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Peter Vandamme - One of the best experts on this subject based on the ideXlab platform.
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Draft genome and description of Orrella dioscoreae gen. nov. sp. nov., a new species of Alcaligenaceae isolated from leaf acumens of Dioscorea sansibarensis
Systematic and Applied Microbiology, 2017Co-Authors: Aurélien Carlier, Margo Cnockaert, Peter Vandamme, Linda Fehr, Leo EberlAbstract:Dioscorea sansibarensis is a monocot species of inedible yam native of tropical Africa and Madagascar. Leaves of D. sansibarensis feature prominent acumen glands that are densely colonized by bacteria. We describe here the isolation and characterization of bacteria from leaf glands of D. sansibarensis specimens obtained from various botanical gardens. Phylogenetic and phenotypic characterizations indicate that the isolates belong to a novel genus and species of the Alcaligenaceae family for which we propose the name Orrella dioscoreae gen. nov. sp. nov., with type strain LMG 29303(T) [=CIP 111009(T)]. Strains isolated from different plants show limited phylogenetic and phenotypic diversity, indicating specific and tight association of the bacteria with the host plant. The analysis of the draft genome of strain LMG 29303T reveals features consistent with a recently evolved plant-associated lifestyle
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Candidimonas nitroreducens gen. nov., sp. nov. and Candidimonas humi sp. nov., isolated from sewage sludge compost
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Ivone Vaz-moreira, Peter Vandamme, Vânia Figueira, Ana R. Lopes, Evie De Brandt, Olga C. Nunes, Célia M. ManaiaAbstract:Two bacterial strains (SC-089T and SC-092T) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 °C, at pH 7 and with 1 % (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the strains were observed to be members of the family Alcaligenaceae, but could not be identified as members of any validly described genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa, together with comparative analysis of phenotypic traits and chemotaxonomic markers, supported the proposal of a new genus within the family Alcaligenaceae, for which the name Candidimonas gen. nov. is proposed. Strains SC-089T and SC-092T, which shared 99.1 % 16S rRNA gene sequence similarity, could be differentiated at the phenotypic level, and DNA–DNA hybridization results supported their identification as representing distinct species. The names proposed for these novel species are Candidimonas nitroreducens sp. nov. (type strain, SC-089T = LMG 24812T = CCUG 55806T) and Candidimonas humi sp. nov. (type strain, SC-092T = LMG 24813T = CCUG 55807T).
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Advenella incenata gen. nov., sp. nov., a novel member of the Alcaligenaceae, isolated from various clinical samples.
International journal of systematic and evolutionary microbiology, 2005Co-Authors: Tom Coenye, Enevold Falsen, Elke Vanlaere, Emly Samyn, Peter Larsson, Peter VandammeAbstract:A polyphasic taxonomic study of 14 isolates recovered from various human and veterinary clinical samples was performed. Phenotypically these isolates shared several characteristics with members of the Alcaligenaceae and related genera. Random amplified polymorphic DNA fingerprinting and whole-cell protein analysis suggested the presence of multiple genomic groups, which was confirmed by DNA-DNA hybridization experiments. 16S rRNA gene sequence analysis indicated that these isolates were related to the genera Pelistega, Taylorella, Oligella, Pigmentiphaga, Alcaligenes, Kerstersia, Achromobacter and Bordetella and belonged to the family Alcaligenaceae. Based on the results of the present study the organisms were classified in a novel genus, Advenella gen. nov. This genus comprises one named species, Advenella incenata sp. nov. (type strain LMG 22250T=CCUG 45225T) and five currently unnamed genomic species. The DNA G+C content of members of the novel genus Advenella is between 54.0 and 57.7 mol%.
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kerstersia gyiorum gen nov sp nov a novel alcaligenes faecalis like organism isolated from human clinical samples and reclassification of alcaligenes denitrificans ruger and tan 1983 as achromobacter denitrificans comb nov
International Journal of Systematic and Evolutionary Microbiology, 2003Co-Authors: Tom Coenye, Margo Cnockaert, Jean Swings, Marc Vancanneyt, Enevold Falsen, Peter VandammeAbstract:A polyphasic taxonomic study was performed on nine isolates recovered from various human clinical samples. Phenotypically, these isolates resembled Alcaligenes faecalis. Whole-cell protein analysis distinguished two different species, and this was confirmed by DNA–DNA hybridizations. Cellular fatty acid analysis and 16S rDNA sequence analysis indicated that these isolates were related to the genera Alcaligenes, Bordetella, Achromobacter and Pigmentiphaga and belonged to the family Alcaligenaceae. On the basis of the results of this study, the organisms were classified in a novel genus, Kerstersia gen. nov. This genus comprises one species, Kerstersia gyiorum sp. nov. (type strain LMG 5906T=API 184-2-84T=CCUG 47000T), and several unnamed isolates. The DNA G+C content of members of the genus Kerstersia is between 61·5 and 62·9 mol%. On the basis of previously published DNA–DNA hybridization results and data from chemotaxonomic studies, it is proposed that Alcaligenes denitrificans Ruger and Tan 1983 be reclassified as Achromobacter denitrificans comb. nov.
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bordetella trematum sp nov isolated from wounds and ear infections in humans and reassessment of alcaligenes denitrificans ruger and tan 1983
International Journal of Systematic and Evolutionary Microbiology, 1996Co-Authors: Peter Vandamme, Karel Kersters, Bart Hoste, Marc Vancanneyt, Marc Heyndrickx, Enevold Falsen, K H HinzAbstract:Ten strains recognized on the basis of a computer-assisted numerical comparison of whole-cell protein patterns as members of a novel species belonging to the family Alcaligenaceae were examined by using an integrated phenotypic and genotypic approach. This species, for which we propose the name Bordetella trematum sp. nov., was more closely related to the type species of the genus Bordetella (Bordetella pertussis) than to the type species of the genus Alcaligenes (Alcaligenes faecalis) and had the general characteristics of members of this family (i.e., a DNA base ratio in the range from 57 to 70 mol%, a fatty acid profile characterized by high percentages of 16:0, 17:0 cyclo, and 14:0 30H, nonsaccharolytic metabolism, and several classical biochemical characteristics, including aerobic and microaerobic growth, catalase activity, assimilation of citrate, an absence of anaerobic growth, and an absence of acetylmethylcarbinol and indole production, gelatin liquefaction, and esculin hydrolysis). A reevaluation of the criteria used to classify Alcaligenes denitrificans Ruger and Tan 1983 and Achromobacter xylosoxidans Yabuuchi and Ohyama 1971 as subspecies of Alcaligenes xylosoxidans and additional evidence provided in recent studies revealed that, consistent with present standards, it is appropriate to consider these two taxa distinct species of the genus Alcaligenes.
Wriddhiman Ghosh - One of the best experts on this subject based on the ideXlab platform.
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Genome Implosion Elicits Host-Confinement in Alcaligenaceae: Evidence from the Comparative Genomics of Tetrathiobacter kashmirensis, a Pathogen in the Making
2016Co-Authors: Wriddhiman Ghosh, Ashish George, Atima Agarwal, Masrure Alam, Prosenjit Pyne, Chayan Roy, Ranadhir Chakraborty, Saikat Majumder, Sheolee Chakraborty, Subrata MajumdarAbstract:This study elucidates the genomic basis of the evolution of pathogens alongside free-living organisms within the family Alcaligenaceae of Betaproteobacteria. Towards that end, the complete genome sequence of the sulfur-chemolithoautotroph Tetrathiobacter kashmirensis WT001T was determined and compared with the soil isolate Achromobacter xylosoxidans A8 and the two pathogens Bordetella bronchiseptica RB50 and Taylorella equigenitalis MCE9. All analyses comprehensively indicated that the RB50 and MCE9 genomes were almost the subsets of A8 and WT001T, respectively. In the immediate evolutionary past Achromobacter and Bordetella shared a common ancestor, which was distinct from the other contemporary stock that gave rise to Tetrathiobacter and Taylorella. The Achromobacter-Bordetella precursor, after diverging from the family ancestor, evolved through extensive genome inflation, subsequent to which the two genera separated via differential gene losses and acquisitions. Tetrathiobacter, meanwhile, retained the core characteristics of the family ancestor, and Taylorella underwent massive genome degeneration to reach an evolutionary dead-end. Interestingly, the WT001T genome, despite its conserved architecture, had only 85 % coding density, besides which 578 out of its 4452 protein-coding sequences were found to be pseudogenized. Translational impairment of several DNA repair-recombination genes in the first place seemed to have ushered the rampant and indiscriminate frame-shift mutations across the WT001T genome. Presumably, this strain has just come out of a recent evolutionary bottleneck, representing a unique transition state where genome self
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Genome implosion elicits host-confinement in Alcaligenaceae: evidence from the comparative genomics of Tetrathiobacter kashmirensis, a pathogen in the making.
PloS one, 2013Co-Authors: Wriddhiman Ghosh, Ashish George, Atima Agarwal, Masrure Alam, Prosenjit Pyne, Chayan Roy, Ranadhir Chakraborty, Saikat Majumder, Sheolee Chakraborty, Subrata MajumdarAbstract:This study elucidates the genomic basis of the evolution of pathogens alongside free-living organisms within the family Alcaligenaceae of Betaproteobacteria. Towards that end, the complete genome sequence of the sulfur-chemolithoautotroph Tetrathiobacter kashmirensis WT001(T) was determined and compared with the soil isolate Achromobacter xylosoxidans A8 and the two pathogens Bordetella bronchiseptica RB50 and Taylorella equigenitalis MCE9. All analyses comprehensively indicated that the RB50 and MCE9 genomes were almost the subsets of A8 and WT001(T), respectively. In the immediate evolutionary past Achromobacter and Bordetella shared a common ancestor, which was distinct from the other contemporary stock that gave rise to Tetrathiobacter and Taylorella. The Achromobacter-Bordetella precursor, after diverging from the family ancestor, evolved through extensive genome inflation, subsequent to which the two genera separated via differential gene losses and acquisitions. Tetrathiobacter, meanwhile, retained the core characteristics of the family ancestor, and Taylorella underwent massive genome degeneration to reach an evolutionary dead-end. Interestingly, the WT001(T) genome, despite its conserved architecture, had only 85% coding density, besides which 578 out of its 4452 protein-coding sequences were found to be pseudogenized. Translational impairment of several DNA repair-recombination genes in the first place seemed to have ushered the rampant and indiscriminate frame-shift mutations across the WT001(T) genome. Presumably, this strain has just come out of a recent evolutionary bottleneck, representing a unique transition state where genome self-degeneration has started comprehensively but selective host-confinement has not yet set in. In the light of this evolutionary link, host-adaptation of Taylorella clearly appears to be the aftereffect of genome implosion in another member of the same bottleneck. Remarkably again, potent virulence factors were found widespread in Alcaligenaceae, corroborating which hemolytic and mammalian cell-adhering abilities were discovered in WT001(T). So, while WT001(T) relatives/derivatives in nature could be going the Taylorella way, the lineage as such was well-prepared for imminent host-confinement.
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Whole-Genome Shotgun Sequencing of the Sulfur-Oxidizing Chemoautotroph Tetrathiobacter kashmirensis
Journal of bacteriology, 2011Co-Authors: Wriddhiman Ghosh, Ashish George, Atima Agarwal, Praveen Raj, Masrure Alam, Prosenjit Pyne, Sujoy K. Das GuptaAbstract:The chemolithoautotrophic betaproteobacterium Tetrathiobacter kashmirensis belongs to the family Alcaligenaceae and is phylogenetically closely related to pathogens such as Taylorella and Bordetella species. While a complete inorganic sulfur oxidation gene cluster, soxCDYZAXWB, is present in its genome, pathogenicity islands or genes associated with virulence, disease, cellular invasion, and/or intracellular resistance are completely absent.
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conjugative type 4 secretion system of a novel large plasmid from the chemoautotroph tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae
Applied and Environmental Microbiology, 2009Co-Authors: Bomba Dam, Wriddhiman Ghosh, Sujoy Das K GuptaAbstract:The genus Tetrathiobacter includes environmentally important betaproteobacteria belonging to the family Alcaligenaceae. Members of this family inhabit diverse habitats, ranging from animals and humans to soil, sewage, and sludge. They are also metabolically diverse and include facultative chemolithotrophs, versatile heterotrophs, xenobiotic degraders, fastidious parasites, and pathogens (15). While the type species, Tetrathiobacter kashmirensis, isolated from a temperate orchard soil, has been recognized as a thiosulfate- and tetrathionate-oxidizing facultative chemolithoautotroph (11, 15), Tetrathiobacter mimigardefordensis, isolated from compost, can utilize the organic disulfide 3,3′-dithiodipropionic acid for growth (42). More recently isolated soil-dwelling strains of T. kashmirensis can detoxify selenite by reducing it to insoluble elemental red selenium (18). Strains identified as T. kashmirensis on the basis of 16S rRNA gene sequence similarity (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"EU523111","term_id":"170674436","term_text":"EU523111"}}EU523111) are allegedly involved in the biodegradation of thiodiglycol, the hydrolysis product of yperite, a highly hazardous derivative of mustard gas used in chemical weapons. In addition, bacteria isolated from a deep-sea environment and phylogenetically identified as T. kashmirensis (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"EF619402","term_id":"148751435","term_text":"EF619402"}}EF619402) have been observed to degrade alkanes. Species of Alcaligenaceae possess a wide repertoire of plasmids (21, 32), a feature pertinent to their biodegradative and biogeochemical roles in the environment. Many of these plasmids are well known for harboring genes involved in biodegradation (14, 39, 44). However, not many of them have been studied at the molecular level. In the present study, we have identified, partially sequenced, and characterized a large (∼60-kb), low-copy-number, self-transmissible, novel plasmid, designated pBTK445, from T. kashmirensis strain WGT. We have characterized the minimal replication region of this plasmid and have subsequently constructed shuttle vectors that could be used for diverse members of the Alcaligenaceae, including Tetrathiobacter. A major part of the sequenced region was found to be occupied by genes homologous to constituents of various type 4 secretion systems (T4SSs) (5-7, 9). This locus was found to be involved in the conjugal transfer function of the new plasmid. Many features of pBTK445 resemble those of IncP plasmids, but the new plasmid also possesses several characteristics distinct from those of IncP plasmids. We discuss in detail those characteristics of pBTK445 that make it an interesting model for the study of the diversity and evolution of large plasmids.
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Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae.
Applied and environmental microbiology, 2009Co-Authors: Bomba Dam, Wriddhiman Ghosh, Sujoy K. Das GuptaAbstract:Tetrathiobacter spp. and other members of the Alcaligenaceae are metabolically versatile and environmentally significant. A novel, approximately 60-kb conjugative plasmid, pBTK445, from the sulfur chemolithoautotroph Tetrathiobacter kashmirensis, was identified and characterized. This plasmid exists at a low copy number of 2 to 3 per host chromosome. The portion of pBTK445 sequenced so far ( approximately 25 kb) harbors genes putatively involved in replication, transfer functions, partition, and UV damage repair. A 1,373-bp region was identified as the minimal replicon. This region contains a repA gene encoding a protein belonging to the RPA (replication protein A) superfamily and an upstream, iteron-based oriV. A contiguous 11-gene cluster homologous to various type 4 secretion systems (T4SSs) was identified. Insertional inactivation demonstrated that this cluster is involved in the conjugative transfer functions of pBTK445, and thus, it was named the tagB (transfer-associated gene homologous to virB) locus. The core and peripheral TagB components show different phylogenetic affinities, suggesting that this system has evolved by assembling components from evolutionarily divergent T4SSs. A virD4 homolog, putatively involved in nucleoprotein transfer, is also present downstream of the tagB locus. Although pBTK445 resembles IncP plasmids in terms of its genomic organization and the presence of an IncP-specific trbM homolog, it also shows several unique features. Unlike that of IncP, the oriT of pBTK445 is located in close proximity to the oriV, and a traL homolog, which is generally present in the TraI locus of IncP, is present in pBTK445 in isolation, upstream of the tagB locus. A significant outcome of this study is the construction of conjugative shuttle vectors for Tetrathiobacter and related members of the Alkaligenaceae.
Sujoy K. Das Gupta - One of the best experts on this subject based on the ideXlab platform.
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Whole-Genome Shotgun Sequencing of the Sulfur-Oxidizing Chemoautotroph Tetrathiobacter kashmirensis
Journal of bacteriology, 2011Co-Authors: Wriddhiman Ghosh, Ashish George, Atima Agarwal, Praveen Raj, Masrure Alam, Prosenjit Pyne, Sujoy K. Das GuptaAbstract:The chemolithoautotrophic betaproteobacterium Tetrathiobacter kashmirensis belongs to the family Alcaligenaceae and is phylogenetically closely related to pathogens such as Taylorella and Bordetella species. While a complete inorganic sulfur oxidation gene cluster, soxCDYZAXWB, is present in its genome, pathogenicity islands or genes associated with virulence, disease, cellular invasion, and/or intracellular resistance are completely absent.
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Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae.
Applied and environmental microbiology, 2009Co-Authors: Bomba Dam, Wriddhiman Ghosh, Sujoy K. Das GuptaAbstract:Tetrathiobacter spp. and other members of the Alcaligenaceae are metabolically versatile and environmentally significant. A novel, approximately 60-kb conjugative plasmid, pBTK445, from the sulfur chemolithoautotroph Tetrathiobacter kashmirensis, was identified and characterized. This plasmid exists at a low copy number of 2 to 3 per host chromosome. The portion of pBTK445 sequenced so far ( approximately 25 kb) harbors genes putatively involved in replication, transfer functions, partition, and UV damage repair. A 1,373-bp region was identified as the minimal replicon. This region contains a repA gene encoding a protein belonging to the RPA (replication protein A) superfamily and an upstream, iteron-based oriV. A contiguous 11-gene cluster homologous to various type 4 secretion systems (T4SSs) was identified. Insertional inactivation demonstrated that this cluster is involved in the conjugative transfer functions of pBTK445, and thus, it was named the tagB (transfer-associated gene homologous to virB) locus. The core and peripheral TagB components show different phylogenetic affinities, suggesting that this system has evolved by assembling components from evolutionarily divergent T4SSs. A virD4 homolog, putatively involved in nucleoprotein transfer, is also present downstream of the tagB locus. Although pBTK445 resembles IncP plasmids in terms of its genomic organization and the presence of an IncP-specific trbM homolog, it also shows several unique features. Unlike that of IncP, the oriT of pBTK445 is located in close proximity to the oriV, and a traL homolog, which is generally present in the TraI locus of IncP, is present in pBTK445 in isolation, upstream of the tagB locus. A significant outcome of this study is the construction of conjugative shuttle vectors for Tetrathiobacter and related members of the Alkaligenaceae.
Enevold Falsen - One of the best experts on this subject based on the ideXlab platform.
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paenalcaligenes hominis gen nov sp nov a new member of the family Alcaligenaceae
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Peter Kämpfer, Enevold Falsen, S Langer, N Lodders, Hans-jürgen BusseAbstract:A beige-pigmented bacterium (strain CCUG 53761AT) was isolated from human blood from an 85-year-old man in Goteborg, Sweden. Comparative analysis of 16S rRNA gene sequences showed that this bacterium displayed <95 % similarity to all described species of the genera of the family Alcaligenaceae. It grouped within the radiation of the genus Alcaligenes, but showed only 93.0–94.8 % similarity to type strains of members of this genus (Alcaligenes faecalis subsp. parafaecalis, 94.8 %; Alcaligenes faecalis subsp. faecalis, 94.2 %; Alcaligenes faecalis subsp. phenolicus, 93.4 %). This discrimination was supported by chemotaxonomic differences. The polyamine pattern consisted of the predominant compound putrescine, moderate amounts of spermidine and minor to trace amounts of spermine and cadaverine; 2-hydroxyputrescine was not detectable. The quinone system was ubiquinone Q-8 with minor amounts of Q-7. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylethanolamine and moderate amounts of phosphatidylglycerol and an unknown phospholipid; minor lipids were also detected. The fatty acid profile, with large amounts of C16 : 0 and C17 : 0 cyclo and the absence of C12 : 0 2-OH as hydroxylated fatty acid, also differed significantly from those reported for Alcaligenes species. On the basis of these data, it is proposed that strain CCUG 53761AT represents a novel genus and species, for which the name Paenalcaligenes hominis gen. nov., sp. nov. is proposed. The type strain of Paenalcaligenes hominis is CCUG 53761AT =CCM 7698T.
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Paenalcaligenes hominis gen. nov., sp. nov., a new member of the family Alcaligenaceae.
International journal of systematic and evolutionary microbiology, 2009Co-Authors: P Kämpfer, Enevold Falsen, S Langer, N Lodders, H-j BusseAbstract:A beige-pigmented bacterium (strain CCUG 53761A(T)) was isolated from human blood from an 85-year-old man in Göteborg, Sweden. Comparative analysis of 16S rRNA gene sequences showed that this bacterium displayed
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Advenella incenata gen. nov., sp. nov., a novel member of the Alcaligenaceae, isolated from various clinical samples.
International journal of systematic and evolutionary microbiology, 2005Co-Authors: Tom Coenye, Enevold Falsen, Elke Vanlaere, Emly Samyn, Peter Larsson, Peter VandammeAbstract:A polyphasic taxonomic study of 14 isolates recovered from various human and veterinary clinical samples was performed. Phenotypically these isolates shared several characteristics with members of the Alcaligenaceae and related genera. Random amplified polymorphic DNA fingerprinting and whole-cell protein analysis suggested the presence of multiple genomic groups, which was confirmed by DNA-DNA hybridization experiments. 16S rRNA gene sequence analysis indicated that these isolates were related to the genera Pelistega, Taylorella, Oligella, Pigmentiphaga, Alcaligenes, Kerstersia, Achromobacter and Bordetella and belonged to the family Alcaligenaceae. Based on the results of the present study the organisms were classified in a novel genus, Advenella gen. nov. This genus comprises one named species, Advenella incenata sp. nov. (type strain LMG 22250T=CCUG 45225T) and five currently unnamed genomic species. The DNA G+C content of members of the novel genus Advenella is between 54.0 and 57.7 mol%.
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kerstersia gyiorum gen nov sp nov a novel alcaligenes faecalis like organism isolated from human clinical samples and reclassification of alcaligenes denitrificans ruger and tan 1983 as achromobacter denitrificans comb nov
International Journal of Systematic and Evolutionary Microbiology, 2003Co-Authors: Tom Coenye, Margo Cnockaert, Jean Swings, Marc Vancanneyt, Enevold Falsen, Peter VandammeAbstract:A polyphasic taxonomic study was performed on nine isolates recovered from various human clinical samples. Phenotypically, these isolates resembled Alcaligenes faecalis. Whole-cell protein analysis distinguished two different species, and this was confirmed by DNA–DNA hybridizations. Cellular fatty acid analysis and 16S rDNA sequence analysis indicated that these isolates were related to the genera Alcaligenes, Bordetella, Achromobacter and Pigmentiphaga and belonged to the family Alcaligenaceae. On the basis of the results of this study, the organisms were classified in a novel genus, Kerstersia gen. nov. This genus comprises one species, Kerstersia gyiorum sp. nov. (type strain LMG 5906T=API 184-2-84T=CCUG 47000T), and several unnamed isolates. The DNA G+C content of members of the genus Kerstersia is between 61·5 and 62·9 mol%. On the basis of previously published DNA–DNA hybridization results and data from chemotaxonomic studies, it is proposed that Alcaligenes denitrificans Ruger and Tan 1983 be reclassified as Achromobacter denitrificans comb. nov.
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bordetella trematum sp nov isolated from wounds and ear infections in humans and reassessment of alcaligenes denitrificans ruger and tan 1983
International Journal of Systematic and Evolutionary Microbiology, 1996Co-Authors: Peter Vandamme, Karel Kersters, Bart Hoste, Marc Vancanneyt, Marc Heyndrickx, Enevold Falsen, K H HinzAbstract:Ten strains recognized on the basis of a computer-assisted numerical comparison of whole-cell protein patterns as members of a novel species belonging to the family Alcaligenaceae were examined by using an integrated phenotypic and genotypic approach. This species, for which we propose the name Bordetella trematum sp. nov., was more closely related to the type species of the genus Bordetella (Bordetella pertussis) than to the type species of the genus Alcaligenes (Alcaligenes faecalis) and had the general characteristics of members of this family (i.e., a DNA base ratio in the range from 57 to 70 mol%, a fatty acid profile characterized by high percentages of 16:0, 17:0 cyclo, and 14:0 30H, nonsaccharolytic metabolism, and several classical biochemical characteristics, including aerobic and microaerobic growth, catalase activity, assimilation of citrate, an absence of anaerobic growth, and an absence of acetylmethylcarbinol and indole production, gelatin liquefaction, and esculin hydrolysis). A reevaluation of the criteria used to classify Alcaligenes denitrificans Ruger and Tan 1983 and Achromobacter xylosoxidans Yabuuchi and Ohyama 1971 as subspecies of Alcaligenes xylosoxidans and additional evidence provided in recent studies revealed that, consistent with present standards, it is appropriate to consider these two taxa distinct species of the genus Alcaligenes.
Bomba Dam - One of the best experts on this subject based on the ideXlab platform.
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conjugative type 4 secretion system of a novel large plasmid from the chemoautotroph tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae
Applied and Environmental Microbiology, 2009Co-Authors: Bomba Dam, Wriddhiman Ghosh, Sujoy Das K GuptaAbstract:The genus Tetrathiobacter includes environmentally important betaproteobacteria belonging to the family Alcaligenaceae. Members of this family inhabit diverse habitats, ranging from animals and humans to soil, sewage, and sludge. They are also metabolically diverse and include facultative chemolithotrophs, versatile heterotrophs, xenobiotic degraders, fastidious parasites, and pathogens (15). While the type species, Tetrathiobacter kashmirensis, isolated from a temperate orchard soil, has been recognized as a thiosulfate- and tetrathionate-oxidizing facultative chemolithoautotroph (11, 15), Tetrathiobacter mimigardefordensis, isolated from compost, can utilize the organic disulfide 3,3′-dithiodipropionic acid for growth (42). More recently isolated soil-dwelling strains of T. kashmirensis can detoxify selenite by reducing it to insoluble elemental red selenium (18). Strains identified as T. kashmirensis on the basis of 16S rRNA gene sequence similarity (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"EU523111","term_id":"170674436","term_text":"EU523111"}}EU523111) are allegedly involved in the biodegradation of thiodiglycol, the hydrolysis product of yperite, a highly hazardous derivative of mustard gas used in chemical weapons. In addition, bacteria isolated from a deep-sea environment and phylogenetically identified as T. kashmirensis (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"EF619402","term_id":"148751435","term_text":"EF619402"}}EF619402) have been observed to degrade alkanes. Species of Alcaligenaceae possess a wide repertoire of plasmids (21, 32), a feature pertinent to their biodegradative and biogeochemical roles in the environment. Many of these plasmids are well known for harboring genes involved in biodegradation (14, 39, 44). However, not many of them have been studied at the molecular level. In the present study, we have identified, partially sequenced, and characterized a large (∼60-kb), low-copy-number, self-transmissible, novel plasmid, designated pBTK445, from T. kashmirensis strain WGT. We have characterized the minimal replication region of this plasmid and have subsequently constructed shuttle vectors that could be used for diverse members of the Alcaligenaceae, including Tetrathiobacter. A major part of the sequenced region was found to be occupied by genes homologous to constituents of various type 4 secretion systems (T4SSs) (5-7, 9). This locus was found to be involved in the conjugal transfer function of the new plasmid. Many features of pBTK445 resemble those of IncP plasmids, but the new plasmid also possesses several characteristics distinct from those of IncP plasmids. We discuss in detail those characteristics of pBTK445 that make it an interesting model for the study of the diversity and evolution of large plasmids.
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Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae.
Applied and environmental microbiology, 2009Co-Authors: Bomba Dam, Wriddhiman Ghosh, Sujoy K. Das GuptaAbstract:Tetrathiobacter spp. and other members of the Alcaligenaceae are metabolically versatile and environmentally significant. A novel, approximately 60-kb conjugative plasmid, pBTK445, from the sulfur chemolithoautotroph Tetrathiobacter kashmirensis, was identified and characterized. This plasmid exists at a low copy number of 2 to 3 per host chromosome. The portion of pBTK445 sequenced so far ( approximately 25 kb) harbors genes putatively involved in replication, transfer functions, partition, and UV damage repair. A 1,373-bp region was identified as the minimal replicon. This region contains a repA gene encoding a protein belonging to the RPA (replication protein A) superfamily and an upstream, iteron-based oriV. A contiguous 11-gene cluster homologous to various type 4 secretion systems (T4SSs) was identified. Insertional inactivation demonstrated that this cluster is involved in the conjugative transfer functions of pBTK445, and thus, it was named the tagB (transfer-associated gene homologous to virB) locus. The core and peripheral TagB components show different phylogenetic affinities, suggesting that this system has evolved by assembling components from evolutionarily divergent T4SSs. A virD4 homolog, putatively involved in nucleoprotein transfer, is also present downstream of the tagB locus. Although pBTK445 resembles IncP plasmids in terms of its genomic organization and the presence of an IncP-specific trbM homolog, it also shows several unique features. Unlike that of IncP, the oriT of pBTK445 is located in close proximity to the oriV, and a traL homolog, which is generally present in the TraI locus of IncP, is present in pBTK445 in isolation, upstream of the tagB locus. A significant outcome of this study is the construction of conjugative shuttle vectors for Tetrathiobacter and related members of the Alkaligenaceae.
