permaculture

[Alia Tsang <alia@dietrick.org>]

On Wed, Mar 6, 2013 at 12:20 AM, Douglas Hinds <cedecor@gmx.net> wrote:

> On 03/05/2013 01:39 PM, John D'hondt wrote:
> > These days there are machines that automatically analyse DNA of the
> > gazillions of micro organisms in soil. They spew out a list of all the
> > different species names with relative abundance. I know they are being
> used
> > in Australian universities.
>
> If you'll tell me the name of a university using them I'll contact them,
> although I'm not sure what this signifies. For one thing, Elaine has
> stated that most of the soil's microorganisms haven't even been
> identified yet and if that is the case, the substances they produce, the
> activity of each and the environmental conditions required to produce
> them is information that no one is even looking for, much less have on
> hand, so if the machines you mentioned ARE actually able to identify the
> organisms contained in a given soil same, that wont tell us much able
> who they are and what they do, but it would be a start.
>
>  From there, even if the genome of a given organism has been defined
> (which have to be true in order to identify it), that doesn't tell us
> what substances they produce, because a given genome can code for a high
> number of proteins, depending on the environmental conditions, and no
> one is developing a data base to define those relationships in a
> methodical manner, AFAIK.
>
>
I believe you can use similar sequencing methods to get the
"transcriptome," the part of the genome that's being transcribed when you
take the sample. But the samples have to be handled very particularly (i.e.
frozen immediately in liquid nitrogen), because the microbial activity
changes very quickly when you dig it up. This would be looking at the RNA,
rather than the DNA.

Another thing some researchers have been doing is describing microbial
communities in terms of functional genes (genes for various enzymes, i.e.
nitrogen-fixing genes, nitrifying/denitrifying genes, genes to break down
various food sources) rather than by "species" or the equivalent. This has
the same issues with not knowing which of these genes are actually being
used, but can tell you about the potential activity of the microbial
community.

Noah Fierer spoke at my university recently, the group he is part of is
doing a lot of metagenomics stuff. Here's an example of the kind of work
they're doing in soils:
http://www.pnas.org/content/early/2012/12/13/1215210110.abstract

Alia