how 2 ID soil microbes
K N and P J Harris
ecoli at cix.compulink.co.uk
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
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 !
Peter, Reading, UK.
AKA P.J.Harris at reading.ac.uk
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