Antibiotics act as an ecological factor in the environment that could potentially affect microbial communities. The effects include phylogenetic structure alteration, resistance expansion, and ecological function disturbance in the micro-ecosystem. Numerous studies have detected changes of microbial community structure upon addition of antibiotics in soil and water environment. However, the causal relationship between antibiotic input and resistance expansion is still under debate, with evidence either supporting or declining the contribution of antibiotics on alteration of antibiotic resistance. Effects of antibiotics on ecological functions have also been discovered, including nitrogen transformation, methanogenesis, and sulfate reduction. In the latter part, this review discusses in detail on factors that influence antibiotic effects on microbial communities in soil and aquatic environment, including concentration of antibiotics, exposure time, added substrates, as well as combined effects of multiple antibiotics. In all, recent research progress offer an outline of effects of antibiotics in the natural environment. However, questions raised in this review need further investigation in order to provide a comprehensive risk assessment on the consequence of anthropogenic antibiotic input.

1,1,1-Trichloroethane (TCA) and chloroform are two notorious groundwater pollutants. Here we report the isolation and characterization of Desulfitobacterium sp. strain PR that rapidly dechlorinates both compounds. In pyruvate-amended medium, strain PR reductively dechlorinates ∼ 1.0 mM TCA completely to monochloroethane within 15 days. Under the same conditions, strain PR dechlorinates ∼ 1.2 mM chloroform to predominantly dichloromethane (∼ 1.14 mM) and trace amount of monochloromethane (∼ 0.06 mM) within 10 days. Strain PR shares 96.7% 16S rRNA gene sequence similarity with its closest relative - Desulfitobacterium metallireducens strain 853-15; however, it distinguishes itself from known Desulfitobacterium strains by its inability of utilizing several of their commonly shared substrates such as lactate, thiosulfate and sulfite. A reductive dehalogenase gene (ctrA) in strain PR was identified to be responsible for dechlorination of both TCA and chloroform, showing a maximum expression level of 5.95 ∼ 6.25 copies of transcripts cell(-1) . CtrA shares 94% amino acid sequence identity with CfrA in Dehalobacter sp. strain CF50 and DcrA in Dehalobacter sp. strain DCA. Interestingly, strain PR could tolerate high aqueous concentrations (up to 0.45 mM) of trichloroethene, another groundwater pollutant that often coexists with TCA/chloroform. As the first chloroform-respiring and the second TCA-respiring isolate that has been identified, Desulfitobacterium sp. strain PR may prove useful in remediation of halogenated alkanes with trihalomethyl (-CX₃) groups.

Polybrominated diphenyl ethers (PBDEs) are widespread global contaminants due to their extensive usage as flame retardants. Among the 209 PBDE congeners, tetra-brominated diphenyl ether (tetra-BDE) (congener 47) and penta-BDEs (congeners 99 and 100) are the most abundant, toxic, and bioaccumulative congeners in the environment. However, little is known about microorganisms that carry out debromination of these congeners under anaerobic conditions. In this study, we describe a coculture GY2 consisting of Dehalococcoides and Desulfovibrio spp., which is capable of debrominating ∼1180 nM of congeners 47, 99, and 100 (88-100% removal) to the nonbrominated diphenyl ether at an average rate of 36.9, 19.8, and 21.9 nM day(-1), respectively. Ortho bromines are preferentially removed during the debromination process. The growth of Dehalococcoides links tightly with PBDE debromination, with an estimated growth yield of 1.99 × 10(14) cells per mole of bromide released, while the growth of Desulfovibrio could be independent of PBDEs. The growth-coupled debromination suggests that Dehalococcoides cells in the coculture GY2 are able to respire on PBDEs. Given the ubiquity and recalcitrance of the tetra- and penta-BDEs, complete debromination of these congeners to less toxic end products (e.g. diphenyl ether) is important for the restoration of PBDE-contaminated environments.

Polybrominated diphenyl ethers (PBDEs) are a class of environmental pollutants that have been classified as persistent organic pollutants since 2009. In this study, a sediment-free enrichment culture (culture G) was found to reductively debrominate octaand penta-BDE technical mixtures to less-brominated congeners (tetra-, tri-, and di-BDEs) via a para-dominant debromination pattern for the former and a strict para debromination pattern for the latter. Culture G could debrominate 96% of 280 nM PBDEs in an octa-BDE mixture to primarily tetra-BDEs in 21 weeks. Continuous transferring of culture G with octa-/penta-BDEs dissolved in n-nonane or trichloroethene (TCE) yielded two strains (Acetobacterium sp. strain AG and Dehalococcoides sp. strain DG) that retained debromination capabilities. In the presence of lactate but without TCE, strain AG could cometabolically debrominate 75% of 275 nM PBDEs in a penta-BDE mixture in 33 days. Strain AG shows 99% identity to its closest relative, Acetobacterium malicum. In contrast to strain AG, strain DG debrominated PBDEs only in the presence of TCE. In addition, 18 out of 19 unknown PBDE debromination products were successfully identified from octa-and penta-BDE mixtures and revealed, for the first time, a comprehensive microbial PBDE debromination pathway. As an acetogenic autotroph that rapidly debrominates octa-and penta-BDE technical mixtures, Acetobacterium sp. strain AG adds to the still-limited understanding of PBDE debromination by microorganisms.

No abstract