Microbes and the World

Types of Microorganisms

Microorganisms make up a large part of the planet's living material and play a major role in maintaining the Earth's ecosystem.

Microorganisms or microbes are microscopic organisms that exist as unicellular, multicellular, or cell clusters. Microorganims are widespread in nature and are beneficial to life, but some can cause serious harm. They can be divided into six major types: bacteria, archaea, fungi, protozoa, algae, and viruses.

Bacteria

Bacteria are unicellular organisms. The cells are described as prokaryotic because they lack a nucleus. They exist in four major shapes: bacillus (rod shape), coccus (spherical shape), spirilla (spiral shape), and vibrio (curved shape). Most bacteria have a peptidoglycan cell wall; they divide by binary fission; and they may possess flagella for motility. The difference in their cell wall structure is a major feature used in classifying these organisms.

According to the way their cell wall structure stains, bacteria can be classified as either Gram-positive or Gram-negative when using the Gram staining. Bacteria can be further divided based on their response to gaseous oxygen into the following groups: aerobic (living in the presence of oxygen), anaerobic (living without oxygen), and facultative anaerobes (can live in both environments).

According to the way they obtain energy, bacteria are classified as heterotrophs or autotrophs. Autotrophs make their own food by using the energy of sunlight or chemical reactions, in which case they are called chemoautotrophs. Heterotrophs obtain their energy by consuming other organisms. Bacteria that use decaying life forms as a source of energy are called saprophytes.

Archaea

Archaea or Archaebacteria differ from true bacteria in their cell wall structure and lack peptidoglycans. They are prokaryotic cells with avidity to extreme environmental conditions. Based on their habitat, all Archaeans can be divided into the following groups: methanogens (methane-producing organisms), halophiles (archaeans that live in salty environments), thermophiles (archaeans that live at extremely hot temperatures), and psychrophiles (cold-temperature Archaeans). Archaeans use different energy sources like hydrogen gas, carbon dioxide, and sulphur. Some of them use sunlight to make energy, but not the same way plants do. They absorb sunlight using their membrane pigment, bacteriorhodopsin. This reacts with light, leading to the formation of the energy molecule adenosine triphosphate (ATP).

Fungi

Fungi (mushroom, molds, and yeasts) are eukaryotic cells (with a true nucleus). Most fungi are multicellular and their cell wall is composed of chitin. They obtain nutrients by absorbing organic material from their environment (decomposers), through symbiotic relationships with plants (symbionts), or harmful relationships with a host (parasites). They form characteristic filamentous tubes called hyphae that help absorb material. The collection of hyphae is called mycelium. Fungi reproduce by releasing spores.

Protozoa

Protozoa are unicellular aerobic eukaryotes. They have a nucleus, complex organelles, and obtain nourishment by absorption or ingestion through specialized structures. They make up the largest group of organisms in the world in terms of numbers, biomass, and diversity. Their cell walls are made up of cellulose. Protozoa have been traditionally divided based on their mode of locomotion: flagellates produce their own food and use their whip-like structure to propel forward, ciliates have tiny hair that beat to produce movement, amoeboids have false feet or pseudopodia used for feeding and locomotion, and sporozoans are non-motile. They also have different means of nutrition, which groups them as autotrophs or heterotrophs.

Algae

Algae, also called cyanobacteria or blue-green algae, are unicellular or multicellular eukaryotes that obtain nourishment by photosynthesis. They live in water, damp soil, and rocks and produce oxygen and carbohydrates used by other organisms. It is believed that cyanobacteria are the origins of green land plants.

Viruses

Viruses are noncellular entities that consist of a nucleic acid core (DNA or RNA) surrounded by a protein coat. Although viruses are classified as microorganisms, they are not considered living organisms. Viruses cannot reproduce outside a host cell and cannot metabolize on their own. Viruses often infest prokaryotic and eukaryotic cells causing diseases.

Multicellular Animal Parasites

A group of eukaryotic organisms consisting of the flatworms and roundworms, which are collectively referred to as the helminths. Although they are not microorganisms by definition, since they are large enough to be easily seen with the naked eye, they live a part of their life cycle in microscopic form.  Since the parasitic helminths are of clinical importance, they are often discussed along with the other groups of microbes.

Classification of Microorganisms

Microorganisms are classified into taxonomic categories to facilitate research and communication.

Life on Earth is famous for its diversity. Throughout the world we can find many millions of different forms of life. Biologic classification helps identify each form according to common properties (similarities) using a set of rules and an estimate as to how closely related it is to a common ancestor (evolutionary relationship) in a way to create an order. By learning to recognize certain patterns and classify them into specific groups, biologists are better able to understand the relationships that exist among a variety of living forms that inhabit the planet.

The first, largest, and most inclusive group under which organisms are classified is called a domain and has three subgroups: bacteria, archae, and eukarya. This first group defines whether an organism is a prokaryote or a eukaryote. The domain was proposed by the microbiologist and physicist Carl Woese in 1978 and is based on identifying similarities in ribosomal RNA sequences of microorganisms.

The second largest group is called a kingdom. Five major kingdoms have been described and include prokaryota (e.g. archae and bacteria), protoctista (e.g. protozoa and algae), fungi, plantae, and animalia. A kingdom is further split into phylum or division, class, order, family, genus, and species, which is the smallest group.

The science of classifying organisms is called taxonomy and the groups making up the classification hierarchy are called taxa. Taxonomy consists of classifying new organisms or reclassifying existing ones. Microorganisms are scientifically recognized using a binomial nomenclature using two words that refer to the genus and the species. The names assigned to microorganisms are in Latin. The first letter of the genus name is always capitalized. Classification of microorganisms has been largely aided by studies of fossils and recently by DNA sequencing. Methods of classifications are constantly changing. The most widely employed methods for classifying microbes are morphological characteristics, differential staining, biochemical testing, DNA fingerprinting or DNA base composition, polymerase chain reaction, and DNA chips.

Microbes and the Origin of Life on Earth

Life on Earth is thought to have originated from the oldest single-cell archaea and bacteria.

Scientific evidence suggests that life began on Earth some 3.5 billion years ago. Since then, life has evolved into a wide variety of forms, which biologists have classified into a hierarchy of taxa. Some of the oldest cells on Earth are single-cell organisms called archaea and bacteria. Fossil records indicate that mounds of bacteria once covered young Earth. Some began making their own food using carbon dioxide in the atmosphere and energy they harvested from the sun. This process (called photosynthesis) produced enough oxygen to change Earth's atmosphere.

Soon afterward, new oxygen-breathing life forms came onto the scene. With a population of increasingly diverse bacterial life, the stage was set for more life to form. There is compelling evidence that mitochondria and chloroplasts were once primitive bacterial cells. This evidence is described in the endosymbiotic theory. Symbiosis occurs when two different species benefit from living and working together. When one organism actually lives inside the other it's called endosymbiosis. The endosymbiotic theory describes how a large host cell and ingested bacteria could easily become dependent on one another for survival, resulting in a permanent relationship.

Over millions of years of evolution, mitochondria and chloroplasts have become more specialized and today they cannot live outside the cell. Mitochondria and chloroplasts have striking similarities to bacteria cells. They have their own DNA, which is separate from the DNA found in the nucleus of the cell. And both organelles use their DNA to produce many proteins and enzymes required for their function. A double membrane surrounding both mitochondria and chloroplasts is further evidence that each was ingested by a primitive host. The two organelles also reproduce like bacteria, replicating their own DNA and directing their own division.

Mitochondrial DNA (mtDNA) has a unique pattern of inheritance. It is passed down directly from mother to child, and it accumulates changes much more slowly than other types of DNA. Because of its unique characteristics, mtDNA has provided important clues about evolutionary history. For example, differences in mtDNA are examined to estimate how closely related one species is to another.

Conditions on Earth 4 billion years ago were very different than they are today. The atmosphere lacked oxygen, and an ozone layer did not yet protect Earth from harmful radiation. Heavy rains, lightning, and volcanic activity were common. Yet the earliest cells originated in this extreme environment. Extremophiles archaea still thrive in extreme habitats. Astrobiologists are now using archaea to study the origins of life on Earth and other planets. Because archaea inhabit places previously considered incompatible with life, they may provide clues that will improve our ability to detect extraterrestrial life. Interestingly, current research suggests archaea may be capable of space travel by meteorite. Such an event termed panspermia could have seeded life on Earth or elsewhere.

The presence of archaea and bacteria changed Earth dramatically. They helped establish a stable atmosphere and produced oxygen in such quantities that eventually life forms could evolve that needed oxygen. The new atmospheric conditions calmed the weather so that the extremes were less severe. Life had created the conditions for new life to be formed. This process is one of the great wonders of nature.

Environmental Diversity of Microbes

Microbes are ubiquitous on Earth and their diversity and abundance are determined by the biogeographical habitat they occupy.

The microbial world encompasses most of the phylogenetic diversity on Earth, as all Bacteria, all Archaea, and most lineages of the Eukarya are microorganisms. Microbes live in every kind of habitat (terrestrial, aquatic, atmospheric, or living host) and their presence invariably affects the environment in which they grow. Their diversity enables them to thrive in extremely cold or extremely hot environments. Their diversity also makes them tolerant of many other conditions, such as limited water availability, high salt content, and low oxygen levels.

Not every microbe can survive in all habitats, though. Each type of microbe has evolved to live within a narrow range of conditions. Although the vast majority of microbial diversity remains undetermined, it is globally understood that the effects of microorganisms on their environment can be beneficial. The beneficial effects of microbes derive from their metabolic activities in the environment, their associations with plants and animals, and from their use in food production and biotechnological processes.

In turn, the environment and the recent temperature anomalies play a crucial role in driving changes to the microbial communities. For instance, the assemblage of microbes that exists on the surface of seawater is thought to have undergone tremendous change with respect to composition, abundance, diversity, and virulence as a result of climate-driving sea surface warming.

For microbiologists, it is critical to study microbial adaptation to different environments and their function in those environments to understand global microbial diversity, ecology, and evolution. They rely on specific physical and chemical factors such as measuring temperature, pH, and salinity within a certain geography to formulate a comparison among microbial communities and the environment different species can tolerate. Researchers collect samples from geographical areas with different environmental conditions and between seasons to determine how dispersal patterns shape microbial communities and understand why organisms live where they do. As such, microbial communities from coastal and open oceans, polar regions, rivers, lakes, soils, atmosphere, and the human body can be tested. These samplings create a starting point to understand how the abundance and composition of microbial communities correlate with climatic perturbations, interact to effect ecosystem processes, and influence human health. Interfering with natural microbial biomass disrupts the balance of nature and the ecosystem and leads to loss of biodiversity.