Mineralization of the herbicide swep by a two-strain consortium and characterization of a new amidase for hydrolyzing swep

Abstract

Background: Swep is an excellent carbamate herbicide that kills weeds by interfering with metabolic processes and inhibiting cell division at the growth point. Due to the large amount of use, swep residues in soil and water not only cause environmental pollution but also accumulate through the food chain, ultimately pose a threat to human health. This herbicide is degraded in soil mainly by microbial activity, but no studies on the biotransformation of swep have been reported. Results:In this study, a consortium consisting of two bacterial strains, Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34, was enriched from a contaminated soil sample and shown to be capable of mineralizing swep. Swep was first transformed by Comamonas sp. SWP-3 to the intermediate 3,4-dichloroaniline (3,4-DCA), after which 3,4-DCA was mineralized by Alicycliphilus sp. PH-34. An amidase gene, designated as ppa, responsible for the transformation of swep into 3,4-DCA was cloned from strain SWP-3. The expressed Ppa protein efficiently hydrolyzed swep and a number of other structural analogues, such as propanil, chlorpropham and propham. Ppa shared less than 50% identity with previously reported arylamidases and displayed maximal activity at 30 °C and pH 8.6. Gly449 and Val266 were confirmed by sequential error prone PCR to be the key catalytic sites for Ppa in the conversion of swep. Conclusions:These results provide additional microbial resources for the potential remediation of swep-contaminated sites and add new insights into the catalytic mechanism of amidase in the hydrolysis of swep.

Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates

“…Consequently, an aryl acylamidase, a deaminase, and hydroquinone 1,2-dioxygenase were proposed as enzymes potentially involved in the biodegradation pathway of APAP ( Grignet et al., 2022 ; Lee et al., 2015 ; Żur et al., 2018b ). In fact, five amidases have been shown to transform APAP to 4-AP or to a brown compound (Supplementary Table S1) ( Chen et al., 2016 ; Ko et al., 2010 ; Lee et al., 2015 ; Yun et al., 2017 ; Zhang et al., 2012 2020 2019 ). Besides, 1,2,4-trihydroxybenzene could be an intermediate of APAP degradation since it was measured in a Burkholderia sp.…”

Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates

“…A phylogenetic tree was created with the top 150 most expressed amidases in the metagenome, the uncharacterized amidases (enzymes annotated as "amidase" and whose function is not known) present in both Pseudomonas isolates, and five amidases known to degrade APAP obtained from literature and databases (Supplementary Figure S2, Supplementary Table S1). All the uncharacterized amidases from the metagenome and the Pseudomonas isolate genomes clustered together (green cluster in Supplementary Figure S2), including four amidases known to degrade paracetamol (Ko et al, 2010;Lee et al, 2015;Yun et al, 2017;Zhang et al, 2012;Zhang et al, 2020;Zhang et al, 2019). This group belongs to the Amidase Signature (AS) enzyme family [EC:3.5.1.4] characterized by a highly conserved signature region of approximately 160 amino acids that includes a canonical catalytic triad (Ser-cisSer-Lys) and a Gly/Ser-rich motif (GGSS[GS]G).…”

“…Consequently, an aryl acylamidase, a deaminase, and hydroquinone 1,2-dioxygenase were proposed as enzymes potentially involved in the biodegradation pathway of APAP (dos S. Grignet et al, 2022;Lee et al, 2015;Żur et al, 2018b). In fact, five amidases have been shown to transform APAP to 4-AP or to a brown compound (Supplementary Table S1) (Chen et al, 2016;Ko et al, 2010;Lee et al, 2015;Yun et al, 2017;Zhang et al, 2012;Zhang et al, 2020;Zhang et al, 2019). Besides, 1,2,4-trihydroxybenzene could be an intermediate of APAP degradation since it was measured in a Burkholderia sp.…”

A Path Forward: Promoting Microbial-Based Methods in the Control of Invasive Plant Species

“…Several studies have explored the role of particular microbes for biocontrol or plant protection services. However, there have only been limited investigations into field-scale investigations and utilization of a consortia approach to either control invasive plants, or benefit native plants to shift competitive outcomes when threatened with invasive plants [ 79 , 125 , 126 , 127 , 128 ]. Here, we advocate for additional research to advance sustainability and an integrated microbiological approach to help suppress invasive plant fitness as a potential additional tool for land managers.…”