[compost_tea] Re: Dr. Ingham

From: chuck whelan <chazfw_at_yahoo.com>
Date: Tue, 19 Aug 2003 11:29:35 -0700 (PDT)

Dr. E :
i have been a member of this group for some months now-- i am quiet by nature- so tend to find comfort as a "lurker"-----& i fully appreciate that the focus of this group is not to stray off course toward the personal tangent------ with that said--& i beg the groups indulgence-- may i personally Thank You for being a part of this experience----woman- i can't imagine where you find the time- how you maintain the interest- my gosh, do all the things you do ?--- but i-for one- am extremely grateful--- i have learned a great deal from this group-- most of all- i have learned that we- as a group- are so very fortunate to be within your presence-- take very good care- and again-- Thank You

soilfoodweb_at_aol.com wrote:
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


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Received on Tue Aug 19 2003 - 17:00:49 EDT

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