Abundance and expression of enantioselective rdpA and sdpA dioxygenase genes during degradation of the racemic herbicide (R,S)-2-(2,4-dichlorophenoxy)propionate in soil

Potential Risks of Tebuconazole during Wine Fermentation at the Enantiomer Level Based on Multiomics Analysis

The enantioselectivity and potential risks of tebuconazole enantiomers (R-tebuconazole and S-tebuconazole) in wine fermentation were investigated in this study using Cabernet Sauvignon grapes. Tebuconazole was mainly degraded during the alcoholic fermentation stage, and no obvious transformation between R-tebuconazole and S-tebuconazole was observed. Selective degradation between these two enantiomers occurred, with R-tebuconazole degrading faster than S-tebuconazole. The residual tebuconazole inhibits glucose metabolism and the unsaturated fatty acid formation in the wine fermentation system and inhibits gene expression in the late phase of Saccharomycetales, affecting its cell wall formation. Overall, the findings highlight that R-tebuconazole exhibited a higher risk than S-tebuconazole in these processes. These insights are potentially exploitable to understand chiral pesticides at the enantiomer level using multiomics technology in food-processing systems.

Potential and limitations for monitoring of pesticide biodegradation at trace concentrations in water and soil

Pesticides application on agricultural fields results in pesticides being released into the environment, reaching soil, surface water and groundwater. Pesticides fate and transformation in the environment depend on environmental conditions as well as physical, chemical and biological degradation processes. Monitoring pesticides biodegradation in the environment is challenging, considering that traditional indicators, such as changes in pesticides concentration or identification of pesticide metabolites, are not suitable for many pesticides in anaerobic environments. Furthermore, those indicators cannot distinguish between biotic and abiotic pesticide degradation processes. For that reason, the use of molecular tools is important to monitor pesticide biodegradation-related genes or microorganisms in the environment. The development of targeted molecular (e.g., qPCR) tools, although laborious, allowed biodegradation monitoring by targeting the presence and expression of known catabolic genes of popular pesticides. Explorative molecular tools (i.e., metagenomics & metatranscriptomics), while requiring extensive data analysis, proved to have potential for screening the biodegradation potential and activity of more than one compound at the time. The application of molecular tools developed in laboratory and validated under controlled environments, face challenges when applied in the field due to the heterogeneity in pesticides distribution as well as natural environmental differences. However, for monitoring pesticides biodegradation in the field, the use of molecular tools combined with metadata is an important tool for understanding fate and transformation of the different pesticides present in the environment.

A Synergistic Consortium Involved in rac-Dichlorprop Degradation as Revealed by DNA Stable Isotope Probing and Metagenomic Analysis

rac-Dichlorprop, a commonly used phenoxyalkanoic acid herbicide, is frequently detected in environments and poses threats to environmental safety and human health. Microbial consortia are thought to play key roles in rac-dichlorprop degradation. However, the compositions of the microbial consortia involved in rac-dichlorprop degradation remain largely unknown. In this study, DNA stable isotope probing (SIP) and metagenomic analysis were integrated to reveal the key microbial consortium responsible for rac-dichlorprop degradation in a rac-dichlorprop-degrading enrichment. OTU340 (Sphingobium sp.) and OTU348 (Sphingopyxis sp.) were significantly enriched in the rac-[¹³C]dichlorprop-labeled heavy DNA fractions. A rac-dichlorprop degrader, Sphingobium sp. strain L3, was isolated from the enrichment by a traditional enrichment method but with additional supplementation of the antibiotic ciprofloxacin, which was instructed by metagenomic analysis of the associations between rac-dichlorprop degraders and antibiotic resistance genes. As revealed by functional profiling of the metagenomes of the heavy DNA, the genes rdpA and sdpA, involved in the initial degradation of the (R)- and (S)-enantiomers of dichlorprop, respectively, were mostly taxonomically assigned to Sphingobium species, indicating that Sphingopyxis species might harbor novel dichlorprop-degrading genes. In addition, taxonomically diverse bacterial genera such as Dyella, Sphingomonas, Pseudomonas, and Achromobacter were presumed to synergistically cooperate with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. IMPORTANCE Understanding of the key microbial consortium involved in the degradation of the phenoxyalkanoic acid herbicide rac-dichlorprop is pivotal for design of synergistic consortia used for enhanced bioremediation of herbicide-contaminated sites. However, the composition of the microbial consortium and the interactions between community members during the biodegradation of rac-dichlorprop are unclear. In this study, DNA-SIP and metagenomic analysis were integrated to reveal that the metabolite 2,4-dichlorophenol degraders Dyella, Sphingomonas, Pseudomonas, and Achromobacter synergistically cooperated with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. Our study provides new insights into the synergistic degradation of rac-dichlorprop at the community level and implies the existence of novel degrading genes for rac-dichlorprop in nature.

Transcriptional regulation of organohalide pollutant utilisation in bacteria

Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.

Gene-Centric Model Approaches for Accurate Prediction of Pesticide Biodegradation in Soils

Pesticides are widely used in agriculture despite their negative impact on ecosystems and human health. Biogeochemical modeling facilitates the mechanistic understanding of microbial controls on pesticide turnover in soils. We propose to inform models of coupled microbial dynamics and pesticide turnover with measurements of the abundance and expression of functional genes. To assess the advantages of informing models with genetic data, we developed a novel "gene-centric" model and compared model variants of differing structural complexity against a standard biomass-based model. The models were calibrated and validated using data from two batch experiments in which the degradation of the pesticides dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxyacetic acid (MCPA) were observed in soil. When calibrating against data on pesticide mineralization, the gene-centric and biomass-based models performed equally well. However, accounting for pesticide-triggered gene regulation allows improved performance in capturing microbial dynamics and in predicting pesticide mineralization. This novel modeling approach also reveals a hysteretic relationship between pesticide degradation rates and gene expression, implying that the biodegradation performance in soils cannot be directly assessed by measuring the expression of functional genes. Our gene-centric model provides an effective approach for exploiting molecular biology data to simulate pesticide degradation in soils.

Enantioselective biodegradation and enantiomerization of dichlorprop in soils

The dissipation of racemic, R-, and S- dichlorprop (DCPP) in four soils were studied in the laboratory. The half-lives of racemic DCPP were from 10.5 to 19.8 days. Preferential degradation of R- or S-DCPP was detected in all soils, even in one soil that the apparent enantiomeric fraction remained constant during incubation. The enantiomerization of DCPP was found to proceed in both directions, except in forest soil that no enantiomerization of S- to R-DCPP was observed. The isomerization equilibrium constant (K = k_RS/k_SR) in two vegetable soils were 0.54 and 0.53, respectively, favoring herbicidally active R enantiomer, while in paddy soil K was 1.60, favoring an inversion of R into S enantiomer. Real-time PCR showed that the rdpA gene was not detected in all indigenous and DCPP amended microcosms probably because of relative short incubation time and low amendment concentrations. In contrast, the sdpA gene was present in indigenous soils and significantly elevated after DCPP addition with the highest relative abundance around day 10 in all microcosms. Illumina sequencing of the 16S rRNA gene showed that the relative abundance of Proteobacteria significantly increased in all DCPP treated soils. DCPP-degrading related families, Sphingomonadaceae and Comamonadaceae, enhanced in all soils, while Burkholderiaceae elevated only in paddy soil with preferential degradation of S-DCPP and Pseudomonadaceae only in forest soil with R-enantiomer preference. The sdpA gene sequencing revealed that about 92%-99% of bacteria harboring sdpA genes in studied soils belong to Alphaproteobacteria.

Methanotrophic contribution to biodegradation of phenoxy acids in cultures enriched from a groundwater-fed rapid sand filter

Drinking water supply is in many parts of the world based on groundwater. Groundwater often contains methane, which can be oxidized by methanotrophs upon aeration. Sand from rapid sand filters fed with methane-rich groundwater can remove some pesticides (Hedegaard and Albrechtsen in Water Res 48:71-81, 2014). We enriched methanotrophs from filter sand and investigated whether they could drive the degradation of various pesticides. To enrich for methanotrophs, we designed and operated four laboratory-scale, continuously methane-fed column reactors, inoculated with filter sand and one control column fed with tap water. When enrichments were obtained, methane was continuously supplied to three reactors, while the fourth was starved for methane for 1 week, and the reactors were spiked with ten pesticides at groundwater-relevant concentrations (2.1-6.6 μg/L). Removal for most pesticides was not detected at the investigated contact time (1.37 min). However, the degradation of phenoxy acids was observed in the methanotrophic column reactor starved for methane, while it was not detected in the control column indicating the importance of methanotrophs. Phenoxy acid removal, using dichlorprop as a model compound, was further investigated in batch experiments with methanotrophic biomass collected from the enrichment reactors. Phenoxy acid removal (expressed per gram of matrix sand) was substantially improved in the methanotrophic enrichment compared to parent filter sand. The presence of methane did not clearly impact dichlorprop removal but did impact mineralization. We suggest that other heterotrophs are responsible for the first step in dichlorprop degradation, while the subsequent steps including ring-hydroxylation are driven by methanotrophs.

Inoculation of soil with cadmium-resistant bacterium Delftia sp. B9 reduces cadmium accumulation in rice (Oryza sativa L.) grains

Bioremediation of heavy metal polluted soil using metal-resistant bacteria has received increasing attentions. In the present study, we isolated a heavy metal-resistant bacterial strain from a Cd-contaminated soil, and conducted pot experiments to evaluate the effect of bacterial inoculation in soil on soil Cd speciation, rice grain biomass and Cd accumulation. We find that the isolated bacterial strain is a Gram-negative bacterium, and named as Delftia sp. B9 based on the 16S rDNA gene sequence analysis. TEM-EDS manifests that Cd can be bioaccumulated inside cell, resulting in intracellular dissolution. The Cd contents of rice grain in the two rice cultivars (early and late rice) are all below the standard limit for Food Safety of People's Republic of China (0.2 mg/kg) after the treatment of both living and non-living cells. Non-living cells are more applicable than the use of living cells for the short time bioremediation. The average content of soil exchangeable fraction of Cd decreases whereas the residual fraction increases with bacterial inoculation. All our results suggest Delftia sp. B9 is able to the stabilization of Cd in soil and reduce Cd accumulation in rice grain, therefore, this strain is potentially suitable for the bioremediation of Cd-contaminated paddy soils.

Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH

Bacterial degraders of chlorophenoxy herbicides have been isolated from various ecosystems, including pristine environments. Among these degraders, the sphingomonads constitute a prominent group that displays versatile xenobiotic-degradation capabilities. Four separate sequencing strategies were required to provide the complete sequence of the complex and plastic genome of the canonical chlorophenoxy herbicide-degrading Sphingobium herbicidovorans MH. The genome has an intricate organization of the chlorophenoxy-herbicide catabolic genes sdpA, rdpA, and cadABCD that encode the (R)- and (S)-enantiomer-specific 2,4-dichlorophenoxypropionate dioxygenases and four subunits of a Rieske non-heme iron oxygenase involved in 2-methyl-chlorophenoxyacetic acid degradation, respectively. Several major genomic rearrangements are proposed to help understand the evolution and mobility of these important genes and their genetic context. Single-strain mobilomic sequence analysis uncovered plasmids and insertion sequence-associated circular intermediates in this environmentally important bacterium and enabled the description of evolutionary models for pesticide degradation in strain MH and related organisms. The mobilome presented a complex mosaic of mobile genetic elements including four plasmids and several circular intermediate DNA molecules of insertion-sequence elements and transposons that are central to the evolution of xenobiotics degradation. Furthermore, two individual chromosomally integrated prophages were shown to excise and form free circular DNA molecules. This approach holds great potential for improving the understanding of genome plasticity, evolution, and microbial ecology.

Degradation of mecoprop in polluted landfill leachate and waste water in a moving bed biofilm reactor

Mecoprop is a common pollutant in effluent-, storm- and groundwater as well as in leachates from derelict dumpsites. Thus, bioremediation approaches may be considered. We conducted batch experiments with moving bed biofilm (MBBR)-carriers to understand the degradation of mecoprop. As a model, the carriers were incubated in effluent from a conventional wastewater treatment plant which was spiked to 10, 50 and 100 μg L^-1 mecoprop. Co-metabolic processes as well as mineralization were studied. Initial mecoprop concentration and mecoprop degradation impacted the microbial communities. The removal of (S)-mecoprop prevailed over the (R)-mecoprop. This was associated with microbial compositions, in which several operational taxonomic units (OTUs) co-varied positively with (S)-mecoprop removal. The removal-rate constant of (S)-mecoprop was 0.5 d^-1 in the 10 μg L^-1 set-up but it decreased in the 50 and 100 μg L^-1 set-ups. The addition of methanol prolonged the removal of (R)-mecoprop. During mecoprop degradation, 4-chloro-2-methylphenol was formed and degraded. A new metabolite (4-chloro-2-methylphenol sulfate) was identified and quantified.

Establishment of Bacterial Herbicide Degraders in a Rapid Sand Filter for Bioremediation of Phenoxypropionate-Polluted Groundwater

In this study, we investigated the establishment of natural bacterial degraders in a sand filter treating groundwater contaminated with the phenoxypropionate herbicides (RS)-2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP) and (RS)-2-(2,4-dichlorophenoxy)propanoic acid (DCPP) and the associated impurity/catabolite 4-chlorophenoxypropanoic acid (4-CPP). A pilot facility was set up in a contaminated landfill site. Anaerobic groundwater was pumped up and passed through an aeration basin and subsequently through a rapid sand filter, which is characterized by a short residence time of the water in the filter. For 3 months, the degradation of DCPP, MCPP, and 4-CPP in the sand filter increased to 15 to 30% of the inlet concentration. A significant selection for natural bacterial herbicide degraders also occurred in the sand filter. Using a most-probable-number (MPN) method, we found a steady increase in the number of culturable phenoxypropionate degraders, reaching approximately 5 × 10(5) degraders per g sand by the end of the study. Using a quantitative PCR targeting the two phenoxypropionate degradation genes, rdpA and sdpA, encoding stereospecific dioxygenases, a parallel increase was observed, but with the gene copy numbers being about 2 to 3 log units higher than the MPN. In general, the sdpA gene was more abundant than the rdpA gene, and the establishment of a significant population of bacteria harboring sdpA occurred faster than the establishment of an rdpA gene-carrying population. The identities of the specific herbicide degraders in the sand filter were assessed by Illumina MiSeq sequencing of 16S rRNA genes from sand filter samples and from selected MPN plate wells. We propose a list of potential degrader bacteria involved in herbicide degradation, including representatives belonging to the Comamonadaceae and Sphingomonadales.

Establishment of Bacterial Herbicide Degraders in a Rapid Sand Filter for Bioremediation of Phenoxypropionate-Polluted Groundwater

In this study, we investigated the establishment of natural bacterial degraders in a sand filter treating groundwater contaminated with the phenoxypropionate herbicides (RS)-2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP) and (RS)-2-(2,4-dichlorophenoxy)propanoic acid (DCPP) and the associated impurity/catabolite 4-chlorophenoxypropanoic acid (4-CPP). A pilot facility was set up in a contaminated landfill site. Anaerobic groundwater was pumped up and passed through an aeration basin and subsequently through a rapid sand filter, which is characterized by a short residence time of the water in the filter. For 3 months, the degradation of DCPP, MCPP, and 4-CPP in the sand filter increased to 15 to 30% of the inlet concentration. A significant selection for natural bacterial herbicide degraders also occurred in the sand filter. Using a most-probable-number (MPN) method, we found a steady increase in the number of culturable phenoxypropionate degraders, reaching approximately 5 × 10(5) degraders per g sand by the end of the study. Using a quantitative PCR targeting the two phenoxypropionate degradation genes, rdpA and sdpA, encoding stereospecific dioxygenases, a parallel increase was observed, but with the gene copy numbers being about 2 to 3 log units higher than the MPN. In general, the sdpA gene was more abundant than the rdpA gene, and the establishment of a significant population of bacteria harboring sdpA occurred faster than the establishment of an rdpA gene-carrying population. The identities of the specific herbicide degraders in the sand filter were assessed by Illumina MiSeq sequencing of 16S rRNA genes from sand filter samples and from selected MPN plate wells. We propose a list of potential degrader bacteria involved in herbicide degradation, including representatives belonging to the Comamonadaceae and Sphingomonadales.

Development of Tools for Genetic Analysis of Phenanthrene Degradation and Nanopod Production by Delftia sp. Cs1-4

The bacterium Delftia sp. Cs1-4 produces novel extracellular structures (nanopods) in conjunction with its growth on phenanthrene. While a full genome sequence is available for strain Cs1-4, genetic tools that could be applied to study phenanthrene degradation/nanopod production have not been reported. Thus, the objectives of this study were to establish such tools, and apply them for molecular analysis of nanopod formation or phenanthrene degradation. Three types of tools were developed or validated. First, we developed a new expression system based on a strong promoter controlling expression of a surface layer protein (NpdA) from Delftia sp. Cs1-4, which was ca. 2,500-fold stronger than the widely used lactose promoter. Second, the Cre-loxP system was validated for generation of markerless, in-frame, gene deletions, and for in-frame gene insertions. The gene deletion function was applied to examine potential roles in nanopod formation of three genes (omp32, lasI, and hcp), while the gene insertion function was used for reporter gene tagging of npdA. Lastly, pMiniHimar was modified to enhance gene recovery and mutant analysis in genome-wide transposon mutagenesis. Application of the latter to strain Cs1-4, revealed several new genes with potential roles in phenanthrene degradation or npdA expression. Collectively, the availability of these tools has opened new avenues of investigation in Delftia sp. Cs1-4 and other related genera/species with importance in environmental toxicology.