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1.
Int J Syst Evol Microbiol ; 70(8): 4531-4536, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32614764

RESUMO

A Gram-staining-negative bacterium, designated 345S023T, was isolated from a sea water sample from the Indian Ocean. The results of 16S rRNA gene sequence analysis revealed that 345S023T represents a member of the genus Alteromonas, with closely related type strains Alteromonas fortis 1T (98.7 %), Alteromonas hispanica F-32T (98.6 %) and Alteromonas genovensis LMG 24078T (98.6 %). Up-to-date bacterial core gene set analysis revealed that 345S023T formed a phyletic lineage with Alteromonas australica H 17T. The case for 345S023T representing a novel species was supported by genomic results. Pairwise in silico DNA-DNA hybridization and average nucleotide identity values were much lower than the proposed and generally accepted species boundaries. Strain 345S023T contains ubiquinone-8 (Q-8) as the sole isoprenoid quinone, summed featured 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the dominant cellular fatty acids (>10 %), and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genome of strain 345S023T consisted of a 4.4 Mb chromosome with a DNA G+C content of 44.4 %. On the basis of these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species: Alteromonas profundi sp. nov. The type strain is 345S023T(=JCM 33893T=MCCC 1K04570T).


Assuntos
Alteromonas/classificação , Filogenia , Água do Mar/microbiologia , Alteromonas/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Oceano Índico , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
2.
Int J Syst Evol Microbiol ; 70(6): 3839-3844, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32496184

RESUMO

A Gram-stain-negative bacterium, designated strain 501str8T, was isolated from a sediment sample collected from the East Pacific Ocean. 16S rRNA gene sequence analysis revealed that strain 501str8T belonged to the genus Muricauda, with closely related type strains Muricauda aquimarina SW-63T (98.5 %), Muricauda lutimaris SMK-108T (98.3 %) and Muricauda ruestringensis B1T (97.9 %). Up-to-date bacterial core gene set analysis revealed that strain 501str8T represented one independent lineage with M. aquimarina SW-63T. The average nucleotide identity values of strain 501str8T with M. aquimarina SW-63T and M. lutimaris SMK-108T were 80.2 and 81.3 %, respectively. In silico DNA-DNA hybridization values between strain 501str8T and M. aquimarina SW-63T and M. lutimaris SMK-108T were 22.8 and 32.9 %, respectively. The predominant isoprenoid quinone was menaquinone-6, and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G were the dominant cellular fatty acids. The G+C content of the genomic DNA was 42.8 mol%. Differential phylogenetic distinctiveness and chemotaxonomic differences, together with the phenotypic properties observed in this study, revealed that strain 501str8T could be differentiated from closely related species. Therefore, we propose that strain 501str8T represents a novel species of the genus Muricauda, for which the name Muricauda oceani sp. nov. is suggested. The type strain is 501str8T (=JCM 33902T=MCCC 1K04567T).


Assuntos
Flavobacteriaceae/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Hibridização de Ácido Nucleico , Oceano Pacífico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
3.
Int J Syst Evol Microbiol ; 70(7): 4345-4350, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32584750

RESUMO

A Gram-stain-negative bacterium, designated strain 40Bstr34T, isolated from a sediment sample from the West Pacific Ocean, was taxonomically characterized by using a polyphasic approach. The strain was phylogenetically close to Jiella aquimaris LZB041T and Jiella endophytica CBS5Q-3T, with 16S rRNA gene sequence similarities of 98.5 and 97.1 %, respectively. The genome of strain 40Bstr34T featured a G+C content of 65.7 % for a 5.8 Mb chromosome. Up-to-date bacterial core gene set analysis revealed that strain 40Bstr34T represents one independent lineage with J.aquimaris LZB041T. In silico DNA-DNA hybridization values between strain 40Bstr34T and its phylogenetic neighbours ranged from 30.3-34.2 %, below the cutoff of 70 %. In addition, the corresponding average nucleotide identity values were between 81.8-83.7 %, which are lower than 95 % threshold. The predominant cellular fatty acids of strain 40Bstr34T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), cyclo-C19 : 0 ω8c and iso-C17 : 0 3-OH, and ubiquinone-10 as the predominant respiratory quinone. The major polar lipids included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and two unidentified lipids. Based on the results of phenotypic, chemotaxonomic and genetic analyses, strain 40Bstr34T is identified as representing a novel species of the genus Jiella for which the name Jiella pacifica sp. nov. is proposed. The type strain is 40Bstr34T (=JCM 33903T=MCCC 1K04569T).


Assuntos
Alphaproteobacteria/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Água do Mar/microbiologia , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Oceano Pacífico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
4.
Int J Syst Evol Microbiol ; 70(1): 340-345, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31596199

RESUMO

A Gram-stain-negative bacterium, designated IO390501T, was isolated from a sea water sample from the Indian Ocean and taxonomically characterized using a polyphasic approach. The strain is phylogenetically close to 'Devosia lucknowensis' L15 and Devosia chinhatensis IPL18T, with 16S rRNA gene sequence similarity of 97.7 and 97.4 %, respectively. The genome of IO390501T has a DNA G+C content of 61.9 mol% for the 3.9 Mb chromosome. Genome-based phylogenetic trees indicated that IO390501T clusters as an independent lineage with 'D. lucknowensis' L15. Genomic relatedness of in silico DNA-DNA hybridization between IO390501T and phylogenetic neighbours ranged from 18.8 to 21.5 %, below the cutoff of 70 %, and corresponding average nucleotide identity values were between 71.4 and 79.0 %, lower than the 95.0 % threshold. The predominant cellular fatty acids of IO390501T are summed feature 8 (C18 : 1ω7c/C18  : 1ω6c) and C16  :  0. IO390501T contains ubiquinone-10 as the sole respiratory quinone, and phosphatidylglycerol and glycolipids as the major polar lipids. On the basis of the results of phenotypic, chemotaxonomic and genetic analyses, strain IO390501T represents a novel species of the genus Devosia for which the name Devosia indica sp. nov. is proposed. The type strain is IO390501T.


Assuntos
Hyphomicrobiaceae/classificação , Filogenia , Água do Mar/microbiologia , Microbiologia da Água , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Hyphomicrobiaceae/isolamento & purificação , Oceano Índico , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
5.
Int J Syst Evol Microbiol ; 69(7): 1974-1979, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31046895

RESUMO

A Gram-stain-negative bacterium, designated CM5-1T, was isolated from a sediment sample collected from the East Pacific Ocean. 16S rRNA gene sequence analysis revealed that strain CM5-1T belongs to the genus Devosia, with closely related type strains Devosia submarina KMM 9415T (98.6 %), Devosia psychrophilaCr7-05T (98.6 %) and Devosia psychrophilaE84T (98.2 %). Up-to-date bacterial core gene set analysis revealed that strain CM5-1T represents one independent lineage with D. submarina KMM 9415T. The average nucleotide identity values of CM5-1T with D. submarina KMM 9415T and D. psychrophila Cr7-05T are 80.1 and 77.9 %, respectively. In silico DNA-DNA hybridization values between strain CM5-1T and D. submarina KMM 9415T and D. psychrophila Cr7-05T are 23.8 and 21.9 %, respectively. Strain CM5-1T contains diphosphatidylglycerol, phosphatidylglycerol and glycolipid as major polar lipids. The sole isoprenoid quinone is ubiquinone-10, and C18 : 1ω7c and 11-methyl C18 : 1ω7c are the dominant cellular fatty acids. The G+C content of the genomic DNA is 61.4 mol%. Differential phylogenetic distinctiveness and chemotaxonomic differences, together with the phenotypic properties observed in this study, revealed that strain CM5-1T could be differentiated from closely related species. Therefore, we propose strain CM5-1T as a novel species of the genus Devosia, for which the name Devosia naphthalenivorans sp. nov. is suggested. The type strain is CM5-1T (=JCM32509T=CGMCC 1.13553T).


Assuntos
Sedimentos Geológicos/microbiologia , Hyphomicrobiaceae/classificação , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Hyphomicrobiaceae/isolamento & purificação , Hibridização de Ácido Nucleico , Oceano Pacífico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
6.
Antonie Van Leeuwenhoek ; 112(6): 927-933, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30737708

RESUMO

Strain IO390502T, isolated from surface seawater in the Indian Ocean, was characterised using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain IO390502T belongs to the genus Paracoccus and is closely related to Paracoccus seriniphilus DSM 14827T (97.6%), followed by P. zeaxanthinifaciens JCM 21774T (97.5%), P. homiensis DSM 17862T (97.3%), P. marcusii DSM 11574T (97.2%), P. haeundaensis BC 74171T (97.0%) and P. carotinifaciens E-396T (97.0%). Cells are Gram-negative, aerobic, poly-ß-hydroxybutyrate-accumulating, motile, rod-shaped, and forms creamy-white colonies. Optimal growth occurred at 25-30 °C, pH 5-8, and in the presence of 3-8% NaCl. The genome of strain IO390502T has a G+C content of 64.9 mol% and a 3.5 Mb chromosome. The in silico DNA-DNA hybridisation and average nucleotide identity values between strain IO390502T and the three closely related taxa, P. seriniphilus DSM 14827T, P. zeaxanthinifaciens JCM 21774T and P. homiensis DSM 17862T, are 19.6%, 21.9% and 20.6%, and 76.0%, 79.9% and 77.8%, respectively. Phosphatidylglycerol is the major lipid present, ubiquinone-10 (Q-10) is the sole isoprenoid quinone, and the major cellular fatty acid is C18:1ω7c. Based on data from phenotypic tests and genotypic differences between strain IO390502T and its close phylogenetic relatives, strain IO390502T represents a new species belonging to the genus Paracoccus, for which the name Paracoccus indicus sp. nov. is proposed. The type strain is IO390502T (= JCM 32637T = CCTCC AB 2018071T).


Assuntos
Paracoccus/isolamento & purificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Ácidos Graxos/metabolismo , Oceano Índico , Paracoccus/classificação , Paracoccus/genética , Paracoccus/metabolismo , Filogenia , RNA Ribossômico 16S/genética
7.
Int J Syst Evol Microbiol ; 68(12): 3881-3885, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30351269

RESUMO

A Gram-stain-negative bacterium, designated strain IO390401T, was isolated from a seawater sample from the sulphide region of the Indian Ocean. Phylogenetic trees based on 16S rRNA gene sequences showed that strain IO390401T is a member of the genus Alteromonas, sharing 97.0-97.4 % 16S rRNA gene sequence similarity with Alteromonas additaR10SW13T, A. stellipolaris LMG 21861T, A. naphthalenivorans JCM 17741T, A. gracilis 9a2T and A. australica H17T, and 94.8-96.8 % with the type strains of other species of the genus Alteromonas. Strain IO390401T contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone, C16:0 and C16:1ω7c/C16:1ω6c as the dominant cellular fatty acids, and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genome of strain IO390401T consists of a 4.4 Mb chromosome with a G+C content of 48.2 mol%. Average nucleotide identity values between strain IO390401T and the three closest phylogenetic neighbours, namely A. additaR10SW13T, A. stellipolaris LMG 21861T and A. naphthalenivorans JCM 17741T, were 70.5, 70.4 and 70.6 %, respectively, and the corresponding in silico DNA-DNA hybridization values were 20.6, 20.7 and 21.1 %. Phylogenetic distinctiveness and chemotaxonomic differences, together with phenotypic properties determined in this study, revealed that strain IO390401T could be differentiated from closely related species. It is therefore proposed as representing a novel species in the genus Alteromonas, for which the name Alteromonas indica sp. nov. is suggested. The type strain is IO390401T (=JCM 32638T=CGMCC 1.13554T=CCTCC AB 2018072T).


Assuntos
Alteromonas/classificação , Filogenia , Água do Mar/microbiologia , Alteromonas/genética , Alteromonas/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Oceano Índico , Hibridização de Ácido Nucleico , Fosfatidiletanolaminas/química , Fosfatidilgliceróis/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
8.
Int J Syst Evol Microbiol ; 68(5): 1672-1677, 2018 May.
Artigo em Inglês | MEDLINE | ID: mdl-29616891

RESUMO

A novel, alkaliphilic, psychrotolerant, facultative anaerobe, designated CP1T, was isolated from sandy soil near the Davis Station in Antarctica. The short-rod-shaped cells displayed Gram-positive staining and did not form spores. Strain CP1T was able to grow at temperatures between 4 and 36 °C, pH 6.0-9.5, and in the presence of up to 5.0 % (w/v) NaCl. 16S rRNA gene and multilocus (pheS, rpoA, and atpA) sequence analysis revealed Carnobacterium mobile DSM 4848T and Carnobacterium iners LMG 26642T as the closest relatives (97.4 and 97.1 % 16S rRNA gene sequence similarity, respectively). The genomic G+C content was 38.1 mol%, and DNA-DNA hybridization with DSM 4848T revealed 32.4±3.4 % similarity. The major fatty acid components were C14 : 0 and C16 : 1ω9c. The cell wall contained meso-diaminopimelic acid and was of peptidoglycan type A1γ. Based on physiological, genotypic and biochemical characteristics, strain CP1T represents a novel species of the genus Carnobacterium for which the name Carnobacterium antarcticum sp. nov. is proposed. The type strain is CP1T (=DSM 103363T=CGMCC 1.15643T).


Assuntos
Carnobacterium/classificação , Filogenia , Microbiologia do Solo , Regiões Antárticas , Técnicas de Tipagem Bacteriana , Composição de Bases , Carnobacterium/genética , Carnobacterium/isolamento & purificação , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
9.
J Biotechnol ; 266: 34-38, 2018 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-29223718

RESUMO

Staphylococcus sp. AntiMn-1 is a deep-sea bacterium inhabiting seafloor sediment in the Clarion-Clipperton Zone (CCZ) that is highly tolerant to Mn(II) and displays efficient Mn(II) oxidation. Herein, we present the assembly and annotation of its genome.


Assuntos
Organismos Aquáticos/genética , Genoma Bacteriano , Manganês , Staphylococcus/genética , Organismos Aquáticos/isolamento & purificação , Staphylococcus/isolamento & purificação
10.
Virus Genes ; 53(2): 317-322, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-27943061

RESUMO

We have previously shown that non-structural protein p35, encoded by Scylla serrata reovirus (SsRV) S10, may act as a viroporin. To characterize the role of p35 protein in the modulation of cellular function, a yeast two-hybrid system was used to screen a cDNA library derived from S. serrata to find its interacting partner. Protein interactions were confirmed in vitro by GST pull-down. Full cDNAs of p35 interactors were cloned by the rapid amplification of cDNA ends. After two-hybrid library screening, we isolated partial cDNAs encoding hemocyanin, cryptocyanin, and TAX1BP1. Interaction of p35 with each of hemocyanin, cryptocyanin, and TAX1BP1 was confirmed by GST pull-down. The full-length cDNA fragments of hemocyanin, cryptocyanin, and TAX1BP1 were 2287, 2422, and 3437 bp, respectively, and they encoded three putative proteins with molecular masses of ~76.9, ~79.2, and ~107.2 kDa, respectively. This study casts new light on the function and physiological significance of p35 during the SsRV replication cycle.


Assuntos
Braquiúros/virologia , Interações Hospedeiro-Patógeno/genética , Reoviridae/genética , Proteínas não Estruturais Virais/genética , Sequência de Aminoácidos , Animais , DNA Complementar/genética , Dados de Sequência Molecular , Filogenia , Reoviridae/patogenicidade , Proteínas não Estruturais Virais/metabolismo
11.
Genome Announc ; 4(4)2016 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-27445381

RESUMO

Carnobacterium sp. strain CP1 was isolated from Antarctic sandy soil and predicted to be a novel species belonging to the genus Carnobacterium Herein, we report the complete genome sequence, which consists of a circular 2,605,518-bp chromosome and an 8,883-bp plasmid with G+C contents of 38.13% and 31.63%, respectively.

12.
Genome Announc ; 4(2)2016 Mar 24.
Artigo em Inglês | MEDLINE | ID: mdl-27013039

RESUMO

Here, we report the complete genome sequence ofAlteromonas stellipolarisLMG 21856, which was isolated from seawater collected from the Southern Ocean.A. stellipolarisLMG 21856 is a budding, psychrotrophic, brown pigment-producing, and oligotrophic bacterium.The complete genome of this bacterium contains 4,686,200 bp, with a G+C content of 43.6%.

13.
Wei Sheng Wu Xue Bao ; 56(9): 1434-49, 2016 Sep.
Artigo em Chinês | MEDLINE | ID: mdl-29738216

RESUMO

Objective: The objective of this study was to assess bacterial diversity in sediment samples from two stations (WBC1305 and WBC1316A) in the Pacific polymetallic nodule province. Methods: The environmental total DNAs were extracted, and 6 bacterial 16S rRNA gene libraries were generated from 6 sediment layers. The Shannon diversity index and Simpson dominance index were calculated for each bacterial community and then compared. The bacterial community structure of each sediment sample was analyzed, and the results were used to construct phylogenetic trees. Results: In total, 533 bacterial clones were obtained from 6 bacterial clone libraries. Among these 533 clones, 472 clones could be assigned to 16 phylogenetic groups (Acidobacteria, Actinobacteria, Alpha, Beta, Delta, gamma-Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Elusimicrobia, Hydrogenedentes, Chlorobi, and Nitrospinae), whereas the remaining 61 clones could not be classified into any known groups. Conclusion: The bacterial communities in sediments from WBC1305 are dominated mainly by gamma-Proteobacteria and from WBC1316A by Firmicutes. In addition, the bacterial community structure at WBC1316A is more abundant and complex than that at WBC1305.


Assuntos
Bactérias/isolamento & purificação , Biodiversidade , Sedimentos Geológicos/microbiologia , Água do Mar/microbiologia , Bactérias/classificação , Bactérias/genética , DNA Bacteriano/genética , DNA Ribossômico/genética , Oceano Pacífico , Filogenia , RNA Ribossômico 16S/genética
14.
Genome Announc ; 3(2)2015 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-25931596

RESUMO

Rhodococcus sp. B7740 was isolated from Arctic seawater and selected for its capacity to synthesize carotenoids. Here, we report the complete genome sequence of Rhodococcus sp. B7740 to provide the genetic basis for a better understanding of its carotenoid-accumulating capabilities, and we describe the major features of the genome.

15.
Folia Microbiol (Praha) ; 60(4): 309-16, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25787019

RESUMO

We describe the isolation and identification of a gene encoding 4-hydroxyphenylpyruvate dioxygenase (HPPD (EC 1.13.11.27)) from the red-brown pigment-producing bacterium Alteromonas stellipolaris LMG 21856. HPPD directs the synthesis of 2,5-dihydroxyphenylacetic acid (homogentisic acid (HGA)). The sequence of the deduced peptide showed homology to HPPDs from other strains of Alteromonas; the greatest similarity was to the hypothetical HPPD from Alteromonas sp. SN2. As observed for HPPDs from other sources, expression of the A. stellipolaris HPPD gene in Escherichia coli cells could be detected by the gradual development of a brown pigment in cultures as a result of the spontaneous oxidation and polymerization of HGA.


Assuntos
4-Hidroxifenilpiruvato Dioxigenase/genética , 4-Hidroxifenilpiruvato Dioxigenase/metabolismo , Alteromonas/enzimologia , Alteromonas/genética , Ácido Homogentísico/metabolismo , Clonagem Molecular , Escherichia coli/genética , Escherichia coli/metabolismo , Oxirredução , Pigmentos Biológicos/metabolismo , Homologia de Sequência de Aminoácidos
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