TY - JOUR
T1 - Isolation and identification of Ktedonobacteria using 16S rRNA gene sequences data
AU - Rachmania, M. K.
AU - Ningsih, F.
AU - Sakai, Y.
AU - Yabe, S.
AU - Yokota, A.
AU - Sjamsuridzal, W.
N1 - Publisher Copyright:
© Published under licence by IOP Publishing Ltd.
PY - 2020/2/21
Y1 - 2020/2/21
N2 - The aims of this study were to isolate and identify the members of Ktedonobacteria from soil samples in Cisolok geysers area, West Java, Indonesia. To isolate the bacteria, sample was spread on 10-fold-diluted Reasoner's 2A medium and the plates were incubated at 30 °C until the Ktedonobacteria-like colonies appeared. Ktedonobacteria-like colonies showed the characteristics of a firm pale orange colony. The colonies were purified and colony PCR was performed using Ktedonobacteria specific and universal eubacterial primers for 16S rRNA gene. Almost full-length of 16S rRNA gene sequences were obtained in order to know the identity of the taxonomic affiliation of the isolates. Three Ktedonobacteria-like isolates, designated S3.2.1.5, S3.2.1.6 (isolated from soil under Bamboo tree) and S3.2.2.5 (isolated from soil in decayed Bamboo stems) were obtained. The detection using Ktedonobacteria specific primers showed positive results, which confirmed that all of three isolates belong to class Ktedonobacteria. The sequence homology search using EzBioCloud showed that these isolates (S3.2.1.5, S3.2.1.6, and S3.2.2.5) were belonged to the family Dictyobacteraceae and closely related to Bacterium SOSP1-79 (99.20%, 98.83%, 99.34%, respectively) and Dictyobacter aurantiacus S-27T (97.41%, 97.41%, 98.00%, respectively). The low percentage of sequence homology to type strains indicates that they could be a candidate of novel taxa of the genus Dictyobacter. Further characterizations such as morphology, physiology, and chemotaxonomy are needed in order to clarify the taxonomic position of these potential novel species of Dictyobacter.
AB - The aims of this study were to isolate and identify the members of Ktedonobacteria from soil samples in Cisolok geysers area, West Java, Indonesia. To isolate the bacteria, sample was spread on 10-fold-diluted Reasoner's 2A medium and the plates were incubated at 30 °C until the Ktedonobacteria-like colonies appeared. Ktedonobacteria-like colonies showed the characteristics of a firm pale orange colony. The colonies were purified and colony PCR was performed using Ktedonobacteria specific and universal eubacterial primers for 16S rRNA gene. Almost full-length of 16S rRNA gene sequences were obtained in order to know the identity of the taxonomic affiliation of the isolates. Three Ktedonobacteria-like isolates, designated S3.2.1.5, S3.2.1.6 (isolated from soil under Bamboo tree) and S3.2.2.5 (isolated from soil in decayed Bamboo stems) were obtained. The detection using Ktedonobacteria specific primers showed positive results, which confirmed that all of three isolates belong to class Ktedonobacteria. The sequence homology search using EzBioCloud showed that these isolates (S3.2.1.5, S3.2.1.6, and S3.2.2.5) were belonged to the family Dictyobacteraceae and closely related to Bacterium SOSP1-79 (99.20%, 98.83%, 99.34%, respectively) and Dictyobacter aurantiacus S-27T (97.41%, 97.41%, 98.00%, respectively). The low percentage of sequence homology to type strains indicates that they could be a candidate of novel taxa of the genus Dictyobacter. Further characterizations such as morphology, physiology, and chemotaxonomy are needed in order to clarify the taxonomic position of these potential novel species of Dictyobacter.
UR - http://www.scopus.com/inward/record.url?scp=85080941442&partnerID=8YFLogxK
U2 - 10.1088/1755-1315/439/1/012031
DO - 10.1088/1755-1315/439/1/012031
M3 - Conference article
AN - SCOPUS:85080941442
SN - 1755-1307
VL - 439
JO - IOP Conference Series: Earth and Environmental Science
JF - IOP Conference Series: Earth and Environmental Science
IS - 1
M1 - 012031
T2 - 6th International Symposium of Innovative Bio-Production Indonesia on Biotechnology and Bioengineering, ISIBio2019
Y2 - 23 October 2019 through 24 October 2019
ER -