Search

A taxonomic study of 24 Gram-stain-negative rod-shaped bacteria originating from the Antarctic environment is described. Phylogenetic analysis using 16S rRNA gene sequencing differentiated isolated strains into two groups belonging to the genus Flavobacterium. Group I (n = 20) was closest to Flavobacterium aquidurens e WB 1.1-56T (98.3% 16S rRNA gene sequence similarity) while group II (n = 4) showed Flavobacterium hydatis DSM 2063T as its nearest neighbour (98.5–98.9% 16S rRNA gene sequence similarity). Despite high 16S rRNA gene sequence similarity, these two groups represented two distinct novel species as shown by phenotypic traits and low genomic relatedness assessed by rep-PCR fingerprinting, DNA-DNA hybridization and whole-genome sequencing. Common to representative strains of both groups were the presence of major menaquinone MK-6 and sym -homospermidine as the major polyamine. Common major fatty acids were C 15:0 iso, C 15:1 iso G, C 15:0 iso 3-OH, C 17:0 iso 3 OH and Summed Feature 3 (C 16:1 ω7c /C 16:1 ω6c). Strain CCM 8828T (group I) contained phosphatidylethanolamine, three unidentified lipids lacking a functional group, three unidentified aminolipids and single unidentified glycolipid in the polar lipid profile. Strain CCM 8825T (group II) contained phosphatidylethanolamine, eight unidentified lipids lacking a functional group, three unidentified aminolipids and two unidentified glycolipids in the polar lipid profile. These characteristics corresponded to characteristics of the genus Flavobacterium. The obtained results showed that the analysed strains represent novel species of the genus Flavobacterium , for which the names Flavobacterium circumlabens sp. nov. (type strain CCM 8828T = P5626T = LMG 30617T) and Flavobacterium cupreum sp. nov. (type strain CCM 8825T = P2683T = LMG 30614T) are proposed. [ABSTRACT FROM AUTHOR]

A group of thirteen bacterial strains was isolated from rock samples collected in a deglaciated northern part of James Ross Island, Antarctica. The cells were rod-shaped, Gram-stain-negative, non-motile, catalase positive, and produced moderately slimy, ultraviolet light (UVC)-irradiation-resistant and red–pink pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, extensive biotyping, fatty acid profile, chemotaxonomy analyses, and whole genome sequencing were applied in order to clarify the taxonomic position of these isolates. Phylogenetic analysis based on the 16S rRNA gene indicated that all isolates constituted a coherent group belonging to the genus Hymenobacter. The closest relatives to the representative isolate P5136T were Hymenobacter psychrophilus BZ33rT and Hymenobacter rubripertinctus CCM 8852T, exhibiting 97.53% and 97.47% 16S rRNA pairwise similarity, respectively. Average nucleotide identity calculated from the whole-genome sequencing data supported the finding that P5136T represents a distinct Hymenobacter species. The major components in fatty acid profiles were Summed Feature 3 (C 16:1 ω7c /C 16:1 ω6c), C 16:1 ω 5 c , C 15:0 iso and C 15:0 anteiso. The cellular quinone content contained unanimously menaquinone MK-6 and MK-7 (ratio 1:5.1). The predominant polar lipid was phosphatidylethanolamine, and moderate to minor amounts of two unknown polar lipids, two unknown aminolipids, one unknown glycolipid and two unknown glycophospholipids were present. The G + C content of genomic DNAs is 60.31 mol%. Based on all the obtained results, we propose a novel species for which the name Hymenobacter amundsenii sp. nov. is suggested, with the type strain P5136T (= CCM 8682T = LMG 29687T). [ABSTRACT FROM AUTHOR]

A polyphasic taxonomic approach was used to characterize the four strains P2653T, P2652, P2498, and P2647, isolated from Antarctic regolith samples. Initial genotype screening performed by PCR fingerprinting based on repetitive sequences showed that the isolates studied formed a coherent cluster separated from the other Pseudomonas species. Identification results based on 16S rRNA gene sequences showed the highest sequence similarity with Pseudomonas graminis (99.7%), which was confirmed by multilocus sequence analysis using the rpo B, rpo D, and gyr B genes. Genome sequence comparison of P2653T with the most related P. graminis type strain DSM 11363T revealed an average nucleotide identity of 92.1% and a digital DNA-DNA hybridization value of 46.6%. The major fatty acids for all Antarctic strains were C 16:0 , Summed Feature 3 (C 16:1 ω7c /C 16:1 ω6c) and Summed Feature 8 (C 18:1 ω7c /C 18:1 ω6c). The predominant respiratory quinone was Q-9, and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The regolith strains could be differentiated from related species by the absence of arginine dihydrolase, ornithine and lysine decarboxylase and by negative tyrosine hydrolysis. The results of this polyphasic study allowed the genotypic and phenotypic differentiation of four analysed strains from the closest related species, which confirmed that the strains represent a novel species within the genus Pseudomonas , for which the name Pseudomonas petrae sp. nov. is proposed with P2653T (CCM 8850T = DSM 112068T = LMG 30619T) as the type strain. [ABSTRACT FROM AUTHOR]

Nitroaromatic compounds are toxic and rather recalcitrant pollutants of water and soil. Microbial degradation of the individual nitroaromatic compounds has already been well described in the literature. However, because several compounds often occur in the environment mutually influencing each other’s degradation, further research into the biodegradation of their mixtures is still needed. We investigated the degradation of a mixture of 4-nitrophenol (4-NP) and 4-nitrotoluene (4-NT) by a mixed microbial culture immobilized in a continuously operated packed-bed reactor (PBR) and by free suspended cells in shake flasks. Each compound was at first degraded separately, then in a mixture, and their degradation characteristics were compared. When treated separately, 4-NP and 4-NT were degraded with efficiency over 99 and 95%, respectively. When in a mixture, 4-NP was still completely removed from the media but the 4-NT removal efficiency dropped by a half and remained about the same during the whole experiment regardless the increasing 4-NP concentration at the PBR inlet. The shake flask experiments corroborated our finding that 4-NP negatively influenced 4-NT degradation by competitive inhibition and also indirectly on the adaptation level. [ABSTRACT FROM PUBLISHER]

A taxonomic study was conducted on 16 bacterial strains isolated from wild Adélie penguins (Pygoscelis adeliae) from Seymour (Marambio) Island and James Ross Island. An initial screening by repetitive sequence-based PCR fingerprinting divided the strains studied into four coherent groups. Phylogenetic analysis based on 16S rRNA gene sequences assigned all groups to the genus Corynebacterium and showed that Corynebacterium glyciniphilum and Corynebacterium terpenotabidum were the closest species with 16S rRNA gene sequence similarities between 95.4 % and 96.5 %. Further examination of the strains studied with ribotyping, MALDI-TOF mass spectrometry, comprehensive biotyping and calculation of average nucleotide identity and digital DNA–DNA hybridisation values confirmed the separation of the four groups from each other and from the other Corynebacterium species. Chemotaxonomically, the four strains P5828T, P5850T, P6136T, P7210T representing the studied groups were characterised by C 16:0 and C 18:1 ω9c as the major fatty acids, by the presence of meso -diaminopimelic acid in the peptidoglycan, the presence of corynemycolic acids and a quinone system with the predominant menaquinone MK-9(H 2). The results of this study show that the strains studied represent four new species of the genus Corynebacterium , for which the names Corynebacterium antarcticum sp. nov. (type strain P5850T = CCM 8835T = LMG 30620T), Corynebacterium marambiense sp. nov. (type strain P5828T = CCM 8864T = LMG 31626T), Corynebacterium meridianum sp. nov. (type strain P6136T = CCM 8863T = LMG 31628T) and Corynebacterium pygosceleis sp. nov. (type strain P7210T = CCM 8836T = LMG 30621T) are proposed. [ABSTRACT FROM AUTHOR]

Abstract: Thirteen coagulase-negative, oxidase-negative, and novobiocin-susceptible staphylococci were isolated from human clinical specimens. The isolates were differentiated from known staphylococcal species on the basis of 16S rRNA, hsp60, rpoB, dnaJ, tuf, and gap gene sequencing, automated ribotyping, (GTG)5-PCR fingerprinting, and MALDI-TOF MS analysis. Phylogenetic analysis based on the 16S rRNA gene sequence indicated phylogenetic relatedness of the analyzed strains to Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus devriesei, and Staphylococcus lugdunensis. DNA–DNA hybridization experiments between representative strains CCM 8418T, CCM 8421T, and the closest phylogenetic neighbors confirmed that the isolates represent novel Staphylococcus species, for which the name Staphylococcus petrasii sp. nov. is proposed. Genotypic and phenotypic analyses unambiguously split the strains into two closely related subclusters. Based on the results, two novel subspecies S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov. are proposed, with type strains CCM 8418T (=CCUG 62727T) and CCM 8421T (=CCUG 62728T), respectively. [Copyright &y& Elsevier]

Abstract: A group of 212 type and reference strains deposited in the Czech Collection of Microorganisms (Brno, Czech Republic) and covering 41 Staphylococcus species comprising 21 subspecies was characterised using rep-PCR fingerprinting with the (GTG)5 primer in order to evaluate this method for identification of staphylococci. All strains were typeable using the (GTG)5 primer and generated PCR products ranging from 200 to 4500bp. Numerical analysis of the obtained fingerprints revealed (sub)species-specific clustering corresponding with the taxonomic position of analysed strains. Taxonomic position of selected strains representing the (sub)species that were distributed over multiple rep-PCR clusters was verified and confirmed by the partial rpoB gene sequencing. Staphylococcus caprae, Staphylococcus equorum, Staphylococcus sciuri, Staphylococcus piscifermentans, Staphylococcus xylosus, and Staphylococcus saprophyticus revealed heterogeneous fingerprints and each (sub)species was distributed over several clusters. However, representatives of the remaining Staphylococcus spp. were clearly separated in single (sub)species-specific clusters. These results showed rep-PCR with the (GTG)5 primer as a fast and reliable method applicable for differentiation and straightforward identification of majority of Staphylococcus spp. [ABSTRACT FROM AUTHOR]

• Four novel Massilia species from extreme environment in Antarctica. • Characteristics of their adaptation to survive in extreme conditions. • Large number of genes enabling them to compete with other bacterial species. • Genes typical for rhizosphere-colonizing bacteria suggest ancient symbiosis. • Biotechnology potential of putative genes for aromatic compounds degradation. Bacteria of the genus Massilia often colonize extreme ecosystems, however, a detailed study of the massilias from the Antarctic environment has not yet been performed. Here, sixty-four Gram-stain-negative, aerobic, motile rods isolated from different environmental samples on James Ross Island (Antarctica) were subjected to a polyphasic taxonomic study. The psychrophilic isolates exhibited slowly growing, moderately slimy colonies revealing bold pink-red pigmentation on R2A agar. The set of strains exhibited the highest 16S rRNA gene sequence similarities (99.5–99.9%) to Massilia violaceinigra B2T and Massilia atriviolacea SODT and formed several phylogenetic groups based on the analysis of gyrB and lepA genes. Phenotypic characteristics allowed four of them to be distinguished from each other and from their closest relatives. Compared to the nearest phylogenetic neighbours the set of six genome-sequenced representatives exhibited considerable phylogenetic distance at the whole-genome level. Bioinformatic analysis of the genomic sequences revealed a high number of putative genes involved in oxidative stress response, heavy-metal resistance, bacteriocin production, the presence of putative genes involved in nitrogen metabolism and auxin biosynthesis. The identification of putative genes encoding aromatic dioxygenases suggests the biotechnology potential of the strains. Based on these results four novel species and one genomospecies of the genus Massilia are described and named Massilia rubra sp. nov. (P3094T = CCM 8692T = LMG 31213T), Massilia aquatica sp. nov. (P3165T = CCM 8693T = LMG 31211T), Massilia mucilaginosa sp. nov. (P5902T = CCM 8733T = LMG 31210T), and Massilia frigida sp. nov. (P5534T = CCM 8695T = LMG 31212T). [ABSTRACT FROM AUTHOR]

Staphylococcus petrasii is recently described coagulase negative staphylococcal species and an opportunistic human pathogen, still often misidentified in clinical specimens. Four subspecies are distinguished in S. petrasii by polyphasic taxonomical analyses, however a comparative study has still not been done on the majority of isolates and their genome properties have not yet been thoroughly analysed. Here, we describe the phenotypic and genotypic characteristics of 65 isolates and the results of de novo sequencing, whole genome assembly and annotation of draft genomes of five strains. The strains were identified by MALDI-TOF mass spectrometry to the species level and the majority of the strains were identified to the subspecies level by fingerprinting methods, (GTG) 5 repetitive PCR and ribotyping. Macrorestriction profiling by pulsed-field gel electrophoresis was confirmed to be a suitable strain typing method. Comparative genomics revealed the presence of new mobile genetic elements carrying antimicrobial resistance factors such as staphylococcal cassette chromosome (SCC) mec , transposones, phage-inducible genomic islands, and plasmids. Their mosaic structure and similarity across coagulase-negative staphylococci and Staphylococcus aureus suggest the possible exchange of these elements. Numerous putative virulence factors such as adhesins, autolysins, exoenzymes, capsule formation genes, immunomodulators, the phage-associated sasX gene, and SCC-associated spermidine N-acetyltransferase gene, pseudouridine and sorbitol utilization operons might explain clinical manifestations of S. petrasii isolates. The increasing recovery of S. petrasii isolates from human clinical material, the multi-drug resistance including methicillin resistance of S. petrasii subsp. jettensis strains, and virulence factors homologous to other pathogenic staphylococci demonstrate the importance of the species in human disease. [ABSTRACT FROM AUTHOR]