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World Surf League Donates $1.5 Million for Ocean Research at Lamont - Grind TV

Featured News - Fri, 04/08/2016 - 12:00
The World Surf League just launched a non-profit, WSL PURE. It will help researchers at Columbia University's Lamont-Doherty Earth Observatory study climate change and the ocean.

World Surf League Grants $1.5 Million for Ocean Science - Surfing Life

Featured News - Wed, 04/06/2016 - 09:40
The World Surf League has just launched a whole new wing of their organisation, WSL PURE. This time, it's all about giving back. The new philanthropic wing is putting $1.5 million in first-year funding into ocean science at Lamont-Doherty Earth Observatory.

It’s Not Just Antarctica — Why Greenland Could also Melt Faster than Expected - Washington Post

Featured News - Tue, 04/05/2016 - 12:00
“More melting creates more darkening and accelerates the melting itself — a positive feedback effect,” Lamont's Marco Tedesco said.

Hudson River Lab Works to Revive New York Waterways - CU's New York Stories

Featured News - Mon, 04/04/2016 - 12:00
“You won’t open your mouth in the Hudson River, and that’s symbolic of a lot of things,” says Wade McGillis, an associate research professor at Lamont. “We want to figure out if we can restore it to a pristine system. If you don’t know what you’re doing to it, you can’t figure out ways to fix it. ”

Even in a Warming World, It Will Still Snow Somewhere - New York Times

Featured News - Sat, 04/02/2016 - 12:00
Lamont's Adam Sobel reminds readers to differentiate between weather and climate. If you really want to know what is going on with climate change, he said, look at the long-term averages over large areas. Do not be fooled by short-term weather fluctuations.

The Alarming Science Behind Projections of Much Higher Seas This Century - Washington Post

Featured News - Wed, 03/30/2016 - 15:09
Lamont's Robin Bell talks about the urgent need for Antarctic research. A recent study found that, with very high carbon emissions, melting ice from Antarctica could cause seas to rise 1.14 meters (3.74 feet), give or take 36 centimeters, by 2100 — and much more by 2500.

The End of Ice - The New Yorker

Featured News - Mon, 03/28/2016 - 12:00
The New Yorker talks to a team of scientists, including Lamont Associate Research Professor Mike Kaplan and Adjunct Associate Research Scientist Aaron Putnam, who are researching how quickly the ice in the Himalayas is melting.

Tutorial: Annotating metagenomes with paprica-mg

Chasing Microbes in Antarctica - Sat, 03/26/2016 - 03:00

This tutorial is both a work in progress and a living document.  If you see an error, or want something added, please let me know by leaving a comment.

Starting with version 3.0.0 paprica contains a metagenomic annotation module.  This module takes as input a fasta or fasta.gz file containing the QC’d reads from a shotgun metagenome and uses DIAMOND Blastx to classify these reads against a database derived from the paprica database.  The module produces as output:

  1.  Classification for each read in the form of an EC number (obviously this applies only to reads associated with genes coding for enzymes).
  2. A tally of the occurrence of each EC number in the sample, with some useful supporting information.
  3. Optionally, the metabolic pathways likely to be present within the sample.

In addition to the normal dependencies paprica-mg requires DIAMOND Blastx.  Follow the instructions in the DIAMOND manual, and be sure to add the location of the DIAMOND executables to your PATH.  If you want to predict metabolic pathways on your metagenome you will need to also download the pathway-tools software.  See the notes here.

There are two ways to obtain the paprica-mg database.  You can obtain a pre-made version of the database by downloading the files paprica-mg.dmnd and (large!) to the ref_genome_database directory.  Be sure to gunzip before continuing.  If you wish to build the paprica-mg database from scratch, perhaps because you’ve customized that database or are building it more frequently than the release cycle, you will need to first build the regular paprica database.  Then build the paprica-mg database as such: -ref_dir ref_genome_database

If you’ve set paprica up in the standard way you can be execute this command from anywhere on your system; the paprica directory is already in your PATH, and the script will look for the directory “ref_genome_database” relative to itself.  Likewise you don’t need to be in the paprica directory to execute the script.

Once you’ve downloaded or  built the database you can run your analysis.  It is worth spending a little time with the DIAMOND manual and considering the parameters of your system.  To try things out you can download a “smallish” QC’d metagenome from the Tara Oceans Expedition (selected randomly for convenient size):

## download a test metagenome wget ## execute paprica-mg for EC annotation only -i ERR318619_1.qc.fasta.gz -o test -ref_dir ref_genome_database -pathways F

This will produce the following output:

test.annotation.csv: The number of hits in the metagenome, by EC number.  See the paprica manual for a complete explanation of columns. The DIAMOND format results file.  Only one hit per read is reported. A text file of the DIAMOND results.  Only one hit per read is reported.

Predicting pathways on a metagenome is very time intensive and it isn’t clear what the “correct” way is to do this.  I’ve tried to balance speed with accuracy in paprica-mg.  If you execute with -pathways T, DIAMOND is executed twice; once for the EC number annotation as above (reporting only a single hit for each read), and once to collect data for pathway prediction.  On that search DIAMOND reports as many hits for each read as there are genomes in the paprica database.  Of course most reads will have far fewer (if any) hits.  The reason for this approach is to try and reconstruct as best as possible the actual genomes that are present.  For example, let’s say that a given read has a significant hit to an enzyme in genome A and genome B.  When aggregating information for pathway-tools the enzyme in genome A and genome B will be presented to pathway-tools in separate Genbank files representing separate genetic elements.  Because a missing enzyme in either genome A or genome B could cause a negative prediction for the pathway, we want the best chance of capturing the whole pathway.  So a second enzyme, critical to the prediction of that pathway, might get predicted for only genome A or genome B.  The idea is that the incomplete pathways will get washed out at the end of the analysis, and since pathway prediction is by its nature non-redundant (each pathway can only be predicted once) over-prediction is minimized.  To predict pathways during annotation:

## execute paprica-mg for EC annotation and pathway prediction -i ERR318619_1.qc.fasta.gz -o test -ref_dir ref_genome_database -pathways T -pgdb_dir /location/of/ptools-local

In addition to the files already mentioned, you will see:

test_mg.pathologic: a directory containing all the information that pathway-tools needs for pathway prediction.

test.pathways.txt: A simple text file of all the pathways that were predicted.

test.paprica-mg.txt: A very large text file of all hits for each read.  You probably want to delete this right away to save space.

test.paprica-mg.daa: A very large DIAMOND results file of all hits for each read.  You probably want to delete this right away to save space.

testcyc: A directory in ptools-local/pgdbs/local containing the PGDB and prediction reports.  It is worth spending some time here, and interacting with the PGDB using the pathway-tools GUI.


Almost Home, with Another 7 Million Years of Climate History

When Oceans Leak - Fri, 03/25/2016 - 17:54
 Tim Fulton/IODP

Expedition 361’s scientists aboard the JOIDES Resolution, near the end of a successful two-month expedition. Photo: Tim Fulton/IODP

Read Sidney Hemming’s first post to learn more about the goals of her two-month research cruise off southern Africa and its focus on the Agulhas Current and collecting climate records for the past 5 million years.

We reached our last site yesterday morning, off Cape Town, South Africa, and the first core was on deck at 11:15 a.m. It was pretty stiff at the bottom, and its microfossils indicated it was more than 250,000 years at 1 meter. We decided to start again, and ended up with 6 meters in the first core of the B hole, with further indications of a very low sediment accumulation rate of approximately 1.5 cm per thousand years. The next few cores gave us troubles with shattered liners and low recovery, so Ian and I went back to the data from the alternative sites to consider moving. Luckily we decided not to, because things really started looking up.

We just completed the first hole with 300 meters of sediment and a base age of more than 7 million years, and with a quite pleasing accumulation rate below the very top part. We still don’t have quite enough information to evaluate the situation in the upper 1 million years, but it seems very clear that the rest of the site will be excellent. The sediment composition is very similar from top to bottom and very rich in carbonate (so called nannofossil ooze). The gamma ray (measures radioactivity and thus is a sensitive measure of clay) and color measurements give a very nice signal and are varying in concert with each other. The weather has gotten nicer since the beginning of the first hole, and we are hoping the conditions hold and that the sea conditions were the reason for the troubles at the beginning of our first hole. Meanwhile, we have just enough time to complete the triple coring of this site back to 7 million, with maybe enough time for logging of the final hole.

 Jens Gruetzner, Alfred-Wegener-Institut for Polar and Marine Research)

Crew members retrieve the beacon. Photo: Jens Gruetzner, Alfred-Wegener-Institut for Polar and Marine Research

So, the good fortune continues. Each site on this cruise has provided real prize material, and the team members are very eager to get started on the work back at home. We have been burning the midnight oil (or midday, depending on your shift), meeting about the various plans for post-cruise science. There remain a couple of conflicts to resolve, but overall it looks like there will be plenty of great science for each participant, and plenty of opportunities to develop career-long collaborations.

It has been a great privilege to be part of this, and it really makes you realize how powerful these huge efforts, that require the cooperation of so many countries and their scientists, are. It is a very different way of doing science, and not always convenient for the individual, but overall the benefits are huge.

Meanwhile, this is my last post for this cruise. We are less than a week from arriving at our dock in Cape Town, and there is no question that we are all quite eager to get there. The JOIDES Resolution is amazing and the (multiple) staffs of the ship company, catering service, and IODP are truly remarkable. They are friendly, professional and very eager to help us to get the best we can out of this amazing scientific discovery process.

Sidney Hemming is a geochemist and professor of Earth and Environmental Sciences at Lamont-Doherty Earth Observatory. She uses the records in sediments and sedimentary rocks to document aspects of Earth’s history.

 Tim Fulton/IODP

The crew and scientists of Expedition 361. Photo: Tim Fulton/IODP

Antarctic wind-driven bacterial dispersal paper published

Chasing Microbes in Antarctica - Thu, 03/24/2016 - 12:53
Frost flowers over young sea ice in the central Arctic Ocean. Photo Mattias Wietz.

Frost flowers over young sea ice in the central Arctic Ocean. Photo Mattias Wietz.

I’m happy to report that one of the appendices in my dissertation was just published in the journal Polar Biology.  The paper, titled Wind-driven distribution of bacteria in coastal Antarctica: evidence from the Ross Sea region, was a long time in coming.  I conceived of the idea back in 2010 when it looked like my dissertation would focus on the microbial ecology of frost flowers; delicate, highly saline, and microbially enriched structures found on the surface of newly formed sea ice.  Because marine bacteria are concentrated in frost flowers we wondered whether they might serve as source points for microbial dispersal.  This isn’t as far-fetched as it might seem; bacteria are injected into the atmosphere through a variety of physical processes, from wind lofting to bubble-bursting, and frost flowers have been implicated as the source of wind deposited sea salts in glaciers far from the coast.

At the time we’d been struggling to reliably sample frost flowers at our field site near Barrow, Alaska.  Frost flowers form readily there throughout the winter, but extremely difficult sea ice conditions make it hard to access the formation sites.  We knew that there were more accessible formation sites in the coastal Antarctic, so we initiated a one year pilot project to sample frost flowers from McMurdo Sound.  By comparing the bacterial communities in frost flowers, seawater, sea ice, terrestrial snow, and glaciers, we hoped to show that frost flowers were a plausible source of marine bacteria and marine genetic material to the terrestrial environment.  Because the coastal Antarctic contains many relic marine environments, such as the lakes of the Dry Valleys, the wind-driven transport of bacteria from frost flowers and other marine sources could be important for continued connectivity between relic and extant marine environments.

Frost flowers are readily accessible in McMurdo Sound throughout the winter, however, this does not mean that one can simply head out and sample them.  While the ice conditions are far more permissible than at Barrow, Alaska, the bureaucracy is also far more formidable.  The can-do attitude of our Inupiat guides in Barrow (who perceive every far-out field plan as a personal challenge) was replaced with the inevitable can’t-do attitude at McMurdo (this was 2011, under the Raytheon Antarctic Support Contract, and does not reflect on the current Lockheed Antarctic Support Contract, not to suggest that this attitude doesn’t persist).  Arriving in late August we were initially informed that our plan was much to risky without helicopter support, and that nothing could be done until mid-October when the helicopters began flying (we were scheduled to depart late October).  Pushing for a field plan that relied on ground transport ensnared us in various catch-22’s, such as (paraphrased from an actual conversation):

ASC representative: You can’t take a tracked vehicle to the ice edge, they’re too slow.

Me: Can we take a snowmobile to the ice edge?  That would be faster.  We do long mid-winter trips in the Arctic and it works out fine.

ASC representative: No, because you have to wear a helmet, and the helmets give you frostbite.  So you can only use a snowmobile when it’s warm out.

Ultimately we did access the ice edge by vehicle several times before the helicopters started flying, but the samples reported in this publication all came from a furious two week period in late October.  What we found really surprised us.

Sampling frost flowers is as easy as scraping them from the ice surface with a clean shovel into a sterile plastic bin.

Sampling frost flowers on a warm day in September, 2011, in McMurdo Sound.

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

Sampling some of the frost flowers used in this study over much thinner ice north of Ross Island in October, 2011.

 Shelly Carpenter.

Sampling “blue ice” on Taylor Glacier a few days earlier.  Comparing various terrestrial ice environments with the marine samples gave us some interesting insights on how bacteria are dispersed by strong winter winds in the coastal Antarctic.

There is ample evidence for the wind-driven transport of bacteria in this region but, contrary to our hypothesis, most of that material is coming from the terrestrial environment.  The major transportees were a freshwater cyanobacterium from the genus Pseudanabaena and a set of sulfur-oxidizing Gammaproteobacteria (GSO).  The cyanobacterium was pretty easy to understand; it forms mats in a number of freshwater lakes and meltponds in the region.  In the winter these freeze, and since snow cover is low, ice and microbial mats are ablated by strong winter winds.  Little pieces of mat are efficiently scattered all over, including onto the sea ice surface.


Easily dispersed: desiccated microbial mat in Lake Chad, 2005
(photo by A. Chiuchiolo), taken from

The GSO threw us for more of a loop; the most parsimonious explanation for their occurrence in frost flowers is that they came from hydrothermal features on nearby Mt. Erebus.  We did some nice analysis with wind vectors in the region and while you don’t get a lot of wind (integrated over time) to move material from Mt. Erebus to our sample sites, you do get some occasional very strong storms.

Wind velocity and magnitude for the study region in October, 2011. Taken from Bowman and Deming, 2016.

Wind velocity and magnitude for the study region in October, 2011. Taken from Bowman and Deming, 2016.

What all this means is that, consistent with other recent findings, there is high regional dispersal of microbes around the coastal Antarctic.  While I’m sure there are some endemic microbes occupying particularly unique niches, in general I expect microbes found in one part of the coastal Antarctic to be present in a similar environment in a different part of the coastal Antarctica.  There are however, quite a few ways to interpret this.  Bacteria and Archaea can evolve very fast, so the genome of a clonal population of (for example) wind deposited Pseudanabaena newly colonizing a melt pond can diverge pretty fast from the genome of the parent population.  This has a couple of implications.  First it means that the coastal Antarctic, with all it’s complex topography yet high degree of microbial connectivity, is an excellent place to explore the dynamics of microbial adaptation and evolution, particularly if we can put constraints on the colonization timeline for a given site (non trivial).  Second, it raises some questions about the propriety of commercially relevant microbes obtained from the continent.  The commercialization of the continent is probably inevitable (I hope it is not), perhaps the potential ubiquity of Antarctic microbes will provide some defense against the monopolization of useful strains, enzyme, and genes.

Tracking Earthquakes in the New York Area - Fox News

Featured News - Thu, 03/24/2016 - 12:00
The devastation caused by earthquakes is evident all across the world, but could something like this happen in our area? Fox news talks with Jim Gaherty.

Heavy Breathing Plants Producing Less Carbon than Feared - Geographical

Featured News - Wed, 03/23/2016 - 12:00
When plants respire, they contribute a massive carbon flux to the atmosphere so their response to higher temperatures is a major concern for scientists. A new study from Lamont's Kevin Griffin finds plants might not respond to warming as thought.

Wine-Lovers Raise a Glass to Climate Change, but There May Be a Hangover - Guardian

Featured News - Mon, 03/21/2016 - 13:00
Higher temperatures in France are producing exceptional vintages, but the run will come to an end if global warming continues at the current rate, a new study from Lamont's Ben Cook suggests.

France's Top Wines Face Climate Tipping Point - AFP

Featured News - Mon, 03/21/2016 - 12:00
Climate change has pushed French wines into uncharted territory, and could force producers to relocate or abandon the grapes that helped to make their vineyards famous, according to a study from Lamont's Ben Cook.

Warming Pushes Wine Harvests Earlier – Not Necessarily for the Better - The Conversation

Featured News - Mon, 03/21/2016 - 12:00
"Our analysis showed that wine harvests are happening earlier, which has historically been a harbinger of high-quality wines. But we also found that changing local weather conditions could make it harder to determine when to expect high-quality wines, and that higher temperatures could force wine growers to use different grape varieties," writes Lamont's Ben Cook.

Carbon Emissions Top Even Those of 56 Million Years Ago - Christian Science Monitor

Featured News - Mon, 03/21/2016 - 12:00
Carbon emissions hit a dramatic high nearly 10 million years after the demise of the dinosaurs some 66 million years ago. But emissions now far surpass that. "What we're doing today is much more extreme than what happened in Earth's history," says Lamont's Bärbel Hönisch.

Will Our Trees Survive the Warming Temps? - Public News Service

Featured News - Mon, 03/21/2016 - 09:37
A crew of scientists led by Lamont's Park Williams has been making its way through the Ozark Mountains, dodging snakes and poison ivy to study tree rings, to see how they're reacting to climate change.

Finding Microfossils Off Southern Africa

When Oceans Leak - Sat, 03/19/2016 - 19:13
 Dick Norris and Jason Coenen. Illustration by Deborah Tangunan

Expedition 361 micropaleontologists with their nannofossil specialties (not quite to scale …): Top, left to right: Margit Simon, Thiago Pereira dos Santos, Luna Brentegani and Deborah Tangunan. Bottom: Dick Norris and Jason Coenen. Illustration by Deborah Tangunan

Read Sidney Hemming’s first post to learn more about the goals of her two-month research cruise off southern Africa and its focus on the Agulhas Current and collecting climate records for the past 5 million years.

Limpopo was awesome! We ended up with close to 4 million years of sediment from our latest coring site, off Mozambique near the Limpopo River. The accumulation rate for the last 2 million years is close to 10 cm per thousand years, so there is potential for highly resolved records in that interval. The accumulation rate between about 2 million and 4 million years is much lower, probably about a quarter, but that is also good news because we only had permission to go 250 meters, and if there had been more sediment we wouldn’t have covered nearly as much time.

The foraminifera are spectacular – translucent, glassy and “very pretty” throughout the whole sedimentary section. We do have a gap or two, as hard as we tried to avoid it, but we have overlap among holes for most of the site, and a continuous record back to close to 2 million years.

During coring at the Zambezi site earlier this week, the micropaleontologists had less to do since there were only two biostratigraphic datums (one foraminifera and one nannofossil), so nannofossil specialist Debs Tangunan made some cute art (above) with each of the biostratigraphers upon a fossil type of his or her specialty. Debs and Luna are the nannofossil specialists; Dick and Thiago are the planktonic (shallow floating) foraminifera specialists; Margit is the benthic (from the bottom) foraminifera specialist; and Jason is the diatom specialist. Jason’s pouting because most of our sites have not been good for diatom biostratigraphy, except the Agulhas Plateau. He has been a great sport though and has been helping with sample preparation and picking benthic foraminifera for a preliminary stable isotope record to help refine the age models for our sampling party.

The Agulhas Current. Image courtesy of Arnold Gordon.

The Agulhas Current. Image courtesy of Arnold Gordon.

We finished up at Limpopo this afternoon and now we are heading south to our final site, which is in the Cape Basin, and only eight hours from the harbor at Cape Town, South Africa. The catering staff put on a fantastic show for the 5-7 p.m. meal – it was sushi!  And what a beautiful layout, with butter carved into the shapes of fish and various melons and other food. It was delicious and amazing!

During the transit to the Cape Basin, which will take a little over four days, we will have a busy time finishing the cores from Limpopo and the Mozambique Channel. We had to put ~1/2 of a hole’s worth of cores to the side to get the shallow sites completed, and we will finish up those cores as we transit to the CAPE site. We must have all the data collected and reports finished before we arrive at CAPE because we are going to have to devote our full attention to the CAPE site in order to get the report finished on that site before we get to port.

CAPE is located right were the eddies that constitute the “leakage” from the Agulhas Current enters the Cape Basin. So this site is going to be very important for tying together the story of how the Agulhas Current system is connected to global ocean circulation. The water depth of CAPE (as well as the other three of our deeper sites from this cruise: Natal Valley, Agulhas Plateau and Mozambique Channel) is in North Atlantic Deep Water (NADW). So we should be able to obtain some great co-registered records of how the shallow and deep ocean circulation are changing through time, as well as how the productivity and temperature and salinity have varied and how these are related in time to southern African climates.

//">Cardiff Half Marathon</a> to raise money for a charity by running the distance aboard ship. Photo: Tim Fulton/IODP

Stephen Barker (left) and Ian Hall prepare to participate in the March 26 Cardiff Half Marathon. They’ll be raising money for a South African education charity by running the 13.1 miles in laps around the ship’s helideck. Photo: Tim Fulton/IODP

Another exciting thing that is going to happen while we are at CAPE on March 26, is that Co-Chief Scientist Ian Hall and Stratigraphic Correlator Steve Barker, both from Cardiff University, are going to be running a half marathon around the deck of the JOIDES Resolution at the same time the Cardiff Half Marathon is underway in the UK. Steve is a former Lamont postdoc and an adjunct associate research scientist at Lamont.

Their goal is to raise funds for a charity that supports children in South Africa. The small South African charity, located in the Western Cape, is called the Goedgedacht Trust, and it promotes education to help poor rural African children escape grinding poverty.  We are also planning to provide some of the Trust’s children with a tour of the ship during our visit in Cape Town. Ian and Steve will appreciate any support you (or your colleagues) can give!  Donations can be made online. I’m planning to contribute, and I hope you will too.

Sidney Hemming is a geochemist and professor of Earth and Environmental Sciences at Lamont-Doherty Earth Observatory. She uses the records in sediments and sedimentary rocks to document aspects of Earth’s history.

China's Forest Conservation Program Shows Proof of Success - Christian Science Monitor

Featured News - Sat, 03/19/2016 - 12:00
"When it comes down to climate and carbon sequestration, these are global problems," says Lamont's Kevin Griffin.

California City Worries About Expansion and Future Water Supply - The Tribune

Featured News - Sat, 03/19/2016 - 12:00
Worried about how climate change will affect rainfall in the coming decades, some San Luis Obispo residents are calling on the city to stop allowing developers to build new homes — at least until the city recalculates its future water supply.



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