Introducing Nitrosocaldus

August 3, 2011

Since I started this blog with a brief introduction of myself, I figured I’d briefly introduce our study organism, Nitrosocaldus yellowstonii.

Our study organism is a thermophilic ammonia oxidizing archaea isolated from a hot spring in Yellowstone National Park. Since its cultivation in 2008, we have kept it continuously in culture. Every seven to ten days we take an aliquot of the culture and “passage” it into fresh media. While it sounds straightforward, there are a few factors to consider when growing these organisms. Transfer too late and you run the risk of passaging dead cells; too soon and you risk passaging a fraction of the culture with no cells.

Heart Lake region - Home sweet home

In addition to Nitrosocaldus, our culture contains a few other bacteria. This paper goes into further detail about the bacteria in our culture. I am frequently asked by other scientists how we conduct experiments when our culture is mixed. The bacteria represent <10% of the total population. Despite the heterogeneity, Nitrosocaldus is the dominant organism in our culture. While several have attempted to remove or kill the bacteria, it appears that Nitrosocaldus can’t survive without the bacteria. This has left us all wondering – what could our archaea possibly need from these bacteria?

Me diligently preparing their feed. Those red and green gas tanks in the background contain the nitrogen/carbon dioxide/oxygen gas mixture.

Nitrosocaldus is kept in gas-tight glass tubes that are filled with a proprietary blend of  UV treated water, vitamins, and salts. They prefer to munch on dissolved carbon dioxide present in the water (we add research-grade baking soda) and seem to hate organic carbon. Unlike atmospheric air (78% nitrogen, 21% oxygen, 1% argon) these archaea prefer to respire a mixture of gas that consists of 70% nitrogen, 20% carbon dioxide, and 10% oxygen. Once prepared, the cells are transferred and incubated at 72 C. Their optimal growth temperature (the temperature at which they will divide the fastest) is supposedly higher, but it’s difficult enough trying to handle these bottles at 72 C.  According to my lab mates, the optimal growth temperature is actually lower. If they grow better at lower temperatures, why are we growing them at a higher temperature?! That’s for me to know and you to think about.

I hope to discover a couple of things about this organism before I part ways with the lab:

  1. I’d like to know where ammonia oxidation is occurring in the cell. The annotated genome helped us determine models for how it occurs, but I am hoping to localize the proteins involved in ammonia oxidation.
  2. These ammonia oxidizing archaea are ubiquitous. They’ve been identified in exotic (sediment from the Gulf of Mexico), modest (greenhouse soil), and lowly (wastewater sewage) locales. Furthermore, Nitrosocaldus’ marine and soil brethren appear to greatly impact the global nitrogen cycle and I hope to learn a little more about how this particular class of archaea might collectively impact the environment.

Stay warm, kids!

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

w

Connecting to %s

%d bloggers like this: