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Classification
A Natural System
Difficulties in
Classifying Microbes

Molecular Phylogeny
Eucarya
Archaea
Bacteria
Molecular Ecology
Footnotes


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Bacteria (Eubacteria, or Typical Bacteria)

©2000 Gary Olsen, University of Illinois

Some Major Groups within the Bacteria

Some major phylogenetic divisions within the eubacteria and representative genera are listed below. Additional divisions continue to be found. To illustrate the scattered distribution of some physiological characteristics, they are marked on the corresponding genera: photosynthetic with an asterisk (*); gliding motility with a bar (|), lack of a cell wall with a paragraph mark (), and thermophilicity by a section mark (§).

Hydrogen oxidizers
(oxygen reducers)
Aquifex§
ThermotogalesThermotoga§, Fervidobacterium§
Thermodesulfobacterium groupThermodesulfobacterium§
Green nonsulfurChloroflexus*|, Herpetosiphon, Thermomicrobium§
Deinococcus groupDeinococcus, Thermus§
Thermodesulfovibrio groupThermodesulfovibrio§
Synergistes groupSynergistes
Low G+C Gram positiveBacillus, Clostridium, Eubacterium, Heliobacterium*, Lactobacillus, Mycoplasma, Spiroplasma
High G+C Gram positiveBifidobacterium, Mycobacterium, Propionibacterium, Streptomyces
CyanobacteriaOscillatoria*|, Prochlorococcus*, Synechococcus*, chloroplasts*
PlanctomycetalesPlanctomyces
ChlamydialesChlamydia
Green sulfurChlorobium*
Cytophaga groupBacteriodes, Cytophaga|, Flexibacter|, Flavobacterium, Rhodothermus§
Fibrobacter groupFibrobacter
SpirochetesBorrelia, Leptonema, Spirochaeta (including Spirochaeta sp. str. Antarctic), Treponema
Proteobacteria (Purple bacteria):
alpha subdivisionAgrobacterium, Anaplasma, Rhodobacter*, Rhodospirillum*, Rickettsia, mitochondria
beta subdivisionNeisseria, Rhodocyclus*
gamma subdivisionBeggiatoa|, Chromatium*, Escherichia, Haemophilus, Legionella, Pseudomonas, Salmonella, Vibrio, Yersinia
delta/epsilon subdivisionBdellovibrio, Campylobacter, Desulfovibrio, Helicobacter, Myxococcus|, Wolinella
Insights into the origin and evolution of other properties can be gained by similarly examining their distribution among the groups (preferably directly on a tree, as discussed below).

Chlorophyll-Based Photosynthesis

Five of the major phylogenetic groups of Bacteria listed above include photosynthetic genera. Given the complexity of the process, it is unlikely to have been invented multiple times. Instead, it seems much more likely that it originated early in eubacterial evolution, and has been lost (or gained by lateral transfer) in many lineages.

Some of the branches that diverge earliest in the Bacterial domain (notably the hydrogen oxidizers and the Thermotogales) have no known photosynthetic members. This suggests, but does not prove, that chlorophyll-based photosynthesis was invented after these groups diverged from the rest of the Bacterial lineages.

Oxygenic Photosynthesis: Cyanobacteria and Chloroplasts

Although chlorophyll-based photosynthesis is widely distributed among the Bacteria, those that perform oxygenic photosynthesis form a phylogenetically monolithic group: all members of the cyanobacterial group share this physiology, and no organisms outside of the cyanobacteria have it.

Photosynthetic eukaryotes all contain chloroplasts (more generally called plastids). One of the great triumphs of molecular phylogenetic analyses has been the demonstration that the chloroplast genome is of bacterial origin. That is, the chloroplast was once a bacterium (more specifically, a cyanobacterium), and, after incorporation into the eukaryotic host cell, it has degenerated into a much simpler cellular organelle (it is an "endosymbiont'). Because of its loss of autonomy, the organelle is maintained by the host cell. In return, it allows the host cell to harvest light energy and to convert carbon dioxide and water into useful organic compounds.

The cyanobacterial lineage is responsible for essentially all biologically produced oxygen, whether by eukaryotic plants and algae, or by free-living cyanobacteria.24

The Alpha Subgroup of the Proteobacteria (Purple Bacteria): The Origin of Mitochondria

Although most eukaryotes are aerobic (many obligately), their ability to respire oxygen is due completely to their mitochondria. As in the case of chloroplasts, the mitochondrion is of bacterial origin. In this case, the source of the endosymbiont was the alpha subgroup of the Proteobacteria. Once again, the definitive evidence for the bacterial origin was provided by molecular sequence analyses.

Given that the mitochondrion is derived from an acquired bacterium, are there eukaryotes without mitochondria? Yes, a number of eukaryotes lack mitochondria, and they are all anaerobic. In some cases, such as anaerobic ciliates, this is due to loss of the mitochondrion. In other cases, such as the microsporidia (represented by Vairimorpha in the tree), it might be that the lineage has never had a mitochondrion, that is, the lineage is primitively amitochondrial.25

ORGANIZING DATA ON A TREE

Thermophilia

Thermophilia is represented in, or is the exclusive phenotype of, all of the deepest groups in the Archaea and the Bacteria. The simplest explanation is that the ancestral organisms were also thermophilic. This is appealing since it is believed that the early Earth was hot compared to its condition today.

Anaerobic Origins

Many of the deeply branching lineages are also anaerobic or microaerophilic (i.e., they use little or no oxygen). This is consistent with an early environment with less oxygen (certainly < 1%) than the present atmosphere. The geological evidence supports this low concentration. Higher oxygen levels had to await the invention of oxygenic photosynthesis.

Genetically-Defined Properties that have Changed Relatively Often

Some properties of organisms are volatile; they seem to be frequently invented and/or lost.

Cell shapeThe basic bacterial shapes (especially rods and cocci) are often intermixed within groups of related species. The most interesting exception is the spirochetes, most which fall in a single group.
AerobiosisThe aerobic life-style is distributed (discontinuously) throughout the prokaryotic groups. This is in some respects puzzling, since there were not large amounts of atmospheric oxygen until about 2 billion years ago. It is highly unlikely that the separation of all of the different lineages that include aerobes is more recent than this date. Therefore one of the exciting questions confronting microbiologists is how did so many different lineages invent or acquire the required genes.
Ability to use various electron donors and acceptorsWithin several of the bacterial groups, closely related organisms can use quite different compounds as electron donors or acceptors. For example, sulfur oxidation is scattered throughout most of the major prokaryotic lineages.
Chlorophyll-based photosynthesisAlthough it is almost certain (given its complexity) that chlorophyll-based photosynthesis was only invented once, the property is found broadly scattered throughout the Bacteria. It appears that it was invented very early is eubacterial evolution, and has been lost many times.
MotilityOne of the most surprisingly variable properties of various lineages is motility. Although it is easy to understand how motile organisms could have non-motile relatives (it could just be the loss of a single gene), it has also been found that gliding motility is found at several different places in the tree as well.
G+C contentWithin very closely related species, the mole percent G+C in the genome will tend to be within a few percent. However, as one considers progressively deeper groups in the tree, the variation can become quite large. The net effect of this is that having similar G+C contents cannot be taken as an indication of a close relationship, but having a very different base content means that the organisms are not closely related.

Genetically-Defined Properties that have Changed Relatively Rarely

Not all cellular properties display as much variability. These properties are among those for which knowledge of an organism's phylogenetic position is most predictive.
 

Cell wall structureA muramic-acid-containing cell wall indicates that the organism is a member of the Bacteria, since this structure is not found among Archaea or Eucarya. Some of the more specific cell walls are also quite diagnostic. One example would be the Gram positive cell wall. If an ultrastructural study shows a new organism to have a typical Gram positive cell wall, then the organism will almost certainly belong in this phylogenetic group. In addition, a cell known to be within one of the major groups of mycoplasmas will almost certainly lack a cell wall.26
Membrane lipidsStructure of lipids is particularly valuable in distinguishing bacterial membranes (mostly fatty acids) from the archaeal membranes (mostly phytyl alcohols). There are other lipids that have proven valuable for recognizing other specific groups, particularly among the eubacteria. One of the most interesting applications of this information is to characterize the organisms that contributed to ancient oil deposits. This area is undergoing a recent renewal, with the introduction of better techniques and instrumentation.
Oxygenic photosynthesisAlthough chlorophyll-based photosynthesis is widely distributed among Bacteria, only the cyanobacteria and chloroplasts (which are phylogenetically part of the cyanobacterial group) are able to extract the required electrons from water (thereby releasing oxygen). To date, all organisms known to perform oxygenic photosynthesis are members of the cyanobacterial group, and all free-living members of the phylogenetic group are able to perform oxygenic photosynthesis. It seems that members of the group are irreversibly committed to this mode of making a living.
MethanogenesisAll known methanogens belong to one of four identified related lineages within the Archaea. Although the methanogens have given rise to other organisms that are not methanogenic, it appears that methanogenesis has only been invented once.

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