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Teaching Resources

Microbial Gifts

Farmers grow food by cultivating plants and animals, with plants using sunlight for energy and water from the soil. Both plants and animals need nitrogen for protein production and phosphorus for genetic material and cell membranes. Since soil has little nitrogen or phosphorus in usable forms, farmers add fertilizers to boost crop yields. 

When we eat, our gut microbes also feed on these nutrients. The unused nutrients, along with microbes, are excreted in wastewater. Domestic wastewater contains organic matter, nitrogen, and phosphorus, which can be converted by microbes in anaerobic digesters into methane, a form of natural gas. Microbes also convert organic nitrogen into ammonium, which can be captured and reused as fertilizer. Phosphorus can also be recovered, and the water can be purified and reused after nutrient removal.

Recycling wastewater, recovering resources, and obtaining clean water contribute to sustainable development.

Recovery of Resources from Wastewater

Daddy: Our teacher told us this morning that we should not waste wastewater anymore but use our microbial friends to recover valuable resources

Image designed using resources from Freepik.com

Microorganisms, like humans, survive by using available substances as food, converting them into cell materials for growth and reproduction. Through trial and error, combined with natural selection, they adapt and specialize in specific tasks over time. 

In our industrial society, waste and byproducts require safe treatment. By studying natural processes, we can harness and enrich microorganisms to degrade waste or even recover raw materials from production. However, microorganisms act purely for their survival, not to benefit us. Bioengineers play a key role in creating systems where both humans and microorganisms benefit from waste processing and resource recovery.

While other frameworks discuss microorganisms in water treatment and biogas production, this one focuses on their role in promoting planetary sustainability through bioengineering.

Recycling and Biorecovery of Waste Materials

Dad: I want to become a bio-engineer and contribute to the survival of the planet. Where do I start?

Environmental pollution is a global issue caused by harmful substances from human activities. Everyday consumption and waste disposal, along with industrial operations such as mining, energy production, farming, manufacturing, and healthcare, contribute to pollution. The nuclear industry adds radioactive waste from energy, medicine, and weapons production. 

Cleaning up pollution is vital to protect human health, wildlife, and the environment. This framework explores how biology can remediate metal and radioactive pollution in soil and water (bioremediation), supporting Sustainable Development Goals for healthy environments and pollution elimination.

Metals and Radioactive Substance Bioremediation

Mummy, how can we clean up the horrible mess where the old factory was?

Modern life relies heavily on energy from fossil fuels like coal, natural gas, and crude oil—a mix of liquid petroleum hydrocarbons (LPHs). These organic molecules, made of carbon and hydrogen, are toxic, mutagenic, and carcinogenic. Formed 50–350 million years ago, crude oil is found deep underground and must be extracted and transported. Accidents during these processes can cause severe environmental contamination. 

Oil spills, the accidental release of LPHs into oceans from ships, refineries, or oil rigs, are among the most devastating marine disasters. They kill fish, marine mammals, and birds, and when oil reaches shores, it damages habitats, beaches, and human settlements. Notable spills, like the Amoco Cadiz, MT Haven, and BP/Deepwater Horizon disasters, have caused long-lasting environmental and economic damage, often requiring months or years of cleanup. 

To address these challenges, significant efforts focus on advanced technologies, especially biotechnology, to mitigate oil spills and support Sustainable Development Goals (SDGs).

Oil spills

Mum: Grandma and I watched TV today and heard that a ship accident at sea caused an “oil spill” that seriously damaged the environment. What does it mean, an “oil spill”?

Biogas is a mixture of methane and carbon dioxide produced by microorganisms during the decomposition of organic waste, such as sewage sludge, industrial wastewater, food scraps, and animal manure. It can replace fossil fuels for electricity, heating, cooking, and even vehicle fuel, as methane is the main component of natural gas. 

Producing biogas reduces waste and greenhouse gas emissions but requires strict control since it occurs in oxygen-free environments. The microorganisms involved need specific physical and chemical conditions to grow, making the process complex. Additionally, removing carbon dioxide from biogas improves efficiency but demands careful operation, and transporting biogas, like fossil fuels, adds to its carbon footprint. Despite these challenges, biogas offers significant benefits, contributing to various Sustainable Development Goals (SDGs).

Biogas

Mum: Today, granny and I took a bright green bus around the city. It said “biogas bus” on it. What does it mean?

Much of the energy powering our lives comes from non-renewable fossil fuels like coal, natural gas, and petroleum. These sources are depleting and pollute air, water, and soil, while their extraction and use contribute significantly to global warming. Transitioning to clean, renewable energy is essential for a sustainable future.

Microbes can produce biofuels from plant materials, offering renewable alternatives to fossil fuels. Expanding the biofuel industry can reduce carbon footprints and create quality rural jobs. While bioethanol and biodiesel are already available, advancements are paving the way for more sophisticated fuels.

Using Microbes to make Biofuels

Grandad: When we visited our relatives during the spring vacation, I saw a sticker on the airplane that said ‘sustainable biofuel’. What is biofuel and is it good for the environment?

Microbial polymers and bio-based plastics

Dad, why do you now wrap my sandwiches with paper? You were always using plastic

Concrete is crucial for modern construction, forming the foundation of buildings for healthcare, industry, education, and transport. However, its production has a significant environmental impact, contributing 4–8% of global CO2 emissions and driving climate change. 

Combining architecture with microbiology offers sustainable solutions. For instance, bacteria can be used to create "self-healing" materials, enhancing durability and reducing environmental costs. Innovations like biofilm communities and stone microbiomes could pave the way for eco-friendly buildings with self-repairing capabilities, transforming traditional construction methods.

Living Concrete

Mummy: how can concrete be alive?

Mushrooms are often linked to disease, decay, and death, as reflected in names like death trumpet, witch boletus, and devil's egg. While some fungi do harm trees—such as a honey mushroom in Oregon that killed many trees and is the largest organism on Earth—mushrooms are only the reproductive structures of fungi. Most of a fungus grows unseen as a network of thread-like hyphae called mycelium, which colonizes soil, wood, or living organisms and produces mushrooms to release spores when conditions are right. The Oregon honey mushroom’s mycelium spans 10 km² and has grown over thousands of years.

Mushrooms can also harm humans; about 1–2% are poisonous. For example, Roman Emperor Claudius was allegedly poisoned in AD 54 with a deadly mushroom, the sticky turnip amanita, hidden in a dish of Caesar’s mushroom. Yet mushrooms are not just harmful—they’re highly beneficial. They provide food, support health, and offer sustainable alternatives to materials like plastics, making them vital to achieving Sustainable Development Goals.

Uses of Fungi: Our world is molding!

Miss: I love mushrooms in food (especially in pasta), but I just heard of dresses made of mushrooms: can that be possible?

Image courtesy of Hanneke Wetzer

"Oil and water don’t mix!" While true, we often need to make them mix—like when washing dishes with detergent, which contains surfactants to remove oily residue. Similarly, microbes produce biosurfactants and bioemulsifiers to break oil into tiny droplets, increasing its surface area and "bioavailability" for degradation, such as during oil spill cleanup. 

These substances are crucial for microbial biology and ecology but also have broad applications for humans. They are used in food production, beverages, medicine, personal care products, textiles, construction, and many other industries.

Microbial biopolymers and surfactants

Dad: we learned at school that microbes can be used to clean up fatty wastes. When we wash up, we use detergents to remove fats from the dishes. Do microbes also use detergents?

Plastic, a group of synthetic materials made from organic polymers, is widespread in nature and poses risks to wildlife and humans. While natural polymers like cellulose and chitin can be broken down by microorganisms using specialized enzymes, plastic remains largely resistant. Some microbes have evolved to degrade plastic, offering hope for solutions to plastic pollution. However, their enzymes are not yet efficient enough to tackle the large-scale plastic waste problem. While microbial enzymes hold potential for biotechnological solutions, careful evaluation is needed to balance environmental benefits with our reliance on durable plastics.

Plastic-degrading microbes

Why is there so much plastic in nature, but dead trees and animals disappear?

In 1928, Alexander Fleming discovered a fungus that produced a chemical capable of killing bacteria, marking the start of antibiotics. Since then, antibiotics have been found in various microorganisms and plants, transforming infectious disease treatment. Microorganisms and plants also yield medicines for conditions like cancer. However, bacteria evolve resistance to antibiotics, posing a future challenge for treating infections and necessitating ongoing discovery of new antibiotics.

Historically, soil microorganisms like Streptomyces and fungi have been major sources of antibiotics, but repeated screening often rediscovers known compounds. Exploring non-soil microorganisms may uncover truly new antibiotics. Oceans cover 70% of the globe and 95% of the biosphere, hosting microorganisms adapted to salt, high pressure, and low nutrients. They also contain halogens like bromide and iodine, suggesting marine bacteria produce different chemicals from terrestrial ones. Therefore, exploring marine bacteria for novel antibiotics and drugs is a growing research and commercial area.

New Medicines from Microbes of the Oceans

The sea gives us fish for food and water for swimming; do we get other useful things from the ocean?

Cells are surrounded by a membrane made of lipids and proteins, which separates the cytoplasm from the environment. Some proteins naturally move to the membrane, decorating the cell's surface.

Microbial surface display involves fusing a chosen protein to these membrane proteins, so it extends into the environment. This technique is valuable in biotechnology for creating protein therapeutics, enhancing enzymes, and developing diagnostic tests.

Surface display is beneficial because it allows easier assessment of protein activity, speeding up the identification of the best variants. This accelerates biotechnology projects, contributing to health and environmental solutions, and supporting sustainable development goals.

Microbial Surface-Display

Mommy- are microbes smooth like a beach ball
or rough like a tennis ball?

Proteins play crucial roles in living organisms, yet their small size makes them challenging to study. Fortunately, some proteins exhibit fluorescence or produce colorful compounds, making them easily observable. These properties are naturally present in many organisms and have been instrumental in microbiology research for years. Reporter proteins, endowed with fluorescence or luminescence, can be fused with other proteins of interest. This fusion helps illuminate the intricacies of microorganisms and molecular biology, facilitating the development of biosensors for detecting pollutants or diagnosing diseases.

Study Tools: Glowing and colourful proteins

Granddad, is it true that scientists make bacteria glow by using spare parts from a jellyfish?

Our ability to respond to food, water contamination, and diseases relies on effective diagnostics. These tools detect specific molecules, nucleic acid sequences, proteins, and toxins in both environmental samples and within our bodies, providing vital hazard information. Diagnostics employ various microbiological methods to convert these analytes into easily interpretable outputs like color changes or digital readings.

Used correctly, diagnostics ensure safe food and water, aid in medical diagnosis and treatment, and help control infectious diseases such as COVID-19. As 'point-of-care' diagnostics become more common—tests conducted where the patient is located—it's important to manage their disposal responsibly to avoid environmental impacts. The use of diagnostics thus significantly influences Sustainable Development Goals.

Diagnostics

Miss: Why do they take my blood when I go to the doctor?

We often categorize microbes as "good" or "bad." Good microbes, or our microbiota, live on and in our bodies, aiding our immune system, nutrition, and protection against harmful pathogens. Most microbes we encounter are either beneficial or neutral, but pathogens can sometimes invade, evade the immune system, and produce harmful toxins. The line between good and bad microbes is blurred, as our microbiota can cause harm if the immune system is weakened, and some pathogens can reside unnoticed. The outcome depends on both the microbe and the host. Interestingly, some pathogen toxins can be turned to beneficial uses.

Applications of microbial toxins and virulence factors

Mummy, Aunt Sarah used to have those funny lines between her eyes and look grumpy, but now they are gone. What happened?

Microorganisms thrive in harsh environments like salt lakes by producing compatible solutes, which retain water and protect against stress. These solutes shield proteins, membranes, and cells from heat, dryness, freezing, thawing, and radiation. Ectoine, a key compatible solute, is used in sunscreens, cosmetics, and anti-inflammatory products due to its protective properties. It may also prevent amyloid protein misfolding linked to Alzheimer's and prion diseases and enhance vaccine stability for longer storage and transport without refrigeration.

Compatible Solutes: Our and Their Protectants

Mummy: why do you smear cream on your face every day?

Photo by Karolina Grabowska from Pexels Photo by Shiny Diamond from Pexels

A crucial part of forensic investigation is identifying evidence at a crime scene, including witnesses, fingerprints, DNA, and trace evidence. Trace evidence, like dirt from a suspect's shoe or fibers from their clothing, can link them to the crime scene.

Recently, investigators have explored using microbiomes for identification. Humans shed millions of unique microbial cells into their environment, making microbes a promising tool for tracking and profiling, similar to fingerprints and DNA. This could become a valuable resource in forensic science.

Microbial Forensics

My microbiome is unlike anyone else’s, and there is evidence to prove it.

Food protection is essential to keep our meals free from physical, chemical, or biological contaminants, which can enter the food supply unintentionally or through criminal adulteration, turning a "treat" into a "trick."

Food adulteration results in billions of dollars in losses and public health risks, often involving harmful ingredients added for profit or malicious purposes like bioterrorism.
Fortunately, many prevention strategies exist, such as analyzing food microbiomes to identify "microbial signatures" and ensure authenticity.
How do scientists verify if a food product is genuine? Is that expensive cheese with Designation of Origin authentic, or was it carelessly made elsewhere?

Food authentication by microbiome analysis

Mummy: how can daddy possibly like that smelly cheese?

Unknown author, Public domain, via Wikimedia Commons

Amino acids and vitamins are essential for life. Amino acids are the building blocks of proteins, crucial as enzymes or structural components in all cells. While vitamins are needed in small amounts, they play key roles in metabolic reactions. Humans and animals must obtain eight essential amino acids and most vitamins from their diet since they cannot produce them internally.

Shortages of these essential nutrients can occur, requiring supplementation. Industrial processes utilize microorganisms to produce nearly all amino acids and some vitamins. For example, the production of L-lysine, a feed additive, amounts to several million tons annually. Adding biotechnologically produced amino acids to vegetable feed not only enhances feed efficiency but also benefits the environment.

Food supplements: amino acids and vitamins

Mummy: we heard of a nasty disease of sailors in the olden days called scurvy: what is it?

Providing sustainably produced, healthy food for the growing global population is a challenge. Fish and shellfish are high-quality protein sources, but wild catches have stagnated since the late 1980s. Fortunately, aquaculture, which now supplies half of our fish, can meet this demand with lower greenhouse gas emissions compared to livestock farming.

However, infectious diseases, mostly bacterial, significantly impact aquaculture. Antibiotics, commonly used to control these diseases, lead to antibiotic resistance, posing a threat to both fish and human health. The WHO has identified antibiotic resistance as a major global issue.

Vaccination has successfully reduced antibiotic use in some fish species, but it is ineffective for fish larvae and shellfish, which lack developed immune systems. Probiotics, beneficial microorganisms that improve health by providing nutrients, boosting immunity, or inhibiting pathogens, offer a promising alternative for disease control in aquaculture.

Aquaculture: Disease Control in Fish Farming based on Probiotics

Mommy: do fish get sick like us? And how do we cure them?

In a world in which the gut microbiome and its relationship with human health is a hot topic, fermented foods are becoming increasingly popular, with consumption increasing 149% in 2018 according to FORBES. But fermented foods are not just associated with a healthier gut: fermentation can also create flavors that cannot be accomplished any other way. According to the Rockefeller University, “fermentation is a culinary exploitation of a microbial system”. Even more, fermented foods are rich in nutrients, have a longer shelf-life, and display unique textures and organoleptic properties. Nevertheless, fermented foods must be manufactured and stored in a controlled environment to ensure safety, quality and constant organoleptic properties in the final product. Fermented foods are associated with multiple sustainable development goals.

Fermented foods

How can bacteria turn something liquid, like milk, into something solid, like yogurt?

Photo by Gustavo Fring (Pexels)

Chemicals are essential in modern society, used widely in food, medicine, fabrics, plastics, fuels, and various industrial products. Many of these products originate from the petrochemical industry, which relies on fossil resources like natural gas and crude oil. However, this reliance has led to significant contributions to climate change and environmental pollution. Typical chemical production processes often involve environmentally harmful conditions and energy-intensive methods with metal catalysts.

Introduced in the 1990s, green chemistry addresses these issues by promoting sustainable practices in the chemical industry based on 12 principles. Microorganisms, with their diverse metabolisms developed over evolutionary history in various habitats, play a pivotal role. Through metabolic engineering, researchers utilize microorganisms to produce a wide range of compounds from renewable resources.

Looking forward, biorefineries are poised to replace traditional petroleum refineries, adhering closely to the principles of green chemistry. Biorefineries not only aim to reduce environmental impact but also contribute to achieving Sustainable Development Goals.

Green Chemistry

Mom, can green chemicals be produced by chemistry?

Indigo has been one of humankind’s favourite dyes since prehistoric times, and remains today one of the most important textile dyes, largely due to the enduring popularity of denim jeans. Indigo is insoluble in water, and to be used as a dye it has to be chemically reduced to a soluble, colourless chemical form, which is called indigo white. For the past hundred years the dyeing industry has relied on the reducing power of alkaline sodium dithionite, (also known as sodium hydrosulphite) but this results in large quantities of sulphur waste to be disposed of. Before the introduction of chemical methods, indigo was dissolved in a fermentation vat, where anaerobic bacteria reduced the indigo. This method is still used on a small scale commercially in India. Harnessing the power of bacteria to dissolve indigo industry-wide would help lessen the environmental impact of producing blue jeans.

Using bacteria to dissolve indigo for dyeing

Sir: I’ve heard that dyeing blue jeans causes a lot of chemical pollution. How could this be lowered?

Image: by Louise Cornelissen, via Pexels.com

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