Subject: Re: Species diversity

From: Elaine Ingham <[email-masked]>
Date: Tue, 5 Nov 2002 14:14:14 EST

If there are no individuals of a species, or if there are no species present,
the number involved is zero.  You can't have a negative number of species, or
a negative number of individuals.  A "species richness" or a "species
diversity" index that assigns a negative number to species that is present is
mis-leading and inappropriate.  At the very least, an explanation of why a
negative value would be assigned is required.

There is no species diversity or species richness index found in any
introductory text book - certainly not Shannon-Weiner or Simpsons - that
calculate a negative species richness or species diversity for any part of
the community of any set of organisms.

No one in ecology makes the mistake of calling something Species Richness
Diversity.  Species richness is simply the number of species per unit area or
volume.  Species diversity requires knowledge about the number of individuals
of each species per unit area or volume.  Species diversity requires a
knowledge of species richness.  The calculations in text books are either for
species richness or for species diversity.  Do not mix the two up.

To quote researchers at Cornell University, the plate count approach is
"worthless" for assessment of species diversity in environmental samples.
Joel Gruver from North Carolina State University has had his say about the
usefulness of plate counts in assessing species diversity in soil or compost
samples on this list serve already.  Plate counts as an approach to assessing
species diversity in environmental samples are not worth the money you pay
for them.

Can plate count information be useful?  That's a different question.  Plate
counts can be used to assess the number of individuals (colony forming
units), or a "most probable number" of individuals, of certain species, if
you KNOW that the species you want to know about grow in a certain specific
set of conditions that you can reproduce in the laboratory.

Most bacteria or fungi in soil or compost do not grow on any plate medium.
Estimates are that less than 0.1% of the known species of bacteria can grow
on any plate medium.  Even if you run six different media, you can't begin to
get a reasonable assessment of species diversity using plate count
approaches.

There has been some serious mis-information about the number of species of
bacteria and fungi in compost, for example, because people do not understand
that plate counts assess less than 0.1% of the set of species present in the
compost.  People tell me often that compost doesn't have many species of
bacteria or fungi, based on plate count information.

Can we all, from this point on, please, exit this mis-information from our
understanding?  Compost has a huge number of bacterial and fungal species in
it, based on the diversity of starting materials put into the compost, based
on the number of unique DNA sequences that occur in compost, or soil or
compost tea.  Using molecular techniques, we can assess diversity.

Plate counts are NOT APPROPRIATE for assessing numbers of species of bacteria
or fungi in any soil, compost or compost tea.  Plate counts can be useful for
assessing numbers of individuals a few species that we know the conditions
for their growth, but that's about it.

Elaine Ingham
President, Soil Foodweb Inc.
www.soilfoodweb.com

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From: Joel Gruver <[email-masked]>
Date: Tue, 5 Nov 2002 21:46:58 -0500

Hello to all,

Elaine Ingham wrote:

>Plate counts are NOT APPROPRIATE for assessing numbers of species of
> >bacteria or fungi in any soil, compost or compost tea.  Plate counts >can
>be useful for assessing numbers of individuals a few species that >we know
>the conditions for their growth, but that's about it.

I agree with the first statement, however I hesitate to be as critical  as
Elaine concerning the use of plate counts to evaluate the quality of compost
teas.

Even though plate counts only represent a tiny fraction of the biodiversity
in soil/compost, they may have good predictive value withrespect to the
disease suppression and plant growth promotion effects of compost teas.

Consider routine soil testing... the extraction/analysis methods used in
routine soil testing are not designed to measure the total quantities of
nutrients contained in soil... rather they measure relatively soluble pools
of soil nutrients that have experimentally been determined (through
extensive field testing) to be strongly predictive of crop response to
fertilizer.

Do plate counts have value in predicting the functional value of    compost
teas ? I have not seen the data but Joel Reiten seems to think so... I
expect that the Xanthamonas article he refered to in his recent post may
present evidence of the predictive value of plate counts.

Do microscopy methods have value in predicting the functional value of
compost teas ? I don't know... Perhaps Elaine can recommend an article which
reports a significant relationship between direct counts and the function
value of compost teas.

Joel

Joel Gruver
Dept of Soil Science
NC State University
[email-masked]

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From: Elaine Ingham <[email-masked]>
Date: Tue, 5 Nov 2002 23:16:27 EST

Hi Joel -

The data we have is written up in the Compost Tea Brewing Manual.  There is a
clear predictive value between direct assessment and ability to prevent
disease.  When 70% or more of the leaf surface is covered with compost tea
organisms (at least 5% of the coverage has to be fungal), we have been able
to prevent colonization of the leaf surface by any foliar pathogen.

We see the same thing when it comes to roots.

We also see a great deal of usefulness in direct counts for assessing which
organisms are present, right now, in tea, or soil, or compost.  We can
discern which as ACTIVE, and performing a function, right now.

Plate counts cannot differentiate between spores and dormant stages, and
things that are alive and active now.  Spores and dormant stages germinate
and grow during the several day time period it takes for the colonies to get
large enough to count.

Extraction of a soluble nutrient from soil isn't like assessing diversity or
trying to predict whether a bacterium will suppress disease.  The connection
between nitrate and plant uptake and response is easy to see, because nitrate
is so soluble and so mobile.  But this isn't the case for P, for example.  Or
Fe.   Most likely, many of the bacteria and fungi that have beneficial
effects on plants are not culturable.

Mycorrhizal fungi, for example, cannot be cultured on any plate medium.  That
seems a huge set of beneficial organisms that are completely missed by plate
counts.  Mycorrhizal fungi play very important roles in both plant uptake and
 in disease suppression.  They are not included in any plate assessment.

There are many instances that a nutrient is present in soil, and yet the
plant tissues remain low in that nutrient.  Just because we can extract it
does not mean the plant will be able to take it up.

Dr. Eric Nelson has mentioned a paper coming out that shows that the pathogen
inhibition method means nothing when it comes to predictability of disease
inhibition in soil samples.  There was no relationship between inhibition on
plates and inhibition in soil.  I'm waiting patiently to see it in print.

But it makes sense that there isn't any real relationship.  The interaction
between a pathogen growing on a plate in the lab, and organisms in the tea,
growing on a plate, bears no relationship to how either the pathogen or the
set of tea organisms will grow in soil, on the leaf surface, on the bark or
blossom.

The ways that organisms respond in artificial lab conditions is nothing like
the way they behave in the field.  So, how predictive can lab trials be?

Now, in the case of trying to detect whether Xanthomonas is present before or
after application of compost tea, that's a different story.  We know the
conditions that allow Xanthomonas to grow on plates,  And in this instance,
plate counts can be useful at detecting whether the tea has reduced the
disease-causing organisms.

I think I made the usefulness of plate counts for that sort of approach clear
in my previous post.  But using plate counts to assess diversity?  No way.

Elaine Ingham