Sunfish!

I'd never heard of the Ocean Sunfish before; we spotted this one on a sampling expedition this week. I'm not sure which species this is, I suspect it's a Mola Mola but feel free to correct me if I'm wrong. here are a few photos, and check out this
website for more info:
http://www.oceansunfish.org

The fish is lying on its side in the photo above, and from the tail fin shape I think it was a Mola mola (Roundtailed or Common mola).

Beautiful bacteria!

This is an image of a gorgeous sulfurous spring at one of my field sites, note the purple sulfur (unconfirmed, possibly purple non-sulfur) bacteria in the center. The image is about 10 cm widthwise.

I used an inoculum of these bacteria for a Winogradsky column I started a month ago, they are growing beautifully - stay tuned for more photos!

Taming the fastidious organism

Biogeomicro term of the day: Fastidious organism

"An organism that has complex nutritional requirements"
ref: http://www.biology-online.org/dictionary/Fastidious_organism

Here is an open access paper using this term:
Degnan AJ, Sonzogni WC & Standridge JH (2003) Development of a Plating Medium for Selection of Helicobacter pylori from Water Samples. Appl. Environ. Microbiol. 69(5): 2914-2918
http://aem.asm.org/cgi/reprint/69/5/2914


Though I don't study human pathogens, I do work with organisms that are difficult to isolate from their more persistent "weedy" companions. The following quote from this paper seemed to sum up the challenge particularly well:

developing an acceptable selective medium for H. pylori in water presented the classical microbiological problem of finding a medium that is nutritionally rich enough to resuscitate and grow a fastidious organism while managing to inhibit the growth of all the other organisms found in water samples.

This sentence really sums up the focus of my quest for this week!

virtual journal club - vocab in context

Ok, I have a plan!

I'm going to post various geomicrobiological vocabulary words to this blog and to my Twitter account. First to Twitter, then compiled once a week to this blog. With each definition I'd post a link to an open-access journal article where the word is used in context.

So for the scientists who follow this blog (hopefully a few eventually!) it could function as a sort of virtual bite-sized journal club. Don't worry, I won't ask you to make any presentations!

For the non-scientists you'll get some insight into what sort of work is being done out there in geomicrobiology and related fields - the kind of work that may not be sexy enough to get into science news but is still exciting (IMHO!). Science literature is pretty heavy stuff to the uninitiated of course, so here is some advice to get you started: just read the abstract, the intro, and the conclusion. They are generally written to be fairly comprehensible to the average scientist who isn't an expert in the specific topic of the paper. So you might have a fighting chance of understanding it if you read those bits, and you won't get bogged down in the minutiae of the methods and results sections. Unless you want to of course!

If anyone wants to post back references to peer-reviewed papers they'd like to highlight on the topics I cover, you are welcome to post them in the comments on my blog. I'm going to stick with journals that provide public access so anyone looking at the blog can see the articles I post. I would recommend you do the same but don't let it hold you back from highlighting a good one if you are itching to share it.

A few (oversimplified) definitions before we get started:

geomicrobiology (and biogeochemistry): science occurring at the interface of the fields of biology, microbiology, geology, and geochemistry.

Journal club: a group of students and/or scientists getting together to discuss papers from the peer-reviewed literature (scientific journals). The point is to learn more about new scientific discoveries, and also to critically evaluate other scientists' work.

Bio-Geo-Micro-Blog!

I am creating this blog as a companion page to my twitter account of the same name, as a place where I can expound a bit more if I don't have enough space on twitter, and for posting pictures. It's an experiment. :-)