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Bacterial Taxonomy

About microscopic forms of life, including Bacteria, Archea, protozoans, algae and fungi. Topics relating to viruses, viroids and prions also belong here.

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Bacterial Taxonomy

Postby wildfunguy » Sat Oct 19, 2013 6:12 pm

Introduction and Purpose Statement

I am studying bacterial taxonomy. I want you to criticize my associations. Doubted statements are in red text, awaiting confirmation. Questions are in green text.
I prefer sources, but I can look for sources to confirm your claims if you give enough detail.

I want to organize this information to make it memorable and easy to apply, and to fill in the gaps. I will post one chart that I am already working on.
Image
Uploaded with ImageShack.us → Is that technically advertising? It came with the image code.

I plan to make more such charts. I would particularly like a chart that relates Gram-staining to taxonomy, one that makes note of all the common exceptions. Maybe there is already one out there. I would also like a chart that gives the most common traits of each taxonomic group and how frequent those traits are among the group, and maybe a chart of unique traits, such as the formation of filamentous structures or reproductive bodies, that are only found within a few taxonomic groups.

Here it goes.

Bacteria in General

Bacteria reproduce asexually, with the most common method being binary fission. They all have peptidoglycan cell walls, unlike archaea.

Deeply Branching Bacteria

The major phyla of the deeply branching bacteria are Chlorflexi, Deinococcus-Thermus, and Aquificae.
What are their cell walls and membranes like? Deinococcus has an outer membrane similar to that of Gram-negatives, but it stains as Gram-positive, so it somehow retains the crystal violet.
The deeply branching bacteria are all autotrophs. For example, the Chloroflexi are the green nonsulfur bacteria, which are phototrophs containing bacteriochlorophyll.
Why do deeply branching bacteria prefer conditions similar to what the early Earth was like? Assuming that all taxonomic groups evolve at the same rate, no group should be more similar to the first organisms than any other group.

Fusobacteria, Firmicutes, and Actinobacteria

If a bacteria stains as Gram-positive, it is probably a member of Firmicutes, Actinobacteria, or a deeply branching phylum.
Virtually all members of Firmicutes or Actinobacteria stain as Gram-positive
, but genus Veillonella is an exception, staining as Gram-negative rods. Oh nevermind, Wikipedia says they're cocci? I thought Clostridians were rod-shaped!!!
Are there any other exceptions within domain bacteria that erroneously stain positive or negative? Particularly from the deeply branching phyla, since my textbook places those phyla nearer to the Gram-negative phyla than the Gram-positive phyla, but does not seem to categorize them according to their Gram reaction.

Actinobacteria may form filamentous structures that may have reproductive spores.
A unique feature is the mycolic acid of Mycobacterium and Nocardia, which gives resistance to dessication, but also makes colony growth significantly slower. These stain as acid-fast cells. If you've got acid-fast cells, you've got Actinobacteria.

Firmicutes (said like "firm-ick-cuties") is a diverse group that is better divided into subgroups.

Fusobacteria (said like "few-so-bacteria") stain as Gram-negative even though they're closely related to Firmicutes (conveniently, these phyla both begin with letter F). What are Fusobacteria cell walls and membranes like? Did Fusobacteria split off by developing a Gram-negative feature, or did Firmicutes branch off by developing a Gram-positive feature. In the former case, I would expect Fusobacteria to have a unique form of Gram-negative structure.

Other Gram-Negative Phyla

Phylum Cyanobacteria consists of bacterial phototrophs, thus they have have photosynthetic lamellae. However, their use of chlorophyll instead of bacteriochlorophyll makes them unique among the bacteria. They're Gram-negative cocci or disks. Like Actinobacteria, disk-shaped cyanobacteria may form filamentous structures with reproductive spores, but the presence of heterocysts or the ability to reduce nitrogen gas to ammonia is unique to Cyanobacteria.

Proteobacteria are very, very diverse and better discussed in terms of the individual classes alpha, beta, gamma, delta, and epsilon.
Prosthecae indicate membership in alphaproteobacteria.

And I'll leave it at that for now.
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Postby Sophiahotep » Thu Nov 14, 2013 10:12 pm

Could you help in taxonomy of beneficial plant/soil bacteria?

I am growing some veggies and will be making some bacteria cultures in petri dishes using swabs from outside, and from my own body and those of friends and pets.

I will then attempt to identify beneficial bacteria and help it take over the Petri. Then I will cultivate it in a larger area, and use that as a pre-compost pile with some fungi and nematodes.
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Postby Sophiahotep » Thu Nov 14, 2013 10:40 pm

Also, Archaea... How can I tell the difference between them and bacteria with a 200x microscope? (getting a 1000x and 2000x as soon as possible)

And what Archaea is beneficial to plant and soil life?
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Re: Bacterial Taxonomy

Postby wildfunguy » Tue Dec 03, 2013 12:21 am

There probably aren't any archaea that you have to worry about. Archaea are rare, and no archaeans are known pathogens.
However, if you do happen to be looking at an archaean, it may have hami instead of fimbriae. Hami are similar to fimbriae—both are long projections from the cell that serve a common function—but hami are "barbed" helical projections with hooked tips.
I don't know how an archaean would Gram stain.
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