Microorganisms are defined as life forms too small to see with the naked eye. But while we don't typically see them, microbes are everywhere, doing good things like helping our digestion or making yogurts and wine, to not-so-good things like causing infection or disease.
Speaking of infections, back in 1928, Alexander Fleming returned to his laboratory from vacation, and noticed a strange fungus contamination on one of his bacterial culture plates. Interestingly, the bacterial colonies immediately around the contamination had been destroyed. This observation led to much further research, eventually culminating in the development of penicillin and other antibiotics that could treat bacterial infections. Yet, although they may live side-by-side in the microscopic world, we know from studying their forms and phylogenies that bacteria and fungi are vastly different and diverse organisms. Let's walk through some of the defining characteristics of these two major groups briefly.
Bacteria are unicellular prokaryotes, meaning that that they are single-celled organisms without a nucleus. All bacteria have a cell wall, but its composition and thickness vary. Gram positive bacteria have a cell wall with a thick peptidoglycan layer, which readily retains crystal violet molecules in gram staining. However, gram negative bacteria have a thin cell wall surrounded by an outer lipopolysaccharide membrane, and they only retain the counterstain, the red-colored safranin. Gram staining allows observation of bacterial shapes as well. Round bacteria are called cocci. Rod-shaped bacteria are called bacilli. And spiral-shaped bacteria are called spirilla. Furthermore, bacterial colonies can also be characterized with the naked eye, using traits such as color, shape and size of the colony.
Now, let's take a look at the fungi. Unlike the bacteria, fungi are eukaryotes, and thus their cells have membrane-bound organelles and a nucleus. They are commonly classified into groups based on their reproductive strategies. For instance, Ascomycota, or sac fungi, which includes morels, penicillium, and truffles, have fruiting bodies called ascocarps. Morels are filled with these structures. If we look at these more closely, they contain many smaller structures called asci, which in turn contain many ascospores formed during sexual reproduction. However, Ascomycota often reproduce asexually by budding. The second major fungal group we will examine is the Basidiomycota, or club fungi. Most edible and poisonous mushrooms in the forest are actually reproductive structures of the Basidiomycota. In this group, what we would refer to as the mushroom cap is technically known as the basidiocarp. In gilled fungi, gills under the basidiocarp are lined with tiny structures know as basidia, and these produce basidiospores, microscopic reproductive spores, during sexual reproduction. These spores are typically disbursed by wind, similar to many plant seeds. Here, we have examined several major bacteria and fungi groups, and the characteristics that define them in a very simplified fashion. However, due to the vast numbers of microbial species, upwards of one trillion by many estimates, scientists often identify and group them using additional methods, including examination of their DNA.
In this lab, you will identify different bacteria species using gram staining, and examine colony characteristics. You will also examine fungi species to identify their reproductive structures.
Bacteria and fungi are two highly diverse groups of organisms that can have significant beneficial or detrimental impacts on human health. For this reason, it is important to understand and distinguish between individual species of these groups. As you will recall, biological taxonomists group organisms based on their phylogenetic relatedness. The three domains of life, Bacteria, Archaea, and Eukaryota segregate life into three distinct groupings. While all bacteria fall within the domain Bacteria, fungi are found in the domain Eukaryota (Kingdom Fungi). In addition to Archaea, domain Bacteria exclusively includes single-celled prokaryotes, meaning their cells lack both a nuclear membrane and membrane-bound organelles. In contrast, fungi of domain Eukaryota have membrane-bound organelles and include both unicellular and multicellular organisms.
Bacteria are found nearly everywhere on Earth and are highly adapted to the environments in which they grow. As a result, this domain includes a staggering amount of diversity. The impact of these organisms on human health is equally diverse. For example, species like Streptococcus thermophilus can be used to produce fermented foods like yogurt, while spores of the bacteria Bacillus anthracis are responsible for the potentially deadly disease anthrax.
To aid in the identification of such organism, microbiologist have developed a myriad of tests to characterize both individual cells and entire colonies of bacteria1. One of the most common methods for identifying bacteria is by Gram staining. This test uses colored dyes to determine the composition of the bacteria’s cell wall. Gram-positive bacteria, which bear a thick cell wall made up of a protein called peptidoglycan, retain a dye called crystal violet and thus appear purple. In contrast, gram-negative bacteria have a thinner cell wall without peptidoglycan and do not retain the crystal violet. Instead, these cells appear pink due to a counter stain called safranin. The use of Gram staining often serves as a preliminary step in the identification of a bacterial species. Further classification requires the identification of additional characteristics. This can include the shape of individual bacteria, which may be either cocci (round), spirillum (spiral), or bacilli (rod-shaped). Additionally, the color, shape, sheen, texture, and even smell of bacterial colonies can be used to distinguish between species.
Fungi of domain Eukaryota are also highly ecologically diverse and can range in size from microscopic yeast to the largest organism on earth, the honey fungus (Armillaria ostoyae). All fungi are heterotrophic, meaning that they must acquire their food from the environment. These organisms also exhibit diversity in their specific activities, niches, and potential effects on human health. For example, some fungi are consumed or used to produce food by humans while others can cause severe or even deadly infections2.
Within kingdom Fungi, two distinct taxonomic divisions exist based on the reproductive strategy of the species. First, Ascomycota, known as the sac fungi, have a reproductive structure called an ascus. Together, many asci form the ascocarp, or “fruiting body” of the fungi. These fungi can reproduce sexually or asexually by budding. Ascomycota consist of some economically important species like the yeast used in brewing beer and baking bread, and some species popular in cuisine, such as morels and truffles. The second group, Basidiomycota, includes organisms commonly known as “club fungi” due to the presence of a large club-shaped reproductive structure called the basidium. In contrast to Ascomycota, most Basidomucota reproduce exclusively by sexual reproduction. This occurs when two haploid mycelia join to form a basidiocarp. On a button mushroom, this is the cap structure. On the underside of the basidiocarp, reproductive structures called gills lined with structures called basidia produce haploid nuclei that eventually form basidiospores. Basidiospores are then dispersed by the wind. This taxonomic division includes many commonly eaten button mushrooms, as well as wild puff mushrooms.
Overall, it is clear that the diverse functions and properties of microorganisms make their identification extremely important for human health and well-being. While a vast number of species of fungi and bacteria have been identified to date, it is estimated that millions more have yet to be identified and classified. In addition, human disciplines that explore Fungi and Bacteria are as diverse as the organisms themselves and will undoubtedly continue to grow. The relevance of microorganisms to the medical fields is more prevalent now then ever, as multi-antibiotic resistant species of infectious bacteria threaten human health. Understanding the structure and biological characteristics of infectious and non-infectious species provides key insights necessary for the creation of new antibiotic treatments and preventative strategies3-4.
Microbiology is also critical to the food industry. Numerous products, including yogurt, cheese, kombucha, bread, and alcohol are made using specific categories or species of microbes. At the same time, food scientists focus on engineering chemical compounds and preservatives that will reduce the growth of unwanted microbes on food. In all these processes, an understanding of how microbes survive, reproduce, and affect their environment is necessary.
