The Microorganisms
Those of us who do not work with or study microscopic organisms have a tendency to clump the living world that is invisible to the naked eye into large, non-descriptive categories: germs, microbes, or even simply bugs. Biologists themselves have historically been guilty of tossing single-celled creatures to into catch-all groups irrespective of their actual relationships. You may remember learning the five-kingdom classification in school. This system split single-celled organisms into two groups - Kingdom Monera for the Bacteria and Kingdom Protista for every other unicellular creature. While this classification overlooked the great diversity of microorganisms, it was actually an improvement over the previous system, one that labeled every living thing as either Animal or Plant!
Starting in the 1970’s, researchers used improvements in genetic techniques to piece together a classification system that more accurately reflects evolutionary history and the vast genetic diversity in the microbial world. By focusing on the similarities and differences in the DNA code used by all living things, scientists could build a “family tree” based on true relatedness, rather than on superficial resemblance.
The basis for finding evolutionary relationships is fundamentally simple. Biologists have exploited the fact that all organisms share the DNA molecule as genetic blueprint and that differences in the DNA sequence are what make each species unique. Thus, DNA can act as a marker by which we can trace the descent of species from a common ancestor. When two groups diverge into separate lineages, their DNA begins to accumulate differences, called mutations, which are passed down to their descendents. By comparing sequences from several different organisms, you can measure how closely related those organism are. Distantly related groups are those that split long ago and have accumulated many genetic differences.
Biologists can now compare the DNA sequences of many species and use this information to build a phylogenetic tree, with a branching pattern reflecting evolutionary divergence. Closely related groups appear near each other on short branches while distant relatives split nearer the base of the evolutionary tree. By using DNA sequences, the relationships between all known living things can be measured. Prior to these approaches, it was difficult to determine how humans were related to plants and fungi, and how these groups were related to single-celled organisms.
It turns out that certain regions of the genetic code are more useful in assembling the Tree of Life than others. One of the most useful regions helps build cellular organelles called ribosomes. All living things rely on ribosomes to translate genetic information into functional proteins within cells. As a result, the regions that encode them can be found in any group of organisms. Fortunately for researchers, their specific sequences vary enough that they can be used to compare even closely related species. With these techniques forming the basis of comparison, researchers continue to fill out the tree of life, which binds all creatures, past, and present, into a universal family
The picture that has emerged from such phylogeneticinvestigations (see insert) is radically different from that of traditional classification. No longer did the macroscopic plants and animals dominate as in the five-kingdom system. Instead, the fundamental divisions of living things became the three domains: Bacteria, Archaea and Eukarya.
Three Domains
It is difficult to briefly characterize the three domains, for each carries an enormous amount of diversity in habitat, metabolism and lifestyle. Nevertheless, we may make some broad generalizations in order to form a picture of the microbial world. Bacteria present an enormously diverse group of organisms. Their cells can take the shape of spheres, rods, filaments or various other forms. They exist in nearly every conceivable habitat, from the gut of an animal to the open ocean, and may be free-living or act as parasites. Some of the most intensely studied bacteria are those that cause human disease, though the vast majority do not interact with humans at all. Despite such diversity, domain Bacteria is united by commonalities. All bacteria are single-celled and reproduce asexually. The chemical makeup of the cell wall that surrounds each bacterium is unique to the domain, a fact that allows researchers to quickly identify a microorganism as a bacterial species.
Hot spring regions host a great range of different bacteria. Several of these, such as Aquifex and Thermotoga, branch from the Tree of Life near its base and thus represent some of our most distant relatives. Photosynthetic bacteria, called cyanobacteria also inhabit thermal environments. We are greatly indebted to these organisms as they are likely responsible for the introduction of oxygen into the early earth’s environment!
Archaea is the most recently recognized domain of life. Our late discovery of the group stems directly from aspects of their lifestyle. First, no archaeans exist as known pathogens of humans or other animals. Also, members of Archaea tend to cluster at either extreme of the temperature spectrum; besides the hyperthermophiles of terrestrial hot springs and marine vents, archaeans also dwell in the frigid waters of the polar seas. Finally, many archaea have proven difficult to isolate in the lab. As a result, their characterization awaited the development of culture-independent molecular techniques, which sample microbial communities based on gene sequences.
Along with Sulfolobus, volcanic regions are home to archaeans such as Picrophilus, the most extreme acidophile of all. A unique cell membrane allows this hardy organism to grow below pH 0! Also present is the motile archaean Thermoplasma, which utilizes multiple flagella to propel itself through hot, sulfur-rich pools. In contrast to these oxygen-tolerant hot spring residents, many archaeans are strict anaerobes. For Thermoproteus, a rod-shaped thermophile, exposure to oxygen means certain death.
Bacteria and Archaea are often grouped together as prokaryotes, as distinct from the eukaryotes. The prokaryotic designation does not reflect evolutionary history- archaeans are actually more closely related to eukaryotes than to the bacteria- but rather links Bacteria and Archaea based on similarities in size and cellular organization.
Prokaryotic cells are small compared to those of eukaryotes; several dozen bacterial cells could fit inside a typical animal cell, though ranges of each vary considerably. Prokaryotes also show less structural complexity. Their cells lack the membrane-bound organelles found in eukaryotes, such as an enclosed nucleus, mitochondria, or chloroplasts. Instead, their cells consist of a cell wall surrounding the fluid cytoplasm, a solution of proteins, nucleic acids, inorganic ions and other cellular structures and substances. Prokaryotic genetic information is stored in a circular DNA molecule massed within the cytoplasm.
In contrast, eukaryote DNA is organized in linear strands, tightly packed in multiple chromosomes and surrounded by a nuclear membrane. In addition, their cells contain mitochondria, organelles vital for energy production, and chloroplasts (in the case of photosynthetic cells only). These organelles carry an amazing history; DNA and structural evidence have revealed their origins as ancient, free-living prokaryotes that were enveloped by a larger cells and found a stable existence within eukaryotes!
Long thought to be the entire living world, domain Eukarya remains the most familiar cellular life. The morphological diversity of the eukaryotes is impressive, stretching from humans to yeasts and from redwood trees to single-celled Paramecium. But even this eclectic company comprises only a small portion of the genetic variability of eukaryotes. Vastly more diversity lies between microbes such as Giardia, responsible for a common intestinal ailment, and the cellular slime molds, which can form macroscopic colonies and migrate as a multi-cellular conglomeration! Even with such variability within the domain, the eukaryotes share many common cellular features and similarities in genetic organization not found in Bacteria or Archaea (see insert: Prokaryotes vs. Eukaryotes).
While no eukaryotes can match the feats of the prokaryotic extremophiles, hot springs do play host to a variety of thermophilic fungi and algae. In waters too acidic for cyanobacteria (pH 4-5) algae such as Cyanidium take on the role of photosynthesizers. The rich microbial mats that they inhabit are thought to be held together by filamentous fungi that live off algal waste products. Diversity studies carried out on these fungi have revealed several lineages closely related to species found as far away as submarine vents in the Atlantic Ocean! Together with bacterial and archaeal decomposers within the mats, these eukaryotes form an remarkable community: all three domains of life intertwined in single, mutually dependent web.
A Microbial World
To the casual observer, the three domain classification may seem to give disproportional weight to microorganisms, which occupy all of the first two domains and much of Eukarya, as well! But there are a number of compelling reasons to view macroscopic life as a small piece of the overall picture.
First, the vast majority of genetic variation on earth comes from the microbial world. In fact, genetically, humans have more in common with oak trees than many bacteria have with each other! This fact may seem astounding, but it makes sense when we remember that bacteria have had at least three and a half billion years to diversify, while plants and animals are relative newcomers.
Next, microorganisms show far more diversity in ways to make a living. While all plants and animals are fuel their energetic needs by carbon-based metabolism, the microbial world contains a whole array of different energy pathways. Individual bacteria and archaea may derive their energy from hydrogen, nitrogen, carbon, sulfur, iron or a host of other chemical compounds. In addition to using sunlight for photosynthesis, some microorganisms can utilize the energy of chemical compounds for chemosynthesis. While humans respire using oxygen, there are microorganisms that can respire using a whole range of other compounds, such as iron and manganese and even plutonium and uranium!
Microbes have also exploited nearly every imaginable ecological niche on the planet. Besides colonizing hot springs, hydrothermal vents and polar ice, these organisms have diversified to live within the cells of plants or animals! They have evolved as parasites within a host species or as symbiotic partners, trading their unique services for the relative protection of an internal environment. Bacteria such as Rhizobium live in the roots of plants gathering nitrogen without which the plant could not grow. Other bacteria live within your own intestines, helping to break down nutrients and even synthesizing essential vitamins! Though we may overlook them with the naked eye, it is difficult to find any location that does not provide a habitat for microbial life.
Finally, in terms of sheer numbers, the microbes dominate the earth’s bio-sphere. For every single macroscopic organism living on the planet, we could count millions of microbial creatures. So, who are the microorganisms? By many standards, nearly everyone!
Armed with an appreciation of the earth’s astounding microbial diversity, we can now tackle the question of how single-celled creatures, and hot spring thermophiles specifically, go about the business of making living: an examination of metabolic diversity.
Our tour of life in Lassen Volcanic National Park continues with a look at: