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.
Along with colleagues from New Zealand, Argentina, and Malaysia I’m convening a session on microbial ecology and evolution at the upcoming biennial SCAR meeting in Kuala Lumpur (because there’s no better place to talk about ice than the tropics). If this sounds like your sort of thing check it out!S23. Microbes, diversity, and ecological roles Walter MacCormack, Argentina; Charles Lee, New Zealand; Chun Wie Chong, Malaysia; Jeff Bowman, USA
The ecology of Antarctica is largely shaped by microbes, with microbial life, including prokaryotes and unicellular eukaryotes, serving as the main drivers of ecosystem function. Given this, it is perhaps surprisingly that our current understanding of Antarctic biota has been derived primarily from studies of metazoans. Despite major advances in the field of Antarctic microbiology in recent years there remains a knowledge gap in our understanding of the distribution, functions, and adaptations of Antarctic microbes. There is a general consensus that Antarctic microorganisms are highly diverse, and in many cases encompass endemic gene pools with unique physiological and genetic adaptations to the extreme conditions of their environment. Relatively recently, the advent of ‘omics platforms has allowed researchers to observe these processes in great detail. This session welcomes submissions on all aspects of microbial ecology and evolution in Antarctica and the Southern Ocean. This includes ‘omics-based approaches to understanding prokaryotic and unicellular eukaryotic diversity, function, adaptation, as well as laboratory and field-based studies of microbial and ecological physiology. Special consideration will be given for abstracts addressing the following issues: (1) Microbial biogeography, functional redundancy, and ecosystem services; (2) Trophic connectivity between prokaryotes and eukaryotes; (3) Cold adaptation strategy and evolution; and (4) Multiple ‘omics integration addressing systems biology of Antarctic ecosystems.
Six of us headed out on Oct. 8 for Brahmanbaria, northeast of Dhaka. Our target is a large winding abandoned river valley that we believe used to be the course of the Meghna River. Currently, the much smaller Titas River flows northward in the channel. Why would a river in the world’s largest delta flow the wrong way? We think that an earthquake uplifted the Comilla District area to the south. That caused the Meghna River to shift westward to its present channel and the Titas to flow up the old channel. A well drilled in the channel in 2012 shows a layer of muds overlying coarser sands.
We think the sands represent sediments from the old Meghna and the muds are sediments filling up the channel. We will be using resistivity to image the channel and an auger to first sample and describe the sediments and then to collect samples for dating.
Finding organic matter to date by carbon 14 is rare, so we plan to use a technique called OSL dating. OSL stands for Optically Stimulated Luminescence. Electrons from the radioactivity of all rocks get trapped in defects in quartz grains. However, they
are so weakly trapped that sunlight can release them. When traveling down the river, the electrons are released and then start accumulating when they are buried. By measuring the light released by the sample when optically stimulated, we can calculate the time since the sample last was exposed to light. By sampling the top of the sands and the bottom of the muds, we can date the time the river switches, or avulsed. The details of the procedure to get an OSL age are pretty complicated, but if this works, we
will date the earthquake that caused the river avulsion.
This technique is new to me. I helped with some sampling the last time I was here, but I have not been in charge of doing it. I am also more comfortable with the quantitative data from the resistivity than the qualitative geologic descriptions we will make of the sediments. Luckily I have a good team with me, Céline, my postdoc, Matt, my former teaching assistant, and Alamgir, Atik and Basu from Dhaka University. I have spent time in the field with Alamgir and
Atik before. Alamgir has conducted his own resistivity surveys. Basu was recommended to me as someone with a lot of experience in describing sediments.
We set out early in the morning for the four-hour drive. However, when we reached the river valley, we found it was almost completely flooded. We walked out on an elevated road and there was pani—the Bangla word for water—everywhere. The abandoned valley is still slightly lower in elevation than the surrounding land. Even that land has the rice fields flooded with shallow water, although the
boundaries between the fields are above water. But our main target is submerged! In the winter this will be dry land, but we are a month and a half too early. A number of scheduling issues required me to come now, although I knew it was too soon after the monsoon, but I didn’t expect so much of the land to still be flooded. Time to come up with an alternative plan.
For the resistivity, we need long straight stretches of dry land. We decided to
do it west of the valley to try to image the thickness of the entire Holocene (last 10,000 years) section. It should vary because of the folding of the strata from the tectonics. Mapping the thickness will help us to map the position of the buried fold. For augering, we only need a small patch of land to stand on. To find it we headed south towards where the valley was uplifted more and might be drier. Not as ideal as the original location, but possible. The next morning we headed farther south and crossed the river valley. It was drier and we noted some potential augering sites. We continued to a location for resistivity. The six of us set up the >350 m long resistivity line, then Céline, Basu and I headed back to try augering while the resistivity data was collected. The augering proved very difficult. We were very slow describing the core that the auger brought up, and while we were doing it the hole would start to collapse. The muddy sediment was very stiff, and we had to hammer the auger in. We only got to 2.7 m when we stopped, nowhere near the depth we needed. Things were pretty discouraging.
I’m really excited (and relieved) to report that my review on the taxonomy and function of sea ice microbial communities was recently published in the journal Elementa. The review is part of a series on biological exchange processes at the sea ice interface, by the SCOR working group of the same name (BEPSII). I’m deeply appreciative of Nadja Steiner, Lisa Miller*, Jaqueline Stefels, and the other senior members of BEPSII for letting (very) junior scientists take such an active role in the working group. I conceived the review in a foggy haze last year while writing my dissertation, when I assumed that there would be “plenty of time” for that kind of project before starting my postdoc. Considering that I didn’t even start aggregating the necessary data until I got to Lamont I’m also deeply appreciative of my postdoctoral advisor for supporting this effort…
The review is really half review, half meta-analysis of existing sea ice data. The first bit, which draws heavily on the introduction to my dissertation, describes some of the history of sea ice microbial ecology (which goes back to at least 1918 for prokaryotes). From there the review moves into an analysis of the taxonomic composition of the sea ice microbial community, based on existing 16S rRNA gene sequence data, takes a look at patterns of bacterial and primary production in sea ice, and then uses PAPRICA to infer metabolic function for the observed microbial taxa (after 97 years we still don’t have any metagenomes for sea ice – let alone metatranscriptomes – and precious few isolates).
There is a lot of info in this paper but I hope a few big points make it across. First, we have a massive geographical bias in our sea ice samples. This is to be expected, but I don’t think we should just accept it as what has to be. More disconcerting, there has been very little effort to integrate physiological measures in sea ice (such as bacterial production) with analyses of microbial community structure. A major exception is the work of the Kaartokallio group at the Finnish Environmental Group, but their work has primarily taken place in the Baltic Sea (an excellent system, but very different from the high Arctic and coastal Antarctic). This all translates into work that needs to be done however, which is a good thing… we are just barely at the point where we can make reasonable hypothesis regarding the functions of these communities.
*This image of Lisa pops up a lot. If you can identify what, exactly, is going on in this picture I’ll buy you a beer.