Spanning time zones for a joint UK-US Bai-call

This week the U.S.-based Baikal Dimensions team sat down for a Skype with a U.K.-based Baikal team to update each other on our respective projects, and look for areas where we can help each other and collaborate. Our first joint Bai-call! Many but not all of us met in-person last year at what we all thought might be Lake Baikal’s first tweet-up (or at least the first one at Bolshie Koty?)!

In 2013, UK-based team of Baikal researchers met our team at ISU's Bolshie Koty research station. Not quite what our Skype call this week looked like, but this is how we might imagine it! Photo: Kara Woo, 2013.

In 2013, a UK-based team of Baikal researchers met our team at ISU’s Bolshie Koty research station. Not quite what our Skype call this week looked like, but this is how we might imagine it! Photo: Kara Woo, 2013.

The U.S.-based team recently had a chance to coalesce a lot of our work at the in-person All Hands Meeting on the Dimensions project, so we turned on a firehose of information about our work from genomics to time series statistics, and then braced ourselves as they reciprocated – it was 90 minutes jam-packed with information, a great science exchange! As we all anticipated, it elicited a number of topics on which we will stay in touch – from nutrient-temperature-plankton relationships, to DOC-microbial dynamics, to the biogeochemistry of seal teeth!

Shoreline of Lake Baikal near Bolshie Koty. This blog post is about a Skype call - I can't bring myself to post a picture of people on a Skype call, so let's look at the lake instead! Photo: Stephanie Hampton, 2013.

Shoreline of Lake Baikal near Bolshie Koty. This blog post is about a Skype call – I can’t bring myself to post a picture of people on a Skype call, so let’s look at the lake instead! Photo: Stephanie Hampton, 2013.

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Message in a Microscope

Today’s post comes from Elena Litchman:

Kirill has been very successful growing multiple strains of the Baikal’s endemic diatom Aulacoseira baicalensis! To the point that it is communicating with him–its filaments are growing as words (see the photo)! It surely helps that both Kirill and Aulacoseira baikalensis are Baikal expats. Kirill is growing multiple strains at a range of temperatures and we will be taking samples for transcriptomics, proteomics and lipid analyses to understand why Aulacoseira baicalensis is a psychrophile (cold-loving organism).

A message written in Aulacoseira baicalensis. Photo: Kirill Shchapov.

A message written in Aulacoseira baicalensis (look closely). Photo: Kirill Shchapov.

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Bringing the pieces together: the Baikal team face-to-face in Michigan

The Dimensions team got together for an exciting All Hands Meeting in Grand Haven MI last week – we had a chance to both find out how much progress has been made and converge on new ideas for synthesizing our results, in ways we had not previously imagined. Hooray for collaboration!

Aulacoseira baicalensis Photo: Irkutsk State University

Aulacoseira baicalensis Photo: Irkutsk State University

The Michigan State University team has successfully cultured a number of Baikal species, including the finicky little diva Aulacoseira baicalensis! [knock on wood] Getting this beauty into culture aids not only MSU experimentation that characterizes functional diversity, but also the genetic work on Baikal endemics at University of Texas. Our Russian colleague Kirill is in residence with the MSU team right now, supported by a prestigious Russian fellowship, and he has been busy isolating phytoplankton for cultures and otherwise making progress in research towards his dissertation at Irkutsk State University in Siberia. From nutrient and temperature experiments to transcriptomics and theoretical modeling, the MSU team is working in high gear, with active collaborations across all of the universities.

Ted and Marianne at Wellesley have just about finished up the functional diversity zooplankton experiments (e.g., “eggsperiments“) that will help to parameterize theoretical models, and relate to zooplankton genetic characterizations at East Tennessee State University. Ted has also been busy pulling together all the pieces of the Saprolegnia parasitism story that began two summers ago at the lake – the prevalence of Saprolegnia infections on Epischura caught us a bit offguard at the time and then turned into a project in which we all found ways to lend expertise – genetics of Saprolegnia, mortality experiments, theoretical modeling, and statistical analysis of long-term data. If we would all stop suggesting new, cool things that we need to do with Saprolegnia, Ted might have a chance to get that paper together!

Saprolegnia infection of Lake Baikal endemic zooplankton Epischura baicalensis. Photo: Ted Ozersky, 2013

Saprolegnia infection of Lake Baikal endemic zooplankton Epischura baicalensis. Photo: Ted Ozersky, 2013

Naturally, Wellesley College stole the show when they told us about the preliminary results of studying the biogeochemical records preserved in the archived teeth of Baikal seals (!) with seal experts at Irkutsk State University – Ted promises he is going to write a blog post about it so I won’t steal his thunder here… Ted seems awfully busy wrapping up manuscripts, so that he can move on to a new faculty job at the Large Lakes Observatory at University of Minnesota-Duluth – congratulations, Ted!

The Lake Baikal seal on ice (photo: Kantor/Greenpeace)

The Lake Baikal seal on ice (photo: Kantor/Greenpeace)

At UT-Austin, Mariska and Ed have been buried in lab work to do the genetic characterizations of Baikal algae, for many months, and are expecting the results back any day now. Stay tuned…

Larry successfully defended his Masters thesis and participated in his commencement at ETSU the day before arriving at the All Hands Meeting. Not only was he an active GK-12 Fellow at ETSU, teaching kindergarteners but he also did field work in Russia and the lab work to show us that there appears to be genetic differentiation among Epischura across basins. Larry is now madly writing this up for peer review, and wrapping up other Baikal projects, so that he can move on to his next adventure – a Ph.D. program at Yale with David Post – congratulations, Larry!

Kara, Steve and I recently moved from UC-Santa Barbara (NCEAS) to Washington State University. Luckily, since we focus on mainly data, data, data… the move has not put us too far behind in our Baikal work! Together with our Siberian colleagues Lyubov, Kirill and Zhenya, and the rest of the Dimensions team, we are working out some of the main drivers of “melosira years” in Lake Baikal, a long-standing mystery – why in some years does Aulacoseira (Melosira) have massive under-ice blooms, and in other years it does not? Ice is mysterious stuff…

Clear ice at Lake Baikal (photo: onurati at flickr.com)

Clear ice at Lake Baikal (photo: onurati at flickr.com)

The circumbaikal cruise in 2013 has yielded a ton of data that we are excited to be bringing together. Our ISU colleagues have many years of data from stations throughout the lake that provide a great context for the 2013 distributed sampling of plankton and other limnological variables. We are also looking forward to comparing notes with our colleagues from University of Nottingham and University College London who have been working across all basins of the lake in the past several years as well!

At the lake last year, Ed drew up this planning map for our circumBaikal cruise – the map brought back very fond memories when he showed it at our All Hands Meeting – we were lucky with the weather and achieved even better spatial coverage than we originally planned using this map!

The hand drawn map our Baikal Dimensions team used to plan the 2013 cruise. We hit more stations than initially planned, and the map sparks lots of great memories. Photo: Ed Theriot, 2013.

The hand drawn map our Baikal Dimensions team used to plan the 2013 cruise. We hit more stations than initially planned, and the map sparks lots of great memories. Photo: Ed Theriot, 2013.

Putting the pieces together – from genetic to taxonomic and functional diversity – is now becoming a reality, and this revelation at the All Hands Meeting was very energizing for us all. Science is never enough, of course, and some team-building activities (aka karaoke) provided the extra edge that all collaborative groups need in order to achieve the highest levels of creativity!

The MSU team and The Intrepid Kara Woo arranged a number of the travel logistics, including bringing a coffee grinder and a french press to keep us well supplied with delicious coffee – for which we are all extremely grateful! Of course, no one but Lev could be responsible for logistics which resulted in him and Larry arriving by ferry across Lake Michigan in the early morning – they are the only ones who will ever know the full accounting of red-eye planes, trains, boats and automobiles… Regardless of those mysterious details, we were delighted to see Lev arrive on the ferry holding a plankton net aloft… and they both jumped right into talking good science for several intense days!

Lev and Larry on Lake Michigan ferry, arriving with plankton net held aloft, May 2014. Photo: Paul Wilburn.

Lev and Larry on Lake Michigan ferry, arriving with plankton net held aloft, May 2014. Photo: Paul Wilburn.

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Breathtaking Baikal

RT recently produced a nice short clip about Lake Baikal and what makes it unique. In the video, correspondent Thabang Motsei travels over the ice by hovercraft, visits the Limnological Museum, and speaks to local people about the lake’s biodiversity, beauty, and place in culture and history.

 

Although Baikal is still frozen over (as is typical for this time of year), Siberia is experiencing abnormally high temperatures. The lake froze later than usual this winter, and this year’s April 1st was the hottest on record for several Siberian cities. The combination of high temperatures and low precipitation have caused the forest fire season to begin early.

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My job is done.

About 5 years ago Elena called me and asked, without much introduction: – Can you characterize the genetics structure of Baikal zooplankton population? – What, right now? – said I. – No, in the future, if we get funded? – I can try, said I. Lots of time elapsed. We did get funded. The plans to characterize the genetic differentiation of Baikal Epischura changed from microsats (oh so 20th century) to RADseq to, finally, pooled RNAseq, which is what we ended up doing. So. Is there or is there no genetic differentiation among samples of Epischura from different parts of Baikal? On Wednesday Larry will have his MS defense and, with his permission, I am posting some of our results here.

Fig. 1. Principle component analysis based on minor allele frequency of 2000 randomly selected SNPs. Individual points are pooled RNAseq biological replicates, 3 per sample. Blue – South Baikal (“St.1″), red – Central Baikal, yellow – North Baikal, green – Maloe More.
Fig. 1
Fig. 2. Actual (green) and expected based on random assignment of alleles to populations distribution of Fst values in 4 samples shown on Fig.1.
Fig. 2
We expect to add 2 more samples from each region plus separate top 50 and 250-100 m depth layers at Station 1. Hopefully before summer.

 

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Shoutout to Baikal at the 2014 Olympics

This short film kicked off coverage of the 2014 Winter Olympics on Russian TV. The film begins with an alphabet primer in which each letter corresponds to some facet of Russian history and culture, and it goes on to depict major moments in the history of Russian civilization up to the present. In the alphabet section, the Russian letter “Б” is for “Байкал” (Baikal) and the film’s protagonist is shown taking a nice, cool drink from the waters of the lake.

Baikal was also featured in the Olympic spotlight a few months ago when SCUBA divers took the Olympic torch below its surface.

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A first glance at differential gene expression in Epischura baikalensis from different parts of Baikal

This plot (called a heatmap) is essentially a table with genes as rows and populations as columns. Genes (rows) are arranged in such a way that genes with the most similar expression profile across populations are next to each other (clustered together, see the cluster dendrogram on the right; populations (columns) are arranged in such a way that two populations with the most similar expression profile are next to each other (see cluster dendrogram on top). Each cell of the table is painted by a scale of colors from red to black to green; red means that this gene is up-regulated (transcribed at a higher rate) in this population, relative to overall mean, green means that this gene is down-regulated in this population.

You can see a clear 2 clusters of genes: up-regulated in the North Basin and upregulated in Maloe More. Maloe More is also the highest fat content samples by far. We plan to sequence more samples from each region.

heatmap12samples

NB: North Baikal station 2, MM – Maloe More station 2, CB: Central Baikal station 2, SB: South Baikal station 2.

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