We finished our work at the river transect. Now we had one more sample to collect. It was to the north where the abandoned valley is still flooded at the site of the tube well that started this idea. It is well BNGB013 along one of the transects that was done for the BanglaPIRE project. It was done along the side of a major “highway”, so will be accessible and it not far out of our way home. Alamgir had a contact in a nearby village and arranged, and rearranged a driller. We were glad to be heading back
to Dhaka. The hotel we stayed in was the best in Brahmanbaria, but it had bedbugs. In this moderate sized town, the choice of restaurants was limited.
The drillers arrived at our meeting place late. There was a fight between two villages the night before and some people were stabbed. They own a plot of land along the main road in the other village. Those villagers wanted them to swap it for land perpendicular to the road, but they refused. The land along the road is valuable for shops. The result was a fight until the police broke it up, but several people ended up injured. They came without their equipment so
they could sneak quickly through the other town. They got what they needed at the store where we met about 2 km west of the well site. I went ahead and located the exact place we wanted to sample.
Since the well had already been logged and sampled, we only needed to drill down to the sands, making sure the stratigraphy agreed. Relooking at the logs of the well, I realized that we barely had enough extension rods to make it to the sampling depth. Luckily we hit the sands with a couple of feet to spare. We
got our sample and headed for Dhaka. Of course, we hit terrible traffic and were late to dinner with other scientists from our project that just arrived from the U.S. Over dinner I learned that Kazi Matin Ahmed, one of the Dhaka University professors we work with was from a town right near our sampling. He said that growing up he would go to school by boat during the monsoon. The next day was packing up at the university and making copies of everything. We also had to pack up a number of GPS and seismic recorders that need to be returned to the U.S. for repairs. Unsalvageable was one from Madhupur that was destroyed in a fire. This trip was very successful; we achieved all our goals, although as usual, there were a lot of changes of plans on the fly. In Bangladesh, nothing goes as planned, but we always get everything
done. Bangladesh is a country of resilient people who know how to get things done.
Catastrophes naturelles : un spécialiste américain s’inquiète du manque de prépa - Insurance & Investment Journal
We planned to drill four or five tube wells across the abandoned channel and pick one for OSL dating samples. With the success of yesterday’s tube well drilling, we were optimistic that we could actually do the sampling. We met the drillers in the morning and headed to the next site. Since only two or three people are needed for logging the well, we left Céline and Basu and the rest of us headed off to do a short resistivity line near the first drill site. We scouted it during the drilling of the first well. On the way to the resistivity
site, we selected locations for three more wells. Depending on time, we will either drill two and then the sampling well or just three stratigraphic wells. Since it will be only 2 meter spacing between the electrodes, it will be quicker to set up despite less people. We are only trying to image the channel, so we don’t need a larger spacing. The site was also drier than the first two resistivity lines. We laid it out and started collecting data. My only concern was that the route was used as a path for local farmers collecting hay. I didn’t want them to knock off the electrode connections or to have them
shocked by the pulses of electricity we sent through the electrodes.
Once the line was running, I headed back to the drill site. They once again found a think mud layer over sand. They continued drilling deeper and found the silt clay that marks the boundary between the Holocene and Pleistocene, when sea level rose following the end of the last ice age. This was a bonus and confirmed that we were on line with the Lalmai anticline farther south. We shifted to the next line, a more difficult location next to a pond, but they managed. I headed back to the resistivity line and found them starting to pack up the equipment. When I went to take a look at the instrument, I found it hadn’t finished. It had run out of memory for recording line and stopped. We quickly reinstalled the electrodes that had been
pulled that we still needed. I deleted some older files that had already been downloaded and restarted acquisition. We had only lost four of 584 command lines.
By the time the second well and the resistivity line were done, it was questionable as to whether we could do the sampling well, which will take longer. The drillers going off for a lunch break settled it. We would do a third tube well today. During the drilling, the skies that had been threatening all day opened up.
The drillers and loggers got completely soaked, but kept going and we completed our five-well transect of the river valley. In the evening we compiled all the logs and discussed a sampling plan. Rather than take four samples in one well, we decided to take two, one above and one below the sand-mud transition in two different wells.
The OSL sample is over 2” wide and the wells we drilled were 1.5” wide. The driller decided it was best to drill a 1.5” well to the depth of the first sample, a few feet above the transition, and then overcore it to 3.5”. Then 3” wide PVC pipe
was lowered to keep the well from collapsing. Finally, we put the sampler on the auger rods and lowered it to the bottom of the well. We, actually people younger and stronger than me, pounded the sampler 30 cm into the bottom. Then we all had to pull up on it to get it out. The next step was to extrude the sample in its liner into a thick PVC pipe casing. The sample must be kept in the dark, so this was done inside a black plastic bag. Then the entire sample is wrapped in the black plastic bag and taped securely. The ends and outside of the sample will be discarded and only the core of the sample will be used for dating. Later, sample preparation will all have to be done in a darkroom. I helped sample on my last trip, but the was the first time I was in charge of the procedure. It went well. After the first sample, the drillers drilled to 1 ft. past the contact, overcored to the same depth, added the PVC liner and we sampled again. We
repeated everything for the second well and we had four OSL samples. We celebrated with green coconuts.
I’m currently sitting in the Dallas airport waiting for a flight to Santiago, Chile, enroute to Palmer Station for the 2015 spring season. Since there is no airfield at Palmer we’ll go in and out by boat (the ARSV Laurence M. Gould). Hopefully we’ll be at the station by October 28 and able to start doing some science not too long after that. There are a couple of reasons why I’m excited about the upcoming season. First, as I discuss in this post, conditions are highly unusual this year, with the extent of sea ice reaching a level not seen at Palmer Station for many years. The reason for this seems to be the persistent warm El Niño conditions in the tropical Pacific Ocean, now complemented by a near zero to negative Southern Annual Mode (negative SAM values are correlated to high sea ice conditions). This increase in sea ice is a counter intuitive but very real effect of global climate change; increased heat in one area of the globe alters global wind patterns and decreases the flow of heat to other areas of the globe. It hasn’t actually been very cold at Palmer Station (the high today was a balmy 24 °F at the time of writing) and how long the sea ice lasts will be depend very much on what happens to winds in the region.
Coming in an era defined by decreasing sea ice along the West Antarctic Peninsula the presence of heavy ice cover could have some interesting ecological impacts. There is a strong likelihood that it will be good for the Adélie penguins, but my primary interest is a little lower down in the food web. I’ll be studying interactions between phytoplankton, the basal food source for the WAP ecosystem, and bacteria at the onset of the spring bloom, hoping to identify cooperative interactions through patterns in bacterial gene expression. Toxic compounds produced by phytoplankton, for example, may be cleaned up by bacterial partners, allowing photosynthesis to proceed more efficiently (ultimately meaning more food for the whole food web). Observing the expression of genes coding for the bacterial enzymes that carry out these processes would be strong evidence for this kind of synergy, which leads me to the second reason I’m excited about the upcoming season.
This year I’m joined by Colleen Hansel and Jamie Collins from the Woods Hole Oceanographic Institute. Colleen and Jamie are chemical oceanographers and experts in identifying specific compounds produced by phytoplankton. Colleen has pioneered a technique to measure superoxide, a damaging free radical, directly in the water column. This is not a trivial undertaking as the half-life of superoxide is only seconds, making traditional oceanographic sampling techniques (such as a Niskin bottle) impossible to employ. Instead we will focus on sampling water in the first few meters of the water column, just above the maximum zone of primary production. Superoxide is produced during photosynthesis, when energetic electrons glob onto free oxygen. The extra electron makes oxygen highly reactive (hence superoxide; it’s a superoxidant) and physiologically damaging. Bacteria have some interesting molecular tools to deal with superoxide however, so perhaps they’ve evolved the ability to perform this service for phytoplankton in exchange for fixed carbon. Coupling observations of gene expression with measures of superoxide and other reactive chemical species is much more powerful, and will tell a much more complete story, than either does alone.
It’s impossible to anticipate how the ice will impact our science plan until we’re at the station and get a feel for how logistics will work this season. Typically sampling at Palmer Station is done by zodiac, which requires reasonably ice-free conditions. The zodiacs can push around a small amount of brash ice but lack the mass (and shrouded propeller) to deal with large quantities. The ice is solid enough this year that we may be allowed to use this ice as a sampling platform – something I’ve got plenty of experience with from previous trips to the Arctic and Antarctic. This is a little out of the norm for Palmer Station however, so we’ll have to see how negotiations proceed.
In our worst-case scenario the ice conditions deteriorate to the point that we can’t sample from it, but not so much that we can push a zodiac through it. The normal sampling procedure in this case is to use a plumbed seawater intake to sample from below the ice (with the added benefit that you can sample from the comfort of the lab), however, this won’t work given the short half-life of superoxide. In this eventuality I think we can salvage the project by focusing on ice algae in place of phytoplankton. Ice algae are essentially phytoplankton which have given up their free-living lifestyle and formed colonies on the underside of the sea ice. These dense mats are a very important food source for juvenile krill, but are understudied in the region given the inconsistent nature of sea ice along the WAP. If we can access some decent ice floes from shore I think we can make a good study of the superoxide gradient, and bacterial response, toward the ice algal colonies. Previous work has shown that ice algae can be under significant oxidative stress so they may have good reason to solicit a little help from bacteria.
The next day we went out again for resistivity and augering. Céline picked out two alternative sites that might be drier. We drove through the abandoned valley to the site. We took the direct route and found the local road to be in a terrible state of disrepair. The vans could barely make it through. Then we hit a spot where slumping off each side of the road narrowed it too much. The villagers helped make a temporary road with bricks and wood, but it was still too narrow. Then they filled a sandbag and together with the bricks, wood and other
handy items we got across. It turned out that since the Upazila (county) voted for the opposition party, they have not had their roads repaired for over a decade. This level of politicization of everything in Bangladesh really hurts the country. When we reached the location of the line, we found that ponds between the road and the fields limited our access. We walked around and found a site next to a brick factory. The line was along an irrigation ditch. Fine to walk on either side, but submerged to mid-shin if you
stepped in the middle. The data looked very good after processing. We may have found the top of the Pleistocene as relatively shallow depths consistent with the site being the top of a buried anticline (folded hill).
The delays from the bad road, site searching, and a longer distance to lug the equipment meant that we couldn’t do augering. We came to the conclusion that we have to alternate days of resistivity and drilling. Not enough time in a day to do both properly. That meant
the next day was for augering. We went back to the soccer field site, officially BNGTi1, and started augering with all six of us. We hurried past the section we had already described. To minimize hole collapse, we switched between two augers and tried to work quickly on the descriptions. It took all of us all morning to make it to 4.8 meters. The mud was too hard. We needed to go to plan B. We would drill tube wells and sample inside the wells. Alamgir and Basu went off to the village to find a driller. The rest of us
cleaned off the equipment and ourselves at a nearby pond and well and had lunch. After several attempts, they found a driller, but he couldn’t come until 3 p.m. I like to use all the available time I have here, but we now had a few hours break.
The three-person drill team arrived right at 3, unusual in this part of the world. I have seen the drilling technique before, but never the initial set up. In 20 minutes they set two vertical bamboo poles in the ground, tied on the cross piece to make a large H, attached a lever arm and the drill pipe, dug a mud pit for water and a
channel to the actual well location. Then they started drilling. It was so much faster and easier than augering! In 10-20 minutes they were past the depth we reached. We don’t get continuous samples described every 10 cm (4 in.), but the lithology averaged every 5 ft. Muds come up as solid cylinders that we collect, sands as a slurry that we decant. We subdivide the 5 ft. sections if there is a lithology change. The driller caught on quickly to what we wanted and kept us informed of all changes in sediment type, which he could easily feel. Céline and Basu, an experienced logger of tube wells, did most of the sediment work,
with some help from the rest of us. As expected, the section was primarily mud with some silt. We reached the sands from the abandoned channel at 42 ft., a little deeper than I expected but reasonable. It was still early enough for us to do another. Alamgir and I scouted a second location as they finished and packed up the equipment. We completed that one, with the sands at only 20 ft. North of our transect looks like there was an island splitting the channel in two. Here would have been downstream of the island, so we
expected it to be shallow. Finally, things were going well. Using tubewells, we should have plenty of time to drill several stratigraphic wells and then pick one for sampling. We celebrated with dinner at the local Chinese restaurant.
A couple of months ago I published paprica v0.11, a set of scripts for conducting a metabolic inference from a collection of 16S rRNA gene reads. This approach allows you to estimate the functional capabilities of a microbial community if you don’t have access to a metagenome or metatranscriptome. Paprica started as a method for a paper I was writing but eventually became complex enough to warrant it’s own publication. Paprica v0.11 reflected this origin – it produced nice results but was cludgy and cumbersome.
Over the last couple of weeks I’ve given paprica a complete overhaul and am happy to introduce v0.20. There are a number of major differences between v0.11 and v0.20, but the most significant difference is a more clear division between construction of the database for those who want full control (and access to the PGDBs) and sample analysis, which can proceed with only the provided, light-weight database (however you will not have access to the PGDBs). Executing paprica v0.20 is as easy as (from your home directory, for the provided file test.fasta):git clone https://github.com/bowmanjeffs/genome_finder.git cd genome_finder chmod a+x paprica_run.sh ./paprica_run.sh test
One really important distinction between this version and v0.11 is that metabolic pathways are NOT predicted directly on internal nodes. This was done for reasons of organization and efficiency, but I’m not sure that it made much sense to do this anyway. Instead the pathways likely to be found for an internal node are inferred from their appearance in terminal daughter nodes (that is, the completed genomes that belong to the clade defined by the internal node). If a given pathway is present in some specified fraction (0.90 by default) of the terminal daughters it is included in the internal node. You can change this value by modifying the appropriate variable in pathway_profile.txt. Some (including myself) might like to have a PGDB for an internal node for purposes of visualization or modeling. In the near future I’ll release a utility to create a PGDB for an internal node on demand.
Some other major improvements…
- Fewer dependencies. For the scripts called in paprica_run.sh you need pplacer, seqmagick, infernal, and some Python modules that you should probably have anyway.
- Improved reference tree. I’m still working on this, but the current method uses RAxML for phylogenetic inference and Infernal for aligment, which seems to work much better than the previous (albeit much faster) combo of Fasttree and Mothur. Thanks to Eric Matsen for helpful suggestions in this regard.
- More genome parameters. I have a particular interest in how genome parameters (e.g. length, coding density, etc.) are distributed in the environment. Paprica gives you a whole list of interesting metrics for the terminal and internal nodes.
Paprica is still in heavy development and I have a lot of improvements planned for future versions. If you try v0.20 I’d love to know what you think – good, bad, or otherwise! You can create an issue on Github or email me.