Exploring the complex response to linuron of bacterial communities from biopurification systems by means of cultivation-independent methods

Abstract

On-farm biopurification systems (BPSs) treat pesticide-contaminated wastewater at farms through biodegradation and sorption processes. However, information on the microbiota involved in pesticide removal in BPSs is scarce. Here we report on the response of BPS bacterial communities to the herbicide linuron (BPS(+)) compared with the control (BPS(-)) in a microcosm experiment. Both denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of 16S rRNA gene fragments amplified from community DNA indicated shifts in the bacterial community after linuron application. Responding populations belonged to taxa that were previously reported from linuron degrading consortia cultivated from soil (Hyphomicrobiaceae, Comamonadaceae, Micrococcaceae). In addition, numerous taxa with increased relative abundance were identified that were previously not associated with linuron degradation. The relative abundance of IncP-1 korB copies increased in response to linuron application. Amplicon pyrosequencing of IncP-1 trfA genes revealed a high IncP-1 plasmid diversity and suggested that populations carrying IncP-1β plasmids increased in relative abundance. Transferable mercury resistance plasmids were exogenously captured from BPS(+)/BPS(-), and in three transconjugants from BPS(+) the gene hylA was detected. Our data suggest the existence of a multispecies linuron degrading bacterial food web and an involvement of IncP-1 plasmids in the adaptation of bacterial communities to pesticide pollution in BPSs.

Targeted metagenomics demonstrates the ecological role of IS1071in bacterial community adaptation to pesticide degradation

“…Degradation of atrazine and mineralization of linuron was shown in the BPS samples while mineralization of linuron was previously shown in the L SM A sample (Bers et al ., ), hence linking observed genotype with a community phenotype. The detection of the hylA/dca ‐genes corroborates previous observations in both L SM A and another BPS environment, either using targeted PCR, exogenous plasmid isolation or cultivation‐dependent techniques (Horemans et al ., ; Bers et al ., ; Dealtry et al ., ; Martini et al ., ). Interestingly, all three genotypes could also be linked to occurrence of the respective pesticide substrates the samples were exposed to, i.e.…”

“…The latter is often the case for xenobiotica‐degrading bacteria as the xenobioticum only represents a minor fraction of the available carbon for growth. For instance, several recent studies show no major changes in community profiles in pesticide amended environments compared to non‐amended controls unless the compound is added at unrealistic high loading rates (Sniegowski et al ., , ; Bers et al ., ; Dealtry et al ., ). A recent metagenomic analysis by Fang et al .…”

Proma Plasmids are Instrumental in the Dissemination of Linuron Catabolic Genes between Different Genera

“…Plasmid pEN1 was exogenously captured from a biopurification system material (Kortrijk, Belgium) spiked with linuron in a microcosm experiment (Dealtry et al, 2016). In brief, Pseudomonas putida KT2442 : gfp was used as a recipient strain for plasmids conferring mercury chloride resistance (20 µg mL-1).…”

“…H7 (Fan et al, 2019). The third new PromA plasmid is plasmid pEN1, which was obtained by biparental exogenous isolation from a BPS operating on a farm near Kortrijk, Belgium (Dealtry et al, 2016), selecting for mercury resistant exconjugants of the recipient strain. We compared the full sequences of three new plasmids with each other and with other previously reported PromA plasmids including those discovered in the linuron degrading Variovorax in order to deduce their evolution and the role that PromA plasmids play in the dissemination of linuron degradation genes in different genera and environments.…”

Molecular processes underlying synergistic linuron mineralization in a triple‐species bacterial consortium biofilm revealed by differential transcriptomics

“…The metabolic interaction between the three strains is further reflected in their close colocalization when grown as biofilms on linuron (Breugelmans et al., ). Conservation of species composition of linuron‐degrading consortia as suggested by the isolation of such consortia from geographically separated and physicochemically different soils (Breugelmans, D'Huys, De Mot, & Springael, ) and from molecular ecology studies (Breugelmans et al., ; Dealtry et al., ; Horemans, Bers, et al., ) underlines the ecological relevance of this multispecies bacterial organization. Although metabolic association during linuron degradation appears the major driving force of the consortium composition and functionality, we do not know whether other interactions underlie the synergistic degradation of linuron.…”