Abstract/Summary

The soil microbiome is the principal reservoir of rhizosphere bacteria, and agricultural management has a significant impact on it. The aim of the study was to understand how changes in cultural practises, such as tillage levels and field cropping history, have influenced soil characteristics and extracellular enzyme activity and how the soil bacterial communities may be altered using the technique of host mediated microbiome selection. In host-mediated microbiome selection, the microbiome is selected based on specific plant traits (for example plant growth, disease resistance, flowering) and the microbiome associated with this trait is passed onto next generation of plants through multigeneration selection progressively enriching plants or their growth environment with microbiota associated with a specific plant trait. This facilitates the use of more complex communities instead of a single microbial strain and provides a potential platform for exploring plant–microbiome interactions. In this study, soybean (Glycine max) plants were grown in an autoclaved coir: sand mix that was inoculated with soil suspensions from the field soils, classified as untilled, tilled and legume soils based on management practices and cropping history. Plant height was used as a trait to select for a microbiome that can produce better plant growth under nutrient limiting conditions. The rhizosphere soil of plants from the first plant generation selected based on plant height (high growth) was used as inoculum for the growth of second generation of plants. The initial field soils (untilled, tilled and legume) varied significantly in physical, chemical and soil enzyme activities. Absence of tillage for extended periods of time (more than 5 years) resulted in high organic matter content in untilled soils and the activity of both the soil enzymes, N-acetyl beta glucosaminidase (NAG) and phosphatase (PHOS), measured in this study were high in untilled soils. Next generation sequencing (NGS) analysis indicated significant differences in bacterial composition between the three field soils, and distance-based redundancy analysis revealed that organic matter content in soil had a major impact on bacterial composition. The results also showed that legumes nourish the soil by boosting the diversity of bacteria. In host mediated selection study, soil enzyme activity was found to be a strong indicator of biological activity in the rhizosphere and the activity of enzyme NAG showed significant positive correlation with plant height and above ground dry mass in this study. The results on root exudation confirms that the soil type is a major factor influencing the bacterial community composition of rhizosphere soils and that plants can select for specific bacterial community to establish a mutual relationship with the help of their root exudates. The three field soils when mixed in equal proportions generated novel combinations of bacterial community with beneficial effects. The results from linear discriminant analysis (LDA) effect sizes (LEfSe) showed that the plants in each soil displayed significantly varied relative abundances of distinct bacterial species in their rhizosphere and many of these species were reported to play roles in soil nutrient cycling. This suggests that when plants are under nutrient stress, they recruit specific taxa in their rhizosphere that help the plants grow under nutrient deficient conditions, and their selection is significantly influenced by the source of inoculum. The findings of this study showed that host-mediated microbiome selection is a viable platform for studying plant-soil-microbe interactions, and that a microbiome rich in plant beneficial bacteria capable of stimulating plant growth in nutrient-limited conditions can be obtained even after two generations of selection.