Microbiology

Cyanobacteria began the process of oxygenating Earth’s atmosphere. Triggered by the increase in O2, multicellular eukaryotes evolved and continued to increase in complexity.

Domains of Life:

There are three recognized domains of life: the Archaea, the bacteria, and the eukarya.

In this course, we will study Bacterial and Eukaryotic (Fungal) Microorganisms.

The Impact of Microorganisms on Humans

Microorganisms as Agents of Disease

We all live from birth until death in a world filled with microbes and we all have a variety of microorganisms that live inside and on our bodies. These microorganisms make up our normal microbiome. Only a minority of microorganisms are pathogenic. Microorganisms that cause harm are called pathogens, and the ability of a pathogen to cause disease is called pathogenicity. An opportunistic pathogen causes disease only in the absence of normal host resistance.

At the beginning of the twentieth century, the major cause of human death were infectious diseases caused by microbial pathogens. Today, however infectious diseases are much less deadly. Control of infectious diseases has come from a combination of causes including: a) improved sanitary and health practices, b) vaccines, c) anti-microbial agents.

Although many infectious diseases are now controlled, many others can still be a threat particularly in immunocompromised people and in developing countries. Both Prokaryotic and Eukaryotic Organisms are opportunistic pathogens leading to serious pathologies in Immunocompromised people. Examples of opportunistic prokaryotic pathogen is Staphylococcus aureus a usual member of the microbiota of the body, frequently found in the upper respiratory tract and on the skin.

An estimated 20% to 30% of the human population are long-term carriers of S. aureus which can be found as part of the normal skin flora, in the nostrils, and as a normal inhabitant of the lower reproductive tract of women S. aureus can cause a range of illnesses, from minor skin infections to life-threatening diseases such as pneumonia, meningitis. It is still one of the five most common causes of hospital-acquired infections and is often the cause of wound infections following surgery. The emergence of antibiotic-resistant strains of S. aureus such as methicillin-resistant S. aureus (MRSA) is a worldwide problem in clinical medicine.

Examples of opportunistic eukaryotic pathogens are the fungal pathogens Candida albicans and Cryptococcus neorformans. Candida albicans lives as part of normal flora on mucous membranes and in the digestive tract of humans and animals. It causes the widest range of infections caused by yeasts. From superficial to systemic and disseminated infections involving any deep organ as liver, kidney, lung, etc., meningitis, endocarditis, pericarditis, peritonitis. It is the most common human fungal pathogen causing almost half million death every year.

In addition, humans worldwide are under threat from diseases that could quickly emerge, such as bird flu or Ebola fever; these are primarily animal diseases that under certain circumstances can be transmitted to humans and spread quickly through a population.

Microorganisms Agriculture and Human Nutrition

Microorganims can impact the agriculture in both positive and negatives ways.

Examples of Positive impact

•            Nitrogen fixation

Nitrogen is a critical limiting element for plant growth and production. It is a major component of chlorophyll, the most important pigment needed for photosynthesis, as well as amino acids, the key building blocks of proteins. It is also found in other important biomolecules, such as ATP and nucleic acids. Even though it is one of the most abundant elements (predominately in the form of nitrogen gas (N2) in the Earth’s atmosphere), plants can only utilize reduced forms of this element.

The Rhizobium or Bradyrhizobium bacteria colonize the host plant’s root system and cause the roots to form nodules to house the bacteria (Figure 4). In the nodule the bacteria convert atmospheric N2 into ammonia (NH3) that the plants use as a nitrogen source for growth. This process is called Nitrogen Fixation. To express genes for nitrogen fixation, rhizobia require a plant host: they cannot fix nitrogen independently.  Access to the fixed nitrogen allows the plant to produce leaves fortified with nitrogen that can be recycled throughout the plant. This allows the plant to increase photosynthetic capacity, which in turn yields nitrogen-rich seed. The consequences of legumes not being nodulated can be quite dramatic, especially when the plants are grown in nitrogen-poor soil. The resulting plants are typically chlorotic, low in nitrogen content, and yield very little seed

•            Microorganisms and ruminant animals

A diverse group of microbes live within the digestive systems of ruminants (such as cows, sheep and goats). In the rumen microorganisms digest and ferment the polysaccharide cellulose, the major component of plant cell walls. Without these symbiotic microorganisms, ruminants could not thrive on cellulose-rich food such as grass and hay. 

• Human microbiome

Trillions of microorganisms (also called microbiota or microbes) of thousands of different species live in our bodies. These include not only bacteria but fungi, parasites, and viruses. In a healthy person, these “bugs” coexist peacefully, with the largest numbers found in the small and large intestines but also throughout the body. The microbiome is even labeled a supporting organ because it plays so many key roles in promoting the smooth daily operations of the human body.

Each person has an entirely unique network of microbiota that is originally determined by one’s DNA. A person is first exposed to microorganisms as an infant, during delivery in the birth canal and through the mother’s breast milk.  Exactly which microorganisms the infant is exposed to depends solely on the species found in the mother. Later on, environmental exposures and diet can change one’s microbiome to be either beneficial to health or place one at greater risk for disease.

The microbiome consists of microbes that are both helpful and potentially harmful. Most are symbiotic (where both the human body and microbiota benefit) and some, in smaller numbers, are pathogenic (promoting disease). In a healthy body, pathogenic and symbiotic microbiota coexist without problems. 

Microbiota stimulate the immune system, break down potentially toxic food compounds, and synthesize certain vitamins and amino acids,  including the B vitamins and vitamin K. For example, the key enzymes needed to form vitamin B12 are only found in bacteria, not in plants and animals.

Sugars like table sugar and lactose (milk sugar) are quickly absorbed in the upper part of the small intestine, but more complex carbohydrates like starches and fibers are not as easily digested and may travel lower to the large intestine. There, the microbiota help to break down these compounds with their digestive enzymes. The fermentation of indigestible fibers causes the production of short chain fatty acids (SCFA) that can be used by the body as a nutrient source but also play an important role in muscle function and possibly the prevention of chronic diseases, including certain cancers and bowel disorders. Clinical studies have shown that SCFA may be useful in the treatment of ulcerative colitis, Crohn’s disease, and antibiotic-associated diarrhea. The microbiota of a healthy person will also provide protection from pathogenic organisms that enter the body such as through drinking or eating contaminated water or food.

Examples of Negative impact

Microbial diseases of plants and animals used for human food cause major economic losses every year.

Example Fusarium and Onion

Onion (Allium cepa) is an important horticultural crop which is cultivated by every agricultural nation in the world with an annual production of 78.5M tonnes and a value of £9,500M. It is the second most valuable vegetable crop in the world behind the tomato and in the UK, production is valued at approx. £110M per year. Fusarium basal rot (FBR) caused by Fusarium oxysporum fsp. cepae (FOC) and Allium white rot (AWR) caused by the fungus Sclerotium cepivorum and are two major soilborne diseases of onions and other Allium crops. Both diseases are very difficult to control as they form long-lived survival structures which remain in the soil for many years; chlamydospores for F. oxysporum and sclerotia for S. cepivorum. FOC infects roots directly through germination of spores in the soil and predominantly causes a bulb rot on onions later in the season or more often in store. However, the pathogen can also cause symptoms at any stage of plant development. It is an increasing problem for onion growers in the UK and globally it is predicted to worsen under current climate change models. S. cepivorum sclerotia germinate and infect roots through hyphae in response to specific chemical compounds released from onion roots. This results in wilting and subsequent plant death during the growing season with more sclerotia being produced and returned to the soil.

Microorganisms and Food, Energy and the Environments

Micro-organisms, in relation to food, can have one of these 3 roles:

Pathogenic micro-organisms can cause infections or intoxications

Saprophytic micro-organism play a role in biodegradation and cause food spoilage

Cultured micro-organisms like probiotic bacteria are used in food processing.