Later, more holistic studies extended this discovery to the whole bacterial history and clearly demonstrated that a great part of bacterial genomes has been acquired by horizontal gene transfer (Dagan et al., 2008 Wiedenbeck & Cohan, 2011) to such an extent that it was paramount in several speciation events (De la Cruz & Davies, 2000 Gogarten & Townsend, 2005 Ochman et al., 2000). Seminal work on genome content evolution soon indicated that these variations can arise at an unexpectedly rapid pace relative to mutations (Ochman et al., 2000). One of the most striking revelations after two decades of whole bacterial genome sequencing is the great variability in gene content that closely related bacteria can exhibit (Baltrus et al., 2017 Cordero & Polz, 2014 Hyun et al., 2012 Shapiro et al., 2012 Tenaillon et al., 2010). A massive sequencing effort on environmental Lysobacteraceae is therefore required to refine our understanding of how this reservoir fuels the emergence and the spread of genes among this family and its potential impact on plant, animal and human health. Genes associated with pathogenicity or antibiotic and metal resistance were among those that most importantly structured the network, highlighting the imprints of human-mediated selective pressure on pathogenic populations. In the network, bacterial lifestyles shaped substructures of isolates colonizing specific ecological niches and harbouring specific types of resistance genes. We detected multiple plasmid–chromosome gene transfers, including the known sharing of a heavy metal resistance transposon. Most inferred plasmid gene sharing events involved a few genes only, and evidence of full plasmid transfers were restricted to taxonomically closely related taxa. While plasmid genes are openly shared between the bacteria of the family Lysobacteraceae, taxonomy strongly defined the boundaries of these exchanges, which only barely reached other families. We searched for homologues of plasmid gene sequences from this family in the entire diversity of available bacterial genome sequences and built a network of plasmid gene sharing from the results. The bacterial family Lysobacteraceae includes plant commensal, plant pathogenic and opportunistic human pathogens for which plasmid-mediated adaptation has been reported.

Network approaches are particularly suitable to represent multipartite relationships and are useful tools to characterize plasmid-mediated gene sharing events. Plasmids provide an efficient vehicle for gene sharing among bacterial populations, playing a key role in bacterial evolution.

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