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1. Identification of the phylotypes involved in cis-dichloroethene and 1,4-dioxane biodegradation in soil microcosms.

   https://doi.org/10.1016/j.scitotenv.2021.148690  

   Dang, Hongyu and (November 2021, Science of the total environment)

   Co-contamination with chlorinated compounds and 1,4-dioxane has been reported at many sites. Recently, there has been an increased interest in bioremediation because of the potential to degrade multiple contaminants concurrently. Towards improving bioremediation efficacy, the current study examined laboratory microcosms (inoculated separately with two soils) to determine the phylotypes and functional genes associated with the biodegradation of two common co-contaminants (cis-dichloroethene [cDCE] and 1,4-dioxane). The impact of amending microcosms with lactate on cDCE and 1,4-dioxane biodegradation was also investigated. The presence of either lactate or cDCE did not impact 1,4-dioxane biodegradation one of the two soils. Lactate appeared to improve the initiation of the biological removal of cDCE in microcosms inoculated with either soil. Stable isotope probing (SIP) was then used to determine which phylotypes were actively involved in carbon uptake from cDCE and 1,4-dioxane in both soil communities. The most enriched phylotypes for 13C assimilation from 1,4-dioxane included Rhodopseudomonas and Rhodanobacter. Propane monooxygenase was predicted (by PICRUSt2) to be dominant in the 1,4-dioxane amended microbial communities and propane monooxygenase gene abundance values correlated with other enriched (but less abundant) phylotypes for 13C-1,4-dioxane assimilation. The dominant enriched phylotypes for 13C assimilation from cDCE included Bacteriovorax, Pseudomonas and Sphingomonas. In the cDCE amended soil microcosms, PICRUSt2 predicted the presence of DNA encoding glutathione S-transferase (a known cDCE upregulated enzyme). Overall, the work demonstrated concurrent removal of cDCE and 1,4-dioxane by indigenous soil microbial communities and the enhancement of cDCE removal by lactate. The data generated on the phylotypes responsible for carbon uptake (as determined by SIP) could be incorporated into diagnostic molecular methods for site characterization. The results suggest concurrent biodegradation of cDCE and 1,4-dioxane should be considered for chlorinated solvent site remediation. 

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2. Isolation and characterization of a halophilic Modicisalibacter sp. strain Wilcox from produced water

   https://doi.org/10.1038/s41598-021-86196-0  

   Marsh, William S.; Heise, Brenden W.; Krzmarzick, Mark J.; Murdoch, Robert W.; Fathepure, Babu Z. (December 2021, Scientific Reports)

   Abstract We report the isolation a halophilic bacterium that degrades both aromatic and aliphatic hydrocarbons as the sole sources of carbon at high salinity from produced water. Phylogenetic analysis of 16S rRNA-gene sequences shows the isolate is a close relative of Modicisalibacter tunisiensis isolated from an oil-field water in Tunisia. We designate our isolate as Modicisalibacter sp. strain Wilcox. Genome analysis of strain Wilcox revealed the presence of a repertoire of genes involved in the metabolism of aliphatic and aromatic hydrocarbons. Laboratory culture studies corroborated the predicted hydrocarbon degradation potential. The strain degraded benzene, toluene, ethylbenzene, and xylenes at salinities ranging from 0.016 to 4.0 M NaCl, with optimal degradation at 1 M NaCl. Also, the strain degraded phenol, benzoate, biphenyl and phenylacetate as the sole sources of carbon at 2.5 M NaCl. Among aliphatic compounds, the strain degraded n-decane and n-hexadecane as the sole sources of carbon at 2.5 M NaCl. Genome analysis also predicted the presence of many heavy metal resistance genes including genes for metal efflux pumps, transport proteins, and enzymatic detoxification. Overall, due to its ability to degrade many hydrocarbons and withstand high salt and heavy metals, strain Wilcox may prove useful for remediation of produced waters. 

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3. Lead or cadmium co-contamination alters benzene and toluene degrading bacterial communities

   https://doi.org/10.1007/s10532-023-10021-w  

   Konya, Aniko; Fiddler, Brice A.; Bunch, Olivia; Hess, Kendra Z.; Ferguson, Cade; Krzmarzick, Mark J. (February 2023, Biodegradation)

   Abstract Co-contamination of hydrocarbons with heavy metals in soils often complicates and hinders bioremediation. A comprehensive characterization of site-specific degraders at contaminated sites can help determine if in situ bioremediation processes are sufficient. This study aimed to identify differences in benzene and toluene degradation rates and the microbial communities enriched under aerobic conditions when different concentrations of Cd and Pb are introduced. Microcosms were used to study the degradation of 0.23 mM benzene or 0.19 mM toluene under various concentrations of Pb (up to 240 µM) and Cd (up to 440 µM). Soil collected from a stormwater retention basin receiving runoff from a large parking lot was utilized to seed the microcosms. The hydrocarbon degradation time and rates were measured. After further rounds of amendment and degradation of benzene and toluene, 16S rRNA gene amplicon sequencing and quantitative PCR were used to ascertain the microbial communities enriched under the various concentrations of the heavy metals. The initial degradation time for toluene and benzene was 7 to 9 days and 10 to 13 days, respectively. Degradation rates were similar for each hydrocarbon despite the concentration and presence of metal co-contaminant, however, the enriched microbial communities under each condition differed. Microcosms without metal co-contaminant contained a diversity of putative benzene and toluene degrading bacteria. Cd strongly reduced the richness of the microbial communities. With higher levels of heavy metals, genera such asRalstonia,Cupriavidus,Azoarcus, andRhodococcusbecame more dominant under various conditions. The study finds that highly efficient benzene- and toluene-degrading consortia can develop under variations of heavy metal co-contamination, but the consortia are dependent on the heavy metal type and concentrations. 

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4. Desulfonation and defluorination of 6:2 fluorotelomer sulfonic acid (6:2 FTSA) by Rhodococcus jostii RHA1: Carbon and sulfur sources, enzymes, and pathways

   https://doi.org/10.1016/j.jhazmat.2021.127052  

   Shih-Hung Yang Ying Shi Mark Strynar Kung-Hui Chu (February 2022, Journal of hazardous materials)

   6:2 fluorotelomer sulfonic acid (6:2 FTSA) is one per- and poly-fluoroalkyl substances commonly detected in the environment. While biotransformation of 6:2 FTSA has been reported, factors affecting desulfonation and defluorination of 6:2 FTSA remain poorly understood. This study elucidated the effects of carbon and sulfur sources on the gene expression of Rhodococcus jostii RHA1 which is responsible for the 6:2 FTSA biotransformation. While alkane monooxygenase and cytochrome P450 were highly expressed in ethanol-, 1-butanol-, and n-octane-grown RHA1 in sulfur-rich medium, these cultures only defluorinated 6:2 fluorotelomer alcohol but not 6:2 FTSA, suggesting that the sulfonate group in 6:2 FTSA hinders enzymatic defluorination. In sulfur-free growth media, alkanesulfonate monooxygenase was linked to desulfonation of 6:2 FTSA; while alkane monooxygenase, haloacid dehalogenase, and cytochrome P450 were linked to defluorination of 6:2 FTSA. The desulfonation and defluorination ability of these enzymes toward 6:2 FTSA were validated through heterologous gene expression and in vitro assays. Four degradation metabolites were confirmed and one was identified as a tentative metabolite. The results provide a new understanding of 6:2 FTSA biotransformation by RHA1. The genes encoding these desulfonating- and defluorinating-enzymes are potential markers to be used to assess 6:2 FTSA biotransformation in the environment. 

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5. Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b

   https://doi.org/10.3390/biom12040560  

   Samanta, Dipayan; Govil, Tanvi; Saxena, Priya; Gadhamshetty, Venkata; Krumholz, Lee R.; Salem, David R.; Sani, Rajesh K. (April 2022, Biomolecules)

   Particulate methane monooxygenase (pMMO), a membrane-bound enzyme having three subunits (α, β, and γ) and copper-containing centers, is found in most of the methanotrophs that selectively catalyze the oxidation of methane into methanol. Active sites in the pMMO of Methylosinus trichosporium OB3b were determined by docking the modeled structure with ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene. The docking energy between the modeled pMMO structure and ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene was −5.2, −5.7, −4.2, and −3.8 kcal/mol, respectively, suggesting the existence of more than one active site within the monomeric subunits due to the presence of multiple binding sites within the pMMO monomer. The evaluation of tunnels and cavities of the active sites and the docking results showed that each active site is specific to the radius of the substrate. To increase the catalysis rates of methane in the pMMO of M. trichosporium OB3b, selected amino acid residues interacting at the binding site of ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene were mutated. Based on screening the strain energy, docking energy, and physiochemical properties, five mutants were downselected, B:Leu31Ser, B:Phe96Gly, B:Phe92Thr, B:Trp106Ala, and B:Tyr110Phe, which showed the docking energy of −6.3, −6.7, −6.3, −6.5, and −6.5 kcal/mol, respectively, as compared to the wild type (−5.2 kcal/mol) with ethylbenzene. These results suggest that these five mutants would likely increase methane oxidation rates compared to wild-type pMMO. 

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