Life is DNA, and to DNA, life shall return

Life is everywhere on earth thanks to evolution. DNA, the code of life, is found in the cells of all living organisms, and in some viruses as well. Death is part of the life cycle, too.

In any environment, there is a clear distinction between DNA found inside living cells (both metabolically active and dormant cells) and extracellular DNA (exDNA) linked to dead cells such as autolysis, senescence, viral infection, or predation. Together, these sources of mortality can create large pools of exDNA, especially in soil environments where exDNA represents a large fraction of total microbial DNA (33% on average). (3)

However, the exDNA cycle in the soil is not a closed system; it is continually replenished by DNA released into the soil by living and decomposing organisms. The fact that this cycle is an open, interconnected system is vital for several reasons.

Once released into the environment, exDNA is used as a nutrient and energy source for plant and microbial growth, especially in soils with low nutrient input. Extracellular DNA can account for over 10% of extractable P in soil and contains essential elements such as N and C. Smaller exDNA molecules are also taken up by microbial cells, where they either serve as building blocks for newly synthesized nucleic acids or are further broken down into essential nutrients. (1)

The rate of exDNA degradation is affected by inorganic and organic substances in soils and sediments and also because biofilms, aggregates, and outer membrane vesicles can protect relic DNA from hydrolytic enzymes. Which is a good thing. ExDNA that persists by binding to soil minerals and humic substances plays a crucial role in the formation of biofilms, exhibiting mainly structural functions to increase water retention, particularly in the topsoil of arid soils. (1)

ExDNA carries a genetic message that may be picked up by foreign soil microbes through natural transformation and thereby crosses the species barrier. The natural transformation of foreign DNA into native soil microbial populations is an important component of prokaryotic evolution. (1)

Microbes play a critical role in soil biogeochemistry and the maintenance of fertility. With that in mind, Biome Makers has developed and now offers their proprietary products, powered by BeCrop Technology, a DNA-based amplicon sequencer that determines the composition, diversity, ecology, and putative functions of soil microbial communities. Soil microbiome has been established as a perfect biomarker of biogeography, the nutrition cycle, disease risk, and plant growth promotion, and Biome Makers is using this information collected in our biology soil lab as the basis for sustainable farming applications.

During the last year, some experts have warned about the potential overestimation or underestimation of soil microbial diversity due to the exDNA pool presence in soil. At a technological level, it is actually a non-issue thanks to a photoreactive DNA-binding dye known as Propidium monoazide (PMA) that preferentially binds exDNA. This process renders the DNA insoluble and results in its’ loss during subsequent genomic DNA extraction. (4)

To date, the documented effects of exDNA on estimates of microbial diversity are idiosyncratic. But also, if PMA is not used, the latest studies show that - despite accounting for a substantial portion of the total DNA - soil exDNA has a minimal effect on estimates of richness, evenness, phylogenetic diversity (PD), or the species abundance distribution based on 16S rRNA gene sequences. Plus, it was reported that the presence of soil exDNA is unlikely to obscure broad biogeographical patterns. (3)

Depending on the application, the question to answer, and experimental design, exDNA can be a potential issue or the perfect biomarker, for example with application in management practices certification or in other emergent microbiome applications like archeology or criminology. In conclusion, by utilizing soil genomics and the power of soil science to analyze soil microbes and DNA, scientists and researchers can present new solutions in agriculture.

Bibliography

(1) Levy-Booth, D. J., Campbell, R. G., Gulden, R. H., Hart, M. M., Powell, J. R., Klironomos, J. N., … Dunfield, K. E. (2007). Cycling of extracellular DNA in the soil environment. Soil Biology and Biochemistry, 39(12), 2977–2991.

https://doi.org/10.1016/j.soilbio.2007.06.020

(2) Carini, P., Marsden, P. J., Leff, J. W., Morgan, E. E., Strickland, M. S., & Fierer, N. (2016). Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nature Microbiology.

https://doi.org/10.1038/nmicrobiol.2016.242

(3) Lennon, J. T., Muscarella, M. E., Placella, S. A., & Lehmkuhl, B. K. (2018). How, when, and where relic DNA affects microbial diversity. MBio, 9(3), 1–14.

https://doi.org/10.1128/mBio.00637-18

(4) Nocker, A., Sossa-Fernandez, P., Burr, M. D., & Camper, A. K. (2007). Use of propidium monoazide for live/dead distinction in microbial ecology. Applied and Environmental Microbiology, 73(16), 5111–5117.

https://doi.org/10.1128/AEM.02987-06

Originally published April 6, 2021, updated May 25, 2022.