ArticleBMC microbiology2026
Depth-dependent differences between direct total DNA and an intracellular-DNA-enriched fraction in bulk-soil bacterial and fungal communities of a Lonicera japonica field.
Article in BMC microbiology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundDirect total-DNA (tDNA) extraction from soil recovers both cell-associated and extracellular (relic) DNA, which can distort amplicon-based views of microbial communities; how strongly this biases bacteria versus fungi, and whether it varies with soil depth, remains poorly resolved for cultivated soils. Using a paired split-sample design, we compared bacterial 16S rRNA gene and fungal ITS profiles from directly extracted tDNA and an operationally defined intracellular-DNA-enriched (iDNA) fraction in bulk soil sampled at three depths from a continuously cultivated Lonicera japonica field.
resultsThe two DNA pools gave related but clearly non-interchangeable pictures of the community, and the two kingdoms responded asymmetrically: bacteria were consistently the more sensitive, with higher richness recovered from tDNA and a marked separation between DNA pools throughout the profile, whereas the fungal contrast was smaller overall and, for alpha diversity and within-pair divergence, concentrated in the surface soil. DNA-pool choice acted mainly by selectively redistributing specific lineages rather than replacing the dominant community, while the measured soil physicochemical variables explained only a small share of community variation within either pool.
conclusionsDirect total DNA and an iDNA-enriched fraction offer kingdom- and depth-dependent windows on the same soil, so the choice of DNA pool is a consequential design decision-especially for bacteria and for surface horizons-that should be matched to the ecological question and independently validated when a cell-associated fraction is the goal. More broadly, a single total-DNA snapshot cannot be assumed to represent the cell-associated community equally across taxa or depths; treating the DNA-extraction strategy as an ecological variable rather than a neutral technical step would strengthen the comparability and interpretation of bulk-soil bacterial and fungal community surveys.
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