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Today I would like to write about a very exciting new and free science project for upper school and nature groups all around the UK called The Microverse.


You may not have thought about what a microbe is before, but there are millions - possibly billions - of different kinds. So why should we care? Well, firstly, most life on earth exists because of one group - the cyanobacteria. Then there are all those important ecosystem services that microbes provide. And remember the 'healthy bacteria' in your gut, which have been linked to all sorts of health benefits (or diseases, when things go wrong).


We now know that human activity is changing the world we see, but what is it doing to the world we can’t? Nobody really knows. There are many questions to answer about about the microbial diversity that can be found in urban environments in cities, towns and villages. What is microbial diversity like on concrete pavements and glass skyscrapers? How can they survive the temperature extremes, lack of nutrients and high levels of pollutants?


The Microverse project is asking schools and nature groups to take samples from buildings for analysis at the Natural History Museum in London. Are our cities a disaster for microbial diversity, or are there thriving, species-rich communities out there? Who knows? It’s a whole new world we’re entering. More information on the biology, science and activities in this Microverse clip.





It is is easy and free to join the project. Just sign up on the The Microverse webpage.


This year, we went back to Lake Joyce to study the benthic biology in the McMurdo Dry Valleys. The 3D microbial structures that are growing out of the mat are particularly interesting because most of them have a calcite skeleton. This is the only lake in the Dry Valleys where microbial mats have such distinctive calcite skeletons.


The calcite skeleton makes these microbialites particularly interesting for geobiology, where modern microbial mats are studied to enable a better interpretation of microbialite fossils from early Earth. 


Over the last three weeks we collected samples that will allow us to investigate if the water chemistry, light and sedimentation effect the growth of microbialites in the lake. We also collected mat material to carry out DNA and microscopy analysis to evaluate the role that cyanobacteria, other bacteria and eukaryotes play on the formation of microbialites and their calcite skeleton.



Microscopy image of Phormidium cyanobacterial filaments in Lake Joyce mats. Most of the Phormidium filaments have a strong purple pigmentation though the production of Phycoerythrin for a better utilisation of the limited light that is available in Lake Joyce.



Anne working at the microscope.



Close-up image of microbialites with calcite skeleton covered by thin microbial mat webs .



Microbialite structures with calcite skeleton collected from Lake Joyce by diving.



The team getting ready for a dive to collect microbial mats.


The main efforts of the field event led by researchers from UC Davis, California, were to map the distribution of the microbial structures in the lake and to test what the influence of sedimentation is on the microbial structures.


The imaging is done by a drop camera that is held on a rope through a hole in the ice. The team installed several traps in the ice that will collect sediment from now until next season.Each hole is individually drilled with a jiffy drill in order to insert the traps and document the microbial mas and microbial structures.



The team drilling a hole in the ice.


Back online! We just got back from our wonderful field camp at Lake Joyce and are busy cleaning our camping equipment and repacking equipment and samples for shipping back to our home institutions. Meanwhile, here is an update on what we have been doing during the last few weeks by Lucy Coleman. Lucy is a teacher in California and part of PolarTrec, and in her blog she talks about the science happening on the cyanobacterial mats, microbialites, sampling, and camp life.


PolarTrec is an amazing programme that allows teachers and researchers to come together through hands-on field experience in Antarctica. It is great to have a chance to work together and learn about teaching, education and outreach!



               Lucy working on blog, video and image updates that will later be taken back to the station and posted online.


After a day of busy packing, submitting a request for a helicopter and some sequence data analysis, I went for an evening walk. It was a cloudy day and a little chilly as well. Over summer around 1,000 people are at McMurdo station and therefore you can find a little bit of everything that you would also find in any small town or village around the world.



Scott's Discovery Hut and McMurdo Station.



Cary labs, where a lot of the science is happening.


McMurdo shop.



Departure for Antarctica

Posted by Anne D Jungblut Nov 17, 2014

After spending several lovely days in Christchurch and having a look around to see how more and more buidlings are being rebuilt after the earthquake, it was time to pick up my ECW (Extreme Cold Weather Gear) for our Ice Flight.



Entrance to the US Antarctic Program clothing distriubtion center in Christchurch.


Extreme Cold Weather Gear.


The flight was originally scheduled for 9am with a pick-up by the shuttle bus at 6am from the place I was staying. However, weather conditions can change very quickly in Antarctica, therefore I was told to ring the flight information… lucky I did so at 5.40 am.


Our flight was delayed by 3 hours, which meant I got another 2 hours of sleep. Finally, we left Christchurch just after 12 noon. As always, the C17 was pretty full with people and cargo.



Inside the C17 aircraft.


After a bit more than 5 hours, we arrived in Antarctica!



....arrival in Antarctica!


Summer student Josi has been working with Dr Anne Jungblut on the Museum's cyanobacteria collections. Here's her final post on cyanobacterial diversity.

Anne is already gearing up to head to Antarctica again! High time I wrap up my mini-series and show you my results. Last time, we sent the cyanobacterial samples for DNA sequencing. This is done in-house at the Museum, so it only takes a few days. Initially, the sequencing files are fairly innocuous - just long strings of letters representing the DNA code.


Here's an example of the first 50 letters of sample 1:




The file continues like this for 770 more base pairs.


To get a first idea of  the easiest way to analyse such data is to carry out a BLAST search. BLAST stand for “basic local alignment search tool” and this is an online resource anyone can use. BLAST compares the uploaded sequences against a vast database.


In my case, the results are all cyanobacteria sequences that scientists have uploaded in the past. Under “query cover” you can see the percentage of identity between the sample and the database entry. In this particular case, we have a number of “uncultured cyanobacteria” entries, which means that somebody uploaded a sequence but didn’t add in much details. But the entry at the bottom shows a 99% match to Chamaesiphon, which is a unicellular cyanobacteria first described in the 1830s.



Different Chamaesiphon genera © 2004–2014 J. Komárek & T. Hauer



Microscopy images of cyanobacteria culture with highest BLAST match to Chamaesiphon.



In the image above you can see the sketch commonly found in scientific books on cyanobacteria for the order Chamaesiphon. Imagine having the microscope image on the top and using the drawings to try and identify the species - they don’t look too similar! Modern sequencing is a powerful tool to identify microorganisms.


However, BLAST results are not always straightforward. At times, the quality of the sequencing result isn’t good enough to carry out a good alignment or a sequence could correspond to more than one database entry. Sometimes, there is no entry to correspond to the uploaded sequence. This means that no similar DNA sequence has been uploaded to the BLAST database, and this may indicate a novel type of cyanobacteria. Therefore, for our case, further detailed phylogenetic analysis are now required to test if our preliminary BLAST result provided a correct assignment of the cyanobacterial isolate to the genus Chamaesiphon.


Sample9.jpg Samples13.jpg










Microscopy images of cyanbacteria isolates 9 and 13






Some of the other cyanobacterial isolates were samples 9 and 13. Sample 9 was sequenced and had 100% similarity to Phormidium priestleyi, while sample 13 had less certain results. In the case of sample 13, the sequence results itself is of low quality – a lower number of base pairs was analysed, and the signal intensity is very weak. This will either be due a low quality PCR-product or potentially a not pure cyanobacterial isolate.


After sequencing and BLAST, the next step is to carry out a phylogenetic analysis and to discuss the results in context of the metadata e.g. habitat, water chemistry etc to see if there are some common features. But sadly, my time at the Museum is over. I reckon there is still a lot do for another summer student !!!


The days are getting shorter in London and the Museum's Ice Rink has opened, but this also means that the days are getting longer in Antarctica with the austral summer approaching. This year, I am very lucky to be invited to join an Antarctic expedition to carry out field work at Lake Joyce, a perennially ice-covered lake in McMurdo Dry Valleys.


While I am still packing the cargo and organsing how many woollen and thermal socks I need, half of the team is already there. This year our field work is part of the US Antarctic Program and our main station is McMurdo Station on Ross Island. Here's a webcam with a view over McMurdo.


We will continue our work on microbial diversity and the ecology of benthic cyanobacteria-based microbialite structures to better understand why and how microbialite structures are forming in Antarctic lakes.



US Antarctic Program bag tags and travel documents.



Perennially ice-covered Lake Joyce and Taylore Glacier in the Pearse Valley, McMurdo Dry Valleys, Antarctica.


Summer student Josi has been working with Dr Anne Jungblut on the Museum's cyanobacteria collections. Her next post on cyanobacterial diversity is all about DNA lab work.


At the end of my last post, we determined which cyanobacteria isolates were unialgal by microscopy and suitable for DNA analysis. These samples were initially collected during the Antarctic fieldwork featured on this blog, stored, and brought back to the Museum. Now we want to know what type of cyanobacteria we’re dealing with! One method to determine the species is by DNA sequencing. For cyanobacteria it is really important to use DNA analysis, as cyanobacteria have very varible morphologies that can change under under different growth conditions.


Analysing DNA


The first step of preparing the samples is to carry out a DNA extraction. This step destroys the cell wall of cyanobacterial cells, and removes everything but the DNA from the test tube. A cyanobacterial genome is fairly large, around 1-10 megabases. That’s as much information as fits on a CD-ROM! Therefore we want to look only at a smaller section of DNA at this stage. The step after DNA extraction is called a PCR (polymerase chain reaction), which amplifies a small part of the DNA and generates multiple copies of it. We are using a cyanobacteria-specific protocol that only targets the DNA of cyanobacteria.


Sounds straightforwards, right? Well, this summer I was the victim of the PCR ghoul - none of the reactions worked...or rather, they worked too well. Below you can see the results of one of my (many…) failed PCRs. Each white stripe corresponds to the amplified DNA after PCR of each sample. The 'ladders' on each side are the equivalent of rulers to allow you to verify the size of your amplified DNA. Looks pretty good, right? We’ve got a good yield for each reaction!


Wrong - unfortunately, the white stripe on the far right is a negative control. I set up the PCR for that reaction without any DNA, so actually, there shouldn’t be any stripe showing up at all! So what’s going wrong here?


pos neg control blog.jpgPCR results from Cyanobacteria (16S rRNA gene) isolated from Antarctica and contamination in negative control.


Well, the PCR amplifies only cyanobacteria DNA - so there can be only one explanation for the 'positive' negative control. One of the reagents for the PCR has DNA contamination! The only solution to this is trial-and-error elimination - each reagent must be replaced individually to figure out the culprit. Unfortunately, a PCR reaction requires about 8 different reagents to work, and any one of them could contain a  tiny trace amount of cyanobacterial DNA.


You can imagine that this process takes time, and can at times be disheartening, especially as the contaminants cannot be seen with the naked eye. However, luckily, the PCR ghoul finally released me from my odyssey and my negative control was finally 'negative' without  a white strip, and I was able to send my samples for DNA sequencing. More on the results next time!


PCR blog.jpg

PCR results from Cyanobacteria (16S rRNA gene) isolated from Antarctica without contamination.


Summer student Josi has been working with Dr Anne Jungblut on the Museum's cyanobacteria collections. She shares her experience of working in the lab with some very chilly samples.


My name is Josi and I'm in the middle of a summer studentship here at the Museum. I have been working with Dr Anne Jungblut on her cyanobacteria project and would love to share what I've been doing over the last several weeks at the Museum.


My summer project is supported by funding from the British Phycological Society, which focuses on research on microalgae, seaweeds, cyanobacteria etc. The society supports research projects through grants and has a biannual publication called The Phycologist.


Antarctic samples


One of my responsibilities over the summer has been to take care of the cyanobacteria in Anne's cyanobacteria culture collection. In the lab, biological samples, or cultures, need to grow in conditions similar to their natural habitats. This keeps them alive and allows us to carry out experiments even when the organisms have been removed from their orginal sites. For example, some of the cyanobacteria samples were collected during Antarctic expeditions featured on this blog and they are now kept in growth chambers here at the Museum.



Growth chamber for Antarctic cyanobacteria.


In the photo, you can see one of these growth chambers or illuminators with each cyanobacteria sample on its separate media place. The bright light on the inside of the door always stays on - it allows the cyanobacteria to carry out photosynthesis. I think of this illuminator as a "cyanobacteria garden" where we wait for the samples to grow. As these cyanobacteria are used to growing under Antarctic conditions, they are quite hardy! But every half year or so the cyanobacteria need to be re-cultured. This process of transferring cells to new medium provides them with fresh nutrients to grow.


I also used light microscopy to figure out if the samples are uni-algal - whether they are only one cyanobacterium morphotype or still a mixture of cyanobacteria. This is important because we can only use them for DNA characerisation when they are unialgal.


pic2.jpgMicroscopy image of unialgal cyanobacteria culture (L) and mixed sample with unicellular and filamentous cyanobacteria (R).


I have got a few more impressions to share on our camp life. We have an amazing view from our cooking area, out across Lake Fryxell and towards Mt Erebus in the background.


View while cooking



We brought a lot of equipment and some days the camp is turned into a workshop to get everything installed, assembled, checked and running for our measurements in the lake.


Preparing equipment for measurements in lake




Another important task is to keep the heater running in the camp.


Lighting the heater



The ice mass on Antarctica is the largest body of frozen water in the world so it is unsurprising that our drinking water is melted glacier ice. Our camp is near Canada Glacier and for several days some of us go over to Canada Glacier to collect chunks of ice that have fallen off the glacier. These chunks of ice are called glacier berries by the locals.


Trip to Canada Glacier to collect glacier berries



Standing among the glacier berries



Diving in Lake Fryxell

Posted by Anne D Jungblut Nov 27, 2012

As I wrote previously, all our microbial mat samples are collected by the divers in our team. AND the divers are back in the water! The diving is happening through a hole in the ice. It takes several days to make the hole. First a smaller hole is drilled and then a coil called a hot finger is used to widen the hole to ca 1 m in diameter.


We are not only collecting benthic cyanobacterial mat samples, but the divers are also collecting water from above the microbial mats for nutrient analysis and to determine oxygen concentration, as well as measuring the light conditions under the ice.


The scientific diving at Lake Fryxell is done with surface supplied air and there are always several dive tenders at each dive. Their responsibilities include tendering to the tethered diver or operating the console for the air supply and communication between the tender and diver.


We are getting ready for a dive



My job is dive tender




It is the end of a dive and we are getting the diver out of the water



Full face mask diving set-up



This afternoon we went for a walk on the Lake Fryxell. The ice is incredible clear in the moat regions, and one can find everywhere cyanobacterial mats frozen into the ice. These cyanobacterial mats were originally from the bottom of the lake, and are called lift-off mats. Microbial mats often drift to the top of the water when they are pushed upwards through the formation of gas bubbles. Although mats are now frozen, it is very likely that many of the cyanobacteria in the mats are still viable.


Lake Fryxell with Canada Glacier in the background




Dried cyanobacterial mats in the ice



Today, I collected water samples to study the diversity of cyanobacteria found in the water column of Lake Fryxell.  The water is sampled through a hole in the ice. We are very lucky the hole is covered by a heated tent, which makes it a lot easier. 


The phytoplankton biomass is concentrated on a filter. Some of the filters turned orange and brown because of the pigments of the phototrophic microbial community. After my return to the NHM, I will extract the DNA in order to characterise the cyanobacterial diversity.


Water sampling




Niskin bottle



Water filtration set-up



Water filter coloured by the pigments of the phototrophic microbes in Lake Fryxell water



.....and a little quiz: What is wrong in the following pictures?



This year, we will be be out in the field for 5 weeks. Our first camp is at Lake Fryxell. During our time at Lake Fryxell, we will be able to use the facilities by the US Antarctic Programme, which is pretty cool! The camp consist of a James Way as living area with heating, internet and even a telephone line to Scott Base and McMurdo. We sleep in tents but spend most of the day out on the lake or in the labs and hut.


Lake Fryxell camp


Inside the hut


Our drinking water is melted glacier ice

Snack corner


Frozen Veggies


Camping at Lake Fryxell



My tent



Solar  energy



Wind energy


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Anne D Jungblut

Anne D Jungblut

Member since: Sep 2, 2010

I'm Anne Jungblut from the Botany Department. Join me as I head to Antarctica to study cyanobacterial diversity in ice-covered lakes of the Dry Valleys and Ross Island where already scientists on Scott's and Shakleton's expeditions made many discoveries.

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