The phylogenetic relationships of multiple enterobacterial species were reconstructed based on 16S rDNA gene sequences to evaluate the robustness of this housekeeping gene in the taxonomic placement of the enteric plant pathogens Erwinia, Brenneria, Pectobacterium, and Pantoea. Four data sets were compiled, two of which consisted of previously published data. The data sets were designed in order to evaluate how 16S rDNA gene phylogenies are affected by the use of different plant pathogen accessions and varying numbers of animal pathogen and outgroup sequences. DNA data matrices were analyzed using maximum likelihood (ML) algorithms, and character support was determined by ML bootstrap and Bayesian analyses. As additional animal pathogen sequences were added to the phylogenetic analyses, taxon placement changed. Further, the phylogenies varied in their placement of the plant pathogen species, and only the genus Pantoea was monophyletic in all four trees. Finally, bootstrap and Bayesian support values were low for most of the nodes, and all nonterminal branches collapsed in strict consensus trees. Inspection of 16S rDNA nucleotide alignments revealed several highly variable blocks punctuated by regions of conserved sequence. These data suggest that 16S rDNA, while effective for both species-level and family-level phylogenetic reconstruction, may underperform for genus-level phylogenetic analyses in the Enterobacteriaceae.

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A Gram-negative, oxidase-positive, catalase-negative, facultatively anaerobic, motile, curved rodshaped bacterium, strain N384 T , was isolated from a marine sponge (Scleritoderma cyanea; phylum Porifera) collected from a depth of 795 feet (242 m) off the west coast of Curaç ao. On the basis of 16S rRNA gene sequencing, strain N384 T was shown to belong to the genus Vibrio, most closely related to Vibrio brasiliensis LMG 20546 T (98.8 % similarity), Vibrio nigripulchritudo ATCC 27043 T (98.5 %), Vibrio tubiashii ATCC 19109 T (98.6 %) and V. sinaloensis DSM 21326 T (98.2 %). The DNA G+C content of strain N384 T was 41.6 mol%. An analysis of concatenated sequences of five genes (gyrB, rpoA, pyrH, mreB and ftsZ; 4068 bp) demonstrated a clear separation between strain N384 T and its closest neighbours and clustered strain N384 T into the 'Orientalis' clade of vibrios. Phenotypically, the novel species belonged to the arginine dihydrolase-positive, lysine decarboxylase-and ornithine decarboxylase-negative (A+/L"/O") cluster. The novel species was also differentiated on the basis of fatty acid composition, specifically that the proportions of iso-C 13 : 0 , iso-C 15 : 0 , C 15 : 0 , iso-C 16 : 0 , C 16 : 0 , iso-C 17 : 0 , C 17 : 1 v8c and C 17 : 0 were significantly different from those found in V. brasiliensis and V. sinaloensis. The results of DNA-DNA hybridization, average nucleotide identity and physiological and biochemical tests further allowed differentiation of this strain from other described species of the genus Vibrio. Collectively, these findings confirm that strain N384 T represents a novel Vibrio species, for which the name Vibrio caribbeanicus sp. nov. is proposed, with the type strain N384 T (5ATCC BAA-2122 T 5DSM 23640 T ).The family Vibrionaceae is a member of the class Gammaproteobacteria and consists of the genera Vibrio, Photobacterium, Salinivibrio, Grimontia, Enterovibrio and Aliivibrio (Chimetto et al., 2011). At the time of writing, the genus Vibrio consisted of 89 species (http://www.vibriobiology.net). Some vibrios, such as Vibrio cholerae, V. parahaemolyticus and V. vulnificus, are well-known human pathogens (FDA, 2004). Generally, Vibrio species are halophilic, mesophilic and chemo-organotrophic in nature and have a facultatively fermentative metabolism (Thompson et al., 2004). Typically, vibrios are inhabitants of aquatic environments that show a remarkable degree of biodiversity, persisting in a variety of geographical locales and eukaryotic hosts, including corals, molluscs, sponges and zooplankton (Thompson et al., 2004).Sponges can maintain diverse symbiotic microbe populations that differ in composition from the microbial communities Abbreviations: ANI, average nucleotide identity; HGT, horizontal gene transfer; ILD, incongruence length difference; ML, maximum-likelihood; MLSA, multilocus sequence analysis; MP, maximum parsimony. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene, topA, ftsZ, gapA, gyrB, mreB, pyrH, recA and rpoA gene sequences derived in this study are H...

Background Elymus (Poaceae) is a large genus of polyploid species in the wheat tribe Triticeae. It is polyphyletic, exhibiting many distinct allopolyploid genome combinations, and its history might be further complicated by introgression and lineage sorting. We focus on a subset of Elymus species with a tetraploid genome complement derived from Pseudoroegneria (genome St) and Hordeum (H). We confirm the species' allopolyploidy, identify possible genome donors, and pinpoint instances of apparent introgression or incomplete lineage sorting.Methodology/Principal FindingsWe sequenced portions of three unlinked nuclear genes—phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I—from 27 individuals, representing 14 Eurasian and North American StStHH Elymus species. Elymus sequences were combined with existing data from monogenomic representatives of the tribe, and gene trees were estimated separately for each data set using maximum likelihood. Trees were examined for evidence of allopolyploidy and additional reticulate patterns. All trees confirm the StStHH genome configuration of the Elymus species. They suggest that the StStHH group originated in North America, and do not support separate North American and European origins. Our results point to North American Pseudoroegneria and Hordeum species as potential genome donors to Elymus. Diploid P. spicata is a prospective St-genome donor, though conflict among trees involving P. spicata and the Eurasian P. strigosa suggests either introgression of GBSSI sequences from P. strigosa into North American Elymus and Pseudoroegneria, or incomplete lineage sorting of ancestral GBSSI polymorphism. Diploid H. californicum and/or allotetraploid H. jubatum are possible H-genome donors; direct involvement of an allotetraploid Hordeum species would simultaneously introduce two distinct H genomes to Elymus, consistent with some of the relationships among H-genome sequences in Hordeum and Elymus.Conclusions/SignificanceComparisons among molecular phylogenetic trees confirm allopolyploidy, identify potential genome donors, and highlight cases of apparent introgression or incomplete lineage sorting. The complicated history of this group emphasizes an inherent problem with interpreting conflicts among bifurcating trees—identifying introgression and determining its direction depend on which tree is chosen as a starting point of comparison. In spite of difficulties with interpretation, differences among gene trees allow us to identify reticulate species and develop hypotheses about underlying evolutionary processes.