RESUMO
Two Gram-negative, obligately aerobic, rod-shaped bacteria, strains G1-22T and G1-23T, were isolated from the phycosphere of a marine brown alga. Both strains exhibited catalase- and oxidase-positive activities. Strain G1-22T displayed optimal growth at 25 °C, pH 8.0, and 2.0-3.0% (w/v) NaCl, while strain G1-23T exhibited optimal growth at 25 °C, pH 8.0, and 4.0% NaCl. Ubiquinone-8 was identified as the sole isoprenoid quinone in both strains. As major fatty acids (> 5%), strain G1-22T contained C16â:â0, summed feature 3 (C16â:â1 ω7c and/or C16â:â1 ω6c), summed feature 8 (C18â:â1 ω7c and/or C18â:â1 ω6c), C12â:â1 3-OH, and C10â:â0 3-OH, while strain G1-23T contained C16â:â0, summed feature 3 (C16â:â1 ω7c and/or C16â:â1 ω6c), and C14â:â0. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were major polar lipids in both strains. Strains G1-22T and G1-23T had DNA G+C contents of 40.2 and 38.9 mol%, respectively. Phylogenetic analyses based on 16S rRNA and genome sequences revealed that strains G1-22T and G1-23T formed distinct phylogenetic lineages within the genera Psychrosphaera and Paraglaciecola, respectively. Strain G1-22T showed closest relatedness to Psychrosphaera ytuae MTZ26T with 97.8% 16S rRNA gene sequence similarity, 70.2% average nucleotide identity (ANI), and a 21.5% digital DNA-DNA hybridization (dDDH) value, while strain G1-23T was most closely related to Paraglaciecola aquimarina KCTC 32108T with 95.6% 16S rRNA gene sequence similarity, 74.6% ANI, and a 20.1% dDDH value. Based on phenotypic and molecular characteristics, strains G1-22T and G1-23T are proposed to represent two novel species, namely Psychrosphaera algicola sp. nov. (type strain G1-22T=KACC 22486T=JCM 34971T) and Paraglaciecola algarum sp. nov. (type strain G1-23T=KACC 22490T=JCM 34972T), respectively. Additionally, based on the comparison of whole genome sequences, it is proposed that Pseudoalteromonas elyakovii, Pseudoalteromonas flavipulchra, and Pseudoalteromonas profundi are reclassified as later heterotypic synonyms of Pseudoalteromonas distincta, Pseudoalteromonas maricaloris, and Pseudoalteromonas gelatinilytica, respectively.
Assuntos
Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano , Ácidos Graxos , Hibridização de Ácido Nucleico , Filogenia , Pseudoalteromonas , RNA Ribossômico 16S , Análise de Sequência de DNA , Ubiquinona , RNA Ribossômico 16S/genética , DNA Bacteriano/genética , Pseudoalteromonas/genética , Pseudoalteromonas/classificação , Pseudoalteromonas/isolamento & purificação , Phaeophyceae/microbiologiaRESUMO
The Pseudoalteromonas genus comprises members that have been demonstrated to play significant ecological roles and produce enzymes, natural products, and activities that are beneficial to the environment and economy. A comprehensive evaluation of the genus revealed that the genomes of several Pseudoalteromonas species are highly similar to each other, exceeding species cutoff values. This evaluation involved determining and comparing the average nucleotide identity, in silico DNA-DNA hybridization, average amino acid identity, and the difference in G + C% between Pseudoalteromonas type strains with publicly available genomes. The genome of the Pseudoalteromonas elyakovii type strain was further assessed through additional sequencing and genomic comparisons to historical sequences. These findings suggest that six Pseudoalteromonas species, namely P. mariniglutinosa, P. donghaensis, P. maricaloris, P. elyakovii, P. profundi, and P. issachenkonii, should be reclassified as later heterotypic synonyms of the following validly published species: P. haloplanktis, P. lipolytica, P. flavipulchra, P. distincta, P. gelatinilytica, and P. tetraodonis. Furthermore, two names without valid standing, 'P. telluritireducens' and 'P. spiralis', should be associated with the validly published Pseudoalteromonas species P. agarivorans and P. tetraodonis, respectively.
Assuntos
Genoma Bacteriano , Filogenia , Pseudoalteromonas , Pseudoalteromonas/genética , Pseudoalteromonas/classificação , DNA Bacteriano/genética , Composição de Bases , Análise de Sequência de DNA/métodos , Hibridização de Ácido NucleicoRESUMO
Three novel bacterial strains, FE4T, FE10T, and LA51T, which are phylogenetically affiliated to the genera Pseudoalteromonas, Vibrio, or Marinobacter, respectively, isolated from fertilized eggs and juveniles of sea cucumber Apostichopus japonicus were characterized by a genome-based taxonomical approach including multilocus sequence analysis (MLSA) combined with classical phenotypic and chemotaxonomic characterizations. A molecular network reconstructed on the basis of nucleotide sequences of four phylogenetic maker protein genes revealed that the strains FE4T, FE10T, and LA51T were closely related to Pseudoalteromonas shioyasakiensis, Vibrio lentus, and Marinobacter similis, respectively. Average nucleotide identity (ANI) comparisons against phylogenetically related species to FE4T, FE10T, and LA51T demonstrated that each newly described strain could not be identified as any previously described species within each genus showing < 95% ANI: 91.3% of FE4T against P. shioyasakiensis JCM 18891 T, 92.6% of FE10T against "V. bathopelagicus" Sal10, and 92.6% of LA51T against M. similis A3d10T, in maximum, respectively. Here, we show molecular phylogenetic, genomic, phenotypic, and chemotaxonomic features of the newly described species FE4T, FE10T, and LA51T. We also propose Pseudoalteromonas apostichopi sp. nov. with FE4T (JCM 36173 T = LMG 33143 T) as the type strain, Vibrio apostichopi sp. nov. with FE10T (JCM 36174 T = LMG 33144 T) as the type strain, and Marinobacter apostichopi sp. nov. with LA51T (JCM 36175 T = LMG 33145 T) as the type strain.
Assuntos
Marinobacter , Filogenia , Pseudoalteromonas , Stichopus , Vibrio , Pseudoalteromonas/genética , Pseudoalteromonas/isolamento & purificação , Pseudoalteromonas/classificação , Animais , Vibrio/genética , Vibrio/classificação , Vibrio/isolamento & purificação , Stichopus/microbiologia , Marinobacter/genética , Marinobacter/classificação , Marinobacter/isolamento & purificação , Larva/microbiologia , Tipagem de Sequências Multilocus , DNA Bacteriano/genética , Técnicas de Tipagem Bacteriana , RNA Ribossômico 16S/genética , Zigoto/microbiologia , Genoma Bacteriano , Ácidos Graxos/análise , Ácidos Graxos/químicaRESUMO
Three bacterial strains, named hOe-66T, hOe-124 and hOe-125, were isolated from the haemolymph of different specimens of the flat oyster Ostrea edulis collected in Concarneau bay (Finistère, France). These strains were characterized by a polyphasic approach, including (i) whole genome analyses with 16S rRNA gene sequence alignment and pangenome analysis, determination of the G+C content, average nucleotide identity (ANI), and in silico DNA-DNA hybridization (isDDH), and (ii) fatty acid methyl ester and other phenotypic analyses. Strains hOe-66T, hOe-124 and hOe-125 were closely related to both type strains Pseudoalteromonas rhizosphaerae RA15T and Pseudoalteromonas neustonica PAMC 28425T with less than 93.3% ANI and 52.3% isDDH values. Regarding their phenotypic traits, the three strains were Gram-negative, 1-2 µm rod-shaped, aerobic, motile and non-spore-forming bacteria. Cells grew optimally at 25 °C in 2.5% NaCl and at 7-8 pH. The most abundant fatty acids were summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:0 and C17:1 ω8c. The strains carried a genome average size of 4.64 Mb and a G+C content of 40.28 mol%. The genetic and phenotypic results suggested that strains hOe-66T, hOe-124 and hOe-125 belong to a new species of the genus Pseudoalteromonas. In this context, we propose the name Pseudoalteromonas ostreae sp. nov. The type strain is hOe-66T (=CECT 30303T=CIP 111911T).
Assuntos
Ostrea , Filogenia , Pseudoalteromonas , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , França , Hibridização de Ácido Nucleico , Ostrea/microbiologia , Pseudoalteromonas/classificação , Pseudoalteromonas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
Worldwide marine compound contamination by petroleum products and heavy metals is a burgeoning environmental concern. Pseudoalteromonas, prevalently distributed in marine environment, has been proven to degrade petroleum and plays an essential role in the fate of oil pollution under the combined pollution. Nevertheless, the research on the reference genes is still incomplete. Therefore, this study aims to thoroughly investigate the reference genes represented by Pseudoalteromonas sp. JSTW via whole-genome sequencing. Next-generation sequencing technology unfolded a genome of 4,026,258 bp, database including Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were utilized to annotate the genes and metabolic pathways conferring to petroleum hydrocarbon degradation. The results show that common alkane and aromatic hydrocarbon degradation genes (alkB, ligB, yqhD, and ladA), chemotaxis gene (MCP, cheA, cheB, pcaY, and pcaR), heavy-metal resistance, and biofilm genes (σ54, merC, pcoA, copB, etc.) were observed in whole-genome sequence (WGS) of JSTW, which indicated that strain JSTW could potentially cope with combined pollution. The degradation efficiency of naphthalene in 60 h by JSTW was 99% without Cu2+ and 67% with 400 mg L-1 Cu2+ . Comparative genome analysis revealed that genomes of Pseudoalteromonas lipolytica strain LEMB 39 and Pseudoalteromonas donghaensis strain HJ51 shared similarity with strain JSTW, suggesting they are also the potential degradater of petroleum hydrocarbons under combined pollution. Therefore, this study provides a WGS annotation and reveals the mechanism of response to combined pollution of Pseudoalteromonas sp. JSTW.
Assuntos
Genômica , Metais Pesados/metabolismo , Petróleo/metabolismo , Petróleo/microbiologia , Pseudoalteromonas/classificação , Pseudoalteromonas/genética , Pseudoalteromonas/isolamento & purificação , Alcanos , Biodegradação Ambiental , Biofilmes , Sequenciamento de Nucleotídeos em Larga Escala , Hidrocarbonetos , Poluição por Petróleo , Filogenia , Pseudoalteromonas/metabolismo , RNA Ribossômico 16S/genéticaRESUMO
Microbial degradation of organic matter along the vertical profile of the water column is a major process driving the carbon cycle in the ocean. Pseudoalteromonas has been identified as a dominant genus in pelagic marine environments worldwide, playing important roles in the remineralization of organic carbon. However, the current understanding of Pseudoalteromonas was mainly based on shallow water populations or cultivated species. This study analyzed for the first time the structure, activity potential and ecotypes differentiation of Pseudoalteromonas in the water column of the New Britain Trench (NBT) down to 6000 m. Analysis on diversities of the 16S rRNA gene and their transcripts showed that Pseudoalteromonas was greatly enriched in deep-sea waters and showed high activity potentials. The deep-sea Pseudoalteromonas were significantly different from their shallow-water counterparts, suggesting an obvious ecotype division along with the vertical profile. Phylogenetic analysis on the 16S rRNA gene and hsp60 gene of 219 Pseudoalteromonas strains isolated from different depths further showed that the vertical ecotype division could even occur at the strain level, which might be a result of long-term adaptation to environmental conditions at different depths. The discovered depth-specific strains provide valuable models for further studies on adaptation, evolution and functions of the deep-sea Pseudoalteromonas.
Assuntos
Ecótipo , Pseudoalteromonas/isolamento & purificação , Água do Mar/microbiologia , DNA Bacteriano/genética , Filogenia , Pseudoalteromonas/classificação , Pseudoalteromonas/genética , Pseudoalteromonas/metabolismo , RNA Ribossômico 16S/genética , Água do Mar/análise , Reino UnidoRESUMO
Novel antimicrobials are urgently needed due to the rapid spread of antibiotic resistant bacteria. In a genome-wide analysis of Pseudoalteromonas strains, one strain (S4498) was noticed due to its potent antibiotic activity. It did not produce the yellow antimicrobial pigment bromoalterochromide, which was produced by several related type strains with which it shared less than 95% average nucleotide identity. Also, it produced a sweet-smelling volatile not observed from other strains. Mining the genome of strain S4498 using the secondary metabolite prediction tool antiSMASH led to eight biosynthetic gene clusters with no homology to known compounds, and synteny analyses revealed that the yellow pigment bromoalterochromide was likely lost during evolution. Metabolome profiling of strain S4498 using HPLC-HRMS analyses revealed marked differences to the type strains. In particular, a series of quinolones known as pseudanes were identified and verified by NMR. The characteristic odor of the strain was linked to the pseudanes. The highly halogenated compound tetrabromopyrrole was detected as the major antibacterial component by bioassay-guided fractionation. Taken together, the polyphasic analysis demonstrates that strain S4498 belongs to a novel species within the genus Pseudoalteromonas, and we propose the name Pseudoalteromonas galatheae sp. nov. (type strain S4498T = NCIMB 15250T = LMG 31599T).
Assuntos
4-Quinolonas/metabolismo , Anti-Infecciosos/metabolismo , Pseudoalteromonas/metabolismo , Pseudomonas/metabolismo , Pirróis/metabolismo , Cromatografia Líquida de Alta Pressão , DNA Bacteriano/genética , Genes Bacterianos , Biologia Marinha , Espectrometria de Massas , Hibridização de Ácido Nucleico , Filogenia , Pseudoalteromonas/classificação , Pseudoalteromonas/genéticaRESUMO
A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated JBTF-M23T, was isolated from tidal flat sediment collected from the Yellow Sea, Republic of Korea. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M23T fell within the clade comprising the type strains of Pseudoalteromonas species, clustering with the type strains of P. byunsanensis and P. amylolytica. Strain JBTF-M23T exhibited the highest 16S rRNA gene sequence similarity value (98.6â%) to the type strain of P. rubra and sequence similarities of 98.3 and 97.7â% to the type strains of P. byunsanensis and P. amylolytica, respectively. The DNA G+C content of strain JBTF-M23T from genomic sequence data was 41.98â%. The ANI and dDDH values between strain JBTF-M23T and the type strains of P. rubra, P. byunsanensis and P. amylolytica were 71.3-76.6 and 19.4-19.9â%, respectively. Strain JBTF-M23T contained Q-8 as the predominant ubiquinone and C16â:â1 ω7c and/or C16â:â1 ω6c, C16â:â0 and C18â:â1 ω7c as the major fatty acids. The major polar lipids of strain JBTF-M23T were phosphatidylethanolamine and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M23T is separated from recognized Pseudoalteromonas species. On the basis of the data presented, strain JBTF-M23Tis considered to represent a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas caenipelagi sp. nov. is proposed. The type strain is JBTF-M23T(=KACC 19900T=NBRC 113647T).
Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Pseudoalteromonas/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfatidiletanolaminas/química , Pseudoalteromonas/isolamento & purificação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/químicaRESUMO
Strain RA15T was isolated from the rhizosphere of the halophyte plant Arthrocnemum macrostachyum growing in the Odiel marshes (Huelva, Spain). RA15T cells were Gram stain-negative, non-spore-forming, aerobic rods and formed cream-coloured, opaque, mucoid, viscous, convex, irregular colonies with an undulate margin. Optimal growth conditions were observed on tryptic soy agar (TSA) plates supplemented with 2.5â% NaCl (w/v) at pH 7.0 and 28 °C, although it was able to grow at 4-32 °C and at pH values of 5.0-9.0. The NaCl tolerance range was from 0 to 15â%. The major respiratory quinone was Q8 but Q9 was also present. The most abundant fatty acids were summed feature 3 (C16â:â1 ω7c and/or C16â:â1 ω6c), C17â:â1 ω8c and C16â:â0. The polar lipids profile comprised phosphatidylglycerol and phosphatidylethanolamine as the most abundant representatives. Phylogenetic analyses confirmed the well-supported affiliation of strain RA15T within the genus Pseudoalteromonas, close to the type strains of Pseudoalteromonas neustonica, Pseudoalteromonas prydzensis and Pseudoalteromonas mariniglutinosa. Results of comparative phylogenetic and phenotypic studies between strain RA15T and its closest related species suggest that RA15T could be a new representative of the genus Pseudoalteromonas, for which the name Pseudoalteromonas rhizosphaerae sp. nov. is proposed. The type strain is RA15T (=CECT 9079T=LMG 29860T). The whole genome has 5.3 Mb and the G+C content is 40.4âmol%.
Assuntos
Biodegradação Ambiental , Chenopodiaceae/microbiologia , Filogenia , Pseudoalteromonas/classificação , Rizosfera , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , Pseudoalteromonas/isolamento & purificação , RNA Ribossômico 16S/genética , Plantas Tolerantes a Sal/microbiologia , Análise de Sequência de DNA , Espanha , Ubiquinona/química , Áreas AlagadasRESUMO
An agar-degrading Antarctic bacterium was isolated and identified as Pseudoalteromonas sp. NJ21. This strain showed strong agarolytic activity and could use agar as the sole carbon source for growth. A novel ß-agarase gene aga3463 was cloned and identified from the genomic library of Pseudoalteromonas sp. NJ21. It was predicted to encode a peptide of 366 amino acids, including a 21-amino-acid signal peptide. BLAST analysis revealed the deduced amino acid sequence of aga3463 shared less than 36% similarity with any characterized agarase, and phylogenetic analysis showed it belonged to the glycoside hydrolase GH86 family. The recombinant Aga3463 protein had optimal temperature and pH of 50⯰C and 7.0, respectively, and retained more than 60% activity from 10 to 50⯰C. The metal ions Cd2+, Ca2+, Fe3+, and Mn2+ increased Aga3463 activity, whereas Cu2+, Si2+, Fe2+, and Ni2+ decreased Aga3463 activity. Notably, Aga3463 exhibited good thermostability in the presence of Ca2+; however, Ca2+ was not necessary for its catalytic activity. The Km and Vmax values for Aga3463 were 6.17â¯mg/ml and 557â¯U/mg, respectively. Thin layer chromatography, liquid chromatography-mass spectrometry, nuclear magnetic resonance spectroscopy, and enzyme assay using p-nitrophenyl-α/ß-d-galactopyranoside revealed Aga3463 as an exo-type ß-agarase with the ability to degrade agarose to neoagarobiose as the major end product.
Assuntos
Fenômenos Químicos , Glicosídeo Hidrolases/química , Pseudoalteromonas/química , Pseudoalteromonas/enzimologia , Sequência de Aminoácidos , Regiões Antárticas , Cromatografia Líquida , Clonagem Molecular , Dissacarídeos , Expressão Gênica , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/isolamento & purificação , Glicosídeo Hidrolases/metabolismo , Cinética , Espectrometria de Massas , Filogenia , Pseudoalteromonas/classificação , Pseudoalteromonas/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Análise de Sequência de DNA , Especificidade por SubstratoRESUMO
The production of pentabromopseudilin and related brominated compounds by Pseudoalteromonas spp. has recently been linked to the bmp biosynthetic gene cluster. This study explored the distribution and evolutionary history of this gene cluster in the genus Pseudoalteromonas. A phylogeny of the genus revealed numerous clades that do not contain type strains, suggesting considerable species level diversity has yet to be described. Comparative genomics revealed four distinct versions of the gene cluster distributed among 19 of the 101 Pseudoalteromonas genomes examined. These were largely localized to the least inclusive clades containing the Pseudoalteromonas luteoviolacea and Pseudoalteromonas phenolica type strains and show clear evidence of gene and gene cluster loss in certain lineages. Bmp gene phylogeny is largely congruent with the Pseudoalteromonas species phylogeny, suggesting vertical inheritance within the genus. However, the gene cluster is found in three different genomic environments suggesting either chromosomal rearrangement or multiple acquisition events. Bmp conservation within certain lineages suggests the encoded products are highly relevant to the ecology of these bacteria.
Assuntos
Proteínas de Bactérias/genética , Família Multigênica , Pseudoalteromonas/genética , Proteínas de Bactérias/metabolismo , Genoma Bacteriano , Genômica , Filogenia , Pseudoalteromonas/classificação , Pseudoalteromonas/isolamento & purificação , Pseudoalteromonas/metabolismo , Pirróis/química , Pirróis/metabolismoRESUMO
A gene (aga0917) encoding a putative ß-agarase was identified from the genome of Pseudoalteromonas fuliginea YTW1-15-1. The nucleotide sequence analysis revealed that aga0917 had significant homology to the agarase genes of the GH16 family. aga0917 encodes a putative protein of 290 amino acids with an estimated molecular mass of 32.5 kDa, including a 21-amino acid signal peptide. A gene fragment encoding only the putative mature form of Aga0917 (269 amino acids) was overexpressed in Escherichia coli BL21 (DE3) pLysS as a 6 × histine-tagged fusion protein (rmAga0917). The Km, Vmax, and kcat for agarose of rmAga0917 were 39.6 mg/mL, 334 (U/mg) of protein, and 178 (1/s), respectively. According to the results of thin-layer chromatography and mass spectrometry analysis, the main end product from agarose with rmAga0917 was neoagarotetraose, in addition to a small amount of neoagarobiose. Notably, the recombinant protein rmAga0917 showed optimum activity at 60°C and retained approximately 100% agarolytic activity after being kept at 40°C for 1 h and 57% residual activity after incubation at 50°C for 1 h. The rmAga0917 exhibited maximum agarase activity at pH 6.0, and retained more than 80% of activity after incubation over a range of pH 4.0-9.0 for 1 h at 4°C.
Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Expressão Gênica , Glicosídeo Hidrolases/química , Glicosídeo Hidrolases/genética , Pseudoalteromonas/enzimologia , Proteínas de Bactérias/metabolismo , Clonagem Molecular , Escherichia coli/enzimologia , Escherichia coli/genética , Glicosídeo Hidrolases/metabolismo , Concentração de Íons de Hidrogênio , Cinética , Peso Molecular , Sinais Direcionadores de Proteínas , Pseudoalteromonas/classificação , Pseudoalteromonas/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Sefarose/metabolismo , TemperaturaRESUMO
Pseudoalteromonas is a genus of marine bacteria often found in association with other organisms. Although several studies have examined Pseudoalteromonas diversity and their antimicrobial activity, its diversity in tropical environments is largely unexplored. We investigated the diversity of Pseudoalteromonas in marine environments of Panama using a multilocus phylogenetic approach. Furthermore we tested their antimicrobial capacity and evaluated the effect of recombination and mutation in shaping their phylogenetic relationships. The reconstruction of clonal relationships among 78 strains including 15 reference Pseudoalteromonas species revealed 43 clonal lineages, divided in pigmented and non-pigmented strains. In total, 39 strains displayed moderate to high activity against Gram-positive and Gram-negative bacteria and fungi. Linkage disequilibrium analyses showed that the Pseudoalteromonas strains of Panama have a highly clonal structure and that, although present, recombination is not frequent enough to break the association among alleles. This clonal structure is in contrast to the high rates of recombination generally reported for aquatic and marine bacteria. We propose that this structure is likely due to the symbiotic association with marine invertebrates of most strains analyzed. Our results also show that there are several putative new species of Pseudoalteromonas in Panama to be described.
Assuntos
Anti-Infecciosos/metabolismo , Biodiversidade , Filogenia , Pseudoalteromonas/classificação , Pseudoalteromonas/genética , Água do Mar/microbiologia , Anti-Infecciosos/farmacologia , Análise por Conglomerados , DNA Bacteriano/genética , Genoma Bacteriano/genética , Desequilíbrio de Ligação , Panamá , Pseudoalteromonas/metabolismo , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
A Gram-stain-negative, motile, rod-shaped bacterium designated OCN003T was cultivated from mucus taken from a diseased colony of the coral Montipora capitata in Kane'ohe Bay, O'ahu, Hawai'i. Colonies of OCN003T were pale yellow, 1-3 mm in diameter, convex, smooth and entire. The strain was heterotrophic, strictly aerobic and strictly halophilic. Cells of OCN003T produced buds on peritrichous prosthecae. Growth occurred within the pH range of 5.5 to 10, and the temperature range of 14 to 39 °C. Major fatty acids were 16â:â1ω7c, 16â:â0, 18â:â1ω7c, 17â:â1ω8c, 12â:â0 3-OH and 17â:â0. Phylogenetic analysis of 1399 nucleotides of the 16S rRNA gene nucleotide sequence and a multi-locus sequence analysis of three genes placed OCN003T in the genus Pseudoalteromonas and indicated that the nearest relatives described are Pseudoalteromonas spongiae, P. luteoviolacea, P. ruthenica and P. phenolica(97-99â% sequence identity). The DNA G+C content of the strain's genome was 40.0 mol%. Based on in silico DNA-DNA hybridization and phenotypic differences from related type strains, we propose that OCN003T represents the type strain of a novel species in the genus Pseudoalteromonas, proposed as Pseudoalteromonas piratica sp. nov. OCN003T (=CCOS1042T=CIP 111189T). An emended description of the genus Pseudoalteromonas is presented.
Assuntos
Antozoários/microbiologia , Filogenia , Pseudoalteromonas/classificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Havaí , Processos Heterotróficos , Hibridização de Ácido Nucleico , Pigmentação , Pseudoalteromonas/genética , Pseudoalteromonas/isolamento & purificação , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Análise de Sequência de DNARESUMO
Strains JW1T and JW3, isolated from surface seawater of the Arabian Sea, were subjected to polyphasic taxonomic analysis. Cells of both strains were Gram-stain-negative, aerobic, and rod-shaped. They formed violet pigment and produced violacein. On the basis of 16S rRNA gene sequence analysis, strains JW1T and JW3 showed high 16S rRNA gene sequence similarity with Pseudoalteromonas byunsanensis JCM12483T (98.2%), P. shioyasakiensis SE3T (97.8%), P. arabiensis JCM 17292T (97.3%), and P. gelatinilytica NH153T (97.1%). The 16S rRNA gene sequence similarity between JW1T and JW3 was 100%. Phylogenetic analyses revealed that both strains fell within the cluster of the genus Pseudoalteromonas and represented an independent lineage. The average nucleotide identity and in silico DNA-DNA hybridization values between JW1T and type strains of the closely related Pseudoalteromonas species were 70.9-83.3% and 20.0-26.4%, respectively. The sole respiratory quinone in both strains is ubiquinone 8 (Q-8). The principal fatty acids are summed feature 3 (C16:1ω7c and/or iso-C15:0 2OH), C18:1ω7c, and C16:0. The major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, one unidentified glycolipid, one unidentified aminolipid, and one unidentified phospholipid. The DNA G+C content was 43.3 mol%. Differential phylogenetic distinctiveness, chemotaxonomic differences, and phenotypic properties indicated that strains JW1T and JW3 could be differentiated from the Pseudoalteromonas species with validly published names. Therefore, it is proposed that strains JW1T and JW3 represent a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas amylolytica sp. nov. (type strain, JW1T = CGMCC 1.15681T = KCTC 52406T = MCCC 1K02162T) is proposed.
Assuntos
Genômica , Indóis/metabolismo , Pseudoalteromonas/genética , Pseudoalteromonas/fisiologia , Água do Mar/microbiologia , Simulação por Computador , DNA Bacteriano/genética , Fenótipo , Filogenia , Pseudoalteromonas/classificação , Pseudoalteromonas/metabolismo , RNA Ribossômico 16S/genéticaRESUMO
Pseudoalteromonas sp. 520P1 (hereafter referred to as strain 520P1) produces N-acylhomoserine lactones (AHLs), which serve as signaling molecules in Gram-negative bacterial quorum sensing. In a previous genomic analysis of the 5.25-Mb genome of strain 520P1, we detected the presence of at least one homolog of the AHL synthase gene (luxI) and five homologs of the transcriptional regulator protein gene (luxR). The LuxI homolog of strain 520P1 (PalI) contained the conserved amino acid motifs shared by all the LuxI family proteins of the different species examined here. The palI gene expressed in Escherichia coli produced two types of AHLs. In the thin-layer chromatography analysis, these AHLs showed identical mobility to the AHLs produced by strain 520P1. The five LuxR homologs of strain 520P1 (PalR1-PalR5) shared only 17-34% amino acid sequence identity, although higher identities were observed in the C-terminal DNA-binding domain. Among the five PalRs, only PalR5 displayed close homology with LuxR family proteins from other Pseudoalteromonas strains. Notably, the palR3 and palI genes were located close together and only 1021 bases apart in the genome. No cognate luxI homolog associated with the four other palR genes was detected. These characteristics of PalI and the PalRs suggest that AHL autoinducers generated by the PalI enzyme might regulate cellular metabolism in cooperation with five transcriptional regulator PalRs, each of which is presumed to play a distinctive role in bacterial signaling.
Assuntos
Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Ligases/genética , Pseudoalteromonas/genética , Percepção de Quorum/genética , Proteínas Repressoras/genética , Transativadores/genética , Fatores de Transcrição/genética , Acil-Butirolactonas/metabolismo , Sequência de Aminoácidos , Clonagem Molecular , Escherichia coli/genética , Escherichia coli/metabolismo , Genoma Bacteriano , Filogenia , Pseudoalteromonas/classificação , Pseudoalteromonas/enzimologia , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Homologia de Sequência de AminoácidosRESUMO
BACKGROUND: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis. RESULTS: Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds. CONCLUSIONS: This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.
Assuntos
Evolução Molecular , Genoma Bacteriano , Pseudoalteromonas/genética , Regiões Antárticas , Antibacterianos/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Temperatura Baixa , Bases de Dados Genéticas , Transferência Genética Horizontal , Proteínas de Membrana Transportadoras/genética , Proteínas de Membrana Transportadoras/metabolismo , Filogenia , Pseudoalteromonas/classificação , Metabolismo Secundário/genéticaRESUMO
A Gram-stain-negative, rod-shaped, strictly aerobic, motile bacterial strain, designated TP162T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP162T was related to the genus Pseudoalteromonas and had highest 16S rRNA gene sequence similarities with the type strains Pseudoalteromonas shioyasakiensis SE3T (98.2 %), Pseudoalteromonas lipolytica LMEB 39T (97.7 %), Pseudoalteromonas arabiensis k53T (97.4 %) and Pseudoalteromonas aliena KMM 3562T (97.2 %). The predominant cellular fatty acids were summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1ω7c), C17 : 1ω8c and C16 : 0. The quinone system for strain TP162T comprised predominantly ubiquinone-8, and the polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content of strain TP162T was 46.7 mol%. Strain TP162T shared 28 % DNA-DNA relatedness with P.shioyasakiensis JCM 18891T, 21 % with P. lipolytica JCM 15903T, 35 % with P.arabiensis JCM 17292T and 18 % with P.aliena LMG 22059T. Combined data from phenotypic, chemotaxonomic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain TP162T is a representative of a novel species of the genus Pseudoalteromonas, for which we propose the name Pseudoalteromonas profundi sp. nov. (type strain TP162T=KACC 18554T=CGMCC 1.15394T).
Assuntos
Filogenia , Pseudoalteromonas/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Oceano Pacífico , Fosfolipídeos/química , Pseudoalteromonas/genética , Pseudoalteromonas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/químicaRESUMO
A new aerobic marine bacterium, strain S3431, was isolated from swab samples of an unidentified polychaete near Canal Concepción, Chile. This strain was thought to represent a new taxon within the genus Pseudoalteromonas. Although DNA-DNA reassociation values showed less than 70 % genomic DNA relatedness to established Pseudoalteromonas type strains, it shared 78 % DNA-DNA relatedness with Alteromonas fuliginea DSM 15748 (=KMM 216) (Romanenko et al., 1994). A. fuliginea has later been considered a heterotypic synonym of Pseudoalteromonas citrea(Ivanova et al., 1998). Relatedness between strains S3431, A. fuliginea DSM 15748 and the type strain P. citrea LMG 12323T was therefore studied. Physiological traits and genomic information were shared at a high level by strains S3431 and DSM 15748, but not between these and P. citrea LMG 12323T. There was only approximately 20 % DNA-DNA relatedness between P. citrea LMG 12323T and strains S3431 and DSM 15748. Based on the available phylogenetic and phenotypic data, the reclassification of A. fuliginea DSM 15748 (Romanenko et al., 1995) â Pseudoalteromonas citrea(Ivanova et al., 1998) as Pseudoalteromonas fuligineacomb. nov. is proposed, and strain S3431 should be assigned to this new species. The name Pseudoalteromonas fuliginea is proposed with KMM 216T (=DSM 15748T=CIP 105339T) as the type strain.
Assuntos
Alteromonas/classificação , Filogenia , Poliquetos/microbiologia , Pseudoalteromonas/classificação , Animais , Técnicas de Tipagem Bacteriana , Chile , DNA Bacteriano/genética , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
A Gram-stain-negative, facultatively anaerobic, rod-shaped and motile strain, designated PAMC 28425T, was isolated from a sea surface microlayer sample from the Ross Sea, Antarctica. Analysis of the 16S rRNA gene sequence of strain PAMC 28425T showed an affiliation with the genus Pseudoalteromonas. Phylogenetic analyses revealed that strain PAMC 28425T formed a clade with Pseudoalteromonas prydzensis MB8-11T and Pseudoalteromonas mariniglutinosaKMM 3635T with 16S rRNA gene sequence similarities of 98.3-98.6 %. Genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strain PAMC 28425T is clearly distinguished from the phylogenetically close relatives. Cells of strain PAMC 28425T grew optimally at 25 °C and pH 7.5-8.5 in the presence of 1.0-3.0 % (w/v) sea salts. The major cellular fatty acids (>10 %) were C16 : 1ω6c and/or C16 : 1ω7c, C16 : 0, and C18 : 1ω6c and/or C18 : 1ω7c. The genomic DNA G+C content was 39.7 mol%. On the basis of the phylogenetic, genomic, chemotaxonomic and phenotypic data presented, we propose the name Pseudoalteromonas neustonica sp. nov. with the type strain PAMC 28425T (=KCCM 43187T=JCM 31286T).