A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data

Abstract

In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov.

Diversity, Specificity, and Phylogenetic Relationships of Endohyphal Bacteria in Fungi That Inhabit Tropical Seeds and Leaves

“…We optimized (1) taxon sampling and (2) the taxonomic breadth appropriate for obtaining maximum resolution by assessing preliminary reconstructions at the level of bacterial phylum (or at the class level for Proteobacteria) (data not shown), and by considering published phylogenetic hypotheses for focal groups (Ludwig and Klenk, 2001;Vaneechoutte et al, 2004;Kämpfer et al, 2006;Tomitani et al, 2006;Nhung et al, 2007;Williams et al, 2007Williams et al, , 2010Berrendero et al, 2011;Brady et al, 2013;Shih et al, 2013;Verma et al, 2013;Spring et al, 2015;Tank and Bryant, 2015). Overall, we generated 22 alignments that together contained 284 sequences representing EHB from our surveys.…”

DciA is an ancestral replicative helicase operator essential for bacterial replication initiation

“…Regarding these species, we cannot exclude that we missed some dciA or dnaC genes, either because of genome annotation errors or because the signatures of the proteins specified by these genes diverged enough from their consensus domain profiles to prevent their detection. Finally, we identified one order regrouping only dna[CI] and dciA -lacking organisms, the Cellvibrionales13. Whether this genetic isolation is revealing of the acquisition of another replicative helicase operator gene, different from dciA and dna[CI] is an open question that would be interesting to investigate.…”

Autochthonous Dissolved Organic Matter Drives Bacterial Community Composition during a Bloom of Filamentous Cyanobacteria

“…Many Gammaproteobacteria are known to be copiotrophic opportunists (e.g., Lauro et al, 2009;Spring et al, 2015), and capable of high growth rates (Teira et al, 2009). Some of them benefit from algae-derived organic matter (e.g., Teeling et al, 2012;Eronen-Rasimus et al, 2014) and can contribute to the decomposition of algal-derived organic matter during phytoplankton blooms (Teeling et al, 2012).…”