I'm reopening this post. I don't think the original question can be answered directly, but as a "Forum" post it brings up some interesting and important topics in the bioinformatics field.
I think plant biotech and metagenomics both have huge potential in the research and commercial venues.
With plants, there's always going to be a need to engineer plants to be more drought-tolerant, be more weed resistant, and produce a more nutritious and substantial product with more yield. There are countless plant genomes to sequence, and orders of magnitude more questions to answer with those data.
Metagenomics is another big thing. There are so many stories which can be told by simply swabbing a surface and seeing what organisms are represented, along with their relative quantities. I've been doing a lot of work in that area and believe me, if you want to get pretty much anyone's attention, show them some of the patterns you see in metagenomics data related to a familiar location. Once the science behind it gets a little more reliable, there are going to be hundreds of interesting stories coming out in that area.
Like other posters mentioned, it's impossible to know which one will have better job opportunities, but if that's your basis for choosing a Ph.D. you're probably gonna have a miserable time pursuing it.
This question is very subjective and the question cannot be answered because it depends on so many factors. I think what we can say in general is that we cannot tell you what to do with your life. Mostly, your job opportunities depend on your skills and interest in the field. For these reasons we should rather not answer such questions.
also, the fluctuations in job opportunities are a function of time and unpredictable.
Hello anokimchen!
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in the US the plant people end up bouncing around between the same major plant companies - Monsanto, Pioneer, Syngenta, etc. It's a much smaller community than the biomedical side, although I will say for some reason the plant people are much more pleasant to work with than scientists at hospitals