EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences

An actinomycete strain K07-0460 T producing new antitrypanosomal antibiotics, spoxazomicins, was isolated from the roots of a variety of orchid collected in the subtropical Okinawa prefecture. The 16S ribosomal RNA gene sequence analysis indicated that the strain belonged to the genus Streptosporangium and showed high similarities with S. amethystogenes subsp. amethystogenes DSM 43179 T (99.4%), S. amethystogenes subsp. fukuiense IFO 15365 T (99.2%) and S. longisporum DSM 43180 T (98.7%). The DNA-DNA hybridization relatedness values between strain K07-0460 T and the three strains were below 70%. On the basis of phylogenetic analysis, DNA-DNA hybridization relatedness and physiological characteristics, the strain should be classified as a new species Streptosporangium oxazolinicum sp. nov. in the genus Streptosporangium. The type strain of S. oxazolinicum is K07-0460 T (¼JCM 17388 T ).

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“…40 The values of sequence similarities among the closest strains were determined using the EzTaxon server. 41 …”

Section: Methodsmentioning

confidence: 99%

Streptosporangium oxazolinicum sp. nov., a novel endophytic actinomycete producing new antitrypanosomal antibiotics, spoxazomicins

et al. 2011

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“…BLAST homology searches (Altschul et al 1997) were made in the GeneBank database. EzTaxon server 2.1 carried out the determination of the closest type strain (Chun et al 2007). …”

Section: Bacterial Community Analysis By Using T-rflpmentioning

confidence: 99%

Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution

Benedek

Vajna

Táncsics

et al. 2013

World J Microbiol Biotechnol

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Nowadays, because of substantial use of petroleum-derived fuels the number and extension of hydrocarbon polluted terrestrial ecosystems is in growth worldwide. In remediation of aforementioned sites bioremediation still tends to be an innovative, environmentally attractive technology. Although huge amount of information is available concerning the hydrocarbon degradation potential of cultivable hydrocarbonoclastic bacteria little is known about the in situ long-term effects of petroleum derived compounds on the structure of soil microbiota. Therefore, in this study our aim was to determine the longterm impact of total petroleum hydrocarbons (TPHs), volatile petroleum hydrocarbons (VPHs), total alkyl benzenes (TABs) as well as of polycyclic aromatic hydrocarbons (PAHs) on the structure of bacterial communities of four different contaminated soil samples. Our results indicated that a very high amount of TPH affected positively the diversity of hydrocarbonoclastic bacteria. This finding was supported by the occurrence of representatives of the a-, b-, c-Proteobacteria, Actinobacteria, Flavobacteriia and Bacilli classes. High concentration of VPHs and TABs contributed to the predominance of actinobacterial isolates. In PAH impacted samples the concentration of PAHs negatively correlated with the diversity of bacterial species. Heavily PAH polluted soil samples were mainly inhabited by the representatives of the b-, cProteobacteria (overwhelming dominance of Pseudomonas sp.) and Actinobacteria.

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“…Genomic DNA extraction, amplification and 16S rRNA gene sequencing were performed as described previously (Li et al 2007). Identification of phylogenetic neighbours and calculation of pairwise 16S rRNA gene sequence similarities were achieved using the EzTaxon server (http://www.eztaxon.org/) (Chun et al 2007). A phylogenetic tree was constructed with MEGA version 4.0 (Tamura et al 2007) after multiple alignment of data by CLUSTAL_X (Thompson et al 1997).…”

Section: Preliminary Identification Of Actinobacteriamentioning

confidence: 99%

Isolation and characterization of culturable endophytic actinobacteria associated with Artemisia annua L.

Zhao

Huang

et al. 2011

Antonie van Leeuwenhoek

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Endophytic actinobacteria isolated from Artemisia annua were characterized and evaluated for their bioactivities. A total of 228 isolates representing at least 19 different genera of actinobacteria were obtained and several of them seemed to be novel taxa. An evaluation of antimicrobial activity showed that more isolates possessed activity towards plant pathogens than activity against other pathogenic bacteria or yeasts. High frequencies of PCR amplification were obtained for type I polyketide synthases (PKS-I, 21.1%), type II polyketide synthases (PKS-II, 45.2%) and nonribosomal peptide synthetases (NRPS, 32.5%). The results of herbicidal activity screening indicated that 19 out of 117 samples of fermentation broths completely inhibited the germination of Echinochloa crusgalli. This study indicated that endophytic actinobacteria associated with A. annua are abundant and have potentially beneficial and diverse bioactivities which should be pursued for their biotechnical promise.

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EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences

Cited by 1,971 publications

References 12 publications

Streptosporangium oxazolinicum sp. nov., a novel endophytic actinomycete producing new antitrypanosomal antibiotics, spoxazomicins

Streptosporangium oxazolinicum sp. nov., a novel endophytic actinomycete producing new antitrypanosomal antibiotics, spoxazomicins

Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution

Isolation and characterization of culturable endophytic actinobacteria associated with Artemisia annua L.

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