Genomics of high molecular weight plasmids isolated from an on-farm biopurification system

Abstract

The use of biopurification systems (BPS) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. BPS environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (MGEs), which play a key role in bacterial adaptation and evolution in such environments. Here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-farm BPS. The high-throughput-sequencing of the plasmid pool yielded a total of several Mb sequence information. Assembly of the sequence data resulted in six complete replicons. Using in silico analyses we identified plasmid replication genes whose encoding proteins represent 13 different Pfam families, as well as proteins involved in plasmid conjugation, indicating a large diversity of plasmid replicons and suggesting the occurrence of horizontal gene transfer (HGT) events within the habitat analyzed. In addition, genes conferring resistance to 10 classes of antimicrobial compounds and those encoding enzymes potentially involved in pesticide and aromatic hydrocarbon degradation were found. Global analysis of the plasmid pool suggest that the analyzed BPS represents a key environment for further studies addressing the dissemination of MGEs carrying catabolic genes and pathway assembly regarding degradation capabilities.

Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP

“…In this way, according to Guglielmini et al [42] and Smillie et al [43], the presence of a MOB element in contigs 7 and 9 suggests these putative elements are mobilizable but non-conjugative. Contig 5, with 74 kb, was found to contain various integrative and conjugative elements (Table 2) [44]. Besides, this contig contained all antimicrobial resistance genes found in the genome of strain GP ( sul 1, tet (33), aad A1, qac E), as well as two copies of the sad A gene encoding for the previously described sulfonamide monooxygenase [26].…”

“…The coverage of sorted BAM files was evaluated with Qualimap v2.2.1 [117]. Genes typically associated with plasmids [44] were identified by aligning amino-acid sequences against the CDD database (v3.17) using the NCBI conserved domain search on with default settings on November, 2018 [118–120]. Conjugative elements associated with the type VI secretion systems and possible origins of replication were analyzed with CONJscan v1.0.2 using the Galaxy platform at Pasteur [40–42].…”

Targeted metagenomics demonstrates the ecological role of IS1071 in 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.…”

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

“…First, the DTR contigs were used as input to VirFinder v.1.1 with default parameters, and to CheckV to identify viral and microbial marker genes. We additionally searched for genes related to plasmids and other nonviral mobile genetic elements using a database of 141 HMMs from recent publications [57][58][59] . A contig was classified as viral if the number of viral genes exceeded that of microbial and plasmid genes (n = 99,345), or VirFinder reported a P < 0.01 with no plasmid genes and no more than one identified microbial gene (n = 36,084).…”