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Re: RES: [compost_tea] Questions for the new millenium



Hi Jose -

I have a bunch of "old" questions from you I need to work on.

Has Will sent the non-compete, non-disclosure form so we can get going on a Brazil lab?  That's step one.  After you sign and send back, we send the affiliate lab guidelines.  You read it over, decide what you want to do, and then let us know. 

We work with you to get the lab up and running. 

I'd love to come down and meet your people, help you pick someone who can be the lab manager in Brazil, and have them come back to SFI Corvallis for a couple months to learn the things they need to know. 
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We have added beneficial organism assays, so the pleomorphic question becomes important.

But, pleomorphism is related to colony morphology, not shape and size when you look at the organism using direct methods.

Pseudomonads are famous for having bunches of different colony morphologies, for example, but when you pull bacteria from each different-appearing colony from the plate and look at them under the microscope, they are not morphologically different.  You can tell they are the same bacterium.  The slime quality is different, but not the bacterial shape. 

In some cases, Bacillus species can be longer and shorter, based on food resource they are using.  So, you might count something as two species when it is in fact only one species. 

But the real problem in using morphology to estimate species is that different species look exactly the same.  You can't differentiate Azotobacteria species one from species two.  They look the same.  So, type two errors are going to be much more prevalent.  We underestimate species diversity using morphology, not overestimate. 

As long as we know that to be the case, the morphological direct count approach is useful.  Certainly much more useful that plate count approaches.  And alot less expensive, at least for now, than molecular approaches. 

As the molecular approaches become economically feasible, we'll move to using them.  And in fact, part of our analysis in the beneficial organism assay relies on molecular methods.  To assess N-fixation, we rely on molecular techniques.

Most likely, most pathogenic bacteria have more than one name, because they have a name when growing and causing disease on one plant species, but on another plant where they do not cause disease, they have another name.  Molecular approaches are the way to go, but there's millions of dollars of research yet to go before those methods become useful.  Well, there are companies doing that work, but on human pathogens, not soil organisms.  The methods are coming along rapidly, and we're set to jump in and get started on the bacterial and fungal approach once the methods become a bit less expensive.

For example, the machine to help you do the probe replication, and then the ID of fluorescent excitation, costs about $190,000 right now.  There are significant problems with repeatability still.  And you still have to do the PCR, isolation, and probe development, specificity testing.  Give it time, though, and researchers will get it worked out. 

We're watching and waiting.......

Elaine

I mean pleomorphism in microorganisms.
There is a considerable amount of evidence showing
that microrganisms can assume different forms.
That could add to the difficulty in studying them from
a morphological stand point.
Also if you have to kill and fix a microbe in order to see it
that is the end of the story. Some organisms assume different
forms throughout their lives and killing and fixing
destroys the whole dynamic of the cycle.

How do see that particular aspect of the microorganisms and
specially soil microorganisms ? Have you noticed pleomorphism
in any of the organisms you have studied in the soil ?

Can the same organism have more than one name ?

Jose
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