Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

By P. Carini, Patrick J. Marsden, J. Leff, E. E. Morgan, M. Strickland, Noah Fierer. Nature Microbiology, 2016

902 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0461251f3c35d03bab4e3402e0d1f987a728e033

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Citations in the corpus

Temperatures beyond the community optimum promote the dominance of heat-adapted, fast growing and stress resistant bacteria in alpine soils (2020, result): “This confirms that our analysis was based on viable cells which has hampered the interpretability of previous microcosm studies due to the relative stability of DNA of lysed cells (Carini et al., 2016).”
Deciphering the associations between soil microbial diversity and ecosystem multifunctionality driven by long‐term fertilization management (2018, background): “For instance the presence of soil relic DNA may increase the estimation of microbial diversity by ≥40% (Carini et al., 2016).”
Soil Bacterial and Fungal Response to Wildfires in the Canadian Boreal Forest Across a Burn Severity Gradient (2019, methodology): “fungi in a given sample, extracted DNA was amplified via quantitative PCR (qPCR) in triplicate, targeting the 16S rRNA gene v4 region with 515f and 806r primers (Carini et al., 2016) and targeting the 18S gene region with FR1 and FF390 primers (Prévost-Bouré et al.”
Embracing the unknown: disentangling the complexities of the soil microbiome (2017, background): “Although there are some notable exceptions (for example, some prairie soils, which are dominated by lineages in the Verrucomicrobia phylum 20 ), the most abundant bacterial and archaeal species usually account for a relatively small percentage of the prokaryotic DNA recovered from individual samples”
A practical guide to amplicon and metagenomic analysis of microbiome data (2020, background): “A large amount of relic DNA in soil can be physically removed with propidium monoazide (Carini et al., 2016).”
Ten questions concerning the microbiomes of buildings (2016, background): “DNA can be 481 remarkably persistent on surfaces and particles [145].”
Microbiome definition re-visited: old concepts and new challenges (2020, background): “Relic DNA can comprise up to 40% of the sequenced DNA in soil [53] and was up to 33% of the total bacterial DNA on average in a broader analysis of habitats with the highest proportion of 80% in some samples [54].”