Tales from the Microbial Laboratory

Two Thousand and Ten

Coral reefs and climate change, a message for Copenhagen from Earth Touch on Vimeo.

~~~~~

This is a beautiful video - and the narrators child-like voice is a powerful one I think.  Estimates on extinction are similar to ones that I've read, although the easy exchange between the terms 'climate change' and 'ocean acidification' is a bit loosey-goosey for me. It's definitely a video that is playing on our emotions, which isn't necessarily a bad thing - in fact, perhaps it's necessary.?  Nonetheless - there is some beautiful footage here. 

A coral-bleaching menace!

The Microbial Laboratory is pleased to report that Science Daily recently posted a piece titled 'Marine Lab Team Seeks To Understand Coral Bleaching' - that discusses an NMR-based metabolomics study in which, yep, you guessed it, members of the Microbial Laboratory participated in...you can find the abstract for the original publication here.  The best line?

These metabolic changes, the HML team believes, are clues to learning why the small temperature change can turn non-virulent V. coralliilyticus into a coral bleaching menace.

[FYI:  The 'comma-shaped' microorganism in the upper left-hand corner of this blog is the temperature-dependent coral pathogen, Vibrio coralliilyticus.  My group is currently putting the finishing touches on a manuscript focused on the genome of this organism, and on another manuscript focused on the proteome.  We're hoping to submit these two manuscripts to PLoS ONE before Thanksgiving...].   

~"I want more wine."~

I don't think that I ever imagined diving on the Great Barrier Reef.

I'm not certified to dive.  That's a nutty thing, I mean - my lab studies Caribbean corals and we've hung out around sunken ships.  We talk about bottlenose dolphins. 

In other words, there has been opportunity.  I love the water - so, I suppose, there has been little to no impediment to my learning how to dive.

I just never did it.

(Which is ashame.  I know, I know - I still can).

So a friend and I go out on a boat to snorkel on the GBR.  Onboard was a woman who had taken the same boat out a day before, and who had dived for the first time.  She was persuasive.  More than persuasive, she was enamored with what she saw down there.  How could we resist?  We were on the other side of the planet - and it was the Great Barrier Reef, for Christ's sake.  I'd like to say that I was brave while they were loading me up with weights and the tank and everything else required - but I wasn't, I was pretty terrified.  Then they shuffle you over to the end of the boat, and tell you to step off the end (yeah, right) - which I did, and thanks to bouyancy control I came back up to the surface quickly.  They had two horizontal bars at the end of the boat - one about a foot down, one perhaps five feet down - and they allowed you to get comfortable breathing at the first bar and then they moved you down to the second bar.  Unfortunately my mask was leaking pretty badly, so I had to come back up to the surface and get equipped with a different one.  It worked better. 

As quickly as I was back in the water, I was back down to the second bar - and before I had much time to think the 'dive buddy' that took you down had grabbed ahold of my left arm and was taking me out and further down.  We were down for about 30 minutes to a depth of about 6 meters.  The other person being taken down was having problems with her ears - she couldn't clear them and started to panic - so we went back up to the surface where a small boat came to get her.  However the 'dive buddy' and I went back down -  and all I can say is that it was amazing.  I'm thrilled that I did it.  There were giant clams and schools of angelfish over a foot tall, royal blue starfish and a large turtle hiding amongst the corals (partially seen in the imagine above, if you look carefully at the top center).  The corals themselves were just all sorts of colors, exquisite shades of golds and greens and blues - the images that I captured with a little disposable underwater camera don't come close to doing them justice.  But I love the images nonetheless.

~~~~~

And I'm back.  Sorting through a full INBOX and neglecting a pile of mail on my kitchen counter.  Trying to wrap my head around work and where I was -- (which wasn't such a good place to be) -- still in denial that my grass is a foot high and that rabbits have taken up residence (much to Stan's wishes, and perhaps to mine - since more rabbits generally mean fewer large snakes).  The tropics are active and today meetings started up - yes, meetings.  What do you do?  I go to meetings. 

But today there was some talk of science.  We talked about a predominant band in a protein gel (a 'hypothetical' protein), about a student's two outlines for manuscripts, and about how we need to come up with a plan for distinguishing phylotypes of an organism we are studying - there were talks behind closed doors and talks in the hallway, talks in my office and one in the parking lot.  Yes, I am back.  Today during lab meeting Katherine read to us a wonderful poem - a poem about a wooden creature who wanted to do more than what was expected of her.  Perhaps, last Friday, I did more than what I expected of myself - and yes, I want more wine too.

(What a treat it was to see this new world through my own eyes, and not through descriptions and images shown to me!) 

~~~~~

Not Paint and Wood by Martin Espada

I saw her at Neruda’s house,

carved a century ago

to keep vigil over the waves

from the prow of a ship,

with great brown eyes

and hair in a whirl,

now hovering silently

above the poet's table.

That night at the bar

she appeared at my elbow,

the same eyes, the same hair,

not paint and wood but flesh.

He likes for me to be still,

she grinned. I don't like to be still.

I want to climb the steps

at Macchu Picchu.

I want to talk about poetry all night.

I want more wine.

~~~~~

Martin Espada teaches at Amherst.  His most recent collection was a Pulitzer finalist.  Gary Soto has said, "Martín Espada has chosen to go outside the self-absorbed terrain of most contemporary poets into a landscape where others—bus drivers, revolutionaries, the executed of El Salvador—sit, walk, or lie dead 'without heads.' There's no rest here. We're jostled awake by the starkness of these moments."

~~~~~

You see, Neruda collected figureheads and wrote a series of poems about them.  (I'd love to visit that collection one day!  Is that possible?).

Here is one such poem.

To a Ship’s Figurehead (Elegy) by Pablo Neruda

From: ‘Canto general’

From the sands of Magellan we salvaged you, exhausted

voyager, immobile

beneath the storm your sweet twofold breast so many times

defied dividing itself between your nipples.

We lifted you again over the Southern waters, but now

you were the passenger in darkness, of angles, one

with the wheat and the metal you guarded

on the wide water, enveloped by oceanic night.

Today you are mine, goddess whom the giant albatross

grazed with its wingspan extended in flight,

like a cloak of music conducted in rain

by your blind wandering eyelids of timber.

Rose of the sea, bee more pure than dream,

almond-woman who from the roots

of a holm-oak peopled with cantos

made yourself form, force of the nest-filled foliage,

mouth of tempests, delicate sweetness,

that could go conquering the light with its thighs.

When the angels and the queens born with you,

covering themselves with moss, slumbered, fated

to the immobility the dead guard with honour,

you climbed to the narrow prow of the ship

and angel and queen and wave, you were the earth’s tremor.

Man’s shudderings climbed to your

noble tunic with its apple-wood breast.

while your lips oh sweetness! were moistened

by other kisses worthy of your wild mouth.

Beneath strange nights your waist let

fall the pure burden of the ship into the waves

cutting a path through the sombre extent

of overturned flame, of phosphorescent honey.

The wind opened its bag of tempests,

the unbound metal of its groans,

and the light at dawn received you trembling

in the ports, kissing your moist diadem.

Sometimes the trembling vessel heeled

when you halted your path through the sea,

like a heavy fruit that breaks off and falls,

a dead mariner whom the spume,

and the pure motion of time and ship, receive.

And you alone among all the faces

submerged by menace, plunged into barren sadness,

received the scattered salt-brine on your mask,

and your eyes retained the salty tears.

More than one wretched life slipped from your arms

into an eternity of funereal waters,

and the touch of the dead and the living

wore away your heart of ocean timber.

Today we have salvaged your form from the sand.

Finally you were destined for my eyes.

You slumber, perhaps, a slumberer, perhaps you are dead, a dead one:

your motion has finally forgotten the sighing

and the wandering splendour has ceased its journey.

Anger of ocean, blows of the heavens have circled

your proud head with cracks and fissures,

and your face rests like a conch,

with wounds that mark your swaying brow.

For me your beauty holds all of the perfume,

all of the wandering corrosion, all its dark night.

And in your raised breast of lamp or of goddess,

swelling turret, immobile love, life lives.

Salvaged, you sail with me, until that day

in which they let fall what I am into the spume.

~~~~~

 

~misguided, but focused~

Today my intent was to download images of the beautiful flowering plants that that I saw during last week's visit to the Flamingo Gardens in Davie, Florida - but I got distracted (as always) by so many things that needed to be done:  catching up on work email, mowing the lawn - all of those things that catch up with you in a less than pleasant way when ignoring them for awhile.

So this evening, when I sat back down to look at the images, I stopped at the one above.  So much is going on!  Color, light, shadows.  It's not all that good of a photograph, but I couldn't stop looking at it - and dissecting it.  Ah yes, misguided but focused once again - but please bear with me.

~~~~~

As an aside:  head over to NPR to listen to two pieces covering last week's coral meeting that the lab attended - here (Talk of the Nation, 11 July 2008) and here (Morning Edition, 11 July 2008).  I've spent much of the day digesting some of what went on - and need to read the recently published article in Science (Carpenter et al. 2008.  One-third of reef-building corals face elevated extinction risk from climate change and local impacts.  Science DOI: 10.1126/science.1159196).  Here's the abstract:

The conservation status of 845 zooxanthellate reef-building coral species have been assessed using IUCN Red List Criteria. Of the 704 species that could be assigned conservation status, 32.8% are in categories with elevated risk of extinction. Declines in abundance are associated with bleaching and diseases driven by elevated sea surface temperatures, with extinction risk further exacerbated by local-scale anthropogenic disturbances. The proportion of corals threatened with extinction has increased dramatically in recent decades and exceeds most terrestrial groups. The Caribbean has the largest proportion of corals in high extinction risk categories while the Coral Triangle (western Pacific) has the highest proportion of species in all categories of elevated extinction risk. Our results emphasize the widespread plight of coral reefs and the urgent need to enact conservation measures.

It's undeniable that reefs are degrading at a rapid rate.  But an interesting question raised by a colleague was:  How long should a coral colony live?  That is, are many of these colonies old - and as part of their natural decline, are they becoming more susceptible to disease and environmental stressors?  I by no means think this is clearly what is going on - but it was an interesting question raised by my colleague, and one that I need to ask a real coral biologist.  I am definitely not one.  But the question did make me realize how much more I need to learn.  At this site, I saw this written at a National Geographic site with respect to coral lifespan:

Average lifespan in the wild: Polyp, 2 years to hundreds of years; colony, 5 years to several centuries

I know there is information out there dating corals and their skeletons.  I've obviously deficient in my knowledge of their lifespan.  But they are not immortal, that is not news -- so I'll stop rambling for now about something I know very little about.

~~~~~

But - back to the banana leaves.  They are so beautiful.  I've photographed my own recently - along with a luna moth - but the varieties were more diverse in Flamingo Gardens, and the contrast between the leaves and the shadows and the shapes were just wonderful.  I then became obsessed with grayscale images of the leaves above.

~~~~~

The image is dark.  Probably too dark to be any good - but look at the folds and creases in the leaves!  Remarkable.  Here I have a 4 GB card filled with images of flowers - and I can't leave this one image.

I had to look closer.

~~~~~

Perhaps it is the angle of the stalks - in contrast to the leaves.  Perhaps it is the light coming in through the tears in the leaf in the center.  I don't know. 

But there was just so much to look at.

~~~~~~

This one is almost identical to the one above. 

Yet different enough.

~~~~~

There are still things to see.

Yes, I know that I am ignoring the images of the comic spoonbill, the flowering gingers - the bamboo and the sacred fig tree.  I will come back to those, one day - when I am not as enamored with the leaves from banana trees.

I am also ignoring the packing that I need to do - to wrap up, actually.  And the pile of papers and mail on my kitchen counter.  I am also ignoring that I need to replace my lawn mower, but I do believe the time has come.

Perhaps I am hiding in these banana leaves.

~~~~~

I think that this might be my favorite image.  Maybe.  Yes.  For sure.

~~~~~

And then there is Ted Kooser (the US Poet Laurete from 2004-2006) who introduced me this evening (via his site American Life in Poetry) to a Hawaiian Poet, Joseph Stanton (you can read a bit about him here).

Until tonight. I was not familiar with Stanton's poetry.  Nor was I familiar with Pablo Nerudo's poem "United Fruit Company" poem (here is a translation) - I need to come back to this poem, and learn more about the 'Banana Republics' that Neruda writes about.  But for tonight, there is a poem about banana trees.  And my own images of banana leaves - ones that I have not, even yet, grown tired of.

~~~~~

Banana Trees by Joseph Stanton

They are tall herbs, really, not trees,
though they can shoot up thirty feet
if all goes well for them. Cut in cross

section they look like gigantic onions,
multi-layered mysteries with ghostly hearts.
Their leaves are made to be broken by the wind,

if wind there be, but the crosswise tears
they are built to expect do them no harm.
Around the steady staff of the leafstalk

the broken fronds flap in the breeze
like brief forgotten flags, but these
tattered, green, photosynthetic machines

know how to grasp with their broken fingers
the gold coins of light that give open air
its shine. In hot, dry weather the fingers

fold down to touch on each side—
a kind of prayer to clasp what damp they can
against the too much light.

    

~bluebirds, a meeting, and coral shallows~

I've noticed for the past week (and a little more) that the bluebirds have once again taken up their post atop the purple martin pole - like last year, I neglected my purple martin duties over the past few months, and like last year, bluebirds have taken advantage of my neglect (and while I really, truly, wanted to foster purple martins - I must say that watching bluebirds raise two nests of young last year was a pleasure). 

The purple martin house is placed in between two vegetable garden beds, and while I weed or plant or ponder or, quite frankly, simply stand, it is fun to have the bluebirds as my daily companions. 

~~~~~

(Image credit goes to our collaborator).

Today was another Wednesday, another gathering of the laboratory around a conference table for our weekly meeting.  Today the senior graduate student brought in a crockpot of chicken and dumplings, an attempt at a family recipe (his grandmother's I believe) -- and the conversation, typically meandering, had folks talking about their view of the perfect dumpling.  His were homemade, cut into strips, plain - and were quite delicious I thought.

Then we talked about the repair of the Beckman centrifuge (a service quote has been received?), the amount of time it will take to wrap up the bacterial isolations from the most recent sampling trip to Puerto Rico (two weeks perhaps?), and the registration deadline for the ICRS meeting (today!).  Then we raced through a student's presentation, thinking broadly, thinking story, thinking clarity - rename the title of the model, change the histogram colors, perhaps rethink the order (marine natural products then chemical ecology?), defining the mesoglea, maybe a different final slide (revisit the model?)...a presentation that we will scrutinize up until we no longer can. 

However, before launching into the student's run through of the powerpoint presentation (the one in preparation for the student's oral defense of her dissertation proposal), Katherine shared a poem with us.   

~~~~~

Coral Shallows by David St John

From PRISM (2002, ARCTOS Press, Sausalito, CA)

Marble angel are you still there standing

On the coral beach in Key West calling me on

Your cell phone to say I’m sorry it was all just another

Misunderstanding one of so many we seem to be

Having lately as those quaint tongues of death creep

Up the legs of our own shadows but for my part

I keep my talismans close --- my necklace with

Its wing of silver lit by turquoise & red coral

& obsidian which the old woman in the pueblo

Fastened around my neck saying You are a creature

Of blood inflamed as coals & this wing will

Life you above the fields of sorrow

She really said that & you said So here I am 3,000 miles

Away beside shallows reeking of green primeval sex

~PR~

Our sampling trip was once again a quick one - a mad dash down to Puerto Rico's southern coast - returning with samples of coral tissue and mucus and surrounding seawater for microbial community analysis.

This trip we had a special treat:  an Caribbean oceanside view of Wednesday night's lunar eclipse.

~~~~~

As always, we learn a few new things each time we visit Puerto Rico - new things about corals, and about the area.

As always, the trip was too short, leaving much more to learn and explore.

As always, it was nice to wake up and walk out on the balcony and enjoy the stillness of the morning.

~~~~~

Our collaborator, who has an intimate working knowledge of the reefs on Puerto Rico's southern coast, told us that he has observed a 53% loss in the coral cover of this region over the past 4 years.  That's a tough statistic - however, on a more optimistic note, this season he has observed a lessening of the intensity and severity of several diseases, raising questions about the adaptation of these corals to disease (with increased ability to ward off disease) and the natural cycle of the pathogens responsible.

(A segment of Acropora cervicornis tissue).

~~~~~

There were still iguanas.  Lots and lots of ignuanas.  But it seems that someone is now doing a genetic study on Isla Mayaguez's iguana population - and the results may lead to the removal/extermination of the animals.  It seems that the iguana population is the result of a pair of iguanas left behind when Isla Mayaquez was a zoo - and that the animals are not native to the area.  Additionally, people have been dumping off their 'pet' iguanas on the island, and they have been hybridizing with the original population. 

(And in a somewhat sporadic laboratory tradition, we took the lab's rat along for any potentially interesting photo opportunities...hence, 'The Laboratory Rat and Iguana Series' - destined to become a classic.)

~~~~~

The flora was - as usual - spectacular, but I was remiss and really captured very few images.  The next time I make one of these mad dashes, I need to remember to take a pocket book on the flora of Puerto Rico along with me, because, quite honestly, I know next-to-nothing about what I am seeing.  I can recognize a mango - and a few other trees, but that is about it.  And so much was in bloom!  There were so many mysterious blooms - and I need to learn more about them.  Next time.

This flower was from a tree on the island - it had a wonderful fragrance and seemed to be quite common.

~~~~~

We were able to get all of the sampling done on Wednesday, so Thursday - after we finished packing up the samples and meeting with our collaborator - the eclair-making postdoc and I took off for the, yep, you got it - the ever-so-intriguing extraterrestrial highway to the west of La Parguera.

Route 303. 

The countryside was just beautiful.

There were trees that I couldn't identify - and a type of flowering fig lining the roads - and hillsides covered in cacti - and the wind was strong and a beautiful light brown-gold grass was 'waving' as grasses often do.  All of this within eyesight of that blue, blue water.

~~~~~ 

Several years ago, it seems, the Mayor of Lajas, PR named Route 303 the 'Ruta Extraterrestre' since the area seems to be a hotbed of UFO activity.  Evidently the eclair-making postdoc saw a special the last time he was down in PR sampling about this road - so I gladly agreed that it only made perfect sense to go in search of the road and it's infamous green sign.  Tonight, as I was trying to find something online about Route 303, I came across this article (pasted in below, dated today) from UFODigest - you've just gotta love it - a UFO landing strip to welcome extraterrestrials!!  Here's what they wrote:

LAJAS, Puerto Rico Mayor Marcos Irizarry's is supporting the building of a UFO landing strip to welcome extraterrestrials that are frequently seen over the area. A green sign in southwestern Puerto Rico proudly displays a silhouette of a flying saucer and two words: "Extraterrestrial Route," for Route 303.

Lajas support for the idea has provoked outrage among islanders who complained it would be a waste of money. Mayor Irizarry quickly clarified that his municipal government would not invest in the project but would help Reynaldo Rios get the proper building permits to attract tourists to his small town. The majority of the people in the town have seen UFOs and other strange phenomenon. "It's a very mysterious place," said Irizarry, who says he once saw red lights zigzagging above the hills. Francisco Negron, the farmer who put up the sign and allows UFO watchers to gather at his ranch, volunteered his property for the landing strip. They estimate the project could cost up to $100,000. They claim they heard a boom and saw the hill go up in flames when a UFO crashed on the hill in 1997.. The mayor hopes that UFO enthusiasts will flock to Lajas. Hundreds of visitors have already come to check out the Extraterrestrial Route since the new sign went up, Irizarry said.

Lajas is unique because of its numerous UFO sightings and Laguna Cartagena National Wildlife Refuge and lagoon that is known for bird watching.

Besides UFOs, 127 different types of birds have been observed as well as balls of light coming and going into the water. At 10:30 PM, on May 30, 1987, a large red buzzing ball of light was seen descending into the lagoon. At 2:AM on May 31st, people in the area were awakened by a blinding white light and saw a huge disc shaped object with brilliant lights circle slowly over the water, as if looking for something. The following afternoon at 1:55 a huge underground explosion followed by a tremor shook the area. Cracks opened in the ground and cobalt blue smoke issued from them.

As if an earthquake followed by blue smoke wasn't jarring enough, residents whose houses bordered the lagoon were forcibly evacuated by members of the U.S. military in grey HUMVEE's and tan four-wheel drive vehicles sporting radar-like rotating antennae on their tops. As they were being herded away from their homes, residents saw men in what appeared to be decontamination suits sweeping the ground with long-handled devices reminiscent of metal detectors and taking samples of water, plants, mud and grass. The next day a helicopter lowered an instrument package into the lagoon. For the next several days witnesses saw a strange flying dumbbell come in from over the sea and hover over the lagoon. It was a metallic cylinder with large balls of greenish-white light on the ends and a beacon-like red and blue light on its underside. During the next several days reports of UFO activity in the area increased dramatically, but also a large four engine commercial jet made a low pass over the lagoon.

Lajas is also unique in having its main highway designated as an Extraterrestrial Route. To add to the mystery the U.S. military has set up an aerostat tethered blimp with a radar system on the edge of town. A similar blimp is at Cudjoe Key near Key West, Florida. The military says the radar is to detect low-flying drug smuggling planes.

The aerostat is a large fabric envelope filled with helium. It can rise up to 15,000 feet while tethered by a single cable, which has a maximum breaking strength of 26,000 pounds. For security and safety reasons, the air space around Air Force aerostats is restricted for a radius of at least two statute miles and an altitude up to 15,000 feet. The smallest aerostat is about twice the size of the Goodyear Blimp. The 275,000 cubic foot, aerodynamically shaped balloon measures 175 feet long by 58 feet across the hull, with a tip-to-tip tail span of 81 feet. The aerostat system lifts a 1,200 pound payload to operating altitude for low-level radar coverage. Many people believe the true purpose of the radars are to detect UFOs rather than drug runners. It is likely both drug runners and UFOs are detected.

~~~~~

So we flew out of San Juan this morning - knowing a bit more about the coral world that we are studying, not much more about the flora of this tropical island - and we traveled down a road where UFOs - actually USOs (unidentified submersible objects) seem to be a frequent visitor.

~~~~~

It felt good to get out of my world, if only for a few days.

   

~manana~

~~~~~

Tomorrow I'm flying down to San Juan with the eclair-making postdoc to sample coral reefs off the southern coast of Puerto Rico - our base is La Parguera and Isla Mayaguez - and it'll be one of those 'fly-in-drive-down-sample-process-fly-back' kinda trips.

~~~~~

I won't complain:  It'll be warm, and that water - it never hurts one to see the blue of the Caribbean.

~~~~~ 

(Plus, I get good cell phone coverage - so I can check in with my parents often - my niece is there, doing a wonderful job of keeping everyone company.  I am grateful that she is there - otherwise, I don't think that I could make this trip).

~~~~~

Oh, and there will be iguanas.  HUGE ones.  They're protected on the island - and during my last visit, there was one that always hung out at the door to my colleague's laboratory.  The iguanas are a bit - intimidating.  There are LOTS of them.  When you get plantain chips from the vending machine, they jump up at you and grab them out of your hands (and yes, the first time that happened, I went running in the opposite direction).  You get used to them, in a strange sort of way - I think perhaps you just get used to their habits and schedules and adapt.  I think one day though that iguanas will take over the island, and the researchers will go fleeing on boats.  One day.  Perhaps.

~~~~~

Later.

~the mysterious~

Look closely.

Streaks of coral mucus (in folds), the small green dots (prokaryotes), the larger orange spheres (most likely eukaryotic cells of some kind) - an image obtained today by the eclair-making postdoc (who hasn't brought in eclairs in a long, long time). 

It's own universe.

The surface mucopolysaccharide layer of the Caribbean reef-building coral, Montastrea faveolata.

The universe in this image is what we are trying to understand.  It's funny how we're studying the microscopic members of this mysterious universe, but here I am tonight, looking at this image - sensing the vastness of it all.

It's like wandering into a strange and new world.

The most beautiful thing we can experience is the mysterious. It is the source of all true art and all science. He to whom this emotion is a stranger, who can no longer pause to wonder and stand rapt in awe, is as good as dead: his eyes are closed. - Albert Einstein

a Tuesday

I was greeted this morning by the male painted bunting at the feeder - I'm sure that he was thinking 'it's about damned time' because the feeder had sat empty for awhile.  I finally remembered this weekend to pick up some white millet seed (their favorite from my experience).  This is the fourth year in a row that I've had a pair nesting in my yard - and while my intentions have been to be an active member of the Painted Bunting Observer Team, I've failed miserably at my PBOT duties.  Over the past three years, I've always felt that I had the same pair return each year to nest - but this is the first year that I feel as if I have a different (younger) pair (offspring perhaps?).  They've just behaved differently, it's hard to explain.  I think that you can get to know a bird - if only from a distance.  I just don't feel as if I know this pair yet.

Today the laboratory was paid a very generous visit by a Professor Emeritus from Tel Aviv University.  He was in the states for a meeting, and was taking a side trip to visit a cousin in Charleston - so he had contacted me months ago about spending the day with my research group.  His laboratory was the first to isolate and characterize the coral pathogen that we are now sequencing the genome of - our first full genome of a microorganism.  This organism is becoming more and more interesting to us each day:  it's being found more frequently in coral-associated microbial communities, it's temperature-dependent virulence and susceptibility to anti-microbials is fascinating - and I'm eager to see it's similarity to other important Vibrios - cholera, vulnificus, shiloi.  The discussions today were interesting, illuminating, puzzling, comforting - when a senior scientist comes to visit your group, it's always useful to gauge their response to your on-going studies, new data, and hypotheses - especially on something like our coral project which is a field I've only recently joined.  At the end of the day, I felt good - we all felt good - and eager to get on with it.  As one of my doctoral students said as we were all leaving the place we'd gathered for lunch:  we're on the edge of a whole lot of discoveries.  I do believe that is true.  The lab's postdoc heads tomorrow up to Rockville, Maryland, and the J. Craig Venter Institute to generate test metagenomic libraries of our coral microbial communities.  A test library alone will generate more sequence data than the laboratory has ever obtained before.  It's going to be quite a summer.

Now I need to grab the dogs and spend some time in the garden.  Today was warm and it's still dry.  We desperately need rain, although none is predicted in the near future.  A nice summer thunderstorm would be a welcomed end to the day.  But that will have to wait for another day to end.     

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.