Gibbs: A New Soil Biology Index to Quantify Beneficial Bacteria in the Soil.

Microbial diversity has been linked to soil resilience and health but few microbial indices explicitly link diversity to function. Many of the thousands of bacteria species present in soils enhance plant nutrition, confer stress tolerance, and promote plant growth and productivity through specific modes of action.  We present a novel soil biology index (GIBBs: Gene Index of Beneficial Bacteria) that quantifies microbial function through the abundance of several known modes of action of various plant-growth-promoting rhizobacteria (PGPRs).  The index builds on the previously demonstrated linkage between phylogeny and function to estimate gene presence from a single phylogenetic analysis (i.e., 16S rRNA profile).  The index integrates a diverse set of ecosystem functions, such as nitrogen-fixation (nifDH), phosphate solubility (ppq), auxin synthesis (ipdC/ppdC), ethylene degradation (acdS), and disease suppression (bud, hcn, phl).  We show that the soil biology index successfully captures microbial abundance and function across managed and unmanaged sites under a variety of agricultural management practices (e.g., tillage, cover crops).