65 Search Results

Anthropogenic organofluorine compounds are recalcitrant, globally distributed, and a human health concern. Although rare, natural processes synthesize fluorinated compounds, and some bacteria have evolved mechanisms to metabolize organofluorine compounds. Pseudomonas sp. strain 273 grows with 1-fluorodecane (FD) and 1,10-difluorodecane (DFD) as carbon sources, but inorganic fluoride release was not stoichiometric. Metabolome studies revealed that this bacterium produces fluorinated anabolites and phospholipids. Mass spectrometric fatty acid profiling detected fluorinated long-chain (i.e., C₁₂–C₁₉) fatty acids in strain 273 cells grown with FD or DFD, and lipidomic profiling determined that 7.5 ± 0.2 and 82.0 ± 1.0% of the total phospholipids in strainmore » 273 grown with FD or DFD, respectively, were fluorinated. The detection of the fluorinated metabolites and macromolecules represents a heretofore unrecognized sink for organofluorine, an observation with consequences for the environmental fate and transport of fluorinated aliphatic compounds.« less

We report that chlorinated ethanes, including 1,2-dichloroethane (1,2-DCA) and 1,1,2-trichloroethane (1,1,2-TCA), are widespread groundwater contaminants. Enrichment cultures XR_DCA and XR_TCA derived from river sediment dihaloeliminated 1,2-DCA to ethene and 1,1,2-TCA to vinyl chloride (VC), respectively. The XR_TCA culture subsequently converted VC to ethene via hydrogenolysis. Microbial community profiling demonstrated the enrichment of Geobacter 16S rRNA gene sequences in both the XR_DCA and XR_TCA cultures, and Dehalococcoides mccartyi (Dhc) sequences were only detected in the ethene-producing XR_TCA culture. The presence of a novel Geobacter population, designated as Geobacter sp. strain IAE, was identified by the 16S rRNA gene-targeted polymerase chain reactionmore » and Sanger sequencing. Time-resolved population dynamics attributed the dihaloelimination activity to strain IAE, which attained the growth yields of 0.93 ± 0.06 x 10⁷ and 1.18 ± 0.14 x 10⁷ cells per μmol Cl^-1 released with 1,2-DCA and 1,1,2-TCA as electron acceptors, respectively. In contrast, Dhc growth only occurred during VC-to-ethene hydrogenolysis. Our findings discover a Geobacter sp. strain capable of respiring multiple chlorinated ethanes and demonstrate the involvement of a broader diversity of organohalide-respiring bacteria in the detoxification of 1,2-DCA and 1,1,2-TCA.« less

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 envelopesmore » 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. Furthermore, the new findings expand our understanding of the unique cellular ultrastructure and biology of organohalide-respiring Dehalococcoidia.« less

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 amore » DCM-contaminated groundwater plume, the abundance of mec genes strongly correlated with DCM concentrations (R² = 0.71–0.85) indicating their potential value as process-specific bioremediation biomarkers. mec gene clusters were identified in metagenomes representing peat bogs, the deep subsurface, and marine ecosystems including oxygen minimum zones (OMZs), suggesting a capacity for DCM degradation in diverse habitats. Here, the broad distribution of anaerobic DCM catabolic potential infers a role for DCM as an energy source in various environmental systems, and implies that the global DCM flux (i.e., the rate of formation minus the rate of consumption) might be greater than emission measurements suggest.« less

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 abundances from ~103 to 108 cells/mL in aquifer microcosms and correlated the corresponding reductive dehalogenase (RDase) gene and RDase protein abundances with measured reductive dechlorination (RD) rates of cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC). An additional set of microcosms tested the RD rate-predictive power of the regression analyses. These efforts revealed (1) that targeted proteomics quantifies Dhc biomarker proteins (e.g., TceA and VcrA, OmeA) over a relevant range of Dhc cell densities, and (2) that proteinmore » and gene abundances can predict RD rates. Protein detection limits translated to a rate coefficient of 10^–4 day^–1 (0.04 year^–1) for both k_cDCE and k_vc, which is within the range observed at sites undergoing monitored natural attenuation (MNA) (i.e., without the implementation of enhanced bioremediation treatment). Rates predicted using a combination of quantitative biomarker gene and protein measurements generally resulted in the best match with experimentally determined rate constants. These new findings provide evidence that quantitative biomarker measurements may be useful predictors of in situ RD rates, which would constitute a major advance for the cost-effective management of contaminated sites.« less

Urbanization, population growth, and the accelerating consumption of food, energy, and water (FEW) resources bring unprecedented challenges for economic, environmental, and social (EES) sustainability. It is imperative to understand the potential impacts of FEW systems on the realization of the United Nation’s Sustainable Development Goals (SDGs) as the world transitions from natural ecosystems to managed ecosystems at an accelerating rate. A major obstacle is the complexity and emergent behavior of FEW systems and associated networks, for which no single discipline can generate a holistic understanding or meaningful projections. We propose a research enterprise framework for promoting transdisciplinarity and top-down quantificationmore » of the interrelationships between FEW and EES systems. Relevant enterprise efforts would emphasize increasing FEW resource accessibility by improving coordinated interplays across sectors and scales, expanding and diversifying supply-chain networks, and innovating technologies for efficient resource utilization. This framework can guide the development of strategic solutions for diminishing the competition among FEW-consuming sectors in a region or country, and for minimizing existing inequalities in FEW availability when a sustainable development agenda is implemented.« less

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 notmore » 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.« less

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 K_OW of 3.42). Here, 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 reductionmore » 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.« less

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 (N₂O) from the tropics. Toward closing these knowledge gaps, in this study 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 overallmore » distinct community composition, the relative abundances and nucleotide sequences of N₂O 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 N₂O 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.« less

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 MnO_2-bio; however, BPA degradation in cultures of Mn(II)-oxidizing bacteria has not been explored. We assessed MnO_2-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 MnO_2-bio mediated BPA degradation. Increased Mn(II) concentrations up to 100 µM resulted in more MnO_2-bio formation but the highest BPAmore » 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 MnO_2-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 MnO_2-bio, is the key determinant for oxidation activity.« less