Friday, May 26, 2017

Soil metaproteomics of the ground where truffles come from!

I could ramble about the little I actually know regarding metaproteomics for quite a while. And I'm going to get to next week! I'm not lacking in enthusiasm for this exciting new field, but I could definitely increase my knowledge-base.

The best part about metaproteomics papers is that you can learn SO MUCH about the environment, because the authors inevitably have to explain something like why, exactly, they are optimizing protein extraction techniques from this one patch of soil...

Case in point:

Before stumbling across this awesome open access paper, my complete and total knowledge of black truffles is that they are expensive, have a really unique smell and that you hunt them with pigs. This last tidbit of knowledge courtesy of TaleSpin.

Thanks to this paper, I know a lot more. The fungus(es?/i?) form(s) a commensal (sp?) relationship with a tree and a tree that will produce truffles will sometimes have a bare area around it. They call this area a brule (with some funny marks above the vowels I don't know how to reproduce).

These researchers set out to understand what is different about the brule compared to other places in the ground. In metaproteomics, you typically don't know what you're starting with. Here, they are taking samples of soil from the brule and from outside the brule and extracting all the proteins from the soil that they can. There may be thousands -- millions -- more?? different organisms in this soil sample -- bacteria, fungi, who knows?!?  And you do proteomics on it!

The biggest part of this paper is the optimized data processing methodology. They do what I would do -- when in doubt, FASP it! but first they dry the soil, pulverize it and do some chemistry stuff to it first:

What can you learn from proteomics on an unknown mixture of an unknown quantity of organisms? The tools and techniques at a data processing level are where they can make predictions of what fungi are present and in what relative amounts! On top of that there are a lot of proteins that are extremely well conserved among all life forms. They can find what molecular functions are the most represented -- and what they find that is a striking difference at the GO level between the soil inside and outside of the brule. Since cell organisms binding processes are massively over-represented within the area of interest, compared to the outside.

This is a sample of what their output looks like.

How do you translate this into biological relevance? You've got me! This is where you hand these results and writing back to the fun fungi guy to interpret, but at a surface level what seems interesting is that although there doesn't appear to be much life in the brule area -- at least not much vegetation - there is some serious metabolism happening in the soil! The micro-organisms are getting energy from somewhere and are hard at work.

They go much more in-depth and dissect individual GO processes here. They also previously did metagenomics on this soil and comparing the individual species (or..genus) to these results gives them more insight than I have the capacity to absorb.

This is just another cool paper showing where our tools and techniques can answer questions that I know I never thought about asking!

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