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1.
Artigo em Inglês | MEDLINE | ID: mdl-34516364

RESUMO

An aerobic, Gram-stain-negative, rod-shaped and non-motile strain (XY-359T) was isolated from the mouth of a marine invertebrate Onchidium species from the South China Sea. It grew at pH 6.0-8.5 (optimum, pH 7.5), at 15-37 °C (optimum, 30 °C) and in the presence of 0.5-4.5 % (w/v) NaCl (optimum, 2.5 %). It could not hydrolyse Tweens 20, 40, 60 or 80 and no flexirubin-type pigments were produced. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid, six unidentified phospholipids and two unidentified polar lipids. The major fatty acids were iso-C17:0 3-OH, iso-C15:1 G and iso-C15:0 3-OH. The respiratory quinone was MK-6. Strain XY-359T showed the greatest degree of 16S rRNA sequence similarity to Flagellimonas algicola AsT0115T (96.54 %), followed by Muricauda flava DSM 22638T (96.27 %). Phylogenetic analysis based on 16S rRNA gene sequences and 31 core genes indicated that strain XY-359T belongs to the genus Muricauda. The genome size of strain XY-359T was 4 207 872 bp, with 39.1 mol% of DNA G+C content. The average nucleotide identity and digital DNA-DNA hybridization values between strain XY-359T and F. algicola AsT0115T were 74.58 % and 18.5 %, respectively, and those between strain XY-359T and M. flava DSM 22638T were 74.2 % and 18.3 %. The combined phenotypic, chemotaxonomic and phylogenetic data suggest that strain XY-359T represents a novel species of the genus Muricauda, for which the name Muricauda onchidii sp. nov. is proposed. The type strain is XY-359T (=MCCC 1K03658T =KCTC 72218T). Moreover, based on the proposal of nesting Spongiibacterium and Flagellimonas within Muricauda by García (Validation List No. 193) and the analyses of phylogenetic trees and average amino acid identities in this study, the transfers of F. algicola, F. pacifica and F. maritima to the genus Muricauda as Muricauda algicola comb. nov., Muricauda parva nom. nov. and M. aurantiaca nom. nov., respectively, are proposed, with an emended description of the genus Muricauda.


Assuntos
Ácidos Graxos , Gastrópodes , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2
2.
Artigo em Inglês | MEDLINE | ID: mdl-34346862

RESUMO

Four marine bacterial strains were isolated from a thallus of the brown alga Ascophyllum nodosum collected in Roscoff, France. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, gliding, rod-shaped and grew optimally at 25-30 °C, at pH 7-8 and with 2-4 % NaCl. Phylogenetic analyses of their 16S rRNA gene sequences showed that the bacteria were affiliated to the genus Zobellia (family Flavobacteriaceae, phylum Bacteroidetes). The four strains exhibited 97.8-100 % 16S rRNA gene sequence similarity values among themselves, 97.9-99.1 % to the type strains of Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T, and less than 99 % to other species of the genus Zobellia. The DNA G+C content of the four strains ranged from 36.7 to 37.7 mol%. Average nucleotide identity and digital DNA-DNA hybridization calculations between the new strains and other members of the genus Zobellia resulted in values of 76.4-88.9 % and below 38.5 %, respectively. Phenotypic, phylogenetic and genomic analyses showed that the four strains are distinct from species of the genus Zobellia with validly published names. They represent two novel species of the genus Zobellia, for which the names Zobellia roscoffensis sp. nov. and Zobellia nedashkovskayae sp. nov. are proposed with Asnod1-F08T (RCC6906T=KMM 6823T=CIP 111902T) and Asnod2-B07-BT (RCC6908T=KMM 6825T=CIP 111904T), respectively, as the type strains.


Assuntos
Ascophyllum , Flavobacteriaceae , Filogenia , Ascophyllum/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/classificação , Flavobacteriaceae/isolamento & purificação , França , Microbiota , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Água do Mar , Análise de Sequência de DNA
3.
Artigo em Inglês | MEDLINE | ID: mdl-34370661

RESUMO

Two bacterial strains, designated SS33T and Y03T, were isolated from marine sediment and marine red alga collected on the coast of Weihai, PR China. Based on the results of 16S rRNA gene sequence analysis, strain SS33T was found to be closely related to Primorskyibacter marinus PX7T, Pelagivirga dicentrarchi YLY04T, Palleronia marisminoris DSM 26347T and Maribius pontilimi GH1-23T with 94.8, 94.6, 94.5 and 94.5 % sequence similarity; strain Y03T was found to be closest to Flavivirga aquimarina EC2D5T, Flavivirga eckloniae ECD14T and Flavivirga amylovorans JC2681T with 96.4, 96.1 and 96.0 % sequence similarity. Strain SS33T grew at 4-37 °C (optimum, 33 °C), at pH 6.0-9.5 (optimum, pH 7.5-8.0) and in the presence of 0-10 % (w/v) NaCl (optimum, 3.0 %). Chemotaxonomic analysis of strain SS33T showed that the predominant respiratory quinone was ubiquinone-10. The major fatty acids (>10.0 %) included C18 : 1 ω7c and C16 : 0. The major polar lipids included phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid, one unidentified glycolipid, one unidentified polar lipid and two unidentified aminolipids. Strain Y03T grew at 15-40 °C (optimum, 28 °C), at pH 6.5-8.0 (optimum, pH 7.0) and in the presence of 0.5-9.0 % (w/v) NaCl (optimum, 2.0%). Chemotaxonomic analysis showed that the predominant respiratory quinone was menaquinone-6. The major fatty acids (>10.0 %) included iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids included phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and four unidentified polar lipids. Based on the polyphasic data, strain SS33T is considered to represent a novel species of the genus Palleronia, for which the name Palleronia sediminis sp. nov. is proposed, with the type strain SS33T (=KCTC 62986T=MCCC 1H00387T). Strain Y03T is considered to represent a novel species of the genus Flavivirga, for which the name Flavivirga algicola sp. nov. is proposed, with the type strain Y03T (=KCTC 72001T=MCCC 1H00386T).


Assuntos
Flavobacteriaceae , Sedimentos Geológicos/microbiologia , Filogenia , Rhodobacteraceae/classificação , Rodófitas/microbiologia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/classificação , Flavobacteriaceae/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
4.
Artigo em Inglês | MEDLINE | ID: mdl-34402780

RESUMO

A Gram-negative, non-motile, non-spore-forming, aerobic and short rod-shaped bacterial strain R32T, was isolated from seawater of the South Atlantic Ocean. Strain R32T grew at 10-40 °C (optimum 28 °C), at pH 6.0-8.0 (optimum 7.0), and in the presence of 3-8 % NaCl (w/v) (optimum 5 %). Cells were oxidase- and catalase-positive. The 16S rRNA gene sequence of strain R32T shared the highest similarities with Mesonia oceanica (98.3 %), followed by Salegentibacter salarius (93.0 %), Salegentibacter mishustinae (92.8 %), Salegentibacter salegens (92.5 %) and Mesonia maritima (92.4 %). The dominant fatty acids were iso-C15 : 0 (32.7 %) and iso-C17 : 0 3-OH (21.1 %). Menaquinone-6 (MK-6) was detected as the sole respiratory quinone. The polar lipids found were phosphatidylethanolamine, three aminolipids and three unidentified lipids. The DNA G+C content was 35.0 mol%. The ANI value and dDDH value between strain R32T and the Salegentibacter and Mesonia species were 70.5-85.8 % and 18.7-30.5 %, respectively. Based on the results of the polyphasic characterization, strain R32T is considered to represent a novel species of the genus Mesonia, for which the name Mesonia hitae sp. nov. is proposed. The type strain is R32T (=MCCC 1A09780T=KCTC 72004T).


Assuntos
Flavobacteriaceae , Filogenia , Água do Mar/microbiologia , Oceano Atlântico , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/classificação , Flavobacteriaceae/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
5.
Artigo em Inglês | MEDLINE | ID: mdl-34428132

RESUMO

A novel bacterial strain, designated as HN-E44T, was isolated from marine sponge collected from Yangpu Bay, Hainan, PR China. Strain HN-E44T was Gram-stain-negative, non-motile, catalase-positive, oxidase-negative, rod-shaped and yellow-pigmented. Growth occurred at 4-37 °C (optimum, 28 °C), at pH 6-8 (pH 7) and in 0.5-14 % (w/v) NaCl (3-5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HN-E44T formed an independent cluster with Marixanthomonas ophiurae JCM 14121T within the family Flavobacteriaceae and had the highest sequence similarity of 93.6 % to the closest type strain M. ophiurae JCM 14121T. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C15 : 1 G. The polar lipids comprised phosphatidylethanolamine, sphingolipid, four unidentified phospholipids, an unidentified aminophospholipid and an unidentified lipid. The respiratory quinone was identified as MK-6. The genomic DNA G+C content was determined to be 40.6 mol%. The average nucleotide identity (ANI) and average amino acid identity (AAI) values between strain HN-E44T and closest type strain M. ophiurae JCM 14121T were, respectively, 79.6 and 85.2 %, both of which were below thresholds for species delineation (95-96 % ANI and 95-96 % AAI), but were over thresholds for genus delineation (73.98 % ANI and 70-76 % AAI). The combined genotypic and phenotypic distinctiveness demonstrated that strain HN-E44T could be differentiated from closely related genera. Therefore, it is proposed that strain HN-E44T represents a novel species of the genus Marixanthomonas, for which the name Marixanthomonas spongiae sp. nov. is proposed, with the type strain HN-E44T (=MCCC 1K03332T=LMG 30459T).


Assuntos
Flavobacteriaceae , Filogenia , Poríferos , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/classificação , Flavobacteriaceae/isolamento & purificação , Fosfolipídeos/química , Pigmentação , Poríferos/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
6.
Syst Appl Microbiol ; 44(5): 126232, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34399113

RESUMO

Seawater contains free-living and particle-attached bacteria. Only a small fraction is cultivable on plates. As free-living and particle-associated bacteria differ in their physiological traits, their cultivability on plates may coincide with particle association. Using filtration and Imhoff sedimentation cones, particles were collected during a spring phytoplankton bloom off Helgoland (North Sea) in order to obtain particle-associated bacteria as inocula. Direct dilution plating resulted in 526 strains from 3 µm filtration retentates and 597 strains from settled particles. Motile Gammaproteobacteria from the genera Pseudoalteromonas, Shewanella, Psychrobacter, Vibrio and Colwellia, as well as particle-attached Flavobacteriia affiliating with the genera Tenacibaculum and Gramella, were frequently isolated. As a result, a diverse collection comprised of 266 strains was deposited. Two strains were most likely to represent novel genera and 78 strains were probably novel species. Recently, a high-throughput cultivation study from the same site using seawater as an inoculum had retrieved 271 operational phylogenetic units (OPUs) that represented 88% of the 4136 characterized strains at the species level. A comparison of 16S rRNA gene sequences revealed that the collection obtained matched 104 of the 271 seawater OPUs at the species level and an additional 113 at the genus level. This large overlap indicated a significant contribution of particle-associated bacteria to the cultivable microbiome from seawater. The presence of 49 genera not identified in the larger seawater study suggested that sample fractionation was an efficient strategy to cultivate rare members of the planktonic microbiome. The diverse collection of heterotrophic bacteria retrieved in this study will be a rich source for future studies on the biology of particle-associated bacteria.


Assuntos
Flavobacteriaceae , Gammaproteobacteria/classificação , Fitoplâncton , Água do Mar/microbiologia , Técnicas Bacteriológicas , Eutrofização , Flavobacteriaceae/classificação , Mar do Norte , Filogenia , RNA Ribossômico 16S/genética
7.
Artigo em Inglês | MEDLINE | ID: mdl-34323679

RESUMO

A novel Gram-stain-negative, rod-shaped, aerobic, non-motile bacterial strain, designated M5A1MT, was isolated from seawater collected from the South Sea of the Republic of Korea. Based on 16S rRNA gene sequence similarity, strain M5A1MT was closely related to Mariniflexile gromovii KMM 6038T (95.3 %), Mariniflexile fucanivorans SW5T (95.2 %), Mariniflexile soesokkakense RSSK-9T (95.1 %), Yeosuana aromativorans GW1-1T (94.6 %) and Confluentibacter lentus HJM-3T (94.6 %). Genome-based phylogenetic analyses revealed that strain M5A1MT formed a distinct cluster with the type strains of the genus Mariniflexile. The major cellular fatty acid constituents (>5 % of the total fatty acids) were iso-C15:0, anteiso-C15 : 0, iso-C15 : 0 3-OH, iso-C15 : 1 G, iso-C16:03-OH and iso-C17 : 0 3-OH. The respiratory quinone was identified as MK-6. The major polar lipids were phosphatidylethanolamine and one unidentified polar lipid. The genomic DNA G+C content of strain M5A1MT was determined to be 37.7 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain M5A1MT is considered to represent a novel species within the genus Mariniflexile, for which the name Mariniflexile maritimum sp. nov. is proposed. The type strain is M5A1MT (=KCTC 72895T=JCM 33982T).


Assuntos
Ácidos Graxos , Água do Mar , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae , Filogenia , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA
8.
J Chem Phys ; 154(21): 215101, 2021 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-34240976

RESUMO

Photoisomerization in the retinal leads to a channel opening in rhodopsins that triggers translocation or pumping of ions/protons. Crystal structures of rhodopsins contain several structurally conserved water molecules. It has been suggested that water plays an active role in facilitating the ion pumping/translocation process by acting as a lubricant in these systems. In this paper, we systematically investigate the localization, structure, dynamics, and energetics of the water molecules along the channel for the resting/dark state of KR2 rhodopsin. By employing several microseconds long atomistic molecular dynamics simulation of this trans-membrane protein system, we demonstrate the presence of five distinct water containing pockets/cavities separated by gateways controlled by protein side-chains. There exists a strong hydrogen bonded network involving these buried water molecules and functionally important key residues. We present evidence of significant structural and dynamical heterogeneity in the water molecules present in these cavities, with very rare exchange between them. The exchange time scale of such buried water with the bulk has an extremely wide range, from tens of nanoseconds to >1.5 µs. The translational and rotational dynamics of buried water are found to be strongly dependent on the protein cavity size and local interactions with a classic signature of trapped diffusion and rotational anisotropy.


Assuntos
Flavobacteriaceae/química , Simulação de Dinâmica Molecular , Rodopsina/química , Sódio/química , Conformação Proteica , Rodopsina/metabolismo , Sódio/metabolismo , Água/química , Água/metabolismo
9.
Antonie Van Leeuwenhoek ; 114(9): 1407-1416, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34251526

RESUMO

A taxonomic investigation using a polyphasic method was conducted to identify a novel marine flavobacterium, designated as DJ-13T, isolated from the hard coral Acropora sp. collected at Okinawa, Japan. Bacterial cells were Gram-stain-negative, yellow-colored, strictly aerobic, rod-shaped, catalase- and oxidase-positive, non-motile, and chemoorganoheterotrophic. The novel isolate grew at NaCl concentrations of 0.5-7%, pH 6.5-9.0, and 15-37 °C. A phylogenetic study on the basis of the 16S rRNA gene sequence revealed that strain DJ-13T belongs to the family Flavobacteriaceae and that it shared the greatest sequence similarity (95.9%) with Croceivirga lutea CSW06T. Strain DJ-13T comprised iso-C17:0 3-OH, iso-C15:0, and iso-C15:1 G as the main (> 10%) cellular fatty acids. Menaquinone-6 (MK-6) was the only respiratory quinone. The assembled draft genome size of strain DJ-13T was 3.71 Mbp with G + C content of 38.7 mol%. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values of DJ-13T and the species of the genus Croceivirga were found to be 74.9-75.5%, 13.4-14.7%, and 68.2-72.4%, respectively. Strain DJ-13T contained phosphatidylethanolamine, two unidentified aminolipids, and five unidentified lipids as polar lipids. From the polyphasic taxonomic results presented, the strain is considered to represent a novel species of the genus Croceivirga for which the name Croceivirga thetidis sp. nov. is proposed. The type strain of C. thetidis sp. nov. is DJ-13T (= KCTC 72790T = NBRC 114252T).


Assuntos
Antozoários , Flavobacteriaceae , Animais , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , Ácidos Graxos/análise , Flavobacteriaceae/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2
10.
J Phys Chem Lett ; 12(27): 6284-6291, 2021 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-34213348

RESUMO

We report a transient signature in the near-UV absorption of Krokinobacter eikastus rhodopsin 2 (KR2), which spans from the femtosecond up to the millisecond time scale. The signature rises with the all-trans to 13-cis isomerization of retinal and decays with the reisomerization to all-trans in the late photocycle, making it a promising marker band for retinal configuration. Hybrid quantum mechanics/molecular mechanics simulations show that the near-UV absorption signal corresponds to an S0 → S3 and/or an S0 → S5 transition, which is present in all photointermediates. These transitions exhibit a negligible spectral shift by the altering protein environment, in contrast to the main absorption band. This is rationalized by the extension of the transition densities that omits the Schiff base nitrogen. Further characterization and first steps into possible optogenetic applications were performed with near-UV quenching experiments of an induced photostationary state, yielding an ultrafast regeneration of the parent state of KR2.


Assuntos
Absorção Fisico-Química , Flavobacteriaceae/metabolismo , Rodopsina/química , Rodopsina/metabolismo , ATPase Trocadora de Sódio-Potássio/metabolismo , Raios Ultravioleta , Membrana Celular/metabolismo , Flavobacteriaceae/citologia , Simulação de Dinâmica Molecular , Conformação Proteica , Análise Espectral
11.
Curr Microbiol ; 78(8): 3342-3348, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34196770

RESUMO

A novel Gram-stain-negative, aerobic, rod-shaped, non-flagellated, and gliding bacterial strain, designated DF109T, was isolated from the coastal sediment of Jingzi Wharf, Weihai, China. The optimal growth occurs at 28°C, pH 7.0-7.5, and 1.0% (w/v) NaCl environment. The colony was yellow-colored, convex, non-transparent, and circular on 2216E Agar. Phylogenetic analyses of the 16S rRNA gene and genome sequence of this newly isolated strain revealed that it is a member of the genus Gelidibacter within the family Flavobacteriaceae. The phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DF109T has the highest sequence similarity to Gelidibacter japonicus JCM 31967T (98.0%). The average nucleotide identity (ANI) values between genomes of DF109T and G. japonicus JCM 31967T and G. algens DSM 12408T were 86.3% and 78.7% and the digital DNA-DNA hybridization (dDDH) values were 31.4% and 22.4%, respectively. The sole isoprenoid quinone was MK-6 and the major cellular fatty acids were iso-C15:1G, iso-C17:0 3-OH, anteiso-C15:0, and iso-C16:0 3-OH. The major polar lipids of strain DF109T were an aminolipid, a phosphatidylethanolamine, and four unidentified lipids. The genomic DNA G+C content was 37.5 mol%. Strain DF109T is suggested to represent a novel species in the genus Gelidibacter, for which the name Gelidibacter pelagius sp. nov. is proposed. The type strain is DF109T (=MCCC 1H00454T=KCTC 82420T).


Assuntos
Flavobacteriaceae , Água do Mar , Técnicas de Tipagem Bacteriana , China , DNA Bacteriano/genética , Ácidos Graxos , Flavobacteriaceae/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2
12.
Artigo em Inglês | MEDLINE | ID: mdl-34270398

RESUMO

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002T was isolated from island soil. The isolate grew at 20-37 °C (optimum, 30 °C), at pH 6.0-9.5 (optimum, pH 7) and in the presence of 0.5-4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8T and Muriicola jejuensis EM44T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C15 : 1 G and iso-C15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, ß-galactosidase and ß-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002T and M. jejuensis and that between the strain and M. marianensis A6B8T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002T should be recognized as a novel species of the genus Muriicola, for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002T (=KCTC 62790T=JCM 32370T).


Assuntos
Flavobacteriaceae/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Ilhas , Fosfatidiletanolaminas/química , Pigmentação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
13.
J Environ Manage ; 296: 113270, 2021 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-34271348

RESUMO

Wastewater treatment plants are considered as hotspots of emerging antimicrobial genes and mobile genetic elements. We used a shotgun metagenomic approach to examine the wide-spectrum profiles of ARGs (antibiotic resistance genes) and MGEs (mobile genetic elements) in activated sludge samples from two different hospital trains at the wastewater treatment plants (WWTPs) in Daegu, South Korea. The influent activated sludge and effluent of two trains (six samples in total) at WWTPs receiving domestic sewage wastewater (SWW) and hospital wastewater (HWW) samples collected at multiple periods were subjected to high throughput 16S rRNA metagenome sequencing for microbial community diversity. Cloacibacterium caeni and Lewinella nigricans were predominant in SWW effluents, while Bacillus subtilis and Staphylococcus epidermidis were predominant in HWW effluents based on the Miseq platform. Totally, 20,011 reads and 28,545 metagenomic sequence reads were assigned to 25 known ARG types in the SWW2 and HWW5 samples, respectively. The higher abundance of ARGs, including multidrug resistance (>53%, MDR), macrolide-lincosamide-streptogramin (>9%, MLS), beta-lactam (>3.3%), bacitracin (>4.4%), and tetracycline (>3.4%), confirmed the use of these antibiotics in human medicine. In total, 190 subtypes belonging to 23 antibiotic classes were detected in both SWW2 and HWW5 samples. RpoB2, MacB, and multidrug (MDR) ABC transporter shared the maximum matched genes in both activated sludge samples. The high abundance of MGEs, such as a gene transfer agent (GTA) (four times higher), transposable elements (1.6 times higher), plasmid related functions (3.8 times higher), and phages (two times higher) in HWW5 than in SWW2, revealed a risk of horizontal gene transfer in HWW. Domestic wastewater from hospital patients also influenced the abundance of ARGs and MGEs in the activated sludge process.


Assuntos
Águas Residuárias , Purificação da Água , Antibacterianos/farmacologia , Bactérias/genética , Bacteroidetes , Resistência Microbiana a Medicamentos/genética , Flavobacteriaceae , Genes Bacterianos , Hospitais , Humanos , Sequências Repetitivas Dispersas , Metagenoma , Prevalência , RNA Ribossômico 16S , Esgotos
14.
Antonie Van Leeuwenhoek ; 114(10): 1551-1563, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34291355

RESUMO

A novel bright-yellow pigmented bacterial strain SM2-FT was isolated from a mangrove sediment collected at the mangrove coast of Luoyang estuary, Quanzhou, China. Strain SM2-FT was Gram-stain-negative, catalase-weak positive, oxidase-positive, rod-shaped, non-flagellated and non-motile. Growth of strain SM2-FT was observed at 20-40 °C (optimum, 30 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 1.0-4.0% NaCl (optimum, 2.0% NaCl). Flexirubin-pigment was absent, and carotenoid-pigment was present. Phylogenetic analysis of 16S rRNA gene sequence placed strain SM2-FT into the family Flavobacteriaceae and shared the maximum sequence similarity with Aequorivita soesokkakensis RSSK-12 T of 92.5%. Whole genomic comparison between strain SM2-FT and close relatives suggested a novel species of a novel genus. The predominant quinone of strain SM2-FT was menaquinone (MK)-6. The major fatty acids (> 10%) comprised iso-C15:1 G (32.4%) and iso-C15:0 (29.1%). The polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids and four unidentified lipids. The complete genome size was 4,094,245 bp with DNA G + C content of 36.0 mol%. Based on the data of polyphasic study, strain SM2-FT was considered to represent a novel species of a novel genus, for which the name Aegicerativicinus sediminis gen. nov., sp. nov., was proposed. The type strain was SM2-FT (= MCCC 1K04383T = KCTC 82361 T).


Assuntos
Flavobacteriaceae , Água do Mar , Técnicas de Tipagem Bacteriana , Carotenoides , DNA Bacteriano/genética , Ácidos Graxos , Flavobacteriaceae/genética , Fosfolipídeos , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2
15.
Rev Chilena Infectol ; 38(2): 297-299, 2021 Apr.
Artigo em Espanhol | MEDLINE | ID: mdl-34184722

RESUMO

Infections due to Gram-negative bacteria of the genus Myroides are very rare and generally affect the skin and soft tissues of patients with some degree of immunocompromise. We present a case of a 23-year-old patient with a history of myelomeningocele surgically resolved at 3 years of age and bot foot, who presented with a deep infection of the right lower extremity by Myroides odoratimimus. The species identification was carried out with MALDI-TOF and the treatment was initially carried out with meropenem and finally then ciprofloxacin, in addition to right supramaleolar amputation.


Assuntos
Infecções por Flavobacteriaceae , Flavobacteriaceae , Osteomielite , Infecções dos Tecidos Moles , Adulto , Infecções por Flavobacteriaceae/diagnóstico , Infecções por Flavobacteriaceae/tratamento farmacológico , Humanos , Osteomielite/tratamento farmacológico , Infecções dos Tecidos Moles/tratamento farmacológico , Adulto Jovem
16.
Curr Microbiol ; 78(8): 3277-3284, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34081182

RESUMO

The family Flavobacteriaceae forms a major branch within the phylum Bacteroidetes. Whole-genome sequence-based analysis could significantly improve the accuracy of taxonomic assignments. In this study, phylogenomic analyses were carried out to revisit the taxonomic status of a clade of the family Flavobacteriaceae. Taking genome-based phylogeny as the primary guideline and average amino acid identity and phenotypic information as supplements, the following taxonomic proposals were put forward: Arenitalea lutea should be reclassified into the genus Algibacter; Algibacter aquaticus should be reclassified into the genus Flavivirga; Jejuia pallidilutea and Algibacter aestuarii should be reclassified into the genus Hyunsoonleella; Algibacter alginicilyticus should be reclassified into the novel genus Pseudalgibacter gen. nov. This study builds up a solid framework for taxonomic decisions of a clade of the family Flavobacteriaceae and will contribute to further insights into the evolution of this family.


Assuntos
Flavobacteriaceae , Água do Mar , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , Flavobacteriaceae/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
17.
Molecules ; 26(11)2021 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-34073991

RESUMO

Although axenic microbial cultures form the basis of many large successful industrial biotechnologies, the production of single commercial microbial strains for use in large environmental biotechnologies such as wastewater treatment has proved less successful. This study aimed to evaluate the potential of the co-culture of two halophilic bacteria, Marinirhabdus sp. and Marinobacter hydrocarbonoclasticus for enhanced protease activity. The co-culture was significantly more productive than monoculture (1.6-2.0 times more growth), with Marinobacter hydrocarbonoclasticus being predominant (64%). In terms of protease activity, enhanced total activity (1.8-2.4 times) was observed in the co-culture. Importantly, protease activity in the co-culture was found to remain active over a much broader range of environmental conditions (temperature 25 °C to 60 °C, pH 4-12, and 10-30% salinity, respectively). This study confirms that the co-culturing of halophilic bacteria represents an economical approach as it resulted in both increased biomass and protease production, the latter which showed activity over arange of environmental conditions.


Assuntos
Flavobacteriaceae/enzimologia , Marinobacter/enzimologia , Peptídeo Hidrolases/biossíntese , Técnicas de Cocultura , Flavobacteriaceae/crescimento & desenvolvimento , Concentração de Íons de Hidrogênio , Marinobacter/crescimento & desenvolvimento , Salinidade , Temperatura
18.
Artigo em Inglês | MEDLINE | ID: mdl-34085922

RESUMO

Two Gram-stain-negative and non-flagellated bacteria, YSTF-M3T and YSTF-M6T, were isolated from a tidal flat from Yellow Sea, Republic of Korea, and subjected to a polyphasic taxonomic study. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strains YSTF-M3T and YSTF-M6T belong to the genera Kordia and Olleya of the family Flavobacteriaceae, respectively. The 16S rRNA gene sequence similarities between strain YSTF-M3T and the type strains of Kordia species and between strain YSTF-M6T and the type strains of Olleya species were 94.1-98.4 and 97.3-98.3 %, respectively. The ANI and dDDH values between genomic sequences of strain YSTF-M3T and the type strains of five Kordia species and between those of strain YSTF-M6T and the type strains of three Olleya species were in ranges of 77.0-83.2 and 20.7-27.1 % and 79.4-81.5 and 22.3-23.9 %, respectively. The DNA G+C contents of strain YSTF-M3T and YSTF-M6T from genomic sequences were 34.1 and 31.1 %, respectively. Both strains contained MK-6 as predominant menaquinone and phosphatidylethanolamine as only major phospholipid identified. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strains YSTF-M3T and YSTF-M6T are separated from recognized species of the genera Kordia and Olleya, respectively. On the basis of the data presented, strains YSTF-M3T (=KACC 21639T=NBRC 114499T) and YSTF-M6T (=KACC 21640T=NBRC 114500T) are considered to represent novel species of the genera Kordia and Olleya, respectively, for which the names Kordia aestuariivivens sp. nov. and Olleya sediminilitoris sp. nov. are proposed.


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 , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
19.
Syst Appl Microbiol ; 44(3): 126209, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33992955

RESUMO

Two bacterial strains were isolated from a marine sediment sample taken from Jingzi Wharf, Weihai, China. These two strains were characterized at the phenotypic, chemotaxonomic, and genomic level. The two strains possessed almost identical 16S rRNA gene sequences (99.9 %). However, RAPD-PCR fingerprint patterns discriminated that they were not from one clonal origin. The average nucleotide identity (ANI) value and the digital DNA-DNA hybridization (dDDH) value between the two strains were 98.3 % and 85.4 %, respectively, suggestingthat they belonged to the same species. On the basis of the result of phylogenetic analysis of the 16S rRNA gene sequences, the two strains belonged to the genus Salegentibacter and were closely related to S. holothuriorum KCTC 12371T (98.6 %) and S. salegens DSM 5424T (98.2-98.3 %). The ANI and dDDH clearly separated strains F63223T and F60176 from the the most related type strains with values below the thresholds for species. The genome sizes of strains F63223T and F60176 were approximate 3.89 and 3.59 Mbp, respectively. The strain F63223T had 3,335 predicted genes with DNA G + C content of 35.6 %. The major respiratory quinone was MK-6 and the major polar lipids were phosphatidylethanolamine and one unidentified lipid. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic classification and genome analysis, the two isolates could be considered to represent a novel species of the genus Salegentibacter, for which the name Salegentibacter maritimus sp. nov., is proposed, with F63223T (=MCCC 1H00433T = KCTC 82417T) as the type strain.


Assuntos
Flavobacteriaceae/classificação , Sedimentos Geológicos , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Sedimentos Geológicos/microbiologia , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Técnica de Amplificação ao Acaso de DNA Polimórfico , Análise de Sequência de DNA
20.
ISME J ; 15(10): 3062-3075, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-33953365

RESUMO

Algal polysaccharides constitute a diverse and abundant reservoir of organic matter for marine heterotrophic bacteria, central to the oceanic carbon cycle. We investigated the uptake of alginate, a major brown macroalgal polysaccharide, by microbial communities from kelp-dominated coastal habitats. Congruent with cell growth and rapid substrate utilization, alginate amendments induced a decrease in bacterial diversity and a marked compositional shift towards copiotrophic bacteria. We traced 13C derived from alginate into specific bacterial incorporators and quantified the uptake activity at the single-cell level, using halogen in situ hybridization coupled to nanoscale secondary ion mass spectrometry (HISH-SIMS) and DNA stable isotope probing (DNA-SIP). Cell-specific alginate uptake was observed for Gammaproteobacteria and Flavobacteriales, with carbon assimilation rates ranging from 0.14 to 27.50 fg C µm-3 h-1. DNA-SIP revealed that only a few initially rare Flavobacteriaceae and Alteromonadales taxa incorporated 13C from alginate into their biomass, accounting for most of the carbon assimilation based on bulk isotopic measurements. Functional screening of metagenomic libraries gave insights into the genes of alginolytic Alteromonadales active in situ. These results highlight the high degree of niche specialization in heterotrophic communities and help constraining the quantitative role of polysaccharide-degrading bacteria in coastal ecosystems.


Assuntos
Flavobacteriaceae , Gammaproteobacteria , Microbiota , Flavobacterium , Gammaproteobacteria/genética , Polissacarídeos
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