I just got word from BMC Genomics that my most recent paper has just been published (in provisional form; we still have not seen the edited proofs). In this paper (1), which I have co-authored with Anders Blomberg, Magnus Alm Rosenblad and Mikael Molin, we utilize metagenomic data from the GOS-expedition (2) together with fully sequenced bacterial genomes to show that:
- Detoxification genes in general are underrepresented in marine planktonic bacteria
- Surprisingly, the detoxification that show a differential distribution are more abundant in open ocean water than closer to the coast
- Peroxidases and peroxiredoxins seem to be the main line of defense against oxidative stress for bacteria in the marine milieu, rather than e.g. catalases
- The abundance of detoxification genes does not seem to increase with estimated pollution.
From this we conclude that other selective pressures than pollution likely play the largest role in shaping marine planktonic bacterial communities, such as for example nutrient limitations. This suggests substantial streamlining of gene copy number and genome sizes, in line with observations made in previous studies (3). Along the same lines, our findings indicate that the majority of marine bacteria would have a low capacity to adapt to increased pollution, which is relevant as large amounts of human pollutants and waste end up in the oceans every year. The study exemplifies the use of metagenomics data in ecotoxicology, and how we can examine anthropogenic consequences on life in the sea using approaches derived from genomics. You can read the paper in its entirety here.
- Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A: Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities. BMC Genomics. Volume 15, Issue 749 (2014). doi: 10.1186/1471-2164-15-749 [Paper link]
- Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, Van Belle C, Chandonia J-M, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, et al: The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biology. 5:e16 (2007).
- Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, Johnson J, Montgomery R, Ferriera S, Beeson KY, Williamson SJ, Tovchigrechko A, Allen AE, Zeigler LA, Sutton G, Eisenstadt E, Rogers Y-H, Friedman R, Frazier M, Venter JC: Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature. 468:60–66 (2010).
For those of you who are not already fed up with my writings on biology stuff on the web site, two opportunities to hear me talk in real life has popped up in May. The first is already on May 2nd, on the Open Day in Life Sciences, arranged by the Science Faculty at the University of Gothenburg. I will talk about the search for detoxification systems in metagenomic sequence data (from a collections point of view, as that is the theme for the day). There will also be an opportunity be guided in the herbarium and the botanical garden, plus having lunch and an optional after-work drink at Botaniska Paviljongen. But hurry, last day of admission is tomorrow! Register here.
The second opportunity will be at the SocBiN-2011 bioinformatics conference in Helsinki, on the 12th of May. I will present in the session called “Bioinformatics of Metagenomics”, and talk about a software tool for rRNA classification. I really look forward to this Bioinformatics conference, there are a number of highly prominent and interesting speakers, and I have heard that Helsinki in May is very beautiful. Besides, I am going there with extremely nice people, adding up to potentially being the best biology venue I will attend this spring.