Soil biome variation of Lupinus nipomensis in wet-cool vs. dry-warm microhabitats and greenhouse.

Premise: Environmental DNA (eDNA) can be used to determine the composition of the soil biome community, revealing beneficial and antagonistic microbes and invertebrates associated with plants. eDNA analyses can complement traditional soil community studies, offering more comprehensive information for conservation practitioners. Studies are also needed to examine differences between field and greenhouse soil biomes because greenhouse-grown plants are often transplanted in the field during restoration efforts.

Methods: We used eDNA multilocus metabarcoding to test how the soil biome of the federally and state-endangered species, Lupinus nipomensis, differed between wet-cool and dry-warm microhabitats. At Arroyo Grande, California, 20 experimental plots were sampled, representing a factorial combination of wet-cool vs. dry-warm soil and plots that did or did not contain L. nipomensis. In a simultaneous greenhouse study, L. nipomensis was grown in drought and well-watered conditions to compare soil communities between field and greenhouse.

Results: A diversity of carbon-cycling microorganisms but not nitrogen-fixers were overrepresented in the field, and nitrogen-fixing bacteria were overrepresented in some greenhouse treatments. The microbial communities in the field soils were more species-rich and evenly distributed than in greenhouse communities. In field plots, microhabitats significantly influenced community beta diversity, while field plots with or without L. nipomensis had no significant differences in alpha or beta diversity.

Conclusions: Our study shows the utility of eDNA soil analysis in elucidating soil biome community differences for conservation and highlights the influence of plant microhabitats on soil microbe associations.