High diversity of Rhodobacterales in the subarctic North Atlantic Ocean and gene transfer agent protein expression in isolated strains

Abstract

Genes encoding gene transfer agent (GTA) particles are well conserved in bacteria of the order Rhodobacterales. Members of this order are abundant in diverse marine environments, frequently accounting for as much as 25% of the total bacterial community. Conservation of the genes encoding GTAs allows their use as diagnostic markers of Rhodobacterales in biogeographical studies. The first survey of the diversity of Rhodobacterales based on the GTA major capsid gene was conducted in a warm temperate estuarine ecosystem, the Chesapeake Bay, but the biogeography of Rhodobacterales has not been explored extensively. This study investigates Rhodobacterales diversity in the cold subarctic water near Newfoundland, Canada. Our results suggest that the subarctic region of the North Atlantic contains diverse Rhodobacterales communities in both winter and summer, and that the diversity of the Rhodobacterales community in the summer Newfoundland coastal water is higher than that found in the Chesapeake Bay, in either the summer or winter. Approximately one-third of GTA sequences retrieved from the subarctic waters were most closely related to those from bacteria isolated from sea ice or cold regions. Distinguishable diversity patterns were found between the temperate and subarctic waters, providing further support for niche adaptation of specific Rhodobacterales members to unique environments. We also demonstrate that a number of Rhodobacterales strains, from both the subarctic and temperate locations, express the GTA major capsid protein. This provides robust evidence that the widespread conservation of GTA genes in the Rhodobacterales may result in the production of functionally similar and active GTA systems in these bacteria in different environments.

Gene transfer agents: phage-like elements of genetic exchange

“…The presence of GTA capsid proteins has been confirmed in multiple lineages within the order Rhodobacterales, from a range of geographically separated marine environments 46 . The possibility of widespread conservation of GTA production in this particular group of bacteria is especially interesting because roseobacters (within the order Rhodobacterales) appear to account for >25% of the total bacterial and archaeal community in some marine environments 47 .…”

“…As was the case in the work on R. pomeroyi GTAs 43 , no biochemical or genetic analysis was carried out for the R. nubinhibens GTA particles, nor was there a demonstration that GTA genes are required for the observed effects. Such experiments are needed to validate the proposed role of GTAs in the extraordinarily high frequencies of gene transfer reported.The presence of GTA capsid proteins has been confirmed in multiple lineages within the order Rhodobacterales, from a range of geographically separated marine environments 46 . The possibility of widespread conservation of GTA production in this particular group of bacteria is especially interesting because roseobacters (within the order Rhodobacterales) appear to account for >25% of the total bacterial and archaeal community in some marine environments 47 .…”

Isolation and Characterization of a Psychropiezophilic Alphaproteobacterium

“…GTAs are novel virus-like elements that function in the transfer of random fragments of genomic DNA (4.5 kb for the Rhodobacter capsulatus GTA) while conferring no documented negative effects associated with transfer (i.e., cell lysis) (10,38). While the g5 phylogeny has previously been found to be congruent with the 16S rRNA phylogeny (94), a more recent study of Rhodobacterales GTAs from the subarctic North Atlantic demonstrated that using a subset of the gene sequence information does not necessarily reflect the expected phylogenetic relationships (25). Analysis of the PRT1 g5 capsid protein with 156 available Rhodobacterales g5 capsid protein sequences (see Fig.…”

Diversity of Arctic pelagic <i>Bacteria</i> with an emphasis on photoheterotrophs: a review

“…4). Two of them (phylogroups E and F) belonged to the Rhodobacterales that is one of the most common alphaproteobacterial order in polar and subpolar oceans (Fu et al, 2010;Ghiglione and Murray, 2012;Niederberger et al, 2010;Prabagaran et al, 2007;Salka et al, 2008;Selje et al, 2004). Loktanella-like puf M clones (phylotype F) dominated the libraries at both seasons, whereas proportions of Sulfitobacter-related sequences (phylogroup E) increased in winter.…”