Wow – ALVIN submarine has potential to be vector for species movement cc: @deepseanews

Well, it is (relatively) common knowledge that surface ships can serve as unintentional vectors for the movement of organisms via things like ballast water (see for example this recent post on Deep Sea News which discusses this in part).  And the ecological favor wreaked by such ship-based-transport can be immense.

A new paper, and news story, call attention to an analogous process that might occur with deep-sea submarines (see news story here: U.S. News – Deep-sea aliens hitched ride by submarine to pristine area).  The basic summary is – researchers using the deep sea sub ALVIN have discovered that, contrary to expectations, some organisms from the deep were able to survive the sub surfacing, being brought on board the mother ship, and then being sent back down to another site.  Some limpets apparently hung out in some tubing for a day and were then “sampled” by the sub at another site.  Apparently, nobody had thought this might be an issue because they had assumed that the surfacing and bringing on deck and cleaning of ALVIN would kill any organisms from one site before traversing to the next place.  Apparently not.

I note one comment – it seems reasonable to think that microbes might be hitching a ride on ALVIN and other submersibles too … which brings me back to the recent post on Deep Sea News I linked to above.  It is by Holly Bik, a post doc in my lab, and in it she discussed the possibility that microbes might be getting moved around by surface ships.  Well, it seems that submersibles should be looked at too ..

NPR Piece on Discovery of Hydrothermal Vent Oasis

It discusses the story of the discovery of the first hydrothermal vent oases back in 1977. I note this is near and dear to my heart. I worked as an undergraduate and then after graduating in Colleen Cavanaugh’s lab at Harvard on chemosynthetic symbioses. And then amazingly I got to go on the 2002 deep sea cruise celebrating the 25th anniversary of the discovery of the vents. On that cruise Rosebud (mentioned in this article) was discovered.
And I am still fascinating by the deep sea – (with Colleen Cavanaugh’s lab esp. Irene Newton and w/ Tanja Woyke via JGI we sequenced the first chemosynthetic symbiont genome a few years ago). Hat tip to Eileen Choffness for pointing this story out.

C-DEBI Research Support > Request for Research Proposals

Katrina Edwards on the Atlantis

I have always been fascinated by life in extreme places on the planet. And somehow I have managed to do projects on microbes from places like Antarctica, boiling hotsprings in Yellowstone and Kamchatka, acid pools, and more. The extremes are fascinating to me because they tell us a lot about the limits of life as well as indirectly about life in “normal” places.

And of course, I am not alone. Many many scientists are fascinated by life’s extremes. But not everyone ends up studying life in extreme environments of course. One reason for this is that many extreme environments that might be of interest are kind of hard to study. Consider the deep sea. Not so easy to do work there and just getting samples can be a massive undertaking.

Just imagine though. What if there were a way to “tag along” on an existing project studying life’s extremes at no cost to you or your grants? Even better what if there were a way to get extra funds to not just tag along on a project but to carry out detailed research at the same time?

Well, amazingly, there is such a chance right now. The C-DEBI “Center for Dark Energy Biosphere” project is calling for proposals. C-DEBI Research Support > Request for Research Proposals

They have money. They have drills. They have been and will continue to be collecting lots of samples from the bottom of the ocean and the crust below.  They are doing a bunch of microbiology (as well as other things). And they are calling for people out there to join them in various ways including;

And if you are interested they are heading out in a few days on a cruise to study the seafloor at “North Pond” a site in the bottom of the ocean on the Mid=Atlantic Ridge. For more information about this cruise see

I note – I was a visiting scientist for a few days at one of the C-DEBI meetings about evolution earlier this year. It was a great meeting – on Catalina Island – and I wrote a VERY long blog post about it: The Tree of Life: A “work” trip to Catalina Island: USC, Wrigley, C-DEBI, dark energy biosphere, Virgin Oceanic, Deep Five, & more. You can learn more about the C-DEBI project by reading that post.  And you can look at my pretty pictures below:

I note in addition, I am forever in debt to Katrina Edwards the PI of the C-DEBI project ever since she gave a frigging awesome tour to my kids of the Atlantis when it was docked in San Francisco

But regardless of the personal connections I have to C-DEBI, the project is very interesting and the fact that they are offering up funds to support “outsiders” who want to participate in the project in some way is great.

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

Why I am ashamed to have a paper in Science

So I just had a paper published in Science last week. In many ways, it has all the makings of one of those papers I should be really proud of. First, it represents a collaboration with my undergraduate advisor, Colleen Cavanaugh, the person who inspired me to go to graduate school and who got me interested in microorganisms, which I have worked on ever since (I published my first scientific paper on work I did in her lab). The paper is on one of the coolest biological systems on the planet – bacterial symbionts of deep sea animals that allow these animals to function much like plants (they use chemosynthesis in much the same way plants use photosynthesis). Studies of the deep sea and of chemosynthesis are important for understanding the origin and evolution of life, for understanding global carbon cycles, for understanding the rules by which symbioses evolve and much more. And on top of all of this, the paper reports the sequencing and analysis of the complete genome of one of these symbionts (that from the clam Calyptogena magnifica) – and one of my main areas of research is on the evolution of the genomes of symbionts. And, the genome was sequenced at the Joint Genome Institute, where I now have an Adjunct Position and am working with extensively. All sounds good right? And, I should be happy to get a paper in Science too, right?

Actually, in reality, I am not pleased with how this paper has turned out. This is really due to two things. First, my collaborators failed to keep me in the loop that the paper was accepted in Science. Thus I did not find out about the paper until I did a google search for some other reason and noticed this Deep-Sea News Blog which had a story, well, about the paper in Science. It would of course have been nice to know the paper was accepted and coming out. It would have been even better to have seen the page proofs, which might have given me the chance to catch some little and not so little mistakes (e.g., the paper claims that this species has the largest genome of any intracellular symbiont sequenced to date – which is unfortunately not true). Now, admittedly I was out sick for a while and maybe my collaborators just did not want to bother me with this information. More likely- people were just very busy – and this just slipped through the cracks.

But you know – it is a Science paper. I should be happy however it came into being right? Well, no. Completely and thoroughly wrong. You see, I do not support publishing things in Science. I object because Science is not an Open Access journal. I tried and tried to get Irene Newton the first author to submit this to another journal. But in the end, she did the brunt of the work, and thus she and her advisor, Colleen, got to pick the place. And in the time since Irene submitted the paper, I have become even more miltant against publishing in such non Open Access journals. Publishing in a non Open Access journal like Science make me feel icky in every way. In addition, by choosing to publish the paper there but not elsewhere, the field of deep sea symbionts may have been hurt rather than helped.

How could a Science paper hurt the field? Well, for one, Science with its page length obsession forced Irene to turn her enormous body of work on this genome into a single page paper with most of the detail cut out. I do not think a one page paper does justice to the interesting biology or to her work. A four page paper could have both educated people about the ecosystems in the deep sea, about intracellular symbionts in general, and about this symbiosis in particular. The deep sea is wildly interesting, and also at some risk from human activities. This paper could have been used to do more than just promote someone’s resume (which really is the only reason to publish a one page page in Science).

But of course, even more importantly, anyone without a subscription to Science, well, they can’t even read the paper. And AAAS gets to decide what happens to the text and figures in the future. So – count this as one of my papers I am not really proud of. I love that I helped my Undergrad. advisor and one of my favorite people in the world do this work. But by it not being in an Open Access journal, I have unfortunately contributed to a system that I think is bad for the world. And I just fell icky.

Some news stories and blogs are coming out on the paper:

Below I have embedded a video of a dissection of what I think was a deep sea Calyptogena, just for the fun of it.

This was taken during a deep sea cruise I managed to get on. For mroe detail on this cruise, see the NOAA Ocean Explorers site here.