Optimization of RNA extraction for bacterial whole transcriptome studies of low-biomass samples

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  • UGent - Universiteit Gent
  • Centre for Advanced Process Technology for Urban REsource Recovery

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We developed a procedure for extracting maximal amounts of high-quality RNA from low-biomass producing (autotrophic) bacteria for experiments where sample volume is limited. Large amounts of high-quality RNA for downstream analyses cannot be obtained using larger quantities of culture volume. The performance of standard commercial silica-column based kit protocols and these procedures amended by ultrasonication or enzymatic lysis were assessed. The ammonium-oxidizing Nitrosomonas europaea and nitrite-oxidizing Nitrobacter winogradskyi were used as model organisms for optimization of the RNA isolation protocol. Enzymatic lysis through lysozyme digestion generated high-quality, high-yield RNA samples. Subsequent RNA-seq analysis resulted in qualitative data for both strains. The RNA extraction procedure is suitable for experiments with volume and/or biomass limitations, e.g. as encountered during space flight experiments. Furthermore, it will also result in higher RNA yields for whole transcriptome experiments where sample volume and/or biomass was increased to compensate the low-biomass characteristic of autotrophs.


Original languageEnglish
Article number105311
Pages (from-to)1-20
Number of pages20
Publication statusAccepted/In press - 9 Oct 2022


  • High-quality RNA, RNA extraction, Low-biomass samples, Enzymatic lysis, Silica-column

ID: 8056941