Microbiology, Lec 8.

Announcements:

I put some questions from an old exam on the web. This year's test will have fewer multiple choice questions than the last time I taught this course (1994). Please don't ask for the answers to the old exam. If you have trouble figuring out the answer to a specific question then ask me in class next tues. or come to my office.

ARCHAEA (Ch. 19 & 20)

Please refer back to lectures 3 and 4 for an overview of the 3 domains of life. Show universal phylogenetic tree. We have already discussed some of the structural and biochemical similarities among the 3 domains and this info is summarized in Table 19.8 of the book.

Major Groups of the Archaea.

Right now the Archaea are being broken up into 2 groups based on biochemical similarities and sequence data. The 2 groups are:

1) Euryarchaeota

Methanogens,
Extreme Halophiles

2) Crenarchaeota

Extreme Thermophiles.
Mesophilic Crens.

Please note however that there are thermophiles distributed throughout the phylogenetic tree of the Archaea and that the halophiles are closely related to some of the methanogens (see Figure 20.7).

1) Euryarchaeota

Methanogens (= methane generators)

Methane (CH4) or "natural gas" is an odorless gas that is used widely today in industry and the home. Much of this gas was probably created over the eons by methanogens. Methane is also a greenhouse gas that may be contributing to global warming because it is increasing in concentration in the atmosphere.

The methanogens are the most widely distributed of the Archaea and have been found almost everywhere that humans have looked. They are most abundant in anaerobic environments (guts, swamps, sediments etc.) About 30% of adult humans have high populations of methanogens in their guts (all of us have some methanogens inside) and this may explain why some folks emit more gas than others. Methane is odorless so the foul smell of some flatulence comes from microbial fermentations of organic compounds, especially proteins.

Table 20.2 shows some of the huge diversity of methanogens. Note that they come in all shapes and have a wide variety of cell-wall types - ranging from pseudopeptidoglycan ("pseudomurein" in Figure 20.2) to protein or glycoprotein cell walls. Also note that they all have "Methano" as part of their generic names. The % G+C of the methanogens ranges from 26 to 62, again indicating that this is a very diverse group.

The diversity of methanogenic metabolic types is given in Table 20.2. Methanogens all live in very reducing environments where e- acceptors like oxygen, nitrate and sulfate have been depleted and where even fermentable substrates have been mostly used up. Most of the metabolic pathways used by these guys are still not well understood but we know quite a bit about the methanogens that use carbon dioxide and hydrogen to make methane. In general these organisms are using H2 as their e- donor and CO2 as their e- acceptor.

4 H2 + CO2 -----> CH4 + 2 H2O

See overhead; note that methanogens use a bunch of novel co-enzymes ("vitamins") in their metabolism.......

See overhead for a synopsis of role that methanogens play in the breakdown of complex molecules like cellulose in anaerobic environments. Note that they are just one part of complex anaerobic food webs.

Extreme Halophiles.

These organisms require high concentrations of salt in order to live. Their optimal NaCl concentrations for growth range from 2 to 4.5 M. For reference the salt concentration of sea water is about 0.5 M. Thus, they are found in habitats like the Great Salt Lake, Dead Sea and salterns (= evaporation basins for obtaining salt; you can see these in the San Francisco bay) etc. They also colonize some salted foods but no halophiles have been shown to cause food-borne illnesses.

The % G+C of the halophiles ranges from 60 to 71 and the best studied extreme halophile, Halobacterium, has a glycoprotein cell wall. One other unique aspect of some extreme halophiles is that they have a novel form of photosynthesis found in no other living organisms. They have a trans-membrane protein called bacteriorhodopsin (box 20.1) which acts as a light driven proton pump (unlike regular photosynthesis, no electron transport is involved).
When oxygen is present Halobacterium salinarium cells are red-pigmented and grow chemoheterotrophically. Under anaerobic conditions, they produces patches of purple membrane. Purple membrane expresses a protein called bacteriorhodopsin (Box 20.1). This is a protein with a retinal molecule attached. Light causes the protein to undergo a conformational change that pumps protons across the membrane. This mechanism is similar to how our eyes transduce light signals. The proton gradient is used to generate ATP, which allows Halobacteriumto survive temporary oxygen limitation.

2) Crenarchaeota

All cultivated representatives are sulfur-dependent and thermophilic. However, recent data indicate that uncultivated mesophilic Crenarchaeota (see below) are present in many environments.

Metabolic diversity of studied Crenarchaeota is limited.

Extreme Thermophiles.

As noted above, thermophiles are distributed throughout the Archaea, but many of them group on a main branch of the Archaeal tree (see Figures 19.3 and 19.12). Most of the extreme thermophiles have temperature optima for growth above 80 degrees C whereas most thermophilic Eubacteria have temperature optima of 70 degrees or lower (see overhead). This niche separation is further indication that the Archaea are adapted to environmental extremes similar to those that may have been present on earth when life evolved. It is also of ecological significance that the extreme thermophiles exist in environments that are too hot for photosynthesis to take place. Thus, it is not surprising that many of them have unique forms of metabolism that involve sulfur compounds etc.. (see Table 20.1). Metabolic diversity of studied Crenarchaeota is limited: H2/S Pyrodictium, Pyrobaculum, probably Sulfolobus). Some will also oxidize organics, using a variety e- acceptors (wait for Phys. Lectures...).

Because of their high thermostability, enzymes from thermophiles are being used in many commercial applications. For example, proteases from moderate thermophiles are used in laundry detergents and DNA polymerases from extreme thermophiles are used in the polymerase chain reaction (PCR) and other molecular techniques that are carried out at high temperatures.

...

Mesophilic Crenarchaeota

Not much is known about these guys since none have been cultured in the laboratory, but rRNA gene abundance studies indicates that they are a few percent of most environments and in some places much higher (e.g. mesophilic Crens are approx. 50% of marine microbes below 100 meters depth in the oceans, so they may be among the dominant life forms on earth!!

Recent studies also indicate that they very common in soils, but no one has any good ideas for what they are doing there (or in the oceans). A crenarchaeote has been detected as a common symbiont in sponges, but what it is doing there is not known either.