Dueling microbial diversity talks at #UCDavis on May 2 #symbioses #microbiology

Here is a storification of the dueling microbial diversity talks that happened at UC Davis on Wednesday May 2.

Nice #openaccess review on the ecology of chemosynthetic symbioses from @chicaScientific & Guus Roeselers

Figure 1 from 10.1007/s00253-011-3819-9. Sediment cross section 

exposing the characteristic Y-shaped burrow dug by S. velum. 

Positioning itself at the triple junction of the Y, the bivalve alternates

 between actively pumping oxygenated water from the upper arms of

 the burrow through the mantle cavity and across the gills and 

accessing reduced sulfur compounds diffusing up from the anoxic 

zones below and pumped through a ventral incurrent opening in the 

mantle. Scale bar equals 2.5 cm

For those who do not know, I got my first taste of microbiology research when I was an undergrad at Harvard and I did my senior/honors research project in the lab of Colleen Cavanaugh. Colleen studied (and in fact still studies) symbioses between invertebrates and chemosynthetic bacteria. The bacteria basically allow these invertebrates to function like plants in many ways. Some of these invertebrates (like the giant tube worms in hydrothermal vents) have lost their mouths and digestive systems and basically live by bringing in high energy chemicals for their symbionts which then make sugars, vitamins, amino acids and other goodies for the host.

Anyway - I am still very interested in these symbioses and have published a few papers on the topic here and there. All that lead in is to simply point everyone out there to a nice new Open Access review paper by Guus Roeselers and Irene Newton: On the evolutionary ecology of symbioses between chemosynthetic bacteria and bivalves. When I first saw the reference in the "Applied Microbiology and Biotechnology" journal I was worried I would not have access to it, but I clicked on the link and discovered it was published using Springer's version of Open Access. Yippee.  The article is worth a look.

Roeselers, G., & Newton, I. (2012). On the evolutionary ecology of symbioses between chemosynthetic bacteria and bivalves Applied Microbiology and Biotechnology, 94 (1), 1-10 DOI: 10.1007/s00253-011-3819-9

Hydrogen as a fuel? No this is not about cars, this is about animals and their symbionts in the deep sea

As many of you know, I generally avoid writing about non open access publications here.  But occasionally I make exceptions.  And I am making one today.  There is a wicked cool paper out in Nature today.  Entitled "Hydrogen is an energy source for hydrothermal vent symbioses" comes from Nicole Dubilier, Jillian Petersen and others.  It is about my favorite ecosystem(s) on the planet - hydrothermal vents.  I became interested in these vents in 1989 when I met Colleen Cavanaugh who at the time was a Junior Fellow at Harvard.  She told me about her work on bacteria that live inside tubeworms, clams and other creatures in the deep sea that are key to the lives of these animals.  The bacteria are chemosynthetic (i.e., they use the energy of chemicals to drive carbon fixation).  The animals have either no digestive systems or very degenerate ones and the bacteria function much like chloroplasts do for plants.  The bacteria basically make everything for their hosts while the hosts collect energy (chemicals in this case) and oxygen and CO2 for the microbes.

After hearing Colleen tell me about her work on these symbioses and how at the time nobody knew much about the symbionts, I joined her new lab at Harvard (she was just appointed as a junior professor) and worked in her lab in my Senior year and after graduating (and ended up publishing my first paper on symbionts of a clam Solemya velum).  I have been captivated by symbioses ever since.  So much so that many years later I worked with Colleen, Irene Netwon, Tanya Woyke, Dongying Wu and others to sequence and analyze the first genome of any of the chemosynthetic symbiotic bacteria.

Anyway - enough about me.  Prior to this new work, all of the symbioses in the deep sea had been found to involve either H2S (or related S compounds) or methane as energy sources.  What is completely fascinating about the new work is that they show here that H2 can also serve as an energy source for chemosynthetic symbioses.  From the abstract:

The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.

I am personally hoping that the authors post PDFs of the paper somewhere for everyone to read.  I will post a link if they do.

I note - there is also a very accessible News and Views written about this paper.  The News and Views is written by Victoria Orphan and Tori Hoehler and is entitled "Hydrogen for dinner."  I particularly like the last paragraph:

Petersen and colleagues’ work exemplifies the technology-driven revolution that is occur- ring in the biological sciences. The continuous development of ever more powerful and spe- cific molecular tools allows taxonomic identity and gene content to be linked to metabolic potential and activity, and to be visualized in context. As these techniques converge with new instrumentation that allows the in situ characterization of physicochemical parameters — even in environments as remote and extreme as hydrothermal vents — biologists are freed from their reliance on model organisms in artificial surroundings. Now, more than ever, our understanding of biology can be placed in the correct environmental and ecological context, enabling the discovery of previously unknown activities that support life. 

Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R, Hourdez S, Girguis PR, Wankel SD, Barbe V, Pelletier E, Fink D, Borowski C, Bach W, & Dubilier N (2011). Hydrogen is an energy source for hydrothermal vent symbioses. Nature, 476 (7359), 176-80 PMID: 21833083

Selfish DNA, symbionts and parasites - some quick links

I was at a committee meeting yesterday for a great PhD student here at UC Davis, Michael Hornsby and the topic of selfish DNA came up.  After his meeting we sat down and looked for some new papers and review papers on the topic.  I just thought it might be of value to share some of these here:

• The Myth … of the Myth of Junk DNA (blog post by John Farrell)
• A formal theory of the selfish gene
• Capturing the superorganism: a formal theory of group adaptation.
• Bacterial toxin-antitoxin systems: more than selfish entities?
• Genomic islands: tools of bacterial horizontal gene transfer and evolution.
• A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution
• What traits are carried on mobile genetic elements, and why?

We also discussed briefly the evolution of mutualists and parasites and here are a few papers that came up:

• Genomics and evolution of heritable bacterial symbionts.
• From parasite to mutualist: rapid evolution of Wolbachia in natural populations of Drosophila.

If anyone knows of any other good recent papers or blog posts about selfish DNA or mutualists vs. parasites please post them here.  Thanks