MycoFlux - The Mycelium-Powered Bioremediation Unit

The central theme of our project is the recovery of Rare-Earth Elements (REEs) from a solution of electronic waste. We want to achieve this recovery by utilizing cell-surface display technology to express lanthanide binding peptides on filamentous fungi. These recombinant fungi can then be used as a cheap and sustainable biomaterial for a filter system to isolate REEs from the heterogenous solutions. To give this process a physical hull, we designed and constructed the MycoFlux apparatus in which the mycelium can be grown under controlled conditions (monitored by various sensors) and at the same time its capabilities as a biosorption system be applied and tested.


Fig 1. | The MycoFlux.

Inspired by solid-state fermentation and mycofiltration, the MycoFlux apparatus combines the cultivation of filamentous fungi and their deployment as a sustainable filter matrix. The fungi is grown on packages of solid substrate and - once a desired amount of biomaterial is achieved - an integrated liquid distribution system circulates a solution to be filtered.

In the case of Rare-Earth recovery, one would deploy our genetically engineered fungus that expresses metal-binding proteins on its surface. The recombinant fungus can be grown on the substrate within the apparatus and a bioleached solution of e-waste circulated until the Rare-Earth Elements are adsorbed onto the biomaterial. Then, a desorption agent could redissolve the ions into a concentrated solution.

Due to its design, the MycoFlux offers a high degree of modularity, which can be adapted to the specific conditions of a project, i.e., the used fungus, the desired filtrate and retentate. In addition, the handling of the apparatus is designed for convenience, which allows, for example, a quick and easy exchange of old substrate against new one.

A suite of sensors is integrated directly into the box, so it is possible to control the growth parameters of the fungi. Automated data processing and visualization enable the user to monitor the MycoFlux easily.

Democratizing Biotech

Driven by our Sustainable Development Goals, our mission is to provide sustainable synthetic biology to communities worldwide. We envision the MycoFlux in community biolabs and workshops everywhere on earth, where people can come together and deal with their own e-waste in an engaging, safe, and profitable manner. To this end, we oriented ourselves to the following guiding design principles: accessible material, simple building instructions, and comfortable handling.

But equally important, we want to bring the benefits of synthetic biology into the daily lives of people everywhere. We see a great need in the field of synthetic biology to demystify the technologies for the general public and enable hands-on experience. By enabling people to solve real-life problems themselves with the help of synthetic biology, we believe that we can foster more acceptance, innovation and community engagement. See how we connected with our stakeholders to address this need in the community of synthic biology!

The MycoFlux is a great opportunity for communities to gain experience with working with recombinant organisms in real life and its use in the RareCycle process lets them profit from their own e-waste. Moreover, it exemplifies the scale-up of our Rare-Earth recovery process beyond the lab. The MycoFlux is a stepping stone to making people more aware of the potentials of synthetic biology in their daily lives as well as in the industrial processes that ensure a sustainable future.

Access and download the tutorial to replicate this Hardware project here!


CAD Drawings:

Technology Influences

Our MycoFlux reactor and extraction system is rooted in two key technologies that we have adapted and combined to use in synthetic biology. The first technology is mycofiltration. In mycofiltration, the inherent capabilities of fungal mycelium to filter out and bind contaminations from fluids are utilized. Successful applications of mycofiltration include the removal of E. coli from water sources 1 and the conversion of air pollutants to lower-impact compounds like carbon dioxide and water 2, demonstrating the enormous potential of mycofiltration in the field of bioremediation. In mycofiltration, the fungal mycelium often sits in a packed bed of a natural or synthetic support matrix.

Because of our overarching goal of easy reproducibility everywhere in the world, we chose matrix candidates from a set of natural biomasses, e.g., straw or bird feed. To make our technology even more applicable, we decided to combine the growth of our fungal biofilter and the extraction process in one apparatus. However, technical trade-offs must be considered. For example, it is advantageous for mycofiltration applications to provide as much biomass as possible, while in the cultivation of fungi one must guarantee sufficient water, oxygen and substrate supply. Thus, the second technology comes into play: solid-state fermentation. As its name suggests, solid-state fermentation involves the cultivation of biological organisms on solid materials with low moisture content. This technology is applied in soy sauce production (the koji step) and for cellulase production. 3,4 In this field, extensive research has been conducted to optimize the growth of fungi on solid substrates.

One particularly interesting aspect is the use of separate trays for the cultivation of fungi to achieve an optimized heat and mass distribution, which is not guaranteed in a solid block of a mycofilter. 5 It is also our goal to introduce technology that is modular and can be adapted for different purposes. In the context of Rare-Earth recycling this could mean the selective separation of different (groups of) Rare-Earth Elements.

By using trays, scale-up is also more straightforward and it could be possible to accommodate different trays over the height of the apparatus with fungus that exhibits selectivity for different Rare-Earth Elements, thereby realizing multiple separations in a single setup.

Therefore, we decided to incorporate all the above features in a tray-based solid-state bioreactor, which is an interesting approach for fungus cultivation as well as beneficial for the eventual extraction process of Rare-Earth Elements.

Fig 2. | Two trays in the MycoFlux.

Form and Functionality

The primary vision we want to achieve with our Hardware project is to show that our fungi-powered recycling technology can be brought into the daily lives of people everywhere on earth. Therefore, our four main criteria are:

1. Using cheap and easily accessible material with low requirements


Because of our overall vision, we restricted ourselves to recycled or easily accessible building materials. Our choice fell on wooden oriented strand boards (OSB) as this material is generally cheap, uses scrap wood in its production and can also be reused from or for other woodworking projects. Moreover, it enables us to go beyond lab-scale and build a device that could realistically be placed in a community workshop or community biolab.


For the liquid distribution system, we used a simple garden pump and garden hose. On the free end we installed a nozzle to effectively spray the whole area of the underlying filter with the filtered fluid.


We also installed multiple sensors to monitor the conditions inside our apparatus that are crucial to the survival and growth of the fungus, such as humidity, temperature and CO2 concentration.

TABLE 1   Cost Breakdown of Chassis
MaterialCost (€)Comment
Wood (OSB2, pre-cut)101.69price for all wood parts if bought new, we partly used recycled boards
Liquid system47.53pump, hose and nozzle
Accessories91.90rollers, paint, screws, handles etc.

2. Ensuring proper functionality for community workshops

The MycoFlux apparatus serves two purposes: it hosts growth medium to cultivate a filamentous fungus and directly uses the grown biomass as a biofilter medium to extract Rare-Earth ions from a liquid solution of e-waste. As described above, we were inspired by tray-based solid-state fermentation to distribute the solid growth medium on a set of equally spaced trays over the height of the apparatus. Through tests with a wild-type fungus and measurements, we confirmed that we can grow significant amounts of fungal biomass in our trays.

Fig 3-9. | A gallery of pictures of the MycoFlux.

The solution that we want to process in the MycoFlux is filled into a tub at the bottom of the apparatus. Through a pump and hose, it is transported to the top of the apparatus and distributed evenly over the filter medium through a nozzle.

Through the choice of the nozzle and the geometry of the apparatus, we ensured sufficient coverage of the filter with liquid medium while considering the ease of building and maintaining the apparatus. The nozzle used is a stainless-steel spiral nozzle with a spray pattern of multiple concentric cones and is especially well suited against blockage by solid residues in the liquid medium. As we cannot fully prevent the washing out of biomass or filter matrix, this was an important design choice to ensure long-term usage.

We also opted for a square layout of the device instead of a circular one, as this is easier to construct with the low-barrier materials we chose because of our overarching goals. The liquid passes through the filter medium and exits each filtering layer via a metallic mesh at the bottom of every tray. After the filter trays, it trickles into the tub again and can be continuously recirculated until a desired Rare-Earth recovery is achieved.

3. Incorporating user and expert feedback to optimize our designs

The target users of our MycoFlux system are communities everywhere on earth, ranging from neighborhood associations and already existing communal recycling workshops to municipal recycling facilities, or a combination of these. Thus, we want to make our hardware easily accessible, safe and handy to convince these communities to recycle and profit from their own e-waste. Through our Human Practices division, we conducted interviews with potential partners and users worldwide and presented to them our hardware solution to the growing e-waste problem. We also reached out to experts in the field of biosafety to obtain design suggestions that could make the cultivation and housing of genetically modified fungi in MycoFlux possible in the future.

Our key takeaways from the interviews are as follows:

The overall reception was very positive, and many potential partners worldwide are excited to utilize our hardware solution. We received user feedback regarding the handling of our apparatus: as we want to place our system in community workshops and community laboratories, it is important for our future users that the apparatus can be moved and have parts of it manipulated as needed in restricted spaces. To cater to that need, we installed transport rollers at the bottom of the apparatus so it can be moved more flexibly even in smaller areas. We also installed handles to the top lid and mounting for the hose as quality-of-use improvements. We realized that the deployment of our apparatus in community working spaces with genetically modified fungi inside is not in the scope of current legislation. Therefore, we consulted security experts on potential prospects in this field and how we can prepare our technology to be ready to go once the legislative framework is set. The main adjustment to our current build was adding polytetrafluoroethylene (PTFE) lining to each wood surface that touches the fungus to minimize the chance of the fungus growing through gaps in the wood. We also plan to add additional filters to the air and liquid outlets to prevent fungal spores from exiting the apparatus.

Fig 4. | Liquid outlet and transport rollers.

Fig 5. | You can find all our CAD drawings in the tutorial!

We gathered more user feedback by inviting interested students from our university to visit our hardware in person and experience working with it first-hand. From their feedback, we designed an improved bottom drain. In the future, we would also improve the handling of the trays by using a different material for the tray guideways.

Early on, we also consulted woodworking specialists from our university’s community workshop. They advised us to impregnate our wood against humidity and biocontamination by using wood glaze and putty. We are extremely satisfied with the results of these safeguards as our constructions have survived heavy exposure to the elements outside as well as the growing fungus inside.

Sensors and Control

Fig 6. | Sensor system with connected visualization program.

In order to be able to monitor the growth conditions of the mycelium and to maintain a permanently optimal environment, we decided to integrate sensor technology into the MycoFlux.

For our current field-test, we chose an array of sensors that measures temperature, air humidity and CO2 and O2 concentrations. We also created a custom-made sensor data visualization program with Python to get easy access to the generated data. These information sources enable the user to introduce control measures to ensure optimal fungal growth.

When selecting the sensors, there are some points you should consider. First, you must consider which parameters you want to measure at all. We chose temperature, humidity, O2 and CO2 sensors for this purpose because these parameters are important in general mushroom cultivation 6 and our mushroom has no other special requirements for mycelium formation. This can be adapted and extended as desired, depending on the mushroom. When buying, you should also make sure that the sensors have a tolerant working range in terms of temperature fluctuations and humidity so that they do not break. This information can be found in the data sheets of the sensors before purchasing.

Because of our focus on flexibility and customization we decided on the combination of an Arduino as a microcontroller and Python as the programming language for the visualization program. They provide a plethora of tutorials and resources and are very beginner-friendly, allowing the user to adapt the system according to their requirements. For the implementation, we decided on a modular system using plug-in boards, whereby no soldering is necessary in order to make subsequent changes quickly and to maintain the system easily.

Fig 7. | Cheap, water-proof sensor setup.

Fig 8. | Shielding the sensors inside from liquids.

The sensors are located inside the MycoFlux between the individual trays and are protected from direct contact with liquid by a small case made of acrylic glass. The rest of the hardware, such as the microcontroller and the display, is located on the opposite side outside the chassis in a waterproof plastic box. The design allows the user to gain access to the microcontroller quickly and easily, e.g., for testing, making changes to the hardware, changing the battery or reading out the data.

Due to our requirements regarding flexibility and expandability, we decided on the Arduino Mega 2560 as a microcontroller. Compared to the much more common Arduino Uno, this unit provides a larger memory and more I/O Pins, making it possible to easily adapt or extend the current configuration for a specific use case.

The Arduino reads the sensor data in a given frequency, displaying them on the connected display for easy access. Furthermore, it collects the data, internally storing it until being connected via USB to our custom-made data visualization program, through which the data is archived and subsequently deleted from the measurement unit to make room for more data. The visualization program also provides an interface to the unit, which can be expanded according to the user's needs. This includes setting a new time interval and registering a new Arduino unit. The tool also offers a visualization of the stored data, giving the user the ability to monitor and interpret the measurements, and an option to export and import data to enable access from multiple devices.

Fig 9. | A screenshot of the interactive visualization program.

A detailed step by step guide to connect the sensors can be found here! Download the code for the Arduino here and our sensor data visualization program here.

Cost Breakdown of the Sensor Array
TABLE 2   Cost Breakdown of the Sensor Array
MaterialExact NameCost (€)Comment
Arduino Mega 2560 Arduino Mega 2560 Rev 332.80
Temperature and humidity sensor DHT22 DEBO DHT 22 BRD (Joy-IT) 8.85
Infrared CO2 sensor CO2 MH-Z19C-PH 28.10
O2 Gas sensor GRV GAS SENS O2 (Grove, Seeed) 53.55
Display LED 1,8” DEBO TFT 1.8 (Joy-IT) 10.90
Transparent plastic Box 4.99we used a lunch box with rubber seal
Multiple Breadboard Jumper Wires 1 pin dual-male (M2M) and 1 pin female to male (F2M) ~4we bought a 5-litre bag of grown mycelium
Resistors 10K Ohm Resistor ~2buy a set with different resistors in case you need different resistance values
Capacitor220 uF Capacitor~1
2x Breadboard Arduino Breadboard ~4we used two small ones
Acrylic glass plates 2 x (10cm x 15cm x 2mm) 8.99 (prize for 10x)at 2mm thickness it can be easily cut at a table edge
Acrylic glass glue 3.45we bought a 5-litre bag of grown mycelium
Silicone ~7to seal off the internal casing
Screws and nails 4 small screws to fix the box to the wood chassis, possibly nails for sensors
Total ~167.59

Fungus and Field Tests

To test and improve the functionality of the MycoFlux, we performed field tests with a wild-type filamentous fungi analagous to how it would be eventually deployed with a recombinant fungus.

1. Choosing the right fungus for field tests

As we were all beginners in fungi cultivation, it was hard to find a starting point to assess the kind of fungus we wanted to cultivate. We first thought about cultivating fungi that are being used in industrial processes but decided that acquiring colonies of those organisms was way too expensive. We were warned by students outside of the team that working in a non-laboratory environment could easily lead to the loss of the entire colony due to contaminations. Since our fungus was only meant to serve as a testing organism for our Mycoflux-system, we therefore decided to choose our first fungus mainly on cultivation practicability. This meant that our fungus was going to be as cheap and as easy to cultivate as possible which automatically led us to focus on edible fungi, as they can be bought in a variety of forms from a great variety of suppliers.

Another argument for edible mushrooms was the high availability of information regarding the culture conditions and maintenance of those fungi. We recommend looking at the great variety of online forums on the cultivation conditions of fungi, as these can contain valuable practical insights on the cultivation of many different species.

Selection Criteria

1. Susceptibility to contaminations and abiotic
stress (light, O2 and CO2 dependency...)
2. Cost of the fungus
3. Fruiting conditions
4. Substrate (availability, costs...)
5. Mycelial growth time
6. Information availability

Besides the costs of ordering a culture, the composition of the growth medium was also very important for us. Because of the natural hydrophobicity of mycelia, we needed a substrate which would allow the cultivation of a low-density mycelial network. This was of utmost importance, since the mycelium needed to be water permeable to fit the role of a bio-filtration system. For this reason, we limited ourselves to fungi that can grow on straw and possibly softwood sawdust.

As our MycoFlux bioreactor is not sterile and was located outside, the fungus also had to be somewhat resilient to temperature fluctuations and be relatively resilient towards biological contaminants. Lighting, as well as oxygen and CO2 conditions were not as important, as these factors could have been easily adjusted by modifications on the MycoFlux reactor.

We finally decided on Cyclocybe cylindracea, as it does not only fit all previously mentioned criteria, but also has a distinct fruiting induction mechanism. As we were only interested in the mycelium and not the fruiting bodies, this meant that we could prolong the non-fruiting phase of the fungus for as long as we wanted.

Cost Breakdown of Mycelium Field Tests
TABLE 3  Cost Breakdown of Field Tests
MaterialCost (€)Comment
Jars0.00we reused old jars
Substrate5.28substrate costs can greatly differ accourding to the needs of different fungi
Filter0.00we used synthetic pillow filling
Main-Culture Container1.05 per Bagfungi cultivation bag
Duct Tape4.95only a few striped necessary
Injection Ports1.95 per Portonly if you work with liquid culture
Fungus30.96we bought a 5-litre bag of grown mycelium
Total44.19cost can be reduced by ordering smaller starting colony

2. Tests of cultivation conditions

Before choosing a substrate to use in our Mycoflux, we first had to assess what kind of substrate was best suited for our application. As has already been mentioned in our “cultivation criteria” description, we had to rely on substrate that allows the mycelium to form a relatively loose matrix in order to let liquid pass through it. By looking up possible substrates for our fungus, we decided to test Straw and softwood sawdust. We tested the substrates by creating three different pre-cultures, one with straw, one with a mixture of straw and sawdust (roughly 50/50) and one with only sawdust. We stored all three in the same environment (dark and around room temperature) and monitored their growth continuously for roughly 1.5 months. It was evident that the growth rate on straw was the fastest, while the pure sawdust culture barely grew at all. Interestingly, the mixture of both substrates grew only slightly slower than the pure straw. Since the sawdust was cheaper in relation to its provided mass, the mixture was deemed most favourable for the use in our bioreactor.


100% Straw

Straw and Sawdust

50% Straw - 50% Sawdust


100% Sawdust

Please click on the cards to reveal their information.

Secondly, we wanted to assess if our fungus would be able to grow under different conditions of sterility. We therefore used three different methods to treat our substrate and inoculate it. First, we used the earth autoclave at our university to sterilize two bags of mixed substrate. The sterilization was performed for 3 hours with a maximum temperature of 134°C, four times vacuum steaming and two minutes of vacuum drying.

Fig 10. | Mycelium growth in MycoFlux (left) and in autoclaving bag (right).

We used the substrate from one bag to mix it with the mycelium in the MycoFlux drawers, which provide a non-sterile environment and directly inoculated the other bag under sterile conditions. We simultaneously inoculated unsterilized straw in a plastic box.

While the mycelium in the Mycoflux drawers took around two weeks to overgrow the new substrate, the mycelium in the autoclaving bag took around five weeks. This difference in growth speed can likely be explained by the larger quantities of already-existing mycelium in the drawers compared to the relatively small quantities of mycelium used for the autoclaving bag.

In contrast, the mycelium in the unsterilized substrate did not show any signs of growth and died after around four weeks.

It has been concluded that the sterility of the substrate plays a major role in fungal proliferation. However, the environment in which the fungi are cultivated does not need to be completely sterile and can most likely be counteracted by larger amounts of inoculation mycelium.

Fig 11. | Mycelium growth in unsterilized substrate.

Future Improvements

With the introduction of MycoFlux, we have successfully combined the desirable features of a biofiltration system and solid-state fermentation in a tray-based bioreactor to realize both cultivation and REE separation in one apparatus. Using cheap and easily accessible building materials, our MycoFlux apparatus can be utilized by all communities across the globe, and we are one step closer to our vision to use it as a local solution to reduce e-waste. Our first prototypes have received positive feedback from the users and experts regarding practicability. With proper inoculation techniques and control of growth and fruiting parameters for the different stages of mycelial proliferation, MycoFlux has also been proven to be a great tool for the cultivation of our wild-type filamentous fungi - despite being unsterile.

Fig 12. | Made for communal places and application - the MycoFlux.

However, further modifications are necessary to safely grow and accommodate genetically modified fungi that are suitable for the actual extraction and recycling of the REEs. For one, the liquid distribution system could be further optimized by adding improved drainage from the bottom while ensuring that the pump is always below the liquid level.

In our current prototype, the guiding rails for the drawers are uniform so differently sized drawers from both sides can be inserted. While a nice idea in theory, this makes taking the drawers out relatively sluggish. In the future, we would recommend installing a drawer system like those found in cabinets and probably forgo the added modulary for easier handling. A specialized system that allows for both could be designed, however it would come with increased complexity.

There are a few things that could be improved in the future regarding the sensor system. First you could make the Arduino Internet-enabled by a WiFi module to read the data wirelessly and even store it directly on a server in the network. A second improvement would be to add a real time clock module (RTC) to the setup to improve the accuracy of the data points and make the Arduino independent of the visualization program in this regard. Additionally, we propose the following optional improvements to our sensor system: a bigger display, additional options in data processing and support for multiple Arduino setups connected to one data visualization program.

When developing MycoFlux, we came across more possible implementations of this technology in various fields beyond our original intent. As mycofiltration is already a well-researched concept for water treatment (e.g., rain water), integrating this approach in our course should not be far from reach.

We believe, the MycoFlux is an exciting opportunity for communities to unleash the bioremediation powers of fungi within their immediate surroundings, be it cleaning water or extracting valuable resources. Through our documentation and continued development, we want to bring synthetic biology into the daily lives of communities everywhere on earth!

Fig 13. | AI vision of neighbors coming together to deal with their e-waste.

Fig 14. | AI vision of communities reproducing and adapting our hardware systems.

Thinking outside the box, the potential of MycoFlux is not just limited in the field of bioremediation. With a bit of finetuning, MycoFlux could play a key role in developing novel mycelial-based applications. For instance, it could be used as a powerful tool in the optimization of fungal farming of medicinal and edible mushrooms, as the growth and fruiting phases can be optimized by changing the growth environment of the fungus.

By sharing our knowledge in building and adapting the functionalities of MycoFlux with the iGEM communities and interested parties, we look forward to expanding the possibilities of MycoFlux as a multipurpose tool not only for the recycling of REEs, but also for a variety of needs and applications. To achieve this, it is essential to establish a network of users who share their experiences or problems and work together towards solutions. Here, we can count on the network our Human Practices and Sustainable Development Impact have built!

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