how 2 ID soil microbes

K N and P J Harris ecoli at
Wed Aug 9 04:31:46 EST 1995

To ID or not to ID that is the question.
Or rather it starts off a chain of questions. I assume that you are 
talking bacteria and streptomycetes rather than fungi.

Q1. How good is your sample and are you sure that if you took the sample 
just a little to the right or left it wouldn't be different, or perhaps 
just a week later ?
Q2. Are you going to try to identify your organisms straight away, or 
after a while in cultivation ? The reason I ask is that after 30 plus 
years in the soil microbe isolation game I reckon that soil microbes are 
just a little flexible in how many characteristics they hang onto in 
cultivation. No, it's not just lousy technique, I've just seen too many 
fresh isolates change their pigmentation, antibiotic tolerance and heavy 
metal tolerance over a few weeks not to suspect that the "wild type" 
soil organism is a long way removed from the "domesticated" kind of bug 
you can get from the culture collections. The reason that the latter are 
IN collections is that they are reasonably stable (and hence maybe not 
very typical). The taxonomists, understandably enough, don't care for 
this opinion.

Try looking up the "Biolog" system or some of the sets of tests 
available from API. They might help to Genus level even if you don't 
want to trust them any further. This is not a criticism of either 
system, just that they are not designed for soils. (What is ?).

The American Soc Agron has a good collection of methods in their latest 
methods handbook that would be worth a look.

Don't be overawed by all the PCR enthusiasm. I still remain to be 
convinced that the DNA extraction is from living breathing current 
members of the population and has not been lurking around for a few 
hundred years like a lot of the humic material. I'm waiting with baited 
breath for someone to isolate enough DNA from a soil to be able to 
carbon date it !

Good luck,
Peter, Reading, UK.
AKA P.J.Harris at

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