Re: [compost_tea] Re: soil versus compost diversity

From: <soilfoodweb_at_aol.com>
Date: Tue, 19 Aug 2003 08:49:56 EDT

In a message dated 8/18/2003 3:58:26 PM Pacific Daylight Time,
dkemnitz2000_at_yahoo.com writes:


> Dr. Ingham you just answered one of my next questions:How do you know
> there are 25,000 species of bacteria present in a gram of healthy
> soil ? Or am I assuming something I shouldn't here? Seems like
> they're named when identified (like after the researcher). Dennis
>
>
When we ID a unique DNA strand, we don't know which bacterial species that
belongs to. We don't know it's culture requirements. We don't know if it was
performing it's function in the soil. We have to combine the FDA method with
the DNA method, and no one has figured out how to do that - yet.

So, we don't have a good way to name bacterial species identified by DNA
work. We have a sequence identifier, and those sequences are in databases. The
next step is to figure out what the bacterial species that has that DNA does
for a living.

When doing DNA analysis, one can find 25,000 - or more - unique DNA sequences
of DNA. We count as different those sequences that are really different, not
just one or two base changes in the sequence. So, there's an assumption that
if the DNA sequence is signficiantly different, that it is a different
species. Microbiologists are still arguing about that, and it's where I usually
step away from the argument. It just seems that there's a huge amount of species
in natural samples that we cannot culture.

But we can say there are LOTS of species present, much, much more than we can
grow on plate culture media in the lab. So, trying to assess diversity of
the bacteria in any samples by using plate culture media is laughable. When
labs try to say they are at least getting a handle on changes in diversity, just
ask yourself if getting less than 0.1% of the opinions in any city give you
and idea of the diversity of opinions in that city on any topic.

Yep, laughable.

Some labs claim that they can assess changes in functional groups, because
different plate media are chosen, each of which assesses a function. That's
like saying we can look in one pool hall in order to assess the diversity of
kinds of sports that exist in that sity. Less than 0.1% of the species that can
do a function grow on any single medium in the lab. That is not adequate to
even begin to understand how many kinds of species or individuals are performing
sports in that city, or the number of kinds of sports.

If you want to know about a specific sport, or function, and you know, for
example, that all the soccer platers will show up for a practice if each player
gets their favorite food, then maybe you'll get a good idea of how many soccer
players live in that part of the city.

Plate counts for a specific species are like that. If you make the
conditions such that all the E. coli will grow, then you can count all the E. coli in
that sample.

So, molecular methods are the way to go to assess diversity.

Total biomass of bacteria has a relationship with diversity, usually. The
more individuals of bacteria, the greater the probability that diversity is
high. Not perfect, but a better assessment of diversity than plate count
determinations.

Hope this helps!

Elaine Ingham
President, Soil Foodweb Inc.
www.soilfoodweb.com
SFI Oregon, USA
SFI Australia
SFI New York
SFI Europe
SFI New Zealand

"Hope is not a feeling. It is not the belief that things will turn out well,
but the conviction that what we are doing makes sense, no matter how things
turn out." -- Vaclav Havel, former President of the Czech Republic





Received on Tue Aug 19 2003 - 13:48:06 EDT

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