A beige-pigmented, oxidase-positive bacterial isolate, Wesi-4T, isolated from charcoal in 2012, was examined in detail by applying a polyphasic taxonomic approach. Cells of the isolates were rod shaped and Gram-stain negative. Examination of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strains of Pseudomonas matsuisoli and Pseudomonas nosocomialis (both 97.3 %). Phylogenetic analyses on the basis of the 16S rRNA gene sequences indicated a separate position of Wesi-4T, which was confirmed by multilocus sequence analyses (MLSA) based on the three loci gyrB, rpoB and rpoD and a core genome-based phylogenetic tree. Genome sequence based comparison of Wesi-4T and the type strains of P. matsuisoli and P. nosocomialis yielded average nucleotide identity values <95 % and in silico DNA-DNA hybridization values <70 %, respectively. The polyamine pattern contains the major amines putrescine, cadaverine and spermidine. The quinone system contains predominantly ubiquinone Q-9 and in the polar lipid profile diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine are the major lipids. The fatty acid contains predominantly C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1 ω6c). In addition, physiological and biochemical tests revealed a clear phenotypic difference from P. matsuisoli. These cumulative data indicate that the isolate represents a novel species of the genus Pseudomonas for which the name Pseudomonas carbonaria sp. nov. is proposed with Wesi-4T (=DSM 110367T=CIP 111764T=CCM 9017T) as the type strain.
PalleroniNJ.
Genus I. Pseudomonas Migula 1984, 237AL. In
KriegNR,
HoltJG.
(editors) Bergey’s Manual of Systematic Bacteriology1 Baltimore: Williams & Wilkins; pp 141–199
WoeseCR,
BlanzP,
HahnCM.
What isn't a pseudomonad: the importance of nomenclature in bacterial classification. Syst Appl Microbiol1984; 5:179–195 [View Article]
OyaizuH,
KomagataK.
Grouping of Pseudomonas species on the basis of cellular fatty acid composition and the quinone system with special reference to the existence of 3-hydroxy fatty acids. J Gen Appl Microbiol1983; 29:17–40 [View Article]
YarzaP,
RichterM,
PepliesJ,
EuzebyJ,
AmannR et al. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol2008; 31:241–250 [View Article][PubMed]
StamatakisA.
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics2006; 22:2688–2690 [View Article][PubMed]
FelsensteinJ.
PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author Seattle: Department of Genome Sciences, University of Washington; 2005
CriscuoloA,
BrisseS.
AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads. Genomics2013; 102:500–506 [View Article][PubMed]
BankevichA,
NurkS,
AntipovD,
GurevichAA,
DvorkinM et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol2012; 19:455–477 [View Article][PubMed]
LindnerMS,
KollockM,
ZickmannF,
RenardBY.
Analyzing genome coverage profiles with applications to quality control in metagenomics. Bioinformatics2013; 29:1260–1267 [View Article][PubMed]
AnuratP,
DuangmalK,
SrisukN.
Pseudomonas mangiferae sp. nov., isolated from bark of mango tree in Thailand. Int J Syst Evol Microbiol2019; 69:3537–3543 [View Article][PubMed]
MinhBQ,
SchmidtHA,
ChernomorO,
SchrempfD,
WoodhamsMD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol2020; 37:1530–1534 [View Article][PubMed]
CriscuoloA.
A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies. Research Ideas and Outcomes2019; 5:e36178 [View Article]
CriscuoloA.
On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference. F1000Res2020; 9:1309 [View Article][PubMed]
RichterM,
Rosselló-MóraR.
Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A2009; 106:19126–19131 [View Article][PubMed]
KämpferP,
SteiofM,
DottW.
Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol1991; 21:227–251 [View Article][PubMed]
KämpferP.
Evaluation of the Titertek-Enterobac-Automated system (TTE-AS) for identification of members of the family Enterobacteriaceae
. Zentralbl Bakteriol1990; 273:164–172 [View Article][PubMed]
KämpferP,
KroppenstedtRM.
Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol1996; 42:989–1005 [View Article]
TindallBJ.
A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol1990; 13:128–130 [View Article]
BusseH-J,
BunkaS,
HenselA,
LubitzW.
Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Evol Microbiol1997; 47:698–708 [View Article]
AulingG,
BusseH-J,
PilzF,
WebbL,
KneifelH et al. Rapid differentiation, by polyamine analysis, of Xanthomonas strains from phytopathogenic pseudomonads and other members of the class Proteobacteria interacting with plants. Int J Syst Bacteriol1991; 41:223–228 [View Article]