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Screening of nitrogen removal bacteria and its application in aquaculture wastewater treatment
Published in Binoy K. Saikia, Advances in Applied Chemistry and Industrial Catalysis, 2022
The 16S rDNA sequence of the strain was amplified with general primers. The forward primer (27F) is 5'-AGAGTTTGATCCTGGCTCAG-3' and the reverse primer (1492r) is 5'-GGCTACCTTGTTACGACTT-3'. The total volume of the PCR reaction system was 25 uL, which contains 1 µL of DNA template lysate, 12.5 µl of 2X Unique TM Taq Master Mix (With Dye), 9.5 µl of RNase Free Water, 1 µL of 27F, and 1 µL of 1492R. The PCR reaction procedure was as follows: 94°C for 5 min, 94°C pre denaturation for 30 sec, 53°C annealing for 30 sec, 72°C extension for 90 sec, 72°C for 10 min, 30 cycles, and cooling at 4°C. The amplified products were analyzed by agarose gel electrophoresis. The amplified products were sent to Shanghai Shenggong Bioengineering Co., Ltd. for sequencing. The sequences obtained were analyzed by Blast homology in the GenBank database of NCBI. The phylogenetic tree was constructed by MEGA7.0 software and the Neighbor-joining method.
Titania Nanoparticles Biofilm Formation in Environment Bacteria
Published in Y.V. Nancharaiah, Vayalam P. Venugopalan, Microbial Biofilms in Bioremediation and Wastewater Treatment, 2019
Jyoti Kumari, Ankita Mathur, N. Chandrasekaran, Amitava Mukherjee
The collected wastewater was subjected to standard dilution in aseptic conditions. Primary isolation was carried out by streaking the sample on the surface of the nutrient agar plate. The plates were then further incubated at 37°C for 24 h. Single isolated colonies were selected and sub cultured on the nutrient agar plate. This process was repeated until pure cultures were obtained. The dominant bacterial isolates were selected for the study. According to the standard methods, morphology and Gram tests were accomplished with the assistance of microbial taxonomy (Sharifi-Yazdi et al. 2001). The genomic DNA was extracted employing phenol-chloroform method. Sequencing was performed with fluorescent dye terminator method (Big dye terminator cycle sequencing kit, ABI Prism 3.1) (Sambrook and Russel 2001). The sequences were examined with BLAST and aligned with help of CLUSTAL W facilitating neighbor joining method and phylogenetic tree was constructed. The sequences which showed 99% similarity in BLAST were identified. The five bacterial isolates identified were Exiguobacterium acetylicum (VITWW1), Pseudomonas nitroreducens (VITWW2), Bacillus flexus (VITWW3), Brevundimonas diminuta (VITWW4) and Exiguobacterium indicum (VITWW5). The 16SrRNA sequences were submitted to Genbank and the accession IDs obtained as KJ146070 for Exiguobacterium acetylicum, KT272871 for Exiguobacterium indicum, KT272873 for Bacillus flexus, KT272872 for Brevundimonas diminuta and KJ146071 for Pseudomonas nitroreducens.
Growth and nutrient degradation characteristics of an aerobic denitrifying bacterium
Published in Avon Pekano Oscar, Wenxue Chen, Shuren Wang, Innovation and Application of Engineering Technology, 2017
Ling Sun, Wen-ping Cao, Shao-hui Huang, Hui-fang Zhang, Yan Li
The 16S rDNA gene sequences were submitted to NCBI BLAST to retrieve similar sequences, based on the principles of maximum homology sequence alignment, with Mega5.0 software and Clustal X1.83 software were used to implement the neighbor-joining method for construction of the phylogenetic tree. The stability of the branches was analyzed by the bootstrap method with 1000 repeats.
Indel-K2P: a modified Kimura 2 Parameters (K2P) model to incorporate insertion and deletion (Indel) information in phylogenetic analysis
Published in Cyber-Physical Systems, 2022
Asim Kumar Mahadani, Shashank Awasthi, Goutam Sanyal, Partha Bhattacharjee, Sanjeev Pippal
Distance-dependent methods are popularly used in large dataset due to accurately reconstruction of both short branch trees and large evolutionary trees, regardless of their branch lengths [22,23,24]. This method involves construction of tree from the pairwise distances. Among the distance-based methods, the Neighbour Joining (NJ) method is widely accepted by biologist as it is efficient, powerful and simple. Many studies have shown better performances of the NJ method in rebuilding correct evolutionary trees [25]. Here, we have developed new evolutionary model, Indel-K2P based on a continuous Markov process governed by substitution rate matrix where gaps are treated as separate state. Different studies have shown that gaps can be treated as a separate state [14,26,36]. Neighbour Joining (NJ) method is selected to test the performance of the model Indel-K2P in comparison to K2P model on real dataset.
Screening of tea saponin-degrading strain to degrade the residual tea saponin in tea seed cake
Published in Preparative Biochemistry & Biotechnology, 2020
Guiming Fu, Kedan Chen, Jiantao Wang, Mei Wang, Ruyi Li, Xiaojiang Wu, Choufei Wu, Peng Zhang, Chengmei Liu, Yin Wan
A phylogenetic tree was constructed using the neighbor-joining method. The results are shown in Figure 2, which indicated the evolutionary distance between the strains. Citrobacter sp. FCTS301 was similar to Citrobacter murliniae CDC 2970-59 but it appeared more phylogenetically distant from the other members of the same branch. The similarity of Pantoea sp. FCTS302 to Pantoea agglomerans DSM 3493 was 92%. The similarity of Enterobacter sp. FCTS303 to Enterobacter asburiae JCM6051 was 98%.