Updating the taxonomic toolbox: classification of Alteromonas spp. using multilocus phylogenetic analysis and MALDI-TOF mass spectrometry

Ng, Hooi Jun; Webb, Hayden K.; Crawford, Russell J.; Malherbe, François; Butt, Henry L.; Knight, Roy W.; Mikhailov, Valery V.; Ivanova, Elena P.

doi:10.1007/s10482-012-9807-y

Cited by 13 publications

(12 citation statements)

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“…Taxonomically, molecular typing using protein profiles has been useful for bacterial classification at the species and subspecies levels [ 41 , 42 ] and at the strain level, depending on the type and class of bacterial group considered [ 43 ]. In the present study, a combination of MALDI-TOF profiling, consensus mass peak lists, and Bayesian inference was used to cluster the 73 Ralstonia strains into three groups with strong branch support.…”

Section: Resultsmentioning

confidence: 99%

Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species

et al. 2016

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BackgroundThe increased availability of genome sequences has advanced the development of genomic distance methods to describe bacterial diversity. Results of these fast-evolving methods are highly correlated with those of the historically standard DNA-DNA hybridization technique. However, these genomic-based methods can be done more rapidly and less expensively and are less prone to technical and human error. They are thus a technically accessible replacement for species delineation. Here, we use several genomic comparison methods, supported by our own proteomic analyses and metabolic characterization as well as previously published DNA-DNA hybridization analyses, to differentiate members of the Ralstonia solanacearum species complex into three species. This pathogen group consists of diverse and widespread strains that cause bacterial wilt disease on many different plants.ResultsWe used three different methods to compare the complete genomes of 29 strains from the R. solanacearum species complex. In parallel we profiled the proteomes of 73 strains using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF-MS). Proteomic profiles together with genomic sequence comparisons consistently and comprehensively described the diversity of the R. solanacearum species complex. In addition, genome-driven functional phenotypic assays excitingly supported an old hypothesis (Hayward et al. (J Appl Bacteriol 69:269–80, 1990)), that closely related members of the R. solanacearum could be identified through a simple assay of anaerobic nitrate metabolism. This assay allowed us to clearly and easily differentiate phylotype II and IV strains from phylotype I and III strains. Further, genomic dissection of the pathway distinguished between proposed subspecies within the current phylotype IV. The assay revealed large scale differences in energy production within the R. solanacearum species complex, indicating coarse evolutionary distance and further supporting a repartitioning of this group into separate species.ConclusionsTogether, the results of these studies support the proposed division of the R. solanacearum species complex into three species, consistent with recent literature, and demonstrate the utility of proteomic and genomic approaches to delineate bacterial species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2413-z) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species

et al. 2016

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“…MLPA using five housekeeping genes ( dnaK , sucC , rpoB , gyrB and rpoD ) also demonstrated that strain SN2 T forms a phylogenetic lineage with A. stellipolaris LMG 21861 T and A. addita R10SW13 T with a bootstrap value of 100 % (). Sequence similarities of the concatenated sequences of the five housekeeping genes between strain SN2 T and type strains of other species of the genus Alteromonas were less than 95.0 %, which is below the recommended threshold of 98.9 % for the genus Alteromonas (Ng et al , 2013). To support the taxonomic affiliation of strain SN2 T further, a MALDI-TOF MS analysis was performed.…”

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confidence: 70%

“…A phylogenetic tree was reconstructed using the neighbor module of protdist , available in the phylip software, based on the concatenated sequences of these five genes (∼3350 bp). MALDI-TOF MS analysis of strain SN2 T and other members of the genus Alteromonas was carried out according to previously described procedures (Ng et al , 2013; Ivanova et al , 2015). A dendrogram based on the MALDI-TOF MS results was reconstructed using the MALDI Biotyper version 3.0 software package (Bruker Daltonik).…”

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confidence: 99%

Alteromonas naphthalenivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from tidal-flat sediment

Jin

Kim

Jeon

2015

International Journal of Systematic and Evolutionary Microbiology

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A Gram-staining-negative and halotolerant bacterium, designated SN2 T , capable of biodegrading polycyclic aromatic hydrocarbons, was isolated from a tidal flat contaminated with crude oil in Korea. Cells were strictly aerobic, catalase-and oxidase-positive, motile rods, with a single polar flagellum. Growth was observed at 4-37 8C (optimum, 25-30 8C) at pH 6.0-9.0 (optimum, pH 7.0-7.5) and in the presence of 0.5-9.0 % (w/v) NaCl (optimum, 2.0 %). Only ubiquinone 8 was detected as the isoprenoid quinone, and summed feature 3 (comprising C 16 : 1 v7c and/or iso-C 15 : 0 2-OH), C 16 : 0 , C 18 : 1 v7c and C 12 : 0 were observed as the major cellular fatty acids. The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, a glycolipid, an aminolipid and three unidentified lipids. The DNA G+C content was 43.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SN2 T formed a phylogenetic lineage with Alteromonas stellipolaris and Alteromonas addita within the genus Alteromonas, which was consistent with multilocus phylogenetic and MALDI-TOF MS analyses. Strain SN2 T was most closely related to the type strains of A. stellipolaris, A. addita and Alteromonas macleodii, with 16S rRNA gene sequence similarities of 99.5, 99.3 and 98.4 % and DNA-DNA relatedness of 48.7¡6.6, 24.9¡7.5 and 27.9¡8.4 %, respectively. In conclusion, strain SN2 T represents a novel species of the genus Alteromonas, for which the name Alteromonas naphthalenivorans sp. nov. is proposed. The type strain is SN2 T (5KCTC 11700BP T 5JCM 17741 T 5KACC 18427 T ).Polycyclic aromatic hydrocarbons (PAHs), including naphthalene, biphenyl, phenanthrene and pyrene, cause serious environmental concerns because of their persistence, resistance to biodegradation, toxicity, mutagenicity and carcinogenicity (Haeseler et al., 1999). PAH-degrading bacteria that play important roles in PAH biodegradation have been isolated mainly from terrestrial habitats, but they have increasingly been isolated from marine habitats (Collins et al., 1998;Geiselbrecht et al., 1998;Hedlund et al., 1999; Jeon et al., 2003;Sohn et al., 2004;Jin et al., 2012).The genus Alteromonas Baumann et al. 1972 contains phylogenetically and phenotypically diverse, Gram-negative, marine bacteria that are heterotrophic, motile rods with a single polar flagellum. Members of genus Alteromonas are distributed globally in marine environments, copiotrophic and r-strategists that dominate heterotrophic blooms (Acinas et al., 1999;García-Martínez et al., 2002;Ló pez-Ló pez et al., 2005;Vandecandelaere et al., 2008). Currently, the genus Alteromonas includes 13 species, although a number of additional species have been transferred to other genera (Parte, 2014;Matsuyama et al., 2015). Previous studies showed that some members of the genus are probably responsible for hydrocarbon biodegradation, including PAH compounds, in marine environments contaminated by crude oil spills (Cui et al., 2008;Jin et al., 2012; Gutierrez et al., 2013). Tidal flats consist of c...

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“…For DNA-DNA hybridization (DDH) experiments, high quality DNA was isolated according to the modified CTAB method detailed by the DOE Joint Genome Institute (JGI, http:// my.jgi.doe.gov/general/protocols.html) and DDH was performed according to the method described by Gonzalez and Saiz-Jimenez (2005) and Ng et al (2013). For DNA-DNA hybridization (DDH) experiments, high quality DNA was isolated according to the modified CTAB method detailed by the DOE Joint Genome Institute (JGI, http:// my.jgi.doe.gov/general/protocols.html) and DDH was performed according to the method described by Gonzalez and Saiz-Jimenez (2005) and Ng et al (2013).…”

Section: Molar % G ? C Determination and Dna-dna Hybridizationmentioning

confidence: 99%

Thalassospira australica sp. nov. isolated from sea water

Ivanova

López‐Pérez

Webb

et al. 2016

Antonie van Leeuwenhoek

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Two Gram-negative, non-pigmented, motile bacteria were isolated from a sea water sample collected at St. Kilda Beach, Port Philip Bay, Victoria, Australia. The two strains were found to grow between 4 and 40 °C, pH 5-10 and tolerate up to 10 % NaCl. A phylogenetic study, based on a 16S rRNA gene sequence analysis indicated that strains NP 3b2(T) and H 94 belong to the genus Thalassospira. The sequence similarity of the 16S rRNA gene between the two new isolates is 99.8 % and between these strains and all validly named Thalassospira species was found to be in the range of 95-99.4 %. The DNA-DNA relatedness between the two strains was found to be 80.2 %, while relatedness with other validly named species of the genus Thalassospira was between 53 and 65 %. The average nucleotide identity (ANI) and the in silico genome-to-genome distance (GGD) between the two bacteria and T. profundimaris WP0211(T), T. xiamenensis M-5(T), 'T. permensis' NBRC 106175(T) and T. lucentensis QMT2(T) was 76-82 % and 21-25 %, respectively. The results of phylogenetic and genomic analysis, together with physiological and biochemical properties, indicated that the two strains represent a new species of the genus Thalassospira. Based on these data, a new species, Thalassospira australica, is proposed with strain NP 3b2(T) (=KMM 6365(T) = JCM 31222(T)) as the type strain.

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Updating the taxonomic toolbox: classification of Alteromonas spp. using multilocus phylogenetic analysis and MALDI-TOF mass spectrometry

Cited by 13 publications

References 45 publications

Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species

Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species

Alteromonas naphthalenivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from tidal-flat sediment

Thalassospira australica sp. nov. isolated from sea water

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