Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils

Ribosomal RNA (rRNA) has been regarded as a proxy for metabolic activity and population growth in microbes, but the limitations and assumptions of this approach should be better defined, particularly in eukaryotic microalgae. In this study, the 18S rRNA/rDNA ratio of a marine diatom, Skeletonema tropicum, was examined in batch and semi-continuous cultures subjected to low nitrogen and phosphorus treatments at a temperature of 20 °C. In the semi-continuous cultures, the measured 18S rRNA/rDNA ratio ranged from 4.0 × 10 to 5.0 × 10 , and the logarithmic form of this ratio increased linearly with the population growth rate under both low nitrogen and low phosphorus conditions. In batch cultures grown under low nitrogen or low phosphorus conditions, log (rRNA/rDNA) also increased linearly with growth rate when the latter ranged between -0.4 and 1.5 day . The 18S rRNA/rDNA ratios of Skeletonema sampled from in the southern East China Sea were substantially lower than measured from laboratory cultures. Among the field samples, ratios obtained at a coastal station were higher than those obtained farther offshore. These results imply higher growth rate at the coastal station, but the influences of other factors, such as cell size and temperature, cannot be ruled out.

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“…; Dlott et al. ). In addition, the primer set designed for SECS samples amplifies rRNA and rDNA in more than one species of Skeletonema .…”

Section: Discussionmentioning

confidence: 97%

Evaluation of the Relationship Between the 18S rRNA/rDNA Ratio and Population Growth in the Marine Diatom Skeletonema tropicum via the Application of an Exogenous Nucleic Acid Standard

Yang

Kang

Shih

et al. 2018

J Eukaryotic Microbiology

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“…These results suggested that exDNA is released by microorganisms proportional to their activity. Similarly, Dlott et al (2015) found a unexpected low rRNA:rDNA ratio when trying to establish a method to measure individual microbial activity and these ratios were due to high amounts of amplifiable exDNA. Both results suggest that the exDNA fraction, which is suitable in its quality for a qPCR or other downstream molecular methods, seems to derive to a large part from actively released DNA and might thus reflect microbial activity, whilst the exDNA deriving from lysed cells is not yielded using these methods.…”

Section: Applicationsmentioning

confidence: 96%

Extracellular DNA in natural environments: features, relevance and applications

Nagler

Insam

Pietramellara

et al. 2018

Appl Microbiol Biotechnol

190

151

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Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.

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“…Also, the inability to differentiate between active and inactive members of the community in complex environments and biological and environmental eDNA/eRNA can cause under or over estimations of diversity and activity quotients [16,17]. Agricultural systems have a significant advantage in moving forward in uncovering the nuances of plant microbiome interactions due to the natural tendency for fields, farms, and cropping rotations to act as surrogates for landscape level replication [18,19].…”

Section: Introductionmentioning

confidence: 99%