Merging a phylogenetic tree with a heatmap in R

***UPDATE***

I was recently introduced to a great tool for working with phylogenetic trees that can do something similar to what I describe below (and a whole lot more).  Check it out at http://itol.embl.de/.

******

It seemed like a simple enough task at the time.  I have several sets of classified 16S 454 reads from which I’ve tallied the number of members for some genera of interest.  Id like a heatmap showing the abundance of these genera, with a phylogram showing the relationship between genera (rows).  Since the heatmap and heatmap.2 (package gplots) commands in R both support row ordering by dendrograms I thought this would be easy.

The first step was to find a single representative sequence for each of 134 genera that I want in the heatmap.  I used sequences from the RDP for this.  I aligned and trimmed these sequences using standard methods in mothur (my favorite 16S analysis program) That’s the easy bit.

Attempt 1 – A dendrogram should never be confused with a phylogenetic tree.  Despite knowing this I thought I could approximate a phylogenetic tree by building a distance matrix outside of R (in clustalo) and performing the clustering inside R (using hclust).  The result was a nice looking dendrogram that had clear flaws in illustrating evolutionary relationships.  This basic method may actually work, but for reasons that will become clear it didn’t in this case.

Attempt 2 – I decided to build a tree in fasttree (superb tree building program) and then, somehow, get the tree into R and trick R into thinking that it was a dendrogram.  Using package ape this is pretty easy.  Ape even has a method for converting the tree to a dendrogram.  The problem is that the tree must be rooted, bifurcating, and ultrametric (each tip equidistant from the root).  This took a substantial bit of tweaking but I was able to get it:

##### create tree as dendrogram for row order #####

library(ape)

rep_tree <- read.tree(‘../known_degrader_rep.tre’)

#For the root I selected the node between the two Archaea and Planctomyces

rep_tree_r <- root(rep_tree,
                   resolve.root = T,
                   interactive = T
                   )

#can’t have any branch lengths of zero or downstream commands will collapse those nodes…

rep_tree_r$edge.length[which(rep_tree_r$edge.length == 0)] <- 0.00001

rep_tree_um <- chronopl(rep_tree_r,
                        lambda = 0.1,
                        tol = 0)

rep_tree_d <- as.dendrogram(as.hclust.phylo(rep_tree_um))

plot(rep_tree_d)

Great!  When I created the heatmap however, I found that there is a major hitch in this method – and any other method that performs clustering separate from heatmap creation.  The heatmap and heatmap.2 commands don’t match up the rows and dendrogram tips by name (in my case by genera), but by the index of the the data as it was first imported into R.  Since I imported my tree and the abundance table separately each genus was assigned a different index.  Using the root() command prior to converting my tree to a dendrogram made it difficult to reconcile the two, because the index values of the dendrogram were no longer in order.  Reordering my abundance matrix so that it matched the index values, but not their current order, took a bit of thought.  Here’s the code I came up with, I’m sure there is a cleaner way…

#force row order so that it matches the order of leafs in rep_tree_d

clade_order <- order.dendrogram(rep_tree_d)

clade_name <- labels(rep_tree_d)

clade_position <- data.frame(clade_name,
                        clade_order
                        )

clade_position <- clade_position[order(clade_position$clade_order),]

new_order <- match(clade_position$clade_name,
                   row.names(combined_matrix)
                   )

combined_ordered_matrix <- combined_matrix[new_order,]

And that seems to work nicely – combined_ordered_matrix is in the same order as the dendrogram INDEX (not the dendrogram leaves).  When the heatmap is constructed the accompanying phylogeny looks fine.  Note that in the following code I’ve switched all zeros to NAs to differentiate between an abundance of 0 and a low abundance:

##### Generate heatmap #####

library(RColorBrewer)
library(colorRamps)

color <- colorRampPalette(c(‘white’,’blue’,’red’))(100)

row_col_table <- read.table(‘../genera_row_colors.txt’,
                            as.is = T)
row_col <- row_col_table$V1

combined_ordered_matrix[which(combined_ordered_matrix == 0)] <- NA

library(gplots)
heatmap.2(combined_ordered_matrix,  
          margins=c(7,10),
          sepcolor=”white”,
          sepwidth=c(0.01,0.01),
          Rowv = rep_tree_d,
          Colv = F,
          dendrogram=’row’,
          colsep=seq(1,10,1),
          rowsep=seq(1,134,1),
          key = TRUE,
          trace=’none’,
          col=color,
          lwid = c(2,5,5,10),
          lhei = c(1,50),
          cexCol = 0.7,
          cexRow = 0.7,
          RowSideColors = row_col,
          density.info=c(‘none’),
          scale = ‘none’,
          na.color = ‘yellow’
          )

If you run this code you’ll notice that the margins don’t allow the key to show.  Still have to fix that.  Here’s the resulting heatmap and phylogeny with 0 values as yellow and the remaining relative abundances on a white-blue-red scale.

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New blog purpose

This blog was originally intended to share the experiences of our group while we conducted field work in Antarctica during the Austral winter/spring of 2011.  The further I get into analysis however, the more I find myself needing a place to document progress and solutions to problems.  I’ve been using a more “raw” space accessed via the Research Wiki link in the header of this page for this, but will now start using this blog space for more polished ideas and solutions.

A major motivation for doing this is to make my solutions and ideas accessible to others who might be doing similar work.  Almost every day I rely on someone’s blog or forum post to overcome an analytical problem.

For those who followed the Antarctica Blog (thank you!) the format will be a little different.  I envision that the posts will be shorter and more technical, however I’ll try to keep it entertaining and informative.  Due to an excessive number of spam comment posts I’ve disabled new subscriptions, however I might change this in the future.

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And that’s it!

Shelly and Stephanie peering down the observation tube.

In thirty minutes we will catch a ride to the airfield for our flight back to McMurdo.  It’s a good day to fly home, warm with a clear sunny sky.  It’s hard to believe how nice it is after yesterday, when the storm that had been blowing for three days reached its peak.  The winds were pretty incredible, at the height of the storm it was easy to imagine that it would be days before everything calmed down enough for flights to resume.

A cloud of invertebrates hovers below the sea ice, feeding on ice algae and phytoplankton. In a couple more weeks there will be even more life feeding on the algal bloom.

Despite the good weather today our flight was still delayed by the severe drifts that had built up on the runway.  For the first time in nine weeks we enjoyed not having any work to do.  To pass the time Shelly, Stephanie, and I went down to check out the observation tube, a metal and plexiglass tube installed into the sea ice a short distance from the station.  Crawling down into the tube puts you several feet below the bottom of the sea ice and opens up a view otherwise available only to the research divers.

An inch tall sea butterly drifts close to the observation tube window.

A substantial amount of snow covers the sea ice near the observation tube so it’s quite dark below the ice (compared to the sea ice near Tent Island, where we have been sampling).  As a result the spring algal bloom hasn’t really gotten going yet.  Despite this lack of algal growth there was an abundance of invertebrate life, mostly delicate little organisms called sea butterflies.  It was mesmerizing to sit in the cool blue and green light and watch the cloud of butterflies drifting by.  A great last mental image of Antarctica!

Thanks to everyone who followed along on our adventure by reading this blog.  Although this is the last entry we will still answer questions posted to the Q&A page.  The blog itself will remain accessible and searchable.  The best of luck in all of your adventures!

-Jeff

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Fourth time’s the charm

One of the many glaciers that cascade into Taylor Valley on the approach to Taylor Glacier.

Made it! We had great weather Friday and no trouble reaching Taylor Glacier. The whole Taylor Valley is a remarkable place, but it was really something to stand on top of the glacier itself and take it all in. The scenery in the valley on the approach to Taylor is remarkable. The McMurdo Dry Valleys are often described as “Martian”, though I’m not sure how well the description fits. The soil’s the right color but everything else is wrong. The valley is narrow with jugged alpine peaks on both sides (some of the mountains and glaciers have famous namesakes in the Alps, and they really do look the part). Despite the lack of precipitation and the valley’s name it seems that every gully or saddle screams “water!”. It’s just that the water happens to be locked in glacial ice. The Dry Valley’s look Earth-like, just not from this era. Primordial is a word that fits well.

Looking down the nose of Taylor Glacier toward Lake Bonney, visible at middle-left, as we come in to land.

At the foot of Taylor Glacier is Lake Bonney; a bizarre perennially ice covered lake. Seasonal streams feed the lake and others further down the valley (ironically the Dry Valleys contain the continent’s largest river, the Onyx, in nearby Wright Valley). Like everywhere else in Antarctica the biology is hidden away below the ice of Lake Bonney, out of view of the casual observer in a helicopter. Glaciers and ice covered lakes hide rich ecosystems in their depths. Here temperatures are more moderate and bacteria can exploit geologic sources of energy. Life makes a showing at the surface only during the warmest weeks of the summer when parts of the glacial surface began to melt, forming cryoconite holes. These holes form where sand, rock, or other dark material collects at the surface. This material efficiently absorbs energy from the sun, warming a small area on the surface and causing local melting even when the air temperatures are well below freezing. This forms a small pocket which collects more sand causing it to melt a little further. By late summer these cryoconite holes host rich communities of cyanobacteria and other organisms.

Rotor wash on a smooth ice surface leads can lead to lots of scattered gear. On any tenous surface the helicopter unloads us "hot", without shutting down, meaning that the first few minutes at a sampling site are a loud, confusing scramble to get everything unloaded and protected before the helicopter takes off. Here we sort ourselves out after the helicopter departs. Photo: Shelly Carpenter.

We could see evidence for these holes everywhere on the glacier’s surface as puddles of solid, crystal clear ice. There won’t be any melting going on here for some time! Unlike many glaciers in wetter climates, the surface of Taylor is not composed of densely packed snow. The whole glacier is solid, blue tinted ice. Standing on Taylor Glacier is like standing on one giant blue ice cube. This very cold, very solid ice is also proved rather difficult to cut into with our coring equipment. In the same amount of time at Wilson-Piedemont Glacier two weeks ago we collected twice as much ice as we did at Taylor.

With the sampling going slower than expected we had little time to savor our surroundings. Only a few minutes past between filling our last sample container and hearing the thud of the helicopter working its way back up the valley. It was unsatisfying to leave such a beautiful place without a little more time to explore, but it was late in the day and we were exhausted.

Back at McMurdo there was little time to rest. Samples from Tent Island and Taylor Glacier needed to be processed quickly so that we could start packing up the lab. If the weather allows we fly back to Christchurch on Wednesday, which is rapidly approaching! The last ice from Taylor Glacier is still filtering in the lab, but almost everything else has been cleaned, broken down, packed up or returned! A few hours of work tomorrow to wrap up loose ends should be all that we need to conclude a remarkable nine week effort…

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Smelling sulfur

Dense algal growth at the bottom of sea ice cores from our Tent Island site. Photo: Shelly Carpenter.

Shelly and I completed our last round of sampling at Tent Island yesterday. Normally we get a bit of wind protection from the island but not this time, it was possibly the coldest we’ve been in the field on this trip! Two weeks ago when we sampled ice cores from that spot we saw the first signs of the spring ice algal bloom; a slight brown coloration to the bottoms of the ice cores. By now the algal bloom is in full swing, with a thick mat of algae covering the bottom of each core. The growth is so thick that water flooding out of our drill holes is a soupy brown color, very much like the surface of a stagnant marsh pond (except this water isn’t stagnant of course; fresh, nutrient rich water is circulating in from the Ross Sea).

Everything takes longer on a cold, windy day and we had a couple of extra samples to collect. By the time the helicopter came to pick us up we were exhausted. After a good night’s sleep we’re ready for our final sampling effort – our fourth and hopefully final attempt on Taylor Glacier! Right now the weather looks promising, if it holds for a few more hours we’ll have it…

Whenever we bring samples back from the field we start melting them immediately so that we can filter them as quickly as possible. When I opened our sampling bins last night to start melting the samples I was greeted with a very strong odor that I should have anticipated. The samples, particularly the more algae rich samples from the ice core bottoms, reeked of sulfur. The smell was very much like what you might find at a tidal mud flat, but much stronger. The source of the smell is the same in both cases; a compound with the fancy name dimethylsulfanopropianate, or DMSP for short. DMSP is a small hydrocarbon molecule that also contains the element sulfur. When algae or phytoplankton are stressed (for example when trapped in newly forming ice, or on a rapidly drying mudflat) they release this compound. In sea ice DMSP is though to help the ice algae cope with the rapidly changing salinity caused by ice formation.

Water vapor is a potent and abundant greenhouse case. Altering the distribution and structure of water vapor through cloud formation can have a significant impact on climate. Image by Robert Rhode for Global Warming Art.

DMSP has received a lot of attention in recent years because it has some implications for regional and global climate. Many marine bacteria can use DMSP as a source of food, a process which converts DMSP to the volatile compound dimethylsulfide (DMS). DMS is probably the largest pool of sulfur in the atmosphere with a biological source (there are large industrial inputs, as well as natural inputs that don’t directly involve biology). In the atmosphere DMS converts to sulfuric acid, a very efficient nucleator of the droplets that form clouds (check out this YouTube video for a further explanation of how cloud nucleation works).

Clouds are basically water vapor, and water vapor is a very potent greenhouse gas. Scientists are still unsure of how exactly clouds impact climate, and how clouds might change as climate changes. One idea is that high altitude clouds have a different impact on climate than low altitude clouds. Both reflect and absorb solar energy and energy radiated from the Earth’s surface. Clouds must radiate the energy they absorb, how that energy is radiated is determined by the cloud’s temperature. One implication might be that cold high altitude clouds warm the atmosphere less than warm low altitude clouds. Consider a bloom of ice algae in relatively warm water underlying a cold atmosphere and producing copious quantities of a powerful nucleator. The resulting clouds will be very low in the atmosphere.

We don’t really know how communities of ice algae and ice microbes are changing with a changing climate, nor do we know how communities of phytoplankton and marine bacteria are changing. Without that knowledge we can’t predict how biology will influence cloud formation in the future. Taking it a step further we can see the full circle: climate changes biology, which changes clouds, which impacts climate, which further changes biology. It’s an interesting problem, there are three different interactions here that we know very little about!

Clouds distributed on NASA blue marble imagery. From Global Warming Art.

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Win some lose some

We saw Emperor and Adelie penguins at Beaufort Island but no open water anywhere, leading to the question where are these birds feeding? This isn't an idle thought; the colony at nearby Cape Crozier failed to successfully rear any chicks on years when the configuration of icebergs calving from the Ross Ice Shelf trapped sea ice near the colony, blocking access to open water and food.

The last few days have been fast and furious as we try to wrap up our sampling program. We fly back to New Zealand in exactly one week which means that time is quickly running out! Fortunately we’re getting close to complete. We lucked out on Monday with superb weather for our flight to Beaufort Island. A large network of leads often forms around Beaufort at the interface between the freely drifting pack ice and the ice loosely anchored to the island. The most recent satellite images that we could obtain, from late September, looked promising. Unfortunately when reached Beaufort we couldn’t find open water or young sea ice anywhere. The thinnest ice that we could find was over 50 cm thick, suggesting that the leads had frozen over soon after the satellite images were taken.

Pull very short ice cores from young sea ice after sampling frost flowers. You can see one of the short cores in the lower right of the image.

This was very disappointing. With time running short we decided to head to nearby Lewis Bay on the north side of Ross Island where we sampled on Saturday. The ice and frost flowers in Lewis Bay are pretty old, but a lot younger than what we found off Beaufort. Enroute to Lewis Bay however we stumbled across a very large, recently frozen lead with ice only 13 cm thick. Perfect! This is thick enough to work on with little risk of breaking through but thin enough that the lead must have been open just days before. Every surface on the lead was coated with frost flowers. They looked a little droopy in the heat (-15 C and sunny!), but good enough for us…

It takes a while to find solid landing sites next to thin sea ice like this; the pilots need a solid 30 inches to land the helicopter. By the time we found a spot and got sorted out for sampling it was getting late in the day, we are grateful for the helicopter crew’s willingness to stay out a little longer to get the job done!

So close yet so far away. Looking down at Taylor Glacier and Lake Bonney at the point of turnaround. Visibility was good but the winds were too high for a safe landing on slick glacial ice.

Back home there was little time to rest. We had to re-sterilize our equipment and get turned around quickly for a trip to Taylor Glacier the next day. The weather didn’t look too promising from the McMurdo helicopter pad but we decided go ahead and try for it. We made it across the Sound and all the way up the Taylor Valley before high winds forced us to turn around. It was heartbreaking to look down on our sampling site and not be able to reach it, but the pilots here are an experienced bunch and we have to trust their judgment. Conditions continued to deteriorate as we crossed McMurdo Sound back to the Station. We were within 10 minutes of the helo pad when visibility and a rapidly descending ceiling forced us to turn back around and return to the west side of the Sound. Having just been chased east by bad weather it was a little like being caught in a vise.

There are worse places to be stuck. Waiting out the weather at Marble Point.

This sort of thing happens fairly frequently however, and as a result there’s a way out. A small fueling station and field camp is maintained at a site called Marble Point, at the foot of the Wilson-Piedemont Glacier. Three people staff the fueling station and they’re always ready for visitors. The crew of another helicopter, also trapped on the west side of McMurdo Sound, was already there. We sat down for a large, delicious hot lunch, cookies, and lots of coffee before deciding what to do.

Marble Point is very close to our old sampling site on the Wilson-Piedemont Glacier so we decided to take the opportunity to collect fresh snow from nearby. This is a sample we were planning to collect later in the week. It didn’t take too long (it was probably the easiest sample we’ve collected on the whole trip), so we enjoyed the scenery while we waited for the helicopter to take us back to Marble Point for more waiting. And wait we did. Just as we were reconciling ourselves to spending the night at Marble Point (which with their cozy bunkhouse is not a bad thing) a brief weather window opened around McMurdo. We hurriedly loaded the helicopter and went for it. It was an interesting flight. A full ground blizzard was blowing at the sea ice surface as we flew into McMurdo, it looked like a vast river of snow moving underneath. At altitude the helicopter was riding on waves of air, it felt rather like being on a small boat in ocean swells. The motion was never alarming, just a constant reminder of the energy on the other side of the thin plexiglas windows.

Shortly after we landed the weather window closed. Our flight to Taylor was rescheduled today and canceled. We are now 0 for 3 on Taylor Glacier. Tomorrow we will try to visit our Tent Island site which should be easier than reaching a glacier deep in a windy valley. That leaves Friday and Saturday for renewed attempts at Taylor. After that we need to close up shop and get ready to head home!

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Ross Island’s North Shore

The weather finally cooperated with us and we made it out for our reconnaissance flight on Saturday. We even managed to bag a couple of samples along the way. After spending the last 8 weeks on the south side of Ross Island it was very interesting to see the north side. The mountains drop more dramatically into the sea on here, and the ice over the open waters of Ross Sea presents a much more fractured and dynamic surface than we normally see in McMurdo Sound. All together it makes for a much more dramatic backdrop while we work.

On thin ice. Jen belays me at the transition from thick ice to the thinner young sea ice.

We worked our way around Ross Island in the counter-clockwise direction. As soon as we rounded Cope Crozier we started probing the sea ice, looking for ice thick enough to land next to ice thin enough for us to sample. Finding this combination isn’t easy. When we spotted a suitable ice flow that we thought was thick enough to land on the helicopter would set down gently with the pilot keeping the rotors spinning at full power. Working under the spinning blades someone would hop out and quickly drill the ice to see how thick it is.

The recce crew. Me, field safety tech Jen, and Shelly. Very ably transported by Paul and Matt.

There’s a pattern to the distribution of ice thickness in both land fast ice and pack ice (the ice not anchored to the land), but it takes a little while to start to see it in a new area. Successive storms, cold snaps, and the underlying pattern of prevailing winds and currents establish a checkerboard of thick and thin flows. After we checked a few flows and found them too thin to power down the aircraft we started finding flows that were thick enough. Once we were dialed in on the thicker floes we were able to piece together a safe path along them to the younger sea ice.

We didn’t find any truly young sea ice. The thinnest ice that we found was 28 cm, probably about two weeks old, though this ice was covered with old, moderately salty (60 ppt, roughly twice the salinity of the ocean) frost flowers. Although the ice was plenty thick to walk across we took the opportunity to test out techniques for working over thin ice. Hopefully we will need these techniques for our next foray. If the weather allows on Monday we will head back out to the north side of Ross Island, this time working to the northwest toward Beaufort Island. From our reconnaissance flight we could see thick pack ice all the way to Beaufort and a glimmer of sunlight off of the lead that seems to persist in a semicircle around it. With luck that lead will be full of very young ice and frost flowers!

Spectacular scenery on the flight back, including this up close and personal view of the Erebus volcano caldera.

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Further weather woes

Satellite image of Beaufort Island on September 24, 2011. You can see the young ice forming on the large lead network to the southeast of the island.

The weather’s still playing tricks with us. We were supposed to fly to Taylor Glacier today, high in the McMurdo Dry Valleys, to sample more glacial ice. It looked hazy all morning but flights were still heading out. Our flight was scheduled for noon but deteriorating conditions in the Valleys forced us to wash at the last moment. Trying not to lose another sampling day we hurriedly made alternate plans to revisit the Wilson-Piedemont Glacier to collect snow (an effort that was scheduled for next week). WP is much lower than Taylor Glacier and since we’ve already surveyed a landing site there, much less risky to travel to under marginal conditions. Before we could take off for our alternate target however conditions deteriorated to the point that not even WP was a viable target.

We left our gear at the helicopter hanger in the hope of better conditions tomorrow and trudged back up the hill to the Crary Lab. Shelly and I are both pretty tired today; we worked around the clock to get our WP samples processed prior to collecting at Taylor Glacier. We finished filtering the last WP sample only moments before we were due at the helicopter pad. There’s one good thing about that; with no lab work to do we can enjoy a relaxing afternoon off!

If the weather allows us to fly tomorrow we will try to circumnavigate Ross Island looking for open water where we might find new ice forming. That’s a flight few people get to make and I’m really looking forward to it. If we find promising leads next to solid ice floes we will try to land the helicopter and collect frost flowers. More importantly the flight will serve as a reconnaissance for the culmination of our frost flower collection efforts on Monday, a trip to Beaufort Island (if the weather is good…). Beaufort Island is a distinctive mountain of an Island that juts out from the Ross Sea. It is so remote that it is almost never visited, despite the fact that it contains Adélie and Emperor penguin colonies and an abundance of other wildlife. We can’t set foot on the Island – it’s specially protected – but we can visit a distinctive large lead that forms to the south of it. This lead is present in every springtime satellite image that we can find and will be ideal for collecting frost flowers.

We got lots of frost flowers around Cape Royds earlier in the season (and will hopefully get more around Ross Island tomorrow), so why go through all the effort of collecting frost flowers way out in the Ross Sea? The bacteria that are found in frost flowers originate from seawater, and the microbial communities that inhabit coastal seawater and open ocean seawater are very different. In Barrow, Alaska and from within McMurdo Sound we’ve collected lots of frost flowers enriched with coastal marine bacteria. We’ve yet to look at the microbial community within frost flowers forming over the open ocean and this will be a rare opportunity to do so!

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Wilson-Piedemont Glacier

McMurdo Sound, with the Wilson-Piedemont Glacier in the upper left.

Monday was a spectacular day and we had no trouble getting out to collect samples on the Wilson-Piedemont Glacier. WP is a broad coastal glacier at the northwestern most extent of McMurdo Sound. Because the wind often blows from the southeast the WP is ideally located to collect small particles eroded from the surface of sea ice in the Sound. WP, like other glaciers, is almost entirely fresh. Researchers have shown that glaciers do contain small amounts of sea salts however, and there is further evidence that some of these salts may come from frost flowers. Glacial sea salts are just a little bit depleted in sulfate relative to the other ions, suggesting that the salt must have come from ice so cold that it contained no sodium sulfate (see “Pass the salt” for a further explanation). Frost flowers, saline snow, and other similar cold salty features at the sea ice surface seem like a logical source for this salt.

Shelly and Susan from the McMurdo field safety team hunker down while a helo, packed door to door with samples, takes off.

Our task at WP was to collect enough ice to determine whether bacteria and bacterial genes present within frost flowers might also be present within glacial ice. There aren’t a lot of bacteria within glacial ice – maybe 1,000 bacteria per milliliter compared to 100 times that many for sea ice – so we have to collect a lot of it. It took two helicopter flights to get us and all of our sampling containers to and from the glacier. We didn’t count the number of ice cores we pulled from the glacier surface but we later estimated that it took around 60 to fill 12 of our 20 gallon sample containers. Loaded each container weighs around 90 lbs, getting them back on the helicopter for the flight out was no easy chore!

Shelly collapses on a much-cored Wilson-Piedemont Glacier.

The dependence on helicopter flights and large sample volumes meant that we had very little time for exploration. This was too bad as the view from WP is truly spectacular. Our site was located next to the Bay of Sails, so named because large icebergs calving from the Ross Ice Shelf on the other side of Ross Island are frequently trapped in an eddy and driven aground in the bay. It looks like someone anchored a fleet of icebergs here, and the more distant ones really do look like sails. It isn’t difficult to imagine the frustrations of early explorers anxiously awaiting the arrival of a relief ship and trying to convince themselves of what was and wasn’t an iceberg.

On the flight home a tantalizing glimpse of Beaufort Island, with several large icebergs in the foreground. With luck we will be flying to a large lead off Beaufort Island next week for more frost flowers, but weather conditions will need to be ideal.

Fortunately we will be visiting WP one more time, to collect fresh snow drifted near the edge of the glacier. In the meantime we’ll be working hard to get caught up on labwork. We have a flight to Taylor Glacier on Friday and over a thousand pounds of ice to melt and filter before then!

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Multiyear ice

Helo flight to Tent Island. Photo: Shelly Carpenter.

The helicopters started flying last Thursday and with their support we’re getting back on track with sampling. Friday we made it back out to Tent Island for our third sample there. It was great to make the trip in less than 10 minutes after all the hours we’ve spent driving that route! The only downside to this mode of transportation is the need for good weather. We had ambitious plans to fly to the Wilson-Piedemont glacier on the far side of McMurdo Sound Saturday for our first glacial ice sample, but fog grounded the helos for the day. Landing on glaciers is tricky business; the pilots are only willing to attempt it with good visibility. Tomorrow we’ll try again, hoping to net two large samples from a single trip. Time is running short – we leave November 2 – so we need to maximize every trip out!

The helicopter crews take Sundays off so we couldn’t fly yesterday. It was a warm (for Antarctica), sunny day so we decided to take a snowmobile trip to Turtle Rock, a little island tucked into a back pocket of McMurdo Sound. Turtle Rock is an interesting feature because it guards a bay full of sea ice which has not melted in many years. We call this ice “multiyear ice”. Until last year most of the ice in the south end of McMurdo Sound was multiyear ice, but a massive breakup of the ice last spring removed almost all of it. The ice that we have been working on so far is first year ice that only formed this winter.

Have you found the bottom? Shelly digs through several years of snowdrifts ontop of meltiyear ice in McMurdo Sound.

We’ve done a little work on the microbiology of multiyear ice in the Arctic but a lot of questions remain. When sea ice forms in the fall it traps lots of bacteria from the seawater. These organisms aren’t adapted to life within the sea ice, but they persist there through the winter. When spring comes and the ice algae begin photosynthesizing these seawater bacteria are outcompeted by specialized sea ice bacteria that metabolize well under low temperatures and with a lot of organic carbon (produced by the ice algae). If sea ice survives that first summer to become multiyear ice however, what happens to those specialized sea ice bacteria? The ice algae use up the nitrogen, phosphorous, and other nutrients present in sea ice the first summer and can’t maintain the same level of photosynthesis in later years. The sea ice bacteria (which can perform better with little organic carbon) are long gone from the sea ice matrix. Does biological activity slowly grind to a halt, or is there a succession to a new microbial community adapted to low temperatures and low levels of nutrients?

Before we can answer these questions we need to acquire some cores of multiyear ice, something easier said than done. Reaching the multiyear ice behind Turtle Rock was easy enough but coring it proved quite difficult. First we had to reach the ice surface. It’s not uncommon to find a couple feet of hard, wind packed snow on top of the ice you want to core. In this case we had 7 feet of snow to tunnel through! Shelly and I cleared ourselves a pit large enough to work in and started coring. With limited space maneuvering the drilling equipment proved challenging, we were constantly climbing in and out of the pit to help lift the corer in and out of the hole. Multiyear ice can be 5 meters thick or more, after only two meters we had to quit for the day. With luck, time, and a couple of intrepid volunteers we might be able to finish that sampling effort before we leave. In the meantime we have more important objectives… collect our critical glacial ice samples and then start using the helicopters to access the ice edge for more frost flowers!

Satellite image of the southeastern portion of McMurdo Sound from February 24, 2011. This is close the point of minimal ice extent for 2011. The small pocket of ice behind Tent Island was persisted for many years and will persist into the 2011 winter.

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