Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int J Syst Evol Microbiol

Industrial Research Institute Swinburne, Swinburne University of Technology, PO Box 218, Hawthorn, Vic 3122, Australia.
International Journal of Systematic and Evolutionary Microbiology (Impact Factor: 2.51). 10/2004; 54(Pt 5):1773-88. DOI: 10.1099/ijs.0.02997-0
Source: PubMed


The phylogenetic relationships among marine Alteromonas-like bacteria of the genera Alteromonas, Pseudoalteromonas, Glaciecola, Thalassomonas, Colwellia, Idiomarina, Oceanimonas, Oceanisphaera, Shewanella, Moritella, Ferrimonas, Psychromonas and several other genera of the 'Gammaproteobacteria' were studied. Results of 16S rRNA gene sequence analyses revealed that some members of these genera formed several coherent groups at the family level. Characteristic signature oligonucleotides for studied taxa were defined. Signature positions are divided into three classes: (i) single compensatory mutations, (ii) double compensatory mutations and (iii) mutations affecting nucleotides not paired in the secondary structure. The 16S rRNA gene sequence similarity level within genera was 93 % or above. This value can be a useful additional criterion for genus discrimination. On the basis of this work and previous polyphasic taxonomic studies, the circumscription of the family Alteromonadaceae is limited to the genera Alteromonas and Glaciecola and the creation is proposed of the families Pseudoalteromonadaceae fam. nov. to accommodate bacteria of the genera Pseudoalteromonas and Algicola gen. nov. (formerly Pseudoalteromonas bacteriolytica) and Colwelliaceae fam. nov. to accommodate bacteria of the genera Colwellia and Thalassomonas. Bacteria of the genera Oceanimonas and Oceanisphaera formed a robust cluster and shared common signature oligonucleotides. Because of deep branching and lack of association with any other genus, the following families are proposed that include single genera: Idiomarinaceae fam. nov., Psychromonadaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov. and Shewanellaceae fam. nov. Finally, this study also revealed that [Hyphomicrobium] indicum should be reclassified as Photobacterium indicum comb. nov.

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Available from: Richard Christen, Nov 18, 2015
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    • "The family Shewanellaceae was established from the amended description of a group of marine Alteromonas-like bacteria (Ivanova et al. 2004a, b, c). The Shewanellaceae comprises Gram-negative, straight or curved rod-shaped, aerobic or facultative anaerobic and readily cultivated gammaproteobacteria isolated frequently in the marine environment from diverse sources, including red algae (Simidu et al. 1990), a tidal flat (Yoon et al. 2004a), seawater (Ivanova et al. 2001, 2004b; Yoon et al. 2004b), sediments (Venkateswaran et al. 1998) and marine invertebrates (Ivanova et al. 2004c). "
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    ABSTRACT: The rapid expansion of multicellular native and alien species outbreaks in aquatic and terrestrial ecosystems (bioinvasions) may produce significant impacts on bacterial community dynamics and nutrient pathways with major ecological implications. In aquatic ecosystems, bioinvasions may cause adverse effects on the water quality resulting from changes in biological, chemical and physical properties linked to significant transformations of the microbial taxonomic and functional diversity. Here we used an effective and highly sensitive experimental strategy, bypassing the efficiency bottleneck of the traditional bacterial isolation and culturing method, to identify changes of the planktonic microbial community inhabiting a marine coastal lagoon (Varano, Adriatic Sea) under the influence of an outbreak-forming alien jellyfish species. Water samples were collected from two areas that differed in their level of confinement inside in the lagoon and jellyfish densities (W, up to 12.4 medusae m-3; E, up to 0.03 medusae m-3) to conduct a snapshot microbiome analysis by a metagenomic approach. After extraction of the genetic material in the environmental water samples, we deep-sequenced metagenomic amplicons of the V5- V6 region of the 16S rRNA bacterial gene by an Illumina MiSeq platform. Experiments were carried out in triplicates, so six libraries of dual indexed amplicons of 420 bp were successfully sequenced on the MiSeq platform using a 2x250 bp paired-end sequencing strategy. Approximately 7.5 million paired-end reads (i.e. 15 million total reads) were generated, with an average of 2.5 million reads (1.25 M pairs) per sample replicate. The sequence data, analyzed through a novel bioinformatics pipeline (BioMaS), showed that the structure of the resident bacterial community was significantly affected by the occurrence of jellyfish outbreaks. Clear qualitative and quantitative differences were found between the western and eastern areas (characterized by many or few jellyfish), with 84 families, 153 genera and 324 species in the W samples, and 104 families, 199 genera and 331 species in the E samples. Significant differences between the two sampling areas were particularly detected in the occurrence of 16 families, 22 genera and 61 species of microbial taxa. This is the first time that a NGS platform has been used to screen the impact of jellyfish bioinvasions on the aquatic microbiome, providing a preliminary assessment of jellyfish-driven changes of the functional and structural microbial biodiversity.
    Full-text · Article · Nov 2014 · Biological Invasions
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    • "One Gram-negative, grayish-yellow pigmented strain of these isolates, designated MA1-3 T , is described in this study. Comparative 16S rRNA gene sequence analysis showed that the novel strain is most phylogenetically closely related to the genera Colwellia and Thalassomonas, members of the family Colwelliaceae of the Gammaproteobacteria (Ivanova et al. 2004). The genus Colwellia was created by "
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    ABSTRACT: A Gram-negative, non-spore-forming, aerobic, motile and rod-shaped or ovoid bacterial strain, designated MA1-3T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South sea in South Korea. Strain MA1-3T was found to grow optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain MA1-3T fell within the clade comprising Colwellia species, clustering coherently with the type strains of Colwellia aestuarii, Colwellia polaris and Colwellia chukchiensis, showing sequence similarity values of 97.2, 96.4 and 95.6 %, respectively. It exhibited 16S rRNA gene sequence similarity values of 93.9–96.1 % to the type strains of the other Colwellia species. Strain MA1-3T was found to contain Q-8 as the predominant ubiquinone and C16:1ω7c and/or C16:1ω6c, C16:0 and C16:1ω9c as the major fatty acids. The DNA G+C content of strain MA1-3T was determined to be 39.1 mol% and its mean DNA–DNA relatedness value with the type strain of C. aestuarii was 13 ± 5.4 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that the novel strain is separated from other Colwellia species. On the basis of the data presented, strain MA1-3T is considered to represent a novel species of the genus Colwellia, for which the name Colwellia meonggei sp. nov. is proposed. The type strain is MA1-3T (=KCTC 32380T = CECT 8302T).
    Full-text · Article · Sep 2013 · Antonie van Leeuwenhoek
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    • "and a number of reclassifications over the years (Van Landschoot and De Ley 1983; Gauthier et al. 1995; Ivanova et al. 2004a), leaving Alteromonas macleodii (Baumann et al. 1972) as the single representative species of the genus for about a decade. Recently however, the number of validly described species have recently rapidly increased, now reaching nine species (Yoon et al. 2003, 2004; Van Trappen et al. 2004; Ivanova et al. 2005b; Martínez-Checa et al. 2005; Chiu et al. 2007; Vandecandelaere et al. 2008). "
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    ABSTRACT: A non-pigmented, motile, Gram-negative bacterium designated H 17(T) was isolated from a seawater sample collected in Port Phillip Bay (the Tasman Sea, Pacific Ocean). The new organism displayed optimal growth between 4 and 37 °C, was found to be neutrophilic and slightly halophilic, tolerating salt water environments up to 10 % NaCl. Strain H 17(T) was found to be able to degrade starch and Tween 80 but unable to degrade gelatin or agar. Phosphatidylglycerol (27.7 %) and phosphatidylethanolamine (72.3 %) were found to be the only associated phospholipids. The major fatty acids identified are typical for the genus Alteromonas and include C(16:0), C(16:1)ω7, C(17:1)ω8 and C(18:1)ω7. The G+C content of the DNA was found to be 43.4 mol%. A phylogenetic study, based on the 16S rRNA gene sequence analysis and Multilocus Phylogenetic Analysis, clearly indicated that strain H 17(T) belongs to the genus Alteromonas. The DNA-DNA relatedness between strain H 17(T) and the validly named Alteromonas species was between 30.7 and 46.4 mol%. Based on these results, a new species, Alteromonas australica, is proposed. The type strain is H 17(T) (= KMM 6016(T) = CIP 109921(T)).
    Full-text · Article · Jan 2013 · Antonie van Leeuwenhoek
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