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  • From: "Lawrence F. London, Jr." <lflj@intrex.net>
  • To: permaculture <permaculture@lists.ibiblio.org>, Market Farming <marketfarming@lists.ibiblio.org>
  • Subject: [permaculture] Subject: Tests for microorganisms in soils.
  • Date: Sat, 11 Apr 2009 09:38:45 -0400

http://lists.ifas.ufl.edu/cgi-bin/wa.exe?A2=ind0904&L=sanet-mg&T=0&O=D&P=39448
Subject: Re: FW: [SANET-MG] Microorganism tests
From: jcummins <[log in to unmask]>
Reply-To: Sustainable Agriculture Network Discussion Group <[log in to
unmask]>, jcummins <[log in to unmask]>
Date: Sat, 11 Apr 2009 07:02:16 -0400

Hello Krista and all the others,
Just thought I might mention a looming technology such as the PhyloChip,
which targets 8741 bacterial and archaeal taxa, in the soil. The
microchip technology can be reasonably inexpensive once established. The
current chip is geared for bacteria but others have been developed to
include fungi and even protozoa and worms can be added on. That
approach was recently used to study composting to follow the soil
microbial community changes during the process. The fundamental
technology takes all the DNA in the soil then lays it out on a DNA chip
capable of identifying many thousands of individual species. I have
enclosed an abstract below showing how the system works. How long before
it is ready for use in the field at a reasonable price. I think that may
come within the next year or two. sincerely, joe cummins


ISME J. 2009 Mar;3(3):340-51. Epub 2008 Nov 20.
Environmental microarray analyses of Antarctic soil microbial communities.
Yergeau E, Schoondermark-Stolk SA, Brodie EL, Déjean S, DeSantis TZ,
Gonçalves O, Piceno YM, Andersen GL, Kowalchuk GA.

Netherlands Institute of Ecology (NIOO-KNAW), Centre for Terrestrial
Ecology, Heteren, The Netherlands.

Antarctic ecosystems are fascinating in their limited trophic
complexity, with decomposition and nutrient cycling functions being
dominated by microbial activities. Not only are Antarctic habitats
exposed to extreme environmental conditions, the Antarctic Peninsula is
also experiencing unequalled effects of global warming. Owing to their
uniqueness and the potential impact of global warming on these pristine
systems, there is considerable interest in determining the structure and
function of microbial communities in the Antarctic. We therefore
utilized a recently designed 16S rRNA gene microarray, the PhyloChip,
which targets 8741 bacterial and archaeal taxa, to interrogate microbial
communities inhabiting densely vegetated and bare fell-field soils along
a latitudinal gradient ranging from 51 degrees S (Falkland Islands) to
72 degrees S (Coal Nunatak). Results indicated a clear decrease in
diversity with increasing latitude, with the two southernmost sites
harboring the most distinct Bacterial and Archaeal communities. The
microarray approach proved more sensitive in detecting the breadth of
microbial diversity than polymerase chain reaction-based bacterial 16S
rRNA gene libraries of modest size ( approximately 190 clones per
library). Furthermore, the relative signal intensities summed for phyla
and families on the PhyloChip were significantly correlated with the
relative occurrence of these taxa in clone libraries. PhyloChip data
were also compared with functional gene microarray data obtained
earlier, highlighting numerous significant relationships and providing
evidence for a strong link between community composition and functional
gene distribution in Antarctic soils. Integration of these PhyloChip
data with other complementary methods provides an unprecedented
understanding of the microbial diversity and community structure of
terrestrial Antarctic habitats.



  • [permaculture] Subject: Tests for microorganisms in soils., Lawrence F. London, Jr., 04/11/2009

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