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1.
Int J Syst Evol Microbiol ; 70(10): 5467-5472, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32894210

RESUMO

A Gram-stain-positive, facultatively anaerobic, endospore-forming bacterium, designated strain TD8T, was isolated from surface-sterilized rice seeds (Oryza sativa L.). Phylogenetic analysis of the 16S rRNA gene indicated that strain TD8T should be placed within the genus Gracilibacillus (95.2-99.0 % sequence similarity); it exhibited highest similarities to Gracilibacillus ureilyticus CGMCC 1.7727T (99.0 %), 'Gracilibacillus xinjiangensis' CGMCC 1.12449T (98.9 %) and Gracilibacillus dipsosauri CGMCC 1.3642T (97.5 %). Chemotaxonomic analysis showed that menaquinone-7 (MK-7) was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid were the major cellular polar lipids, and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0, which supported the allocation of the strain to the genus Gracilibacillus. The digital DNA-DNA hybridization value between strain TD8T and Gracilibacillus ureilyticus CGMCC 1.7727T was lower than 70 % (22.60 %), and the average nucleotide identity score was 79.54±5.09 %, suggesting that strain TD8T represented a novel species in the genus Gracilibacillus. The genomic DNA G+C content was 37.5 %. Based on physiological and biochemical characteristics and genotypic data, strain TD8T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus oryzae sp. nov. is proposed. The type strain is TD8T (=ACCC 61556T=CICC 24889T=JCM 33537T).


Assuntos
Bacillaceae/classificação , Oryza/microbiologia , Filogenia , Sementes/microbiologia , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
2.
Int J Syst Evol Microbiol ; 70(10): 5211-5216, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32816657

RESUMO

A Gram-stain-positive, endospore-forming, motile and rod-shaped bacterium, designated as strain DSL-17T, was isolated from a tidal sediment of the East China Sea and characterized phylogenetically and phenotypically. The strain could grow at 16-47 °C (optimum 37 °C), at pH 6.0-10.0 (optimum 6.0) and with 1-7% (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DSL-17T was related to members of the genus Metabacillus and shared the highest similarity with Metabacillus litoralis SW-211T (98.6 %), followed by Metabacillus halosaccharovorans E33T (97.9 %), Metabacillus crassostreae JSM 100118T (97.7 %), Metabacillus niabensis 4T19T (97.7 %) and Metabacillus malikii NCCP-662T (97.5 %). 16S rRNA gene sequence similarities between strain DSL-17T and other members of the genus Metabacillus were below 96.6 %. The sole respiratory quinone was MK-7. Strain DSL-17T had a cell-wall peptidoglycan based on meso-diaminopimelic acid. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), three unidentified glycolipids and six unidentified lipids. The strain had iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0, C16 : 0 and iso-C16 : 0 as major fatty acids. The G+C content of the genomic DNA was 35.7 mol%. The combined genotypic and phenotypic data indicated that strain DSL-17T represents a novel species of the genus Metabacillus, for which the name Metabacillus sediminilitoris sp. nov. is proposed The type strain is DSL-17T (=MCCC 1K03777T=DSM 109843T).


Assuntos
Bacillaceae/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Água do Mar/microbiologia , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Peptidoglicano/química , Fosfolipídeos/química , 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): 4145-4150, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32519940

RESUMO

A Gram-stain-positive, catalase-positive, facultatively anaerobic, terminal-spore-forming rod, designated strain BCM23-1T, was isolated from bark of Tamarindus indica collected from Chiang Mai Province, Thailand. This strain produced d-lactic acid from glucose. It grew at 20-45 °C (optimum, 30 °C), pH 3.5-9 (optimum, pH 7.0) and in the presence of 1-4 % (w/v) NaCl. The cell-wall peptidoglycan contained meso-diaminopimelic acid (A1γ). The major isoprenoid quinone was menaquinone 7 (MK-7). Polar lipids analysis revealed the presence of diphosphatidylglycerol, phosphatidylglycerol, an unidentified aminophospholipid, an unidentified phospholipid and an unidentified lipid. The predominant cellular fatty acids were anteiso-C17 : 0, anteiso-C15:0, and iso-C16 : 0 when cultivated on GYP agar plates. The 16S rRNA gene sequence similarity between strain BCM23-1T and Terrilactibacillus laevilacticus NK26-11T was 98.3 %. The draft genome of BCM23-1T was 3.24 Mb in size and contained 3088 coding sequences with an in silico DNA G+C content of 37.1 mol%. The values of ANIb, ANIm and digital DNA-DNA hybridization between strain BCM23-1T and T. laevilacticus NK26-11T were 89.9, 90.8 and 40.4 %, respectively. The results of phenotypic and chemotaxonomic, 16S rRNA gene sequence similarity, and whole genome analyses support strain BCM23-1T as representing a novel species of Terrilactibacillus for which the name Terrilactibacillus tamarindi sp. nov. is proposed. The type strain is BCM23-1T (=LMG 31662T=JCM 33748T=TISTR 2841T).


Assuntos
Bacillaceae/classificação , Filogenia , Casca de Planta/microbiologia , Tamarindus/microbiologia , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tailândia , Vitamina K 2/análogos & derivados , Vitamina K 2/química
4.
Int J Syst Evol Microbiol ; 70(6): 3763-3774, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32496179

RESUMO

Eight Gram-stain-positive, rod-shaped bacterial strains were isolated from faeces of Tibetan antelopes on the Tibet-Qinghai Plateau of China. Genomic sequence analysis showed that the strains belong to the genera Actinomyces (strains 299T and 340), Corynebacterium (strains 2184T, 2185, 2183T and 2189) and Oceanobacillus (strains 160T and 143), respectively, with a percentage of similarity for the 16S rRNA gene under the species threshold of 98.7 % except for strains 160T and 143 with Oceanobacillus arenosus CAU 1183T (98.8 %). The genome sizes (and genomic G+C contents) were 3.1 Mb (49.4 %), 2.5 Mb (64.9 %), 2.4 Mb (66.1 %) and 4.1 Mb (37.1 %) for the type strains 299T, 2183T, 2184T and 160T, respectively. Two sets of the overall genome relatedness index values between our isolates and their corresponding closely related species were under species thresholds (95 % for average nucleotide identity, and 70 % for digital DNA-DNA hybridization). These results, together with deeper genotypic, genomic, phenotypic and biochemical analyses, indicate that these eight isolates should be classified as representing four novel species. Strain 299T (=CGMCC 1.16320T=JCM 33611T) is proposed as representing Actinomyces wuliandei sp. nov.; strain 2184T (=CGMCC 1.16417T=DSM 106203T) is proposed as representing Corynebacterium liangguodongii sp. nov.; strain 2183T (=CGMCC 1.16416T=DSM 106264T) is proposed as representing Corynebacterium yudongzhengii sp. nov.; and strain 160T (=CGMCC 1.16367T=DSM 106186T) is proposed as representing Oceanobacillus zhaokaii sp. nov.


Assuntos
Actinomyces/classificação , Antílopes/microbiologia , Bacillaceae/classificação , Corynebacterium/classificação , Fezes/microbiologia , Filogenia , Actinomyces/isolamento & purificação , Animais , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , Corynebacterium/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tibet
5.
Clin Oral Investig ; 24(6): 2099-2108, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32377864

RESUMO

OBJECTIVES: The aim of this study was to evaluate the composition of microbiota of irreversible pulpitis and primary endodontic infections with respect to clinical and radiographic findings by performing cultures and 16s rDNA sequencing in Iranian patients. MATERIAL AND METHODS: In this prospective cross-sectional study, samples were collected from 41 root canals for 4 main groups of patients. Bacterial identification was performed by the polymerase chain reaction (PCR) and 16s rDNA sequencing of aerobic and anaerobic cultivable colonies taken from patients' culture plates. Additionally, the presence of 13 bacterial species and 3 nonbacterial species was also explored using PCR and species-specific primers. RESULTS: Sixteen microbial species, 1 fungus (Candida albicans), and 1 virus (Herpes simplex virus) were discovered and isolated. Species with the highest prevalence were Dialister invisus (68.3%), Porphyromonas gingivalis (58.8%), Streptococcus salivarius (58.5%), and Treponema denticola (56.1%). Lysinibacillus fusiformis (19.1%) was detected in the root canals for the first time. Candida albicans was seen in 11 cases (26.8%). Herpes simplex virus (HSV) was seen in 4 patients (9.8%). CONCLUSIONS: Our results suggest that Gram-negative anaerobic oral bacteria are the majority of the microbes in primary endodontic infections. Various combinations of bacterial species were related to different clinical and radiographic conditions. Lysinibacillus fusiformis was detected for the first time in primary endodontic infections. CLINICAL RELEVANCE: The results of this investigation might help clinicians choose to identify suspected endodontic pathogens in the etiology of each form of pulpal and periradicular diseases to determine the best therapeutic measures.


Assuntos
Bacillaceae , Infecções , Pulpite , Bacillaceae/isolamento & purificação , Estudos Transversais , DNA Bacteriano , Cavidade Pulpar , Humanos , Irã (Geográfico) , Estudos Prospectivos , Pulpite/diagnóstico , Pulpite/microbiologia , Veillonellaceae
6.
Int J Syst Evol Microbiol ; 70(6): 3701-3710, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32416748

RESUMO

A moderately halophilic strain, designated SCU50T, was recovered from a saline soil sample and characterized by a polyphasic approach. The 16S rRNA gene sequence analysis showed that strain SCU50T belonged to the genus Gracilibacillus and was most closely related to Gracilibacillus thailandensis TP2-8T (98.1 % similarity) and Gracilibacillus orientalis XH-63T (97.7 %). Genomic average nucleotide identity and digital DNA-DNA hybridization analyses confirmed the separate species status of the new isolate relative to other recognized Gracilibacillus species. The genome size was about 5.09 Mbp and the DNA G+C content was 36.7 mol%. The strain grew optimally at 10-15 % (w/v) NaCl, pH 6.5-7.5 and 25-30 °C. It contained anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 as the dominant fatty acids and menaquinone-7 as the major respiratory quinone. The polar lipid profile was examined and found to comprise diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and one unidentified lipid. The cell-wall peptidoglycan type was A1γ based on meso-diaminopimelic acid. Combining the data from phenotypic, chemotaxonomic, genomic and phylogenetic characterization, it was concluded that strain SCU50T should be assigned as representing a novel species within the genus Gracilibacillus. Thus, a novel taxon named Gracilibacillus salitolerans sp. nov. was first established, with SCU50T (=CGMCC 1.17336T=KCTC 43107T) as the type strain.


Assuntos
Bacillaceae/classificação , Filogenia , Salinidade , Microbiologia do Solo , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Cloreto de Sódio , Vitamina K 2/análogos & derivados , Vitamina K 2/química
7.
Int J Syst Evol Microbiol ; 70(5): 3295-3299, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32375943

RESUMO

A Gram-stain-positive, motile, rod-shaped and endospore-forming strain, SYSU K30002T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-west China. SYSU K30002T grew at 28-40 °C (optimum, 37 °C), at pH 5.0-8.0 (optimum, pH 7.0) and in the presence of 0-4 % (w/v) NaCl (optimum in the absence of NaCl). The cell-wall peptidoglycan type was A4α (Lys-Asp). The cell-wall sugars of SYSU K30002T were ribose, galactose and mannose, and MK-7 was the menaquinone. The major fatty acids were iso-C15 : 0, C16 : 1 ω7c alcohol and iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids. The G+C content of the genomic DNA was 36.1 mol%. The average nucleotide identity values between SYSU K30002T and its closest relatives were below the cut-off level (95-96 %) for species delineation. Based on phenotypic, chemotaxonomic and genome comparisons, strain SYSU K30002T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillusantri sp. nov. is proposed. The type strain is SYSU K30002T (=KCTC 33955T=CGMCC 1.13504T).


Assuntos
Bacillaceae/classificação , Cavernas/microbiologia , Filogenia , Microbiologia do Solo , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
8.
PLoS One ; 15(4): e0231426, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32271848

RESUMO

Demand for agricultural crop continues to escalate in response to increasing population and damage of prime cropland for cultivation. Research interest is diverted to utilize soils with marginal plant production. Moisture stress has negative impact on crop growth and productivity. The plant growth promoting rhizobacteria (PGPR) and plant growth regulators (PGR) are vital for plant developmental process under moisture stress. The current study was carried out to investigate the effect of PGPR and PGRs (Salicylic acid and Putrescine) on the physiological activities of chickpea grown in sandy soil. The bacterial isolates were characterized based on biochemical characters including Gram-staining, P-solubilisation, antibacterial and antifungal activities and catalases and oxidases activities and were also screened for the production of indole-3-acetic acid (IAA), hydrogen cyanide (HCN) and ammonia (NH3). The bacterial strains were identified as Bacillus subtilis, Bacillus thuringiensis and Bacillus megaterium based on the results of 16S-rRNA gene sequencing. Chickpea seeds of two varieties (Punjab Noor-2009 and 93127) differing in sensitivity to drought were soaked for 3 h before sowing in fresh grown cultures of isolates. Both the PGRs were applied (150 mg/L), as foliar spray on 20 days old seedlings of chickpea. Moisture stress significantly reduced the physiological parameters but the inoculation of PGPR and PGR treatment effectively ameliorated the adverse effects of moisture stress. The result showed that chickpea plants treated with PGPR and PGR significantly enhanced the chlorophyll, protein and sugar contents. Shoot and root fresh (81%) and dry weights (77%) were also enhanced significantly in the treated plants. Leaf proline content, lipid peroxidation and antioxidant enzymes (CAT, APOX, POD and SOD) were increased in reaction to drought stress but decreased due to PGPR. The plant height (61%), grain weight (41%), number of nodules (78%) and pod (88%), plant yield (76%), pod weight (53%) and total biomass (54%) were higher in PGPR and PGR treated chickpea plants grown in sandy soil. It is concluded from the present study that the integrative use of PGPR and PGRs is a promising method and eco-friendly strategy for increasing drought tolerance in crop plants.


Assuntos
Agricultura , Bacillaceae/fisiologia , Cicer/crescimento & desenvolvimento , Reguladores de Crescimento de Planta/farmacologia , Amônia/metabolismo , Bacillaceae/genética , Bacillaceae/isolamento & purificação , Bacillus megaterium/genética , Bacillus megaterium/isolamento & purificação , Bacillus subtilis/genética , Bacillus subtilis/isolamento & purificação , Bacillus subtilis/fisiologia , Biomassa , Clorofila/análise , Cicer/efeitos dos fármacos , Cicer/metabolismo , Ácidos Indolacéticos/metabolismo , Peroxidação de Lipídeos/efeitos dos fármacos , Reguladores de Crescimento de Planta/metabolismo , Folhas de Planta/metabolismo , Proteínas de Plantas/metabolismo , Raízes de Plantas/metabolismo , Raízes de Plantas/microbiologia , Putrescina/metabolismo , Putrescina/farmacologia , RNA Ribossômico 16S/química , RNA Ribossômico 16S/metabolismo , Chuva , Ácido Salicílico/metabolismo , Ácido Salicílico/farmacologia , Plântula/efeitos dos fármacos , Plântula/crescimento & desenvolvimento , Microbiologia do Solo
9.
Arch Microbiol ; 202(6): 1545-1549, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32246163

RESUMO

A bacterial strain, designated YIM 98839T, was isolated from the hypersaline sediment of Aiding Lake in Xinjiang province, North-West China. The strain was Gram-stain-positive, motile, aerobic, produced oval subterminal or central endospores in swollen sporangia. The whole-cell hydrolysates contain meso-diaminopimelic acid as the diagnostic cell-wall diamino acid. Galactose, fucose and ribose are the major whole-cell sugars. The phospholipids are diphosphatidylglycerol, phosphatidylglycerol and one unknown phospholipid. The predominant menaquinone is MK-7. The major fatty acids are anteiso-C15:0, anteiso-C17:0 and iso-C15:0. The DNA G + C content of the type strain is 37.0 mol%. Phylogenetic analysis indicated that the isolate belongs to the genus Oceanobacillus. However, it differed from its closest relative, Oceanobacillus limi H9BT in many physiological characteristics. Moreover, the DNA-DNA relatedness values between the novel isolate and the relative type strain was 20.2%. Based on comparative analysis of polyphasic taxonomic data, strain YIM 98839T represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus halotolerans sp. nov. is proposed. The type strain is YIM 98839T (= CGMCC 1.17002T = KCTC 43140T).


Assuntos
Bacillaceae/classificação , Bacillaceae/genética , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases/genética , Parede Celular/química , China , DNA Bacteriano/genética , Ácido Diaminopimélico/análise , Ácidos Graxos/análise , Lagos/microbiologia , Fosfolipídeos/análise , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
10.
Arch Microbiol ; 202(6): 1529-1534, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32232517

RESUMO

A Gram-staining positive, motile, rod-shaped and subterminal endospore-forming bacterium, designated strain SYSU K30005T, was isolated from a soil sample collected from a karst cave in Libo county, Guizhou province, south-western China. Strain SYSU K30005T showed the highest 16S rRNA gene sequence similarity with Lysinibacillus fusiformis (98.6%) and Lysinibacillus sphaericus (98.2%). In phylogenetic tree, strain SYSU K30005T clade with the members of the genus Lysinibacillus. Based on the phylogenetic and 16S gene sequence result, strain SYSU K30005T was affiliated to the genus Lysinibacillus. The growth of SYSU K30005T was observed at 15-37 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-4% (w/v) NaCl (optimum in 3.5% NaCl). Cell wall peptidoglycan type was A4α (Lys-Asp). The cell-wall sugars of SYSU K30005T were ribose, galactose and mannose and MK-7 was the only quinone. The fatty acids (> 5% of total fatty acids) were iso-C15:0, anteiso-C15:0, iso-C16:0 and iso-C17:0. The polar lipids profile included diphosphatidylglycerol, phosphatideylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The genomic DNA G + C content was 37.2 mol%. The average nucleotide identity values between SYSU K30005T and its closest relatives were below the cut-off level (95-96%) for species delineation. The results support the conclusion that strain SYSU K30005T represents a novel species of the genus Lysinibacillus, for which we proposed the name Lysinibacillus cavernae sp. nov. The type strain is SYSU K30005T (= KCTC 43130T = CGMCC 1.17492T).


Assuntos
Bacillaceae/classificação , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases/genética , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Solo , Microbiologia do Solo
11.
Arch Microbiol ; 202(6): 1469-1476, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32193578

RESUMO

A novel Gram-stain-positive, motile, moderate halophile, strain L9T, was isolated from hides of white goat in China. The isolate grew optimally at 30 °C, at pH 7 and with 5-10% (w/v) NaCl. The predominant menaquinone was MK-7, and the major cellular fatty acids were identified as iso-C15:0 and anteiso-C15:0. The peptidoglycan amino acid type was determined to be A4ß, containing L-ornithine and D-aspartic as diagnostic amino acids. The phospholipids were dominated by diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid and two unidentified phospholipids. Genome sequencing resulted in a genome size of 4.0 Mbp and a DNA G + C content of 35.9 mol%. Phylogenetic trees based on the 16S rRNA gene sequences showed the isolate to be closely related to Oceanobacillus limi H9BT (98.2% similarity) and Ornithinibacillus halophilus G8BT (97.5% similarity). The ANI and dDDH values between strain L9T and the closely related species were 69.8-76.1% and 13.0-20.5%, respectively. On the basis of the data presented, strain L9T represents a novel species of the genus Ornithinibacillus, for which the name Ornithinibacillus caprae sp. nov. is proposed. The type strain is L9T (= KCTC 43176T = CGMCC 1.17659T).


Assuntos
Bacillaceae/classificação , Bacillaceae/isolamento & purificação , Cabras/microbiologia , Aminoácidos/análise , Animais , Bacillaceae/genética , Técnicas de Tipagem Bacteriana , Composição de Bases/genética , DNA Bacteriano/genética , Ácidos Graxos/análise , Peptidoglicano/química , Fosfolipídeos/análise , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Cloreto de Sódio/metabolismo
12.
Int J Syst Evol Microbiol ; 70(4): 2359-2365, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32065575

RESUMO

A Gram-stain-positive, motile, facultatively anaerobic, non-sporing, and rod-shaped bacterial strain, designated HF60T, was isolated from the Red Maple Lake of Guizhou Province, China. The DNA G+C content of the strain HF60T was 55.0 %. The predominant isoprenoid quinones were identified as MK-7 (56.4 %) and MK-8 (35.7 %). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and aminophosphoglycolipid. The major fatty acids were anteiso-C13 : 0, iso-C15 : 0, C16 : 0 and iso-C13 : 0. The strain had cell wall peptidoglycan type A3α l-Lys-Gly. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain HF60T belonged to the genus Exiguobacterium and was most closely related to Exiguobacterium sibiricum JCM 13490T (97.2 % 16S rRNA gene sequence similarity), followed by Exiguobacterium undae DSM 14481T (97.1 %), Exiguobacterium antarcticum DSM 14480T (96.9 %) and Exiguobacterium aurantiacum NBRC 14763T (94.5 %). The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness indicated that strain HF60T can be considered to represent a novel species of the genus Exiguobacterium, for which the name Exiguobacterium flavidum sp. nov. is proposed, The type strain is HF60T (=MCCC 1H00336T=KCTC 33987T).


Assuntos
Bacillaceae/classificação , Lagos/microbiologia , Filogenia , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
13.
Ecotoxicol Environ Saf ; 192: 110250, 2020 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-32028154

RESUMO

A bacterial strain designated Lysinibacillus fusiformis 15-4 was isolated from oil-free soil on the Qinghai-Tibet Plateau, which can grow well utilizing petroleum hydrocarbons as a carbon source at a lower temperature. To deeply characterize the molecular adaptations and metabolic processes of this strain when grown in a petroleum-containing environment, transcriptome analysis was performed. A total of 4664 genes and the expression of 3969 genes were observed in strain 15-4. When the strain was grown in petroleum-containing medium, 2192 genes were significantly regulated, of which 1312 (60%) were upregulated and 880 (40%) were downregulated. This strain degraded and adapted to petroleum via modulation of diverse molecular processes, including improvements in transporter activity, oxidoreductase/dehydrogenase activity, two-component system/signal transduction, transcriptional regulation, fatty acid catabolism, amino acid metabolism, and environmental stress responses. Many strain-specific genes were involved in the oxidation of hydrocarbon compounds, such as several luciferase family alkane monooxygenase genes, flavin-utilizing monooxygenase family genes, and flavoprotein-like family alkanesulfonate monooxygenase genes. Several cold shock protein genes were also induced suggesting adaptation to cold environments and the potential for petroleum degradation at low temperatures. The results obtained in this study may broaden our understanding of molecular adaptation of bacteria to hydrocarbon-containing environments and may provide valuable data for further study of L. fusiformis.


Assuntos
Bacillaceae/genética , Bacillaceae/metabolismo , Petróleo/metabolismo , Transportadores de Cassetes de Ligação de ATP/metabolismo , Adaptação Fisiológica , Bacillaceae/isolamento & purificação , Biodegradação Ambiental , Proteínas e Peptídeos de Choque Frio/biossíntese , Proteínas e Peptídeos de Choque Frio/genética , Temperatura Baixa , Perfilação da Expressão Gênica , Regulação Bacteriana da Expressão Gênica , Hidrocarbonetos/metabolismo , Oxigenases de Função Mista/biossíntese , Oxigenases de Função Mista/genética , Microbiologia do Solo , Tibet
14.
Int J Syst Evol Microbiol ; 70(3): 1947-1952, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31985396

RESUMO

We performed taxonomic studies on a psychrotolerant strain, designated PB01T, isolated from an Antarctic iceberg. The cells of strain PB01T were Gram-stain-positive, strictly aerobic, white-yellow and rod-shaped. The results of 16S rRNA gene sequence analysis revealed that strain PB01T was closely related to Psychrobacillus psychrodurans DSM 11713T (99.19 % similarity), Psychrobacillus psychrotolerans DSM 11706T (98.91 %) and Psychrobacillus insolitus DSM 5T (98.85 %). Despite high 16S rRNA gene sequence similarity, the degrees of DNA-DNA relatedness between strain PB01T and its three closest phylogenetic neighbours were 62.4±7.3 % for P. psychrodurans DSM 11713T, 61.1±5.4 % for P. psychrotolerans DSM 11706T and 56.1±6.9 % for P. insolitus DSM 5T. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 1ω7с-OH. Menaquinone-8 was the major respiratory quinone, and phosphatidylethanolamine was the major polar lipid. The DNA G+C content of strain PB01T calculated from the complete genome sequence was 36.0 mol%. Based on the phenotypic, chemotaxonomic, genomic and phylogenetic data obtained in the present study, we conclude that strain PB01T represents a novel species of the genus Psychrobacillus, for which we propose the name Psychrobacillus glaciei sp. nov. The type strain is PB01T (=CECT 9792T=KCTC 43041T).


Assuntos
Bacillaceae/classificação , Camada de Gelo/microbiologia , Filogenia , Regiões Antárticas , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
15.
Int J Syst Evol Microbiol ; 70(2): 1398-1403, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31860430

RESUMO

A Gram-stain-positive, rod-shaped (0.3-0.4×1.2-2.0 µm), strictly aerobic and beige-pigmented bacterium, designated B3227T, was isolated from the sediment of a sea cucumber culture pond in Rongcheng, China (122.2° E 36.9° N). Its biochemical characteristics analysis revealed that the cells of this bacterium were catalase-positive and oxidase-negative. Cell growth occurred at 15-45 °C (optimum, 37 °C), pH 6.5-9.0 (pH 7.5-8.0) and in the presence of 0.0-22.0 % (w/v) NaCl (6.0-9.0 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain B3227T exhibited similarities of 95.7, 95.5, 95.5 and 95.3 % to the type strains of Filobacillus milensis, Piscibacillus salipiscarius, Halalkalibacillus halophilus and Piscibacillus halophilus, respectively, and the results of physiological analyses revealed that strain B3227T was most similar to the genus Halalkalibacillus. The cells were endospore-forming and comprised an A1-γ-meso-diaminopimelic acid-type peptidoglycan. The respiratory quinone of strain B3227T was MK-7, and the dominant fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content was 38.7 mol%. The average nucleotide identity values between strain B3227T and H. halophilus JCM 14192T (ANIb 69.5%, ANIm 84.2 %) and F. milensis JCM 12288T (ANIb 70.1 %, ANIm 84.1 %) were below the cut-off level (95-96  %) for species delineation. The results of kegg analysis revealed that strain B3227T could biosynthesize shikimate acid, a base compound for the formulation of the swine flu drug. Based on its morphological and physiological properties, as well as phylogenetic distinctiveness, strain B3227T should be placed into the genus Halalkalibacillus as a representative of a new species, for which the name Halalkalibacillus sediminis sp. nov. is proposed. The type strain is B3227T (=KCTC 33093T=MCCC 1H00193T).


Assuntos
Bacillaceae/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Pepinos-do-Mar/microbiologia , Água do Mar/microbiologia , Animais , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Peptidoglicano/química , Fosfatidiletanolaminas/química , Fosfatidilgliceróis/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
16.
Int J Syst Evol Microbiol ; 70(2): 1139-1144, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31751198

RESUMO

A Gram-stain-positive, moderately halophilic, strictly aerobic, endospore-forming, rod-shaped bacterium, strain JSM 102062T, was isolated from a non-saline farm soil sample collected from Dehang Canyon in Hunan, PR China. Growth occurred with 0.5-20 % (w/v) NaCl (optimum 4-7 %) at pH 5.5-11.0 (optimum pH 8.0) and at 20-50 °C (optimum 30-35 °C). Contained cell-wall peptidoglycan based on meso-diaminopimelic acid and possessed menaquinone-7 (MK-7) as the major respiratory isoprenoid quinone. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, five unidentified phospholipids and an unidentified glycolipid. The DNA G+C content was 44.1 mol%. Phylogeny based on 16S rRNA gene sequences indicated that strain JSM 102062T belonged to the genus Sediminibacillus, sharing high 16S rRNA gene sequence similarities to Sediminibacillus halophilus EN8dT (99.4 %) and Sediminibacillus albus NHBX5T (98.3 %). The whole genomic analysis showed that strain JSM 102062T constituted a different taxon separated from the recognized Sediminibacillus species. Combined data from phenotypic and genotypic studies demonstrated that strain JSM 102062T represents a noval species of the genus Sediminibacillus, for which the name Sediminibacillus terrae sp. nov. is proposed; the type strain is JSM 102062T (=CCTCC AB 2014166T = CGMCC 1.12957T=DSM 28949T=KCTC 33541T).


Assuntos
Bacillaceae/classificação , Fazendas , Filogenia , Microbiologia do Solo , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
17.
Biosens Bioelectron ; 148: 111832, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-31706173

RESUMO

Fluorescence-activated cell sorting (FACS) has rarely been applied to screening of microorganisms because of poor detection resolution, which is compromised by poor stability, toxicity, or interference from background fluorescence of the fluorescence sensors used. Here, a fluorescence-based rapid high-throughput cell sorting method was first developed using a fluorescence resonance energy transfer (FRET) fluorescent nanoprobe NP-RA, which was constructed by coating a silica nanoparticle with Rhodamine B and methyl-red (an azo dye). Rhodamine B (inner layer) is the FRET donor and methyl-red (outer layer) is the acceptor. This ready-to-use NP-RA is non-fluorescent, but fluoresces once the outer layer is degraded by microorganisms. In our experiment, NP-RA was ultrasensitive to model strain Shewanella decolorationis S12, showing a broad detection range from 8.0 cfu/mL to 8.7 × 108 cfu/mL under confocal laser scanning microscopy, and from 1.1 × 107 to 9.36 × 108 cfu/mL under a fluorometer. In addition, NP-RA bioimaging can clearly identify other azo-respiring cells in the microbial community, including Bosea thiooxidans DSM 9653 and Lysinibacillus pakistanensis NCCP-54. Furthermore, the fluorescent probe NP-RA is compatible with downstream FACS so that azo-respiring cells can be rapidly sorted out directly from an artificial microbial community. To our knowledge, no fluorescent nanoprobe has yet been designed for tracking and sorting azo-respiration functional microorganisms.


Assuntos
Compostos Azo/química , Transferência Ressonante de Energia de Fluorescência/métodos , Corantes Fluorescentes/química , Rodaminas/química , Shewanella/isolamento & purificação , Bacillaceae/isolamento & purificação , Técnicas Biossensoriais/métodos , Bradyrhizobiaceae/isolamento & purificação , Infecções por Bactérias Gram-Negativas/microbiologia , Humanos , Nanopartículas/química , Dióxido de Silício/química
18.
Int J Syst Evol Microbiol ; 70(2): 882-888, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31833832

RESUMO

A facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive rod, designated as strain Z8T, was isolated from red fox (Vulpes vulpes) faeces sampled at Tablas de Daimiel National Park, Ciudad Real, Spain. Strain Z8T grew at 0-37 °C (optimum, 28 °C), in the presence of 0-5.5 % (w/v) NaCl (2.5 %, w/v) and at pH 6-10 (pH 7). The strain was motile and positive for catalase, oxidase, H2S and siderophore production, acid and alkaline phosphatases, and N-acetylglucosamine, adipic acid and malate assimilation. It hydrolysed starch, DNA, l-tyrosine, Tween 20, Tween 80 and lecithovitellin. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Z8T is a member of the genus Psychrobacillus, showing high sequence similarity to Psychrobacillus lasiicapitis NEAU-3TGS17T (99.2 %) and Psychrobacillus soli NHI-2TT (99.1 %), and around 98 % to other known species of the genus Psychrobacillus. Digital DNA-DNA hybridization and average nucleotide identity values were lower than 24 and 79 %, respectively, with the most related species. In silico G+C content was 35.9 mol%. The major cellular fatty acids of strain Z8T were iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. The novel strain contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as predominant polar lipids, and the main respiratory isoprenoid quinone was MK-8. Based on the 16S rRNA phylogenetic analysis, together with MLSA (recA, rpoB and gyrB), phylogenomic, chemotaxonomic and phenotypic results, we demonstrate that strain Z8T represents a novel species of the genus Psychrobacillus, for which the name Psychrobacillus vulpis sp. nov., is proposed. The type strain is Z8T (=CECT 9721T=LMG 31001T).


Assuntos
Bacillaceae/classificação , Raposas/microbiologia , Filogenia , Animais , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fezes/microbiologia , Genes Bacterianos , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espanha , Vitamina K 2/análogos & derivados , Vitamina K 2/química
19.
J Microbiol ; 57(11): 997-1002, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31659686

RESUMO

A Gram-stain-positive, rod-shaped, alkalitolerant, and halophilic bacterium-designated as strain NKC3-5T-was isolated from kimchi that was collected from the Geumsan area in the Republic of Korea. Cells of isolated strain NKC3-5T were 0.5-0.7 µm wide and 1.4-2.8 µm long. The strain NKC3-5T could grow at up to 20.0% (w/v) NaCl (optimum 10%), pH 6.5-10.0 (optimum pH 9.0), and 25-40°C (optimum 35°C). The cells were able to reduce nitrate under aerobic conditions, which is the first report in the genus Salicibibacter. The genome size and genomic G + C content of strain NKC3-5T were 3,754,174 bp and 45.9 mol%, respectively; it contained 3,630 coding sequences, 16S rRNA genes (six 16S, five 5S, and five 23S), and 59 tRNA genes. Phylogenetic analysis based on 16S rRNA showed that strain NKC3-5T clustered with bacterium Salicibibacter kimchii NKC1-1T, with a similarity of 96.2-97.6%, but formed a distinct branch with other published species of the family Bacillaceae. In addition, OrthoANI value between strain NKC3-5T and Salicibibacter kimchii NKC1-1T was far lower than the species demarcation threshold. Using functional genome annotation, the result found that carbohydrate, amino acid, and vitamin metabolism related genes were highly distributed in the genome of strain NKC3-5T. Comparative genomic analysis revealed that strain NKC3-5T had 716 pan-genome orthologous groups (POGs), dominated with carbohydrate metabolism. Phylogenomic analysis based on the concatenated core POGs revealed that strain NKC3-5T was closely related to Salicibibacter kimchii. The predominant polar lipids were phosphatidylglycerol and two unidentified lipids. Anteiso-C15:0, iso-C17:0, anteiso-C17:0, and iso-C15:0 were the major cellular fatty acids, and menaquinone-7 was the major isoprenoid quinone present in strain NKC3-5T. Cell wall peptidoglycan analysis of strain NKC3-5T showed that meso-diaminopimelic acid was the diagnostic diamino acid. The phephenotypic, genomic, phylogenetic, and chemotaxonomic properties reveal that the strain represents a novel species of the genus Salicibibacter, for which the name Salicibibacter halophilus sp. nov. is proposed, with the type strain NKC3-5T (= KACC 21230T = JCM 33437T).


Assuntos
Bacillaceae/classificação , Bacillaceae/isolamento & purificação , Alimentos e Bebidas Fermentados/microbiologia , Filogenia , Bacillaceae/genética , Bacillaceae/fisiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/metabolismo , Ácidos Graxos/química , Genes Bacterianos/genética , Genômica , Halobacteriales , Concentração de Íons de Hidrogênio , Peptidoglicano/química , RNA Ribossômico 16S/genética , República da Coreia , Tolerância ao Sal , Análise de Sequência de DNA , Cloreto de Sódio/metabolismo , Vitamina K 2/análogos & derivados , Vitamina K 2/química , Sequenciamento Completo do Genoma
20.
Int J Syst Evol Microbiol ; 69(11): 3529-3536, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31424384

RESUMO

A Gram-stain-positive, aerobic, spore-forming, moderately halophilic bacterium, SSKP1-9T, was isolated from traditional salted shrimp paste (Ka-pi) produced in Samut Sakhon Province, Thailand. This strain grew optimally at 37-40 °C, pH 7.0 and in the presence of 8-16 % (w/v) NaCl. The 16S rRNA gene sequence similarity values between strain SSKP1-9T and Lentibacillus juripiscarius TISTR 1535T and Lentibacillus halophilus TISTR 1549T were 98.7 and 97.2 %, respectively. Based on 16S rRNA gene sequence similarity, strain SSKP1-9T represents a distinct novel species, as shown by phenotypic traits, DNA-DNA hybridization and average nucleotide identity values. In addition, the whole-cell protein profile confirmed the novelty of the taxon. The genomic DNA G+C content was 44.6 mol%. The major isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipid analysis revealed the presence of phosphatidylglycerol, diphosphatidylglycerol, four unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis support that strain SSKP1-9T represents a novel species of Lentibacillus, for which the name Lentibacilluslipolyticus sp. nov. is proposed. The type strain is SSKP1-9T (=JCM 32625T=TISTR 2597T).


Assuntos
Bacillaceae/classificação , Microbiologia de Alimentos , Filogenia , Alimentos Marinhos/microbiologia , Animais , Bacillaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Crustáceos/microbiologia , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tailândia , Vitamina K 2/análogos & derivados , Vitamina K 2/química
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