I’m not a microbial ecologist, though I’ve studied the field a bit. I was invited to speak at the International Symposium on Microbial Ecology in the climate change session, to talk about my work on the Paleocene/Eocene Thermal Maximum and what magnetofossils indicate about changing microbial ecology during that ancient global warming event.
The big new breakthrough since I last took a microbial ecology class four years ago seems to be a technique known as “tag sequencing”, in which researchers target short, highly variable sub-sequences of small sub unit RNA. Rather than sequencing the whole SSU RNA (the gene sequencing traditionally used for identifying organisms), which is typically a couple thousand base pairs long, they focus on regions of a hundred base pairs or so that are subject to relatively rapid evolutionary change. The shorter sequence length allows sequences from many more organisms to be sampled, which means that environmental studies capture a more accurate profile of all the microbes in a community.
In a session on the human microbiome, Rob Knight presented a comparison of tag sequencing analyses from a variety of environments. It turns out that the first order division in microbial community composition is between freshwater and saltwater environments. Invertebrate gut microbiota resembles those of the environment they live in; vertebrate gut microbiota resemble neither freshwater or saltwater environments. Among the vertebrate gut microbiota, the second order division of diversity is based upon diet: carnivores, omnivores, hind-gut herbivores, and fore-gut herbivores all fall into different classes. Humans have fairly typical omnivore gut microbiota.
But… that’s the higher order pattern of diversity. When looked at in detail, there’s quite a bit of variability in microbes between different individuals. They are very few specific taxa that are common to all human gut microbiota, and it’s similar for the rest of the human microbiome. Fun fact: on average, less than 20% of the taxa present in the skin microbiome of your right hand are present in the skin microbiome of your left hand.
On another topic, a number of people talked about the interaction between methane oxidation and nitrogen cycling in soil. Apparently, fertilizing soil with ammonium causes some bacteria to shift from oxidizing methane to oxidizing ammonium, thereby increasing the flux of methane into the atmosphere. Nobody presented estimates as to how significant this effect is globally, but it’s something worth thinking about.
Something else I learned: the word “Eocene” in a title apparently frightens audiences away. It shouldn’t be this way. The Eocene needs to become as much a popular concept as the Jurassic, and a representing of the sort of world that can develop under global warming. Eocene Park, anybody?