I, For One, Welcome Our Gammaproteobacterial Arsenic-Using Overlords: Why Old School Microbiology Still Matter

I don’t see the need to redescribe the recent paper about the discovery of bacteria that can might replace, in extremis, phosphorus with arsenic, which was overhyped by NASA, was poorly covered by most journalists, and which has compromising methodological problems (for good coverage, read here, here, and here; and snark). But what the paper does demonstrate is the importance of culturing microorganisms, knowledge about which is becoming rapidly lost by younger scientists.

With the advent of DNA-based, culture-independent techniques, where we can look at the DNA and RNA of microbes without actually having to grow any bacteria–the most famous example of this is the Human Microbiome Project–a lot of microbiology, especially microbial ecology, is conducting less culturing (growing) of microorganisms. Tthe inane mantra of ‘99.9% of bacteria can’t be cultured’ (if we’re stupid and lazy), hasn’t helped either. And the phenomenon of trainees ‘inheriting’ a bug/study system from their advisors has led to a technical specialization, where the academic progeny don’t know how to culture other organisms. Finally, isolating new organisms isn’t viewed as sexy by funding agencies*.
All of this has lead to a loss of expertise in all the tricks old school microbiologists use to isolate novel organisms. When I speak to older and crankier microbiologists (hard to believe, but true!), they constantly lament this. My personal, anecdotal observation is that many microbiologists would be unable to culture bacteria other than E. coli and a couple of other easy-to-grow bacteria.
But this paper, which obviously involved being able to grow the organism (otherwise the lab experiments couldn’t have been done), demonstrates the need for culturing organisms. That’s something we should emphasize when we train students and post-docs.
*One interesting area of cross-fertilization between genomics and traditional culturing is the use of single-cell culture techniques. Here, cells are individually isolated into separate microchambers (or droplets of emulsion oil), killed, and then using a technique analogous to PCR, their genomes are amplified and sequenced. This will be very useful in generating genomes for difficult-to-culture organisms.
Cited article: Wolfe-Simon et al, “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus” Science, 10.1126/science.1197258

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