[USCC] Vermicompost microbiology

[Allison L H Jack]

>Dear Dr. Byvoz,

Something interesting that has come out of previous work done in Dr. Eric 
Nelson's lab is that there may be emergent properties involved when 
considering compost mediated suppression of plant diseases. One of his 
studies compared a disease suppressive and a disease conducive compost. 
They isolated the seed-colonizing microbes at a critical time point when 
they had observed suppression to occur. Then they looked at how each 
individual isolate performed as a treatment protecting the seed from 
Pythium. They didn't exhaustively sample individuals from each community, 
but even this small study has interesting implications.

What they found was that the disease conducive compost (the one that did 
not protect the plants from disease) had many species that were suppressive 
when tested individually, while the disease suppressive compost did not 
have as many species that were individually suppressive. The amazing thing 
was that when they combined the isolates together and used them as a seed 
treatment, the community with the high proportion of individually 
suppressive isolates was NOT suppressive. [See table 4] So the bottom line 
is that "the whole is greater than the sum of the parts" which is a 
prevalent concept in ecology. The ecological interactions that are taking 
place between microbial species are so incredibly complex. There is a lot 
going on that we do not yet understand.

McKellar, M.E. and E.B. Nelson (2003) Compost-induced suppression of 
Pythium damping-off is mediated by fatty-acid-metabolizing seed-colonizing 
microbial communities. Applied and Environmental Microbiology, 69(1): p. 
452-460.

The implication of this and other findings is that although we are able 
measure total numbers and possibly activity of known "beneficial" and 
"pathogenic" microorganisms in compost, it may not actually tell us 
anything about how that compost will perform with respect to disease 
suppression. Merely the presence or absence of certain species does not 
always correlate with suppression.

I'm familiar with your work on Actinomycetes and I agree that they are 
potentially major players in disease suppression because of their 
antibiotic capability. In this same study however, they found 
actinobacteria present on the seed surface, but they were not implicated in 
the actual suppression and no inhibitory substances like antibiotics were 
found. Instead a group of microbes capable of metabolizing fatty acids was 
most likely responsible for the suppression. With this important chemical 
signal degraded, Pythium sporangia never germinated, and were unable to 
infect the seeds. Pythium infections happen so quickly (within 2 hours) 
that it is unlikely the actinobacteria would have time to colonize a 
germinating seed and switch their metabolism over to the production of 
antibiotics, which is common in later stages of growth.

So it is most likely that there are different complex mechanisms involved 
for specific pathogens. I believe that scientists are still a long way off 
from being able to make sound predictions of compost quality with relation 
to disease suppression because we don't know enough about how it works. 
Even with all the molecular methods we have available, we still need to 
know what we're looking for and have sound data linking it to the function 
we want to predict. I know as an industry we need to have some working 
estimates of compost quality to use now, but I think we should also focus 
some energy on uncovering the exact mechanisms so we can develop better 
predictive tools in the future.

I look forward to hearing more comments on this topic :-).

Take care,
Allison

p.s. I'll send the pdfs to Dr. Byvoz individually, and if anyone else is 
interested in taking a look at them, let me know and I can send them out.



>Thinking about standardization of vermicompost properties, I mean those
>microbiological parameters that correlate with its fertility and suppressive
>activity. I partially agree with those people who consider presence (and
>activity) of just “beneficial” and “harmful” microorganisms to be 
>the only
>useful properties to measure.
>
>
>
>However, we need to know who are “beneficial” and who are 
>“harmful”? With
>the harmful ones is more or less clear. These are phytopathogenic fungi and
>bacteria.
>
>
>
> >From our experience, vermicomposts (just two samples we have studied)
>contain high abundance of the fungus Aspergillus flavus and other A. spp.,
>which are known to be phytotoxic. However, we have many other species of
>fungi that are potentially harmful. Using luminescent microscope, we found
>around 1000000 spores/g (!) of fungi in vermicompost (45% moisture) made of
>cow manure, but practically no mycelium. Who are they? What will happen to
>these spores when they come to soil?
>
>
>
>To isolate and identify them sometimes we need specific methods and
>experience. Here we can use both dilution plate and molecular methods. The
>latter I think is more preferable, but requires equipment and experience of
>the personal. Using molecular technique, we can follow the population
>dynamics of those microorganisms that are potentially important for
>vermicomposts.
>
>
>
>Beneficial microorganisms are much less clear. Growth promoting or
>antagonistic microbes? How can we follow them?
>
>
>
>Again form our experience, vermicomposting process promotes actinomycetes to
>grow. Spores of some actinomycetes can proliferate during passage through
>the earthworm digestive tract (our works in 90ths). We found more
>actinomycete mycelium in vermicasts comparing to excrement and in
>vermicompost vs. food substrate (Byzov et al., 1995). Actinomycetes are
>known as producers of antibiotics. May be this is an important parameter?
>
>
>
>Therefore, we need to find a set of such SOIL microorganisms that could be
>indicators of bad and good quality of vermicomposts. May be some of them can
>be eliminated or introduced to compost to improve its quality. But, it is a
>labor and time-consuming work.
>
>
>
>Integral parameters (which are easier to measure) such as BIOLOG, Degens,
>Harris’ catabolic diversity and others, could be useful too, but we have to
>find how they correlate with the quality of product.
>
>
>
>Regards,
>
>
>
>Boris
>
>

**************************************************************************************
Allison L H Jack
Graduate Student
Department of Plant Pathology
Cornell University
335 Plant Science
Ithaca, NY 14850
607.273.5762
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