The Hidden World of Microorganisms

Microorganisms have been around on Earth possibly since the earliest of life began 3.5 billion years ago, and they inhabit nearly every terrestrial, marine, and even some aerial environments. Tiny and invisible to the naked eye, these organisms comprise the world’s most diverse and abundant form of life. As a whole, these organisms are known as microorganisms, and include essential members of the bacteria, virus, protist, and fungi kingdoms.

Bacterial World 

Bacteria, single-cell microorganisms, form a large and highly diverse domain of microbes, and over 65% of the phylogenetic tree is composed of bacteria from all ancient branches of evolution. Bacteria are relatively efficient at absorbing and using organic forms of energy and nutrients, making them vital for the cycling of organic materials in the environment. Bacterial species can be divided into three main classes – proteobacteria, cyanobacteria, and actinobacteria – based on their phylogenetic and genomic differences.


Proteobacteria are the most abundant and highly diverse bacterial domain. They are found in almost all types of habitats, from terrestrial and aquatic environments to the intestinal tracts of animals and humans. They can be further divided into five classes – Alpha, Beta, Gamma, Delta, and Epsilon – based on characteristics such as their 16S rDNA and their metabolic pathways. While some pathways may offer various benefits to their host, some are decidedly harmful and allow proteobacteria to be opportunistic pathogens.

Alpha Proteobacteria 

Alpha proteobacteria are a group of species that are found in numerous habitats, ranging from soil and ponds to the hindgut of humans and other mammals. Most known species are free-living, although some are known to be parasitic. These species are highly metabolically active, possessing a variety of metabolic pathways, such as the tricarboxylic acid cycle, which allows them to interact with their environment in beneficial ways, such as carbon and nitrogen cycles by producing metabolites.

Beta Proteobacteria

eta-proteobacteria are the second phylogenetically diverse class of proteobacteria, and they inhabit numerous habitats, from soil to polluted water, and even the human body. Beta-proteobacteria are a metabolically diverse group of species, containing pathways for respiration, methylation, and nitrification, enabling them to survive in harsh environments. Like Alpha-proteobacteria, Beta-proteobacteria can also be opportunistic pathogens. Most members are free-living, but some species are parasitic, such as Rhizobium, which infects plant roots, causing nitrogen fixation and plant growth.


Cyanobacteria form a large and distinct group of earth’s oldest organisms, as they are believed to have existed as far back as 3.5 billion years ago. They are photosynthetic bacteria, capable of transforming light energy into chemical energy, which helps them to produce essential substances such as carbohydrates, proteins, lipids, and pigments. They are found in a variety of habitats, ranging from the ocean and soil to the atmosphere, and even in dormant form inside the eggs of some species of birds.


Actinobacteria are a distinct class of bacteria, most of which are aerobic and decomposers. They are well-known for the production of useful metabolites, such as antibiotics and biodegradable polymers. These bacteria have slow growth rates, form a resistant spore when unfavourable environmental conditions occur, and inhabit numerous terrestrial and aquatic habitats, ranging from soil to the skin of humans and other animals.

Viral World 

Viruses are a distinctive type of microorganism. Unlike any other organism, they do not contain any metabolic pathways and are instead dependent on pre-existing host-cells for replication. Viruses can be further divided into three main categories – DNA viruses, RNA viruses, and Retroviruses – based on the type of nucleic acid that forms the viral genetic material.

DNA Viruses 

DNA viruses are a large class of viruses that use double-stranded DNA as the main building block for their cores. These viruses are composed of a nucleic acid capsule, which contains the viral genetic information, and a proteinaceous layer, which acts as a protective shield to the nucleic acid core. They are found amongst almost all taxonomic groups, such as bacteria, plants, animals, and fungi, and exhibit host-specificity, meaning they infect and replicate within one species.

RNA Viruses 

RNA viruses are a distinct class of viruses, which use single-stranded RNA as the viral information packet. RNA viruses are far more diverse than DNA viruses in terms of disease-causing potential, although they tend to cause milder cases of sickness in comparison to their DNA counterpart. Having existed since prehistoric times, they can be found in almost all habitats, including plant, invertebrate, and vertebrate species.


Retroviruses are a distinct class of virus, which are distinct from other virus classes in terms of their genetic material. Unlike DNA viruses, which use double-stranded DNA as the genetic blueprint, Retroviruses use single-stranded RNA. They are obligate intracellular parasites, meaning they depend on a cellular host for replication, and their virion composition contains two identical copies of a single-stranded retroviral RNA molecule.

Protist World 

Protists are a diverse and varied group of eukaryotic organisms, which are found in a variety of habitats, ranging from marine and freshwater environments to soil and even the digestive tracts of animals. This group encompasses numerous smaller phyla, such as flagellates, ciliates, amebas, and green algae, and unlike bacteria and viruses, are able to form complex multicellular organisms.


Flagellates are a diverse and varied taxon, originating from the protist kingdom, and are capable of movement by means of a single or multiple flagella. Although there are multiple genera within the flagellate group, the most prominent are Massisteria, Spirostomum, and Volvox. Flagellates are distributed across all habitats, including soil, fresh and salt water, and have been found in the heterotrophic soil environment, the lower atmosphere and even polar regions.


Ciliates, sometimes known as ciliates, are a diverse group of protists, containing a great deal of species. They are named after their defining feature of cilia, tiny hair-like structures covering their bodies, which allow efficient metabolic uptake and reparative processes. Ciliates inhabit diverse environments, ranging from ponds and other aqueous habitats to the intestinal tracts of animals and humans.


Amebas, also called amoebas, are single-celled, eukaryotic organisms, and are able to form temporary, unicellular aggregates when exposed to food. Amebas are ubiquitous, meaning they can survive in a variety of conditions, including aqueous habitats and the intestinal tracts of animals and humans. They are capable of aerobic and anaerobic respiration and exhibit a number of nutritional strategies, ranging from pure autotrophy to obtaining nutrition from animal sources.

Green Algae 

Green algae are a diverse group of single-celled and multi-cellular eukaryotes. They are mainly found in aquatic habitats, although some species can also inhabit moist soils, and are capable of photosynthesis. Their cell walls are composed of cellulose, and they possess a variety of pigments, such as chlorophyll a, carotenoids, and phycobilins, allowing them to conduct photosynthesis. Green algae have been used as a food source and as a source of biofuel.

Fungal World 

Fungi are a large and diverse group of eukaryotic organisms, which mainly decompose dead organic matter but can also cause the spoilage of food. They generally live in the soil or on decaying organic matter, and can form complex, multicellular colonies. Fungi can be divided into three distinct phyla – Ascomycota, Basidiomycota, and Zygomycota – based on their characteristics, such as the structure of their reproductive spores.


Ascomycota, also known as the sac fungi, are fungi that are characterised by the fact that they produce their spores in a sac-like structure known as an ascus. They are an incredibly diverse group, containing a variety of species, from tiny yeasts to large mushrooms, and possess an array of metabolic capabilities, such as aerobic and anaerobic respiration, and fermentation. Ascomycota are found in a wide range of habitats, from the ocean to soil.


Basidiomycota, which are commonly known as mushrooms, are another diverse and fascinating class of fungi. These fungi are characterised by their production of their spores in a particular type of spore-producing organ known as a septate basidium. Basidiomycota form a crucial role in ecosystems as decomposers, breaking down decaying organic matter, and often provide food and shelter to other organisms.