Unlocking soil health: Are microbial functional genes effective indicators?

Soil microbial community plays crucial roles in promoting soil functions and maintaining soil health. Microbial functional gene abundances are actively involved in soil processes which supports soil functions and wider soil health. However, their suitability as indicators to assess soil health is still debatable. In this study, we sampled soils from a 10-year long-term fertilization experiment in a wheat-maize cropping system on the North China Plain. The treatment included no fertilizer (Control), chemical fertilizers only (NPK), NPK + organic manure, NPK + straw, and NPK + manure + straw. We quantified seventeen functional genes involved in carbon ( cbbL, GH31 ), nitrogen ( nifH, ureC, chiA, A-amoA, B-amoA, narG, nirK, nirS, norB and nosZ ), and phosphorus ( gltA, bpp, phoD, phoC, pqqC ) cycling. These genes were correlated with a suite of soil properties representing indicators of carbon (total carbon, organic carbon, and permanganate oxidizable carbon, α-1,4 glucosidase and carbon dioxide emission), nitrogen (total nitrogen, inorganic nitrogen, β-N-acetylglucosaminidase, and nitrous oxide emission), and phosphorous (available phosphorus, acid and alkaline phosphatase) pools/cycling. Soil microbial functional genes exhibited high coefficients of variation and strong sensitivity to fertilization treatments, while showing low variability among replicates within the same treatment. The abundances of functional genes, especially GH31, cbbL, B-amoA, chiA, phoC , and phoD were strongly correlated with their proxy indicators of carbon, nitrogen and phosphorus cycling. In addition, organic fertilization enhanced carbon and nutrients relevant functional gene abundances, generating positive effects on maize yield. These results indicate that microbial functional genes are sensitive to organic inputs and could provide a more detailed and mechanistic understanding of soil processes than conventional indicators by capturing the biochemical processes that govern nutrient dynamics. Our study underscores the potential of microbial functional genes as sensitive and valuable indicators for advancing soil health assessments and management practices. • Microbial functional genes were related to carbon and nutrient cycling. • Functional genes and proxy indicators for soil processes were highly correlated. • Functional genes were more sensitive to fertilization than proxy indicators. • Models showed strong relationships between functional genes and crop yield.