Tales from the Microbial Laboratory

A Microbial Voyage

A few weeks lago, one Wednesday during lab meeting, when everyone was feeling swallowed up by the scale of the number of microorganisms we were trying to archive from Puerto Rican coral reefs, a person on the project, Katherine (who is a scientist-poet), read us this wonderful poem that she had discovered that just summed up everything we were feeling:  we were on a voyage, perhaps even a great ocean voyage, and we had nothing left to do but to continue uncovering our story .

Voyage by Tony Hoagland (from Hard Rain)

I feel as if we opened a book about great ocean voyages
and found ourselves on a great ocean voyage:
sailing through December, around the horn of Christmas
and into the January Sea, and sailing on and on

in a novel without a moral but one in which
all the characters who died in the middle chapters
make the sunsets near the book's end more beautiful.

— And someone is spreading a map upon a table,
and someone is hanging a lantern from the stern,
and someone else says, "I'm only sorry
that I forgot my blue parka; It's turning cold."

Sunset like a burning wagon train
Sunrise like a dish of cantaloupe
Clouds like two armies clashing in the sky;
Icebergs and tropical storms,
That's the kind of thing that happens on our ocean voyage —

And in one of the chapters I was blinded by love
And in another, anger made us sick like swallowed glass
& I lay in my bunk and slept for so long,

I forgot about the ocean,
Which all the time was going by, right there, outside my cabin window.

And the sides of the ship were green as money,
             and the water made a sound like memory when we sailed.

Then it was summer. Under the constellation of the swan,
under the constellation of the horse.

At night we consoled ourselves
By discussing the meaning of homesickness.
But there was no home to go home to.
There was no getting around the ocean.
We had to go on finding out the story
                                                          by pushing into it —

The sea was no longer a metaphor.
The book was no longer a book.
That was the plot.
That was our marvelous punishment.

Got koi?

Every had one of those days?  When everything just seemed really crazy?  So I was at the Eastern Fish Health Workshop (fish you say?) and I was sitting through a session before the coral session with presentations by "exotic" veterinarians, more specifically, a few that focused on really expensive koi.  Now I know there's a difference if you want to get picky, but I've always heard that koi was just a fancy name for "expensive goldfish".  A carp in other words.  Now, this one talk focused on two pet koi's owned by a woman - this woman lived in Niagara Falls and used to drive to Buffalo to take her fish to a koi specialist.  I had to check this out on the web, and when I googled "koi veterinarian" I just got 149,000 hits...so foolish me.  But what was so funny about this talk wasn't that the veterinarian came to the pond to check water quality, health status of the fish, etc - but these LARGE koi traveled in big coolers 6 hours one way to visit this veterinarian.  The vet justified all of this by saying that the owner had spent alot of money on these fish - ended up she purchased them for $125 on Ebay (which doesn't put these koi in the expensive koi category).  I never knew Ebay was in the koi business, but I guess why not - they're into everything else.  So I went to Ebay and saw that alot of koi-related stuff was on sale, and if you looked up "live koi" - there they were, live koi for bid.  Even stranger, on one website they featured a PLAYKOI of the Month (for this month - just look to your left).  Anyway, I digress (who wouldn't?).  This woman traveled regularly to her koi veterinarian - and these two fish had tumors removed and eyes removed and tumors biopsied and their tanks redecorated with soft objects for the blind koi and one of them was finally treated twice a day with rimadyl (pain meds) injections and when it wasn't swimming much they devised a sling to help exercise the fish.  All of this was explained quite scientifically, with photos of the koi in all sorts of positions (including in the sling, doing exercises) and with cross sections of tumors and epidermal samples...the end was that after numerous trips to the koi vet, the woman made one final trip and had the koi euthanized.  I must admit by this point in the talk the entire audience was a little stunned (and it wasn't by the subsequent autopsy photos) and we'll probably all think about koi (and their care) much differently now.  That's pretty much guaranteed.

So, my talk went okay (the only question I was asked involved a gorgonian species that I've never heard of before - figures, doesn't it?).  What sucks is that my ankle is more swollen than it was two days ago, and it's turning a great color...which is a huge bummer since (1) I have never had a sprained ankle before, and (2) I am really bummed that I got one a few days before the Cooper River Bridge Run on the year I actually TRAINED and have my brother flying in to run with me. 

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! 

What's up with the Francis Marion?

In an attempt to understand what is going on in my backyard regarding the selling of some parcels of National Forest land, I found information on the following sites that was useful:

(1)  The Coastal Conservation League's website.   More specifically, they have a link regarding the Francis Marion National Forest  and stresses on the forest due to Mt Pleasant expansion pressures, as well as a link which allows you to respond directly to the US Forest Service (they are accepting comments until Thursday, 30 March 2006).

(2)  The USDA Forest Service's website.    This site has a link to "lands potentially eligible for sale by State and National Forest."  For South Carolina, this is 4,656 acres in the Francis Marion and Sumter National Forests.  The size of these parcels range from 4.43 acres to 373.51 acres (for a pdf of Francis Marion parcels potentially for sale, click here).

I also ran across a washingtonpost.com article (dated 21 March 2006) on the selling of National Forest land with this chilling quote:

"A recent U.S. Forest Service study predicted that more than 44 million acres of private forest land, an area twice the size of Maine, will be sold over the next 25 years. The consulting firm U.S. Forest Capital estimates that half of all U.S. timberland has changed hands in the past decade. The Bush administration also wants to sell off forest land, by auctioning more than 300,000 acres of national forest to fund a rural school program."

Okay, I'm all for funding rural school programs, hell, I'm for funding just about any school program.  But have we gotten ourselves into such an economic mess that we can only sell our National Forests in order to educate our children well?  I certainly hope not.

But so far, it's still an emotional issue for me.  I think the land should be protected, not sold.  In case you're wondering why a forest is so special anyway, take a look at this site that I saw linked on www.musetomuse.com.   

Selling our National Forests...

So,today I was reading yesterday's NYTimes editorial "Selling the Forests" and a more local reminder "What's at Stake in Forest Plan" -- and thinking about the loss of about 1,100 acres in the Francis Marion National Forest.  The Francis Marion is my backyard.  Almost literally.  Over the past few weeks and months I've been thinking about the selling of forest land, and I think I've been so appalled that I've been in denial.  Like...it simply couldn't happen.  I haven't followed the specifics nor have I written my representatives or local newspapers.  Instead I've just assumed it couldn't possibly happen.  That's naive of me, and I've realized this is a purely emotional issue for me - the land should not be sold, under any circumstances. It's a closed issue.  But tonight I sit here and realize what an idiot I am - because I feel the same way about our forests as I have about recent issues related to our individual civil liberties ...we have to fight like hell to not lose them, to preserve them, because once reliquinshed (or sold), then it will be next-to-impossible to get them back again.  Regardless of whether they are civil rights or parcels of land...even if they are "only" a 121 acre parcel of land surrounded by new developments.  I don't care.  I want that 121 acre parcel saved, because perhaps it is an important link in the migration of painted buntings, perhaps even an important link in the migration of a single pair of painted buntings that come every spring to my feeder  and nest somewhere in my one acre of land.  I can't tell you how wonderful it is to have them visit each year.  What a gift!  (The fact that they came this year almost a month earlier than normal is another discussion).  I sit and think about how to improve the habitat in my one acre (more wax myrtles?), while the federal government ponders selling their land for development.  There's a disconnect somewhere, and while I should try and figure out what I don't understand about all of this, I don't what to understand.  I don't want to understand why my government wants to sell this land to developers, and I don't want to understand why they want to reduce my civil liberties.  Call me naive.  I don't care. 

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.

Trained observers...

These are tales from our laboratory, about events or discoveries, both routine and extraordinary, that interest us. Like science, some of these tales will seem mundane, even trivial, and some will seem like wonderful dreams, but between the four walls that comprise our space, these tales enlighten and motivate us. If science is more about how we acquire knowledge than about the specific reactions that occur in a test tube or what microorganism grows on a Petri dish, then this is our acquisition process. So if the lines between science and art and the world in general blur, then we’re probably on the right track. In the words of a friend and colleague Bill, scientists are “trained observers.”

So, these are our observations.  About coral reefs and poetry, laboratory life and art, nanoparticles and music, soils and the Lowcountry, oil and sunken ships...about microorganisms and gardens.

Eyeing the world through slits in my eyes...

I’ve had my own laboratory for about 12 years now. Sounds like a lot of years when I think about it, but I generally don’t have much time to think about it. We started off in a very small space – where we learned how to cram a lot of equipment and supplies and people together – and now we’re in a larger space with a nice view of the lowcountry coastal marshes and we’re still cramming everything and everyone in just the same. We’re a small lab though – in terms of the number of people. I’d like to say the lab has changed along the way – of course the faces have changed and equipment has been replaced and added to and I’m 12 years older than I was – but I’m not so sure those changes are what I’m talking about. I think what we really do is still the same: to take what has been written by others and our own observations and distill them into something to think about, to possibly test, or even take in a new direction. It’s a slow process, sometimes just a dream – and we have to remember (just like with dreams) that if we don’t write our thoughts down right away, that they might just disappear for awhile, maybe even forever. So I guess you could say we have fleeting visions about science, some that prove to be pretty good, and some that might make you wonder “what were they thinking?”.  We can only work hard and hope that there are more of the former (remembered visions) than the latter (lost ones). 

Recently I’ve been taking a painting class by the aeronautical engineer-turned-artist Matt Overend, and several classes ago Matt asked us to choose a painting and copy it. Since then, I’ve become obsessed with a Pierre Bonnard painting titled “The Garden” and have been trying to copy it using watercolors. I couldn’t find this painting online (I didn’t really look all that long), but I did find a reproduction.  Anyway, after obsessing about this painting for weeks I realized that what I was obsessed with was the garden itself, that deep down I thought my very own garden looked the same way. If you squint, I think you can see the similarities…right?   

Anyway, while obsessing about this painting and being swamped in the lab at the same time with a sea of microorganisms collected from coral reefs just off the southern coast of Puerto Rico (La Parguera), I realized that I squint when I look at my lab too. I’m not sure what painting it looks like when I do that, but I know it helps me to blur the lines between the day-to-day failures and the frustrations and the small discoveries and the enjoyment that I get out of the place and it’s transient inhabitants. So I guess Tales from the Microbial Laboratory is the start of chronicling what I (“we”) see and hear and think about when pondering the laboratory and the world that surrounds it through slits in my ("our") eyes.