B.Y.A. Studios All we need is a cow...

1. Thermophiles are type of extremophile. Extremophile is absolutely an actual science word, it's just not very specific. It includes thermophiles, psychrophiles, acidophiles, alkalinophiles, chemophiles, and lots of other -philes.
2. I'm not looking for any type of thermophile at all. Right now at least, I'm just trying to estimate the number of thermophilic cells present in different soils.
3. There were some issues with funding and scheduling, so my only hot-springs soil has been refrigerated since 1988. I have soil from a couple of local parks, and soil from two compost heaps -- both of which were cold at the time of sampling, and were therefore inactive.
4. I haven't looked very closely at any of the organisms that grew. I grew a couple of fungi that I didn't bother to identify. There are these funky soil bacteria called actinomycetes that look a lot like fungal hyphae, and they were originally classified as fungi. There were a bunch of colonies that grew on the surface of my plates that formed (or collected, I can't say for sure) a fairly large volume of sticky fluid. Don't know what's in the fluid, but it could be something pretty cool, possibly antibiotics. There were a lot of colonies with pigmentation, mostly orange-reddish.
5. I never observed the microbes under high enough magnification to see the individual cells (which would have been 1000x, which is the oil immersion lens). I used a technique called dilution plating to get an estimate of the number of cells present in an amount of soil. You take 10g soil and shake it for 20 minutes in 90ml dH2O. That gives you a dilution of 10:1. You pour molten agar onto a plate with 1ml of diluted sample, mix it gently but thoroughly, let it solidify, then incubate it. You'll get a lot of colonies from that if your soil is any good, so you also perform a dilution series in which you plate multiple dilutions of your original sample (10:1, 100:1, 1000:1, 10000:1, 100000:1) and hope that that gives you a dilute enough sample that you don't overgrow your plates. Then you count the number of colonies formed after incubation, and assume that each colony was formed by a single original bacterial cell. Then you do a bit of math and end up with the number of cells in a gram of soil. It's not a terribly exciting method, but it gives good results that are easy to interpret and fairly accurate. The biggest problem is that if you do it properly, with a few duplicates at each dilution, you end up having to make a shitload of plates. Since I'm also doing 3 different temperatures, I ended up having to make 48 plates for each sample. The first time I did it it took me almost 5 hours. I subsequently figured out a few shortcuts and the rest of the samples only took ~2 hours to plate.
6. The work in Hawaii is completely unrelated to this. In Hawaii I'll be collecting samples for somebody else's project at Stanford. It would be very interesting though to test Hawaiian soil.
7. Yes, mostly industry. Some of the hydrocarbons are just straight out of crude oil, some are from processed gasoline, some are organic solvents used in chemical reactions. Most of them are carcinogenic to humans (or at least they are in California!). If you were to use these bacteria to clean up an oil spill or something, you would call it bioremediation. There's a lot of money being spent on this kind of research right now, because it's extraordinarily expensive and ineffective to clean up these kinds of chemicals with the current methods, which are mostly detergents.
8. I do have some data, but I'm not done processing it just yet. I think I'll wait until I'm completely done with the project, and just send you my entire paper. That would make a lot more sense than just raw data.

Keep the questions coming! Don't be afraid to ask me things that you think are obvious either.