Genome-Centric Metatranscriptomic Characterization of a Humin-Facilitated Anaerobic Tetrabromobisphenol A-Dehalogenating Consortium.

Tetrabromobisphenol A (TBBPA), a widely used brominated flame retardant in electronics manufacturing, has caused global contamination due to improper e-waste disposal. Its persistence, bioaccumulation, and potential carcinogenicity drive studies of its transformation and underlying (a)biotic interactions. This study achieved an anaerobic enrichment culture capable of reductively dehalogenating TBBPA to the more bioavailable bisphenol A. 16S rRNA gene amplicon sequencing and quantitative PCR confirmed that successive dehalogenation of four bromide ions from TBBPA was coupled with the growth of both Dehalobacter sp. and Dehalococcoides sp. with growth yields of 5.0 ± 0.4 × 108 and 8.6 ± 4.6 × 108 cells per µmol Br- released (N = 3), respectively. TBBPA dehalogenation was facilitated by solid humin and reduced humin, which possessed the highest organic radical signal intensity and reducing groups -NH2, and maintained the highest dehalogenation rate and dehalogenator copies. Genome-centric metatranscriptomic analyses revealed upregulated putative TBBPA-dehalogenating rdhA (reductive dehalogenase) genes with humin amendment, cprA-like Dhb_rdhA1 gene in Dehalobacter species, and Dhc_rdhA1/Dhc_rdhA2 genes in Dehalococcoides species. The upregulated genes of lactate fermentation, de novo corrinoid biosynthesis, and extracellular electron transport in the humin amended treatment also stimulated TBBPA dehalogenation. This study provided a comprehensive understanding of humin-facilitated organohalide respiration.

Sustained detoxification of 1,2-dichloroethane to ethylene by a symbiotic consortium containing Dehalococcoides species.

1,2-Dichloroethane (1,2-DCA) is a ubiquitous volatile halogenated organic pollutant in groundwater and soil, which poses a serious threat to the ecosystem and human health. Microbial reductive dechlorination has been recognized as an environmentally-friendly strategy for the remediation of sites contaminated with 1,2-DCA. In this study, we obtained an anaerobic microbiota derived from 1,2-DCA contaminated groundwater, which was able to sustainably convert 1,2-DCA into non-toxic ethylene with an average dechlorination rate of 30.70 ± 11.06 µM d-1 (N = 6). The microbial community profile demonstrated that the relative abundance of Dehalococcoides species increased from 0.53 ± 0.08% to 44.68 ± 3.61% in parallel with the dechlorination of 1,2-DCA. Quantitative PCR results showed that the Dehalococcoides species 16S rRNA gene increased from 2.40 ± 1.71 × 108 copies∙mL-1 culture to 4.07 ± 2.45 × 108 copies∙mL-1 culture after dechlorinating 110.69 ± 30.61 µmol of 1,2-DCA with a growth yield of 1.55 ± 0.93 × 108 cells per µmol Cl- released (N = 6), suggesting that Dehalococcoides species used 1,2-DCA for organohalide respiration to maintain cell growth. Notably, the relative abundances of Methanobacterium sp. (p = 0.0618) and Desulfovibrio sp. (p = 0.0001995) also increased significantly during the dechlorination of 1,2-DCA and were clustered in the same module with Dehalococcoides species in the co-occurrence network. These results hinted that Dehalococcoides species, the obligate organohalide-respiring bacterium, exhibited potential symbiotic relationships with Methanobacterium and Desulfovibrio species. This study illustrates the importance of microbial interactions within functional microbiota and provides a promising microbial resource for in situ bioremediation in sites contaminated with 1,2-DCA.

Nanoscale zero-valent iron reduction coupled with anaerobic dechlorination to degrade hexachlorocyclohexane isomers in historically contaminated soil.

Hexachlorocyclohexane (HCH) isomers pose potential threats to the environment and to public health due to their persistence and high toxicity. In this study, nanoscale zero-valent iron (nZVI) coupled with microbial degradation by indigenous microorganisms with and without biostimulation was employed to remediate soils highly polluted with HCH. The degradation efficiency of total HCHs in both the "nZVI-only" and "Non-amendment" treatments was approximately 50 %, while in the treatment amended with nZVI and acetate, 85 % of total HCHs was removed. Addition of nZVI and acetate resulted in enrichment of anaerobic microorganisms. The results of quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing revealed that Desulfotomaculum, Dehalobacter, Geobacter, and Desulfuromonas likely contributed to the depletion of HCH isomers. Moreover, some abiotic factors also favored this removal process, including pH, and the generation of iron sulfides as revealed by the result of Mössbauer spectrometer analysis. Our research provides an improved remediation strategy for soils polluted with HCH isomers and an understanding of the synergistic effect of nZVI and indigenous microorganisms.

Ornithine and breast cancer: a matched case-control study.

In vivo and vitro evidence indicates that ornithine and its related metabolic products play a role in tumor development. Whether ornithine is associated with breast cancer in humans is still unclear. We examined the association between circulating ornithine levels and breast cancer in females. This 1:1 age-matched case-control study identified 735 female breast cancer cases and 735 female controls without breast cancer. All cases had a pathological test to ascertain a breast cancer diagnosis. The controls were ascertained using pathologic testing, clinical examinations, and/or other tests. Fasting blood samples were used to measure ornithine levels. The average age for cases and controls were 49.6 years (standard deviation [SD] 8.7 years) and 48.9 years (SD 8.7 years), respectively. Each SD increase in ornithine levels was associated with a 12% reduction of breast cancer risk (adjusted odds ratio [OR] 0.88; 95% confidence interval [CI] 0.79-0.97). The association between ornithine and breast cancer did not differ by pathological stages of diagnosis or tumor grades (all P for trend > 0.1). We observed no effect measure modification by molecular subtypes (P for interaction = 0.889). In conclusion, higher ornithine levels were associated with lower breast cancer risk in females.

Identification of key gene modules and hub genes of human mantle cell lymphoma by coexpression network analysis.

PURPOSE: Mantle cell lymphoma (MCL) is a rare and aggressive subtype of non-Hodgkin lymphoma that is incurable with standard therapies. The use of gene expression analysis has been of interest, recently, to detect biomarkers for cancer. There is a great need for systemic coexpression network analysis of MCL and this study aims to establish a gene coexpression network to forecast key genes related to the pathogenesis and prognosis of MCL. METHODS: The microarray dataset GSE93291 was downloaded from the Gene Expression Omnibus database. We systematically identified coexpression modules using the weighted gene coexpression network analysis method (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis were performed on the modules deemed important. The protein-protein interaction networks were constructed and visualized using Cytoscape software on the basis of the STRING website; the hub genes in the top weighted network were identified. Survival data were analyzed using the Kaplan-Meier method and were compared using the log-rank test. RESULTS: Seven coexpression modules consisting of different genes were applied to 5,000 genes in the 121 human MCL samples using WGCNA software. GO and KEGG enrichment analysis identified the blue module as one of the most important modules; the most critical pathways identified were the ribosome, oxidative phosphorylation and proteasome pathways. The hub genes in the top weighted network were regarded as real hub genes (IL2RB, CD3D, RPL26L1, POLR2K, KIF11, CDC20, CCNB1, CCNA2, PUF60, SNRNP70, AKT1 and PRPF40A). Survival analysis revealed that seven genes (KIF11, CDC20, CCNB1, CCNA2, PRPF40A, CD3D and PUF60) were associated with overall survival time (p < 0.05). CONCLUSIONS: The blue module may play a vital role in the pathogenesis of MCL. Five real hub genes (KIF11, CDC20, CCNB1, CCNA2 and PUF60) were identified as potential prognostic biomarkers as well as therapeutic targets with clinical utility for MCL.

Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, ß-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene.

Intensive historical and worldwide use of pesticide formulations containing hexachlorocyclohexane (HCH) has led to widespread contamination. We derived four anaerobic enrichment cultures from HCH-contaminated soil capable of sustainably dechlorinating each of α-, ß-, γ-, and δ-HCH isomers stoichiometrically to benzene and monochlorobenzene (MCB). For each isomer, the dechlorination rates, inferred from production rates of the dechlorinated products, MCB and benzene, increased progressively from <3 to ∼12 µM/day over 2 years. The molar ratio of benzene to MCB produced was a function of the substrate isomer and ranged from ß (0.77 ± 0.15), α (0.55 ± 0.09), γ (0.13 ± 0.02), to δ (0.06 ± 0.02) in accordance with pathway predictions based on prevalence of antiperiplanar geometry. Data from 16S rRNA gene amplicon sequencing and quantitative PCR revealed significant increases in the absolute abundances of Pelobacter and Dehalobacter, most notably in the α-HCH and δ-HCH cultures. Cultivation with a different HCH isomer resulted in distinct bacterial communities, but similar archaeal communities. This study provides the first direct comparison of shifts in anaerobic microbial communities induced by the dechlorination of distinct HCH isomers. It also uncovers candidate microorganisms responsible for the dechlorination of α-, ß-, γ-, and δ-HCH, a key step toward better understanding and monitoring of natural attenuation processes and improving bioremediation technologies for HCH-contaminated sites.

Natural Attenuation and Anaerobic Benzene Detoxification Processes at a Chlorobenzene-Contaminated Industrial Site Inferred from Field Investigations and Microcosm Studies.

A five-year site investigation was conducted at a former chemical plant in Nanjing, China. The main contaminants were 1,2,4-trichlorobenzene (TCB) reaching concentrations up to 7300 µg/L, dichlorobenzene (DCB) isomers, monochlorobenzene (MCB), and benzene. Over time, these contaminants naturally attenuated to below regulatory levels under anaerobic conditions. To confirm the transformation processes and to explore the mechanisms, a corresponding laboratory microcosm study was completed demonstrating that 1,2,4-TCB was dechlorinated to 1,2-DCB, 1,3-DCB, and 1,4-DCB in approximately 2%/10%/88% molar proportions. The DCB isomers were dechlorinated via MCB to benzene, and, finally, benzene was degraded under prevailing sulfate-reducing conditions. Dechlorination could not be attributed to known dechlorinators Dehalobacter or Dehalococcoides, while anaerobic benzene degradation was mediated by microbes affiliated to a Deltaproteobacterium ORM2, previously associated with this activity. Unidentified organic compounds, possibly aromatic compounds related to past on-site production processes, were fueling the dechlorination reactions in situ. The microcosm study confirmed transformation processes inferred from field data and provided needed assurance for natural attenuation. Activity-based microcosm studies are often omitted from site characterization in favor of rapid and less expensive molecular surveys. However, the value of microcosm studies for confirming transformation processes, establishing electron balances, assessing cocontaminant inhibition, and validating appropriate monitoring tools is clear. At complex sites impacted by multiple compounds with poorly characterized transformation mechanisms, activity assays provide valuable data to incorporate into the conceptual site model to most effectively inform remediation alternatives.