Open AccessIsolation and identification of Ktedonobacteria using 16S rRNA gene sequences data
Author(s) -
M. K. Rachmania,
Fitria Ningsih,
Yasuteru Sakai,
Shuhei Yabe,
Akira Yokota,
Wellyzar Sjamsuridzal
Publication year - 2020
Publication title -
iop conference series. earth and environmental science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.179
H-Index - 26
eISSN - 1755-1307
pISSN - 1755-1315
DOI - 10.1088/1755-1315/439/1/012031
Subject(s) - 16s ribosomal rna , biology , bacteria , homology (biology) , ribosomal rna , gene , botany , microbiology and biotechnology , genetics
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-27 T (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 .