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1.
Int J Syst Evol Microbiol ; 69(11): 3362-3367, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31622228

RESUMO

A novel Gram-stain-negative bacterium, designated as SCSIO 06110T, was isolated from a deep-sea sediment of the West Pacific Ocean. Cells were 0.5-0.8 µm in width and 3.0-4.0 µm in length, spore-forming, rod-shaped with peritrichous flagella. Positive for catalase and urease, negative for oxidase and nitrate reduction. Growth occurred at 15-37 °C, pH 6-9 and 1-5 % (w/v) NaCl, with optimum growth at 28 °C, pH 7 and 3 % (w/v) NaCl. MK-7 was the only menaquinone. The strain possessed diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified phospholipids. Iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0 were the major fatty acids. The novel isolate clustered with genera in the family Paenibacillaceae, but formed a separated branch with the closest relative Chengkuizengella sediminis J15A17T (91.1 % sequence similarity) when compared in a phylogenetic analysis of 16S rRNA gene sequences. The DNA G+C content of strain SCSIO 06110T was 38.5 mol%. Based on the polyphasic data presented, a new genus, Longirhabdus gen. nov., is proposed in the family Paenibacillaceae with the type species Longirhabdus pacifica sp. nov. and the type strain SCSIO 06110T (=DSM 105158T=CGMCC 1.16550T).


Assuntos
Bacillales/classificação , Sedimentos Geológicos/microbiologia , Fontes Hidrotermais/microbiologia , Filogenia , Bacillales/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Oceano Pacífico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
2.
Microbiol Res ; 229: 126331, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31521945

RESUMO

The uses of halotolerant bacteria isolated from naturally saline habitats have the potential to be useful crop protection agents for plants in stressful conditions. These beneficial microbes generate several plant growth regulators and bioactive molecules, which enhance plant protection from adversities, such as plant pathogens, salts and metals stresses. In this study, 15 halotolerant bacterial strains endowed with important antimicrobial activities were isolated from Sfax solar saltern (Tunisia). All of these strains were characterized by biochemical and molecular tools aiming to investigate their in-vitro and in-vivo antifungal potentialities, plant growth promotion capabilities and metal tolerance abilities under saline stress condition. The 16S rRNA gene sequencing showed that the isolated strains were affiliated to different phylum and three species were described for the first time as plant growth promoting strains (Idiomarina zobelli FMH6v, Nesterenkonia halotolerans FMH10 and Halomonas janggokensis FMH54). The tested strains exhibited several potentialities: to tolerate high salt and heavy metal concentrations, to produce biosurfactants, exopolysaccharides and extracellular hydrolytic enzymes, to form biofilms and to liberate plant promoting substances. Eight strains were able to protect tomatoes fruits from the proliferation of the fungal disease caused by Botrytis cinerea and six strains improved plant vigor indexes. Principal component analysis showed an important correlation between in-vitro and in-vivo potentialities and two strains Bacillus velezensis FMH2 and Bacillus subtilis subsp. spizizenii FMH45 were statistically considered as the most effective strains in protecting plants from fungal pathogens attack and promoting the growth of tomatoes seedlings under saline and multi heavy-metals stress conditions.


Assuntos
Bactérias/isolamento & purificação , Fenômenos Fisiológicos Bacterianos , Lycopersicon esculentum/microbiologia , Água do Mar/microbiologia , Cloreto de Sódio/metabolismo , Bactérias/classificação , Bactérias/genética , Botrytis/fisiologia , Lycopersicon esculentum/crescimento & desenvolvimento , Doenças das Plantas/microbiologia , Salinidade , Água do Mar/química , Plântula/crescimento & desenvolvimento , Plântula/microbiologia , Cloreto de Sódio/análise , Estresse Fisiológico , Tunísia
3.
J Microbiol ; 57(9): 759-768, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31376108

RESUMO

The cultivation of microbial species remains a primary challenge in microbiology and obtaining pure cultures is essential for the study of microbial physiology and function. When isolating microorganisms from aquaculture environments, Vibrio are the most dominate isolates on the media that are commonly used. In order to expand our ability to study microbial species, an easy-operation and low-cost medium that can reduce the interference of Vibrio strains and increase the cultivability of other bacteria is urgently needed. We compared viable cell counts on conventional media (CM; including Marine Agar 2216 and LB media) and diluted media (DM; including 1/10-Marine Agar 2216, 1/10-LB). We also assessed the diversity of cultivable microorganisms under high and low nutrient conditions by a plate-wash strategy coupled with high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene. The results show that microbial communities from DM, especially 1/10-Marine Agar 2216, are more diverse than those obtained from CM. Vibrio isolates were reduced on DM. PICRUSt analysis revealed that nutrient composition is a significant contributor to the diversity and function of the cultivable microbial communities. Bacteria grown on CM possess more pathogenic characteristics, whereas DM favors the growth of bacteria that have multiple metabolic functions. Collectively, our data provide strong evidence that dilution of CM influences the cultivability of bacteria from aquaculture seawater. It also supports that DM can expand the range of microbial species that can be cultivated. This study also provides insights for media design in microbial cultivation from aquaculture systems.


Assuntos
Meios de Cultura/metabolismo , Água do Mar/microbiologia , Vibrio/crescimento & desenvolvimento , Bactérias/classificação , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Bactérias/isolamento & purificação , Meios de Cultura/química , DNA Bacteriano/genética , Filogenia , RNA Ribossômico 16S/genética , Vibrio/genética , Vibrio/isolamento & purificação , Vibrio/metabolismo
4.
World J Microbiol Biotechnol ; 35(9): 133, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31432254

RESUMO

There is a significant increase in the discovery of new antimicrobial compounds in recent past to combat drug resistant pathogens. Members of the genus Bacillus and related genera have been screened extensively due to their ability to produce wide range of antimicrobial compounds. In this study, we have isolated and characterized a new antimicrobial peptide from a marine bacterium identified as Virgibacillus species. The low molecular mass and stability of the antimicrobial substance pointed towards the bacteriocinogenic nature of the compound. The RAST analysis of genome sequence showed presence of a putative bacteriocin biosynthetic cluster containing genes necessary for synthesis of a lanthipeptide. Translated amino acid sequence of mature C-terminal propeptide showed identity with salivaricin A (52.2%) and lacticin A (33.3%). Accordingly, the mass (2417 Da) obtained by MALDI analysis was in agreement with posttranslational modifications of the leader peptide to yield three methyl lanthionine rings and a disulfide bond between two free cysteine residues. The lanthipeptide was named as virgicin, which selectively inhibited the growth of Gram-positive bacteria and biofilm formation by Enterococcus faecalis. Inhibition of biofilm formation by E. faecalis was also observed in in vitro model experiments using hydroxyapatite discs. Thus, virgicin appears to be a promising new bacteriocin to control oral biofilm formation by selective pathogens.


Assuntos
Bacteriocinas/isolamento & purificação , Bacteriocinas/farmacologia , Enterococcus faecalis/efeitos dos fármacos , Enterococcus faecalis/crescimento & desenvolvimento , Peptídeos/isolamento & purificação , Peptídeos/farmacologia , Virgibacillus/metabolismo , Bacteriocinas/química , Bacteriocinas/genética , Biofilmes/efeitos dos fármacos , Biofilmes/crescimento & desenvolvimento , Vias Biossintéticas/genética , Genoma Bacteriano , Peso Molecular , Família Multigênica , Peptídeos/química , Peptídeos/genética , Água do Mar/microbiologia , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Virgibacillus/classificação , Virgibacillus/isolamento & purificação
5.
J Agric Food Chem ; 67(34): 9611-9617, 2019 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-31385500

RESUMO

Pullulanase is a commonly used debranching enzyme in the starch processing industry. Because the starch liquefaction process requires high temperature, a thermostable pullulanase is desired. Here, a novel hyperthermostable type II pullulanase gene (pulPY) was cloned from Pyrococcus yayanosii CH1, isolated from a deep-sea hydrothermal site. PulPY was optimally active at pH 6.6 and 95 °C, retaining more than 50% activity after incubation at 95 °C for 10 h. The thermostability was significantly higher than those of most pullulanases reported previously. To further improve its activity and thermostability, the N-terminal and C-terminal domains of PulPY were truncated. The optimum temperature of the combined truncation mutant Δ28N + Δ791C increased to 100 °C with a specific activity of 32.18 U/mg, which was six times higher than that of wild-type PulPY. PulPY and the truncation mutant enzyme could realize the combined use of pullulanase with α-amylase during the starch liquefaction process to improve hydrolysis efficiency.


Assuntos
Proteínas de Bactérias/metabolismo , Glicosídeo Hidrolases/metabolismo , Pyrococcus/enzimologia , Água do Mar/microbiologia , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Estabilidade Enzimática , Glicosídeo Hidrolases/química , Glicosídeo Hidrolases/genética , Concentração de Íons de Hidrogênio , Hidrólise , Cinética , Domínios Proteicos , Pyrococcus/química , Pyrococcus/genética , Pyrococcus/isolamento & purificação , Amido/metabolismo , Especificidade por Substrato , Temperatura Ambiente
6.
Int J Syst Evol Microbiol ; 69(10): 3022-3030, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31364965

RESUMO

Two novel strains, designated YLB-02T and YLB-04T, were isolated from the deep-sea sediments of Yap Trench located in the Pacific Ocean. Cells of the strains were Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YLB-02T belonged to the genus Oceanobacillus and strain YLB-04T belonged to the genus Bacillus. Strain YLB-02T showed similarities of 96.9 % with Ornithinibacillus contaminans CCUG 53201T, 96.3 % with Oceanobacillus profundus CL-MP28T, 96.1 % with Oceanobacillus halophilus J8BT and 95.7 % with Oceanobacillus bengalensis Ma-21T. Strain YLB-04T showed the highest sequence similarity of 97.4 % with Bacillus notoginsengisoli SYP-B691T. The average nucleotide identity (ANI) and the DNA-DNA hybridisation (DDH) estimate values for strain YLB-02T and YLB-04T with their related type strains were below the respective threshold for species differentiation. The G+C contents of strains YLB-02T and YLB-04T were 37.3 and 45.4 mol%. The predominant (>10 %) cellular fatty acids of strain YLB-02T were iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 1ω7c alcohol, and those of strain YLB-04T were C16 : 0, iso-C15 : 0, anteiso-C15 : 0 and C18 : 0. Their predominant ubiquinone was MK-7. The cell-wall peptidoglycan of strain YLB-02T contained glutamic acid, alanine, aspartic acid, lysine and ornithine, but no meso-diaminopimelic acid, while strain YLB-04T contained meso-diaminopimelic acid, glutamic acid, alanine, aspartic acid, lysine and ornithine. In addition to diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG), the polar lipids of strain YLB-02T also consisted of an unidentified glycolipid (GL), two unidentified polar lipids (L1 and L2) and two unidentified phospholipids (PL1 and PL2), and those of strain YLB-04T also consisted of phosphatidylethanolamine (PE) and an unidentified phospholipid (PL). Based on phenotypic, genotypic and chemotaxonomic characteristics, two novel species are proposed, Oceanobacillus piezotolerans sp. nov. with YLB-02T (=MCCC 1A12699T=JCM 32870T) and Bacillus piezotolerans sp. nov. with YLB-04T (=MCCC 1A12711T=JCM 32872T) as the type strains.


Assuntos
Bacillaceae/classificação , Bacillus/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Água do Mar/microbiologia , Bacillaceae/isolamento & purificação , Bacillus/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Oceano Pacífico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
7.
Int J Syst Evol Microbiol ; 69(10): 3293-3298, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31385783

RESUMO

A Gram-negative, rod-shaped, non-motile and strictly aerobic bacterium, designated ZQ420T, was isolated from marine sediment sampled on Zhoushan Island located in the East China Sea. Strain ZQ420T was able to grow at 10-45 °C, 0-12.0 % (w/v) NaCl and pH 5.5-9.0. Catalase and oxidase activities, nitrate reduction, H2S production, hydrolysis of starch, casein, Tween 20, 40 and 80 were positive. Indole, methyl red, Voges-Proskauer test, hydrolysis of gelatin and Tween 60 were negative. The major cellular fatty acids were C18 : 1 ω7c, C16 : 0 and 11-methyl C18 : 1ω7c. Ubiquinone-10 (Q-10) was the only detected respiratory quinone. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids, three unidentified glycolipids, two unidentified aminolipid and two unidentified lipids. The DNA G+C content was 64.8 mol%. According to 16S rRNA gene sequence similarities, strain ZQ420T shared 97.9, 96.3 and 96.3 % similarities to the following species with validated names Pararhodobacteraggregans D1-19T, Pseudo rhodobacter psychrotolerans PAMC27389T and Pseudo rhodobacter collinsensis 4-T-34T, respectively. While sharing lower sequence similarities (<96.0 %) to other type species. Phylogenetic analyses showed that strain ZQ420T and P. aggregans D1-19T formed an independent cluster in the phylogenetic trees. The average nucleotide identity value between strain ZQ420T and P. aggregans D1-19T was 79.1 %. The in silico DNA-DNA hybridization analysis revealed that strain ZQ420T shared 21.5 % DNA relatedness with P. aggregans D1-19T. On the basis of its phenotypic, chemotaxonomic and genotypic characteristics, strain ZQ420T is considered to represent a novel species in the genus Pararhodobacter, for which the name Pararhodobactermarinus sp. nov. is proposed. The type strain is ZQ420T (=KCTC 62579T=MCCC 1K03530T).


Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/química
8.
Int J Syst Evol Microbiol ; 69(10): 3305-3309, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31418672

RESUMO

A novel Gram-stain-negative, rod-shaped, beige-coloured, motile, facultatively anaerobic bacterium, designated as E84T, was isolated from sediment sampled from a marine solar saltern in Wendeng, PR China. Phylogenetic analysis based on 16S rRNA gene sequencing showed that Rhodosalinus sediminis WDN1C137T was the closest phylogenetic relationship, with 16S rRNA gene sequence similarity of 96.9 %. Optimal growth occurred at 33-37 °C (range, 20-40 °C), at pH 7.5 (pH 7.0-8.5) and with 6.0 % (w/v) NaCl (0.5-20.0 %). The sole respiratory quinone was Q-10. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C18 : 0 and cyclo C19 : 0ω8c. The polar lipids were phosphatidylglycerol, one unidentified glycolipid, two unidentified phospholipids and two unidentified lipids. The genomic DNA G+C content of strain E84T was 69.8 mol%. Based on the results of physiological, genotypic, phylogenetic and chemotaxonomic analyses, we concluded that strain E84T represents a novel species of the genus Rhodosalinus, for which the name Rhodosalinus halophilus sp. nov. is proposed. The type strain is E84T (=KCTC 52697T=MCCC 1H00231T).


Assuntos
Filogenia , Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Rhodobacteraceae/isolamento & purificação , Salinidade , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
9.
Int J Syst Evol Microbiol ; 69(11): 3405-3413, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31373895

RESUMO

Strain CECT 7735T, a marine Gram-reaction negative, aerobic, non-motile bacterium, was isolated from coastal seawater in Valencia, Spain. Strain CECT 7735T is chemoorganotrophic, mesophilic, slightly halophilic, grows at 15-28 °C but not at 4 or 37 °C, requires seawater for growth and grows up to 6 % salinity. The major cellular fatty acid is summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The G+C content of the genome is 55.7 mol%. Comparative analysis of the 16S rRNA gene sequence shows the strain is affiliated to the family Rhodobacteraceae, in the class Alphaproteobacteria, with highest similarities to Phaeobacter species (97.0-97.5 %), Shimia species (96.5-97.3 %) and Pseudopelagicola gijangensis (96.5 %). Further phylogenomic analysis through the up-to-date-bacterial core gene (UBCG) set showed P. gijangensis to be its closest relative. Average nucleotide identity and in silico DNA-DNA hybridization values are lower than 85 and 21 %, respectively, with its phylogenetic relatives, suggesting that strain CECT 7735T represents a new species. The average amino acid identity value was over 70 % with the genome of the type strain of P. gijangensis and with all those of Shimia species. These values, together with UBCG set trees, suggest that the new species and P. gijangensisbelong to the same genus and that Pseudopelagicola should be reclassified as a Shimia species. We conclude that strain CECT 7735T represents a new species in the genus Shimia, for which we propose the name Shimiathalassica sp. nov. In addition, Pseudopelagicola gijangensis is reclassified as Shimiagijangensis comb. nov. From the same phylogenomic study, it can be concluded that Thalassobius activus should be reclassified in the genus Cognatishimia as Cognatishimiaactiva comb. nov.


Assuntos
Filogenia , Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espanha
10.
Int J Syst Evol Microbiol ; 69(11): 3414-3419, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31380736

RESUMO

A Gram-negative bacterium, namely strain ANRC-JHZ47T, was isolated from a seawater sample collected at Biological Bay, Fildes Peninsula, Antarctica. Cells of strain ANRC-JHZ47T were rod-shaped and motile by a single polar flagellum. Strain ANRC-JHZ47T was aerobic, oxidase-negative, and catalase-positive. The strain grew at 4-37 °C (optimum, 25 °C), pH at 3.5-10.0 (optimum, pH 5.5) and in NaCl at 1-7.0 % (w/v; optimum, 2-3 %). Strain ANRC-JHZ47T used Q-8 as the predominant respiratory quinone. Its predominant fatty acids were C16 : 0 (21.9 %), C12 : 0 (12.6 %), C19 : 0cyclo ω8c (12.4 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 13.1 %), C10 : 0 3-OH (11.3 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 6.0 %). Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified aminolipid and five unknown polar lipids. The DNA G+C content was 42.6 mol%. Strain ANRC-JHZ47T showed the highest 16S rRNA gene sequence similarity to Marinomonas arenicola KMM 3893T (97.9 %), followed by Marinomonas primoryensis KMM 3633T (97.6 %), Marinomonas profundimaris D104T (97.2 %) and Marinomonas pollencensis IVIA-Po-185T (97.0 %). Furthermore, the average nucleotide identity values between strain ANRC-JHZ47T and M. arenicola KMM 3893T, M. primoryensis KMM 3633T and M. profundimaris D104T were 79.8, 74.0, and 74.1 %, respectively. The in silico DNA-DNA hybridization values between them were 22.5±2.5, 20.4±2.3 and 19.9±2.3 %, respectively. Based on the results of phenotypic and phylogenetic analyses, strain ANRC-JHZ47T is considered to represent a novel species of the genus Marinomonas, for which the name Marinomonas flavescens sp. nov. is proposed. The type strain is ANRC-JHZ47T (=MCCC 1K03604T=KCTC 72113T).


Assuntos
Marinomonas/classificação , Filogenia , Água do Mar/microbiologia , Regiões Antárticas , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Marinomonas/isolamento & purificação , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
11.
Int J Syst Evol Microbiol ; 69(11): 3593-3598, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31460859

RESUMO

A Gram-stain-negative, yellow-pigmented, aerobic bacterial strain, designated LPB0140T, was isolated from sea water. The 16S rRNA gene sequence similarity analysis demonstrated that the closest relative of the isolate is Sphingorhabdus contaminans (96.4 %), but the new isolate formed an independent phyletic line within the genus Sphingorhabdus. Its genome is composed of a circular chromosome of 2.53 Mb with DNA G+C content of 46.1 mol%. The genome includes 2359 protein-coding genes, and two copies of rRNA operons. Strain LPB0140T possessed C14 : 0 2-OH, C16 : 1ω7c and/or C16 : 1ω6c, and C18 : 1ω7c and/or C18 : 1ω6c as the major cellular fatty acids and Q-10 as the isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, and sphingoglycolipid, but phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine were also detected as minor polar lipids. The chemotaxonomic properties and enzymatic activities of the novel isolate clearly differed from those of its closest relatives. Thus, based on the phylogenetic and phenotypic data presented in this study, strain LPB0140T should be classified as a novel species in the genus Sphingorhabdus. The type strain is LPB0140T (=KACC18891T=JCM31568T).


Assuntos
Filogenia , Água do Mar/microbiologia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Sphingomonadaceae/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/química
12.
Int J Syst Evol Microbiol ; 69(9): 2892-2898, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31259677

RESUMO

A Gram-stain-negative, non-flagellated, catalase-positive, oxidase-positive bacterial strain, designated YLY08T, was isolated from the gut microflora of sea bass (Dicentrarchus labrax L.) collected from the coast of Yuanyao Wharf, Weihai, PR China, and subjected to a polyphasic taxonomic study. Strain YLY08T grew optimally at 28-30 °C, at pH 7.0-7.5 and in the presence of 2.0-3.0 % (w/v) NaCl. Poly-ß-hydroxybutyrate granules were produced. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain YLY08T clustered with the type strain of Oceaniglobus indicus, with which it exhibited 95.3 % sequence similarity, while the similarity to other genera was below 95.0 %. Genomic analyses, including average nucleotide identity and the digital DNA-DNA hybridization, clearly separated YLY08T from O. indicus MCCC 1A11863T with values below the thresholds for species delineation. The major cellular fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The sole respiratory quinone detected was Q-10. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, one unidentified aminolipid and one unidentified phospholipid. The genome of strain YLY08T, with 38 assembled contigs, was 3.9 Mb long with a G+C content of 59.0 mol%. The results of the phenotypical, phylogenetic and biochemical analyses between the strain YLY08T and the related type strain indicated that this strain represents a novel species in genus Oceaniglobus within the family Rhodobacteraceae, for which the name Oceaniglobus ichthyenteri sp. nov. is proposed. The type strain is YLY08T (=MCCC 1H00318T=KCTC 62182T).


Assuntos
Bass/microbiologia , Microbioma Gastrointestinal , Filogenia , Rhodobacteraceae/classificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hidroxibutiratos , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Poliésteres , RNA Ribossômico 16S/genética , Rhodobacteraceae/isolamento & purificação , Alimentos Marinhos/microbiologia , Água do Mar/microbiologia , Análise de Sequência de DNA
13.
Int J Syst Evol Microbiol ; 69(9): 2834-2840, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31274398

RESUMO

A Gram-stain-negative strain, designated FM6T, was isolated from surface seawater sampled at the port in Xiamen, PR China. Strain FM6T showed less than 96.3 % 16S rRNA gene sequence similarity to the type strains of species with validly published names. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FM6T belonged to the family Sphingomonadaceae and was closely related to species of the genera Sphingomonas (96.3 %) and Stakelama (96.0 %). Ubiquinone-10 was the predominant respiratory quinone. Cells were motile with a single polar flagellum. Growth occurred at temperatures from 20 to 45 °C (optimum, 30 °C), at pH values between pH 6.0 and 8.0 (optimum, pH 7.0) and in 0-4.0 % (w/v) NaCl (optimum, 1.0-1.5 %). Predominant polar lipids were sphingoglycolipid, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, five unidentified glycolipids and five unidentified polar lipids. The major fatty acids were summed feature 8 (containing C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of the type strain was 63.8 mol%. On the basis of the results of phylogenetic analysis, combined with phenotypic and chemotaxonomic data, strain FM6T is considered to represent a novel species in a new genus in the family Sphingomonadaceae for which the name Sphingosinithalassobacter portus gen. nov., sp. nov. is proposed. The type strain of Sphingosinithalassobacter portus gen. nov., sp. nov. is FM6T (=MCCC 1K03501T=JCM 32714T).


Assuntos
Filogenia , Água do Mar/microbiologia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sphingomonadaceae/isolamento & purificação , Ubiquinona/química
14.
J Agric Food Chem ; 67(33): 9307-9313, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31352784

RESUMO

Porphyra is one of the most consumed types of red algae. Porphyran is the major polysaccharide extracted from Porphyra, and it is composed of alternating 4-linked α-l-galactopyranose-6-sulfate (L6S) and 3-linked ß-d-galactopyranose (G) residues. ß-Porphyranases are promising tools for degrading porphyran; however, few enzymes have been reported, and the biochemical properties of porphyranases are still unclear. Here, a novel GH16 ß-porphyranase, designated as Por16A_Wf, was cloned from Wenyingzhuangia fucanilytica and expressed in Escherichia coli. Its biochemical properties and hydrolysis pattern were characterized. Por16A_Wf exhibited stable activity on a wide pH scale from 3.5 to 11.0. Glycomics analysis using LC-MS revealed that Por16A_Wf specifically hydrolyzed the glycosidic linkage of G-L6S, whereas it tolerated 3,6-anhydro-α-l-galactopyranose and methyl-d-galactose in -2 and +2 subsites, respectively. Por16A_Wf could be applied as a biotechnological tool for tailoring porphyran, which would serve in directional preparation of its disaccharide, producing products with various molecular weights and facilitating investigation of the structural heterogeneity of Porphyra polysaccharides.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Flavobacteriaceae/enzimologia , Glicosídeo Hidrolases/química , Glicosídeo Hidrolases/genética , Água do Mar/microbiologia , Sefarose/análogos & derivados , Sequência de Aminoácidos , Proteínas de Bactérias/metabolismo , Biocatálise , Biotecnologia , Clonagem Molecular , Estabilidade Enzimática , Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Flavobacteriaceae/isolamento & purificação , Glicosídeo Hidrolases/metabolismo , Concentração de Íons de Hidrogênio , Hidrólise , Peso Molecular , Filogenia , Porphyra/química , Porphyra/metabolismo , Sefarose/química , Sefarose/metabolismo , Alinhamento de Sequência
15.
Int J Syst Evol Microbiol ; 69(9): 2854-2861, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31274408

RESUMO

A Gram-stain-negative, non-motile, mesophilic, short rod-shaped, aerobic bacterium designated as 318-1T was isolated from a marine sediment collected from Masan Bay, South Korea. Strain 318-1T grew optimally at pH 6-7, at 30 °C and in the presence of 2-3 % (w/v) NaCl, tolerant of up to 8 % (w/v) NaCl, and accumulated poly-ß-hydroxybutyrate (PHB). A comparative analysis of 16S rRNA gene sequences revealed that strain 318-1T formed a distinct phyletic lineage in the genus Ruegeria (family Rhodobacteraceae, class Alphaproteobacteria) and showed high sequence similarity to Ruegeria halocynthiae DSM 27839T (96.5 %) and Shimia haliotis DSM 28453T (96.3 %). Comparing the genome sequence of 318-1T with those of the type strains of seven species of the genus Rugeria and two species of the genus Shimia, the values obtained were below the thresholds with analysis of average nucleotide identities (ANI, 71.6-76.8 %) and in silico DNA-DNA hybridisation, Genome-to-Genome Distance Calculator (GGDC, 18.5-20.6 %). The DNA G+C content was 65.75 mol%. Chemotaxonomic data [predominant quinone ubiquinone Q10; polar lipid profile consisting of major compounds phosphatidylcholine (PC), phosphatidylglycerol (PG), an unidentified aminolipid and an unidentified lipid; major fatty acids summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c)] supported the affiliation of strain 318-1T to the genus Ruegeria. Genomic, chemotaxonomic, and phenotypic differentiation of strain 318-1T from the members of the genus Ruegeria support it as a novel species. On the basis of the results in this study, a novel species, Ruegeria lutea sp. nov., is proposed. The type strain is 318-1T (=JCM 30927T=KEMB 7306-525T=KCTC 72105T).


Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Baías , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
16.
Int J Syst Evol Microbiol ; 69(10): 3049-3055, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31287397

RESUMO

A Gram-stain-negative, strictly aerobic, non-motile and ovoid- or rod-shaped bacterial strain, JBTF-M29T, was isolated from tidal flat sediment sampled from the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain JBTF-M29T clustered with the type strains of Maribius species and this cluster joined the clade comprising Pseudomaribius and Palleronia species. Strain JBTF-M29T exhibited 16S rRNA gene sequence similarity values of 96.2-96.6 % to the type strains of three Maribius species, of 96.4 % to the type strain of Pseudomaribius aestuariivivens and of 93.9-94.7 % to the type strains of three Palleronia species. In the UPGMA dendrogram based on the ANI values of genomic sequences, strain JBTF-M29T formed an evolutionary lineage independent of the genera Maribius and Palleronia and some other taxa. Strain JBTF-M29T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C18 : 0 as the major fatty acids. The major polar lipids of strain JBTF-M29T were phosphatidylglycerol and one unidentified aminolipid. The DNA G+C content of strain JBTF-M29T was 64.5 mol%. The differences in fatty acid and polar lipid profiles and other differential phenotypic properties including nitrate reduction and casein hydrolysis made it reasonable to distinguish strain JBTF-M29T from the genera Maribius, Pseudomaribius and Palleronia. Therefore, on the basis of the polyphasic taxonomic data presented here, strain JBTF-M29T constitutes a new genus and species within the class Alphaproteobacteria, for which the name Paenimaribius caenipelagi gen. nov., sp. nov. is proposed. The type strain is JBTF-M29T (=KACC 19867T=NBRC 113548T).


Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfatidilgliceróis/química , RNA Ribossômico 16S/genética , República da Coreia , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
17.
Int J Syst Evol Microbiol ; 69(10): 3109-3115, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31334695

RESUMO

A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated MYP11T, was isolated from seawater around Jeju island, Republic of Korea and identified by polyphasic taxonomic study. A neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain MYP11T joined the cluster comprising the type strains of Shimiaabyssi, Shimiaaestuarii and Shimiaaquaeponti, showing 16S rRNA gene sequence similarities of 96.3-96.8 %. Strain MYP11T exhibited 16S rRNA gene sequence similarity values of 94.2-94.9 % to the type strains of other Shimia species. In the upgma dendrogram based on the average nucleotide identity values of genomic sequences, strain MYP11T formed an evolutionary lineage independent of those of Shimia species and other taxa. Strain MYP11T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and cyclo C19 : 0 ω8c as the major fatty acids. The major polar lipids of strain MYP11T were phosphatidylcholine, phosphatidylglycerol, two unidentified lipids and one unidentified aminolipid. The DNA G+C content of strain MYP11T was 63.1 or 61.5 mol%. The differences in the fatty acid and polar lipid profiles and DNA G+C contents made it reasonable to distinguish strain MYP11T from the type strains of S. abyssi, S. aestuarii and S. aquaeponti and those of other Shimia species. On the basis of the polyphasic data presented here, strain MYP11T is considered to constitute a new genus and species within the class Alphaproteobacteria, for which the name Aliishimia ponticola gen. nov., sp. nov. is proposed. The type strain is MYP11T (=KCTC 62899T=NBRC 113544T).


Assuntos
Filogenia , Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
18.
Environ Pollut ; 252(Pt B): 1633-1642, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31284205

RESUMO

AmpC beta-lactamase genes are some of the most common antibiotic resistance genes and require special attention once they have become mobilised. The detection of these genes is well documented in clinical settings. However, there is insufficient knowledge of both plasmid and genomic AmpC genes in aquatic environments. This systematic review aimed to determine the extent of the knowledge gap in the literature regarding the prevalence of AmpC beta-lactamase genes in aquatic systems. Using selected criteria, a total of 27 databases were searched for applicable peer-reviewed journal articles. No date and language restrictions were applied. Journal articles that highlighted the detection of AmpC beta-lactamase genes in environmental aquatic systems, including wastewater treatment plants, were included. Of the 950 literature sources that were identified, 50 were selected for full text analysis based on predetermined criteria. Studies on AmpC genes detection were traced in 23 countries. These studies focused on surface water (24), wastewater (17), sea water (4) and both surface and wastewater (5). Most studies did not specifically aim to detect AmpC genes, but to detect antibiotic resistance genes in general. Presently no surveillance protocols, standardised detection methods or environmental limits exist for these genes and, due to a paucity of research in this field, it is unlikely that such systems will be implemented in the near future. The implications and dynamics of AmpC genes in aquatic systems remain unclear and require intense research to ensure the sustainability of environmental systems and human health.


Assuntos
Proteínas de Bactérias/genética , Farmacorresistência Bacteriana/genética , Água Doce/microbiologia , Genes Bacterianos , Água do Mar/microbiologia , Águas Residuárias/microbiologia , beta-Lactamases/genética , Humanos , Plasmídeos/análise
19.
Environ Pollut ; 252(Pt B): 1659-1670, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31284208

RESUMO

The Yangtze River, which is the largest in Euro-Asian, receives tremendous anthropogenic nitrogen input and is typically characterized by severe eutrophication and hypoxia. Two major processes, denitrification and anaerobic ammonium oxidation (anammox), play vital roles for removing nitrogen global in nitrogen cycling. In the current study, sediment samples were collected from both latitudinal and longitudinal transects along the coastal Yangtze River and the East China Sea (ECS). We investigated community composition and distributions of nosZ gene-encoded denitrifiers by high throughput sequencing, and also quantified the relative abundances of both denitrifying and anammox bacteria by q-PCR analysis. Denitrifying communities showed distinct spatial distribution patterns that were impacted by physical (water current and river runoffs) and chemical (nutrient availability and organic content) processes. Both denitrifying and anammox bacteria contributed to the nitrogen removal in Yangtze Estuary and the adjacent ECS, and these two processes shifted from coastal to open ocean with reverse trends: the abundance of nosZ gene decreased from coastal to open ocean while anammox exhibited an increasing trend based on quantifications of hzsB and 16S rRNA genes. Further correspondence correlation analysis revealed that salinity and nutrients were the main factors in structuring composition and distribution of denitrifying and anammox bacteria. This study improved our understanding of dynamic processes in nitrogen removal from estuarine to open ocean. We hypothesize that denitrification is the major nitrogen removal pathway in estuaries, but in open oceans, low nutrient and organic matter concentrations restrict denitrification, thus increasing the importance of anammox as a nitrogen removal process.


Assuntos
Amônia/metabolismo , Estuários , Ciclo do Nitrogênio , Nitrogênio/metabolismo , Rios/microbiologia , Água do Mar/microbiologia , China , Desnitrificação , Genes Bacterianos , Ciclo do Nitrogênio/genética , Oceanos e Mares , Oxirredução , Rios/química , Salinidade , Água do Mar/química
20.
Microbiol Res ; 226: 65-73, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31284946

RESUMO

Bacterial communities are resilient to the environmental changes, yet the effect of long term ecological changes on bacterial communities remain poorly explored. To study the effect of prolonged environmental changes, a 25 m long sediment core was excavated from a paleo beach ridge located on the Cauvery delta, south east coast of India. Geological evidences suggested that the site has experienced multiple marine transgressions and regressions. The three paleosols from Vettaikaraniruppu (VKI) beach ridge, VKI-2 (2.8 m bgl; 3 kybp), VKI-5 (7.2 m bgl; 6 kybp) and VKI-14 (24.5 m bgl; 146 kybp) was chosen for bacterial community analysis based on their formation period. Bacterial community structure of paleosols was reconstructed using V3 hypervariable region of bacterial 16S rDNA targeted Illumina sequencing. The VKI-5 sediment layer which formed under marine environment contained highest bacterial diversity, and the community was a mix up of terrestrial and marine bacterial population. The final community VKI-2 exhibited an approximate structural pattern witnessed in the native bacterial community VKI-14 which formed during marine regression. Furthermore, marine transgression and regression experienced in VKI resulted in the formation of distinct biogeographic patterns.


Assuntos
Bactérias/classificação , Biodiversidade , Ecossistema , Microbiota , Água do Mar/microbiologia , Bactérias/genética , DNA Bacteriano/genética , DNA Ribossômico/genética , Ecologia , Sedimentos Geológicos/microbiologia , Índia , Biologia Marinha , Microbiota/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência
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