Relationship between enantioselective transformation of racemic quizalofop‐ethyl and soil bacterial diversity: A destructive approach

Characterization of two novel hydrolases from Sphingopyxis sp. DBS4 for enantioselective degradation of chiral herbicide diclofop-methyl

Diclofop-methyl, an aryloxyphenoxypropionate (AOPP) herbicide, is a chiral compound with two enantiomers. Microbial detoxification and degradation of various enantiomers is garnering immense research attention. However, enantioselective catabolism of diclofop-methyl has been rarely explored, especially at the molecular level. This study cloned two novel hydrolase genes (dcmA and dcmH) in Sphingopyxis sp. DBS4, and characterized them for diclofop-methyl degradation. DcmA, a member of the amidase superfamily, exhibits 26.1-45.9% identity with functional amidases. Conversely, DcmH corresponded to the DUF3089 domain-containing protein family (a family with unknown function), sharing no significant similarity with other biochemically characterized proteins. DcmA exhibited a broad spectrum of substrates, with preferential hydrolyzation of (R)-(+)-diclofop-methyl, (R)-(+)-quizalofop-ethyl, and (R)-(+)-haloxyfop-methyl. DcmH also preferred (R)-(+)-quizalofop-ethyl and (R)-(+)-haloxyfop-methyl degradation while displaying no apparent enantioselective activity towards diclofop-methyl. Using site-directed mutagenesis and molecular docking, it was determined that Ser175 was the fundamental residue influencing DcmA's activity against the two enantiomers of diclofop-methyl. For the degradation of AOPP herbicides, DcmA is an enantioselective amidase that has never been reported in research. This study provided novel hydrolyzing enzyme resources for the remediation of diclofop-methyl in the environment and deepened the understanding of enantioselective degradation of chiral AOPP herbicides mediated by microbes.

Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition

This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.

Microbial Communities Associated with Methylmercury Degradation in Paddy Soils

Bioaccumulation of the neurotoxin methylmercury (MeHg) in rice has raised worldwide concerns because of its risks to human health. Certain microorganisms are able to degrade MeHg in pure cultures, but the roles and diversities of the microbial communities in MeHg degradation in rice paddy soils are unknown. Using a series of microcosms, we investigated MeHg degradation in paddy soils from Hunan, Guizhou, and Hubei provinces, representing three major rice production regions in China, and further characterized one of the soils from the Hunan Province for microbial communities associated with MeHg degradation. Microbial demethylation was observed in all three soils, demonstrated by significantly more MeHg degraded in the unsterilized soils than in the sterilized controls. More demethylation occurred in water-saturated soils than in unsaturated soils, but the addition of molybdate and bromoethanesulfonic acid as the respective inhibitors of sulfate reducing bacteria and methanogens showed insignificant effects on MeHg degradation. However, the addition of Cu enhanced MeHg degradation and the enrichment of Xanthomonadaceae in the unsaturated soil. 16S rRNA Illumina sequencing and metatranscriptomic analyses of the Hunan soil consistently revealed that Catenulisporaceae, Frankiaceae, Mycobacteriaceae, and Thermomonosporaceae were among the most likely microbial taxa in influencing MeHg degradation in the paddy soil, and they were confirmed by combined analyses of the co-occurrence network, random forest modeling, and linear discriminant analysis of the effect size. Our results shed additional light onto the roles of microbial communities in MeHg degradation in paddy soils and its subsequent bioaccumulation in rice grains.

Enantioselective Catabolism of the Two Enantiomers of the Phenoxyalkanoic Acid Herbicide Dichlorprop by Sphingopyxis sp. DBS4

Dichlorprop [(RS)-2-(2,4-dichlorophenoxy)propanoic acid; DCPP], an important phenoxyalkanoic acid herbicide (PAAH), is extensively used in the form of racemic mixtures (Rac-DCPP), and the environmental fates of both DCPP enantiomers [(R)-DCPP and (S)-DCPP] mediated by microorganisms are of great concern. In this study, a bacterial strain Sphingopyxis sp. DBS4 was isolated from contaminated soil and was capable of utilizing both (R)-DCPP and (S)-DCPP as the sole carbon source for growth. Strain DBS4 preferentially catabolized (S)-DCPP as compared to (R)-DCPP. The optimal conditions for Rac-DCPP degradation by strain DBS4 were 30 °C and pH 7.0. In addition to Rac-DCPP, other PAAHs such as (RS)-2-(4-chloro-2-methylphenoxy)propanoic acid, 2,4-dichlorophenoxyacetic acid, 4-chloro-2-methylphenoxyacetic acid, and 2,4-dichlorophenoxyacetic acid butyl ester could also be catabolized by strain DBS4. Bioremediation of Rac-DCPP-contaminated soil by inoculation of strain DBS4 exhibited an effective removal of both (R)-DCPP and (S)-DCPP from the soil. Due to its broad substrate spectrum, strain DBS4 showed great potential in the bioremediation of PAAH-contaminated sites.

Application of enantiomeric fractions in environmental forensics: Uncertainties and inconsistencies

The assumption that only biological processes are enantioselective introduces challenges in the reliability of enantioselective analysis as a tool for discriminating biotic and abiotic processes in the environmental fate of chiral pollutants. Enantioselectivity does not depend on the nature of the fate process a chiral contaminant undergoes but on the interaction of the chiral contaminant with homochirality inducing external agents (e.g. chiral molecules, macromolecules or surfaces such as enzymes, blood plasma, proteins, chiral co-pollutants, humic acid and soil organominerals). The environmental behavior of a chiral contaminant is difficult to anticipate because the interactions between the chiral contaminants and the homochirality inducing external agents is often complex and strongly influenced by local environment conditions such as pH, redox conditions, organic carbon, organic nitrogen, humic acid, and redox conditions. Furthermore, the use of enantioselective analysis in environmental forensics depend on the adequate separation and accurate identification and quantification of the enantiomers of the chiral contaminant. Matrix effects, instrument effects, inadequate enantioselective separation, and poor quantification techniques introduce uncertainties in the determination of enantiomeric composition. Here we present the weaknesses of this assumption and recommend using enantiomeric fractions as chemical markers of biotransformation with caution. We recommend using stable isotopes, including abiotic controls to determine if enantioselective sorption occurs, and determining stability of enantiomers in solvent or at elevated temperatures to account for confounding factors arising from matrix effects, enantioselective abiotic processes, and enantiomerization due solvent and thermal lability of the chiral analyte, respectively to maintain the integrity of the utility of enantiomeric composition changes as an environmental forensics tool.