The eco-evolutionary dynamics of extrachromosomal elements in environmental vibrio

Abstract

Plasmids and other extrachromosomal elements (ECEs) are recognized as key factors mediating horizontal gene transfer; however, their diversity and dynamics among ecologically structured host populations in the wild remains poorly understood. Here we take a population-genomic approach to determine carriage of different types of ECEs in a recently established model for ecologically and genetically cohesive bacterial populations, asking whether different ECE types (i) are primarily associated to host phylogeny or ecology, (ii) have distinct transfer (and loss) patterns, and (iii) display different microevolutionary dynamics. We employed two models of environmental bacterial populations: a Vibrio cholerae population isolated from a coastal brackish pond (Oyster Pond, Woods Hole, MA), and diverse co-existing Vibrio populations comprising several species from Plum Island Sound (Ipswich, MA). High frequency (>40%) of a novel filamentous phage, VCYD, was detected in a collection of 531 isolates of V. cholerae. VCYD occurs both in the host-genome integrative form (IF) and a plasmid-like replicative form (RF). The relative frequency of each form differed among isolates from portions of the pond displaying different salinities, suggesting potential impact of host habitat on the biology of bacteriophages. Using the second model, we isolated 187 ECEs from 660 isolates previously categorized into 25 different ecologically and genetically cohesive populations. We identified the following elements: 22 bacteriophages, and 24 conjugative, 38 mobilizable and 103 so-called non-transmissible ECEs. While mobilizable ECEs require co-occurring conjugative plasmids for successful transfer, non-transmissible ECEs do not encode any genes for self-transfer. We further found that ECEs were significantly enriched in free-living cells, suggesting association of ECEs with host environment. The finding of phage as a major and stable ECE component is surprising and the absence of any integrase genes suggests that these are lysogens that do not integrate into the host genome. Finally, our data show that a type of plasmids previously defined as "non-transmissible" appears to be most common among Vibrio ECEs and that they have been transferred recently and frequently among distantly related populations through mechanisms yet to be uncovered. Overall, this study suggests a dynamic mobile gene pool with high turnover among host populations.