Bio-Organic Fertilizers Manipulate Abundance Patterns of Rhizosphere Soil Microbial Community Structure To Improve Tomato Productivity

Abstract Background Bio-organic fertilizers has been shown to improve crop yields, partially because of the effects on the structure and function in resident soil microbiome. Purpose and methods Whereas, it is unknown if such improvements have been facilitated by the particular action of microbial inoculants, or the compost substrate. To understand the ecological mechanisms to increase crop productivity by bio-organic fertilizers, we conducted a pot experiment tracking soil physicochemical factors and extracellular enzyme activity over two growth stages and variations of soil microbial communities caused by fertilization practices as below: Bacillus subtilis CY1 inoculation, swine compost, and bio-organic fertilizer. Results Results showed that different fertilization measures, especially bio-organic fertilizers, increased soil nutrients, enzyme activity, and the diversity of microbial communities. For quantifying the “effect size” of microbiota manipulation, we discoverd that, respectively, 19.94% and 48.99% of variation in the bacterial and fungal communities could be interpreted using tested fertilization practices. Fertilization-sensitive microbes showed taxonomy diversity and gave responses as guilds of taxa to specific treatments. The microbes exhibited medium to high degree of co-occurrence in the network and could be recruited, directly or indirectly, by B. subtilis CY1, suggesting that bio-organic fertilizer may allow manipulation of influential community members.Conclusion Together we demonstrated that the increase in tomato productivity by bio-organic fertilizer was caused by the synergistic effect of organic fertilizer and beneficial microorganisms, thus providing novel insights into the soil microbiome manipulation strategies of biologically-enhanced organic fertilizers.