PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera

Abstract

PromA plasmids are broad host range (BHR) plasmids, which are often cryptic and hence have an uncertain ecological role. We present three novel PromA γ plasmids which carry genes associated with degradation of the phenylurea herbicide linuron, two of which originated from unrelated Hydrogenophaga hosts isolated from different environments (pPBL-H3-2 and pBPS33-2), and one (pEN1) which was exogenously captured from an on-farm biopurification system (BPS). Hydrogenophaga sp. plasmid pBPS33-2 carries all three necessary gene clusters (hylA, dca, ccd) determining the three main steps for conversion of linuron to Krebs cycle intermediates, while pEN1 only determines the initial linuron hydrolysis step. Hydrogenophaga sp. plasmid pPBL-H3-2 exists as two variants, both containing ccd but with the hylA and dca gene modules interchanged between each other at exactly the same location. Linuron catabolic gene clusters that determine the same step were identical on all plasmids, encompassed in differently arranged constellations and characterized by the presence of multiple IS1071 elements. In all plasmids except pEN1, the insertion spot of the catabolic genes in the PromA γ plasmids was the same. Highly similar PromA plasmids carrying the linuron degrading gene cargo at the same insertion spot were previously identified in linuron degrading Variovorax sp. Interestingly, in both Hydrogenophaga populations not every PromA plasmid copy carries catabolic genes. The results indicate that PromA plasmids are important vehicles of linuron catabolic gene dissemination, rather than being cryptic and only important for the mobilization of other plasmids.

Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria

“…Both the IncP-1 and PromA incompatibility groups are BHR groups, but in contrast to IncP-1 plasmids very few PromA plasmids have been identified so far ( Ito and Iizuka, 1971 ; van Elsas et al, 1998 ; Schneiker et al, 2001 ; Tauch et al, 2002 ; Gstalder et al, 2003 ; Mela et al, 2008 ; Van der Auwera et al, 2009 ; Li et al, 2014 ; Dias et al, 2018 ; Yanagiya et al, 2018 ; Werner et al, 2020 ). PromA plasmids are known for their BHR and their ability to (retro)-mobilize other less or non-transmissible plasmids within the bacterial community ( van Elsas et al, 1998 ).…”

DNA-SIP and repeated isolation corroborate Variovorax as a key organism in maintaining the genetic memory for linuron biodegradation in an agricultural soil

“…In all linuron-degrading isolates, the examined catabolic genes are located on plasmids of high promiscuity, like IncP-1 and PromA, or on larger megaplasmids with unknown promiscuity (Dealtry et al 2016; Öztürk et al 2020; Werner et al 2020). On these plasmids, the linuron catabolic genes, either encoding the hydrolase, DCA dioxygenase or chlorocatechol catabolism, are always embedded in a composite transposon characterized by flanking IS1071 insertion sequences (Dunon et al 2013, 2018b).…”

“…The results for IncP-1 were less clear, but the catabolic genes might have been associated with other (conjugative) plasmids, as is the case in Variovorax sp. PBS-H4 that hosts a PromA plasmid carrying hylA and the ccd cluster and in the strain WDL1 populations that carry a megaplasmid containing hylA or the dca cluster, as well as the ccd cluster (Breugelmans et al 2007; Öztürk et al 2020; Werner et al 2020).…”

“…However, other genera also harbour linuron-degrading soil isolates. Linuron-utilizing Achromobacter and Hydrogenophaga strains were isolated from the same Halen soil, of which the Hydrogenophaga strains depend on the same gene functions as Variovorax to degrade linuron, likely acquired by horizontal gene transfer (Breugelmans et al 2007; Werner et al 2020). Recent studies have further expanded the group of soil-borne linuron degraders with the isolation of a new consortium from soil near a pesticide producing factory in China.…”

“…As such, even though a plethora of information regarding the biodegradation of linuron exists, new degraders and gene functions involved in linuron degradation are still being identified, suggesting that the in situ ecology of linuron degrading bacteria in agricultural soil is more complex than currently known. Additionally, as mentioned above, potential biases associated with the enrichment and isolation of degraders from environmental samples, question the actual role of such linuron-degrading isolates in in situ biodegradation (Dealtry et al 2016; Albers et al 2017; Werner et al 2020). This was highlighted by our recent study which suggested that cultivation might result in biased representation of in situ linuron degraders in an on-farm biopurification system (BPS) that treats pesticide contaminated wastewater.…”