Molecular systematic and phylogenetic analysis of indigenous bacterial isolates with potential as bioremediation agent based on 16S rRNA gene analysis

Abstract

Liquid biomedical waste is a form of medical waste from community health centers (Pusat Kesehatan Masyarakat or Puskesmas) with high levels of health hazardous organic contaminants. Bioremediation is an alternative way to eliminate toxic components in liquid waste. A bacteria community that can be used as component of organic waste bioremediation is indigenous hydrolytic and non-pathogenic to low-pathogenic bacteria. From previous studies, 4 hydrolytic indigenous bacterial isolates with such characteristics were obtained from liquid clinical wastes of two health centers in Semarang City, namely H1, H3, H5 (from Puskesmas Halmahera), and T3 (from Puskesmas Tlogosari Kulon). This study aimed to reveal the molecular identity and kinship these bacterial isolates to understand more of their properties as consortium of bioremediation agent. Molecular identification and phylogenetic tree construction works were carried out based on 16S rRNA gene sequences. Sequences of 16S rRNA gene sequences were obtained by isolation and gene amplification using the PCR method followed by sequencing. Based on the results of molecular identification, the four isolates studied were in the same class, namely Gammaproteobacter with Phylum Proteobacter. H1 bacterial isolates have 98.01% similarity with Acinetobacter schindleri. H3 and H5 isolates share the same genus, Stenotrophomonas, with 99.79% similarity with S. maltophiphila and 97.69% with S. acidaminiphila, respectively. T3 isolate had a similarity of 98.85% with Pararheinheimera aquatica species, which was widely known as a potent bioremediation agent. The phylogenetic tree design with the MEGA 6 program showed that the H3 and H5 isolates had the closest kinship compared to the other two isolates, while the T3 isolates had the farthest relationship with the 3 other isolates. This is in line with the fact that T3 isolate was originated from a different location separating it from 3 other isolates.

Investigating the Antifungal Potential of Genetically Modified Hybrid Chitinase Enzymes Derived from Bacillus subtilis and Serratia marcescens

“…The precise identi cation of bacterial isolates was essential in this study to comprehend their biological characteristics, potential for causing disease, and ecological importance. To accomplish this, the bacterial isolates underwent 16S rRNA gene sequencing, a method renowned for its strong conservation and inclusion of both variable and conserved regions (Iskandar et al 2021;Ahmed et al 2022). The sequencing technique was successful in accurately identifying the bacterial isolates at the species level.…”

Bacterial communities of Iradiator Gamma Karet Alam (IRKA) pool water

“…Although not as abundant as Pseudomonas stutzeri and Priestia flexa, the following species have some identified potential benefits. Novosphingobium ginsenosidimutans is known to convert ginsenoside [45], Pararheinheimera aquatica or its basonym Rheinheimera aquatica [46,47] is known to have antimicrobial ability [46] and bioremediation agent [48]. Aquabacterium parvum has potential as nitrate-dependent Fe(II)-oxidizing bacteria [49].…”

Optimization of Crude Protease Production from Bacillus thuringiensis HSFI-12 and Thrombolytic Activity Its Enzyme Dialysate

“…DNA sequencing was carried out on the ABI PrismTM 310 Genetic Analyzer, while the resulted sequences were assembled and analyzed using DNA-Baser (Heracle BioSoft, Romania) program [19,20]. Sequencing aimed to determine the sequence of nucleotides in DNA fragments so that they can be used to determine the identity and function of genes by comparing their sequences with other known DNA sequences in the Genbank database using BLAST [21,22].…”

“…BLAST analysis was performed on the nucleotide sequence of the 16S rRNA gene online via https://blast.ncbi.nlm.nih. gov/Blast.cgi [22,35]. The results of the BLAST analysis of the HSFI-12 isolate bacteria obtained the sequence of the 16s rRNA gene fragment which showed a homology level of 99.80 % with that of the bacterial isolate Bacillus thuringiensis FDAARGOS_791 (Acc.…”