A method for isolation of soil microbial DNA that is suitable for analysis of microbial cellulase genes

Kobayashi, Yoshiki; Hayashida, Erika; Yokoyama, Keiichi; Fujii, Katsuhiko

doi:10.1080/01496395.2015.1119847

Cited by 2 publications

(2 citation statements)

References 47 publications

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“…Microbial DNA was extracted from microorganism-containing retentate using the Power Water DNA isolation kit (Mo Bio Laboratories, USA). To exclude DNA contamination, the microbial DNA was also extracted from microorganism-containing retentate by the cetyltrimethylammonium bromide (CTAB) method ( 46 ). For each sample, DNA was extracted three times and then the DNAs were pooled.…”

Section: Methodsmentioning

confidence: 99%

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Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

Liu

Zhang

2017

mBio

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Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions.

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Section: Methodsmentioning

confidence: 99%

“…The purified virions were examined under a JEM-1230 transmission electron microscope (TEM) operating at 120 kV. The viral DNA was isolated by formamide lysis and the CTAB method ( 46 ). For each sample, DNA was extracted three times.…”

Section: Methodsmentioning

confidence: 99%