I. Microbial wander at Biohack  Waag Academy 2024

with Maro Pebo 

1.The exploration of microbial posthumans interweaves the human microbiome with broader philosophical inquiries into human identity, positing an intrinsic connection between humans and microorganisms. This concept is vividly illustrated in the art and research of various thinkers and creators:

a.Travis Bedel (bedelgeuse) – His artwork merges botanical illustrations with human anatomical diagrams, highlighting the integral role of microbes in human biology.

More than half of your body is not human, say scientists. (click the link)

“Human cells make up only 43% of the body’s total cell count. The rest are microscopic colonists.”

The last universal common ancestor (LUCA) is the hypothesized common ancestral cell from which the three domains of life, the Bacteria, the Archaea, and the Eukarya originated

b. Ken Rinaldo – His installations focus on the symbiotic relationship between humans and microbes, 

He is internationally recognized for interactive art installations developing hybrid ecologies with animals, algorithms, plants, and bacterial cultures.

“Opera for Dying Insects by Ken Rinaldo 2020. Photo by Ken Rinaldo. Acquired Immunity at Ars Electronica exhibits The Opera for Dying Insects video work curated by Marta de Menezes.” (click the link)

2. Historical Insight – The invention of the microscope in the 17th century was a pivotal moment, shifting our understanding of microorganisms from invisible entities to crucial components of life.

Louis Pasteur – A pioneering microbiologist who advanced the germ theory of disease, illustrating how microorganisms can cause illness but also serve beneficial roles in processes like fermentation.

Louis Pasteur (1822-1895) was a French biologist who is often regarded as the father of modern microbiology because of his many contributions to science. He was the first to demonstrate that infectious diseases are caused by microbes, disproved the concept of spontaneous generation (the idea that microbes could appear out of nothing), developed the process of pasteurization (as well as being its namesake), and developed some of the world’s first vaccines.

3. Artistic Endeavors:

  a. Marta de Menez – Inspired by Piet Mondrian, she creates microbial art that uses microorganisms as living paint, forming geometric patterns that reflect Mondrian’s abstract style. (click the link)

 

b.   Joey Davis – His ‘Microvenus’ project embeds binary code representing the feminine and masculine within DNA sequences, demonstrating the intersection of art, biology, and digital culture.

4. Biotechnological Applications – Scientists utilize microorganisms as tools in various industries, producing everything from gold to perfume, and even storing genetic information.

5. Theoretical Perspectives:

   Rosi Braidotti – A philosopher who discusses posthuman versus transhuman concepts, advocating for a post-anthropocentric understanding that includes recognizing our microbial connections. (click the link)

Rosi Braidotti is a contemporary philosopher known for her work on posthumanism, a philosophical perspective that seeks to move beyond traditional humanistic notions of the human being. Her discussions often focus on the differences between posthumanism and transhumanism, two concepts that, although related, diverge in their philosophies and implications for the future of humanity.

Posthumanism

Braidotti’s posthumanism is grounded in a critical approach to the notion of human exceptionalism and the anthropocentrism embedded in Western humanism. It challenges the idea of an inherent hierarchy that places humans above other forms of life and emphasizes an ethical obligation towards non-human entities. Her version of posthumanism advocates for a new way of thinking about the self that is relational and interconnected with the environment, other animals, and technology. It promotes a vision where identities are fluid and multiple, encouraging a transformative approach to our understanding of life.

Transhumanism

In contrast, transhumanism is often associated with the enhancement of human capabilities through advanced technologies. It represents a techno-optimistic view that seeks to transcend human limitations through science and technology, such as genetic engineering, artificial intelligence, and cybernetics. Transhumanists generally focus on augmenting human intelligence, health, and lifespan.

Braidotti’s Critique

Braidotti is critical of transhumanism for several reasons. She views it as overly reliant on technology and as perpetuating a form of human exceptionalism—it’s still about making ‘humans’ better, rather than transforming what it means to be human in relational terms. Her critique extends to the neoliberal motivations behind some transhumanist visions, which she sees as exacerbating inequalities and promoting a market-driven approach to technological enhancement.

Contributions to Philosophy

Braidotti’s work encourages a profound reconsideration of how we understand subjectivity, ethics, and our relationships with the ‘other’—whether that be non-human animals, the environment, or artificial systems. She advocates for a politics and ethics that are not confined to humans but are inclusive of all forms of life, stressing the importance of developing sustainable ways of living on a damaged earth. Her perspective urges an embrace of a future where being is multiple, complex, and deeply interconnected.

Through her discussions on posthuman versus transhuman concepts, Braidotti not only critiques the present limitations of our human-centered thinking but also provides a vision for a more inclusive, resilient, and adaptable future.

   Tobias Rees– Explores how our understanding of the human microbiome reshapes our views on health, identity, and biology.

These individuals and concepts collectively foreground a future where the boundary between biological and non-biological, human and microbial, becomes increasingly blurred, enriching our understanding of life’s interconnectedness.

book recommended:

Simians, Cyborgs and Women by Donna J Haraway

The Posthuman by Rossi Braidotti

The Mushroom at the end of the world by Anna Lowenhaupt Tsing

Rendering Life Molecular by Natasha Myers

II. MICROBIAL DYES

with Maarten Smith

Microbial dyes are sustainable and eco-friendly pigments produced by microorganisms, offering an alternative to synthetic dyes by utilizing the natural color-producing capabilities of bacteria, fungi, and algae.

Textile dyeing with bacteria (click the link)

“River Blue” is a compelling environmental documentary that chronicles the devastating impact of the fashion industry on rivers worldwide. Through the eyes of conservationist Mark Angelo, the film explores how toxic chemicals used in clothing manufacturing are polluting waterways, destroying ecosystems, and affecting the health of communities. The documentary highlights the destructive practices of the textile industry and calls for significant environmental stewardship and sustainable practices to protect our global water resources. It serves as a wake-up call, urging consumers, manufacturers, and governments to take action towards more sustainable and ethical fashion.

The history of textile dyes dates back over 4,000 years, beginning with natural dyes derived from plants, animals, and minerals, and evolving into synthetic dyes with the discovery of mauveine in 1856, which revolutionized the industry and expanded the palette of colors available for fabric dyeing.

a. Berlin design studio Blond and Bieber’s project that uses algae to create colourful dyes for textile printing

b. Fabulous Fungi by Ilse Kremer

c. Living Colour by Laura Luchtman & Ilfa Siebenhaar

COLABORATION WITH MICROBIAL LIFE FORMS

Shibori is a Japanese manual resist dyeing technique, which produces patterns on fabric. (click the link)

Serratia (click the link)

Janthinobacterium (click the link)

III. Imagining the ecological microbiome

with Justin D. Stewart

…. involves using microscopic imaging and staining techniques to visually explore and understand the complex interactions within microbial communities. By employing microscopes, researchers can observe the morphology and arrangement of microorganisms, while gram staining—a method that differentiates bacteria into Gram-positive and Gram-negative based on their cell wall composition—helps in identifying and classifying microbial species. These imaging techniques provide crucial visual data that aid in the mapping of microbial diversity and dynamics, revealing how microorganisms influence their environment and interact with each other, thus offering insights into their ecological roles and potential applications in biotechnology and medicine.

a. GRAM STAINING

procedure for gram staining of a Gram-negative bacterium such as Janthinobacterium, and the use of equipment:

1. Sterilization: The inoculating loop should be sterilized using a Bunsen burner. Heat the loop until it is red hot to ensure that all microbial life on the loop is eliminated before obtaining a sample.
2. Staining Procedure:
   • Crystal Violet: Treat the smear with crystal violet stain for 1 minute to stain all cells.
   • Iodine: Apply iodine solution for 1 minute, which acts as a mordant and forms a complex with the crystal violet, fixing it to the bacterial cell wall.
   • Decolorization: Decolorize with alcohol or acetone for about 10. This step is crucial as it is the differential step that removes the crystal violet-iodine complex from the thinner cell walls of Gram-negative bacteria, while Gram-positive bacteria retain the stain.
   • Safranin: Counterstain with safranin for 1 minute. This stains the decolorized Gram-negative bacteria pink for contrast against the purple Gram-positive bacteria.
3. Observation under Microscope:
   • Place the slide under the microscope to observe the results. Ensure that the slide is properly mounted and the microscope is correctly set up for viewing at the appropriate magnifications.

This detailed, step-by-step gram staining guide ensures a clear distinction between Gram-positive and Gram-negative bacteria, crucial for accurate microbiological analysis.

IV. SYMBIOTIC ORGANISMS: Lichens

with Adriana Knouf (tranxxeno lab)

Lichens are fascinating symbiotic organisms composed of a fungus (usually an ascomycete) and one or more photosynthetic partners, typically algae and/or cyanobacteria. These organisms live in a mutually beneficial relationship: the fungus provides a protective environment and structure, while the algae or cyanobacteria contribute food through photosynthesis. This unique partnership enables lichens to thrive in harsh environments where few other organisms can survive, such as on rocky surfaces, tree bark, and even on bare soil or exposed rock surfaces.

Lichens are extraordinary organisms that consist of a mutualistic relationship between a fungus (mainly from the Ascomycota phylum) and one or more photosynthetic partners, which can be either green algae or cyanobacteria. This symbiosis allows them to live in a wide range of environments, from arctic tundras to deserts, thriving on surfaces as varied as tree bark, rocks, and decaying wood.

In lichens, spores typically originate from the fungal partner of the symbiotic relationship. Lichens consist of a fungus (usually an ascomycete) living in close association with algae or cyanobacteria. The fungal component is primarily responsible for reproduction through the production of spores.

The process generally occurs as follows:

1. Spore Formation: The fungal partner develops specialized structures known as fruiting bodies. These fruiting bodies can take various forms, such as apothecia (cup-shaped) or perithecia (flask-shaped), depending on the species of fungus.
2. Spore Release: Within these fruiting bodies, spores are produced through a sexual reproductive process. Once mature, the spores are released into the air.
3. Dispersal and Germination: The released spores disperse through the environment, typically via wind. When they land in suitable conditions where they can access light and nutrients, they germinate to form new fungal hyphae.
4. Re-establishment of Symbiosis: For a new lichen to form, the germinating fungal spores must encounter compatible photosynthetic partners (algae or cyanobacteria). Once they meet, they can establish a new symbiotic relationship, leading to the formation of a new lichen thallus.

This reproductive strategy emphasizes the role of the fungal partner in the dispersal and propagation of lichens, relying on the successful meeting of the spore with a suitable photosynthetic partner to form new lichen individuals.

Exposure to Environmental Factors: Lichens are particularly notable for their ability to endure extreme conditions by entering a dormant state when resources are scarce. Here are some key aspects of how lichens interact with their environment:

Sunlight: Lichens require sunlight for photosynthesis, which is performed by their algal or cyanobacterial partner. They are adapted to varying levels of light exposure, from direct sunlight on exposed rock faces to the dappled light of forest canopies.

Temperature: Lichens can survive in extreme temperatures ranging from the hot surfaces of deserts to the cold of arctic regions. They can withstand freeze-thaw cycles that would kill most other organisms.

Moisture: Lichens do not have roots and do not absorb water through the ground but can quickly absorb water from rain, fog, or ambient humidity directly through their surface. They can become desiccated during dry periods and rapidly reactivate when moisture becomes available.

Pollution: Lichens are known bioindicators of air quality. Their ability to absorb water and nutrients from the air makes them sensitive to airborne pollutants. A decline in lichen populations often signals increased levels of air pollution, particularly sulfur dioxide.

Nutrient Cycling: By breaking down rock substrates and accumulating atmospheric nutrients, lichens contribute to soil formation and nutrient cycling in ecosystems, facilitating colonization by other plants.

Radiation: Lichens can also endure high levels of solar radiation and even survive in outer space conditions, as demonstrated in experiments where lichens were exposed to open space and retained their viability.

Scientific and Practical Applications: Lichens are used in various applications, from traditional dyes and medicines to potential modern uses in pharmaceuticals and cosmetics. Their remarkable resilience makes them subjects of study in astrobiology, where scientists investigate the possibilities of life on other planets.

By studying lichens, scientists gain insights into adaptation, survival strategies in extreme conditions, and the potential for life beyond Earth, making them a crucial subject in both terrestrial and extraterrestrial biological research.

Eukaryotes and Prokaryotes

Eukaryotic Cells

A eukaryotic cell contains a nucleus.

• Plant and animal cells are eukaryotic. A eukaryotic cell tends to be fairly large and complex. Animal and plant cells are both eukaryotic cells.
• Plant and animal cells have common organelles:
  • Cell membranes
  • Cytoplasm
  • Nucleus

Prokaryotic Cells

A prokaryotic cell does not contain a nucleus.

• Bacterial cells are prokaryotic cells. Prokaryotes cells are smaller and more simplistic. One prokaryotic cell forms a unicellular prokaryotic organism.
• Bacterial cells have similarities to plant and animal cells.Animal, plant and bacterial cells all have a cytoplasm and a cell membrane.
• Bacterial cells have a cell wall. In addition to the cell membrane, bacterial cells have a cell wall which surrounds the cell membrane.
• Bacterial cells do not have a nucleus. Instead they have genetic material in a loop. They also have smaller rings of DNA called plasmids.

book recommended: LICHEN BIOLOGY

microscope

V. MYCELIUM (GROWING BIOMATERIALS)

with Anne Vlanderen

Creating a mycelium corset

involves cultivating mycelium, the root structure of fungi, to form a natural and sustainable material that can be used in innovative fashion design. Here’s how you can grow Ganoderma lucidum mycelium specifically for crafting a corset:

Step 1: Preparing the Substrate

1. Choose Substrate: For a mycelium-based textile, substrates such as agricultural waste (e.g., straw, hemp, or flax fibers) are ideal as they provide the necessary nutrients and structural support for mycelium growth.

2.Prepare and Sterilize Substrate: Shred the substrate into small pieces and sterilize it by autoclaving or steaming to kill any existing microorganisms. This ensures that the mycelium can colonize without competition.

Step 2: Inoculation

1. Cool the Substrate: Allow the sterilized substrate to cool to room temperature.
2. Inoculate with Mycelium: Introduce Ganoderma lucidum spawn into the prepared substrate. This can be done in a sterile environment to prevent contamination.

3. Mix Thoroughly: Ensure the spawn is evenly mixed with the substrate to promote uniform growth.

Step 3: Incubation

1. Enclose the Substrate: Place the inoculated substrate into a mold that is shaped like a corset. This could be a custom-made mold based on the desired size and shape of the final product.

2. Set Optimal Conditions: Keep the mold in a dark, humid environment with temperatures around 25°C (77°F) to encourage mycelium growth.

3. Monitor Growth: Allow the mycelium to colonize the substrate completely, which can take several weeks. The substrate will bind together as the mycelium grows through it.

Step 4: Harvesting

1. Check for Completion: Once the mycelium has fully colonized the substrate and the material feels cohesive and firm, it’s ready to be harvested.
2. Remove from Mold: Carefully remove the mycelium-based material from the mold. At this stage, the material will have the rough shape of a corset but will require further processing.

Step 5: Drying and Curing

1. Dry the Material: Allow the mycelium corset to dry in a well-ventilated area to remove moisture. This step is crucial to stop the growth process and harden the material.
2. Cure if Necessary: Depending on the desired texture and durability, you may need to cure the corset in an oven at a low temperature to further harden the material.

Step 6: Finishing Touches

1. Shape and Trim: Once dried, you can trim and shape the corset to ensure a perfect fit. Mycelium material can be sanded or cut as needed.
2. Add Fasteners: Attach zippers, laces, or other fastening systems to make the corset wearable.
3. Seal and Protect: Optionally, apply a natural sealant to protect the corset from moisture and wear.

Tips for Success

• Maintain Sterility: Throughout the process, maintain a sterile environment to prevent contamination.
• Monitor for Contaminants: Regularly check for any signs of mold or other contaminants during the growth process.
• Experiment: Mycelium behaves differently depending on the substrate and growth conditions, so it might take a few trials to perfect your technique.

Using Ganoderma lucidum mycelium to create a corset is an innovative approach that merges fashion with sustainability, yielding a product that is not only eco-friendly but also a unique piece of biofabricated art.

Recommended video: FANTASTIC FUNGI (click the link)

Recommended book: The Mycocultural Revolution: Transforming Our World with Mushrooms, Lichens, and Other Fungi

Fungi have specific environmental and nutritional needs that are crucial for their growth and reproduction. Understanding these needs is essential whether you’re cultivating fungi for culinary purposes, gardening, or scientific research. Here’s a detailed breakdown of the primary requirements for fungal growth:

1. Substrate and Nutrition

Fungi are heterotrophic organisms, meaning they obtain their nutrients by absorbing dissolved molecules. They require organic substrates from which they can extract these nutrients:

• Carbon Sources: Fungi need organic carbon for growth, which they typically get from decomposing material. This can include wood, leaves, other plant debris, or specialized fungal growth media.
• Nitrogen Sources: Essential for protein synthesis, nitrogen can be sourced from the environment, either from organic material in the substrate or inorganic fertilizers.
• Vitamins and Minerals: Certain fungi also require small amounts of vitamins and minerals to facilitate biochemical processes.

2. Moisture

• Water is crucial for fungal metabolism and spore dispersal. Fungi absorb water through their mycelium, the network of filaments that make up their body. The right level of moisture in the substrate is critical to prevent either desiccation or overly wet conditions that could lead to bacterial growth and rot.

3. Temperature

• Optimal temperature ranges vary widely among fungal species. Most fungi thrive in temperatures between 20°C to 30°C (68°F to 86°F). However, some species are adapted to extreme conditions, from freezing temperatures to very hot environments.

4. pH Levels

• Fungi can grow in a wide range of pH levels, but most prefer slightly acidic to neutral pH (around pH 5.0 to 7.0). The pH can affect enzyme activity and nutrient availability.

5. Oxygen and Carbon Dioxide Levels

• Aerobic fungi require oxygen for cellular respiration. They consume oxygen and release carbon dioxide as a waste product. Ensuring adequate ventilation or air exchange is important in fungal cultivation to maintain the oxygen supply and prevent the buildup of carbon dioxide.

6. Light

• Most fungi do not require light for growth and are not photosynthetic. However, light can influence fungal behavior such as spore germination and the direction of growth (phototropism). Some fungi require light to trigger fruiting body formation.

7. Space

• Fungi need space to grow. As the mycelium expands, it requires more area to continue its growth. In confined spaces, fungi can become stressed, which might hinder their development or lead to contamination issues.

Management in Cultivation

In controlled environments like laboratories or mushroom farms, these conditions need to be carefully managed to maximize growth and yield:

• Hygiene: To prevent contamination from bacteria or other fungal species, cleanliness is crucial.
• Monitoring and Control: Regular checks and adjustments to environmental conditions such as humidity, temperature, and substrate moisture are necessary.
• Rotation and Harvesting: Timely harvesting and substrate rotation can help maintain healthy fungal cultures and prevent depletion of nutrients

Contamination is a significant challenge in fungal cultivation, whether it’s in a laboratory setting, commercial mushroom farming, or even casual home cultivation. Contamination refers to the unwanted presence of other microorganisms such as bacteria, molds, or competing fungi, which can inhibit growth, reduce yields, and even ruin entire cultures. Here’s an overview of the types of contamination, its sources, and how to manage it:

Types of Contamination

1. Bacterial Contamination: Bacteria can outcompete fungi for nutrients and space. They often thrive in overly wet or improperly sterilized substrates.
2. Mold and Competing Fungi: Other fungal species, especially fast-growing molds like Trichoderma, can overtake the intended fungal cultures. These usually appear as different colored patches on the substrate or culture media.
3. Yeast: Yeasts can also contaminate fungal cultures, typically resulting from poor aseptic techniques. They can change the pH of the substrate, negatively impacting the growth of the target fungi.
4. Viruses and Pests: In outdoor settings or large-scale farms, insects and mites can introduce viruses and other pathogens to fungi, which can be particularly destructive.

Sources of Contamination

• Improper Sterilization: Using substrates or equipment that hasn’t been adequately sterilized can introduce contaminants.
• Airborne Spores: Molds and other fungi release spores that can be carried by air currents into cultivation areas.
• Human Handling: Improper handling techniques or unclean workspaces are common sources of contamination.
• Water and Environmental Conditions: Using non-sterile water or maintaining conditions that favor the growth of unwanted organisms can lead to contamination.

Management and Prevention Strategies

1. Sterilization: Properly sterilize all substrates, equipment, and cultivation areas before starting cultures. Pressure cooking, autoclaving, or chemical sterilants are commonly used methods.
2. Aseptic Technique: When handling fungi and substrates, use aseptic techniques to prevent introducing contaminants. This includes wearing gloves, using laminar flow hoods for lab work, and minimizing exposure to open air.
3. Environmental Control: Maintain optimal growth conditions for the specific fungi you are cultivating. This includes controlling humidity, temperature, and airflow to discourage the growth of unwanted organisms.
4. Regular Monitoring: Inspect cultures regularly for signs of contamination, such as unusual colors, textures, or smells. Early detection is crucial for managing potential outbreaks.
5. Isolation: Keep different cultures isolated from each other to prevent cross-contamination. Use separate rooms or containment systems if possible.
6. Use of Antifungals and Antibiotics: In some cases, especially in laboratory settings, it might be necessary to use antifungal agents or antibiotics to control bacterial and fungal contaminants. However, these should be used judiciously to avoid developing resistance.

Dealing with Contaminated Cultures

• Isolation: If contamination is detected, isolate the affected cultures immediately to prevent it from spreading.
• Disposal: Sometimes, the best action is to dispose of contaminated cultures safely to avoid further risks.
• Analysis and Adjustment: Analyze what caused the contamination and adjust practices accordingly to prevent future occurrences.

Managing contamination effectively is crucial for successful fungal cultivation and requires diligent practices and careful monitoring of environmental conditions and cultural practices.