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.
I am heading back to Bangladesh, but this time I am stopping in New Delhi before heading to Bengal (West Bengal and Bangladesh). It is the first time that I will be in a part of India that is not adjacent to Bangladesh. Several of us are meeting there to plan for a new project that will span Bangladesh to India to Myanmar. I arrived a few hours before Nano Seeber and Paul Betka and used the time to get a new Indian SIM for my phone. After meeting up, we headed to the guesthouse of the Ministry of Earth Sciences, where we will be staying. If only the U.S. had a cabinet level department for earth sciences. It was difficult to find at night without a Hindi speaker, but we managed.
Over the next few days we had meetings about the project, but also some time for sightseeing, while
discussing the project in the car. Most of our meals were vegetarian, and Gandhi’s birthday, which occurred while we were there, is celebrated by eating vegetarian. When two more scientists arrived from Singapore, we started the day by visiting the Qutub Minar, dating back to the 1200s and the arrival of the Muslim Delhi Sultanate, followed by the Mughal Empire in the 1500s. In the Quwwat-ul-Islam mosque, there is the famous Iron Pillar originally erected by Chandragupta in the 4th century, probably at Patna, and brought here much later. Near the beginning of the inscription it says: “in battle with the Vanga countries, he kneaded (and turned) back with (his) breast the enemies who, uniting together came against (him).” Vanga is Bengal, now split into West Bengal in India and Bangladesh.
After mostly finishing discussions, the others decided to take a day trip to Agra to see the Taj Mahal. I was able to change my flight to Kolkata to the following morning and joined them, continuing to talk science on the 4-hour drive. We had to buy the expensive tickets at 750 rupees rather than the 10 rupees the Indians were paying. However, the premium ticket lets us bypass the long lines. The Taj Mahal is the tomb of Mumtaz Mahal,
the beloved wife of Shah Jahan, the Mughal Emperor. It was built over 17 years from 1631-1648. She died in childbirth of her 14th child. He was buried there as well when he died in 1668, after being overthrown by his son. I have seen many pictures but was not expecting how enormous the structure is. The entire place is beautiful and enormous with flanking buildings, gardens and gateways. I kept wondering about the cost of building it and how many man-years of India’s peasants financed it. Perhaps this excess was why this was the peak of the Mughal Empire. Within a 100 years, the British were
taking over. Afterwards we went to Agra Fort, which is similarly gigantic, and another seat of the Mughals. There are palaces and a throne inside the red fort with views of the Taj. There are 30 buildings left, the rest having been leveled by the British to erect barracks for their troops. We didn’t get back to our hotel until 11.
I left early the next morning for Kolkata, the British Indian capital until 1911, when they moved it to Delhi. It was done to punish the Bengalis for opposing the
splitting of the Bengal Presidency into more manageable size, which would have cut Bengal in two. I spent the day at Calcutta University then headed back to the airport to fly to Dhaka. At my usual hotel, I met up with Jenn Pickering, a student at Vanderbilt University, and Céline Grall, my postdoc. They were teaching a short course at Dhaka University. I spent the next few days in multiple meetings and making arrangements for a week of fieldwork. It will be good to get out into the countryside.
Completing an ‘Ice Station’ means collecting samples over a wide range of Arctic water and ice conditions. Each station means a major orchestration of people and resources. The teams gather, equipment is assembled, and the trek off the ship begins. After the first off ship exodus the sample teams are well practiced in moving equipment and setting up work areas so as not to interfere with the other stations. There is no shortage of space so spreading out is not a challenge!
Collecting a wide range of samples at multiple Arctic locations allows GEOTRACES to get an integrated look at the trace elements moving through the Arctic ocean ecosystem, and to better understand how these elements connect to the larger global ocean. Each is carefully collected. Whether the elements are ‘contaminants’ or essential nutrients there is a specific protocol in order to quantify the inputs without ‘dirtying’ the sample. It may seem odd to think of ‘dirtying’ something we label a contaminant, but in order to fully understand the concentrations and methods of transport for each element, every sample is handled with the same amount of care.
The following photo essay showcases the various ice/water sampling stations and reviews what is being collected at each.
Snow Samples: The snow collected at this station is being used in part to determine the presence/absence of contamination related to the March 11, 2011 Fukushima event.
Both the snow samples and the ice core sections will be analyzed and examined along with the information collected from seawater, suspended particulates, and bottom sediments, in order to better understand the influence of processes specific to the Arctic on the transport and distribution of several anthropogenic radionuclides.
Ice core samples: The ice cores are sections of sea ice, and again are being collected to determine the presence/absence of contamination related to Fukushima. In general the samplers were able to obtain 1.5 – 2 meters of ice in the cores.
Melt Ponds: Surface melt ponds form on the sea ice in the long says of the Arctic summer. The warmth of the sun creates ponds that sit on top of the ice. The water collected in these ponds carries different properties than the either the sea ice from which it melted, or the ocean water from which the sea ice formed. Most often these ponds have a frozen surface layer that needs to be drilled through before water is pumped out for collection.
Beryllium-7 (7Be) Samples: Produced in the atmosphere when cosmic rays collide with nitrogen atoms, 7Be is constantly being added to the surface of the water, and therefore is a great surface water tracer. With its very short half-life, ~ 53 days, 7Be can be used to track water parcel circulation as it moves between surface and deep water (which has no significant source of the 7Be isotope). The surface water pulls the 7Be with it as it moves down deeper into the ocean, allowing us to track and time the mixing process.
Dirty Ice Samples: The dirty ice work is more opportunistic, and therefore is not be part of each ice station. If dirty ice is spotted it will be sampled, and while it may not be part of each ice station, it is part of the overall GEOTRACES protocol. While most of the stations sample for quantification, i.e. grams of sediment/ml ice, the dirty ice samples are used more for characterization, i.e. composition or mineralogy. For Tim’s work the collection of dirty ice is used to look at sediments originating from continental shelves bordering the Arctic, with the goal of evaluating or characterizing dirty ice as a transport vector for anthropogenic radionuclides.
Minimal Processing of the samples collected at the stations will occur on the Healy. The snow and Ice gets melted and the seawater acidified. The focus of the trip is to collect as much material as possible. There will be plenty of time for processing when the researchers are back at their home institutions.
Margie Turrin is blogging for Tim Kenna, who is reporting from the field as part of the Arctic GEOTRACES, a National Science Foundation-funded project.
For more on the GEOTRACES program, visit the website here.