A simplified quick microbial genomic DNA extraction via freeze–thawing cycles

Chen, Fei Fei; Ye, Jian‐Ren; Chio, Chonlong; Liu, Wanhui; Shi, Jiyuan; Khatiwada, Janak Raj

doi:10.1007/s11033-019-05176-w

Cited by 18 publications

(10 citation statements)

References 19 publications

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“…Genomic DNA was extracted by boiling [43]. DNA extracted by NanoDrop was checked for accuracy and concentration [44]. Universal primers were used for the amplification of the 16s rRNA gene fragment with a length of 20 bp (total length 40 bp), 27F (Forward-5'-AGAGTTTGATCCTGGCTCAG-3'), and 1492R (Reverse-5'-GGGTTACCTTGTTACGACTT-3').…”

Section: Molecular Identification Based On 16s Rrnamentioning

confidence: 99%

Single-cell Oil Production Using Low-Cost Carbon Sources by Newly Isolated Kocuria Y205

2021

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Background & Aims of the Study: This study aimed to investigate, for the first time, the ability of single-cell oil production from low-cost carbon sources using Kocuria Y205 native Iranian bacterial isolates from the soil.Materials and Methods: Whey and lignocellulose compounds were used as carbon sources and yeast extract as a nitrogen source. Also, the isolated cultivation was done on Mineral Salts Medium (MSM) culture media. Molecular analysis based on 16s rRNA gene sequence was performed to identify isolated. Fourier-Transform Infrared Spectroscopy (FTIR) analysis was used to confirm the presence of carbon groups. GC analysis was also used to identify the fatty acids Sudan black. Finally, a Transmission Electron Microscopy (TEM) electron microscopy image was taken to view the stored lipid granule. Results:The highest rate of lipid production among all carbon sources in different periods of cultivation by whey was 24.57% after 48 hours, and also, the highest rate of lipid production for lignocellulose compounds was 15.29% after 48 hours. Conclusion:This study shows that the newly isolated Kocuria Y 205 has excellent ability to use whey and lignocellulose compounds as waste containing carbon resources for the growth, production, and storage of microbial oil. It can be used in industrial applications, too.

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Section: Molecular Identification Based On 16s Rrnamentioning

confidence: 99%

Single-cell Oil Production Using Low-Cost Carbon Sources by Newly Isolated Kocuria Y205

2021

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“…Generally, the antibacterial mechanism of Cm and Kan is that they bind to the ribosome of the bacteria (Cm binds to the 50S subunit, Kan binds to the 30S subunit) to inhibit protein synthesis. However, B. pyrrocinia JK‐SH007 could produce glycocalyx (Chen, Ye, Chio et al, 2020) and biofilm (Fu et al., 2020), which may limit the entry of Cm and Kan into the cell and affect the function of Cm and Kan.…”

Section: Discussionmentioning

confidence: 99%

Knockout of a highly GC‐rich gene in Burkholderia pyrrocinia by recombineering with freeze‐thawing transformation

Chen

Liu

et al. 2021

Molecular Plant Pathology

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The ability to manipulate the bacterial chromosome in molecular genetics and genetic engineering studies can provide significant insight into gene function (Fan et al., 2016;Ito et al., 2005). In vivo analysis of gene function and construction of the engineered bacteria require reliable genetic transformation (Cao et al., 2017;Matheka et al., 2019;Riglar & Silver, 2018). An optimal genetic transformation system generally includes an efficient transformation system, a reliable gene-editing system, and a simplified screening method (Niyomtham

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“…CCTCC M2012439 ). This strain was routinely incubated in Luria-Bertani (LB) liquid media at 28°C with shaking for 24 h. Genomic DNA was extracted using a modified freeze–thawing method ( Chen et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Genome Sequencing of Rahnella victoriana JZ-GX1 Provides New Insights Into Molecular and Genetic Mechanisms of Plant Growth Promotion

et al. 2022

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Genomic information for bacteria within the genus Rahnella remains limited. Rahnella sp. JZ-GX1 was previously isolated from the Pinus massoniana rhizosphere in China and shows potential as a plant growth-promoting (PGP) bacterium. In the present work, we combined the GridION Nanopore ONT and Illumina sequencing platforms to obtain the complete genome sequence of strain JZ-GX1, and the application effects of the strain in natural field environment was assessed. The whole genome of Rahnella sp. JZ-GX1 comprised a single circular chromosome (5,472,828 bp, G + C content of 53.53%) with 4,483 protein-coding sequences, 22 rRNAs, and 77 tRNAs. Based on whole genome phylogenetic and average nucleotide identity (ANI) analysis, the JZ-GX1 strain was reidentified as R. victoriana. Genes related to indole-3-acetic acid (IAA), phosphorus solubilization, nitrogen fixation, siderophores, acetoin, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, gamma-aminobutyric acid (GABA) production, spermidine and volatile organic compounds (VOCs) biosynthesis were present in the genome of strain JZ-GX1. In addition, these functions were also confirmed by in vitro experiments. Importantly, compared to uninoculated control plants, Pyrus serotina, Malus spectabilis, Populus euramericana (Dode) Guinier cv. “San Martino” (I-72 poplar) and Pinus elliottii plants inoculated with strain JZ-GX1 showed increased heights and ground diameters. These findings improve our understanding of R. victoriana JZ-GX1 as a potential biofertilizer in agriculture.

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A simplified quick microbial genomic DNA extraction via freeze–thawing cycles

Cited by 18 publications

References 19 publications

Single-cell Oil Production Using Low-Cost Carbon Sources by Newly Isolated Kocuria Y205

Single-cell Oil Production Using Low-Cost Carbon Sources by Newly Isolated Kocuria Y205

Knockout of a highly GC‐rich gene in Burkholderia pyrrocinia by recombineering with freeze‐thawing transformation

Genome Sequencing of Rahnella victoriana JZ-GX1 Provides New Insights Into Molecular and Genetic Mechanisms of Plant Growth Promotion

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