Individual Final Project

SoilBuddy

Gemini AI-Generated in response to prompt [1] Gemini AI-Generated in response to prompt [1] Gemini AI-Generated in response to prompt [1]

1 Abstract

As an expansive substitute to manual geochemical sampling, and cheap complement to existing agritech workflows, SoilBuddy is synbio’s answer to the need for real-time soil health monitoring in humanity’s quest to end world hunger. SoilBuddy captures key metrics such as oxygenation, pH and macronutrient levels through an authentically biological chassis, and conveys actionable insights through naturally-occurring reporter systems. SoilBuddy scales naturally over the space of a farm while implementing safety switches which prevent ecological leakage and facilitate regulatory compliance.

The key contribution of the project is a demonstration of safety-first persistent microbiome monitoring and regulation. Specifically, within the confines of HTGAA, I will be designing and verifying the function of an AND genetic circuit in E. coli to express GFP if and only if local bacterial cell density is high (~chemiluminescence threshold) and external pH is excessively high (>pH 7).

In broad strokes, this will be achieved through Genetic circuit design and simulation on Asimov Kernel; Cassette design on Benchling; Heat-shock transformation; and ultimately triplicate verification of fluorescence against -ve controls using OpenTrons.

Due to my limitations as a remote committed listener, I will be focusing on the first segment of the project: the design and verification of my gene cassette.

2 Project Aims

The first aim of my final project is to design and verify the function of an AND genetic circuit in E. coli to express GFP if and only if local bacterial cell density is high (~chemiluminescence threshold) and external pH is excessively high (>pH 7). This will be achieved through the utilization of Asimov Kernel for genetic circuit design and simulation; Cassette design on Benchling; Heat-shock transformation in competent E. coli, and ultimately triplicate verification of fluorescence in response to the AND condition and AND condition only using OpenTrons.

The next steps in the development of SoilBuddy will be the incorporation of several more reporter systems orthogonal to the GFP to test for different soil conditions such as oxygenation and macronutrient levels, as well as optimization studies to calibrate the quorum sensing bioswitch. A stretch goal would be the incorporation of signaling pathways which indicate microbiome health, and the secretion of prebiotics / phages which regulate biotic diversity and abundance.

In the long term, we hope to replace harmful chemical fertilizers in commercial agriculture and insure the supply of food against fluctuations in fertilizer supply through a solution that scales naturally over the space of a farm while implementing safety switches which prevent ecological leakage and facilitate regulatory compliance.

3 Background

The first publication by Zhang et. al., 2025 describes the realization of a multi-channel bioelectronic E. coli-based sensor that utilizes multiplexing to sense multiple heavy metals and ions in soil solution. However, a key limitation is that the research group’s biosensor relies on microelectronic readout to generate human-interpretable signals, which can’t scale cheaply over the area of a commercial farm.

The second publication by Jansson et. al, 2023 describes current approaches towards soil microbiome curation and explores the possibility of community gene editing and isolate application on large scales to supplant or enhance the action of conventional chemical fertilizers. However, this solution is neither safe from a biocontainment perspective, nor sustainable since constant reapplications of isolate would be required.

Crucially SoilBuddy addresses both of these issues. Firstly, it utilizes an all-biological chassis that is reproducible, allowing it to scale organically without the reapplication of SoilBuddy treatment and in a cost-efficient manner. Secondly, the biosafety switch within SoilBuddy, together with its encapsulation within a single bacterium cell, allows for a higher degree of biocontainment and protection from ecological contamination.

In 2026, commercial agriculture produces enough food to meet the caloric needs of all humans on Earth, yet, frictions in production and trade limit the geographies in which food can be grown, and subsequently where it is distributed. At the same time, the vendor lock-in of commercial fertilizer suppliers both chains commercial farmers to inefficient modes of food distribution and introduces supply chain risks especially in a time of global trade uncertainty (Eg uncertain petroleum supplies driving up the price of nitrogenous fertilizer). Existing bioremediation options don’t scale well to commercial farms and across biomes. SoilBuddy solves all this and more using the power of bioengineering: it replicates in the soil, thus solving issues with the flows of power and money in the global agriculture industry; it supplants commercial fertilizers that have to be constantly reapplied, and provides inherent biocontainment through its AND switch.

While I was inspired by the four tenets of biomedical ethics, I reckoned the most important goals relevant to SoilBuddy are Non-Maleficence and Justice. Given the echoes of the GMO debate from earlier in the century, and the proliferative capacity of bacterial systems, prioritizing safeguards against ecological contamination are crucial for governing our bacteria-based platform. At the same time, given the long history of agricultural intervention being wielded as a political tool to harm access to food and development, it’s crucial that we prioritize justice in the administration of SoilBuddy to ensure its applications prove to be a tool for good.

Goal 1: Non-Maleficence

In the context of SoilBuddy, a commitment to non-maleficence - articulated in the credos “first, do no harm” - involves a rejection of utilitarian logic to instead foreground safeguards against proliferation and mitigation of unintended consequences before the launch of SoilBuddy.

1.1: Counter-Proliferation

SoilBuddy must be governed to prevent runaway proliferation in wild ecosystems and spillover events should be minimized as far as possible.

1.2: Mitigation

Before applying SoilBuddy, practitioners in the SoilBuddy ecosystem must enact measures that mitigate the harm caused by both foreseen unintended consequences (ie. known risks of biotech in agriculture per se, such as gene contamination) as well as unforeseen unintended consequences (ie. put in place inherent safeguards or plans of action to manage unknown unknowns).

Goal 2: Justice

In the context of SoilBuddy, our construction of justice pertains to its distribution and development into perpetuity – I mean to open-source soil health.

2.1: Material Equity

Governance should focus on ensuring geographic and socioeconomic equity in access to the materiel of SoilBuddy, administering its distribution on the basis that food ought to be a human right, in line with the UN’s SDGs.

2.2: IP Equity

Governance should guard against the privatization of developments on SoilBuddy as a platform, recognizing that, again, access to food as a human right contributes to the common good of the species. Insomuch as SoilBuddy will start off open-source, its derivative art should also be accessible to all.

4 Experimental Design

Designing DNA relevant to your final project + Code Include specific methods/tools/technologies/biological concepts for each part of the final project and analysis This section will be used to determine whether the experiments are well designed, feasible, and likely to succeed in testing your hypothesis Often this section is broken into discrete tasks/sub-aims For each experiment and/or analysis, include a description of your expected results If possible, include figure(s) that visually shows a broad workflow of your project or a specific aspect of your experimental plan Reminder: All HTGAA projects must include some DNA design! Make sure this form is submitted.

5 Results & Quantitative Expectations

As a remote committed listener, I decided to focus on the in silico portions of my project: designing the genetic circuit using Asimov Kernel and implementing the gene cassette using Benchling.

Write down a detailed protocol of how you validated this aspect of your final project. (Numbered list or paragraph is fine)

I used Asimov Kernel (ie. in silico gene circuit simulation), Benchling (ie. in silico DNA design), OpenTrons (ie. lab automation technologies) and heat shock treatment (ie. heat-shock based bacterial transformation)

Asimov Kernel Gene Casette

Challenge 1 Challenge 2 Challenge 3 Challenge 4

6 Additional Information

  1. List all references cited in this assignment
  • [1] As an expansive substitute to manual geochemical sampling, and cheap complement to existing agritech workflows, SoilBuddy is synthetic biology’s answer to the need for real-time soil health monitoring in humanity’s quest to end world hunger. SoilBuddy captures key metrics such as oxygenation, pH and macronutrient levels through an authentically biological chassis, and conveys actionable insights through naturally-occurring reporter systems. SoilBuddy scales naturally over the space of a farm while implementing safety switches which prevent ecological leakage and facilitate regulatory compliance.

The key contribution of the project is a demonstration of safety-first persistent microbiome monitoring and regulation. Specifically, within the confines of HTGAA, I will be designing and verifying the function of an AND genetic circuit in E. coli to express GFP if and only if local bacterial cell density is high (~chemiluminescence threshold) and external pH is excessively high (>pH 7).

  1. Create a supply list and budget for your project
  • Benchling Genetic Cassette Order - $400
  • OpenTrons Flex Robot Timeslot - $25 equivalent (assuming ~10,000hr Minimum Mean Time Between Failures)
  • Competent E. coli (eg O157:H7 E. coli) - $200
  • Heat-shock treatment reagents and labware (eg recovery medium, bain marie, stopwatch, micropipette, LB medium w/ kanamycin, elliptical shaker) - $200
  • 0.1M HCl (aq), DI water, LB Broth - $50 equivalent
  • OD Spectrophotometer, Cuvettes - Included with OpenTron Flex

$875 Total