Ecotype diversification of an abundant Roseobacter lineage

Abstract

The Roseobacter DC5-80-3 cluster (also known as the RCA clade) is among the most abundant bacterial lineages in temperate and polar oceans. Previous studies revealed two phylotypes within this cluster that are distinctly distributed in the Antarctic and other ocean provinces. Here, we report a nearly complete genome co-assembly of three closely related single cells co-occurring in the Antarctic, and compare it to the available genomes of the other phylotype from ocean regions where iron is more accessible but phosphorus and nitrogen are less. The Antarctic phylotype exclusively contains an operon structure consisting of a dicitrate transporter fecBCDE and an upstream regulator likely for iron uptake, whereas the other phylotype consistently carry a high-affinity phosphate pst transporter and the phoB-phoR regulatory system, a high-affinity ammonium amtB transporter, urea and taurine utilization systems. Moreover, the Antarctic phylotype uses proteorhodopsin to acquire light, whereas the other uses bacteriochlorophyll-a and the sulfur-oxidizing sox cluster for energy acquisition. This is potentially an iron-saving strategy for the Antarctic phylotype because only the latter two pathways have iron-requiring cytochromes. Therefore, the two DC5-80-3 phylotypes, while diverging by only 1.1% in their 16S rRNA genes, have evolved systematic differences in metabolism to support their distinct ecologies.

Microbial Niche Diversification in the Galápagos Archipelago and Its Response to El Niño

“…While most roseobacters have large genomes with diverse metabolic and regulatory capabilities, HTCC2255 has a relatively small genome (half the size and number of genes typical of roseobacters), and a relatively restricted set of metabolic capabilities and transcriptional regulators (Newton et al, 2010;Luo and Moran, 2014) suggestive of a more specialist, oligotrophic lifestyle (Giovannoni et al, 2014;Billerbeck et al, 2016). While most Roseobacter genomes lack photo-driven supplemental energy conservation or use aerobic anoxygenic phototrophy, HTCC2255 is one of the only Roseobacter genomes to contain a proteorhodopsin (Newton et al, 2010;Sun et al, 2017).…”

The interplay between iron limitation, light and carbon in the proteorhodopsin-containing Photobacterium angustum S14

“…Considering that Fe-limitation typically results in a decline in energy levels within the cell (Tortell et al 1999), a possible link may exist between PR-based phototrophy and the ability to enhance energy production within Fe-limited cells (Raven 2009;Marchetti et al 2012Marchetti et al , 2015Sun et al 2017;Cohen et al 2018). The formation of a proton gradient by the PR photosystem does not require Fe, while phototrophic systems containing Type I and Type II reaction centers, such as those found in oxygenic phototrophs, require Fe-containing cytochromes in order to sustain electron flow (Blankenship 2010).…”

“…The formation of a proton gradient by the PR photosystem does not require Fe, while phototrophic systems containing Type I and Type II reaction centers, such as those found in oxygenic phototrophs, require Fe-containing cytochromes in order to sustain electron flow (Blankenship 2010). The comparison of three closely related Roseobacter strains, indicated that the two strains isolated from Fe-replete regions contained a Type II reaction centre (bacteriochlorophyll complex), while the strain isolated from an environment characterised by Fe-limitation (Antarctic waters) contained a PR gene (Sun et al 2017). It was hereby suggested that the presence of a PR gene was a potential adaptation for a Roseobacter strain subjected to low Fe-concentrations.…”

Genomic comparison of Clostridium species with the potential of utilizing red algal biomass for biobutanol production

“…Genomes from strains WA and WB, together with those from 33 other bacterial strains from the Clostridium genus and an outgroup strain ( Bacillus licheniformis ATCC 14580) affiliated to the same Clostridiaceae family were analyzed to establish their phylogenetic relationship. By referring to the method from Sun et al [ 65 ], a Clostridial phylogenetic tree was finally constructed with the LG substitution matrix and the gamma model using the RAxML tool (V8.0) based on a concatenation of 10793 amino acid sites over 129 single-copy gene families shared by 36 available genomes [ 38 ] and finally demonstrated via MEGA6 [ 66 ].…”