococcoidia, phylum Chloroflexi, characterized by streamlined genomes and a strict requirement for organohalogens as electron acceptors. Here, we used cryo-electron tomography to reveal morphological and ultrastructural features of Dhc strain BAV1 and “Candidatus Dehalogenimonas etheniformans” strain GP cells at unprecedented resolution. Dhc cells were irregularly shaped discs (890 ± 110 nm long, 630 ± 110 nm wide, and 130 ± 15 nm thick) with curved and straight sides that intersected at acute angles, whereas Dhgm cells appeared as slightly flattened cocci (760 ± 85 nm). The cell envelopes were composed of a cytoplasmic membrane (CM), a paracrystalline surface layer (S-layer) with hexagonal symmetry and ∼22-nm spacing between repeating units, and a layer of unknown composition separating the CM and the S-layer. Cell surface appendages were only detected in Dhc cells, whereas both cell types had bundled cytoskeletal filaments. Repetitive globular structures, ∼5 nm in diameter and ∼9 nm apart, were observed associated with the outer leaflet of the CM. We hypothesized that those represent organohalide respiration (OHR) complexes and estimated ∼30,000 copies per cell. In Dhgm cultures, extracellular lipid vesicles (20 to 110 nm in diameter) decorated with putative OHR complexes but lacking an S-layer were observed. The new findings expand our understanding of the unique cellular ultrastructure and biology of organohalide-respiring Dehalococcoidia. IMPORTANCE Dehalococcoidia respire organohalogen compounds and play relevant roles in bioremediation of groundwater, sediments, and soils impacted with toxic chlorinated pollutants. Using advanced imaging tools, we have obtained three-dimensional images at macromolecular resolution of whole Dehalococcoidia cells, revealing their unique structural components. Our data detail the overall cellular shape, cell envelope architecture, cytoskeletal filaments, the likely localization of enzymatic complexes involved in reductive dehalogenation, and the structure of extracellular vesicles. The new findings expand our understanding of the cell structure-function relationship in Dehalococcoidia with implications for Dehalococcoidia biology and bioremediation.

Bisphenol A (BPA), a high production volume chemical and potential endocrine disruptor, is found to be associated with sediments and soils due to its hydrophobicity (log KOW of 3.42). We used superfine powdered activated carbon (SPAC) with a particle size of 1.38 ± 0.03 μm as a BPA sorbent and assessed degradation of BPA by oxidized manganese (Mn) species. SPAC strongly sorbed BPA, and desorption required organic solvents. No degradation of adsorbed BPA (278.7 ± 0.6 mg BPA g-1 SPAC) was observed with synthetic, solid α-MnO2 with a particle size of 15.41 ± 1.35 μm; however, 89% mass reduction occurred following the addition of 0.5 mM soluble Mn(III). Small-angle neutron scattering data suggested that both adsorption and degradation of BPA occurred in SPAC pores. The findings demonstrate that Mn(III) mediates oxidative transformation of dissolved and adsorbed BPA, the latter observation challenging the paradigm that contaminant desorption and diffusion out of pore structures are required steps for degradation. Soluble Mn(III) is abundant near oxic-anoxic interfaces, and the observation that adsorbed BPA is susceptible to degradation has implications for predicting, and possibly managing, the fate and longevity of BPA in environmental systems.

Biostimulation to promote reductive dechlorination is widely practiced, but the value of adding an exogenous nitrogen (N) source (e.g., NH4+) during treatment is unclear. This study investigates th...

The delivery of fermentable substrate(s) to subsurface environments stimulates Fe(III)-bioreduction and achieves detoxification of organic/inorganic contaminants. Although, much research has been conducted on the microbiology of such engineered systems at lab and field scales, little attention has been given to the phage-host interactions and virus community dynamics in these environments. The objective was to determine the responses of soil bacterial communities and viral assemblages to stimulated anaerobic Fe(III)-bioreduction following electron donor (e.g. acetate) addition. Microbial communities, including viral assemblages, were investigated after 60 days of Fe(III)-bioreduction in laboratory-scale columns continuously fed with acetate-amended artificial groundwater. Viral abundances were greatest in the influent section and decreased along the flow path. Acetate availability was important in influencing bacterial diversity, microbial interactions and viral abundance and community composition. The impact of acetate addition was most evident in the influent section of the columns. The increased relative abundance of Fe(III)-reducing bacteria coincided with an increase in viral abundance in areas of the columns exhibiting the most Fe(III) reduction. The genetic composition of viruses in these column sections also differed from the control column and distal sections of acetate-treated columns suggesting viral communities responded to biostimulated Fe(III)-bioreduction.

Dichloroacetate (DCA) is ubiquitous in the environment due to natural formation via biological and abiotic chlorination processes and the turnover of chlorinated organic materials (e.g., humic substances). Additional sources include DCA usage as a chemical feedstock and cancer drug and its unintentional formation during drinking water disinfection by chlorination., Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising “Candidatus Dichloromethanomonas elyunquensis” strain RM utilizes DCA as an energy source, and the transient formation of formate, H2, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated “Candidatus Dichloromethanomonas elyunquensis” strain RM in DCA degradation. An (S)-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg−1 protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota.

The phylogenetic and functional diversities of microbial communities in tropical rainforests and how these differ from those of temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N(2)O) from the tropics. Toward closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity compared to those of temperate grasslands or agricultural soils. In contrast to the overall distinct community composition, the relative abundances and nucleotide sequences of N(2)O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N(2)O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest than in temperate soils, i.e., 20% versus 0.1 to 0.3% of bacterial genomes in each soil type harbored the gene, respectively. Finally, unlike temperate soils, LEF soils showed little stratification with depth in the first 0 to 30 cm, with ∼45% of community composition differences explained solely by location. Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities and should facilitate future ecological studies of these ecosystems. IMPORTANCE Tropical rainforests are the largest terrestrial sinks of atmospheric CO(2) and the largest natural source of N(2)O emissions, two greenhouse gases that are critical for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. To close this knowledge gap, the present study applied shotgun metagenomics to samples selected from three distinct life zones within the Puerto Rico rainforest. The results advance our understanding of microbial community diversity in rainforest soils and should facilitate future studies of natural or manipulated perturbations of these critical ecosystems.

Bioremediation of chlorinated ethenes in anoxic aquifers hinges on organohalide-respiring

Bisphenol A (BPA), a chemical of environmental concern, is recalcitrant under anoxic conditions, but is susceptible to oxidative degradation by manganese(IV)-oxide (MnO2). Microbial Mn(II)-oxidation generates MnO2-bio; however, BPA degradation in cultures of Mn(II)-oxidizing bacteria has not been explored. We assessed MnO2-bio-mediated BPA degradation using three Mn(II)-oxidizing bacteria, Roseobacter sp. AzwK-3b, Erythrobacter sp. SD-21, and Pseudomonas putida GB-1. In cultures of all three strains, enhanced BPA degradation was evident in the presence of Mn(II) compared to replicate incubations without Mn(II), suggesting MnO2-bio mediated BPA degradation. Increased Mn(II) concentrations up to 100 µM resulted in more MnO2-bio formation but the highest BPA degradation rates were observed with 10 µM Mn(II). Compared to abiotic BPA degradation with 10 μM synthetic MnO2, live cultures of strain GB-1 amended with 10 μM Mn(II) consumed 9-fold more BPA at about 5-fold higher rates. Growth of strain AzwK-3b was sensitive to BPA and the organism showed increased tolerance against BPA in the presence of Mn(II), suggesting MnO2-bio alleviated the inhibition by mediating BPA degradation. The findings demonstrate that Mn(II)-oxidizing bacteria contribute to BPA degradation but organism-specific differences exist, and for biologically-mediated-abiotic-degradation (BMAD), Mn-flux, rather than the absolute amount of MnO2-bio, is the key determinant for oxidation activity.

Sulfurospirillum sp. strain ACSDCE couples growth with reductive dechlorination of tetrachloroethene to cis-1,2-dichloroethene at pH values as low as 5.5. The genome sequence of strain ACSDCE consists of a circular 2,737,849-bp chromosome and a 39,868-bp plasmid and carries 2,737 protein-coding sequences, including two reductive dehalogenase genes.

Correction to: Nature Microbiology https://doi.org/10.1038/s41564-020-0733-x , published online 8 June 2020. In the version of this Consensus Statement originally published, Pablo Yarza was mistakenly not included in the author list. Also, in Supplementary Table 1, Alexander Jaffe was missing from the list of endorsees. These errors have now been corrected and the updated Supplementary Table 1 is available online.

“Candidatus Dehalogenimonas etheniformans” strain GP couples growth with the reductive dechlorination of vinyl chloride and several polychlorinated ethenes. The genome sequence comprises a circular 2.07-Mb chromosome with a G+C content of 51.9% and harbors 50 putative reductive dehalogenase genes.

“ Candidatus Dehalogenimonas etheniformans” strain GP couples growth with the reductive dechlorination of vinyl chloride and several polychlorinated ethenes. The genome sequence comprises a circular 2.07-Mb chromosome with a G+C content of 51.9% and harbors 50 putative reductive dehalogenase genes.

Here, we report the complete genome sequence of the tetrachloroethene-to-trichloroethene dechlorinator Sulfurospirillum sp. strain ACSTCE. The genome consists of a 38.05-kb circular plasmid and a 2.69-Mb circular chromosome, which encodes 3 identical reductive dehalogenases with 91.47% amino acid identity to the PceA of Sulfurospirillum multivorans strain DSM 12446.

8 pages, 2 figures, 1 table, 2 boxes, supplementary information https://doi.org/10.1038/s41564-020-0733-x.-- Author Correction: Roadmap for naming uncultivated Archaea and Bacteria: n the version of this Consensus Statement originally published, Pablo Yarza was mistakenly not included in the author list. Also, in Supplementary Table 1, Alexander Jaffe was missing from the list of endorsees. These errors have now been corrected and the updated Supplementary Table 1 is available online, The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity, Support for this effort was provided by the National Science Foundation (grant no. DEB-1841658). We extend deep appreciation to all who attended the Microbial Taxonomy 2018 seminars, the Microbial Systematics for the Next Decade workshop held in Hood River, Oregon, USA, in October 2018, and those that participated in subsequent, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

As a global environmental pollutant, mercury (Hg) threatens our water resources and presents a substantial risk to human health. The rate and extent of immobilization of Hg2+ (hereafter, Hg) on engineered sorbents (Thiol-SAMMS®, pine biochar, SediMite™, Organoclay™ PM-199, and quartz sand as a control) was evaluated using flow-through column experiments. The effectiveness of the sorbents was based on (1) the percentage of Hg removed in relation to the total amount of Hg passing the sorbent column, and (2) the rate of Hg uptake compared to the nonreactive tracer bromide (Br−). All sorbents removed Hg to a certain extent, but none of the sorbents removed all the Hg introduced to the columns. Thiol-SAMMS showed the highest mean percentage of Hg removed (87% ± 2.9%), followed by Organoclay PM-199 (71% ± 0.4%), pine biochar (57% ± 22.3%), SediMite (61% ± 0.8%), and the control quartz sand (11% ± 5.6%). Thiol-SAMMS was the only sorbent to exhibit retardation of Hg in comparison to the conservative tracer Br−. For the remaining sorbents, Br− along with low concentrations of Hg were eluted within the first 3 pore volumes, indicating limited retardation of Hg. Overall, removal of Hg by sorbents was substantial, suggesting that sorbents might be suitable for deployment in contaminated environments. High concentrations of DOM leaching from the soil columns likely influenced the speciation of Hg and inhibited sorption to the sorbents. Incomplete removal of Hg by any sorbent suggests that additional optimization is needed to increase efficiency.