Processing rocks for microbiology sampling

In today's blog, I'll walk you through my sampling process- I realized I've shown some of the experimental methodology I use out here, but nothing about how I get to that point.  That's what I'll cover here.

In the teaser image, you see me waiting for a sample in the core splitting room.  I'm looking through the core liner at the rock samples retrieved in this core.  This room is where the sample goes immediately after recovery on the catwalk, and when I find a piece I like, I collect it on a sheet of pre-combusted aluminum foil (baked at 400 degrees Celcius for three hours to kill any microbes and leave the foil sterile) and bring it downstairs.  Then I wash it three times with sterile filtered seawater in a fresh ziplock bag and begin hacking away! 

Above, you see what that sample looks like before I begin breaking it open.  This one was pretty small, it's 6 cm (~2.4 inches) across.  The box you see is steel, and the box and chisel are flame sterilized before use to avoid contamination.

Above you see me with a hammer and chisel, trying to extract chips from the interior of the whole round core sample.  After I get some large chunks from the interior (I want to avoid sampling the outside of the rock, which is in contact with the drill fluid and possibly contaminated), I transfer them to a mortar and pestle (also flame sterilized) to grind them into smaller pieces:

Here's what that looks like when I'm done, the rock chips are now small enough to work with.  For reference, the width across the circle is 9 cm (3.5 inches), so those smaller pieces are <1 cm.

I take these rock chips and put them into tubes and freeze them for DNA analysis (molecular biology) following the cruise.  I typically try to collect a few of these tubes to be sure there is enough material to work with.  Those tubes look like this:

Ok, maybe that's not so exciting, but it's part of the process.  I also collect some rock chips in the same tubes and add formaldehyde to preserve cells for cell counts.  And then there's the larger chunks of rock that I place to the side for analysis of in situ stable isotopes.  Note that this is different from the stable isotope addition incubations I discussed a few posts ago, where I am adding stable isotopes and measuring how quickly they are taken up.  With these samples, I look at stable isotope levels present on the rock when it was collected to tell me about microbial metabolisms on the rocks (but not rates).  Those samples go in a special bag that i seal in the anaerobic chamber (remember from the blog about culturing) and keep in the refrigerator.  It looks like this:

Finally, here's a view of the inside of the rock box after I finished processing this sample.  I showed that sample who's boss!

I'll point out here that this rock may not be what you were expecting basalt to look like.  It's not!  This sample was a volcanic sandstone, which has an orangish color to it, and it is somewhat soft (especially compared to basalt).  Basalt looks dark grey and is very hard.

I hope that was clear, this is my routine a few times a day out here.  Hitting those rocks sure is fun.  Until next time! 

Comments

Sterilization

Naturally, sterilization is important to any project. However, I notice a severe lack of any lab coat or pulling your long hair back to prevent contamination. What gives?

Hi, thanks for your comment.

Hi, thanks for your comment. I've been pretty lucky with my work so far to not contaminate my samples with hair or skin (based on previous results from rock and water sampling during my career), but a lab coat is not a bad idea. My hair isn't long enough to tie back currently, despite two months of growth during this cruise, but a hat may be useful. Since I haven't had problems before, I think these samples should be OK as well, but more caution against contamination does not hurt.