Improving soil health using beneficial microbiomes in urban agriculture

Project Overview

Project Type: Graduate Student
Funds awarded in 2021: $14,991.00
Projected End Date: 11/30/2023
Grant Recipient: Cornell University
Region: Northeast
State: New York
Graduate Student:
Faculty Advisor:
Jenny Kao-Kniffin
Cornell University


  • Vegetables: tomatoes


  • Sustainable Communities: urban agriculture

    Proposal abstract:

                Urban agriculture is an emerging food production system in which farmers grow crops within cities. Urban agriculture not only provides local food with a low carbon footprint, but also promotes sustainability by increasing urban ecosystem services and biodiversity. However, many urban farmers face challenges with their soils, including poor soil structure and low nutrient availability. This research aims to resolve these issues using two particular soil microbes, arbuscular mycorrhizal fungi (AMF) and bacterial polyphosphate accumulating organisms (PAOs). AMF are known to improve soil aggregation and organic carbon storage, while PAOs are mostly studied by scientists without the context of plants and agriculture, yet these bacteria contribute substantially to biological phosphorus (P) cycling. Although the agricultural impacts of PAOs are yet undiscovered, this proposed study will first investigate their impacts on soil P cycling and P uptake by plants. We will work with three urban farms in New York City, and aim to evaluate 1) how AMF and PAOs influence soil carbon and P pools; 2) what types of PAOs interact with AMF; and 3) how PAOs can alter the function of soils in urban crops (i.e., tomatoes in this study). The outreach activities will involve collaborating with youth interns at each urban farm, and sharing the outcomes of the initiative with local urban farmers at conferences and within extension networks.

    Project objectives from proposal:

                The overall aim of this research is to improve the physical and biological health of soils in urban tomato farms by increasing soil aggregation, accumulation of SOC, and P cycling. The specific research objectives include:


                1) To discover how different combinations of AMF and PAOs impact the production of the soil-aggregating glomalin-related soil protein (GRSP), SOC accumulation, different species of P in soils, and P uptake by tomatoes, consequently impacting the growth and yield of tomatoes in urban agriculture.



                This objective is designed to measure how AMF and PAOs contribute to SOC accumulation, soil P cycling, and plant P uptake and growth. AMF are known to increase SOC accumulation by producing a sticky and hydrophobic glue-like glycoprotein, GRSP, which can bind adjacent small-sized aggregates and enlarge them. Hypothetically, increased organic carbon (C) in soils becomes an energy source for PAOs to grow, thereby facilitating P cycling and P supply for plant uptake22. The growth and yield of tomatoes can also be affected by increased SOC and P availability in soils.


                2) To identify the genotype, phenotype, and phylogeny of the PAOs derived from manure that are abundant in the rhizosphere of tomatoes in urban agriculture.



                PAOs are widely studied in EBPR system to recycle water contaminated by high levels of P, because of their high capacity to retrieve P and store it as a long linear chain of inorganic phosphate, polyphosphate (PolyP) in their body23. However, little is known about biological and genetic characteristics of PAOs that inhabit soils and contribute to P cycling. This objective will allow us to identify the genotypes and phenotypes of these functioning PAOs that closely interact with AMF and tomatoes. 


                3) To compare microbial community compositions and metabolic functions using integrated omics studies on the soils of urban farms growing tomatoes under the treatment of AMF and PAOs.



                This objective aims to elucidate how AMF and PAO treatments affect soil biochemical metabolisms and soil nutrient enrichment by examining the protein expressions for N, C, and P cycling in urban agricultural soils. By integrating shotgun metagenomics with metaproteomics26, we can identify how the inoculation of AMF and PAOs creates a shift in soil protein expressions in relation to SOC accumulation and soil nutrient metabolisms, and how this can relate to tomatoes’ nutrient uptake and growth27,28.

    Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.