The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

/pdf/analysis-of-1-000-type-strain-genomes-substantially-improves-57hicbb77a.pdf

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.

Four orange-pigmented isolates, L7-456, L7-484T, L9-479 and L9-753T, originating from surface-sterilized leaf tissues of Jatropha curcas L. cultivars were characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that all four isolates belong to the genus 
Aureimonas
. In these analyses, strain L7-484T appeared to be most closely related to 
Aureimonas ureilytica
5715S-12T (95.7 % sequence identity). The 16S rRNA gene sequences of strains L7-456, L9-479 and L9-753T were found to be identical and also shared the highest similarity with 
A. ureilytica
5715S-12T (97.5 %). Both L7-484T and L9-753T contained Q-10 and Q-9 as predominant ubiquinones and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, sulfoquinovosyldiacylglycerol and an aminophospholipid as the major polar lipids. C18 : 1ω7c and C16 : 0 were the major fatty acids. Similar to other species in the genus 
Aureimonas
, hydroxylated fatty acids (e.g. C18 : 1 2-OH) and cyclic fatty acids (C19 : 0 cyclo ω8c) were also present. The DNA G+C contents of L7-484T and L9-753T were 66.1 and 69.4 mol%, respectively. Strains L7-484T and L9-753T exhibited less than 40 % DNA–DNA hybridization both between themselves and to 
A. ureilytica
KACC 11607T. Our results support the proposal that strain L7-484T represents a novel species within the genus 
Aureimonas
, for which the name Aureimonas jatrophae sp. nov. is proposed, and that strains L9-753T, L7-456 ( = KACC 16229  = DSM 25023) and L9-479 ( = KACC 16228  = DSM 25024) represent a second novel species within the genus, for which the name Aureimonas phyllosphaerae sp. nov. is proposed. The type strains of Aureimonas jatrophae sp. nov. and Aureimonas phyllosphaerae sp. nov. are respectively L7-484T ( = KACC 16230T  = DSM 25025T) and L9-753T ( = KACC 16231T  = DSM 25026T).

Aureimonas jatrophae sp. nov. and Aureimonas phyllosphaerae sp. nov., leaf-associated bacteria isolated from Jatropha curcas L.

A Gram-stain-negative, strictly aerobic and rod-shaped motile bacterium with peritrichous flagella, designated strain LZB041T, was isolated from offshore surface seawater of the East China Sea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LZB041T formed a lineage within the family ‘
Aurantimonadaceae
’ that was distinct from the most closely related genera 
Aurantimonas
(96.0–96.4 % 16S rRNA gene sequence similarity) and 
Aureimonas
(94.5–96.0 %). Optimal growth occurred in the presence of 1–7 % (w/v) NaCl, at pH 7.0–8.0 and at 28–37 °C. Ubiquinone-10 was the predominant respiratory quinone. The major fatty acids (>10 % of total fatty acids) were C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8) and cyclo-C19 : 0ω8c. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, one unknown aminolipid, one unknown phospholipid and one unknown polar lipid. The DNA G+C content of strain LZB041T was 71.3 mol%. On the basis of polyphasic analysis, strain LZB041T is considered to represent a novel species of a new genus in the class 
Alphaproteobacteria
, for which the name Jiella aquimaris gen. nov., sp. nov. is proposed. The type strain of the type species is LZB041T ( = JCM 30119T = MCCC 1K00255T).

Jiella aquimaris gen. nov., sp. nov., isolated from offshore surface seawater

Four yellow-pigmented, Gram-stain-negative, rod-shaped bacteria, strains PP-WC-4G-234T, PP-CE-2G-454T, PP-WC-1G-202 and PP-CC-3G-650, were isolated from the phyllosphere of Galium album. The strains shared 99.7–100 % 16S rRNA gene sequence similarity but could be differentiated by genomic fingerprinting using rep- and random amplification of polymorphic DNA PCRs. Phylogenetic analysis based on the 16S rRNA gene placed the strains within the family Aurantimonadaceae with highest 16S rRNA gene sequence similarity of 97.2–97.3 % to the type strain of Aureimonas phyllosphaerae. Sequence similarities to all other Aurantimonadaceae were below 97 %. The main cellular fatty acids of the strains were C18 : 1
ω7c as the predominant fatty acid followed by C16 : 0 and summed feature 3 (C16 : 1
ω7c/C16 : 1
ω8c). The polyamine patterns of strains PP-WC-4G-234T and PP-CE-2G-454T contained sym-homospermidine as a major compound, and the major respiratory quinone was ubiquinone Q-10. Predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine, sulfoquinovosyldiacylglycerol, three unidentified phospholipids and one unidentified lipid only detectable after total lipid staining. The DNA G+C content was 66.4, 68.9, 67.4 and 70.5 mol% for strains PP-WC-4G-234T, PP-CE-2G-454T, PP-WC-1G-202 and PP-CC-3G-650, respectively. Based on phylogenetic, chemotaxonomic and phenotypic analyses we propose two novel species of the genus Aureimonas, Aureimonas galii sp. nov. with PP-WC-4G-234T (=LMG 28655T=CIP 110892T) as the type strain and Aureimonas pseudogalii sp. nov. with PP-CE-2G-454T (=LMG 29411T=CCM 8665T) as the type strain and two further strains representing the same species, PP-WC-1G-202 and PP-CC-3G-650.

Aureimonas galii sp. nov. and Aureimonas pseudogalii sp. nov. isolated from the phyllosphere of Galium album.

A temperate phage (termed AmM-1) was identified from the psychrotolerant Rhizobiales bacterium Aurantimonas sp. C5-1, which was isolated from bathypelagic water (water depth = 1,500 m) in the northwest Pacific. The AmM-1 genome is 47,800 bp in length and contains 67 coding sequences. Although phage AmM-1 morphologically belongs to the family Myoviridae, its genomic structure, particularly modular genome organization, is similar to that of lambda-type phages of Siphoviridae. Genetic and phylogenetic analyses of the structural core genes also revealed that AmM-1 has a mosaic genomic structure that includes a lambda-like head (Siphoviridae) and P2-like tail (Myoviridae). The sequences of the structural core genes of AmM-1 are distinct from those of previously characterized phage groups but similar to those of recently identified one prophage element and one phage of marine Rhizobiales bacteria: a potential prophage element in the marine psychrotolerant Aureimonas ureilytica DSM 18598 genome and the temperate phage RR-1A infecting Rhizobium radiobacter P007 isolated from deep subseafloor sediment. The mosaic genome structure of AmM-1 suggests the occurrence of genetic exchange between distinct temperate phages in marine Rhizobiales populations.

Genomic characterization of a temperate phage of the psychrotolerant deep-sea bacterium Aurantimonas sp.

Members of the genera Aurantimonas and Fulvimarina have largely been described on the basis of 16S rRNA gene sequence analyses, biochemical tests and limited chemotaxonomic data. Examination of the polar lipid compositions of members of these two genera indicated that although the patterns were similar with regards the phospholipid and amino lipid compositions, there were clear differences in the presence or absence of the glycolipid sulfoquinovosyldiacylglycerol (SQDG). This glycolipid was absent in members of the species Aurantimonas coralicida and Fulvimarina pelagi but was present in Aurantimonas altamirensis, Aurantimonas ureilytica and Aurantimonas frigidaquae. These results are also consistent with the 16S rRNA sequence-based grouping. We therefore propose that the genus Aurantimonas be divided further to reflect this additional information. Thus, it is recommended that Aurantimonas altamirensis, Aurantimonas ureilytica and Aurantimonas frigidaquae are transferred to a new genus, Aureimonas gen. nov., as Aureimonas altamirensis gen. nov., comb. nov. (type strain S21BT  = CECT 7138T  = CIP 109525T  = KCTC 22106T  = LMG 23375T  = DSM 21988T), Aureimonas ureilytica comb. nov. (type strain 5715S-12T  = KACC 11607T  = DSM 18598T  = CIP 109815T) and Aureimonas frigidaquae comb. nov. (type strain CW5T  = KCTC 12893T  = JCM 14755T  = DSM 21987T). The type species of the new genus is Aureimonas altamirensis. Additionally, emended descriptions of the genera Aurantimonas and Fulvimarina are provided.

Reclassification of Aurantimonas altamirensis (Jurado et al. 2006), Aurantimonas ureilytica (Weon et al. 2007) and Aurantimonas frigidaquae (Kim et al. 2008) as members of a new genus, Aureimonas gen. nov., as Aureimonas altamirensis gen. nov., comb. nov., Aureimonas ureilytica comb. nov. and Aureimonas frigidaquae comb. nov., and emended descriptions of the genera Aurantimonas and Fulvimarina.

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