Deep Sequencing II: the seq-uel.



Deep Seq II: Cast – Dr Sara Rassner, Dr Andy Mitchell, PhD student André Soares. Many thanks to our miner minders Paul & Byron.

As mentioned in Science, we had a go at sequencing metagenomes in the subsurface last December. We extracted and sequenced DNA underground as a proof of principle for battery powered, standalone sequencing. As Elizabeth Pennisi, the writer of the Science article noted, we still had “a few kinks to iron out” in terms of read length and taxonomic classification on site. Since our main motivation is to go from sample to microbiological insight on-site, wherever that may be, we felt we ought to iron out these kinks. So, yesterday we headed back to the Big Pit coal museum, armed with our MinION sequencer.

What did we keep the same?

We sampled the same ochreous biofilm at the same site

We used the same rapid library preparation kit (RAD001, even though it is now outdated)

We used the same library loading protocol (SpotON, no beads) to the same version of flow cell (our last R9.4)

We used the same version of offline MinKNOW and local basecaller

(Note: We took an R9.5 and a RAD002 kit as a backup, but didn’t use them. Working in the field means that “two is one, one is none” when it comes to technical processes.)

What did we change?

Obviously: the time of year we sampled the biofilms. We have data suggesting ochreous biofilms at the surface of South Wales coalmines change seasonally in their bacterial community structures, but the scope for temporal changes in their subsurface equivalents is unknown. This factor, coupled with the n=1 nature of the study means temporal comparisons in metagenome composition should be approached very cautiously.

The DNA extraction protocol: PhD student André Soares has worked to optimize the extraction protocol to address two challenges:

  1. Compatibility with the battery centrifuge to avert, er, spoaradic yet catastrophic sample tube loss
  2. DNA yield and integrity

As we hoped, it appears that modification of the DNA extraction protocol made a very positive difference.

OK, so it’s the DNA extraction, stupid.

On the basis of experience with surface ochre, we were disappointed in the yield of DNA and the read length obtained in Deep Seq I: we used a standard PowerSoil protocol but with TerraLyzer bead-beating. Ultimately, using 10% of the recommended DNA input for nanopore sequencing we were pleasantly surprised to get any worthwhile reads at all. As biofilmed sediments such as the ochre sampled are characterized by a high ratio of mineral surfaces to biomass, they are particularly challenging. Exposed mineral surfaces can adsorb DNA during extraction, resulting in the loss of DNA before it can be purified.

Others have faced this challenge and developed improved DNA extraction protocols as a result. This protocol, developed by astrobiologists, uses a mixture of ethanol and phosphate buffer coupled with an additional heat treatment to help the dissociation of biomass from minerals, lysis, and crowding of mineral surface to reduce adsorption of DNA.



André extracting DNA

Faced with this situation, it isn’t uncommon for folk to simply extract from more starting material. But a 2 mL bead beating tube is a finite volume, and free movement of beads, buffer and sample is essential for effective bead beating, and incomplete suppression of inhibitors by downstream steps is likely. We felt it better to bead beat and remove inhibitors from standard volumes of sample, then combine samples onto the same spin column and elute in a standard 100 microlitre volume. With the use of the ethanol/phosphate buffer plus 2x30s bead beating and 20 minutes hot soak in André’s travel mug the yields of DNA from subsurface ochre improved considerably. But still not enough for the 200 ng DNA in 7.5 microlitres demanded for rapid library prep.

This left us with two options. Oxford Nanopore have recently released rapid low input kits which permit PCR amplification of transposase tagged DNA, permitting sequencing of 10 ng DNA (and with barcodes too). As attractive as this possibility is, we discounted it for several reasons

  1. Time. Due to the working patterns of Big Pit, our time on site is very limited. The PCR step took 1.5h on a lab based thermal cycler, plus Qubit quantification and AMPure clean up. It would take longer on a mini-PCR cycler
  2. Using (long) PCR would limit the read length to 5-10 Kbp. We’re not avid whale watchers, but I can admit we like seeing the occasional long read sneak through a pore.
  3. PCR in the field: one more thing to go wrong, one more source of contaminants, one more thing for the bias police.

So, in the end we decided to just go for a final AMPure bead based clean up of the PowerSoil eluate, to provide a quick additional cleaning step, and critically, up to a 20 fold concentration from 2×100 microlitre eluates to 10 microlitres which could be quantified and sequenced. Trials in the lab showed it did not affect DNA integrity adversely.

On the day itself though, we needn’t have worried: our duplicate extractions yielded 36-38 ng per microlitre when quantified by Qubit. Enough to exceed the 200 ng specification for the rapid kit. We occasionally take yes for an answer. So, in the interests of time we proceded without AMPure.


I think I’m starting to get the hang of this SpotON loading malarkey.

What did we find?


André inspects the taxonomic classification of metagenomic reads: from sample to insight, underground.

Overall, the read length distribution improved considerably. While our longest reads were just 59 kbp, using the older version of MinKNOW we couldn’t expect much longer.

The first 120 reads to land in the pass folder were hived off to a second laptop for Centrifuge based taxonomic classification, which provided identities for about 68% of those reads in 5 minutes. While visualization with Pavian didn’t pan out underground inspection of the csv file showed some interesting overlaps with DeepSeq I in terms of the proteobacteria detected, and the prevalence of Streptomycete reads among the Actinobacteria was again noteable.  Melinabacteria and Pandoravirus were among the one read wonders: we’ll look into these data more carefully over the coming weeks.

What happened next?



Sara marching out the MinION.

As the run was still going at the end of the day underground, once more we moved the MinION out of the underground pumphouse, down a roadway and up the mineshaft to an office. The sequencing run continued unabated despite the shift of 100 metres elevation and 10 °C. As we had to return to Aberystwyth, we kept the MinION running in the back of the van on the way home, before putting the run out of its misery with a minimum of ceremony in a carpark in Builth Wells.

An uphill struggle?

On the way home I noticed a slight tendency for the number of pores actively generating sequence to change in relation to road conditions. Coming up from the Valleys means there’s a lot of uphills, downhills and roundabouts. Hardly sequencing at 17,000 kph but not the gentlest of rides either. Thanks to Matt “Maverick” Loose it’s clear MinIONs are resistant to inversion, so if this was a real effect, the mechanism is unclear. Who knows?

What now?

I think it’s time to update both our nanopore pre-prints and prepare for a long, cold summer.

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“Deep” sequencing

big pit

We’ve sat on this one for a while as we thought we could do better next time round. Back in December 2016 we decided to trial our tools and protocols for nanopore sequencing without mains electricity or access to the internet using a lightweight assemblage of kit. We thought about various places we could try: the beach in Aberystwyth, the summit of Snowdon, the International Space Station. But then we realised we had an ideal location: somewhere we could reach in the department van rather than a rocket. A coal mine.

Although a considerable portion of Earth’s biomass lives in the subsurface, as far as we know, until now nobody has been silly enough to try DNA sequencing while still within the subsurface. To see how our kit performed, we thought we would give it a go.

We managed to extract, quantify, library prep and run the sequencer while at a depth of -100m, but we faced some challenges along the way which mean we would like to try again to improve the data. For now, because others have had an interest in offline, off-grid sequencing we thought we’d share our protocol and kit as a preprint which we’ll update in due course.

Things which worked well:

  • The sequencing itself. Our MinION had no problem sucking strands through >1100 active pores while underground. MinKNOW basecalled the reads while offline too. Thanks to our miner minder Paul Green for pressing the go button on the run
  • Quantification on Qubit. Sara Rassner got consistent dsDNA yields from our extracts using the Qubit while it was powered by a lithium powerpack.
  • Library prep: Gloved hands and a thermos mug provided the 30 and 75 degrees Celsius incubation steps. Our MiniPCR cycler had to stay at home as the powerpack had to be hooked up to the Qubit at all times.
  • The workflow. We had very limited time to spend underground. Everyone worked like greased gazelles and the process ran smoothly for the most part
  • The not having a methane explosion while underground bit. Coal mines present this additional hazard. We had to take detailed precautions, risk assessments and clearances to get our kit underground. One precaution meant connecting up and running all electrical kit while aboveground – limiting our flexibility and battery life.

Things we need to work on

  • DNA extraction yield and integrity from low biomass high mineral content samples. We settled on ochreous biofilms as our target substrate as a result of prior positive experience, but our yields from a conventional PowerSoil protocol were very poor. On the basis “one molecule, one read” and that we had a very happy flow cell on the MinION we decided to crack on. I put as much DNA as we could in to the library, squeezing 3x the normal library volume in to the flow cell whereever we could (SpotON port, normal port…bit more into the SpotON…etc). This still totaled <10% of the recommended input of DNA. This is the likely cause of the short read length and low percentage of identified reads. We’re working on this.
  • The battery powered centrifuge. True, non-electric drill based battery powered centrifuges are thin on the ground. We found a 12V DC option which we hacked to run off a battery. It has a disconcerting habit of shattering some bead tubes every so often. Other than rescaling & pooling extracts we’re not sure how to solve this.

PhD student and caving bioinformatician André Soares was in his element running the “data mining” for this project. He made a video of the event. He’s also won a competition to attend London Calling thanks to his #deepseq tweet and I gather he’ll have a poster to present there too. Lucky fella.

Our thanks to all the staff at The Big Pit museum who made the sequencing run possible.

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Reflections on #nanoporeconf

Reflections on #nanoporeconf

Another departure lounge, another blog. It has been a fun but also draining couple of weeks, skipping between the EU ITN MicroArctic kick off meeting plus some polar night fieldwork and duty as an (un)hired gunman for field parties on Svalbard, and then directly to New York City for the Oxford Nanopore Technologies (ONT) Community Meeting, where I had the honour of an invited talk about our metagenomics misdemeanours. While I kill some time at the gate, I thought I would share some thoughts on the New York side of the trip.

Disclosure – ONT kindly paid my travel expenses to present at the meeting, and I have had access to the MinION kit from MAP. That said, if I had something less positive to say, I would say it just the same.

Hardware from #nanoporeconf

Lots of exciting stuff is coming out from ONT. While high throughput, benchtop kit like PromethION would readily excite some of my colleagues at IBERS who are in to crop genomics, I was far more piqued by the lower throughput but higher portability kit. Specifically the SmidgION and the Flongle, which respectively are a mobile phone powered sequencer and a “flow cell dongle” to allow MinION users to run a smaller, SmidgION like flow cell. The potential for these platforms to do quicker and cheaper sequencing for focused applications is impressive, and I understand ONT will pursue diagnostics approval for them. For environmental applications, the potential to do cheeky on site, real time 16S profiling for ca. 20 USD a run will be a game changer. There are glaciers on Svalbard and certain spots on the Greenland Ice Sheet with good GSM signal and 3G so I would love to try some supraglacial SmidgIONing someday soon. (I am of course assuming that the app would require connection to the cloud in some way, given the reliance on a phone. I could be wrong about that.)

Disruptive technology…literally

All this said, the bit of hardware that impressed me the most is a flow cell dongle prototype which integrates sample prep with an on-MinION beadbeater. I will wait to see if this actually performs, and on what range of samples (insect bits were mentioned, but soil like matrices would be top of my list) but the impressive thing in my mind is that ONT “gets it”. Sample prep is the bottleneck. I have been saying and thinking this for a long time, but for the microbial ecologist there has been no real innovation in sample prep approaches for well over a decade. Yet it remains pivotal to good sequence quality and obtaining a “representative” view of the community of interest. Simply put the hard work invested elsewhere in developing an array of bioinformatics tools for microbiota research has not been mirrored upstream of the sequencer. So it is great to see a sequencing company explicitly considering this aspect.

Wetware from #nanoporeconf

So far my interest has been drawn to shotgun metagenomics based approaches for characterizing microbiota. As I stated in my talk, the direct sequencing of ca. 200 ng of community DNA avoids PCR amplification which incurs potential primer biases and risks coamplifying contaminants which are likely to be abundant in more rustic field settings. However ribosomal RNA has a foundational significance in microbial diversity exploration, so it was great to see Andy Herron, Andrew Smith and Lee Kerkhof present different strategies targeting rRNA in various forms, as the rRNA full operon, as 16S rRNA directly sequenced and by enrichment of 16S rRNA. My one note of alarm was the finding that data from 16S rRNA genes and 16S rRNA overlapped considerably in a trial environmental sample. I would not expect this as these compare apples and oranges.


Science from #nanoporeconf

It would be hard to provide a comprehensive list here, so I will just cherry pick some personal highlights

Jane Carlton sequencing malaria genomes from clinical samples in remote Indian field labs. Knowing how much attention is needed to cold chain flow cells and reagents to Arctic locations, this work by Prof Carlton and her parasitologists was all the more impressive.

Lee Kerkhof with 16S to 23S rRNA operon amplicon sequencing. Something that ONTs long reads readily lends itself to. Nice to see it is being done well. Kudos to Prof Kerkhof for unashamedly stating that the ensuing bioinformatics had to be point and click, GUI, Excel spreadsheet based. As an unapologetic mudfetcher I feel this is exactly what is required if one has the primary goal of understanding a microbial community, rather than simply processing the data. Until that script produces a functional stacked bar chart, PCoA-or-nMDS, ANOSIM and network with a passable cover letter for ISMEJ I feel it is a distraction.

Julie Hachey on the potential for MinION to sequence extraterrestrial nucleotides for life detection on Mars. Enough said.

Johanna Rhodes on real time fungal genomic epidemiology in a hospital outbreak of an emerging Candida species associated with a high case fatality rate. By now my sole interaction with medical mycology is giving a couple of second year lectures on key fungal pathogens, and I emphasize to the class just how ferocious fungi can be, especially for patients with immune system dysfunction. I always detect some scepticism about mycoses from folk in the class who have been enticed by HIV, Ebola, Zika et al. as the “big killers” so it was nice to see UK medical mycology being put firmly on the map in this context.

The Talk

It is fair to say I was severely bricking it. The list of speakers was impressive, let alone what they had to say. I very rarely speak at conferences, given the cost of attendance, and I would not really count myself as one of the “nanoporati” or “illumina-ti” to say the least.

Hopefully some of what I had to say about the importance of generating a genomics based perspective of environmental change in the cryosphere got through. These are very rapidly changing environments where microbes are both sensitive to the change in play and consequently drive landscape scale feedbacks which make the situation worse (e.g. methane production, biological darkening of ice). But we lack baseline data as genomic variation in space, time and phylogenomic dimensions of cold environments remains severely undersampled. We can use MinION to help change that.

Introducing the MetagenNomad

MetageNomadToothbrush sawn in half style kit and philosophy required to let metagenomics break free from the lab. May involve roughing it, cuffing it and duct tape. c.f. Patagucci.

What seemed to create most buzz (if my twitter timeline is any indication) is that we have assembled all the kit and consumables to go from environmental DNA extraction, QC, shotgun library or PCR prep, through to nanopore sequencing and offline bioinformatics in a 45 litre by 7 kilogram package. Even the choice of rucksack got some attention. A UK military issue daysack was not the first choice. I really wanted a yellow Tespack solar backpack, as it would visually resemble a Minion cartoon character, or failing that just a Minion daysack, but the requirements analysis for a resilient bit of kit scotched the minion bag, and the Tespack seemed less important as the first first few missions with the kit are in dark environments. So I went with a rucksack we used on Greenland last year which has the advantage of detachable side pouches to allow users to carry field safety gear (bullets, chocolate) or more plasticware or powerpacks. While others are pursuing hardcase based systems, I guess as a rucksack this becomes the first “wearable” sequencing lab. I know what I would prefer to use abseiling into a crevasse.

The key feature of the kit is that it all runs from 12V DC, is comprised of off the shelf kit and our preliminary bioinformatics tools do not require cloud based basecalling or taxonomic analysis. It should have sufficient endurance for a few sequencing runs. As I am continuing to fine tune the kit I will write in a little more detail about the exact content and rationale after our next field based MinION mission in a few weeks’ time.

Time for more coffee.

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Dirty deeds done seq

It’s been a really long time since I wrote anything here. Interesting mix of good and bad stuff in the meantime. Anyway…

We recently uploaded a bioRxiv preprint based on a small project of ours:

Extreme metagenomics using nanopore DNA sequencing: a field report from Svalbard, 78 N

While I have a few minutes between flights in Copenhagen as I’m headed out to the field again, I thought I’d share some thoughts about it.

Extreme metagenomics? Really? In the sense we tried shotgun metagenomics to study an ecosystem people would consider “extreme”, maybe it is. But as this was a preprint, I felt I could indulge a tongue in cheek moment by alluding to this as a science equivalent of Extreme Ironing: Doing a normal task in a new and unusual environment.

So is there a value to sequencing metagenomes in the field? Hopefully. In the preprint we set out the trifecta of problems Arctic microbiologists face in my opinion: Firstly, the Arctic is warming fast, and that has unpredictable impacts on its ecosystems, fuelling microbial feedbacks and disruption to field plans. Secondly, to study these environments there are often challenges around sample integrity and timeliness incurred by transfer and process of samples back to a lab. This means that the insights gained are retrospective. Thirdly, while we can make many measurements of microbial community activities and abundance in field labs, being able to validate the capture of certain taxonomic groups on site could be very useful. For example: imagine wishing to test a hypothesis that genus X does Y using a field experiment – it would be useful to know that your source community contains genus X before starting the experiment, rather than finding out much later that your experiment measured genus Z instead because genus X was on holiday. Similarly, imagine drilling into a subglacial lake and wishing to confirm that your sample(s) are clean/distinct from drilling fluid or surficial contaminants before wrapping up your drilling season. Both applications are helped by on-site sequencing.

Why metagenomics? One could use 16S rRNA gene sequencing, but this necessitates an additional PCR step of course. This introduces  primer biases, and also slows the process. In field conditions rather than a pre-PCR lab it also makes your analyses more vulnerable to contaminants. We preferred to do a quick 10-15 minute transposase based library prep from ca. 200 ng community genomic DNA. Conceptually I’d rather think of the output generated as a non-16S based 16S like taxonomic profile (!) than the kind of depth or coverage one would wish to have to reassemble genomes or delve into potential functionality with great detail.

Did it work? On balance, yes. There are things we’d do differently, principally around DNA extraction and bioinformatics, but we were able to arrive at community profiles comparable to published datasets from glacier community.

What next: I’d like to start some tests with mock communities and optimize the process further. Another area is considering how off-grid we can take this. On our way home from Svalbard I had five hours sitting in this same transfer centre and I decided to hack my way through the extraction, prep and sequencing process. I think we can do the same kind of experiment with a sub-five kilogram package without access to mains electricity or the internet.

Will you publish this in a peer reviewed journal? Hopefully. I’m new to both preprints and nanopore so I have no feel for where & how, or the worth of our observations. Our intention in uploading to bioRxiv now was to illustrate the possibility of going from extraction & sequencing in the field to sharing insights on a faster timescale than before. Given the trends for accelerated warming in the Arctic, speed may be of the essence for future work to be relevant.

I’ll update this as I get time & wifi over the next week.

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So you wanna be an Arctic scientist: Part Deux

Following on from my earlier post, here are the remaining bits of questionable advice I can offer those considering a career in the cold. These are a little more introspective and a bit harder to get “right” than a first aid certificate or reading some polar history.

  1. Play well with others.

Wide open spaces. Stunning panoramas of ice and snow. Terra incognita. Polar regions often have an appeal for those of us who prefer our own company and getting away from it all.

Picture 130

Everywhere you will go, you will go with at least one other person. It’s likely you will get on each other’s nerves sooner or later.

The reality of fieldwork in the polar regions could not be more different. Unless it gets a bit Mawson you will always have other people around. Being able to “rub along” with just the same few people in trying circumstances 24/7 is really important. Similarly, being aware of your own foibles (I snore and fart at an international level – props to any tentmate of mine) is as important as being able to put up with others, so a good sense of humour and humility is vital on all fronts.


(1) Supercomfy shared bedroom in Tarfala research station, Sweden. (2) Scrubbing out the toilets in NERC station, Svalbard while wearing sandals with socks. Such a fashion faux pas is an example of the kind of antisocial behaviour that can lead to toxic group dynamics in a field station.

On this note, it’s worth bearing in mind that while fieldwork is often a land far away from normal civilized behaviour, field plans and conduct should always be utterly inclusive and each member of the team has the right to feel safe, valued and be able to contribute to their full potential irrespective of ethnicity, religion, gender or any other such factor. Everyone has a responsibility in making sure discriminatory or harassing behaviour has no place in 21st century science. It is far too common and should never be tolerated.

  1. Don’t be a tourist.

DSCN0713 DSCN4701

Tourists pay thousands of pounds to catch a glimpse of the lesser spotted Svalbard scientist through their binoculars.

Very few people working in the Polar regions go there because they don’t enjoy working there. We often fill entire memory cards with photos or videos of Yet Another Penguin/Polar Bear/Walrus/Tourist ship. And yes, it is great fun. People pay vast sums of money to see what you get to study. This should not distract you from the reality: if you’re an Arctic scientist, this is the day job. You will have worked hard to get this far and have (almost certainly) used charitable or public cash to bankroll your work. The onus is upon you to come up with the goods.

IMGP1951 IMGP1955

A good day at the office (1) Wet and shitty. Six kilograms of cryoconite bagged,  15 grams at a time (2) Same day, six hours later. View from the field toilet.

A while ago, I was discussing PhD research topics with a prospective member of my group. Impressive CV, great references and technically very capable. But it became clear that the discussion was really a negotiation about the geographic destinations the project could tick off, rather than the scientific and career development voyage that a PhD tends to entail. At that point it became clear that it wouldn’t work out. The person accepted an offer elsewhere to go somewhere at the top of their geo-ticklist, and dropped out after their second season.

If geo-ticking is your driving force and you’ve seen the same patch of ice / tundra / glacier for several field seasons, your motivation will suffer.


Dr Joseph Cook (@tothepoles). Outstanding in the field. For ten hours a day every day for eleven days he would make hundreds of measurements within a 10×10 metre patch of ice, pacing back and forth. Science in the cold demands tenacity sometimes.

If “how can I score a grant/PhD to go to Novaya Zemlya / Deception Island / Dronning Maud Land” is your starting point, your attention will not be focused on asking the best research question or doing the most rigorous or timely science. Your performance will suffer.


Kayakers in Kongsfjorden, Svalbard

If climbing that mountain over there / kayaking in the fjord / abseiling into that moulin is why you want to go somewhere, your scientific priorities will get mislaid. There is also a chance you will get embroiled in a gnarly epic somewhere far, far from home (and without benefit of “free” mountain rescue). Your field time will suffer.

If those are the things that get you out of a five-season sleeping bag at 0400h: great. Go do ‘em. But to expect a career in polar science will be a licence to do those things is as big a mistake in career planning terms as turning up at MI6 and expecting a licence to kill.

In >12 field deployments to various parts of the Arctic and Alps I have had exactly one day of being a tourist. A very nice day it was too. That is not to say I haven’t had plenty of days in which I appreciate the things I get to see and do while I do my job.


Sightseeing at Russell glacier, Greenland.  

  1. Homeward bound.

If you are successful, unless the Arctic is your home, you will spend a lot of time away from home. This will affect your life, in particular your interaction with family and friends back in the real world. It will also affect your career, which may well depend on your being away to gather data, but is progressed by the “right” papers, grants, collaborative networks, courses, teaching, administration, service and performance in the real world.

I write this having had two statistical epiphanies in the last week (‘tis the season):

  1. In the 12 months June 2014-5, my wife / statistically significant other / long haired Co-PI (same person) and I will have spent eight months apart because of our respective research and teaching commitments.
  2. In the 4 years since being appointed to faculty, I will have spent more nights sleeping rough in Scandinavian airports than on leave.

This is by no means unusual within the community of my peers. I am in awe of truly exceptional individuals such as the person who has well over a dozen Antarctic seasons to their name but has never missed Christmas with their kids. The rest of us all too often miss birthdays, anniversaries, social stuff, even entire cultural norms, not to mention things like grant or promotion deadlines. We often work 15-20h a day seven days a week to keep up with a busy academic workload which is not distributed across the usual twelve months because of field commitments. This means that literal and metaphorical fences don’t get mended.

With modern communications, you have to get really remote to be truly off-grid. I have had skype conferences with people overwintering in Antarctica, troubleshot sample archiving issues with people on the worst caravan holiday in the world by email, and have likewise fended off calls from tax inspectors, accountants and solicitors while in the High Arctic. As a PhD student I had a relationship come to an end by instant messaging while in Svalbard. The days of an annual mailbag and 200 letter-messages by Morse code are pretty much over.

This means that you are seldom truly “away” to some people and bad news from back home can reach you pretty easily when you are in no position to do something constructive about it. The consequent feeling of helplessness can be difficult. Priming key people in your life about the illusion of connection can be useful.

On a related note, while social media is a boon for outreach purposes, what goes on fieldwork does not necessarily stay on fieldwork. Enough said.

Balancing your own family’s needs with fieldwork takes careful consideration. I have known some academics take their kids (even infants) on fieldwork, while other hang up their boots for a while. Anything that works out is fine. This post provides some examples and advice from those with actual experience.

While no DNA test has ever been able to prove conclusively that I have children, I do have family at the other end of the age spectrum. Here’s my personal perspective. Try not to judge me more than I do already.

My father is himself no stranger to the world. He ran away to sea in 1947 (insert many tall, but surprisingly well-corroborated, tales here) before returning home thirteen years later at the age of thirty. As I reach the same age, I am aware I have gained just a fraction of the life and world experience he had by thirty.

From his seafaring days he has a tattoo for identification purposes. It reads “Homeward Bound”. He once told me he decided to leave the sea after sitting on a hill overlooking Bergen in Norway and grabbing a fistful of soil, realizing it was the same, but different, soil as his father nurtured on the farm at home.

By now, he lives with dementia. In 2011, not long after the loss of his wife, his condition deteriorated to the extent that I couldn’t care for him safely at home. Likewise there were only so many times I could ask friends and family to cover for me while I slipped away to teach undergraduate classes. The day after my mother died, I taught a three hour lab class. These things do not stop, just because of personal circumstances.

As the n=1 F1 (i.e. only child) these crises meant I had to abandon the project I had planned in Greenland and slot into a team on Svalbard instead. I still have the letter which stated that these events did not present a special circumstance for the research excellence framework as they apparently did not affect my research for more than 12 months. In retrospect it is clear that my professional future as a researcher depended on going away.

Nevertheless, the “easy” option for that year, a field camp in polar bear territory, is no place to grieve for the loss / “loss” of one’s parents and deal with all that the procedural aftermath of bereavement entails. Needs must though.

I recall visiting him a few days before I travelled north. Leaving him was particularly hard in those days, not just for emotional reasons, but as he was quite a savvy escape artist. The previous week he escaped by convincing a visiting priest he was just there to see an old friend. So, I gave him a big hug before beating a hasty retreat:

“So, Dad, I’m off to the Arctic again.”

“Are you? What are you doing there then?”

“Yes. Research. I’m up there for a month this time.”

“But our Attic isn’t big enough to live in for that long.”

We both laughed, and I chuckled until I got to the car, where the tears came.

As time goes by, it goes without saying that your priorities and ability to spend time away are likely to change too. It is certainly possible to balance life away and life in the “real world”, but it takes careful consideration and compromise. I don’t score well in either department, so all I’ll say is: if you want to be an Arctic scientist, always make sure you’re homeward bound.

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So you wanna be an Arctic scientist?


“Ablutions were outstanding. I cannot think of a finer indicator of esteem in our field than being able to note you’ve brushed your teeth in a cryoconite hole.”

Author’s email to collaborator describing life in a field camp, August 2014

Every so often I am approached by students asking how to get into the field of cold region science in general. I’m not the best person to ask. My own introduction to the field was accidental and I still feel as if I’m “getting into it”. With the caveat that there are many people who are vastly more experienced and wise than I, here’s a summary of the advice I tend to give. It will be in two parts. This first part relates more to career and skill development. The second part is a little more introspective. Neither deal with the practicalities of fieldwork in any great detail, or the unwritten rules of “Field Club” (1. Never argue with a man wearing trousers made from a polar bear. 2….). Perhaps a post for another day?

Both parts are entirely subjective and highly prejudicial to my own experience, which is mainly of the Arctic. I will use “Arctic” and “polar” fairly interchangeably though. I expect that aspects of this advice could apply equally to other environments too.

If you disagree, or have some advice of your own you are welcome to post a comment!

  1. Don’t specialize too soon.

It is better to gain a solid grounding in marine biology / biochemistry / terrestrial ecology / geochemistry / whatever than specifically polar marine biology or Arctic biology. Most people take skills and experience they have developed in other fields and transfer it across to research questions pertinent to the Arctic or the Antarctic.

Unless employed/studying at a polar research institute, most “Arctic researchers” have fingers in other pies too. At the moment I work on projects involving deserts, pathogens, subsurface microbiology, coal mines and polar explorer poo too. If you are forced to specialize, specialize in as many different things as you can have some success in / the grownups let you do.

You will appreciate the breadth and depth of your training if you are successful in your ambition as it will give you novel perspectives on the systems you work on, but also as an insurance plan if your career plans take a different direction.

  1. Learn to write. Better.

Getting to the Arctic is a costly business. You will need to win grants and write papers. Notwithstanding Advice subheading #3, the ability to express your science in writing is as vital as your ability to mend a snowmobile at -20*C or catch barnacle geese.


Track changes: up there with crevasses and sledge dog poo in the Arctic annoyance scale.

Scientific writing is a skill which takes time to refine, so if you’re an undergraduate, this endeavour starts with the next essay you research, plan, write and reference.

For more guidance, have a look at (Arctic) microbiologist Joshua Schimel’s book Writing Science.

  1. Bring your other CV to the party.

You will be evaluated on the strength of your academic CV. Depending on the stage of your career, this will mean your grades, your degrees, your papers, your grants. These count for a lot when applying for studentships, funds or jobs. So make your academic CV as strong as possible.

Nevertheless, when it’s freezing, and snow is being driven into your numbed face, your GPS batteries just died and your fieldmate is starting to mumble, fumble and stumble, your first aid skills and above all, the ability to get a tent up and get a brew on are what counts.


Never make camp without at least two means of simultaneously making brews. The third pot is in case someone wants to make hot squash, or the devil’s juice, coffee.

There’s a whole lot of other skills that matter to an Arctic scientist. These range from cold weather camping, backcountry skiing, mountaineering (all fairly obvious) to advanced first aid, VHF or satellite communications, PADI dive certifications, RYA boating qualifications (and generally mucking around in boats), mechanics, weapons handling, mountain & crevasse rescue and ropework, Logistical planning, Working with aircraft and getting permits. This list is abridged from just one (exceptional) colleague’s CV.

These are skills which are seldom taught on any undergraduate curriculum, but many can be developed via assorted clubs and societies, or even just the plain ol’ University of Life. Make the most of any opportunities to gain them.


Boat being steered conventionally. Can also be steered with two bits of paracord if the steering column fails mid fjord.

You don’t have to be MacGuyver (yet) but an ability to solve problems (logistical, medical, scientific) with limited resources is really useful. Similarly, while being “outdoorsy” is a definite asset, for every successful scientist who can winter climb to Scottish V standard there are two that have never used crampons before. The bottom line is that being able to function in a hostile environment is often a prerequisite to get data.

This means keeping your feet warm and dry, the insides of your nostrils sunburn free and being able to make a hot brew under any conditions.


Anyone seen Tonto? Ice sheets are high glare environments and you can indeed get sunburn in unusual places, like inside your nose. I am told it is almost as painful as watching the X Factor.

Oh, and having the right bits of paper count too, especially when the logistical support people evaluate your ability to survive in the field.

  1. Respect your environment / know the system.

It goes without saying that fieldwork in the Arctic entails working in quite fragile places and it’s important to minimize your environmental impacts. But the above point has more to do with knowing your environment. If you’re a biologist focusing on the ecology of a particular shrub, it really pays dividends to know all about the heathland you’re working on. Likewise a glacier microbiologist needs to know about ice structure and glacial processes. Otherwise your work risks losing context.


Situational awareness: Be aware of the broader context of your own specific focus of research.

My advice is to learn as much as you can about the natural environment in which you’re working. Read textbooks from other fields. Attend courses. Talk to people from other disciplines: for a terrestrial or aquatic biologist, collegial links with a good geomorphologist or oceanographer respectively are worth their weight in gold. They will fill in gaps in your knowledge about your experimental system you never knew existed, and it will lead to new hypotheses. Be wary of losing sight of your own discipline though. You will add most value in being able to bring your unique skills to the table.

Knowing the history of your field and polar exploration is quite useful too. I always take a copy of Apsley Cherry-Garrard’s The Worst Journey in the World to read about his exploits with Scott’s last expedition. It reminds me that no matter how bad my field day may be, it could be a lot worse. Although I empathise with Cherry Garrard: a very myopic youngster who accidentally found his way to the ice in his early twenties, it’s also a good reminder of the massive chasm between polar exploration in its golden era and polar science in the Iridium era.

To be continued…

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We’re still processing thousands of samples and recovering from our “cryo monster tour” or “fieldwork marathon” as others have described our summer’s projects across the Arctic and Alps. It’s won awards and for once, not just for most airline coffee consumed, excess baggage hauled or receipts filed for expenses.

Here’s a report of what we got up to, courtesy of MoBio Inc.

and a video too, courtesy of the very talented (not least as the camera didn’t break!) film-maker Sara Penrhyn Jones

It’s not over yet though. I’m gearing up to go south in December in collaboration with the Natural History Museum to South Georgia and the Falkland Islands to conduct projects funded by National Geographic and the Shackleton Fund. Time to haul more excess baggage etc…

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A bear’s eye view

Our blog has been dormant for the best part of six months. That’s not because we haven’t been up to much though. In fact it’s been a very busy spell at Cryoconite Towers. We have been quietly working on samples and data from our last season on Svalbard – and preparing for this summer’s fieldwork. I thought the best way of offering a catchup is from the perspective of team member @icybear79

Who is @icybear79?

In a nutshell, icy bear is smarter than the average bear of little brain. Often thought to be Arwyn Edwards, Tris Irvine-Fynn or Sara Rassner (although they are some of “his people”), icy bear’s origins are shrouded in the mysterious north and will remain a secret as dark and chilling as a particularly filthy cryoconite hole. Icy bear first materialized at Aberystwyth as part of an exhibition on Climate Change last year.

polar bear

It seems wherever ice is in crisis, icy bear is there.

It only seemed fair to bring icy bear with us to Svalbard last year as part our NERC project on glacier ecology


To his credit, icy bear became our constant companion in the field IMGP1037 IMGP1049 IMGP1042 IMGP1005

Icy bear soon became insufferable yet inseparable while on fieldwork – pictured here with Dr Tris Irvine-Fynn and Professor Nozomu Takeuchi.

All too soon it was time for the Aber cryo team to return to the UK. It’s fair to say @icybear79 is at home in the field, but he was soon to become a telly academic in his own right


Appearing on daytime S4C…


…Outreach events…


…and scientific conferences, ranging from the International Glaciological Society’s British Branch, to the ASB Life in the Cold Workshop at Leeds, before reaching the dizzy heights of the Cambrian News


and ITV Wales, as our paper on the surprising microbial abundance of glacier surfaces was published.

But of course – remember that wherever ice is in crisis, icy bear is there. By April it was high time for icy bear to head out again (having broken our lab’s ice machine)


Icy bear first headed South. Further South than any bear had been before.




All the way south to South Island, New Zealand to help with teaching a Geography fieldcourse and looking at evidence of an outburst flood as part of a British Society of Geomorphology fieldwork grant.

As I write this, icybear79 is in Kathmandu in Nepal getting ready to head up to the Khumbu as part of a Royal Society project team looking at glaciers in the Himalaya. Hear the team’s leader, Dr. Ann Rowan, talk on BBC Radio 4 about the planned fieldwork. Icy bear (along with helper Tris Irvine-Fynn) will be looking at the hydrochemistry and maybe some microbiology while they’re there.

Tris will be taking icy bear to Arctic Canada next, where glaciers are changing rapidly, and will be working on a Climate Change Consortium of Wales project led by TrisIMGP0522_smallTris Irvine-Fynn and Arwyn Edwards  extracting a shallow ice core from a glacier. Expect more of this kind of thing!

Meanwhile, Arwyn will be heading to Svalbard for a week at UNIS. Unfortunately, they say you can never go home, and this is the case for Icy Bear too, so he’ll stay in Canada for the duration.


Instead, Tris will bring him with his ice corer to join Arwyn and Dr Joe Cook as part of another Royal Society project, this time in Greenland. Arwyn, Joe and Tris will be camping inland on the Greenland ice sheet to look at glacier ecology in some more detail. The team are joining forces with the DarkSnow collective to study interactions between microbes, melt and pollution on Greenland.  Have a read of Greenland guru Professor Jason Box’s blog about the Dark Snow 2014 project to find out more.

We (Icy Bear, Tris, Arwyn) will head straight from Greenland to join up with PhD students Ottavia & Stephen in Tarfala, in Northern Sweden as part of a EU FP7 InterAct project based there. After a few days’ respite, we then plan to head to finish off the season in the Alps.

After all of this, we may all be roundly sick of glaciers and fieldwork. But there will be no rest for the wicked, and Icy Bear won’t get any time off either. Pretty soon after all of this, Arwyn and Icy Bear will be heading to South Georgia as part of a collaboration with the Natural History Museum and National Geographic to examine its fragile glacial ecosystems.  Finally, just today we received a request for Icy Bear’s very particular skill sets in Drønning Maud Land as part of a UK-US-Swedish project involving Aberystwyth’s Professor Neil Glasser in 2015-6.

It really does look like we’ll be un-bear-ably busy….




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Frequently Asked Questions

Well, on Monday night I had great fun sharing my dirty secrets about microbes and glaciers with a lovely crew of people who turned up to the Aberystwyth Science Café.

Rather than rehash what I said, I thought it might be fun to report some of what the audience asked me at the end of the talk or at the bar. I was really humbled by the interest and pertinence of the questions, which came from a diverse and varied audience. I could recognize many eminent experts in palaeoglaciology, sedimentology, bioinformatics, mycology and botany in the audience, as well as a range of students and people just curious about all of this glacier bugs malarkey. So here’s what I could remember, as I remember it (a government health warning if there ever was!).

I’ve now edited to link to peer reviewed papers supporting my responses and fix typos.

1. Does human pollution affect glacial ecosystems?

Yes. Five kinds of pollution in particular:

Nitrogen – a single deposition event from air masses rich in anthropogenic nitrogen oxides blown up from Europe can meddle with an entire glacial ecosystems. Microbes in Arctic cryoconite no longer need to fix nitrogen for themselves, so long as deposited nitrogen from the snowpack reaches them. This has been a major change for glacial ecosystems in  since Messers Haber and Bosch radically altered our nitrogen economy.

Radionuclides – from accidents and atmospheric nuclear tests. Alpine cryoconite is the most-enriched substance beyond test sites known to science. You can detect the radionuclide signatures of particular events even.

Mercury – Microbes in High Arctic snow have to deal with mercury contamination, and their plasmid genomes reflect this.

Persistent organic pollutants. Mainly on glaciers heavily used for skiing and recreation. Some cryoconite microbes seem very capable of bioremediating these pollutants.

Antibiotics – genes for antibiotic resistance are found on many glaciers.

2. Nature always tries to find a balance. Are the microbes in glaciers collaborating, competing etc?

Yes. Cryoconite, for instance, is a collaboration between phototrophs and heterotrophs. But there’s also lots of competition and bug-eat-bug stuff going on. In particular the viruses – these are highly abundant and their tendency to kill most of the bacteria but produce very few progeny – makes for one of the biggest viral shunts of the microbial loop known. Protozoal grazers are also important.

3. Is the effect of microbes on glaciers being accounted for in models of environmental change?

Not as far as I know, and they probably should be. We have produced climate-reconstruction dependent models of glacier carbon cycles, but how ice-microbe-albedo feedbacks and carbon cycles interact with climate seem to be ignored. An exception is a paper by Jan Oerlemans’ group which suggested that supraglacial dusts induce a melting effect equivalent to an additional +2 degrees Celsius above that from warming predicted by common climate models on Alpine glaciers.

4. What happens to the cryoconite when it goes into the sea as icebergs calve?

This is one of the important questions we have yet to answer fully about how microbes on glaciers influence ecosystems “downstream” – be they terrestrial (glacier forefields), fluvial (streams) or marine. We know that in some marine systems (such as the Gulf of Alaska) that glacial organic carbon is the major source of  organic carbon flux from land to the sea, but uncertainty surrounds the origins of that carbon.

5. How active are the microbes in cryoconite?

Surprisingly so. Rates of microbial activity in cryoconite (sat at 0.1-1 degrees C) have been compared to Mediterranean soils. We still lack really comprehensive, definitive audits of the cryoconite economy as it varies through space and time though.

6.  Do they stay active if cryoconite is buried in the ice?

I don’t know. We’ve thought about this, and have some ideas from labwork about dormancy and resuscitation we’d love to test, (as an undergrad I studied in a lab which did a lot of this work) but we never made a sufficiently compelling case to be funded enough to find out in the real world.

7. The surface of one of Jupiter’s moons, Europa is water ice, and it’s coloured. Is that microbial pigments?

I honestly don’t know. It’s an interesting possibility, but it’s kind of beyond my logistical capabilities to organise a field trip there. I know there are many dedicated researchers working on astrobiology, and agencies which fund cold ecology as an analogue for extraterrestrial life, but I have to admit that I find more pressing concerns closer to home: The one planet we know supports rich and biodiverse life is experiencing warming which first affects the 80% of its biosphere which is colder than your fridge, and we have yet to find all of life on Earth, as we know it.

7. What does life on mean for primary succession in glacier forelands?

It means that it probably isn’t really primary succession. See an earlier blog post of mine which covers aspects of this issue.

8. When does the bar open?

Ages ago. Mine’s a pint. Cheers!

My thanks to the 65 or so people who attended and paid attention to my absurd ramblings, and asked the questions above.

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Dirty Secret: (Microbial) Life and the Death of Glaciers – Aber Science Cafe

I’ll be spilling the beans about cryoconite and how the life of glaciers is surprisingly linked to microbial shenanigans at the Aberystwyth Science Café at 1930h on Monday the 11th of November at Aber Arts Centre. Plus there may be a guest appearance by @icybear79…


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