Team:Lambert GA/Human Practices
OVERVIEW
Figure 1. Lambert iGEM targeted many stakeholders including commercial companies, community organizations, nonprofits, and academia to gain insight on the integration of AgroSENSE for real-word applicabilities.
Lambert iGEM collaborated with a variety of stakeholders including food banks, commercial and local aquaponics producers, and local schools to determine if AgroSENSE is good and responsible for society.
Our project was inspired by Smart Agriculture, a group of students at our high-school who experimented with hydroponics and automation to provide nutritious, efficient, locally sourced produce such as kale and lettuce. A few Lambert iGEM members also participated in this club and proposed integrating aquaponics and synthetic biology. This inspired our initial investigation of biosensors to address nutrient balance concerns within alternative agriculture systems.
We then reached out to aquaponics experts such as Dr. Todd Guerdat to identify barriers in implementing aquaponics. Dr. Guerdat, an environmental engineer at the USDA and author of Recirculating Aquaculture, informed us of the laborious procedures in maintaining aquaponics systems, specifically maintaining nutrient balance. For his large scale aquaponics system, he told us that he had to send his samples to a laboratory and the ion measurement instruments were costly. Our conversations with these aquaponics experts shifted our focus to developing nitrate, nitrite, and phosphate biosensors as well as researching possible bioremediation of Iron from fish waste sludge. This will inform users of the nutrient levels in their system, so they can guide maintenance decisions accordingly such as the addition of fertilizer.
Dr. Mark Styczinski from the Georgia Institute of Technology and Dr. Ichiro Matsumura from Emory University guided us in the development of our biosensors. They helped troubleshoot concerns in Nar and Pho regulons’ inability to measure certain thresholds of nutrients and the interference of the native regulons with our synthesized parts. Meanwhile, Dr. Saad Bhamla from the Georgia Institute Technology mentored us in developing our low cost bead homogenizer OpenCellX, an improvement on our last year’s hardware.
When developing a prototype for our system, Ponix, a commercial hydroponics company provided insight on how our biosensors and arduino sensors could ease maintenance of aquaponics systems for community organizations. We began reaching out to community organizations such as the Gwinnett Coalition and Atlanta Community Food Banks to understand the condition of nutrition in their respective areas and the potential for AgroSENSE to address food insecurity. Our initial idea was to implement our AgroSENSE system in community centers and foodbanks located in Atlanta's food deserts.
However, it was concerns about biosensors raised in conversation with APD Urban Planning that shifted our focus from community based systems to school groups and biotechnology teachers. Instructors could maintain and safely discard biosensors while guiding students to develop hands-on skills in botany, systems maintenance, and biotechnology. Through Georgia Bio, a non-profit association whose mission is to advance the growth of Georgia’s life sciences, we connected with teachers across Georgia to develop plans for implementation of AgroSENSE in schools.
PROBLEM
SMART AGRICULTURE
Our inspiration for this year’s project was sparked by our collaboration with Lambert Smart Agriculture, a group of students at our high-school who experimented with hydroponics and automation to nutritious, efficient, locally sourced produce such as kale and lettuce. Lambert iGEM members participating in this club pitched the integration of synthetic biology and aquaponics at our initial brainstorming meeting in February. We discussed common diseases faced in hydroponics systems such as root rot. However, through more in-depth conversations we discovered that non-nutrient specific sensors have resulted in Smart Agriculture members estimating the concentrations of the distinct nutrients, phosphate, nitrate, and potassium. This led to plant growth variability in their aquaponics systems. The group also gave us insight into key hardware specifics such as the measurements required for PVC pipes to build their hydroponics set-up. Innovating off of our model aquaponics system donated by Ponix, we are continuing our partnership with Smart Agriculture to design a new system that is more frugal and effective. Similarly, we contributed ideas and methods to expand their current hydroponics greenhouse to accommodate aquaponics.
Figure 2. A few Lambert iGEM members helping Smart Agriculture with their hydroponic greenhouse. Disclaimer: This image was taken before the COVID-19 pandemic.
DR. TODD GUERDAT
During the spring, Dr. Todd Guerdat, a Civil/Agricultural Engineer with the Natural Resources Conservation Service at the USDA and a leading expert in aquaponics, aided in redirecting our project away from phosphate and nitrate production towards a method to sense key nutrients and solubilize iron. Our initial project idea revolved around sensing and producing phosphate and nitrate ions to make our aquaponics system self-sufficient. During our call, Dr. Guerdat advised our team to focus on only the sensing portion of Pho (phosphate) and Nar (nitrate) as production of these ions already occur efficiently through fish waste. He also suggested the development of a nitrite sensor. Aquaponics systems naturally contain bacteria that convert ammonia- a fish excrement- to nitrite- an intermediate toxic to fish- to nitrate- a nutrient essential to plants. Therefore, knowing the nitrite concentration in an aquaponics system will help users maintain fish health and nutrient balance while guiding their decision making. Additionally, according to Dr. Guerdat, there is no method to degrade iron (another essential nutrient) from fish excrement and solubilize it to allow plants to utilize it within an aquaponic system. This gap in iron solubility inspired the iron workflow of our project (See WetLab: Iron).
Dr. Todd Guerdat
GEORGIA AQUAPONICS
In early April, Lambert iGEM had a virtual conference call with Mr. Dave Davies and his wife, Marion, from Georgia Aquaponics, a family-owned locally operated aquaponic farm. We discussed the basics of aquaponics, its advantages, set up, complications, their experience, and what they have learned from it. They aided us in further developing our project’s problem statement, directing the focus from hydroponics to aquaponics. After our conference, Mr. Davies suggested focusing more on aquaponic education rather than food production in regards to our Human Practices outlook since the general public is hesitant to try something new and aquaponically grown produce is more expensive than commercially grown produce. Additionally, they described the hardships they encountered with sensing nutrients using test strips, which are imprecise, and further encouraged our team to find alternate methods of sensing, thus confirming our project’s purpose.
DEVELOPMENT
PONIX
During the spring, Lambert iGEM contacted Michael Choi from Ponix, an Atlanta company that currently uses shipping containers to build environment-controlled hydroponics systems to grow produce. During the meeting, our main priority was to understand current hydroponics systems and their impact on local and global markets. We also discussed the potential future impacts of hydroponic systems and how they can further be developed. Mr. Choi explained that hydroponic systems are expected to become a major part of the future since hydroponics offer a myriad of advantages that can not be attained with traditional farming methods, such as a limited amount of required water, an environmentally-conscious organization, and a wider access to requisite and supplemental nutrients for the plants. Additionally, he addressed the basics of building a hydroponic system and methods to grow our food efficiently so that we can design and potentially build our own system. Through our partnership, Ponix was generous enough to donate a 46 inches wide 79 inch by 36 inch system for our project experimentation. Once we began experimenting with our Ponix system, we noticed that for plants with larger root bulbs, water was leaking and therefore not allowing for equal distribution throughout our system. Moreover, the system produced excess algae. To troubleshoot these problems, we discussed with Mr. Choi on future iterations of the system to improve pipe design. Also, Mr. Choi supported our focus in agricultural biotechnology education, and we have been discussing future collaborations with organizations such as EdFarms, a Birmingham, Alabama based organization encouraging innovation and real-world skills among students.
Mr. Michael Choi
Figure 3. Lambert iGEM Members harvesting lettuce from Ponix’s donated system
MR. BOB RATAJCZAK
In mid-April, Lambert iGEM held an online conference with Mr. Bob Ratajczak, an aquaponics researcher at the University of Georgia. The team discussed different nutritional aspects of the fish used within the aquaponics system, including how to calculate the optimal density of food as compared to fish weight, the symbiotic relationship between the plants and the fish, and the general practices used in current aquaponic setups (such as current methods of sensing nutrients and maintaining efficient growth of both the fish and plants). Mr. Ratajczak’s expertise in aquaponics setup was crucial to help Lambert iGEM’s hardware team understand how to convert the donated vertical hydroponics system into an aquaponics system. The main issue the team examined was how to adequately filter the fish sludge to utilize the iron within it. To approach this issue, Mr. Ratajczak suggested using a swirl filter to separate the solid waste from the tank water. Thus, incorporated a swirl filter in our system to ease maintenance.
Mr. Bob Ratajczak
DR. MARK STYCZYNSKI
During a conference in May with the Styczinski Research Group from the Georgia Institute of Technology, Dr. Mark Styczynski and Ms. Elizabeth Chilton guided us in developing the experimental design for our Pho and Nar wet-lab pathways. As their research group primarily works on developing biosensors, they were able to give us advice on our concerns, such as whether the natural Pho/Nar regulon pathways would interfere with our parts. They also confirmed our modeling plan to predict GFP expression of our Pho biosensors for varying phosphate concentrations. Dr. Styczynski and Ms. Chilton also suggested that we start our modeling processes by identifying the rate constants through literature review. With regards to the Nar system, our initial idea was to knock out the natural Nar regulon. However, Dr. Styczinski suggested that CRISPR is difficult to knock out genes within E. coli, and noted that our team simply needs to outcompete the natural Nar system.
Dr. Mark Styczynski
Ms. Yan Zhang
Ms. Elizabeth Chilton
DR. SAAD BHAMLA
Dr. Saad Bhamla is a professor at the Georgia Institute of Technology and the founder of the BhamlaLab. His expertise and experience in Frugal Hardware devices has proven to be very beneficial for both our Drylab teams. This year, the continued support from his lab the OpenCellX Project has enabled our team to test our devices in a wider variety of applications than the original intent of our project. Over the past two years, he has provided valuable feedback on the applicability and design of OpenCellX (See Project: Excellence in Another Area). Specifically, during our 2020 season, Dr. Bhamla highlighted the need for a more resilient and reliable design, specifically through the use of bearings. He has also connected our team with molecular biologists who use bead-beaters for their workflows with the intent on collaborating with them in the future.
Dr. Saad Bhamla
DR. ICHIRO MATSUMARA
Along with the Styczinski Research Group and Dr. Saad Bhamla, we also pitched our project to Dr. Ichiro Matsumura of Emory University’s Biochemistry Department. He recommended that we look at our Iron pathway through an alternative lens, suggesting that solubilizing iron through a recombinant cytochrome protein would be inefficient and instead advised researching the natural ways that iron is recycled, such as in pond ecosystems. He also recommended that a protein extraction approach would be intensive, so it would be in our best interest to identify an internal electron donor to reduce ferric (Fe³⁺) to ferrous (Fe²⁺). Dr. Matsumura redirected our Iron Workflow to research natural bacteria’s role in iron reduction and potential improvements our team can expand upon. (See WetLab: Iron) Additionally, Dr. Matsumura gave us advice on our Nar and Pho workflows. Through literature review we determined that the Pho regulon would only be able measure 4 micromolar of phosphate, and similarly the Nar system would only be able to measure 0-140 ppm of nitrate. Therefore, we were concerned that if the phosphate or nitrate concentrations were not within these thresholds, our biosensors would not be able to provide a readout. Dr. Matsumura advised us to measure concentrations not within the thresholds through serial dilutions. (See Wetlab: Pho and Nar)
Dr. Ichiro Matsamura
DR. SAMMY BELL
Dr. Sammy Bell, head of Formulation Sciences at Boehringer Ingelheim, provided us with a chemist’s perspective on the Iron pathway. He suggested that Iron reduction from ferric to ferrous would be much easier chemically through the addition of an electron donor such as ascorbate. He further advised us that we would have to justify why iron reduction would be preferred through a synthetic biology over a chemical approach. Although a synthetic biology approach would prove to be more reproducible, chemical conversion of iron was deemed simpler. Using Dr. Bell’s guidance, we redirected our Iron Workflow to identify potential plant synthetic biology routes to improve Iron uptake. (See WetLab: Iron) Further, Dr. Bell guided us in our initial experimental design development for the Nar pathway. Our experimental plan was to produce Nitrate through a synthetic biology approach by modeling the nitrification process. However, he suggested that understanding the chemical process underlying conversion of nitrification (conversion of ammonia → nitrite → nitrate) would be difficult and using a synthetic biology approach would not be efficient. Therefore, we decided to pursue nitrate sensing over nitrate production.
Dr. Sammy Bell
IMPLEMENTATION
CAREPOINTE COMMUNITY OUTREACH
In early June, Lambert iGEM contacted Mrs. Mona Hoffman, a Food Pantry Coordinator at CarePointe, to understand our aquaponic system’s potential to supplement produce to food banks and help accessibility for people who cannot afford nutritious foods. She informed us that our aquaponic system could potentially help with the influx of food as she has previously heard of aquaponic options to address food insecurity. Mrs. Mona was also positive to consider a hypothetical implementation of our aquaponic system. Moreover, she aided us in reaching out to the Gwinnett Coalition and the nutrition specialist of Atlanta Food Bank by giving us their contact information.
Figure 4. CarePointe is a food bank and community center.
GWINNETT COALITION
In mid July, Lambert iGEM contacted Mrs. Suzy Bus, a Program Director at Gwinnett Coalition, and Mrs. Lecia Young, a Program Coordinator at Gwinnett Coalition, to understand if our aquaponic system could effectively address food insecurity issues in local communities. They gave us positive responses to our aquaponics system and were optimistic that aquaponics would not only help feed people, but also generate jobs. In terms of the hypothetical implementation of our aquaponics system, Mrs. Bus and Mrs. Young were positive about collaboration and putting our aquaponic system in their site. They also gave an answer to our main concern: people’s receptiveness to aquaponic systems. According to what they’ve heard from the Gwinnett Public Library, people had positive responses to the aquaponic system as they were excited to see the growth of the produce. They were hopeful to incorporate an AgroSENSE system in the future into their community center. Lastly, they gave us a map of food deserts in Atlanta (see Project: Proposed Implementation), so that we could correctly identify the target areas facing food insecurity. Their website: www.gwinnettcoalition.org
Ms. Suzy Bus
Ms. Lecia Young
NUTRITION SPECIALIST FROM ATLANTA COMMUNITY FOOD BANK
In July, Lambert iGEM contacted Ms. Kristen Elliott, a nutrition specialist from Atlanta Community Food Bank. We discussed the status of people in Food Deserts in terms of nutrition and talked about how our aquaponics system can help them. She said the major reason for limited access to nutritious foods for people living in food deserts is lack of money and a tight budget for food, leading them to buy cheap and processed foods. She also added that high consumption of processed foods leads to several consequences, including diabetes and high blood pressure. In terms of our project, she thinks that our aquaponics system would be very beneficial to giving people in food deserts access to nutritious food. Ms. Kristen Elliott especially liked our project as it can go straight from the system to the table, which allows the consumers to get the most nutrition out of it. She suggested that we could market our system by growing plants that are already familiar to the people. Lastly, she gave us several tips for writing cookbooks (See Human Practices: Science Communication and Project: Proposed Implementation), including looking at Feeding America Recipe Guidelines, making the recipes using nine ingredients or less, focusing on salt and sodium content, and more.
Ms. Kristen Elliot
APD URBAN
In early June, Lambert iGEM was able to get in contact with APD Urban, an urban planning consulting firm with experience in the integration of aquaponic systems into city projects. The team wants to get a sense of how our project would fit into the local sphere in a way that would make it as effective and efficient as possible to help mitigate the effects of food deserts across Atlanta. The consultants on call with us were able to provide us with a detailed financial analysis aquaponics system and its implementation, along with highlighting some potential complications that could arise when introducing our system to residents. They brought up a safety aspect (biosensor management and discarding) we had not considered previously, and they provided us with marketing tactics to circumvent the stigma surrounding food grown with GMOs. Finally, they were able to lend us insight on the incentives that citizens of Atlanta could have to utilize our system and helped us modify our project to capitalize on these incentives to make our system an attractive option for people because of the fresh produce. Overall, the firm gave another point of view on our project and helped us combat some of the public perception against food GMOs to help ensure our system would reach the maximum number of people it could. APD Urban were also kind enough to provide us with several contacts for further information on local government involvement, agricultural marketing campaigns, and local authorities that would be willing to take a risk on our progressive project.
Mr. Steven Gonzales
Mr. Carter Coleman
GEORGIA BIO
Lambert iGEM shifted our focus to schools and the education system to implement the first prototype of AgroSENSE because schools could act as community centers and also provide a hands-on learning experience for students. After getting all appropriate releases for our engineered cells, we plan to train teachers on maintaining and discarding biosensor cells while providing students opportunities to innovate in agricultural biotechnology to best serve their communities. With the help of Georgia Bio, we connected with high-school biotechnology teachers to design a curriculum that will integrate with our AgroSense app to help students build, learn, and innovate in aquaponics (See Project: Proposed Implementation). Georgia Bio also alerted us of the need for visual graphics as the shift for many schools to virtual learning has created opportunities to broaden science communication, so we created a series of infographics that supplement our states’ Biology and Biotechnology curriculum (See Human Practices: Science Communication). Georgia Bio also helped us to connect with other stakeholders such as Ponix, a commercial hydroponics company who guided us in the development of our project.
Mrs. Kristin Boscan
Ms. Megan Heaphy
FUTURE WORK
GEORGIA BIO
During Phase II of AgroSENSE, Lambert iGEM plans to continue partnering with Georgia Bio in an effort to make connections with teachers interested in implementing aquaponics into their curriculum in areas such as agricultural science, biotechnology, biology, chemistry, environmental sciences, and botany. We are partnering with Georgia Bio as it maintains an extensive network of teachers and corporate sponsors to provide high impact teacher training across the state of Georgia. Lambert iGEM plans to offer a workshop package consisting of a build day, 4 teaching workshops, and a curriculum implementation session. The workshops will be offered in a virtual and face-to-face setting in an effort to connect with teachers who might be inhibited by distance to our school. The workshops are intended to be synchronous, but will be recorded for reference purposes. The build day will provide the instructions to outfit the school with a basic hydroponics setup. Teacher workshops are designed to re-skill or supplement existing knowledge of teachers in areas of systems maintenance, biosensors, plant physiology, and fish physiology. The last session of the workshop will consist of time spent directly linking existing curriculum with AgroSENSE and building easily implementable lesson plans.
ADAM SILVERMAN
When developing the Nar Biosensors, Lambert iGEM was curious about the ability to convert our biosensor cells into a cell-free system, a method to further our user-friendly system. However, one potential challenge we encountered was how to incorporate our membrane-bound sensor proteins, NarX and NarQ, into this system. We discussed with Adam Silverman, a graduate student in Jewett Labs at Northwestern University, about how he developed sensors using other similar membrane-bound proteins by overexpressing them in E.coli cells and extracting the needed membrane proteins. He theorized that these membrane-bound proteins would still be in a membrane environment since, after lysis, the remaining membrane fragments create vesicles, where the membrane-sensor proteins, now in a high concentration, reside. Mr. Silverman gave us advice on our project and how we could develop cell-free sensors for our own system- a potential direction for our project’s second year.
Mr. Adam Silverman
TEACHER FOCUS GROUP
High-School Biology teacher, Ms. Cynthia Greer provided insight that she used an organic hydroponics tower in her classroom to teach plant botany. She suggested that the experience made students more excited to attend class and taught them their responsibility in maintaining such systems. She also suggested that Lambert iGEM’s project in providing readouts through biosensors and arduino sensors would be helpful because her previous experience in maintaining her hydroponics system was quite laborious. She further guided us to look into Boys and Girls clubs to implement afterschool programs that could be excellent extracurriculars for students interested in agriculture. In addition, we talked with Mrs. Brooke Hollingsworth, an agriculture teacher at Liberty Middle School. She expressed how teachers can tie hydroponics to all middle school science classrooms. 6th graders primarily learn earth science, so they benefited from learning how to test water quality. 7th graders learn life science, so they learn about plant botany and plant growth cycles. 8th graders learn chemistry, so they manage fertilizer addition, testing chemical composition, and adjusting the pH in their school’s hydroponic systems. Mrs. Hollingsworth noted that the integration of aquaponics in middle school classrooms can provide students an insight on future career options and have a hands-on approach to scientific problems. Further, she suggested that having an educational outlook for AgroSENSE would be beneficial since students would learn the responsibility of maintaining systems and can in conjunction learn about a variety of science concepts.
Figure 5. Lambert iGEM discussing with Ms. Cynthia Greer about how AgroSENSE can be integrated in her classroom.