Persistence and degradation of Phytophthora cinnamomi DNA and RNA in different soil types

Abstract

DNA and RNA detected in soil using molecular techniques may originate from a living or dead organism. It is therefore of interest to know how long the DNA and RNA from a decaying organism can persist in soil, and how environmental conditions such as soil temperature, moisture, and microbial populations impact on the survival time. This study determined the difference between the persistence of Phytophthora cinnamomi mRNA and DNA in different soil types. DNA and RNA were extracted from P. cinnamomi and 10 ng/250 mg of soil was applied to five different soil types that were either air‐dried or maintained at 70% field capacity. The persistence of DNA at 20°C was tested after intervals of 0, 3, 7, 14, 90, 241, and 378 days, and for RNA at 0, 1, 3, and 7 days using qPCR and RT‐qPCR techniques, respectively. Persistence was longer in dry than moist soil, P. cinnamomi DNA could be readily detected in dry soil conditions for up to 90 days and was found at extremely low levels at 241 and 378 days. RNA was detected only on day 1, except for dry river sand, and moist sandy loam in which it persisted for 3 days; it was not detected after seven days. These results confirm that RNA degrades very quickly, making it a valuable tool for determining the presence of viable Phytophthora in soil. In contrast, DNA can be remarkably stable in some environments, and positive results could be obtained even after the death of the organism for a year or more prior to the test. For diagnostics, the use of an RNA‐based test avoids the possibility of such false positive results. In the context of the research project, this study is relevant to determining how long viable Phytophthora remains in soil after the eradication protocols have been instigated. In a broader context, the persistence of DNA is relevant to any study using environmental DNA for diagnostics or for metabarcoding when undertaking community ecology or microbiome studies. These results are relevant for studies using detection of P. cinnamomi nucleic acids in soils for purposes of diagnostics, ecological research, or projects on eradication.

The effect of crop species on DNase-producing bacteria in two soils

“…One major fate of extracellular DNA (exDNA) in the soil environment is degradation by indigenous soil microbial extracellular deoxyribonucleases (exDNases) into smaller fragments resulting to the loss of genetic information (Blum et al 1997;Levy-Booth et al 2007;Nielsen et al 2007;Ibáñez de Aldecoa et al 2017). The presence of these restriction enzymes therefore serves as barriers to exDNA introgression into native soil bacteria through HGT (Dodd and Pemberton 1999;Wu et al 2001) and its subsequent long-term persistence in the soil environment (Kunadiya et al 2021). For instance, Stewart and Sinigalliano (1990) reported a decrease in natural transformation frequency in bacteria after incubating marine and artificial sediments with DNase 1.…”

Experimental Evidence for Manure-Borne Bacteria Invasion in Soil During a Coalescent Event: Influence of the Antibiotic Sulfamethazine

“…Their high abundance in manure bacterial community composition may explain the success of their invasion, since a high inoculation rate is more likely to be successful [20,36]. One could argue that the detection of the most abundant bacteria of the manure in soil may be a bias due to DNA from dead cells that did not establish in the soil [37,38]. However, this argument can be rejected since not all the most abundant OTUs from manure were detected in the amended soils.…”

The future of biodiversity monitoring and conservation utilizing environmental DNA

“…While most of the studies in the special issue focus on aquatic systems, Kunadiya et al. (2021) used spiked soil samples of DNA and RNA to study their persistence of an important agricultural soil‐borne plant pathogen, Phytophthora cinnamomi . Detection of this species in both natural and horticulture settings is important for many crops including avocado, pineapple, peach, chestnut, and macadamia.…”