Featured post

before accepting that too good to be true doctoral position….check your contract is legal and correct

I imagine scam contracts is a problem that occurs worldwide, so while my personal experience with this was in Sweden, my warning is to any student thinking of studying overseas. My warning is about fake wage, employment certificates, or contracts. In general, domestic students aren’t going to be stung by these kind of cons as they know the local system, they know their rights or who to speak to to find out their rights. Because foreign students don’t have the same knowledge, may have just spent their last $ moving across the world on a false promise, and have no networks to support them in their new country, they are the most at risk of being conned. Because of this vulnerability some unscrupulous supervisors have been known to send fake employment certificates promising e.g. higher wages than will actually be paid. To avoid this happening to you, you can check with (your future?) university HR, finance, and/or the local student union about what are the accepted normal wages and conditions for a doctoral student at the university you are considering. Do this before you accept the contract, and most definitely before you move.

For Uppsala University basic information on wages is provided by the studentkår: http://www.uppsalastudentkar.se/doktorand/phd-handbook/funding-and-financial-support but each faculty and department will have a more detailed description of their contracts. General guide for doctoral funding in Sweden: http://www.doktorandhandboken.nu/engelska/handbookforpostgraduatestudents/funding.4.24cc9d95134182bfa4a8000107.html

If you have been offered a contract that is in any way different to that typically offered local students be very very cautious about accepting. Be vary cautious about signing anything that looks official or mentions income. Once you sign papers so you can get paid the wages you have earned it is seen as acceptance of the real contract rather than the fake one you were sent and you can no longer demand the wage you were promised. The things is, if you know all this before you move, before you sign papers to get paid, you can get it fixed by notifying HR, finance, head of department, student unions etc and the scamming supervisor will be made to give you the correct contract or the correct wage. In this way the Swedish universities are really good as they have very strictly observed rules about wages and conditions. It also means you will know what your income will be before you move or even decide if you will move. These problems sadly arise as there is no control over scam-artist supervisors and their behavior, it is up to you to check. Just because the Swedish system is amazingly equitable does not mean all who work there are. Just because a certificate has an official university letter-head does not mean it is officially sanctioned by the university!!!

SO whatever you do, DO NOT SIGN any contract that is different to what you were promised… even if it means becoming homeless, or going hungry, or getting kicked out of the country (if you have no proof of wage/contract then you have no residence permit). Once you sign, you have no ability to change your contract. So DON’T sign. But better yet, heed this warning and find out your rights and employment conditions before you decide to take that offer that is too good to be true.

Featured post

microbial models need to focus on bicycles not ferraris

Most microbial lab experiments use the very accommodating and infamous Escherichia coli to test hypotheses. E. coli bacterium have largish genomes (for bacteria anyway) and thrive in nutrient rich environments. E. coli  however is neither an abundant nor keystone species in the most common of natural environments: those that are nutrient poor. The ecological and evolutionary relevance of E. coli is therefore doubtful yet it remains the most commonly used microbe for testing theories in vitro.

Having done a few molecular surveys of the microbes living in a range of terrestrial environments I, like so many before and after me, have become frustrated at the bias and gaps in current databases and of course in our knowledge. My small contribution to balance this out is to focus for my current project on collecting genomic information to use to improve laboratory cultivation. I will be developing methods for culturing and storing new and poorly studied bacterial species. My aim is to focus on organisms sourced from nutrient poor environments that are ecologically abundant and have small genomes. These characteristics are typical of many ecologically significant species. Establishing microbes such as these in culture in a lab will go a long way to redress the gaps and biases in our knowledge of ‘typical’ species.

last conference for the season – EUCOP4

been busy hopping round the northern hemisphere going to conferences and workshops these last few months. The last conference for the season is now rolling round. I’m heading south to the gorgeous city of Évora in Portugal to attend EUCOP4. First I’ll be attending the PYRN, APECS, ADAPT, PAGE21,  workshop and and then on to the conference proper where I’ll be giving a talk: Microbial dynamics in a thawing world. If you’re interested in listening to a very brief summary of my talk check out my frostbyte. While you’re there you might want to have a look at some of the other frostbytes, theres some pretty amasing research and science communication going on right there. If you’re attending EUCOP4 please come up and say high &/or contact me on any of my pages.


Methane producing microbes and reindeer: who wins and loses with climate warming? Ep.01 of 3

Does it matter that the arctic circle is warming? Some people are happy that once ‘frozen wastelands’ will become fertile wetlands. Think Siberia. Thawing will open up mining and agriculture in the north which many people will benefit from. Many hungry and poor people not just the CEOs and investors. Does it matter if the melting ice changes tundra into swampland or the grazing reindeer starve if new farmland is created? An international group of scientists investigating effects and consequences of climate change in northern Sweden can now tell you it matters not just because of environmental services, endangered species or direct impacts on humans, but because of the microbes that live in these frozen soils.

view across Stordalen Mire showing raised palsa with dry light coloured vegetation including the lichens favoured by reindeer, green sections in the process of collapse  and fens where permafrost is completely thawed and standing water can be seen

view across Stordalen Mire showing raised palsa with dry light coloured vegetation including the lichens favoured by reindeer, green sections in the process of collapse and fens where permafrost is completely thawed and standing water can be seen

There’s a group of microbes called archaea that back in the day, before the cyanobacteria helped oxygenate the atmosphere, basked in warm shallow seas and belched methane into the atmosphere. These days most of their descendants hide away in environments where oxygen, which will kill them, doesn’t reach. Many of them still produce methane. For obvious reasons they’re called ‘methanogens’. Some methanogens live in ruminant guts (e.g. cow stomachs) while others live in flooded rice paddy fields. These methanogens contribute to anthropogenic climate warming. Some methanogens however have been domesticated and are used to generate methane for fuel from waste reducing reliance on fossil fuels (yay) and reducing CO2 emmissions (more yay!!). Methanogens that live in permafrost regions have been slowly and quietly living out their existence buried in frozen soil, the small amount of methane they produce trapped beneath ice or consumed by their methane-eating neighbors. Climate warming in arctic regions has altered this status quo and huge stores of cryo-sequestered carbon in permafrost are now available for these methanogens to eat (read up on thermodynamics, enzyme kinetics and how this relates to methanogenesis if you want to explore this). The methanogens eat the newly available carbon and convert it to methane. The methane is released into the atmosphere adding to global warming…. and so the cycle of warming->more tasty carbon-> more methane->even more warming, begins.

frozen palsa: tundra type vegetation showing lichen, tussock grasses and dwarf ericaceous plants

frozen palsa: tundra type vegetation showing lichen, tussock grasses and dwarf ericaceous plants

Starting in 2010 an international group of scientists working at Stordalen Mire northern Sweden, begun studying the microbes living in this peatland with permafrost. Rapid thawing of permafrost and increasing methane emission had been documented from these peat soils over the last 30 years. So it was thought that there might be methanogens living in the peat. But no one knew for sure and no one knew which ones might be there. The scientific team collected hundreds of peat samples, water samples and air samples over several years. The first two years of peat samples were shipped all the way to Australia where I extracted the DNA and RNA of the microbes in the soils. Next the DNA was sequenced and I used the genetic sequence information to catalogue which microbial species where there. I found that the types species and amounts of species of microbes changed dramatically depending on the degree of thaw of the permafrost. The biogeochemists working on the project found that the amount of methane produced depended on the degree of thaw too. We put the pieces together….

thawed fen: standing water with Eriophorum angustifolium

thawed fen: standing water with Eriophorum angustifolium

One of the first things we found was that the peat with tundra vegetation sitting above pristine permafrost had a high number of different species.  A different story however emerged at the site where the permafrost is actively thawing. The soil at this site has collapsed due to permafrost thaw and the surface is now about 1 m below surrounds. The effects of climate change are shockingly clear. The diverse tundra vegetation is gone replaced by sphagnum moss and methane is being produced.

When I looked at the microial species in this peat I found a dramatic increase in the amount of methanogens present. In fact it was so high I checked and re-checked my analysis 20 times before telling anyone. It was that unexpected. What I also found when I took a closer look at the sequences, was a new species of methanogen. You should have seen how much my hand shook and my little heart raced as I pressed the return key to start the first analysis to find out who its closest relatives were! Wow. You don’t get that kind of rush every day.

thawing bog: a sphagnum peat core resting on palsa, midsummer 2011. M. stordalenmirensis is most abundant in the lower section where it is water logged and has a browner colouration

thawing bog: a sphagnum peat core resting on palsa, midsummer 2011. M. stordalenmirensis is most abundant in the lower section where it is water logged and has a browner colouration

This new species, which I named ‘Methanoflorens stordalenmirensis’, is so successfully adapted to the thawing permafrost that it blooms, similar to cyanobacteria (algal) blooms. The problem of course is, because it creates methane when it makes energy for itself, it creates a late summer spike in methane production that can be detected over the Mire. Because this species was so ridiculously abundant in the peat we were able to use some hot new sequencing technology on the DNA I’d got from one sample and  reconstruct the ‘M. stordalenmirensis’ genome.

The ‘methano~’ is because thats how archaea who produce methane are named;

‘florens’ because it blooms;

and the specific ‘stordalenmirensis’ is where this l’il stinky one was found.