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This study examined how different soil sampling methods affect estimates of bacterial diversity across 57 forest and grassland sites in Germany. Researchers found that combining soil cores into homogenized composite samples significantly underestimates plot-level microbial richness compared to analyzing individual cores separately, and can even reverse conclusions about which ecosystems contain more diversity. Plot-level richness increased continuously with more sampling effort and larger spatial coverage without reaching saturation, but sampling completeness decreased when sequencing depth was held constant.
Why it matters
These findings reveal that standard practices of homogenizing soil samples can produce misleading diversity estimates and incorrect ecological conclusions. This has important implications for microbial ecology research, environmental monitoring programs, and any studies comparing microbial diversity across different ecosystems or land uses.
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⚠️ Preprint – Noch nicht peer-reviewed
Dieser Artikel wurde noch nicht von unabhängigen Experten begutachtet. Die Ergebnisse sind vorläufig und sollten mit Vorsicht interpretiert werden.
Soil microbial diversity is shaped by the spatial scale at which communities are sampled, yet standard sampling practices often homogenize samples, obscuring fine-scale spatial structure and diversity patterns. To better understand how sampling effort, spatial extent, and physical homogenization influence plot-level microbial richness estimates, we sampled 57 forest and grassland sites across three regions in Germany using a 14-core cross-transect design and performed 16S rRNA gene metabarcoding. We simulated sampling efforts and a range of spatial extents and compared diversity estimates to those from physically homogenized composite samples. Plot-level richness increased continuously with sampling effort and spatial extent, with no evidence of saturation. However, when sequencing depth was held constant, sampling completeness declined with increasing sampling effort, meaning that more diversity is not captured. Composite samples substantially underestimated plot-level richness and altered apparent diversity relationships between ecosystems; individual cores identified forests as richer than grasslands, whereas homogenized samples suggested the opposite relationship. These results demonstrate that sampling effort, spatial extent, and homogenization fundamentally shape soil microbial diversity estimates. Homogenized composite samples cannot substitute for individual cores when the goal is to reliably quantify plot-level richness or compare diversity across ecosystems.
Source: The illusion of diversity: sampling design drives conflicting estimates of soil bacterial richness