Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Abstract

Soil microbiomes are sensitive to current and previous soil conditions, and bacterial ‘bioindicators’ of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.

Tillage homogenizes soil bacterial communities in microaggregate fractions by facilitating dispersal

“…Increased weighted mean predicted 16S gene copy number under tillage (Fig. 6) was also noted in a recent global metanalysis (Wilhelm et al, 2023), and is consistent with the idea that pulses of resources (e.g., C liberation or litter incorporation via tillage) select for competitors with fast growth potential in soil bacteria (Schmidt et al, 2018). These studies also found that larger mean estimated genome size correlated with lower soil health ratings and tillage, indicating a need for higher metabolic and regulatory capabilities under environmental instability (Schmidt et al, 2018; Wilhelm et al, 2023).…”

“…We also found relative enrichment of Sphingomonas and Geodermatophilus under tillage, both of which have been identified as key tillage responders (Wilhelm et al, 2023). Under no-tillage, we also found enrichment of the genus Gaiella , ( Actinobacteria), which was one of several identified bioindicators of high biological soil health ratings (Wilhelm et al, 2023). We also found enrichment of anaerobic taxa (e.g., Anaerolineae ) (Yamada and Sekiguchi, 2020) in microaggregates (Fig.…”

“…There were several taxa that responded to tillage representing the genus Nocardioides ( Actinobacteria ). A responder to frequent soil disturbance (West and Whitman, 2022), Nocardioides has been negatively correlated with soil health in a global metanalysis (Wilhelm et al, 2023). We also found relative enrichment of Sphingomonas and Geodermatophilus under tillage, both of which have been identified as key tillage responders (Wilhelm et al, 2023).…”

“…A responder to frequent soil disturbance (West and Whitman, 2022), Nocardioides has been negatively correlated with soil health in a global metanalysis (Wilhelm et al, 2023). We also found relative enrichment of Sphingomonas and Geodermatophilus under tillage, both of which have been identified as key tillage responders (Wilhelm et al, 2023). Under no-tillage, we also found enrichment of the genus Gaiella , ( Actinobacteria), which was one of several identified bioindicators of high biological soil health ratings (Wilhelm et al, 2023).…”

Habitat, plant height, and soil nutrients are important determinants of the Hypericum perforatum microbiome

“…Further work should focus on culturing and rigorously testing plant growth promoting effects of these taxa. Both of these taxa we were also recently identi ed as potential bioindicators of soil health (Wilhelm et al 2022(Wilhelm et al , 2023. In this case, rather than directly in uencing plant height they may just be indicating soil microsite variation that is favorable to plant growth.…”