Tales from the Microbial Laboratory

a study

Montastrea faveolata.

This is one of the corals that we are following through the progression of disease.  Our collaborator in Puerto Rico is monitoring them in the field for us - each coral colony that we are following was tagged at the beginning of the study, and as the disease progresses, more samples are taken.

We're using molecular approaches to follow changes in the microbial communities - bacteria and symbiotic algae (zooxanthellea) that are associated with the corals as disease progresses.  We're hoping to couple changes in microbial community structure with changes in the functional gene potential in that community:  in other words, what is going wrong and why from an ecological perspective.

But the bottomline is that the corals are dying.  Some suggest there is hope, but most don't.

The extent of the loss is staggering.  Coral reef ecosystems represent the most biologically diverse ecosystem in the marine environment.  Ultimate bottomline:  much more diversity will be loss (besides the corals themselves) - imagine all of the species dependent on corals and coral reefs (from a structural perspective) for their survival.

There are days when it's hard to not let it get you down.  Today was one of those days.

Update (23 May):  I didn't realize when I wrote this post yesterday that it was International Biological Diversity Day.  I had forgotten (but then I don't think it's extensively promoted in this country either).  The day was established by the UN General Assembly to celebrate the day the Convention on Biological Diversity went into effect.  The focus on this year's convention was - not surprisingly - climate change.  The list of parties involved is an interesting one:  the relative lack of involvement by the US still astonishes me (but just about everything about the current administration astonishes me).  However, it doesn't mean that we can't participate in the Billion Tree Campaign with or without our government's support.  No harm can be done by planting a tree. 

terminal species

I returned to Charleston today - and was greeted by a familiar fragrance in my own garden.  Walking up the stairs to the deck, a few hours ago, I could tell that my wisteria, that has almost taken over the side deck, was in bloom.  Their blooms are fleeting, their aggressive vines have given me headaches for years - but oh - for that week or so when it is in bloom, when I am greeted each day by the familiar scent - I just can't bear to let it go. 

I'm tired.  It was a very good weekend with my parents - good days - and their flower beds are in good shape and their spirits are improved and for a few days I stuffed as many cruciferous vegetables down their throats as I could.  It's time to settle into this new life with a terminal illness in the family - mixing conversations about wigs and scarfs and chemotherapy and fears - with conversations about a cousin's pending new baby, a flower that finally decided to bloom after 25 years (a Fritillaria) and what my mom should put in a Easter basket for her only grandchild.  I'm sure there are books on this to read, that would help me to navigate these new waters - but perhaps for now I'll just think of everyone as being terminal (not in a morbid sense - but in a real one) and accept the days that we have.

So - time to get back to the lab.  Two coolers worth of coral samples arrived from Puerto Rico today - and with disappointment, Katherine told me on the phone that they were unable to find Acropora cervicornis - a magnificant coral that is listed now as 'threatened' under the Endangered Species Act.  On the drive down today, listening to NPR, I recall hearing something (was it today?) on how the Bush Administration is trying to once again loosen restrictions on the Endangered Species Act - you can read a bit about it here.  Groups are calling it the worst attack on the ESA in 35 years.  As our laboratory sits and watches - over the year(s)- reefs change, changing in composition resulting in reductions in overall diversity - it's hard not to see the coral reef as a mirror of other ecosystems.  Thinking back, in Ecology 101:  a diverse ecosystem is a more stable one.  A basic premise of ecosystem science.

But for now, I'll sort through my work emails, and try to remember where I was before I drove up to Virginia.  I'm swamped with work, that's for sure.  I think that for now though, I'll wander my own garden with the Ancient Wonder Beagle and the gallbladder-less (Dog)Wood and feel grateful for the time I just had with my mother.  And water a few things - we are horribly dry here.  We need a spring rain. 

Corals and Impediments (Science and Impediments)

Corals.  The laboratory is gearing up for another coral sampling trip along the southern coast of Puerto Rico.  We sample just off of La Parguera (with our collaborators at the University of Puerto Rico) - at the reef's Enrique and Turrumote and Media Luna.  During my first visit, almost a year ago now, I had tried to prepare myself for what the reefs might look like - but I wasn't prepared for the quiet, for the stillness - for the greyness.  The reefs are still alive - but they are in transition, a transition that is reducing their diversity, their productivity, their vitality - soon they will not be the same coral reefs that my colleagues have visited weekly for years.  During this trip we will expand our sampling efforts to two more coral species (for a total of five) - one of which is on the endangered species list, Acropora cervicornis. 

Corals and Impediments.  Our biggest challenge is transporting our corals - getting them back to the laboratory with as little harm done to their microbial communities as possible - frozen samples, samples at certain required temperatures....getting through the USDA checkpoints in San Juan, crossing our fingers that when the FedEx guy says that they won't irradiate the samples, that he means it -- all of the permits are in place for the sampling, but translating the permits activity to actual transport seems to be a bit challenging sometimes.  Plus, it's not the best time to be transporting microbial cultures - we do our initial plating of coral mucus in the field lab - we do what we can, but during most of the process we just have our fingers crossed, hoping that we've thought through the process and haven't left out something important.  We're getting better at it.

Science.  But each new sampling trip sends the lab into a period of renewed optimism - while this next group of samples confirm what we are observing?  Or will a new trend be observed?  Or will the data only result in more confusion, the need for additional samples, and a new approach?  We recently got some pretty exciting data - the results of running one sample of coral mucus microbial community DNA through a functional gene array.  We 'saw' for the first time what is most likely the predominant functional genes - genes involved in such processes as sulfur and nitrogen cycling and methane generation...and on and on...almost 1,200 genes revealing the role of the microorganisms in key nutrient cycling processes of the coral holobiont.  During this sampling trip, we'll start obtaining samples that will allow us to start following the changes in functional gene potential of the microbial community during coral holobiont disease progression.  Our hypotheses?  That changes in microbial community structure due to disease influences a key sub-population in the community that contributes to coral death.  That corals that can recover from disease events recruit back the necessary community - either the same 'group' of microorganisms or possibly even a different 'group' - but organisms with redundancy in their functional gene potential.  In other words:  who cares what the microbes name is, along as it has the ability to fix nitrogen.

Science and Impediments. Now, here's where it gets challenging.  On more than one occasion I've posted about issues for women in science (well, at least my own issues) - and while sometimes I could state it more broadly, it always seems to come down to the same bottomline:  it's hard to be at the table, to be seen and heard - and the battle for equal footing is a constant one.  I've always said that individually each 'experience' seems trivial - but it's the compilation of daily experiences that combine to create a mountain-sized challenge that is oppressive.  Today's example:  I get stopped by a colleague who mentions that our program had brought in a visiting scientist (a marine mammal) person that has access to different 'pots' of money for marine mammal research (of which I have one grant pending to fund).  It ends up that the program sequestered this person and that only three males in our program had been scheduled to meet with her (I had no idea she was even coming to visit - nor did the other female PI in our program - and we both have an on-going marine mammal project) - and my colleague said "Oh, we do need to remember to include you more often" which is simply condescending as hell...and then the conversation transitions to the fact that they might actually 'need' me - because some of the work that this visiting scientist was interested in was related to hydrocarbon impacts on dolphin health, and of course they know nothing about hydrocarbons.  So my colleague says 'perhaps you could be a consultant or collaborator on a grant we submit so that we can be legitimate in the hydrocarbon arena' and I'm thinking:  A collaborator?  A consultant?  I'm a Prinicipal Investigator - geez, what are these guys thinking?  That I'm here to lend them my CV when they need me - so that I can help them (as tenured Full Professors) to get funding when they do nothing to support me as a more junior Associate Professor?   When they don't even think to include me in the opportunity to begin with?  So I respond that if they need a Co-Principal Investigator on the proposal, to let me know - and I walk away - because these guys are simply so clueless it is hardly worth saying much more (and also because I said more before, over and over again, and gotten nowhere).  So -- individually this was a 7 minute conversation in a long and productive day -- but this treatment every day, every week - results in lost opportunity - lost opportunities, and I'm frankly wondering when it all ends - when my publication list will be long enough, when my grant portfolio will contain enough digits, when my years of experience will be sought out for it's equal contribution and not just as a last minute add-on in a time of need.  It's such bullshit.  Exhausting bullshit.

So it's nights like this, when I feel the lingering excitement of my lab's science, when new ideas have been floating around the lab all day - when one lit search leads to changing an old idea and a new dataset generates a whim of a hypothesis that grows throughout the afternoon - it's after a day when I'm convinced more than ever that we're on the right track but then I have a 7 minute conversation that sidetracks me, attempts to put me in another space - a space where I'm less than I can be, where I feel that I'm only there to support the scientific pursuits of others - it's after those days that I come home and crave (besides a glass of wine) the blossoming blogosphere of sites written by women in science - and find comfort in their battles and their successes and their words and know that what I am doing is very, very much worth it.  (It was only 7 minutes out of an otherwise very good day).  Something new that I found tonight (and hope to contribute to in the future as soon as I figure out how):  Scientiae

This is a blog carnival that compiles posts written about the broad topic of "women in STEM," (STEM=science, technology, engineering and mathematics) and may include posts:

stories about being a woman in STEM

exploring gender and STEM academia

living the scientific academic life as well as the rest of life

discussing how race, sexuality, age, nationality and other social categories intersect with the experience of being a woman in STEM

sharing feminist perspectives on science and technology

exploring feminist science and technology studies

Both men and women (and anyone in-between) are welcome to contribute to the carnival as long as the topics are relevant and respectful.

And another site:  Women in Science

This is in addition to ones that I've already written about here and here...it's definitely a growing - and strong - community.  I'm so glad that they are out there, and I'm glad that they are sharing their experiences. 

A Misc. Second Day in 2007

I can't bear to dismantle my perennial beds yet - there are too many seedpods remaining, interesting ones, like those of Hibiscus coccineus 'Texas Star' (also here).  Plus, the birds are still enjoying them - except for the white-eyed Vireo that still insists upon finding a way to enter through my kitchen window.  He's insistent, I'll say that. 

Today:  reality.  Not too much at once however, I did work from home - and realized that I'm past due on two manuscript reviews, that I need to play 'catch-up' on some literature in order to be of use to my graduate student Ben who has his proposal defense looming, that I need to start the process of finding a new postdoc for the coral grant (since the one that was due to start on 8 Jan seems to have been offered at real job at a much higher salary), that I have a Progress Report due and a grant to get started on, and...on and on.  The list is intimidating to me and I'm sure it's boring for you, so I'll stop there.

The word of the day:  decency.  The creepiness of the day:  blueberry bushes blooming in early January.  The frustrations of the day:  a pipe leaking underneath my house and the appearance of tapeworms in the Ancient Wonder Beagle's poop (meds already taken - but while at the Vet, they said that with all of this warm weather (and happy fleas - and remember, it just takes one), folks who have never had problems with tapeworms before are flocking in for medication - I haven't had a dog with tapeworms, at least that I've been aware of, for about 15 years - since when I lived in Florida).  The good news of the day:  my car's windshield got repaired.  A gorgeous illustration for the day:  Olduvai George's Mammuthus primigenius.  The decision of the day (or evening or week):  whether (or not) to head up to the North Carolina Science Blogging Conference for a road trip with the Xarkers.  I'm thinking yes, but that almost makes this whole blogging them seem real...which it isn't, right?

So - on this misc. 2nd day of 2007 I'll end with this...because we live here near the Atlantic Ocean, in fact - at it's very doorstep - and because I think about this stuff alot - so I thought I'd share a few links with you about our oceans, and what's living there.  It's cool stuff, truly.               

The Census of Marine Life (What lived in the oceans?  What lives in the oceans?  What will live in the oceans?):   2006 Annual Report to the Public.

The Census of Coral Reefs (CReefs). 

Microbial Life in Marine Environments. 

Scrap the To-Do List

Acropora palmata - called Elkhorn Coral for obvious reasons, is one of the threatened reef-building corals in the Caribbean.  I can't imagine not seeing these corals in the underwater landscape - so I am glad that projects like this one are underway.  These images were captured by a colleague at the University of Puerto Rico-Mayaquez, Dr. Ernesto Weil, who helped us last March collect samples for microbial analysis from coral reefs off of La Paguera, PR.  He captures wonderful underwater images, and knows these reefs better than the back of his own hand.  We debated whether he was part fish or not - he hardly needs to breathe underwater.  So today - after being reminded of the beauty of these landscapes, I'll scrap my previous To-Do List and focus on our first manuscript on microorganisms associated with corals.  There's an urgency there.   

Is biodiversity important...and if so, important compared to what?

A student in the lab just emailed me this link to an MSNBC post on what researchers have described as "Earth's richest seascape" - and the diversity of corals in this area, ~6,950 sq. miles off of Bird's Head Peninsula in northwest New Guinea, is incredible.  According to the article:

Researchers have counted 1,200 species of fish there and 600 species of reef-building coral - the latter equal to 75 percent of the world's known total.

Australia's Great Barrier Reef, covering an area 10 times bigger, has more types of fish - 1,464 species - but just 405 species of coral.  And the bigger Caribbean Sea has fewer than 1,000 species of fish and just 58 types of coral.

Wow.

This follows an announcement made last February, about a team of U.S., Indonesian and Australian scientists that surveyed the Foja Mountains, a remote area of Papua province that covers more than two million acres of old growth tropical forest.  Talk about remote - and talk about diversity - it must have been an amazing expedition.  According to the article, the first bird they saw was a new species.

Unfortunately, the Papuan coral reefs are under the same threats that alot of reefs are -  and the use of dynamite/cyanide to capture fish for export and commercial fishing practices/over-fishing must be managed, for a start.  But I also wonder how it's going with regards to oil exploration, since prospective oil fields are in the general region.

A few months ago, I had a post on a bunch of random stuff - and reading the article tonight made me think once again about two questions that the Island of Doubt raised awhile back:

Is every species of living thing on the planet equally deserving of protection?

Is every species worthy of preservation?"

Are the corals in this place of remarkable diversity worth protecting?  As I sit here, reviewing grants about global biodiversity, reading over-and-over again about the spectacular biodiversity on planet Earth, and the numerous threats to this diversity - I can't help but feel sad about what may be lost.  I'm also not so human-centric:  corals are deserving of protection and are worthy of preservation.  It's what we think about everyday in the laboratory - our humble, mostly inadequate, and challenging struggle to understand the impact of threats on these amazing marine animals.  But where - on a globale scale - do threats to biodiversity reside, when one ponders HIV/AIDS and other infectious diseases?  Cancer?  Poverty? Terrorism? War? Climate Change?  How do we prioritize biological diversity?

I don't know.

Global Can of Worms

My laboratory has recently entered the world of coral reef research - a tight knit, strangely competitive group that guards it's reefs and research closely.  One reason is access:  access to some of the critical reefs isn't something you can get everyday (so samples can be hard to come by) and all activities must be permitted - most reef's and their resident corals are protected (due to the Coral Reef Restoration Act - view this site for other legislation related to our oceans).  Our coral reefs are threatened - and many of these reefs have specific corals that are considered to be endangered or threatened species, including species in the Genus Acropora  (Staghorn and Elkhorn corals).  Coral reefs are new to us - as a research area - so we're trying to keep up with what's going on in the world regarding reef health and management.  We're playing catch-up. 

So yesterday, a student in my lab working on our coral project sent me an interesting link to a BBC News article regarding the Belize Barrier Reef.   This was interesting.  Essentially, local scientists in Belize say that their reefs are devastated (which is hard to deny) - and that a hurricane could simply sweep away what remains.  However they don't blame hurricanes for the loss of the reefs.  Scientists from Belize and across the planet are "backing a petition pressing the United Nations World Heritage Sites Committe to acknowledge that climate change is already damaging world heritage sites."  Five sites are being included in the petition:  the Belize barrier reef, the Australian barrier reef, and glacier parks in Nepal, Peru and the Rockies (where glaciers are disappearing).

This is interesting.  Historically, World Heritage Sites are designated as such so that sites are protected during war times - those who sign the treaty are committed to not damaging these sites (I wonder how this holds up?).  If the UN accepts this case involving coral reefs, it would then open the doors for poor countries to sue wealthier nations for damages due to the emission of greenhouse gases.   One of the biggest threats to our planet's coral reefs is rising ocean temperatures - proposed to be a direct consequence of global warming and greenhouse gas emissions. 

So Belize (as an example) could sue the US for the decline of their country's reefs.  Their case is pretty solid - solid scientific evidence exists linking coral death to coral bleaching events and further linking these events to temperature.  The Committee is meeting during the week of 8-16 July.  The US has already announced it's objections to the petition - stating that there is no conclusive evidence linking greenhouse gas emissions and reef decline.  However, the US also states that if the damage is occurring, it is accidential so it does not violate the World Heritage Sites Treaty.  (This point sounds pretty lame to me).  The US also states (according to the article) that "accepting the petition on a controversial issue such as climate change would spoil the harmonious relations of the World Heritage Committee."  Huh?  Is that a reason to not protect and preserve the most diverse ecosystem in our oceans?  The last great place to look for novel anti-microbials, anti-cancer agents, etc?  We should preserve the harmonious relations of a committee over protecting an ecosystem that provides the world with 20% of it's protein (from fisheries)?  The world is a crazy place and I rarely understand the ordering of priorities.

But then I'm a scientist, not a World Heritage Sites Committee member.  It'll be interesting to see what happens.  But this is a global can of worms, for sure.

   

Who said your everyday off-white microbes were boring?

The isolation of microorganisms from coral mucus continues!  We're now feeling that more is behind us (with respect to this sampling trip) than ahead - ~350 isolates are safely frozen back now at -80C in glycerol and DMSO and their pellets are safely stored at -20C for DNA extraction when time allows.  We're pretty confident that most of these organisms are coral-specific and the sequencing will confirm this visual observation.  This is an important first observation for this project!  The other observation is that not all white microorganisms look the same, even though at first glance they might seem very much alike.  We joked with Katherine (the lab's Poet Laureate) today about writing a few poems in honor of the more interesting isolates...I definitely think we need an "Ode to the Off-White Microorganism" to start with! 

A sea of microorganisms...

We’re swamped, snowed under, literally swallowed up by a few coral’s worth of microorganisms.  We’re isolating them from coral mucus (aka coral snot) – a mucopolysaccharide layer that covers the the coral surface.  The mucus was collected a few weeks ago from several reefs off the southern coast of Puerto Rico.  We inoculated agar plates with mucus from three different coral species (from both healthy and diseased corals of each species) - these agar plates were then expressed mailed to our lab in Charleston.  Then Katherine - with Nan's help, a little bit of Ben's and now Maria's (and even myself on ocassion) have been working on isolating the different microorganisms to purity.  When I say "working" I mean pretty much working nonstop, to the point that a little amendment to our lab's sign has appeared which states "We never sleep."

Now, some of the colors of the microbial colonies are sorta fun, but what I'm not

showing you is the hundred's of microbial isolates that might be the same thing, or

might not be.  We won't know until we sequence them to find out exactly what they are - so we won't know for awhile.  In the meantime, we keep going.  There

are two questions in all of this that haunt me.  The first one:  Are our

isolation methods, which are definitely limiting for environmental strains of

bacteria, going to allow us to detect differences in the microbial communities between species?  Or will we have to rely on molecular approaches alone?  Thus far, I would say that we are seeing differences between the organisms we isolated from the different corals, and even between the healthy and diseased corals of the same species (especially for the gorgonian coral).   So I am hopeful that all of this effort will be fruitful.

 

However my second question is a bit different:  Is what we are doing worth exhausting people that work in my laboratory?  On one hand, corals are an extremely threatened marine ecosystem, and the microbial diversity associated with these corals will change (or even be lost) as coral reefs are degraded.  I can therefore say that I do feel that this is an important research direction.  But to the point of exhaustion?  I'm not so sure.