Networking in microbes: conjugative elements and plasmids in the genus Alteromonas

Abstract

BackgroundTo develop evolutionary models for the free living bacterium Alteromonas the genome sequences of isolates of the genus have been extensively analyzed. However, the main genetic exchange drivers in these microbes, conjugative elements (CEs), have not been considered in detail thus far. In this work, CEs have been searched in several complete Alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. Six genomes are reported here for the first time.ResultsWe have found nine different plasmids of sizes ranging from 85 to 600 Kb, most of them were found in a single strain. Networks of gene similarity could be established among six of the plasmids that were also connected with another cluster of plasmids found in Shewanella strains. The cargo genes found in these plasmids included cassettes found before in chromosome flexible genomic islands of Alteromonas strains. We describe also the plasmids pAMCP48-600 and pAMCP49-600, the largest found in Alteromonas thus far (ca. 600 Kb) and containing all the hallmarks to be classified as chromids. We found in them some housekeeping genes and a cluster that code for an exocellular polysaccharide. They could represent the transport vectors for the previously described replacement flexible genomic islands. Integrative and conjugative elements (ICEs) were more common than plasmids and showed similar patterns of variation with cargo genes coding for components of additive flexible genomic islands. A nearly identical ICE was found in A. mediterranea MED64 and Vibrio cholera AHV1003 isolated from a human pathogen, indicating the potential exchange of these genes across phylogenetic distances exceeding the family threshold.ConclusionWe have seen evidence of how CEs can be vectors to transfer gene cassettes acquired in the chromosomal flexible genomic islands, both of the additive and replacement kind. These CEs showed evidence of how genetic material is exchanged among members of the same species but also (albeit less frequently) across genus and family barriers. These gradients of exchange frequency are probably one of the main drivers of species origin and maintenance in prokaryotes and also provide these taxa with large genetic diversity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3461-0) contains supplementary material, which is available to authorized users.

Genome Variation in the Model Halophilic Bacterium Salinibacter ruber

“…This would explain that strains of different CFs and geographical origins can share accessory genome sequences. Similar findings have been reported for different species ( López-Pérez et al, 2013 , 2017 ). Although we failed to find Integrative and Conjugative Elements (ICEs) in the plasmids, we did find some elements coding for proteins involved in integration and excision, including site-specific tyrosine recombinases (XerD) and integrases.…”

“…Although we failed to find Integrative and Conjugative Elements (ICEs) in the plasmids, we did find some elements coding for proteins involved in integration and excision, including site-specific tyrosine recombinases (XerD) and integrases. The presence of the genes comEC and comF in all S. ruber strains, suggests that transformation and transduction may provide alternative mechanisms for the transfer of plasmids, as suggested for A. macleodii ( López-Pérez et al, 2017 ). Incorporation of new genes in GIs can play a role in modulation of transcription and signal transduction ( Coleman et al, 2006 ).…”

Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii

“…1, S1). Synteny of plasmids from A. macleodii Te101 and A. mediterranea DE1 corroborates the role of plasmids for niche specialization within and across species boundaries 13,41 .…”

“…The occupation of different niches 24 , varied interactions with other organisms [25][26][27] and utilization of diverse substrates 28,29 suggests the existence of functionally distinct entities within the A. macleodii species boundary, despite being >99% identical on 16S rRNA gene level. This notion is supported by the diverse flexible genome and a high degree of genetic exchange between A. macleodii and the "sister species" A. mediterranea 13,30 . Consequently, genomic islands and mobile genetic elements are major drivers of genetic and metabolic variability within Alteromonas, influencing surface-associated vs. free-living lifestyles 31 , exopolysaccharide production 30 , heavy metal resistance 32 and polysaccharide utilization 33 .…”

“…Flexible genomic islands, located at equivalent loci in different strains of the same taxon, can provide or replace genetic information and are important factors for intraspecific heterogeneity 9,10 , for instance governing carbon utilization, siderophore production and pilus assembly 11 . These adaptive-evolutionary processes are often amplified by plasmids and other mobile genetic elements, driving horizontal gene transfer (HGT) and diversification on short time scales [12][13][14] . Bacterial adaptations can also relate to single-nucleotide exchanges via homologous recombination or mutations 15,16 .…”