Abstract
Ribosomal RNA (rRNA) is used widely to investigate potentially active microorganisms in environmental samples, including soil microorganisms and other microbial communities that are subjected to pronounced seasonal variation in temperature. This raises a question about the turnover of intracellular microbial rRNA at environmentally relevant temperatures. We analyzed the turnover at four temperatures of RNA isolated from soil bacteria amended with 14C-labeled uridine. We found that the half-life of recently produced RNA increased from 4.0 days at 20°C to 15.8 days at 4°C, and 215 days at −4°C, while no degradation was detected at −18°C during a 1-year period. We discuss the implications of the strong temperature dependency of rRNA turnover for interpretation of microbiome data based on rRNA isolated from environmental samples.
Highlights
Microbial DNA isolated from environmental samples cannot differentiate between the live and dead fraction of the microbiome and is generally believed to persist for longer time spans compared to RNA, e.g., in soils where extracellular DNA from dead organisms may persist for years (Carini et al, 2016)
Bacterial Ribosomal RNA (rRNA) is more stable than messenger RNA likely as a consequence of its incorporation into ribosomes and protection by ribosomal proteins (Deutscher, 2003), but rRNA is degraded by RNases intracellularly during stress, e.g., caused by starvation for organic carbon, amino acids or essential nutrients (Zundel et al, 2009), or when an RNA molecule is defective (Deutscher, 2006)
We assumed that the messenger RNA (mRNA) pool has a faster turnover compared to rRNA and that a large proportion of the initial RNA degradation would be due to degradation of mRNA
Summary
Microbial DNA isolated from environmental samples cannot differentiate between the live and dead fraction of the microbiome and is generally believed to persist for longer time spans compared to RNA, e.g., in soils where extracellular DNA from dead organisms may persist for years (Carini et al, 2016). Numerous studies and commercial laboratory suppliers have described the decay of RNA in bacterial strains or in environmental samples under different conditions (often in combination with substances that inhibit RNase activity), but these studies focus on the decay of mRNA or the total pool of RNA that includes extracellular RNA
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