Different groups of prokaryotes. Evolutionary relationships of bacteria and archaea. Extremophiles.
- The two prokaryote domains, Bacteria and Archaea, split from each other early in the evolution of life.
- Bacteria are very diverse, ranging from disease-causing pathogens to beneficial photosynthesizers and symbionts.
- Archaea are also diverse, but none are pathogenic and many live in extreme environments.
- A DNA sequencing approach called metagenomics lets scientists identify new species of bacteria and archaea, including ones that can't be cultured.
Prokaryotes, which include both bacteria and archaea, are found almost everywhere – in every ecosystem, on every surface of our homes, and inside of our bodies! Some live in environments too extreme for other organisms, such as hot vents on the ocean floor.
Although they are found all around us, prokaryotes can be hard to detect, count, and classify. The prokaryotic species we know of today are a tiny fraction of all prokaryotic species thought to exist. In fact, the very idea of a “species” becomes complicated in the world of prokaryotes!
In this article, we'll first look at major groups of prokaryotes. Then, we'll explore why it’s often tricky to identify and classify them. Finally, we'll see how DNA sequencing methods are helping us get a better picture of the prokaryotes around us.
A prokaryote "family tree"
For a long time, all prokaryotes were classified into a single domain (the largest taxonomic grouping).
However, work by microbiologist Carl Woese in the 1970s showed that prokaryotes are divided into two distinct lineages, or lines of descent: Archaea and Bacteria. Today, these groups are considered to form two out of three domains of life. The third domain (Eukarya) includes all eukaryotes, such as plants, animals, and fungi.
Since splitting off from one another millions of years ago, both Bacteria and Archaea have split off into many groups and species.
Domain Bacteria contains major groups: proteobacteria, chlamydias, spirochetes, cyanobacteria, and gram-positive bacteria.
The proteobacteria are subdivided into five groups, alpha through epsilon. Species in these groups have a wide range of lifestyles. Some are symbiotic with plants, others live in hot vents deep under the sea, and others yet cause human diseases, such as stomach ulcers (Helicobacter pylori) and food poisoning (Salmonella).
The other four major groups of bacteria are similarly diverse. Chlamydias are pathogens that live inside host cells, while cyanobacteria are photosynthesizers that make much of Earth's oxygen. Spirochetes include both harmless bacteria and harmful ones, like the Borrelia burgdorferi that cause Lyme disease. The same is true of Gram-positive bacteria, which range from probiotic bacteria in yogurt to the Bacillus anthracis that cause anthrax.
Domain Archaea contains major groups. Intriguingly, so far, no archaea that are human pathogens have yet been discovered.
Archaea do live in our bodies and those of animals—for instance, in the gut—but all of them seem to be harmless or beneficial. Although there are hypotheses, no one yet knows exactly why archaea are all "friendly," i.e., why no disease-causing species have evolved.
Alongside the archaea that enjoy the comfy environment of the human gut, there are many extremophile species that live in much more inhospitable places. These include volcanic hot springs, undersea hot vents, and very salty places like the Dead Sea.
The many "mystery prokaryotes"
For many years, the main approach to studying prokaryotes was to grow them in the lab. If an organism could be grown on an agar plate or in a liquid culture, then it could be studied, analyzed, and added to our growing catalog of prokaryotic species and strains.
Some prokaryotes, however, can't grow in a laboratory setting (at least, not under the conditions scientists have tried). In fact, an estimated of bacteria and archaea are unculturable!
This represents a pretty huge gap in our understanding of what prokaryotes are out there. For context, there are known eukaryotic species. If the culturability problem applied to eukaryotes in the same degree as prokaryotes, we would only know of of these species. This would make for a very empty tree of life, and a very incomplete understanding of what eukaryotes (as a group) are like. For instance, we might know that there were animals, but be in the dark about plants or fungi!
What is a prokaryotic species?
In order to talk about finding prokaryotic species, we probably need to define what they are. This may seem like a basic question, but it's a complex and even controversial one if you're a microbiologist.
For eukaryotes, most scientists define a species as a group of organisms that can interbreed and have fertile offspring. This definition makes sense for species that reproduce sexually, but it doesn't work so well for organisms like bacteria. Bacteria reproduce asexually to make clones of themselves—they don't interbreed.
Scientists instead classify bacteria and archaea into taxonomic groups based on similarities in appearance, physiology, and genes. Many are given names using traditional Linnean taxonomy, with a genus and species. Still, the question of how and whether prokaryotes should be grouped into species remains a topic of debate among scientists. The right “species concept” for these organisms is still a work in progress.
Metagenomics: A new window on microbes
Scientists estimate there may be millions of prokaryotic species (or species-like groups), but we know very little about most of them. This is starting to change thanks to large-scale DNA sequencing.
DNA sequencing makes it possible for scientists to study entire prokaryotic communities in their natural habitats – including the many prokaryotes that are unculturable, and would previously have been "invisible" to researchers.
The collective genome of such a community is called its metagenome, and the analysis of metagenome sequences is known as metagenomics. Prokaryotic metagenomics is one of the areas of biology that I find coolest and most mysterious.
For example, a DNA sample can be taken from a hot spring microbial mat, such as the beautiful, multicolored mats found in Yellowstone National Park. Even a tiny sample from this rich community includes many, many individuals of different species.
By sequencing and analyzing metagenome DNA samples, scientists can sometimes piece together entire genomes of previously unknown species. In other cases, they use sequence information from specific genes to figure out what types of prokaryotes are present (and how they are related to each other or to known species). The genes found in the DNA samples can also provide clues about the metabolic strategies of the organisms in the community.
Want to join the conversation?
- How did scientists do experiments on archaebacterias if they only live in extreme places?(8 votes)
- They don't live only in extreme environments. Approximately 40 % of your own microflora are actually archaea. In the past few decades we found out that many prokaryotes that we thought were bacteria are actually archaea.(10 votes)
- Why mycoplasmas included in gram positif when it dont have cell wall?(4 votes)
- Because of the criteria used.
Mycoplasma is not classified under 'gram positive' based on Gram staining (which does not give results) but based on genetics.
Comparison of DNA sequences and 16s ribosomal RNA tend to support this idea and Mycoplasma are now categorized as gram-positive.(3 votes)
- If bacteria and archaea are prokaryotes, why does figure 3, the lineage diagram near the top, indicate that archaea and eukarya have a more recent ancestor? Doesn't common ancestry dictate classification?(2 votes)
- Excellent observation!
You are correct, prokaryote is not a good phylogenetic grouping — it really just means "not a eukaryote".
Prokaryote is an old term that is no longer considered valid in a phylogenetic context, but is too useful to give up.
The accepted explanation for the evolution of the Eukarya is that a Bacteria ended up inside (was eaten or infected) an Archaea — this is known as symbiogenesis, or the endosymbiotic theory.
This is the most fundamental example of a limitation in thinking of phylogenies as trees — sometimes the branches fuse!
The diagrams on the right in this wikipedia article may help you visualize the "true" relationship among the three domains:
- Did Archea and Bacteria branch before or after Eukarya appeared? If before, from which of these domains did Eukarya branch?(2 votes)
- Yes, Archea and Bacteria branched before the Eukarya appeared. Only after they branched did the Eukarya branch off from Archea. Evolutionists think this because Archea and Eukarya are similar, Archea and Bacteria are similar, but Eukarya and Bacteria aren't very similar. And using DNA hybridization and things they hypothesized this, though there really is no proof.(4 votes)
- to which kingdom do mold belong(1 vote)
- That depends on the mold!
Most molds are fungi — Kingdom: Fungi
Other things called molds include:
• "water molds" (Kingdom Chromista):
• "slime molds", which aren't Fungi, but whose classification is still uncertain:
- What is the difference between Archea and Bacteria?(1 vote)
- Differences Between Bacteria and Archaea
•Different cell wall proteins
•Different lipids in plasma membrane
•Different ribosomal proteins and RNA
•Archaea ribosomal proteins resemble eukaryotic ribosomal proteins.(3 votes)
- what are Prokaryotes are found in(1 vote)
- Prokaryotes are found practically everywhere, from inside other organisms (like digestive bacteria) to in really extreme environments that have high heat or acidity, for example.(2 votes)
- how will prokaryotes grow in a laboratory?(2 votes)
- mitosis, all you need to grow prokaryotes is a food source, and the right temp to keep them dividing and growing.(1 vote)
- what is an extremophile?(1 vote)
- An organism§ that loves "extreme" environments — of course "extreme" is relative to what we think of as "normal".
These "extreme" environments include:
• undersea thermal vents (e.g. "black smokers") with temperatures up to 122°C
• acidic drainage from mine tailings with pH values less than 1
The wikipedia article on this seems like a good place to start learning more:
§Note: Extremophiles are usually members of the Archaea.(1 vote)