I’ve fallen very far behind on my one-time goal of writing a blog post for each new lab publication. Seeking redemption via a paper out today by former Bowman Lab postdoc Avishek Dutta, now an assistant professor at UGA. His paper, Depth drives the distribution of microbial ecological functions in the coastal western Antarctic Peninsula, is the first study (we believe) to employ high throughput shotgun metagenomics to evaluate the ecological functions of bacteria and archaea across multiple depths and seasons in the Antarctic marine system. It builds on some wonderful work by Tom Delmont in the Amundsen Sea and Joseph Grzymski in the same region as this study.
Avishek selected 48 historic samples collected by our group in collaboration with the Palmer Long Term Ecological Research study for shotgun metagenomic analysis. Although this is not a particularly large sample set by today’s standards, using Avishek’s iMAGine pipeline it was nonetheless sufficient to yield 2,940 bins (collections of contigs that might be from similar genomes) and 137 dereplicated, high quality bins that we considered metagenome assembled genomes (MAGs). MAGs are not perfect constructs; they’re incomplete and likely composites of different, highly similar genomes. Nonetheless, standard genomic tools and analyses can be applied to them to try and infer likely metabolisms and other characteristics.
You really have to stare at the above figure for a while to start to wrap your head around the details, but the main points are: 1) There’s a lot of potential for carbohydrate degradation potential, as we might expect for bacteria and archaea that respond to phytoplankton blooms. 2) There’s a lot of dark carbon fixation potential, and this is often combined with different heterotrophic metabolisms to produce a prokaryotic mixotrophic functional type (i.e. an organism that can switch between autotrophic and heterotrophic metabolisms). This is one of those things that we assume must be fairly common without actually observing it. Right now there is a lot of discussion in various communities about the role of mixotrophic protists in marine foodwebs and the carbon cycle, but mixotrophic bacteria and archaea get surprisingly little attention.
