Urban agriculture (UA) is an emerging food production system in which farmers grow crops within cities. However, many urban farmers face challenges with their compost soils, including poor soil structure and low nutrient availability. This study aimed to utilize beneficial microbes, such as arbuscular mycorrhizal fungi (AMF) and phosphorus solubilizing bacteria (PSB), to address soil aggregation and biological phosphorus (P) cycling in UA soils while also assisting urban farmers in generating higher economic returns. We cultivated Bush Champion II Hybrid Tomatoes (an indeterminate tomato cultivar) in three organic urban farms in New York City in 2022 under four different treatments: 1) Control tomatoes, which were not treated with PSB or AMF; 2) Tomatoes treated with PSB; 3) Tomatoes treated with AMF; and 4) tomatoes treated with PSB and AMF. Our hypothesis posited that the positive interactions of PSB and AMF would synergistically enhance soil phosphorus cycling and carbon accumulation and, thereby, promote plant growth and nutrition. Our findings indicate that the combined application of AMF and PSB increased the overall abundance of soil microbiomes, as measured by flow cytometry. There was also an increase in the production of soil-aggregating proteins and soil acid phosphatase activity. Additionally, the nutrient uptake by tomatoes, including calcium (Ca), potassium (K), and phosphorus (P), was enhanced. We also employed omics approaches using deep sequencing metagenomics and metaproteomics to generate meaningful insights into how AMF and PSB interacted with soil native microbial populations and defined soil microbiome functions. Our findings offer novel insights into the characteristics and functions of soil microbiomes in UA soils. This knowledge will contribute to advancing the potential of beneficial microbes in enhancing food production within urban agriculture systems.
