Difference between revisions of "Team:Newcastle/Description"

 
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                     <p><font size="3">The United Nations estimates global population has increased by over 1 billion since 2005 and will near 9.8 billion by 2050 [ref]. The demand that we place on agricultural products has risen in parallel. We rely on the agricultural sector to provide not only food, but also fuels, shelter and fabrics. In turn, the agricultural sector relies on the application of synthetic fertilisers to maintain crop productivity. Nitrogen, phosphate and potassium (NPK) based fertilisers provide crops with essential macronutrients required for growth. NPK consumption is predicted to increase to 201.7 million tonnes by the end of 2020 [ref].</font></p>
+
                     <p><font size="3">The United Nations estimates global population has increased by over 1 billion since 2005 and will near 9.8 billion by 2050 [1]. The demand that we place on agricultural products rises in parallel. We rely on the agricultural sector to provide not only food, but also fuels, shelter and fabrics. In turn, the agricultural sector relies on the application of synthetic fertilisers to maintain crop productivity. Nitrogen, phosphate and potassium (NPK) based fertilisers provide crops with essential macronutrients required for growth. NPK consumption is predicted to increase to 201.7 million tonnes by the end of 2020 [2]. </font></p>
  
−
                    <p><font size="3">NPK fertilisers significantly increase the yield of staple foods such as maize, wheat and potatoes but they also play a large role in in climate change. Nitrogenous fertilisers are produced using the Haber-Bosch process [ref]. This process is energy intensive, requiring 600kg of natural gas to produce 1000kg of ammonium, and resulting in the release of 670 million tonnes of CO<sub>2</sub> per annum [ref].</font></p>
+
<p><font size="3"><p><font size="3">NPK fertilisers significantly increase the yield of crops such as maize, wheat and potatoes [3] but they also play a large role in climate change. Nitrogenous fertilisers are produced using the Haber-Bosch process. This process is energy intensive, requiring 600 kg of natural gas to produce 1000 kg of ammonium, and resulting in the release of 670 million tonnes of CO<sub>2</sub> per annum [4].</font></p>
  
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                     <p><font size="3">In addition, fertiliser application has been shown to have a negative long-term impact on soil health [ref]. Synthetic fertilisers cause soil pH to decrease, degrading soil crumbs and resulting in compact soils with reduced water drainage and air circulation; both have negative impacts on plant-root health [ref]. Meanwhile, the accumulation fertiliser run-off leads to eutrophication in water courses. Eutrophication impacts water quality and allows algal blooms to form affecting biodiversity through toxin production and promotion of a hypoxic environment[ref]. This reduces the availability of clean drinking water with additional costs incurred to process water for drinking.</font></p>
+
                     <p><font size="3">Fertiliser application has also been shown to have a negative long-term impact on soil health. Synthetic fertilisers cause soil pH to decrease, degrading soil crumbs and resulting in compact soils with reduced water drainage and air circulation; both have negative impacts on plant-root health [5]. Meanwhile, the accumulation of fertiliser run-off leads to eutrophication in water courses. Eutrophication impacts water quality and allows algal blooms to form, affecting biodiversity through toxin production and promotion of a hypoxic environment [6,7]. This reduces the availability of clean drinking water with additional costs incurred to process water for drinking.</font></p>
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                   <p><font size="3">Not all plant species require the addition of large amounts of nitrogen. Legumes, such as peas, beans, clover and soy, form symbiotic relationships with rhizobial bacteria. These bacteria colonise the roots structures where they biochemical fix nitrogen that becomes available for the plant [ref]. </p>
+
                   <p><font size="3">A plant’s demand for resources long predates the era of fertilisers, this demand has led to co-evolution of symbiotic relationships between plants and microbes. The legume-rhizobia symbiosis is one of the most well-known of these interactions. These bacteria are able to colonise the roots of plants such as peas where they fix atmospheric nitrogen. This nitrogen is then readily available for the plant to access [8]. </p>
 +
<img src="https://static.igem.org/mediawiki/2018/6/64/T--Newcastle--RhizobiainRootTom.png"><p><font size="2"><center>Figure 1. <i>Rhizobia</i> spp. colonising the root of broad bean plant in Northumberland, UK. Photo credit: Dr Thomas Howard</center></font></p>
  
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                     <p><font size="3">Mycorrhizal fungi form extensive networks with many plant roots enhancing their access to nutrients and water. And both fungal, bacterial and archeal micro-organisms are known to inhabit the plant tissues. These are a natural and wide ranging phenomenon dating back to the Devonian period. The earliest land plants show evidence of fungal endophytes.</p>  
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                     <p><font size="3">However, it is not just bacteria that plants have evolved these beneficial relationships with. Mycorrhizal fungi  are capable of producing  intricate hyphal networks throughout the root system that enhance the plant’s ability to access nutrients and water [9]. </p>
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<img src="https://static.igem.org/mediawiki/2018/0/03/T--Newcastle--Glomites.jpeg"><p><font size="2"><center>Figure 2. <i>Glomites rhyniensis</i> hyphae growing through the root cortex of <i>Aglophyton major</i> [10]</center></font></p>
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                  <p><font size="3">Plant interactions with soil micro-organisms are nature’s wide-ranging alternative to chemical fertilisers. These natural symbioses date back over 400 million years to the Devonian era, where fossil records show evidence that even the earliest land plants had relationships with fungal endophytes [10]. </p>
 +
 
 +
                    <p><font size="3">Engineering of these symbioses, to open access to crop plants, is a promising solution to aid in mitigating NPK fertiliser dependence. While there have been many attempts to engineer nitrogen fixation into the crop itself, the concept of engineering symbioses themselves is a relatively untouched area. Here we propose an alternative route to reach this goal. Rather than engineering the plant or nitrogen-fixing symbiosis directly, we instead put forward the idea to develop a novel endophytic bacterial chassis to act as a mediator between these beneficial bacteria and the plant roots. </p>  
  
  
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                     <p><font size="3">The need to feed increasing urban populations is placing unprecedented pressure on the agriculture industry. To secure higher productivity, the sector relies upon synthetic fertilisers derived from energy intensive manufacturing methods – the devastating effects of which are outlined in the sustainability imperative section above. In addition, for every 1 °C increase in atmospheric temperature, 10 % of farmland used for crop production will be lost [8]. Over the next 50 years, farming is going to become even more marginalised [9]. </font></p>
+
                     <p><font size="3">This project investigated <i>Pseudomonas</i> sp. (CT 364) due to evidence that members of this genus are capable of colonising plant roots [11]. <i>Pseudomonas</i> are Gram-negative bacteria with a diverse metabolism [12] that enables the reported colonisation of a broad range of plant roots. Because of this, several <i>Pseudomonas</i> species have been proposed as natural plant growth promoters due to their capacity to produce siderophores which are able to liberate iron [13] and phosphorus [14]. The genus has also been implicated with the production of anti-fungal chemicals [15] and nematode repellents [16]. </font></p>
  
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                    <p><font size="3">As a result, there is a growing trend within urban environments to develop local and regional food systems, otherwise known as: urban farms. Urban farming can involve growing in contained environments such as greenhouses - already a well-established practice. </font></p>
+
<p><font size="3"><p><font size="3">Considering these benefits, Alternative Roots investigated whether it would be possible to develop <i>Pseudomonas</i> sp. as the first synthetic biology ready endophytic bacterium.</font></p>
  
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          <p><font size="3">There are many benefits of growing within contained environments in urban spaces, these include;</font></p>
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                    <p><font size="3">In addition to examining the synthetic biology of this proposal we have also examined potential deployment options. Examination of urban agricultural production led us to concepts such as urban farming and contained agriculture. These offer benefits to this proposal as they offer a route to containing any GMOs, as well as many other advantages: </font></p>
  
 +
<p><font size="3">
 
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<li><font size="3">Providing Newcastle with fresh produce all year round.</font></li>
+
<li><font size="3">Producing locally-grown, fresh produce all year round.</font></li>
 
<li><font size="3">Reducing the carbon footprint of crop production due to reduced food millage.</font></li>
 
<li><font size="3">Reducing the carbon footprint of crop production due to reduced food millage.</font></li>
 
<li><font size="3">No agricultural run-off.</font></li>
 
<li><font size="3">No agricultural run-off.</font></li>
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<li><font size="3">Safer crops as there is less risk of contamination.</font></li>
 
<li><font size="3">Safer crops as there is less risk of contamination.</font></li>
 
<li><font size="3">Reduced spoilage because of shorter transportation times and reduced handling.</font></li>
 
<li><font size="3">Reduced spoilage because of shorter transportation times and reduced handling.</font></li>
−
</ul>
+
</ul></font></p>
  
 
<br>
 
<br>
 +
<p><font size="3">With developing technologies in the field of sustainable energy, it could one day be possible to engineer contained growth systems that are self-sustaining regarding its energy usage. By carefully controlling the parameters within these environments, we can emulate perfect surroundings that allow the crops to grow to their full potential, maximising yield.</font></p>
  
−
                     <p><font size="3">With developing technologies in the field of sustainable energy, it could one day be possible to engineer contained growth systems that are self-sustaining regarding its energy usage. By carefully controlling the parameters within these environments, we can emulate perfect surroundings that allow the crops to grow to their full potential, maximising yield. </font></p>
+
                     <p><font size="3">We are attempting to use a system like this in our project. Newcastle City council has recently declared their bold plans to convert Newcastle into a ‘Smart City.’ Looking into the proposed scenarios, we saw an opportunity to propose a ‘sustainable agriculture’ scenario for Newcastle, incorporating our hardware development. To do this we have put together a theoretical design project that outlines how we may implement this idea in Newcastle. </font></p>
  
−
                    <p><font size="3">This method of farming provides a benefit to our concept as it removes the need for release of GMOs. Therefore, it became the focus of our Human Practices.</font></p>
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                     <p><font size="3">We believe engineering endophytes is the new paradigm in plant productivity, as a result our goal was to characterise <i>Pseudomonas</i> sp. endophytic properties and optimise transformation protocols. <i>Pseudomonas</i> sp. Could subsequently be engineered to express genes of interest that could change the physiology of the plant. </font></p>
+
                     <p><font size="3">Our goal was to characterise the endophytic properties of <i>Pseudomonas</i> sp., our proposed endophytic chassis, and to establish transformation protocols. <i>Pseudomonas</i> sp. could subsequently be engineered to express genes of interest resulting in plant physiological changes when colonising plant roots.</font></p>
  
−
                     <p><font size="3">The goal of our Human Practices work was to generate a conversation locally about the use of Newcastle's Victoria Tunnel as an urban farm. In doing so, we wanted to raise larger questions surrounding the use of GM bacteria to increase plant productivity, as opposed to genetically modifying the plant itself - challenging consumer views on GMOs.</font></p>
+
                     <p><font size="3">The goal of our Human Practices work was to generate a conversation locally about the use of Newcastle's Victoria Tunnel as an urban farm. In doing so, we wanted to raise larger questions surrounding the use of GM bacteria to increase plant productivity, as opposed to genetically modifying the plant itself - challenging consumer views on GMOs.</font></p>
  
−
                     <p><font size="3">Alongside this, our goal was to build a hardware prototype for the Victoria Tunnel; and address the lack of suitable hardware that would allow us to grow large numbers of plant seedlings in a controlled environment for the purposes of our project. The hardware needed to be cheap, energy and cost efficient, and a standardised method for growing plants.</font></p>
+
                     <p><font size="3">Alongside this, our goal was to build a hardware prototype for the Victoria Tunnel; and address the lack of suitable hardware that would allow us to grow large numbers of plant seedlings in a controlled environment for the purposes of our project. The hardware needed to be cheap, programmable, energy and cost efficient, and a standardised method for growing plants.</font></p>
 
        
 
        
  
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<p class="about-para"><font size="2"><strong>Attributions: Connor Trotter, Will Tankard, Chris Carty, Frank Eardley, Heather Bottomley, Lewis Tomlinson, Luke Waller, Patrycja Ubysz, Sadiya Quazi, and Umar Farooq.</strong><font></p>
  
  
 +
<p class="about-para"><font size="2">1. United Nations, Department of Economic and Social Affairs., Population Division (2017). "World Population Prospects: The 2017 Revision, Key Findings and Advance Tables." <font></p>
  
  
 +
<p class="about-para"><font size="2">2. United Nations Food and Agriculture Organization (2017) World Fertilizer Trends and Outlook to 2020. <font></p>
  
 +
<p class="about-para"><font size="2">3. Usman MN, MG; Musa, I (2015) Effect of Three Levels of NPK Fertilizer on Growth Parameters and Yield of Maize-Soybean Intercrop. International Journal of Scientific and Research Publications 5(9). <font></p>
  
 +
<p class="about-para"><font size="2">4. Pfromm PH (2017) Towards sustainable agriculture: Fossil-free ammonia. Journal of Renewable and Sustainable Energy 9(3):034702. <font></p>
  
 +
<p class="about-para"><font size="2">5. Bitew YA, M (2017) Impact of Crop Production Inputs on Soil Health: A Review. Asian Journal of Plant Sciences 16(3):109-131. <font></p>
  
 +
<p class="about-para"><font size="2">6. Carmichael WW (2001) Health Effects of Toxin-Producing Cyanobacteria: “The CyanoHABs”. Human and Ecological Risk Assessment: An International Journal 7(5):1393-1407.<font></p>
  
 +
<p class="about-para"><font size="2">7. Yang X-e, Wu X, Hao H-l, & He Z-l (2008) Mechanisms and assessment of water eutrophication. Journal of Zhejiang University. Science. B 9(3):197-209<font></p>
  
 +
<p class="about-para"><font size="2">8. Zahran HH (1999) Rhizobium-Legume Symbiosis and Nitrogen Fixation under Severe Conditions and in an Arid Climate. Microbiology and Molecular Biology Reviews 63(4):968-989. <font></p>
  
 +
<p class="about-para"><font size="2">9. Birhane E, Kuyper TW, Sterck FJ, Gebrehiwot K, & Bongers F (2015) Arbuscular mycorrhiza and water and nutrient supply differently impact seedling performance of dry woodland species with different acquisition strategies. Plant Ecology & Diversity 8(3):387-399.<font></p>
  
−
<p class="about-para"><font size="2">1. Smith. B (2002). "Nitrogenase Reveals Its Inner Secrets" Science Journal 297: 5587<font></p>
+
<p class="about-para"><font size="2">10. Taylor TN, Remy W, Hass H, & Kerp H (1995) Fossil Arbuscular Mycorrhizae from the Early Devonian. Mycologia 87(4):560-573.<font></p>
  
−
<p class="about-para"><font size="2">2. Gómez-Lama Cabanás C, Schilirò E, Valverde-Corredor A, & Mercado-Blanco J (2014) The Biocontrol Endophytic Bacterium <i>Pseudomonas fluorescens</i> PICF7 Induces Systemic Defense Responses in Aerial Tissues Upon Colonization of Olive Roots. Frontiers in Microbiology 5:427.<font></p>
+
<p class="about-para"><font size="2">11. Buddrus-Schiemann K, Schmid M, Schreiner K, Welzl G, & Hartmann A (2010) Root Colonization by Pseudomonas sp. DSMZ 13134 and Impact on the Indigenous Rhizosphere Bacterial Community of Barley. Microbial Ecology 60(2):381-393.<font></p>
  
−
<p class="about-para"><font size="2">3. Gross, H. and J. Loper (2009). Genomics of Secondary Metabolite Production by <i>Pseudomonas</i> spp.<font></p>
+
<p class="about-para"><font size="2">12. Bergey DH, Krieg NR, & Holt JG (1984) Bergey's manual of systematic bacteriology (Williams & Wilkins, Baltimore, MD). <font></p>
  
−
<p class="about-para"><font size="2">4. Sharma SB, Sayyed RZ, Trivedi MH, & Gobi TA (2013) Phosphate Solubilizing Microbes: Sustainable Approach for Managing Phosphorus Deficiency in Agricultural Soils. SpringerPlus 2:587.<font></p>
+
<p class="about-para"><font size="2">13. Sah S, Singh N, & Singh R (2017) Iron acquisition in maize (Zea mays L.) using Pseudomonas siderophore. 3 Biotech 7(2):121. <font></p>
  
−
<p class="about-para"><font size="2">5. Ruffner, B., et al. (2013). "Oral Insecticidal Activity of Plant-Associated Pseudomonads." Environmental Microbiology 15(3): 751-763.<font></p>
+
<p class="about-para"><font size="2">14. Sharma SB, Sayyed RZ, Trivedi MH, & Gobi TA (2013) Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. SpringerPlus 2:587.<font></p>
  
−
<p class="about-para"><font size="2">6. Jousset, A., et al. (2009). "Predators Promote Defence of Rhizosphere Bacterial Populations by Selective Feeding on Non-Toxic Cheaters." The Isme Journal 3: 666<font></p>
+
<p class="about-para"><font size="2">15. Ruffner B, et al. (2013) Oral insecticidal activity of plant-associated pseudomonads. Environmental microbiology 15(3):751-763.<font></p>
  
−
<p class="about-para"><font size="2">7. Vanitha SC & Umesha S (2011) Pseudomonas fluorescens mediated systemic resistance in tomato is driven through an elevated synthesis of defense enzymes. Biologia Plantarum 55(2):317-322.<font></p>
+
<p class="about-para"><font size="2">16. Jousset A, et al. (2009) Predators promote defence of rhizosphere bacterial populations by selective feeding on non-toxic cheaters. The ISME journal 3(6):666-674. <font></p>
  
−
<p class="about-para"><font size="2">8. Despommier D (2011) The vertical farm: Controlled environment agriculture carried out in tall buildings would create greater food safety and security for large urban populations. J fur Verbraucherschutz und Leb 6(2):233–236.</p>
+
<p class="about-para"><font size="2">17. Despommier D (2011) The vertical farm: Controlled environment agriculture carried out in tall buildings would create greater food safety and security for large urban populations. J fur Verbraucherschutz und Leb 6(2):233–236.</p>
  
−
<p class="about-para"><font size="2">9. Despommier D (2011) The vertical farm: Controlled environment agriculture carried out in tall buildings would create greater food safety and security for large urban populations. J fur Verbraucherschutz und Leb 6(2):233–236.</p>
+
<p class="about-para"><font size="2">18. Despommier D (2011) The vertical farm: Controlled environment agriculture carried out in tall buildings would create greater food safety and security for large urban populations. J fur Verbraucherschutz und Leb 6(2):233–236.</p>
  
  

Latest revision as of 23:46, 17 October 2018

Alternative Roots

Alternative Roots

Project Description

Scroll Down



Environmental Imperative

The United Nations estimates global population has increased by over 1 billion since 2005 and will near 9.8 billion by 2050 [1]. The demand that we place on agricultural products rises in parallel. We rely on the agricultural sector to provide not only food, but also fuels, shelter and fabrics. In turn, the agricultural sector relies on the application of synthetic fertilisers to maintain crop productivity. Nitrogen, phosphate and potassium (NPK) based fertilisers provide crops with essential macronutrients required for growth. NPK consumption is predicted to increase to 201.7 million tonnes by the end of 2020 [2].

NPK fertilisers significantly increase the yield of crops such as maize, wheat and potatoes [3] but they also play a large role in climate change. Nitrogenous fertilisers are produced using the Haber-Bosch process. This process is energy intensive, requiring 600 kg of natural gas to produce 1000 kg of ammonium, and resulting in the release of 670 million tonnes of CO2 per annum [4].

Fertiliser application has also been shown to have a negative long-term impact on soil health. Synthetic fertilisers cause soil pH to decrease, degrading soil crumbs and resulting in compact soils with reduced water drainage and air circulation; both have negative impacts on plant-root health [5]. Meanwhile, the accumulation of fertiliser run-off leads to eutrophication in water courses. Eutrophication impacts water quality and allows algal blooms to form, affecting biodiversity through toxin production and promotion of a hypoxic environment [6,7]. This reduces the availability of clean drinking water with additional costs incurred to process water for drinking.



Symbiosis

A plant’s demand for resources long predates the era of fertilisers, this demand has led to co-evolution of symbiotic relationships between plants and microbes. The legume-rhizobia symbiosis is one of the most well-known of these interactions. These bacteria are able to colonise the roots of plants such as peas where they fix atmospheric nitrogen. This nitrogen is then readily available for the plant to access [8].

Figure 1. Rhizobia spp. colonising the root of broad bean plant in Northumberland, UK. Photo credit: Dr Thomas Howard

However, it is not just bacteria that plants have evolved these beneficial relationships with. Mycorrhizal fungi  are capable of producing  intricate hyphal networks throughout the root system that enhance the plant’s ability to access nutrients and water [9].

Figure 2. Glomites rhyniensis hyphae growing through the root cortex of Aglophyton major [10]

Plant interactions with soil micro-organisms are nature’s wide-ranging alternative to chemical fertilisers. These natural symbioses date back over 400 million years to the Devonian era, where fossil records show evidence that even the earliest land plants had relationships with fungal endophytes [10]. 

Engineering of these symbioses, to open access to crop plants, is a promising solution to aid in mitigating NPK fertiliser dependence. While there have been many attempts to engineer nitrogen fixation into the crop itself, the concept of engineering symbioses themselves is a relatively untouched area. Here we propose an alternative route to reach this goal. Rather than engineering the plant or nitrogen-fixing symbiosis directly, we instead put forward the idea to develop a novel endophytic bacterial chassis to act as a mediator between these beneficial bacteria and the plant roots.




A New Chassis

This project investigated Pseudomonas sp. (CT 364) due to evidence that members of this genus are capable of colonising plant roots [11]. Pseudomonas are Gram-negative bacteria with a diverse metabolism [12] that enables the reported colonisation of a broad range of plant roots. Because of this, several Pseudomonas species have been proposed as natural plant growth promoters due to their capacity to produce siderophores which are able to liberate iron [13] and phosphorus [14]. The genus has also been implicated with the production of anti-fungal chemicals [15] and nematode repellents [16].

Considering these benefits, Alternative Roots investigated whether it would be possible to develop Pseudomonas sp. as the first synthetic biology ready endophytic bacterium.






Urban Farming

In addition to examining the synthetic biology of this proposal we have also examined potential deployment options. Examination of urban agricultural production led us to concepts such as urban farming and contained agriculture. These offer benefits to this proposal as they offer a route to containing any GMOs, as well as many other advantages:

  • Producing locally-grown, fresh produce all year round.
  • Reducing the carbon footprint of crop production due to reduced food millage.
  • No agricultural run-off.
  • Limited need for pesticides and fertilisers.
  • Safer crops as there is less risk of contamination.
  • Reduced spoilage because of shorter transportation times and reduced handling.


With developing technologies in the field of sustainable energy, it could one day be possible to engineer contained growth systems that are self-sustaining regarding its energy usage. By carefully controlling the parameters within these environments, we can emulate perfect surroundings that allow the crops to grow to their full potential, maximising yield.

We are attempting to use a system like this in our project. Newcastle City council has recently declared their bold plans to convert Newcastle into a ‘Smart City.’ Looking into the proposed scenarios, we saw an opportunity to propose a ‘sustainable agriculture’ scenario for Newcastle, incorporating our hardware development. To do this we have put together a theoretical design project that outlines how we may implement this idea in Newcastle.




Alternative Roots

Our goal was to characterise the endophytic properties of Pseudomonas sp., our proposed endophytic chassis, and to establish transformation protocols. Pseudomonas sp. could subsequently be engineered to express genes of interest resulting in plant physiological changes when colonising plant roots.

The goal of our Human Practices work was to generate a conversation locally about the use of Newcastle's Victoria Tunnel as an urban farm. In doing so, we wanted to raise larger questions surrounding the use of GM bacteria to increase plant productivity, as opposed to genetically modifying the plant itself - challenging consumer views on GMOs.

Alongside this, our goal was to build a hardware prototype for the Victoria Tunnel; and address the lack of suitable hardware that would allow us to grow large numbers of plant seedlings in a controlled environment for the purposes of our project. The hardware needed to be cheap, programmable, energy and cost efficient, and a standardised method for growing plants.





Description

References & Attributions

Attributions: Connor Trotter, Will Tankard, Chris Carty, Frank Eardley, Heather Bottomley, Lewis Tomlinson, Luke Waller, Patrycja Ubysz, Sadiya Quazi, and Umar Farooq.

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