China 
Africa 
Explore chapters and articles related to this topic
A Brief Review of Earth Microbiomes and Applications
Published in Nwadiuto (Diuto) Esiobu, James Chukwuma Ogbonna, Charles Oluwaseun Adetunji, Olawole O. Obembe, Ifeoma Maureen Ezeonu, Abdulrazak B. Ibrahim, Benjamin Ewa Ubi, Microbiomes and Emerging Applications, 2022
Toochukwu E. Ogbulie, Nwadiuto (Diuto) Esiobu, Ifeoma Enweani-Nwokelo
A series of procedures are required in carrying out the laboratory analyses. Microbes from the environmental samples are cultured, selected/identified and pure culture obtained. Varying purification processes are employed, although it depends on the type of sample. Isolates can equally be identified directly from the sample in which case the chromosomal DNA will be extracted from soil and the microbes too. The DNA extraction can be carried out directly following standard/modified procedures such as alkaline lysis with sodium dodecyl sulfate (SDS) and enzymes such as proteinase K and lysozyme and boiling lysis with Tris Ethylene Diamine Tetraacetic Acid (EDTA) (1X TE) (Sambrook and Russell, 2001) or by using filtration techniques involving commercially available DNA extraction kits made by many biotech companies such as the ZR Soil Microbe DNA Microprep (Zymo Research, CA, USA, www.zymoresearch.com), DNA extraction kit by Norgen Biotek Corp, Canada (www.norgenbiotek.com), Promega Corporation (www.worldwide.promega.com), Ultraclean soil DNA isolation kit – Cambio (www.cambio, co, uk), DNeasy PowerSoil Pro kit – QIAGEN (www.qiagen.com), etc. The type of kit to be used usually depends on the intended protocol to adopt as well as the type of sample/microorganism. This is usually followed by various amplification techniques as multiple displacement amplification, use of primers and PCR protocols following thermal cycler programs to increase DNA yield.
Relation between As(III) oxidation potential and siderophore production: a study of tannery As(III) oxidizers
Published in Yong-Guan Zhu, Huaming Guo, Prosun Bhattacharya, Jochen Bundschuh, Arslan Ahmad, Ravi Naidu, Environmental Arsenic in a Changing World, 2019
Tannery soil and effluent samples were taken from waste disposal site Miraj, India. In enrichment, 3 g soil was inoculated in Tris-mineral medium, supplemented with 0.04% yeast extract (TMM) and 5 mM of As(III). Flasks were incubated on shaker for As(III) at 30°C for 5 days and 3mL of this enrichment culture was inoculated in fresh medium. This procedure was repeated two times. The isolates yielded were initially screened by using silver nitrate plate assay. Sequencing of 16S rRNA gene was performed using genomic DNA isolated by alkaline lysis method (Fig. 1).
Aerosol partitioning potential of bacteria presenting antimicrobial resistance from different stages of a small decentralized septic treatment system
Published in Aerosol Science and Technology, 2023
Gabriela E. Ramos, Hyoungmook Pak, Ryan Gerlich, Anish Jantrania, Brooke L. Smith, Maria D. King
DNA was extracted in three replicate samples from the bioaerosol and water samples using the alkaline lysis method (Zhou et al. 1990). 16S rRNA-based Illumina sequencing was used to delineate the composition and similarities of microbiomes in the water and air samples. Following isolation and purification, DNA extracted from the replicates and time points for each sample were prepared as barcoded libraries and analyzed at the Molecular Genomics Center at Texas A&M for Illumina® paired-end (2 × 250) sequencing on the MiSeq platform (Estrada-Perez et al. 2018). First-round PCR was used to amplify the V4/V5 regions of the 16S rRNA gene using the primers 515 F (5′-GTGYCAGCMGCCGCGGTA-3′) and 909 R (5′-CCCCGYCAATTCMTTTRAGT-3′) (Wang and Qian 2009). Bacterial DNA sequences were processed and analyzed using the QIIME2 (Quantitative Insights into Microbial Ecology) v.1.8 software to determine the 16S rRNA allele distributions among the bacteria before and after aerosolization (Paulson et al. 2013; Caporaso et al. 2010). Sequences were demultiplexed, and forward and reverse reads were merged using FLASH v.1.2.11 (Magoč and Salzberg 2011) with a maximum overlap of 250 bp. Sequences were quality-filtered (-q 19), and chimeras were removed via QIIME2 and USEARCH (Edgar 2010). Taxonomy was assigned using the Ribosomal Database Project classifier (Klappenbach et al. 2001) with the reference database Greengenes13_8 16s rRNA (Klappenbach et al. 2001; McDonald et al. 2012) for bacteria.
Production of recombinant lethal factor of Bacillus anthracis in Bacillus subtilis
Published in Preparative Biochemistry & Biotechnology, 2021
Mahboobeh Gholami, Majid Moghbeli, Farshid Kafilzadeh, Mohammad Kargar, Mariam Bikhof Torbati, Ashkan Tavizi, Sally Bellevile, Javad Hatami, Zahra Eslami
The pXO1 was extracted from Bacillus anthracis using alkaline lysis with sodium dodecyl sulfate (SDS) according to Sambrook’s protocol.[27] In brief, a single colony was inoculated in 10 ml of LB medium containing Ampicillin; the medium was incubatedat 37 °C with vigorous shaking; after 16 h, the bacteria were recovered by centrifugation at 2000 g at 4 °C for 10 minutes. The pellet then was resuspendedin 0.2 ml of Alkaline lysis solution I containing 3.7 g/l of EDTA, 3 g/l of Tris base, and 10 g/l of glucose; 0.4 ml of Alkaline lysis solution II (10 g/l of SDSand 8 g/l of NaOH) as well as 0.3 ml of Alkaline lysis solution III (60 ml of potassium acetate 5 M, 11.5 ml of acetic acid, and 28.5 ml of deionized water) were added to the resuspended solution. Following centrifugation of the solution at 2000 g for 5 minutes, the supernatant was precipitated by adding 0.6 ml of isopropanol; the result of participation was collected after centrifugation for 5 minutes. The pellet was resuspended in 1 ml of 70% ethanol and centrifugated for 2 minutes; the supernatant was removed and the pellet (nucleic acid) was dissolved in 0.1 ml of Tris-EDTA buffer (pH 8). The result was confirmed by 1% agarose gel electrophoresis containing 0.001 ml of EtBr (10 g/l) in 1X Tris-Borate-EDTA buffer at 100 V and visualized under UV illumination.
Characterization, optimization and kinetic study of diclofenac degradation by novel bacterial strains and their synthetic consortia
Published in Bioremediation Journal, 2020
Sunil Chopra, Dharmender Kumar
Gram staining was used for the morphological identification of four bacterial isolates (DSD1, DYD1, PPD2, and DKD1). The alkaline lysis method was used for genomic DNA extraction of these isolates (Wilson 2001). The genomic DNA qualitative analysis was performed with 1.0% agarose gel electrophoresis. Further, the polymerase chain reaction (PCR) was performed with 27F and 1492R (16S rRNA, universal primer) to amplify the 16S rRNA genes of the isolates. The Sanger DNA sequencing method was used for sequencing the PCR amplified product. After sequencing, the freely available DECIPHER 2.13.1 online tool was used to chimeric sequence analysis. The GenBank database of the National Center of Biotechnology Information (NCBI) was used to compare nucleotide of isolate with available other nucleotides by the Basic Local Alignment Search Tool (BLASTn). Further, the Neighbor-Joining (NJ) method (MEGA 7 software) was used to construct a phylogenetic tree among related strains. The UGPMA clustering (MEGA 7 software) was used to study the genetic variances between nucleotides (Kumar, Stecher, and Tamura 2016).