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Biodiversity: Microbes, Earth's Ecosystem and Microbiome

A research by Laura Ann Bocon

Master of Gastronomy at University of Gastronomic Sciences of Pollenzo
Intern at Civran Azienda Agricola

(please note, this is a work in progress)

A “Gastronome Research” on biodiversity applied to Civran Azienda Agricola, that can be analyzed on different angles:

  • in the field (plants variety, micro-organisms variety on the soil, use of self-produced micro-organism as a field nourishment);
  • in the laboratory, so in the products (ingredients variety and “almost unpredictable” flavors variety occurred by spontaneous fermentation);
  • in the guts (micro-organisms variety supplied by the spontaneous fermentation process).

The aim of the research is to create useful content and cultural dissemination to farm’s audience.

Chapter 1.1: Microbes

Chapter's transcript below.

What do plants and animals, even the soil or a jar of fermented sauerkraut have in common? It’s life.
Life, often unseen to the naked eye, is teeming all around us in the form of microbes, or microscopic organisms. When important topics like biodiversity, sustainability and nutrition are discussed, microbes play a very important role in helping us achieve a sustainable and healthy lifestyle. Life on earth is very old. Microbial life, particularly bacteria, are the oldest life forms on earth dating back 3.5 to even 4 billion years ago. Microbes are everywhere, inhabiting some of the most uninhabitable places on earth. There are more microbes on earth than stars in the universe.

When scientists were first attempting to categorize life on earth, the plant and animal kingdoms reigned supreme. As technology improved and new scientific discoveries emerged, scientists continually rethought their categorization. Today, the tree of life is categorized into three main domains: Bacteria and Archaea—both of which fall under the category of prokaryotae—and eukaryota—which includes a widely diverse range of life from plants and animals to protists and fungi. Two of the domains of life are occupied solely by two types of Prokaryotes. This illustrates just how extensive and important microorganisms are to our planet. There are three main categories of microorganisms: those are prokaryotes, eukaryotes and viruses.


Prokaryotes were the first signs of life to emerge on the earth almost 4 billion years ago. Prokaryotes can be found in just about every habitat on earth. They generally have a simpler cellular structure than that of eukaryotes. Most are single celled organisms that don’t contain a nucleus. Prokaryotes can be further classified into bacteria and archaea—both of which are very diverse groups of organisms.


Bacteria can be found in soil, in bodies of water—such as oceans—and in, on or around plants, animals, humans and other organisms. Bacteria play many crucial roles for both the environment and for humans. While not all bacteria are beneficial for the earth and humans, it would be a mistake to disregard them.

One of the oldest organisms in earth’s recorded history is cyanobacteria, also known as blue-green algae. Like other bacteria, they are single celled organisms but will often exist in colonies that are large enough to see with the naked eye. Cyanobacteria often cooperate as if they were a multicellular organism, working together to photosynthesize sunlight and carbon dioxide into energy and oxygen. Because of their size, records of their existence have been discovered in the form of fossils. These date back almost 3.5 billion years. Cyanobacteria are very important to earth’s history. Cyanobacteria contributed to the oxygen atmosphere that we depend on to today because of their ability to produce oxygen through photosynthesis. They are also the precursors to plants. Cyanobacteria perform important functions for soil and plant health, including nitrogen fixation. We wouldn’t be where we are today without the contributions of cyanobacteria to the ecological functions of our planet.


Archaea were only just classified as such in the late 1970s. Prior to that, they were thought of to be another type of bacteria. While archaea initially appear to be similar to bacteria, as they are also single celled organisms that contain no nucleus and can be found in similar environments, they are also evolutionarily very different. They can survive in much more extreme environments compared to bacteria in such places as the freezing waters of the Arctic ocean or in steaming hot springs. These particular species of archaea are known as extremophiles. Archaea are also found on our skin and within our gut. Another remarkable thing about archaea is that they are not known to cause any diseases in humans.


Eukaryotes make up the third (and largest) domain of life and include eukaryotic organisms like algae, fungi and protists.


Protists consist of everything else that cannot be easily classified. Some protists include Protozoa, amoebas, and algae.


Many algae come in a wide range of shapes and sizes; some can be single celled and microscopic while others may be multicellular and macroscopic. Algae can exist alone or may form chains in colonies that may be seen seen with the naked eye, such as an algae bloom. Algae live in both fresh and saltwater environments. While most algae are eukaryotic organisms, there is one type of algae which is actually a prokaryotic organism. It is known as blue-green algae, or cyanobacteria. All other types of algae, including green algae, are a type of eukaryotic organism. Green algae is primarily an aquatic organism which includes the many species of seaweed. However, despite the different types of algae, all contain chlorophyll and thus can create their own food through photosynthesis.


Unlike plants which make their own food through photosynthesis and carbon dioxide, fungi cannot make their own food. Instead they may get their nutrients through one of three ways. Fungi may absorb nutrients from decaying plant or animal matter. Other fungi will feed on living organisms rather than dead and decaying hosts, these fungi are considered parasitic. Lastly, some fungi live with other organisms in a mutually beneficial relationship. This is called a mutualistic relationship in which two species live harmoniously and benefit from one another. Since fungi cannot move to obtain their food, they instead grow in order to cover more surface area to increase their access to potential food sources. Fungi can be single celled or multicellular and contain a nucleus. Types of fungi include yeasts, molds and mushrooms. 

Molds secret digestive enzymes that break down organic matter. This fungi grows on surfaces such as mildew or mold. Having mildew grow on damp surfaces in our homes can be unappealing and damaging to our health. However, there are some favorable molds such as those that contribute to the delicious pungency of blue cheeses. Other types of fungi form large fruiting bodies known as mushrooms. 

Mushrooms come in all shapes and sizes and can be very delicious or very deadly to humans.

Yeast are single celled microscopic organisms about the same size as a red blood cell. They reproduce when daughter cells “bud” or break off of the parent cell. Yeasts play a very important role in the fermentation process of certain foods including beer, wine and bread. One of the more commonly recognized yeast strains is Saccharomyces cerevisiae.

Fungi live mostly on land, in soil or on dead plant matter. Fungi play indispensable roles in breaking down  plant matter which is important to carbon cycling. As the carbon contained in the cell walls of plants is likewise broken down, this vital nutrient is made more readily available to be taken up by plants, thus returning an important nutrient back into the surrounding environment. Some fungi however cause fungal infections such as athlete’s foot, yeast infections or cause diseases on plants.


Lastly, there are viruses. Viruses are the smallest of all microbes and are made up of nucleic acids, proteins and lipids. They only exist to reproduce. What is interesting about viruses is that they are only alive when they are infecting and reproducing through a host. Viruses can only reproduce by infecting prokaryote or eukaryote cells. They burrow inside of their host cell and use the cell’s genetic code to complete the act of replicating for them. As we all know too well with the coronavirus pandemic plaguing the world today, viruses can be truly dangerous and deadly to mankind. 

Why do microbes matter?

Still many more microbes exist and thousands more have yet to be discovered. What is undeniable is the power microbes have to affect the earth and all life within it. They are vitally crucial to the stability and productivity of environmental ecosystems as well as for the functioning of the human body and for sustaining our health. Microbes also perform important functions that transform the food we eat. Without microbes, we wouldn’t be able to enjoy a cup of tea, a slice of bread and a bowl of yogurt before we start our day.


Shige Abe. “The Three Domains of Life.” Astrobiology at NASA, 2001.

Aparna Vidyasagar. “What Are Algae?” Live Science, June 4, 2016.

Shannon Brescher Shea. “Behind the Scenes: How Fungi Make Nutrients Available to the World.”, 2018.

CK-12: Biology Concepts. “8.10: How Fungi Eat.” Biology LibreTexts, September 29, 2016.

Rob Guralnick, Allen Collins, Ben Waggoner, and Brian Speer. “Life on Earth.”, 1994.

Microbiology Society. “What Is Microbiology?” , 2019.

Kenneth Todar. “Overview of Bacteriology.” Online Textbook of Bacteriology, 2012.

Chapter 1.2: Microbial Communities

Chapter's transcript below.

Microbial life is often examined by the ecosystems they inhabit. Like all life in nature, examining only one piece of the puzzle rather than how it fits into its surrounding environment will severely limit our understanding of the functions and significance microbes have on our environment and our health. Microbial communities are called microbiomes. Micro of course, refers to microorganisms, but what is a biome? 


As we discover the world of microorganisms and microbiomes, we must first look at biomes. Biomes are classified as communities characterized by the dominant vegetation and organisms that inhabit it. Biomes will also vary across climates and whether they are on land or underwater. There are six major types of biomes. Those are freshwater, marine, desert, forest, grassland and tundra. Few biomes across the globe have been spared from human influence. Humans have vastly impacted our natural landscape through agriculture by depleting resources and the natural biodiversity and have increased carbon emissions. Nurturing and supporting natural and diverse ecosystems, both large and small, is essential to sustaining life on this planet.


Microbiomes often refer to the worlds unseen by the naked eye. In a jar of sauerkraut, in the soil under our feet and even within our gut, microorganisms inhabit these areas in diverse and expansive microscopic ecosystems. As people are becoming increasingly aware of the roles microbes play in our environment and our bodies, further research and initiatives are being conducted to explore their full potential. One such example is the The Earth Microbiome Project, a collaborative initiative to collect and study data on microbes and their functions in different ecosystems. The Human Microbiome Project likewise is a collaborative initiative aimed at studying human microbiota and its impact and role in human health and disease.


Most microbial life resides in biofilms. That is, microbes like bacteria will often clump together and even cooperate as if they were a multicellular organism rather than a collection of many single celled organisms. Microbes in biofilms adhere to a surface. Biofilms exist within humans as well such as within our mouths and in our digestive tract. Biofilms have the potential to be both beneficial and harmful for the environment or our health. Dental plaque is an example of a biofilm that forms on the surface of teeth. Tooth decay and gum disease are a result of bacteria’s metabolism within the plaque biofilm. Within our digestive tract, biofilms help protect us from pathogenic invaders. Likewise, in our environment biofilms have the potential to help or harm.

Plants and Microorganisms

As I stated in chapter 1, microbes can be found inhabiting even the most uninhabitable regions of our earth. One location that microbes inhabit holds particular significance to agriculture, crop production and the nutrient value of the plants that we consume. Microbes live within the soil and in, on and around plants. The relationship between plants and microorganisms is intricate, codependent and essential to all plant life.

There are a few terms used to describe this relationship. Holobiont is a term which refers to the host and its endocelluar, or internal, microbiome and extracellular, or external, microbiome. Another term is plant microbiome—microbiome as we know is used to describe the community of microorganisms living in a defined habitat. Lastly is the phytobiome (which consists of the plant, or “phyto”, and it’s “biome” which consists of the environment and all organisms living in, on or around it. The plant’s microbiome may consist of several types of microbes including bacteria, archaea, fungi, viruses and protozoa.

Microbes perform important functions for its health and growth. Such functions include protection against harmful pathogens, nutrient acquisition, regulation of the immune system and stress tolerance. Plants may experience stress from both biotic and abiotic sources. Biotic stresses are those caused by living organisms. This can include other microorganisms such as bacteria, yeasts, viruses or fungi, insects, parasitic nematodes, invasive plants or weeds.

Abiotic stresses are caused by nonliving entities such as essential nutrient deficiencies, exposure to toxic substances or environmental stresses such as extreme weather conditions. In agriculture, these stresses can drastically harm a crop and even cause crop failure.

A plant’s ecosystem

There are different microbiomes surrounding a plant. There is the rhizosphere, which includes the soil around the roots of a plant. This is one of the most complex ecosystems on earth. The phyllosphere is the region above ground and on and around the stems and leaves of the plant. Certain fungi called mycorrhizal fungi shared a symbiotic relationship with plant roots known as a mycorrhiza. This relationship is also mutualistic as it benefits both the host and fungi. Fungi feed off the glucose produced by the plant through photosynthesis and the fungi improves the plant’s access to mineral nutrient and water absorption by increasing the surface area of the plant’s root system. The endosphere is within the plant tissue itself.

These three microbiomes, similar to the microbial ecosystems that thrive in humans, are associated with the health of the host organism itself. Essential roles of microbes in these ecosystems include protecting the host against pathogens and increasing nutrient uptake in the host. This relationship is a symbiotic, mutualistic one. For example, roots extract compounds into the soil that microbes may utilize. In turn, microbes in the rhizosphere may help make nutrients such as phosphorus and nitrogen accessible to the plant.

While certain microbes, including various species of bacteria may form harmonious and mutualistic relationships with their plant hosts, there are many that may cause harm. There are parasitic bacteria, also known as pathogens, that may feed off the host or in other ways damage or kill the host in the process.


“Abiotic Stress.” ScienceDirect. Accessed May 17, 2021.

Biomes Group, Biology 1B class, section 115. “The World’s Biomes.” UC Museum of Paleontology, 1996.

“Biotic Stress.” ScienceDirect, n.d.

CK-12: Biology Concepts. “8.10: How Fungi Eat.” Biology LibreTexts, September 29, 2016.

Marilyn Cummins. “What Is a Phytobiome?” Noble Research Institute, 2020.

Frances Gilman. “Beyond Food: Fermentation and Microbiology’s Role in Farming and Agriculture.” Perfumer & Flavorist, 2020.

“NIH Human Microbiome Project.” , 2021.

Joan B. Rose. “Biofilms: The Good and the Bad.” Water Quality and Health Council, December 2, 2011.

“The Earth Microbiome Project.” The Earth Microbiome Project, 2017.

Micaela Tosi, Eduardo Kovalski Mitter, Jonathan Gaiero and Kari Dunfield. “It Takes Three to Tango: The Importance of Microbes, Host Plant, and Soil Management to Elucidate Manipulation Strategies for the Plant Microbiome.” Canadian Journal of Microbiology 66, no. 7 (July 2020): 413–33.

Chapter 1.3: Microbes role in biogeochemical cycles

Subtitles in English and Italian available on Youtube video's settings
Chapter's transcript below.

Microbes play a vital role in biogeochemical cycles. These cycles involve the recycling of primary elements that are essential to all living systems. Examples of these include the carbon, oxygen and nitrogen cycles. A biogeochemical cycle is the pathway an element takes through the environment: passing through the earth’s biosphere (all living organisms), atmosphere (the body of gases that surround earth), hydrosphere (bodies of water on or near earth’s surface) and lithosphere (the earth’s mantle and crust, including all rocks on earth). Microbes’ involvement in these cycles is indispensable. These cycles are essential to the functioning of our planet and human’s impact on our planet is affecting these cycles. Today’s agricultural practices, for example, have been significantly impacting our environment. Nitrogen and phosphorus fertilizers flow in runoff into waterways, carbon is being released into the atmosphere due to carbon emissions particularly from agriculture and livestock farming, including emissions from transportation.


The carbon cycle

In the carbon cycle, microbes perform what is known as CO2 fixation. In carbon fixation, photosynthetic organisms take CO2 from the atmosphere and convert it to organic matter. Such organisms include cyanobacteria and planktonic algae which are responsible for almost half of the carbon fixation production. Likewise, organic matter may be broken down by microorganisms by way of the metabolic processes of fermentation and respiration. The organic matter is converted into CO2 which then returns to the atmosphere. Carbon is vital to the survival of most microbes which consume carbon contained in organic matter from plants or the waste products or bodies of other organisms. 

A study was conducted to discover if there was a way to improve carbon sequestration in order to improve agricultural sustainability by manipulating the soil through an application of various farming techniques and through the manipulation of the soil microbiome. Researchers are interested in finding ways in which microbes may be utilized to help soils regain lost carbon and to curtail carbon emissions which impact climate change. But more research and experimentation need to be done regarding this as this is important to the future of agriculture and the health of our planet.

Intensive agricultural practices degrade soil quality and often have a negative impact on our environment. When plants are harvested during agricultural production, organic matter and nutrients and even topsoil are lost which impacts the soil health. Two common agricultural practices: tillage and drainage, have led to increased aeration of the soil and increased exposure of normally protected organic matter. This in turn, leads to accelerated decomposition of organic matter, subsequently releasing carbon into the atmosphere at an accelerated rate. 

But what can we do to improve soil quality and increase carbon sequestration in the soil? There are various agricultural practices that can improve soil health and reduce the loss of topsoil and nutrients in the soil. These include cover-cropping and intercropping, composting, and to increase the production of plants that have extensive root systems that reach deep into the soil. Another method is with the application of biochar, a type of charcoal that helps in carbon sequestration.


Nitrogen cycle

There are multiple processes which occur in the nitrogen cycle as nitrogen transforms and travels through organic matter, into the soil and water and back into the air.microorganisms are essential to some of these processes. Nitrogen is essential to plant growth and therefore to humans. Despite this, overuse of nitrogen fertilizers can have serious implications for environmental health and sustainability. Nitrogen must be fixed to another compound in order to be accessible by plants and other organisms. Microbes play an essential role in the biological processes by which nitrogen (N2) is converted into various forms of nitrogen compounds such as ammonia, nitrites and nitrates.



Nitrogen fixation

In biological nitrogen fixation, which is the most common process of nitrogen fixation, certain bacteria convert atmospheric nitrogen into a fixed form of nitrogen (such as ammonia, nitrites and nitrates) which may be then taken up by organisms that require the substance. Only some bacteria have the ability, these bacteria may freely live in the soil or share a symbiotic relationship with plants or other organisms.


Microbes consume and decompose organic matter from crops and within the soil. The nitrogen within is converted into ammonium.


Microorganisms convert ammonium to nitrate to use as a source of energy. Nitrate is the most widely available form of nitrogen for plants but can be easily leached from the soil, especially after harvest. Nitrate will easily move from the soil in water, especially if soil drainage is high.


Denitrification is as it sounds, a reserve of nitrification and involves certain bacteria converting nitrate into gaseous forms of nitrogen which return back into the atmosphere.


Within the soil there is also competition for nitrogen. Both microbes and plants use nitrogen and ammonia for energy. Immobilization occurs when there is a high demand for nitrogen and is not readily available for plants. However, as microbes die, that nitrogen will be released back into the soil. 


Managing nitrogen levels

To minimize these nitrogen losses and manage the nitrogen in the soil, as in the case of nitrate leaching, farmers may apply nitrogen fertilizers. However, applying too much or too little during the growing season can have adverse effects and may cause chemical imbalances in the soil and increase greenhouse gas emissions. Other factors may impact crop intake of nitrogen including the temperature, moisture of the soil or whether the nitrogen was applied when the plants are taking it up. Timing is important. 

There are negatives to the use of nitrogen fertilizers however. Overuse is a risk, especially if it is leached from the soil and enters waterways. When bodies of water, both freshwater and saltwater, are over saturated with nutrients like nitrogen, algae blooms can occur. Although algae blooms occur naturally, when formed by nutrient pollution, they can impact the natural ecosystem and produce toxins. Changes in nutrient supply in the water and soil such as this can impact the local plant and animal populations as well as the microbial populations.

Improving and maintaining soil health is vital to sustaining the world’s food supply while supporting sustainable agricultural practices. The use of nitrogen fixing cover crops are also great methods for improving soil health, preventing runoff and topsoil loss and for fixing nitrogen into the soil. Such crops include legumes like clover or certain cereal crops such as winter rye.


Oxygen cycle

Microorganisms also play an essential role in the oxygen cycle. We can thank photosynthetic microorganisms, that is microorganisms that produce their own energy through photosynthesis, for a significant proportion of the world’s oxygen. Photosynthetic microorganisms like algae and cyanobacteria (also known as blue green algae) produce 50% of the oxygen in our atmosphere. Cyanobacteria similarly play a crucial role in the nitrogen cycle.


“Biogeochemical Cycles.” UCAR Center for Science Education, 2011.

Cary Institute of Ecosystem Studies. “Biogeochemistry at Core of Global Environmental Solutions: Coupled-Cycles Framework Key to Balancing Human Needs with Earth’s Health.” ScienceDaily, 2011.

Gougoulias, Christos, Joanna M Clark, and Liz J Shaw. “The Role of Soil Microbes in the Global Carbon Cycle: Tracking the Below-Ground Microbial Processing of Plant-Derived Carbon for Manipulating Carbon Dynamics in Agricultural Systems.” Journal of the Science of Food and Agriculture 94, no. 12 (March 6, 2014): 2362–71.

Huang, L., C.W. Riggins, S. Rodríguez-Zas, M.C. Zabaloy, and M.B. Villamil. “Long-Term N Fertilization Imbalances Potential N Acquisition and Transformations by Soil Microbes.” Science of the Total Environment 691 (November 15, 2019): 562–71.

Johnson, Courtney, Greg Albrecht, Quirine Ketterings, Jen Beckman, and Kristen Stockin. “Nitrogen Basics – the Nitrogen Cycle Agronomy Fact Sheet Series.” Cornell University, 2005.

Lowenfels, Jeff, and Wayne Lewis. Teaming with Microbes : The Organic Gardener’s Guide to the Soil Food Web. Portland, Oregon: Timber Press, 2016.

Miyamoto, Chie, Quirine Ketterings, Jerry Cherney, and Tom Kilcer. “Nitrogen Fixation Agronomy Fact Sheet Series.” Cornell University, 2008.

Todar, Kenneth. “Impact of Microbes on the Environment.” Textbook of Bacteriology, 2012.

Vidyasagar, Aparna. “What Are Algae?” Live Science. Live Science, June 4, 2016.

Chapter 1.4: Biodiversity

Chapter's transcript below.

Industrialization, technological innovations and the streamlining of food production and agriculture have significantly impacted our environment. 

Overexploitation from hunting or fishing has led to deforestation and to habitat loss for many species of flora and fauna and in worse cases, has led to outright extinction of many plant and animal species. This has also been exacerbated by rapid expansion of agricultural farmland. The introduction of non-native species of flora or fauna have similarly negatively impacted and disrupted natural ecosystems. Increased agricultural production and modern farming methods have led to the loss of topsoil and soil contamination, increased greenhouse gas emissions and the resulting global warming. These are all threats we face today regarding the health of our planet and of ourselves.

Biodiversity is important for many reasons. A wide variety of plants or crops in a given region or agricultural plot increase the species, genes and potential biological functions of the area. The diversity of components may improve the biological stability and productivity, especially in regards to the performing of vital ecosystem functions.

Ecosystem functions

Ecosystem functions are defined as processes performed by plants, animals and microorganisms and how they impact their surrounding physical and chemical environment. Essential ecosystem functions include resource capturing, biomass production, decomposition and nutrient cycling. 

Loss of biodiversity, particularly across trophic levels, that is across species along the food chain, will also impact ecosystem functions. A diverse habitat of organisms like plants, animals, insects and microorganisms with a diverse range of traits and functions will increase the productivity of the area especially in regards to particular ecosystem services. For example, the variety of plant litter and other biological waste may improve decomposition and recycling.  These services provide humans with essential resources. 

Ecosystem services

These are the benefits that our ecosystem provides to humanity. There are four which include provisioning, regulating, supporting and cultural services.

Provisioning involves the production of renewable resources such as food, wood, medicines and freshwater. Increasing the biodiversity across species in a given area increases productivity, like in the case of commercial crop yield. Greater biodiversity will increase the products obtained through provisioning services.

Supporting services are those which support other ecosystem services. These include pollination, nutrient cycling and species adaptability to changing climates—such as tolerance to frost or high temperatures, drought or heavy rains. How well these services perform may improve productivity. If insects pollinate farmland that is rich in diverse plant life, crop yield will also increase. Pollination also improves climate conditions by aiding in carbon sequestration. Pollinators help both crops and wild and native plant life reproduce.

Regulating services help regulate environmental change. These include air and water purification, the detoxification of soils and erosion prevention and mitigating the negative impacts of climate change. Increasing biodiversity in a region, will lessen the risk of the spread of invasive plant species and the spread of plant pathogens such as viral and fungal infections. Carbon sequestration is increased as a result of a rich biomass production. Biomass is the debris originating from plants, animals and agricultural production.

Humans hugely impact the biodiversity of regions and it is imperative that we take care in restoring the natural ecosystems or agroecosystems and their biodiversity to improve the ecosystem services since human life depends on it.

Monocropping vs biodiversity

Monocropping came about to simplify the production of certain high demand commodity crops such as corn, wheat, and soy in the production of food, biofuels, fibre and more. This allowed growers to specialize in the production of one crop and to increase the output. However, such tactics can lead to biodiversity loss. There is also a greater risk of continuation due to use of agrochemicals in industrial monocropping.

With monocropping comes a greater risk of losing crops to disease or blight. Higher biodiversity offers greater stability. Organically grown vegetables have been shown to have a higher biodiversity of microbial populations than conventionally grown. More than likely, greater diversity of crops will also diversify the microbes present in the soil. Similarly, a diverse range of native deep-rooted plants offer greater stability to the soil and a more diverse and rich microbial population. The results of which I will discuss in the next chapter.

Microbes aid in the productivity of these services as well. It is possible that no multicellular organisms function completely without the aid of or interaction with microorganisms.

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“Biomass – an Overview.” Science Direct, 2016.

Blum, Winfried E.H., Sophie Zechmeister-Boltenstern, and Katharina M. Keiblinger. “Does Soil Contribute to the Human Gut Microbiome?” Microorganisms 7, no. 9 (August 23, 2019): 287.

Cardinale, Bradley J., J. Emmett Duffy, Andrew Gonzalez, David U. Hooper, Charles Perrings, Patrick Venail, Anita Narwani, et al. “Biodiversity Loss and Its Impact on Humanity.” Nature 486, no. 7401 (June 2012): 59–67.

Cary Institute of Ecosystem Studies. “Biogeochemistry at Core of Global Environmental Solutions: Coupled-Cycles Framework Key to Balancing Human Needs with Earth’s Health.” ScienceDaily, 2011.

Chivian, Eric, and Aaron Bernstein. Sustaining Life : How Human Health Depends on Biodiversity. Oxford ; New York: Oxford University Press, 2008.

El Serafy, Ghada, and Pedro J. Leitão. “Ecosystem Function – GEO BON.” GEO BON: The Group on Earth Observations, n.d.

Helmenstine, Anne Marie, Ph. D. “What Is Fixed Nitrogen or Nitrogen Fixation?” ThoughtCo, 2018.

Orr, Matthew R., Kathryn M. Kocurek, and Deborah L. Young. “Gut Microbiota and Human Health: Insights from Ecological Restoration.” The Quarterly Review of Biology 93, no. 2 (June 2018): 73–90.

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Chapter 1.5: The Role of Microbes in Maintaining Soil Health

Chapter's transcript below.

Current issues

Improving and ensuring the health of our soil can increase the productivity and quality of our agricultural output. Modern agricultural practices and human intervention have impacted the health of our soils. Such issues include loss of topsoil, exposure to contaminants and pollutants, nutrient loss and desertification, or the transformation of healthy soil into sandy soil. Sandy soils contain less micro and macro nutrients and have low fertility and low water retention. These qualities make for poor growing conditions in plant cultivation. 

As forests are cut down to increase farmland, the risk of soil erosion also increases. This could mean a loss of nutrient rich and healthy topsoil. In some areas, soil is being lost at a much faster rate than it can be generated. Arable soil is a vital and often underappreciated resource.

Soil and Microbes

In modern day crop cultivation, widely diverse native crops have been replaced by fewer higher yield shallow-rooted staple crops. As I stated in the previous chapter, monocropping and other modern day agricultural practices have resulted in decreased soil health, soil erosion, and decreased biodiversity, which not only impact flora and fauna populations but the microbial populations as well. 

Soils are home to a great many microorganisms, from protozoa, bacteria and archaea to fungi and algae. These microorganisms provide many essential functions that improve soil and plant health. They recycle dead plant and animal matter into nutrients and nullify pathogens. Microbes in the soil also have the ability to store gases such as CO2 that would otherwise contribute to greenhouse gas emissions. Soil microbes can store up to 1.8 times more carbon and 18 times more nitrogen than plants, making them vital elements to slowing down and even preventing greenhouse gas emissions.

Improving and maintaining soil and plant health is vital to sustaining the world’s food supply while supporting sustainable agricultural practices. There are various microbe-assisted methods currently being used or tested to improve soil health and quality.

Soil Management Methods


Phytoremediation is a method of removing contamination in soil and ground water using plants. Plants may be grown in areas that are contaminated and then harvested, aiding in the removal of pollutants. The plants act as filters or traps, breaking down, filtering or containing organic or metal contaminants. Phytoremediation via microbes is a new but underutilized technology.

AMF: Arbuscular Mycorrhizal Fungi

These particular fungi colonize plant roots to form a symbiotic relationship. These fungi help protect the plants against pathogens and certain stresses, promote growth and yield and help protect the health of the plant and ecosystem. Utilizing these fungi may be a sustainable and environmentally friendly method which may replace certain chemical fertilizers. Utilizing AMF to improve soil conditions is one such example of the potential microbe-assisted phytoremediation methods.

However, there are downsides to this method. AMF may compete for nutrients in the soil and could decrease the microbial richness and diversity in the soil. Combining AMF with organic fertilizers could potentially counteract this. Bacteria, such as nitrogen fixers, may also be inoculated into the soil. As I stated in chapter 1.3, nitrogen fixing bacteria convert nitrogen from the atmosphere into ammonia or other nitrogen compounds that plants may take up more readily. Nitrogen increases plant growth and yield.

Organic fertilizers

The use of organic fertilizers improve the quality and stability of soil and may aid in changing soil’s physicochemical properties, increase nutrient uptake by plants and reduce pests. 


Microbes can be utilized to increase crop yield and plants’ resistance to disease or may be able to prevent disease altogether. It is important to promote microbiome health to keep the soil and plant healthy and to increase the nutritional value of the plant. Microbial products may go by various names depending on their intended use. Such products include soil inoculants, like nitrogen fixing bacteria which are used to stimulate root or plant growth and may also be referred to as biostimulants. Others include biofertilizers, biopesticides or probiotics. These products may be added to the soil or seed. 

The need for substitutes for harsh chemical fertilizers and pesticides which have contributed to environmental contamination due to runoff are driving research into alternative solutions. Microbes are also used to detoxify or to clean industrial wastewater. Through a system called bioremediation, microorganisms are used to break down pollutants in the wastewater. Compared to conventional methods, this method is much more cost effective, environmentally sustainable, and creates no waste byproduct.

Microbial soil inoculants have the potential to be a sustainable and environmentally conscious alternative. That said, it is not without its faults or challenges.


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Huang, L., C.W. Riggins, S. Rodríguez-Zas, M.C. Zabaloy, and M.B. Villamil. “Long-Term N Fertilization Imbalances Potential N Acquisition and Transformations by Soil Microbes.” Science of the Total Environment 691 (November 15, 2019): 562–71.

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Tosi, Micaela, Eduardo Kovalski Mitter, Jonathan Gaiero, and Kari Dunfield. “It Takes Three to Tango: The Importance of Microbes, Host Plant, and Soil Management to Elucidate Manipulation Strategies for the Plant Microbiome.” Canadian Journal of Microbiology 66, no. 7 (July 2020): 413–33.

Zhang, Zhechao, Zhongqi Shi, Jiuyang Yang, Baihui Hao, Lijun Hao, Fengwei Diao, Lixin Wang, Zhihua Bao, and Wei Guo. “A New Strategy for Evaluating the Improvement Effectiveness of Degraded Soil Based on the Synergy and Diversity of Microbial Ecological Function.” Ecological Indicators 120, no. 106917 (January 2021): 106917.

Chapter 2.1: The Human Microbiome

Chapter's transcript below.

The Human Microbiome

Similar to the microbiomes and ecosystems that permeate the earth, microbes also inhabit a variety of diverse ecosystems within and on humans. The human microbiome is the counterpart to the human genome. Microbial genes outnumber the genes in our genome 100 to 1. These microbial communities are made up of bacteria, fungi, archaea, protists and viruses. In the GI tract (i.e. gastrointestinal tract) alone, there are up to 100 trillion microbes. It has the highest known cell densities of any microbiome on earth.

Microbes can be found on and within the human body: in our mouths, intestines and even in women’s vaginal canals and on our skin and teeth. Microbes that live in our mouths attach themselves to our teeth through a sticky adhesive known as a biofilm. These microbes are adapted to the moist and warm environment of our mouths and survive off of food particles, oxygen, water and our saliva. Our skin accommodates a wide variety of microbes that exist in various climates. The surface of our skin may be oily, dry, moist or exposed to much or little sunlight. Microbes that exist in these various climates are adapted to survive these conditions. However, less microbes thrive in the oily parts of our skin since oil is often antimicrobial. 

There are many abiotic, or non-living factors, that influence and impact the microbes that make us their homes. Such factors include temperature, diet, pH, oxygen, water, nutrients and UV light. Microbes that thrive in the various ecosystems that exist within and on the human body must be adapted to such. Any changes our bodies experience can likewise impact the microbial communities that live there. 

Another factor that impacts our microbial residents is age. Babies who are born vaginally will be coated in a film of microorganisms from their mothers whereas babies who are born by cesarean section will be colonized by skin microbes. Where babies are born will also impact by which microbes they are colonized. Babies who breastfeed will take in oligosaccharides present in breast milk. These sugars are actually beneficial to microbes rather than the babies directly. Microbes will consume these sugars and help build up babies’ immune systems. As we grow up, the variety and amount of microbes in and on our bodies changes. There are also significant stages in our lives and events that occur which will impact microbial populations. Such significant events include puberty, pregnancy and menopause. Sickness, antibiotic use, stress, injury, climate and significant changes in diet will also impact our microbiomes.  

We share different relationships with the microbes that reside within or on us. One such relationship is called commensalism. In this relationship, one organism, whether it is us or the microbes, will benefit from the other without causing it harm. Reversely, parasitism is a relationship in which one organism, considered a parasitic organism, benefits off the other, referred to as the host organism, causing it harm. Mutualism is a relationship in which both organisms benefit from each other.

Microbes and Health

Microbes play a variety of roles within our bodies. Some microbes make vitamins our bodies alone cannot. For example, in the large intestine, microbes produce B vitamins which are essential co-enzymes for DNA synthesis and repair. Vitamin B12, which can only be made within our bodies by bacteria and archaea, help build healthy blood and brain tissue. Diets deficient in vitamin B12 and folate, another B vitamin, are associated with depression.

Microbes protect us from infection by helping to decrease inflammation and train the immune system to fight off infections, attacking harmful invaders and sparing the good microbes. Microbial biofilms protect us from harmful invaders, both inside and out. Particularly within our intestines, how we eat will influence how healthy our biofilms are and how well they can protect us. They also influence the functions of our organs and often act as important signals during metabolic processes. However, as I stated in Section 1, not all biofilms are beneficial to humans with dental plaque being one such example. Of course, only a few of the hundreds of microbes that make up the biofilm that forms on our teeth actually cause cavities. Brushing cleans away the bad along with the good. Eating less sugar and processed foods can change the microbes that live in the plaque biofilm. 

Some microbes help us to digest our food. Up to 10% of the calories we absorb are made available by microbes. When trying to improve someone’s health and gut microbiota, it’s an easier solution to target someone’s diet since food has a large impact on one’s microbiota but changing it doesn’t require a huge and expensive medical intervention. A diet that is high in calories, carbohydrates and processed sugars and fats, is usually associated with less diversity of gut microbiota. Microbes help us to digest carbohydrates like sugars, starches and fiber and release nutrients that would otherwise pass through our digestive system. In turn, microbes also feast on the food we consume. Different diets support different microbial communities. A healthier diet means a healthier gut. 

Microbes within our gut may also influence our brains. Nervous tissue surrounds our gut. This collection of neurons is connected to the brain via the vagus nerve. Bacteria in our gut make molecules that transmit signals to the brain. Some microbe related intestinal issues are associated with the symptoms of certain mental disorders such as anxiety or depression. Certain diets, such as the mediterranean diet, which contains fermented foods, can keep our microbes happy and protect our physical and mental health.


Aslam, Hajara, Jessica Green, Felice N. Jacka, Fiona Collier, Michael Berk, Julie Pasco, and Samantha L. Dawson. “Fermented Foods, the Gut and Mental Health: A Mechanistic Overview with Implications for Depression and Anxiety.” Nutritional Neuroscience 23, no. 9 (November 11, 2018): 1–13.

Genetic Science Learning Center. “The Human Microbiome.” University of Utah: Learn Genetics, 2000.

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