Finally an update!

I'm still alive, barely. Just joking. Although it certainly has been a stressful last week. We had two consecutive LD stations with just a short one day breather to get all our stuff together for a final go at all the incubation experiments and other sampling.
Everyone thought that this deep deep blue patch of watery desert would be ideal for studying physical, optical and chemical parameters since there didn't seem to be any biological interference whatsoever. Oh how wrong they were.
Initial microscopy counts and fluorescence data from the CTD suggested that we had loads of UCYN at 60 m of depth and a deep chlorophyll max at ca 140 m of depth. Chlorophyll is the pigment that help the phytoplankton photosynthesize.
Some scientists onboard was of course super excited about this when we later confirmed a UCYNB bloom at 60 m of depth (us included).
So in the end, when looking closer below the surface, this desert-like water mass harbored more microbial activity (in terms of UCYN) than we had ever encountered before on the cruise. Who would have thought?

The reason why I have been slow on posting any updates on the blog is simple. We are nearing the end of the cruise and there's lot and lots of reports, presentations and protocols that needs to be written or files that needs to be filled out with data and whatnot.
I've been super busy and after a day of trying to piece everything together in front of my computer, the last thing I want to do is write another wall of text. Sorry.

Anyway, today was the 14th (out of 15) SD, which means that my last day of science will be tomorrow. After that there will be a lot of packing and organising to be done, to make sure that everything, our precious samples included, get back to Stockholm in one piece.

Now I have to finish an abstract for a conference in August. Deadline is the 1st of April. I might have a more detailed update for you in a couple of days.

Stressful plans

Did I ever mention that we often have change of plans on board? I have a strong feeling I did, more than once. So this post might not come as a surprise. Almost immediately after my last post on the subject of downtime I was reached by the news that we would have an improvised short duration station (SD) 14 at midnight, only using a single CTD cast for everyone interested. Imagine the craze following when 20 scientists more or less battled for their tight water budgets from the CTD rosette.

The purpose of this extremely short SD, where we litteraly just stopped 45 minutes to lower the CTD and get it back up again before setting out for Niue, was to get a picture of the water column in a suggested ultra-oligotrophic area just outside of the large phytoplankton bloom. This site could, depending on the results of the quick survey, become our next and final long duration station (LD).

Extremely local rain cloud on the shores of the small island nation of Niue.

Naturally, when such decisions are to be made, me and my colleague were asked to run the qPCR. This made our water demands a lot easier at least. Concerning pros and cons for this site, our data was more or less the only parameter that could tip the scale in favor of coming back after leaving the injured crewmember at Niue. The chief scientist was hoping to find a UCYN bloom for our final LD, since we missed out on a great opportunity south of Fiji due to the massive tropical cyclone.

So we got our water at midnight and ran the qPCR for half the night and in the end it gave us a clear answer: We are not coming back. The filters were almost empty of anything photosynthesising but we did have quite a few UCYN still. Problem was that their abundance was still half of the LD threshold.

Next morning's meeting concluded that we will keep heading east and initiate the final LD within a large cyclonic eddie in the ultra-oligotrophic (dark blue, remember?) open ocean a few days transit from Tahiti.

Now we have another problem. We are running out of time due to numerous delays out of our control. We will not have time for any more SD's and just barely enough time for a full LD. However, there are conflicting information about the time required for transit to Tahiti. The reason for this is that we have also encountered strong easterly winds that slow us down, typical.

I'm wondering if there is anything else that nature and Murphy can throw at us.

Oceanic transit

Today and possibly also tomorrow will be days of downtime. Even though it might seem comfortable having a couple of days off, it is far from it. I quickly get restless after a few hours no matter what I'm doing. There are always work related issues or tasks at hand, but writing or compiling data is only bearable for so long when the ship is rocking back and forth on its way to our next location.

I think I might actually grab a few DNA/RNA samples off the underway water pump once we are outside of the phytoplankton bloom. At least that will keep me occupied for a few hours each day.

Otherwise these kind of days (or any day really) are well suited for some serious gym time. It is a challenge in itself to work out properly when the room you're in is moving erratically in either direction. Since I'm almost exclusively using body-weights, something that I'm far from used to nowadays, I quickly push myself to a state of nausea. I'm not sure that's a good thing, but on the other hand my muscles begs me to stop, and that I know is a good thing.

I never even dreamed of getting any visible results out of this kind of exercise, and in just 6 weeks, but it seems I was wrong. If that is due to my body's inexperience with "low weights - many reps" workout or just the fact that the dietary supplement (Gainer) I bought consists of creatine, I'll never know. Either way I'm happy about it. By the way, I really hate pull-ups, but they sure are effective.

I previously wrote that I was contacted by a regional newspaper back home. So now I finally got my promised few days of fame (hell yeah), the rockstar-scientist-to-be influences one region at a time. Jokes aside (I think that title might already be claimed by Sam Dupont anyway), I'm happy with how the article turned out and hopefully I'll reach out to some and even inspire others.

I had a very enjoyable afternoon and evening in the hammock on front deck yesterday, even acquired a bit of a tan, and as usual when I have a bit of time to myself with an awesome and myseterious view in front of me, my thoughts start spinning. It is not necesarily a bad thing, most of the time I thoroughly enjoy it. Yesterday the result was a poem. I've been writing poetry before, but many years ago, and only in Swedish, but back then I had nowhere to share my writings. Now I do, and that's why it ended up on my blog.

I've been counting down the days until I'm home again. It's a comforting feeling. I also got a few nice photos from my fiancée which warmed in the already 30 degrees celsius climate.

I miss you so much, and soon it's only two short weeks left.

Open Ocean Poetry

Everywhere I see,
the sky touches the sea.

An infinite nothingness,
dreaming of something more,
but nothing less.
Twinkling stars and waves ashore,
beacons of insignificance sharing their lore.

In this vastness I ought to have a place,
somewhere in time and space.
Stars keep twinkling,
waves keep rolling,
feeding something more.

Everywhere I see,
do you still remember me?

The sun rise hidden from view,
life under waves, beyond stars,
starts anew.
A faint whisper for minds so keen,
open your eyes and see what I mean.

Everywhere I see,
you have a place for me.

Last 8 days of science

We are now leaving the large phytoplankton bloom behind, after five days of intense long duration station (LD) sampling. Today the scientists responsible for measuring physical and optical parameters are fully occupied, but again, not so much for us biologists.

Before heading out on the desert-like waters between Niue and Tahiti we have to get into port of the small island nation of Niue to drop off one of the crew who previosuly injured his knee on board. Apparently he has been coping with his injured knee for some time, but now it has reached a point where he is forced to seek medical attention back in France.
I feel genuinely sorry for him. It must be a horrible situation to find yourself in, and also knowing that this sidetrack will cost the cruise at least 24 hours (for the neat cost of some 60 000 SEK/day).

Although we are leaving these chlorophyll rich waters behind, it is not a different picture that meets the eye when looking out over the horizon. The ocean looks just as azure (or blue) as before, effectively masking the secrets we are here to uncover.
I previously mentioned that the satellite imagery of or next target waters is a cold dark blue color, the color of nothing out on the oceans. A watery dessert. This is not the whole picture though as the satellite can only pierce so far into the water column. I'm looking forward to sampling the first depth profile at our next short duration station (SD). Who knows what we will find further down the photic zone (the upper most layer of the ocean where enough light penetrates for photosynthesis to occur).

The cruise is far from over work-wise although only some two weeks out at sea remain, but when it comes to doing science (sampling and lab work) we only have eight more days (three SD and five days of the final LD). We will then have a short transit of a day or so into Papeete harbour, arriving on the 2nd of April. Once back on land there will be an intense period of packing and shipping everything back to Sweden. Hopefully it will be a smooth process.

Curiosity and collaborative work

The first day of the second long duration station (LD) has certainly been an intense one. I've been working more or less non-stop since 03.00 in the morning (except for a couple of hours of sleep after lunch). Now it is already past midnight and I have another sampling in 3 hours. Thankfully I can sleep after that since there is no need for me to do anything more with those samples than either quickly filter them or incubate them on front deck for filtration during the coming day.

This LD has the same schedule as the first one, which means that I have a lot to do. This first day I might also have gotten a tiny bit over-ambitious, but I'm just too curious about the UCYN abundance in a depth profile at this location since it turned out that the science team listened to my recommendations to place the LD within the large bloom of phytoplankton.

So in summary we collected RNA, microscopy and FISH samples (in a depth profile) for archival and DNA samples for my qPCR run. This meant using some 23 bottles followed by a lot of water filtration. An equal amount of cleaning is then required afterwards, which is probably the most tedious part of my lab work. After that was done, I started extracting DNA for the planned qPCR. I wasn't overly keen on running the qPCR straight after extraction since I by this point was very tired. So I stored the extracted samples in the freezer and went to bed for a few hours. But it didn't end there. I also started up the nutrient amendment experiment after my nap. An experiment which is collaborative work together with a French lab. In practice this means that they fill up all the bottles and add the nutrients (which in my case is only 5 bottles - silicate, iron, dissolved organic phosphate, dissolved inorganic phosphate and control - plus 5 untreated time point zero), and then measure the bulk nitrogen uptake for me when we later spike the bottles with 15N2. So what I did today in addition to filtering my own T0's was also taking care of their DNA/RNA bottles for T0. This will be my responsibility for the breakdown of the experiment too. At the end of the cruise I will ship their archived DNA/RNA together with mine back to Stockholm where the collaboration will continue.

There have certainly been a lot of waiting for filtration today, and I'm happy tomorrow will not be as heavy on that as today. I suppose overseeing water filtration is the biologists equivalent to the saying of something being as "boring as watching paint dry". Filtration is just as exciting.

Oh, and when we're on the subject of excitement. I got the address to my American friend (middle in above picture) Kyle Frischkorn's blog. So if you want to have some further reading and another angle of approach to the same cruise, then check it out. It is really good (although I might be biased, haha). He's a Ph.D. candidate like me, but mainly works with questions concerning the filamentous and colonial diazotroph Trichodesmium, which has been fairly abundant so far during the cruise.

http://blogs.ei.columbia.edu/tag/south-pacific-marine-ecosystems/

Now I'm almost finished with my qPCR run and eagerly awaiting the results, stay tuned.
In the meantime you can enjoy two more really good pictures from the Ship Games, just to prove that you can have great fun with very little means irrespective of who you are and where you are.

 

Liquid Nitrogen

I decided beforehand that this would be my day off. And oh what a day off it became. High-life at sea. I could just leave it at that, I'm feeling happy and relaxed enough about it, but that wouldn't make much of a blog post worth reading now would it?

So for the sake of you guys, I'll go through some of the simplicities that make up a good day at sea.
First of all, I didn't sleep in. Technically I didn't. I had breakfast (choco-pops) and then went back to bed. Huge difference but no less satisfying.
Since lunch is at the relatively early time of 11.00 I could literally, once more, go straight from bed to another meal.
The reason why I decided for this to be a lazy day is that we are preparing for the next long duration station (LD), which in practice means that there's only time and space for the measurements of physical parameters. In addition, hosting the ship games the other day was rather exhausting for me, so I'm recharging my batteries to go all in next LD (03.00 sampling, hell yeah!).
Even though it might sound like I had nothing to do, there's always something to do, which is a good thing because it keeps me occupied. The best part of it though is that any work needed to be done was for me to do whenever I felt like it. No scheduled times for sampling and no results that needed to be reported at a set time. Just calmness.

So writing, reading, cleaning up the lab after yesterday and helping Kyle and Andy refill their liquid nitrogen dewars just turned into a nice pass of time. It is also always extremely cool to be working with liquid nitrogen. Funny, eh?
After digesting my lunch while listening to some music, sleeping another hour and watching the gentle swell roll by, as if the ocean was a living, moving organism, I hit the gym. Somewhat reluctantly after just waking up.
It turned out to be a good session though, and in the end I'm happy I forced myself to go.
Apparently I wasn't the only one having a laugh today. Some people in the crew told some scientists in the labs that they had spotted dolphins. As predicted when conveying such news everyone ran to the railing by the CTD to catch a glimpse of the dolphins. Little did they know that it was all just a ruse and another crewman poured a large volume of water on their heads from up above.

I also made a phone call back home after finally receiving my phone card. It was supposed to be a bit of a surprise for my fiancée, and I think it was. Just hearing her voice and the kids was great and even though it felt like we didn't talk about anything in particular, 15 minutes quickly passed. In the end I felt a bit emotional about it, and made me miss her more, but again, just hearing her voice made it worth it.

In the evening I had a beer out on front deck together with Kyle and Andy. It's absolutely pitch black outside without the moon, and barely any stars could penetrate the clouds. However, it was of no concern as soon as our eyes had adjusted, and by pure chance Andy glimpsed over the railing and down at the swell cause by the moving ship. With every swell the water exploded with green light, like golf ball size orbs of bioluminescence littering the disturbed water. It was almost like watching a show of fireworks exploding, some smaller and some larger than the others. This phenomenon is caused by small plankton called dinoflagellates, but there must have been dense aggregates of them to emit that much light!

The only thing missing was for today to be croissant day, but hey, that's tomorrow!

High frequency sampling a massive bloom

After 15 hours of almost constant work, barely enough time to have lunch and dinner, the 48 time points of our north-south transect are finally completed.
The actual lab work was an ever-flowing routine of fixing microscopy filters in formalin while filtering water for DNA archival. Inside of the bloom my 0.2 µ pore size filters clogged already after 1 liter filtered most of the times! Usually I filter 2.5 liters without a problem.

In addition to my 5-6 hours of shift-work in the lab, I also ran two DNA extractions in parallel with each other after my first shift. When both extractions were completed I did a qPCR run on them which was followed by a meeting to try and decide upon the location of our next long duration station (LD) which we will start at midnight, 14th of March.

Unfortunately I could not attend the whole meeting due to my next shift starting so at this time I don't know what was decided.
The bloom turned out to be mainly diatoms and some Trichodesmium, which apparently have been blooming in this very area for at least a month, probably more. However, everyone seemed at a loss as to what was sustaining this bloom of diatoms, in terms of nutrients like nitrogen, since there seemed to be very few diazotrophs present. The natural conclusion, if not biological is then physical, like upwelling. Someone even mentioned volcanic activity, either on land or at the seafloor. This is extremely interesting but not really within the scope of the cruise since we are focusing on oligotrophic waters where diazotrophs sustain bloom formations at places usually devoid of sufficient nutrients.
This is where my qPCR data over the presence of the diazotrophic UCYN bacteria comes in and the reason why I ran two DNA extractions was for the chief scientist to have numbers to compare outside and inside the bloom of diatoms. To everyone's surprise the abundance of UCYN was almost 10 times higher outside (300k) of the bloom than inside (35k). However, I was sure to point out that the sampling we had conducted was only made at a single depth (5 meters) and was therefore very limited in terms of picturing the abundance of all UCYN in the water column. Data throughout the cruise have shown a clear trend in having the highest number of cells/liter around 35 meters of depth, so we could possibly miss out on a larger community here. To clarify, 35 000 cells/liter is not enough diazotrophs to sustain a bloom at this magnitude for such a long period of time.

There is so much more I would have liked to look into, specially in terms of a depth profile, but time wouldn't allow it. A gradient of abundances from the edge of the bloom to the middle would have been nice too. I have the filters for that at 5 meters at least, but there was no time for me to investigate it on board (and UCYN is not the main subject of my project either).

After I left the meeting to continue my lab work people were trying to find reasons justifying having the LD inside the bloom. In my opinion I hope we do.

L'Atalante Ship Games 2015

Today was a special occasion. I was asked by the chief scientist on board to arrange some kind of activity for the science team during one of our few days off. Naturally, I was up for the challenge, and leaned back on my previous training as an adventure guide and team-building instructor and compiled a serie of activities with what little resources and space I had available.

So I started planning something which I came to name the "L'Atalante Ship Games 2015". Participation was optional but I still had 18 people joining, which was great. They were split into three teams, six people in each, to solve different exercises heavy on teamwork.

In the end we all had a great afternoon with a total of 8 different activities and were able to crown a winning team as the L'Atalante Ship Games 2015 Champions.

Thanks Dalslands Aktiviteter, I never imagined I would be using my experiences from you guys to host games for a group of scientists on a ship in the South Pacific.

Below follows a few pictures from the games.

Kyle makes a leap for it during the first activity; the "Step on stones", which basically meant using four square shaped weights from the gym to cross a small area on front deck, without touching the floor.

Team three makes an impressive try to have the whole team standing on the small square during the activity "Everyone on board".

 
The picture to the left shows team two desperately trying to solve the ingenious puzzle "The T" within 10 minutes. The best part of this activity was actually the beginning when the chief scientist looked at me after I announced the rules and asked me: "Do we really need 10 minutes for this?".
At that point I can understand him because it is only four pieces, but little did he know about the puzzle I had prepared for them. His team didn't solve it.

The picture to the right shows Dominique in the middle of the obstacle course (after crawling under a ping-pong table). The catch was that you had to carry around a ball on a spoon, in your mouth, during the whole course. Quite difficult, and the source of many laughs since you do look plain stupid with that spoon in your mouth while focusing on the ball. Or perhaps constipated is a better word to describe it for some. Good fun either way.

In addition to what the pictures show, we also had activities called "sorting people", "fetching random things", "mini sock-bowling" and concluding it all with a "ping-pong ball race". The ball race is another brilliant activity I took from previous experience. I got some ping-pong balls in the gym, buckets in the lab and cut out "half-pipes" from water bottles. The teams then had to transport the balls using the "half-pipes" from a starting position into their bucket, further down the ship.

Later that night we had a brief prize ceremony with a few speeches and beer before the winning team, team three, finally received the trophy (as seen above) that they had been competing for (in addition to the fame and glory of course).

Dateline reflections

I think it is time for some random photos again, a couple of them including my feet. You know, these regular photos you get on your feed when your (annoying) friends go abroad on a sun trip.

I don't have any white, sparkling beaches as a background but I rather revel in what I have. A metallic hull (or I just want to be annoying, because I can).

So these two guys are the main entertainment on board. The American, Kyle, on the left, self-proclaimed party dude and the most fun guy on board, is also blogging and I will link to his blog in short order for anyone interested in his view of the same cruise.

The guy on the right, Andy, is my German roommate. He has been a source of good advice and opinions throughout the course, when he isn't sleeping that is (which is most of the time).

On this picture they are both sampling for their experiments off the second 200 m CTD cast.

Out of the impending threat of a copyright lawsuit I'm not adding a picture of the Italian and my colleague in lab, Andrea. He is a fancy piece of clothing though, and good fun (No Kyle, he does not sound like Luigi in the Mario Brothers when he speaks). 

First "feet-picture". This is my little hide-out where I'm supposed to get my beauty sleep. These last few nights the waves have increased in size and intensity, so sleep has been a reluctant commodity. Since I prefer sleeping lying on my side, a proper wave hitting the hull of the ship in front would flip me over, every single time. Finally, after two nights of battle with gravity I found that some sweet metal music in my ears did wonders.

Second "feet-picture". See what I mean? It ain't pretty but it sure is comfortable after a hard day at work. My poor numb right pipetting thumb was happy to have a rest in the hammock on front deck. I was even accompanied by dazzling sunlight and a slight breeze of 30 degrees celsius. As always, the clouds put up a show which made me fall asleep.

Finally, I've had an emotionally tough week. The days have been drifting past in a snails pace, and we've had to change our clocks on several occasions (going across time zones) and also re-visiting the same day twice (dateline). It has been fairly calm and harmonic for two weeks after the initial two weeks of badly missing my fiancée and kids. Now, as the 2/3 time mark of the cruise draws near, I find myself with the same feelings of longing and aching loneliness (although I'm far from alone). I've on several occasions pictured my return, embracing her, and it is always a scene where I probably will shed a tear. However, it always feels good.

At least my "out-at-sea-facial-hair" is coming along nicely (and no, no "seastasch").

Crossing the dateline with a monster at our heels

There have been many changes of plans these last few days. Mostly, it has concerned our sampling schedules and locations and I've felt very confused about it all.

In my previous post I mentioned that we might head to Fiji for shelter from the big storm coming our way. Apparently the storm has changed its predicted trajectory, now going in a southeasterly direction, straight over Fiji. A few days back it was supposed to pass west of Fiji.
So as the cyclone also picked up in intensity and size we made a run for it, heading east towards the dateline and Niue waters.
At this very moment the cyclone, now renamed "The Monster" - being the largest storm ever in this region, with wind speeds exceeding 240 km/h - have not yet reached Fiji.
We are presumably safe outside of Tonga but can still feel the waves getting larger and stronger, these past two days I've even had a hard time sleeping properly because of the increased rocking. By the time the Monster reaches our latitude we will be crossing the dateline, many degrees east of it.

I'm happy I'm not particularly superstitious though, because crossing the dateline, heading east, means that we will gain one extra day. In our case it actually means that we will have two friday the 13th. How many people could ever claim to have experienced that?

After that, we will reach our next long duration station (LD), in Niue waters, which is our only option. Thankfully, according to satellite imagery, it seems like we are sailing into a massive, and still expanding bloom. We have no idea what organism(s) make up this bloom, which spans several hundred kilometers in all directions. Of course, me and my colleague have our fingers crossed for DDAs.
Since this is a great opportunity for all of us to sample, we will make a 15 hours transect right through the bloom where we will conduct high profile sampling with most of the team involved. During these 15 hours we will be sampling for several parameters every 20 min from an underway surface water pump. Me and my colleague will also run the qPCR twice.

Barbecue

Today is supposed to be the day when we will make the decision on how to tackle the approaching storm. Everyone is eagerly awaiting our qPCR results of today's run.
We had a brief meeting yesterday afternoon, discussing our options, and either way we are forced to pick a long duration station (LD) in Fiji waters. Next up is Tonga and out of some reason unknown to me, they have demanded to have an observer on board, which responsible personnel on board politely declined. After some debate we were finally allowed to only operate for 24 hours in Tonga waters meaning no LD even though initial satellite imagery looks awesome.
So on the matter of the cyclone, we are strongly leaning towards heading for Suva bay (Fiji), however the captain was skeptical to whether we would be given permission to enter the bay or not since port cities are usually reluctant to allow too many vessels to gather during a storm. I suppose it is due to the consequences of any ship sinking, but as one person in the meeting put it: "we're not a tanker, they wouldn't even be bothered if we sank". Happy thoughts please, happy thoughts.
Hopefully, the only Fijian we have an board will be able to pull some strings, or things might just change once, twice or thrice before we're done with this whole thing...

Barbecue on front deck was an awesome social event last night. I just wished we could have picked a calmer day. With a storm approaching we have already felt the wind and the waves picking up, but between the occasional sea spray from waves breaking on the side of the ship's hull, it was enjoyable. Drinks were free (beer, wine and coke) and what little food I managed to prepare at the dimly lit grill, rocking back and forth, was good.
After tirelessly battling to make ourselves heard in the howling wind, everyone headed inside, but not until all drinks were out.
The evening continued at the electricians workshop, who invited everyone to a party. They had cleared everything out, making the room barely big enough for everyone to fit and still have some room for dancing. They music roared painfully out of the poor speakers, playing some French music mixed with old classics and newer pop. It was terrible...
I'll let you in on a secret; scientists look just as nerdy, when dancing as with anything else, but at least it is fun.
I happily witnessed the spectacle, some of my friends on board really loosening up, which made it even more fun. I had my regular three beers and then water and coke for the rest of the evening, up until the abrupt end when the speakers blew.
Someone got to clean our bottles before sampling tomorrow morning, and I would not miss my choco-pops breakfast at 07.00 for anything.

Tropical cyclone

So the rumors were true. We do have a massive storm in our path, heading straight for us. It is predicted to reach our location in the middle of next week, with 19 meter waves.
The crew doesn't seem to be overly alarmed, our ship is a big and sturdy one, but if we hit a storm like that things (lab equipment included) would inevitably break and we would not be able to run any experiments on board.
Therefore we will attempt to dodge the worst of it by either heading east, somewhat along our intended route (but then miss out on possible long duration station candidates) or head north to seek shelter at Fiji.
The decision will be made within the two coming days, based on our qPCR data and the physical parameters. I think that if we encounter large abundances of UCYN at our our current location (and the next) we will probably head for Fiji.

Last night I ran a qPCR run on water from the short duration station 7, mostly for testing our new standard dilution series aliquots, since the qPCR data wasn't required at that station. I found vast numbers of UCYNB in the top 10 meters of surface water. I think we might have hit a bloom. Perhaps the coming LD candidates will be similar. We're still fairly low on our beloved DDAs though.

Inconsistency and waiting for the CTD

We have now officially entered Fiji waters and crossed into a new time zone, which means that not a single clock on board is showing the actual local time. It also means that I'm now 11 hours ahead of Sweden, which again, feels a bit weird.

It is our 7th short duration station (SD) today, and we are slowly nearing our mid-point (10th of March). The following 2 days will decide where we will have our next long duration station (LD). So today we once again start running the qPCR looking for the UCYN targets.

I don't think I've actually explained what the targets really are. So for those interested, they are small unicellular diazotrophs (nitrogen fixers). Most of them are so small that they can not be identified by any other means than molecular methodologies (e.g. the qPCR). They are currently being subject of some intense research due to their role as diazotrophs but also in their unique characteristics (some arguing that they are in a transitional state between free living and symbiotic, giving an excellent opportunity to study a process similar to the theory of the modern eukaryotic cell, the endosymbiont theory. The reason for this is that some of them have been shown to lack certain genes required for their life history, then being either photoautotrophs or photoheterotrophs. How they still manage without these genes, e.g. for photosystem II essential for photosynthesis, is largely unknown). Some of the other diazotrophs can be seen by the naked eye while others are easily recognised in a microscope.

When we have decided on a location for the second LD, out of three, there will hopefully, be some more consistency in our sampling. At the moment we are trying to save time by sampling whenever we arrive at an intended SD and every single time since LD1 we have had to wait for hours for our first CTD with our water. Tedious, yes.
Anyway, for more detailed information on the cruise plan and goals you can visit the official OUTPACE 2015 webpage at https://outpace.mio.univ-amu.fr/spip.php?article71.

Between rumors of a massive storm, stupid oceanographer community rituals when crossing the dateline and someone spotting a few whales, it is now finally time for sampling.

A day of many things

5/3
So this past day was an intense one. First off, being the first short duration station (SD) in a week, and then so many different things required my attention. I got to bed at 02.30 in the morning and was so tired that I actually missed breakfast, turning off my alarm in the following morning without even noticing. Now it was for once a good thing that the French have their lunch so early (11.00), because I could go straight out of bed, feeling miserable, and down to the mess for brunch, which effectively made me feel less like a hungover teenager.

Firstly, the start of the previous day had us clean out and prepare the lab and qPCR for the SD sampling, which went smooth enough. We even had the time to hit the sunny front deck for an hour.
Secondly, today we also had to decide upon the shipping of samples and equipment back to Sweden after the cruise. I know it is a bit less than a month left but better be prepared and in good time. I would hate to see our samples (which need to be stored and shipped frozen) go to waste because we postponed our decision. We had a bit of a disagreement and communication mishap with our supervisor concerning this, which put me in a foul mood that evening, until I had the time to reply and elaborate on our decision to ship our samples using a recommended French company in Tahiti.
Thirdly, we also had a scientific meeting with one of the research teams on board (this time the physics oceanographers) presenting their data so far, to the rest of the cruise participants.
This took way more time than  I thought it would and since there aren't enough chairs for everyone in the conference room I had to stand (or sit on a sharp edge, numbing my butt) for hours. I quickly got fed up with it.
However, in the middle of the meeting a couple of people from the crew sneaked in and set up a computer with speakers. No one payed them any heed and all of a sudden a silly song in French sounded loudly in the whole room. Startled, everyone started laughing, and they laughed even more when someone in the crew jumped into the room, dressed in the orange immersion suit (environmental life suit, you look really stupid in it) with colorful paper circles taped on his back. He then started dancing in a silly manner, somewhat reminding me of an old friend's poor imitation of Zoidberg from the TV-show Futurama, and hugging everyone in the room. The silly music was still playing by the way.
Apparently today was an annual celebration of some kids TV-show in France. I've never heard of it, but it was a fun distraction from the internal waves measurements in the presentation from the last long duration station (sorry, but you should really get more chairs).
Fourthly, I was contacted by a local newspaper from my home town who asked me to participate in their next issue of "Xtra" which is published once a month (thanks mom). So I had to take a few additional pictures to send them.
Fifthly, SD sampling which was a pain as late as it turned out to be (21.00).

I'm very happy that I despite all the work this day managed to get an hour of calmness on front deck

today, just enjoying the sun and watching the waves roll by as the ship made haste for the next SD.

I know I've said it before, but I can't help being awed by the endless ocean and horizon stretching out around me.
I find it both humbling and inspiring and front deck is a great spot of contemplation. Gazing up at the thin clouds unfolding across the light blue sky like a soothing blanket of white feathers, it made me feel slightly better as the breeze brushed my face and the sun warmed my back.
I felt small but full of possibility. The vast nothingness that is the open ocean is my possibility and I'm right now just a tiny speck in one such ocean of possibilities.
With that thought I once again looked up and tried to point out directions and wondering how far I would be able to see if  I was on the same altitude as the thin clouds. Could I see the curving of the globe? Probably, but not too far in the distance then, even on this bright day, certainly not as far as Sweden. How I miss my fiancée and my kids.

In a hurry towards Fiji

We have now entered a new phase in the cruise. We have left New Caledonia far behind and somewhat entered a  new water mass (at least from a biological perspective). Work-wise it will be the same story though. A "rinse-and-repeat" lab work that we did every day before the first long duration station (LD). The difference now though is that we have a change of schedule. Apparently we are running short on time and consequently are falling behind in the planning, so these coming four days of work, where we would have been contributing with our important data on the UCYN targets abundance in the water column, will instead mean nothing in terms of our qPCR data. The reason for that is that we a rushing over to Fiji waters anyway and we will not stop long enough to consider another LD along that route even though we might hit a bloom of the UCYN.

Sampling will also be done late at night, which is not optimal, and even useless for some of the scientists on board.

The cruise organisers even told us late yesterday evening after we presented our data, that we don't even have to run the qPCR until we get to Fiji unless we really want to. This made me more than a little bit annoyed. How could we be this much behind schedule that they don't even have the time to consider our data. I get the feeling that they have already decided on the spots anyway. This qPCR data is our only real contribution to the cruise and now it's not necessary. I'm more than a little bit curious as to what will happen if we arrive at this intended area, chosen based on satellite surface water imagery, and there are little to no UCYN present.

At least our qPCR run went well. Our data looked good and we had hits on all UCYN targets, the most abundant ones at a magnitude of 10^3. Our initial microscopy sampling also showed decreased abundance of Trichodesmium and finally an increase in the number of DDAs (specifically Rhizosolenia-Richelia). This is good news for me and my colleague. Fingers crossed it will just keep getting better the closer to Fiji we get.

We will probably keep running the qPCR every night for these four days. In the end the data might prove useful and we will at least keep our skills sharp.

Oceanic scientists in need

4/3
So the first long duration station (LD) is officially over and we are well on our way to the next short duration station (SD). We have just rounded the southern tip of Vanatu waters and are heading in a northeasterly direction to get back on route towards Tahiti.
We are estimated to reach the SD at 18.00 local time and me and my colleague will as usual be the first ones to sample of the CTD and get to work on finding any of the UCYN targets using our qPCR. I have a feeling it will be a late workday since our lab procedure usually takes 3,5 hours.
Before that however, we will have to do a test run on our reagents and standards just to make sure they are fine sitting in the freezer for a week. The freezer has proven to be less than reliable regarding the intended temperature of -20 degrees celsius. A higher storage temperature or frequent thawing and freezing will degrade the reagents and standards making them inefficient at best.
After conferring with our supervisor we moved all of it into the -80 degrees celsius freezer instead, but that was no sooner than yesterday.

Apparently a vital instrument called a Winkler for measuring oxygen concentration in the water broke a couple of days ago, so since we are still relatively close to New Caledonia, responsible personnel decided to bring a new one from Nouméa using a helicopter.
This was a procedure which had never been done before so there was a lot of commotion prior to its arrival. Fire fighters were stationed all over the ship in full gear and everyone else, scientists and crew alike (captain excepted), was gathered at back deck for safety reasons. All this just in case anything would go wrong. I know for a fact that the pilot was asked if he was skilled. The answer he gave was that at least he is experienced, meaning that there are no good pilots, they are just either young or old (he being old), which was good enough for everyone involved. I really liked the humble simplicity of that answer.

Anyway, the helicopter arrived and everyone on board started taking pictures of it while it circulated fairly close around the ship. We also realised that they were actually taking pictures of us too. I suppose there was a mutual feeling of respect and awe. I thought it was really cool. The crew in the helicopter was sitting on the edge of the open side door ready to lower down a large crate on deck.
It was all very professional and the actual deliverance was done in less than 10 seconds (the ship was actually still moving too). This was followed by a few more circles around the ship and a wave of goodbye before they disappeared in the horizon, heading south, back to New Caledonia.

Croissant day

It has been two eventful days with a lot of different things going on. Both research wise and not, both immediately concerning my work on board and not.

Either way I might just start out with the things not concerning my research for a change.

As the title says we have a weekly day referred to as croissant day, which happens every sunday. That is also the only way for me to actually know there will be the start of a new week the following day. Anyway, this day we have croissants to eat at every meal of the day, and the bottled red wine (instead of the regular bag-in-box) is served all day too.

As I've previously mentioned I'm not much of a wine drinker but chocolate croissants, yes please! However, I've been told that apparently these aren't good enough for people from Paris. Spoiled French. Whatever. More for me, yay!

The following day marked the end of sampling for this first long duration station (LD), which feels good. It seems that some people have gotten off work earlier though since something reassembling a crude pool turned up on front deck. Beggars can't be choosers, right? So naturally I found myself just hoping they will finish it before we get to Tahiti. Oh, and I also managed to drop a full tray of food on myself at dinner (including a bowl of soup). Don't ask how, because I don't know. I was just in a big hurry to get back to my sampling, typical, and then I had to clean myself up in addition. Previously when someone dropped something there has been a round of applause throughout the cantina, however, after I yelled out a line of less than appropriate words in Swedish at my misfortune, the cantina went dead silent. I'm not sure what would have been worse, the silence or the applause. At least they should all know by now that I'm not American.

The morning of the final day of this LD I was supposed to sample a depth profile from the CTD for use in another, although minor, experiment of mine again involving spiking with 15N2, 13C and filtering for SIMS analysis. But first my bottles needed to be filled, spiked and incubated for 12 hours of light.

I got up at 03.00 to get all set for this experiment, and had decided before hand with the diazotroph team that we would run this experiment together, so once again they would provide me with the 15N2 and 13C while also measuring the bulk nitrogen fixation.

The CTD went down at 03.10. Only me, my colleague, the crane operators and the flying fish being awake. The CTD came back up at 03.45. Still no diazotroph team around. What the hell?

At least there was one more person at the CTD by now who instinctively ran over to one of the cabins of the missing people only to come back with the unimpressive reply that they have their own CTD at 04.00 since they need so much water. God damn it!

Now there are several things wrong with this unfolding early morning so lets just pause there and take it from the beginning.

On the first day of this LD I had a chat with the leading scientist of the diazotroph team and we planned both our schedules so we would be sampling together on the day of the nutrient amendments experiment as well as the depth profile. Mostly since we are both interesting in collaborating now and in the future as well as for me to avoid wasting time and effort running my own bulk samples. On an earlier agreement with my supervisor they are also always providing the 15N2 and 13C since we had some difficulties getting ours delivered to the ship in time.

Anyway, after deciding on our mutual sampling days I went to the cruise organiser to schedule myself and my colleague on the appropriate CTD's during the five days of LD (specifically sampling from the same CTD's as the diazotroph team at two occasions then. At that time there was no mention whatsoever about an extra CTD at 04.00.

The reason is simple. The 03.00 CTD won't be ready for another go until earliest 04.30. The schedule for my CTD also still said that the diazotroph team would be sampling with me.

With that said, we are back at the unimpressive reply which had me, certainly not being a morning person, play out all of my frustration at one go (sorry once more technical personnel), picturing my whole experiment going to hell and getting up at 03.00 for nothing.

Me and my colleague sampled our water anyway and then stored them away in the blue incubators on front deck, for possible use later. 

Sometime after 04.30 part of the diazotroph team merrily entered the lab while whistling and laughing happily. I seized the opportunity and told them of my morning. At least they stopped whistling. They sampled from their CTD and prepared their bottles for incubation using the mooring. To speed things up I helped out as best I could and finally, two and a half hours late, I got my bottles spiked and ready for incubation. After that, karma struck. While we were working on the mooring before grabbing the rest of their samples off the CTD someone had emptied it. I swear it wasn't me.

Break-down of the nutrient amendment experiment

This day marked the end of my major experiment for the long duration stations (LD). After a 36 hour acclimatization, spiking with 15N2 and 13C -bicarb and then incubating for 24 hours it was finally time to filter the bottles with the different treatments.

For my thesis I'm collecting filters for SIMS (secondary ion mass spectrophotometry) analysis. So I want to see if the activity of the nitrogen fixation and growth for the DDAs (diatom - diazotroph association) changes when exposed to non-limiting conditions of certain nutrients.
In my case these nutrients only included iron, DIP (dissolved inorganic phosphorous) and DOP (dissolved organic phosphorous). Of course I also had a control bottle. My ambition was to also include treatments of silicate and vitamin B12, unfortunately there was a last minute change in the availability of these nutrients, so I had to settle with the ones I ran during this LD and a very limited amount of silicate which I will save for an LD where the DDAs are more abundant.

In addition to these SIMS filters I also filtered water for the diazotroph team responsible for measuring the bulk nitrogen fixation which I will use for later comparison. They wanted to specifically preserve filters for DNA and RNA which I will bring back to Sweden after the cruise. Since filtering water for DNA and RNA samples is somewhat my speciality by now, I was happy to assist.
This proved to be a bigger challenge than I had initially thought. There was a lot of multi-tasking involved since the filtration had to be set up for the different bottles and the water for DNA and RNA had to be split up and measured. The different filtrate purposes also required their own special filters and tubes with either a storage medium or nothing, and finally flash freezing in liquid nitrogen or just put in the -20 degrees celsius freezer.
While managing all this, the filtration time for the bottles varied a bit and I had to constantly keep an eye on the bottles and the time taken for each filtration and then get to work on storing the filters in the correct tubes (pre-numbered).
Rockstar filtration! I just missed some metal music in the lab!

All in all it was, as far as I can tell right now at least, a successful experiment. I just hope that I will actually find some DDAs on my filters when it's time to run the SIMS. My hypothesis is that iron will be the biggest stimulant since nitrogen fixation, specifically the nitrogenase complex, requires a lot of iron for its expression. This only takes the symbionts into consideration however. The diatom might need something in addition to iron (which is mainly used in the RUBISCO pigment for carbon fixation) for boosted growth, silicate perhaps.

After this hectic start of the day I treated myself with some quality time on front deck in the hot tropical sun listening to that metal music that I missed in the lab earlier today. The ocean certainly eminates a contagious calmness. I probably watched the gentle waves roll by towards the endless horizon for hours before hitting the gym.

Finally, I have now passed 500 unique views of my blog since I started some 2-3 weeks ago. I'm thrilled about the relatively large interest in my cruise, which far exceeds any expectations I might have had. Thank you all, it is very flattering. In return I give you this picture proving that nature indeed has a sense of humour.