Beautiful Bacterial Networks in the Marsh

“So,” I’m sure you aren’t wondering, how did that creating ‘ecospecies’ from bacterial sequences based on sequence similarity, co-occurrence, and network theory work out for you?”

Quite well, thanks for asking! Heck, have a git repository, why dontcha!

Jen is furiously writing the manuscript, but, the technique indeed seems to indicate that 12% sequence similarity was the optimal number.

Once we got that down, and started plotting the network with individual Operational Taxonomic Units (OTU) each connected to one or more of the 8 plots they were found in, we started seeing some neat things. More more than that, they were just pretty pictures! I mean, come on, these plots are always cool.

Screen Shot 2013-06-26 at 4.18.40 PM

First, you can see that there is indeed some separation of species by plot and treatment (# is plot, letter is treatment). We got really excited about this, and so dug deeper to produce…

Screen Shot 2013-06-26 at 4.19.49 PM

Yes. Not you can see that most OTUs are specialists. True generalists are exceedingly rare.

We had one other piece of information up our sleeve, though. Abundance. We have abundances of OTUs. Playing around with edge widths (abundance in plot) didn’t produce anything striking. But then we looked at total abundance of an OTU across the whole marsh, and resized OTU nodes accordingly. I think this is exceedingly beautiful. And shows some striking patterns with respect to treatment and who is most abundant.

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Jen knows this experiment backwards and forwards, so is writing a much more nuanced discussion of what this means, and analyzing the data in more detail. But it’s pretty awesome. And pretty beautiful.

Just another way of viewing the wonder of nature.

p.s. I am learning to love RColorBrewer in a serious way

Les Miserables Larides

One of the great things about field stations is the silliness they engender. I mean, there you are, in the middle of nowhere, with no one but other scientists thinking about the wonder of the natural world. Awe and wonder can only take you so far. And then, at some point, you cross over, and start to get a little silly.

It leads to things like dressing up as fouling panels, launching serious plans to make an ‘underwater office,’ elaborate nail-polish-marking designs for crab carapaces, and no small number of pranks.

And then, there’s this. This may be on the order of the silliest things ever to come out of field station. I heard the gull interns (seagull science is notorious for producing silliness alongside great science) talking about this idea to sync some of their videos up with the Les Mis soundtrack and now…now I found they’ve… well..

You must see this to believe it. Astounding. My hats off to the SML 2013 Gull crew. Marine science music video of the year?

(also, who is singing on ‘I dreamed a dream’ – amazing voice!)

PeerJ Turns One!

x-posted from openpub

One year ago, one of the more intereting experiments in open access publishing – PeerJ – launched. It’s model of membership rather than paying by the article is still something people are grappling with – it’s just so different, so delightfully disruptive. Not only that, but PeerJ has stepped in to fill the void in providing a biology preprint server (which we have used), as well as coming up with a more intuitive interface for commentary on preprints and published work – along with supplying reviews alongside published work. A number of other great open access journals have tried one or more of these innovations, but few have tried them all *at once*. Not only that, but I have the feeling they’re not going to stop there.

After all, if they’ve tried this many new things in year one, I, for one, want to know what year two is going to hold…

Walkin’ in an Invasive Wonderland

Last day of dives before heading back. We hit two sites on either side of the northern head of Appledore. It’s a remarkable break, as on one side you have fairly decent expsore to waves from the West. On the other, things are fairly protected. So, there’s a strong physical gradient. And, though perhaps just a few hundred meters apart, the two sites could not be more different. At the first site, the photos didn’t come out terribly well, but this gives you a general sense –

It was Halosiphon as far as the eye could see - like diving in a bed of furry ropes.  Or very thin muppet arms.  No, wait, that's just odd... although it would fit nicely in  Dark Crystal or Labyrinth.

It was Halosiphon as far as the eye could see – like diving in a bed of furry ropes. Or very thin muppet arms. No, wait, that’s just odd… although it would fit nicely in Dark Crystal or Labyrinth.

Lots of adorable cunner swimming about, but, man, churned up. A little Heterosiphonia about, but, not too bad.

Then we rounded the corner. And saw…


It’s like somebody defauntated the rumpus room and decided to give the entire subtidal a nice shag carpet. I mean, sure, it hides the stains, but…

More than that, the site was quite bouldery. But what invertebrates were on the boulders?


Oh, look! It’s my old friend Didemnum vexillum from the Left Coast. It’s here, in force. I’ve seen spots of it all week, but, nothing like the giant area covering colonies of the Bodega Harbor jetty or the docks. And yet, here it is. Sure, there’s some Desmerestia thrown in for good measure, but, more or less, it’s all invasives, all the time down here.

What is going on? How long will this state last?

Undersea Carpets?

The second site of the day was a surprise. 10 years ago, Smith’s Cove was a mixed mussel bed and urchin barren. Previous, it has been a Codium meadow. Now… It’s just a giant red algal carpet. Wall to wall. Thick, easily fragmenting, ubiquitous, invasive red Heterosiphonia japonica. Also, big tufts of Ulva. And some other bushy filamentous algae scattered about, along with a few crabs.


What a weird landscape. What is that red carpet doing? Smothering things? Creating habitat for mobile invertebrates? Providing food, or is it not that edible? The reef was like this as far as we swam and looked around – hundreds of square meters. Weird.

Yeah, that's 100% cover.

Yeah, that’s 100% cover.

Kelp on a Ledge!

Day 2 of dives with Sarah out at SML. Today we hit two sites that were quite different – both from each other and from Norwegian Cove the other day. The Ledges are in the channel between Appledore and Smuttynose, so, they get good flow running through. This was key, as it blew sediments from the previous day’s storm out fairly quickly. And viz was really quite nice. While it used to be a barren (at least on one side) 10 years ago, it appears that it’s now a mix of kelps and Desmarestia with some Chondrus, filamentous reds, and others thrown in for good measure.

A nice mixed algal assemblage.  And a mix of kelp ages and sizes.

A nice mixed algal assemblage. And a mix of kelp ages and sizes.

Indeed, some parts were super kelpy, although, not dominated by large adults. The mix of sizes was fairly astounding, even where thing were at high densities.

Note all of the little guys hanging about.  I mean, it is still early June, so, it may be recovery.  But how cute are these little ruffled kelpies!

Note all of the little guys hanging about. I mean, it is still early June, so, it may be recovery. But how cute are these little ruffled kelpies!

Note all of the holes you see, though. The site was also packed with little snails like Lacuna vincta that appeared to be doing quite a job on the kelps.


What will this mean for later in the summer? Particularly with Heterosiphonia around in patches.


All in all, a nice site to sample. More soon on Smith’s Cove. Which was…

Day 1: Back in the field!

Well, today was it. After a 2 year hiatus behind my computer screen, my skin now softer and more delicate from its soothing rays, I hopped back in the water FOR SCIENCE! Not only that, but it was my return to dry suit diving. Oh, dry suit diving. I really didn’t miss you and your weird buoyancy tricks (note to self, get ankle weights, as old ones have desintegrated).

It was a great day, despite feeling kinda like the first day back at school. Ted (lab manager) and I came out to SML to work with a fantastic undergrad I’m advising for the summer, as well as do some site scouting of our own. The weather report said that things would turn awful in the afternoon/early evening (and was right), so, a morning dive on the backside of Appledore was just the thing.

This truck is loaded WITH SCIENCE!

This truck is loaded WITH SCIENCE!

Ted ready to go

Ted ready to go

We were there to help Sarah census the invasive Heterosiphonia japonica to look at its distribution with respect to a depth and exposure gradient (see also this kick butt paper by Christine Newton et al.). And the backside of Appledore is quite exposed. The transects we were sampling are next to a spot in the intertidal that got wiped bare by this winter’s storms.

Photo by Ted of Sarah (L) and I about to plop down our first transect.

Photo by Ted of Sarah (L) and I about to plop down our first transect.

What intrigued me about the transects was two things. I remember this area being super-kelpy. Indeed, the wave exposure limited Codium back when that alga was the big bad (I’ve heard it’s quite rare here, and in a quick checkout at The Cribs, I only saw 3 individuals). But now…well, there are some kelps, but, mostly, it’s red and brown filamentous algae. A lot of Desmerestia viridis to be sure, but a lot of red and brown puffiness. That, and a lot more Chondrus. I mean, we were fairly shallow, but, still. Interesting.

Photo by Sarah of one of her transects

Photo by Sarah of one of her transects

Not a lot of Heterosiphonia, though. It’s going to be interesting to see how Sarah’s project turns out. Some sites have been heavy with it, some light.

I’m just glad to be back in, and seeing how the place has changed. Steneck’s Flips & Locks paper was an interesting update on how this system is doing. I’m going to be curious to browse around and try and take the big whole community perspective I honed at the SBC LTER and see what there is to see here.

A great photo by Sarah of a school I totally missed.

A great photo by Sarah of a school I totally missed.

True Facts About Marine Life

Because there hasn’t been enough ocean silliness lately…

I’ve long been a fan of Ze Frank. But who knew that one of the next places he’d be turning his razor sharp with was on the natural world. And not only that, but, he’d make sure everything is pretty much scientifically kosher. So, I give you three things that nearly made me laugh so hard I was almost glad I wasn’t in a drysuit (because tight neck seals and laughing = no fun?), in escalating order of hilarity. Note, some of this is not so SFW in a mild manner, but certainly always SFDSN.