Friday, October 27, 2006

Source Tracking is Hot!

It must have been good enough, because it convinced them to scrape 2500 euros off of wherever they could scrape it from. “But we need some sexy language,” my adviser informs me. “For scientists, this is good, but non-scientists need to know why microbial source tracking is sexy.” Huh? Sexy?

I had a meeting with my advisers on Thursday where I presented the basics of microbial source tracking (MST) and my proposed study design. It was a good idea to have this meeting because I’ve been doing A LOT of learning, A LOT of literature reviewing, and A LOT of meeting with people who know more than me on such topics as MST and molecular tools. Molecular tools are beginning to govern the environmental engineering field. But the techniques are vast and the methods are complicated. For example, you can be an expert in environmental engineering and know very little about MST.

If you don’t want to read the long winded version, I’ll skip to the punch-line. MST is hot because:

  • It’s fast! It can prevent people from getting sick, or even dieing of waterborne diseases, by letting them know their water is contaminated much quicker than ever before.
  • It’s informative! In addition to finding out that the water is contaminated, we may be able to find out who is responsible and how big of a risk it is.
  • The technology is getting easier and quicker and will be automatable for long term monitoring in places like drinking water treatment plants or swimming beaches.
  • The same protocols may be applicable from Lilongwe to Santiago, that’s one of the things I’m testing (though not those two particular locations).

If you would like to learn some new cocktail party words and some science, keep on reading.

I may have read more papers during my first month in Tampere than I read for my entire thesis. There’s nothing to show it-- no data, no concrete scientific conclusions, no eloquently crafted proposals-- unless I present what I’ve learned to someone else. Thus the adviser meeting.

Tuula is right. Microbial Source Tracking is sexy. If our drinking or swimming water is contaminated, we’ve never been able to tell who is responsible, what type of animal the contamination came from, or where we need to focus our management efforts. With microbial source tracking, this is all possible. One of the biggest challenges of living with so many people on earth is keeping human and animal waste separate from drinking water. It’s an enormous industry for lucky people who have municipalities with drinking and wastewater infrastructure. However, it’s an enormous risk for many rural areas, particularly in less developed nations, that do not have this infrastructure.

Historically, we have monitored water contamination by growing indicator organisms (E. coli, fecal coliform, Enterococci, etc.) from drinking water samples. This tells us if the water is contaminated. It does not tell us what to do about it or where the contamination came from. The options have been either to guess where the contamination came from, or to post signs warning people not to swim if contaminant levels are high. Monitoring indicator organisms is relatively easy, but takes two days (of potentially exposing swimmers to waterborne pathogens) to get the results.

The basic concept of MST is to match microbes from a polluted site to their animal or human hosts. To understand MST, you have to know that microbes are everywhere, on your hands, in your mouth, in the air, on surfaces, and most importantly all over your digestive tract. Most of them don’t cause us problems, and many of them help us. MST capitalizes on microbes to trace contamination to its source. Matching genotypic or phenotypic microbial profiles suggests a link between the origin (septic tank) and contamination site (reservoir or swimming beach). It’s important in watershed management and risk assessment. Microbial source tracking has the potential to be fast. It can also be automated for utilities, once we work out the kinks. We’ll know within a few hours if our water is contaminated and if we should contain the septic tank across the street or the upstream factory farm.

In my study on Finnish well water, I’ll be looking for either cow or human fecal contamination (or both). I’ll use Bacteroides, a type of bacteria found in human and animal digestive systems. Bacteroides is a good MST indicator because:

  1. it cannot grow in the presence of oxygen (it cannot grow in the environment, only in digestive systems)
  2. it is abundant in human and animal digestive tracts
  3. it only grows in rumen, digestive tracts, and body cavities (not on rocks, on bugs, in the soil, etc.—if it’s in the environment, it came from something with a digestive tract)
  4. its DNA varies consistently, depending on the host (animal) in which it resides

I’m using PCR to test for the presence of a DNA sequence in Bacteroides. PCR is a way of amplifying DNA sequences to concentrations that are high enough to visualize using agarose gel electrophoresis. From reading papers on other MST projects, I’ve found some regions of Bacteroides DNA that are found only in humans, and some other regions that are found only in cows. These are the regions that I will amplify.

If the cow specific regions amplify, dairy farms are a likely source. If the human regions amplify, local septic tanks are a likely source. If nothing amplifies, either the well is not contaminated or there’s some other source besides cows or humans (I’ll pick wells that do not have any other likely sources, but nothing is ever 100% certain in science).


Ralph Bodenner said...

Cool project. What is slow about the process as it is implemented today?

The "Post a comment" link is really hard to see, btw.

laurita said...

Hi Ralph.
Today we use indicator organisms that require culturing, or growing. Culturing requires at least processing time plus 24 hours and a possible second 24 hours for a verification step. Many molecular techniques don't require culturing (like the one I'm using) because we can directly detect the DNA of the organisms in the water. It takes me all day anyway, but it's possible to automate the process more that I do.

laurita said...

I haven't given up on the comments link, but I'm having tech difficulties. It's easy to see the post-a-comment link on the main page, but you really can't see it on the individual posts page.