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If you've joined us from our last blog post where we introduced the team, hello again! I'm really excited to be taking part in the Museum's newest citizen science project, The Microverse, that we launched at the end of 2014. This is a research project that will explore what microorganisms are living on UK buildings.



The research is being led by Dr Anne Jungblut, who studies microorganisms in extreme environments, exerting much of her research effort on the microorganisms that are found in Antarctica. Despite taking field trips to Antarctica, Anne is also very keen to explore the life that lives on buildings here in the UK, which - perhaps surprisingly - have received very little attention with respect to their microbiology to date.



Cyanobacteria are the specific type of microorganism that Anne studies in Antarctica.


Like Antarctica, buildings are an extreme environment for life, exposing microorganims to extremes of wet and dry and - sometimes - high levels of pollution, while providing little access to nutrients. Anne approached Lucy Robinson and I to see if we could help her to recruit members of the public into collecting data (it would take Anne years if she collected the data from across the UK herself).


So we want to get 250 secondary schools to step out of the classroom and swab a local building.



Students will find a local building and collect samples from the wall using a cotton swab.


Throughout January and February, A-Level Biology students from across the UK will be swabbing buildings and recording data about the building's environment and form. The students will collect the samples on cotton wool swabs and post them back to the Museum in a preservative. Once here, Anne will then extract DNA from the swabs and sequence it, to reveal what types of microorganism groups are living there and how many different types.



Samples are added to labelled tubes of DNA preservative to be sent back to the museum for analysis.


Schools will literally be contributing the genuine scientific research and to the Museum's collection, because Anne will use the data to publish academic research in a scientific journal and the specimens will be incorporated into our Molecular Collections Facility. This research project aims to determine the diversity of microorganisms on buildings across the UK and what types of variables are impacting on that diversity. It will form a foundation of knowledge from which more detailed questions can be asked.


If you are an A-Level Biology student or teacher, or you know of anyone that might like to get involved in The Microverse, there is still time to join the programme, just visit our webpage to find out how to take part. It's completely free and each school receives a pack with equipment and resources guiding both teachers and students through the method and the science. Data collection has already started in January and will continue throughout February, and the results will be returned to students by the end of March 2015.


Jade Lauren


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 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).


During the first week of our trip, we made an exciting discovery! In one of the ponds in Maiviken Cove, we found cyanobacterial mats.


Maiviken is a a beautiful cove on Thather Peninsula,only a 1 hour walk away from KEP. The cyanobacterial mat were in a small pond close to the scree slopes on the eastern side of the valley. The cyanobacterial-based mats were a lot more gelatinous than, for example, mats from the McMurdo Ice Shelf, but nevertheless clearly definiable as lift-off mats of up to 1 cm thickness.


Back in the lab, I had a look under the microscope and the mats were comprised of various morphotypes of Oscillatoriales includig Phormidium and Leptolyngbya, the unicellular order Chroococcales as well as Nodularia, which is a genus in the nitrogen-fixing order Nostocales.


A few weeks later, I also found cyanobacterial mats with a similar taxa composition in apond in Hapon Bay, which is also on Thather Peninsula. This finding is interesting as there is very little know about mat-forming cyanobacteria from South Georgia. Therefore, we collected material for more detailed microscopic and DNA analyses of the cyanobacterial diversity in these mats.

IMG_8116.jpgCyanbacterial mats in Maiviken Cove


On Barff Peninsula, I found a meltwater stream where the cyanobacterial genus Nostoc was growing on some of the rocks. The Nostoc nodules were ca 1 cm in diameter. It was difficult to get a good image beause of the reflection of the sun in the fast flowing water.

IMG_8398.jpgNostoc in a stream on Barff Peninsula


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



It is November 2012 and it is time to head back to Antarctica. This year we are a team of researchers and students from University of Canterbury (NZ), UC Davis (USA) and the Natural History Museum, London. We are coming from the research areas of Microbial Biodiversity, Microbial Ecology and Geobiology. We will be working in the McMurdo Dry Valleys and study the benthic biology of Lake Fryxell and Lake Vanda. In total, we will be in Antarctica seven weeks, two weeks at Lake Fryxell and three weeks at Lake Vanda, which is very exciting !


Cyanobacteria-based microbial mats and microbialites cover large parts of these lakes. The lakes are ice-covered and meromictic with a stratified water column, which makes them very interesting systems to study how environmental conditions affect microbial diversity and community composition and microbialite morphologies and their assemblages. The microbial communities will be collected by divers ( ...not me but the other members of my team). They will also characterise the different shapes of microbialite structures, as well as light conditions and photosynthesis activity of the lake environment.   We will also do light microscopy to study the cyanobacterial morphotype diversity.


Lake Fryxell at night



Dr Kanako Ishikawa from Lake Biwa Environmental Research Institute, Otsu, Japan, visited Dr Anne D Jungblut (NHM Life Sciences Department) in April 2012 as part of a project supported by a Daiwa Foundation Small Grant that aims to establish a Lake Biwa periphyton species list and carry out public engagement events on biodiversity, management and conservation of Lake Biwa, Japan.



Proliferation of macrophytes and periphyton in Lake Biwa


Lake Biwa is the largest lake in Japan and one of the twenty oldest lakes in the world. It has many endemic species, and supplies 14 million people with drinking water including the megalopolises Osaka, Kyoto and Kobe Cities. It is a breeding ground for freshwater fish and supports commercial fishing.


Microalgae such as cyanobacteria and green algae growing on leaves and stems of submerged water plants (macrophytes) or rock surface are defined as periphyton. These microalgae are not only an important food source for fish and other animals, but can also become nuisance for fishing equipment, water supply system and leisure activities.


Periphyton.jpgPeriphyton collected from Lake Biwa


In recent years macrophytes have become highly abundant in Lake Biwa and as a consequence periphyton growth has dramatically increased. However, little is still known about the species diversity of Lake Biwa periphyton, in particular the presence of non-native and potentially harmful species. During the visit, Kanako Ishikawa and Anne Jungblut carried out DNA-based analyses on periphyton samples collected from Lake Biwa using culture-independent methods.


Lab.jpgKanaka Ishikawa and Anne Jungblut preparing DNA samples for PCR


Anne Jungblut will visit the research laboratory of Dr. Kanako Ishikawa (Lake Biwa Environmental Research Institute) and Dr Taisuke Ohtsuka (Lake Biwa Museum) in Shiga prefecture, Japan, in July.


Anne Jungblut, a botany research scientist at the NHM, has been awarded the US Antarctica Service Medal. The medal was established by US Congress in 1960 to honour service personnel and civilians who contribute to US Antarctic expeditions.




Anne has been taking part in Antarctic expeditions since 2005 with the New Zealand and US Antarctic Program, and has represented The Natural History Museum on these expeditions since 2009.  Her blog gives details of expeditions to look  at cyanobacteria in Antarctica, which form thick mats in meltwater pools.  We are always intrigued by the sampling equipment that appears in some of the photographs!


Most of the cyanobacterial mats that we have found were orange pigmented and the macroscopic structure was flaky to cohesive. The orange colour is due to carotenoids which are an protection against UV and oxidative stress.


I had a small light micrscope with me in the field and the genus Leptolyngbya dominated the orange mats. Leptolyngbya are filamentous non-branching cyanobacteria belonging to the order Oscillatoriales. They are mostly between 0.5-3 micrometre thick. However, the lower side of the orange layers sometimes had green pigmentation, which besides the Leptolyngbya also had some Phormidium. The genus Phormidium also belong to the order Oscillatoriales, but they are thicker with a width of around 5 micrometres.


   Flaky orange-pigmented cyanobacterial mats dominated by Leptolyngbya



Cohesive orange-pigmented cyanobacterial mats



green lower side of cyanobacterial mat with Phormidium


Interestingly, we also found some cyanobacterial mats which were dark purple to black. This colour is due to the UV-screening Scytonemin. We found the genus Schizothrix sp. (Oscillatoriales)  in the mats which is known to produce Scytonemin. We also found several ponds with large accumulations of the genus Nostoc, which belongs to the order Nostocales and has specialist cells called heterocysts for nitrogen-fixation.


Cyanobacterial mats with the Scytonemin-producing genus Schizothrix



Nostoc accumulations in a meltwater pond



We also found a few ponds with green algae. Green algae biofilms are easy to distinguish from cyanobacteria as green algae are very bright green.


Green algae



The Wright Valley is one of the ice-free Dry Valleys. The Upper Wright valley is characterised by the so-called Labyrinth, which is an area of steep-sided canyons and channels. It is mainly dolerite and most rocks are bright red. Based on the literature it was formed by large 'floods during the mid-Miocene era'.


The Labyrinth




In the area you can find many strangely shaped rocks. They are called ventifacts, and are wind- and dirt-sculpted rocks.


Ventifacts in the Labyrinth




Wherever you look you only see rocks and it often reminded me of images showing how it may look on Mars.



Landscapes like on Mars


However, there is life. On one of our walks, we found these lichens. They were on the top of one of the ridges, where the overall humidity seems to be higher due to its location at a height of greater than 750 metres, and the greater influence of clouds and fog. Many of the lichens grow under or in cracks of the rocks, and this enhances the erosion of the rocks.



Lichens on rocks in the Labyrinth





AND, as soon as you get running water and temporary ponds you get thick accumulations of orange-pigmented mats. To date there have only been few morphological descriptions and there is no DNA-based data available at all.



Meltwater ponds covered by ice with bright orange mats





Orange cyanobacterial-based microbial mats




Close-up of microbial mat