early career scientists

Investigation of methane emissions in marine systems

Investigation of methane emissions in marine systems
Ever wondered how we can measure methane emssions from the seafloor ? And ever wanted to steer a mini submarine remotely operating vehicle (ROV)? Well here´s your chance! Have look at this blog post on analyzing methane emissions using ROVs and you´re ready to embark! 


The goal is to determine when the gas leak started and how the fluid flow systems work. With our research, we can contribute to a better understanding at what time methane from the seabed has released to the atmosphere and if more emissions have occurred while the climate of the past was changing.

We have been using ROVs to inspect the seafloor and sample carbonate crusts, gas bubbles released from the seafloor and surrounding sediments (Fig. 1).

Fig. 1: the ROV Ægir 6000 (credit:Maja Sojtaric – CAGE).

The last area investigated is composed by two 2 small canyons where a lot of bacterial mats were observed (Fig. 2). These bacterial mats occur where the methane is in high concentration in sediments and represent a target for investigation on methane-influenced systems.

Fig. 2: sampling area in the Norwegian Sea and pictures of the seabed with bacterial mat (credit:Maja Sojtaric – CAGE ).

Two major tools are used in these environments to identify the past methane emissions, the carbonate crusts and push cores.The carbonate crusts precipitated because of the methane release, isotopes measured on these rocks inform about the date of emission and about the source of methane (Fig. 3 and 4).

Fig. 3: Gastropod in CH4-derived carbonate cemented sediment; aragonite botryoids (upper center; X-pol light) (credit: Maja Sojtaric – CAGE).

The push cores are sampled for porewater to trace geochemical processes related to fluid flow processes. Samples are also taken for gas measurements to determine the amount and its sources (Fig. 4). The response of the biological community on methane seepage is analyzed by means of planktonic and benthic foraminifera.

Fig. 4: Push core sampling in bacterial mat (credit: Maja Sojtaric – CAGE).

Dr. Pierre-Antoine Dessandier, post-doc researcher at CAGE, center for arctic gaz hydrate, climate and environment, university of Tromso, Norway wrote this blog post. After obtaining his PhD at Bordeaux university (France) in 2015 on micropaleontology, Pierre-Antoine moved to Tromso in Norway to continue his work on benthic foraminiferal ecology and paleo-environments. His main research interests are the use of benthic foraminifera as bio-indicators of climate change and methane emissions in the Arctic seas, using ecology of species and isotopic measurements. He is currently working on active methane seepages in the Barents Sea to reconstruct the chronolgy of the past methane emission and their link with climate change.




What´s in your fieldbag? Part 1: measuring freshwater carbon fluxes in the Artic

What´s in your fieldbag? Part 1: measuring freshwater carbon fluxes in the Artic

This bag belongs to

Joshua Dean, Postdoc, Vrije Universiteit Amsterdam

Field Work location

Far Eastern Siberian Arctic: Kytalyk Nature Reserve.

Duration of field work

2 weeks plus 3 days travel either side.

Items in the bag

  • Detecto Pak-Infrared (DP-IR) gas analyser [borrowed from colleagues, protect at all costs]
  • EGM4 CO2 gas analyser [borrowed from another department, protect at all costs]
  • water sample vials [plus many tens of spares]
  • molecular sieve cartridges [for capturing CO2 samples for radiocarbon analysis; Garnett et al., 2016a]
  • foil gas bags [for capturing CH4 for radiocarbon analysis; Garnett et al., 2016b]
  • small and large syringes, needles and stopcocks [for extracting dissolved CO2 and CH4 samples from water]
  • jumbo (1L) syringe [for extracting jumbo water headspace samples for CO2 and CH4 radiocarbon sampling – also good for jumbo sized practical jokes]
  • drink bottle [I normally bring a camelback] and snacks
  • satellite phone [T‑mobile’s Siberian Arctic coverage is woeful]
  • ski goggles as gift for Russian park ranger [so they will show me the protected mammoth graveyards in the nature reserve]
  • waterproof notebook [to protect from the elements and clumsiness]
  • duct tape [or duck tape depending on your tastes]
  • sharpie/permanent markers [2 things you always need in the field, duct tape and permanent markers – always! It’s best if these are colour coded so you know if someone has stolen yours].
 The essentials for aquatic greenhouse gas field sampling campaigns (photo credit: Joshua F. Dean, VU Amsterdam)

The essentials for aquatic greenhouse gas field sampling campaigns (photo credit: Joshua F. Dean, VU Amsterdam)

 Not shown in photo

  • exetainers® [for storing gas samples extracted from water]
  • jumbo degassing vessel(s) [to match the jumbo syringe, see Garnett et al., 2016a and 2016b for more details]
  • assorted spare parts [many, many, many spare parts – finding small bits of equipment that you dropped in the Arctic tundra is a nightmare, I lost a walkie-talkie in the tundra once]
  • field team [for mental and physical assistance – absolutely vital
  • Russian guide [because English is not to be found here]
  • mosquito shirt and bug spray [the mosquitos love foreign blood, for an impression see below]
  • spare food [in case you have an aversion to weird food, see previous post on the Blog].



Mosquito Paradise, Kytalyk Nature Reserve (photo credit: Ove H. Meisel, VU Amsterdam)

Aim of the research

The aquatic pathway is known to be a potentially important export pathway of terrestrial carbon of all forms (Dinsmore et al., 2010), but while this is known to be a significant process in the Arctic (Vonk et al., 2015), we desperately lack in understanding of how this may be affected by the warming climate. We are taking measurements of freshwater carbon fluxes across a range of lakes, pools, rivers and streams in the Siberian Arctic tundra to estimate their contribution to the carbon budget of the landscape. We will compare this to measurements from the eddy covariance tower, both CO2 and CH4 fluxes, that we manage at the site (see previous post on the blog). We are also incorporating radiocarbon measurements within this to see whether climate change induced permafrost thaw is mobilising ancient carbon, which was previously locked up in the organic rich tundra soils, into the aquatic pathway.

One item I can’t live without

Beer… I can live without it, but when everything goes wrong in the field, you fall into a pool and/or stream, your camera gets wet, the batteries in all your equipment die, you lose repeated samples and the mosquitos have laid waste to every inch of your skin, it’s nice to relax with an ice cold beer in the evening. Luckily the permafrost in this area is shallow, so it’s easy to dig a temporary fridge.


Dinsmore, K.J., Billett, M.F., Skiba, U.M., Rees, R.M., Drewer, J., Helfter, C., 2010. Role of the aquatic pathway in the carbon and greenhouse gas budgets of a peatland catchment. Global Change Biology 16(10), 2750–2762.

Garnett, M.H., Gulliver, P., Billett, M.F., 2016a. A rapid method to collect methane from peatland streams for radiocarbon analysis. Ecohydrology 9, 113-121.

Garnett, M.H., Billett, M.F., Gulliver, P., Dean, J.F., 2016b. A new field approach for the collection of samples for aquatic 14CO2 analysis using headspace equilibration and molecular sieve traps: the super headspace method. Ecohydrology, doi:10.1002/eco.1754.

Vonk, J.E., Tank, S.E., Bowden, W.B., Laurion, I., Vincent, W.F., et al., 2015. Reviews and synthesis: Effects of permafrost thaw on Arctic aquatic ecosystems. Biogeosciences, 12, 7129-7167.

Dr. Joshua F. Dean from the VU University Amsterdam wrote this blogpost. He is a postdoctoral researcher who explores the carbon cycle in the Arctic and temperate peatlands to determine methane and carbon dioxide feedbacks under a warming climate. His work involves experimental approaches, modelling, and direct and indirect measurements of carbon dioxide and methane emissions from freshwater environments, with fieldwork campaigns throughout the Arctic and northern hemisphere peatlands.

Coffee break biogeosciences – climate change affects mountain plant’s sex ratios

Coffee break biogeosciences – climate change affects mountain plant’s sex ratios

As climate change progresses, widespread changes in phenotypes in many plant populations are bing observed by scientists around the world. For instance in alpine areas, dominant plant species on lower altitude are shifting towards higher altitude as they adapt to increasing temperatures, thereby competing with high-altitude native plant species. In a recent study by Petry et al. (2016) it was shown that responses to climate change in the plant Valeriana edulis (valerian) are strongly sex-specific, thereby reducing pollen limitation and increasing seedset under climate change scenarios. By comparing the presence of female and male valerian plants at different elevations (from 2500 to 3600m) along slopes in the Rocky Mountains of Colorado, they found that climate change is impacting the sex ratio of plants along their elevation range, with a higher presence of female plants high on the mountain as compared to male plants. As these ratios of female to male plants are changing faster than species are moving uphill, they might be a much more rapid trait to detect responses of plant communities to climate change than migration patterns.

To read more about this research on how warming alters mountain plant´s sex rations in the Rocky mountains, check out the article by Petry et al. (2016).

Keeping a lookout at the edge of the world

Keeping a lookout at the edge of the world


Few places in the world conjure up images of remoteness and harshness like Far Eastern Siberia. Yet, it’s places like these where our science is needed most.

Arctic soils hold vast amount of carbon, protected in thick layers of permafrost, but these stores are becoming more and more vulnerable as temperatures in the Arctic warm, and are set to warm faster than anywhere else on the planet. Recent studies have further suggested that the freezing and thawing activity in permafrost areas plays a crucial role in the overall carbon balance of these regions, trapping and releasing large quantities of gas in unfrozen, still active soil layers during the shoulder seasons (e.g. Zona et al., 2016). Hence the challenge to measure C fluxes in these regions during the early spring and late autumn periods either side of the snow-free growing season.

However, just getting to these sites is often a challenge, both logistically and personally!

I recently travelled to Siberia in April with my boss to set up eddy covariance instrumentation at our Arctic Siberian field site – Kytalyk nature reserve, about 30 km northwest of Chokurdakh, a small town itself a three-and-a-half-hour flight (on a plane that was two generations older than me) northwest of Yakutsk in the Sakha Republic of Russia. Our research group, led by Prof. Han Dolman at Vrije Universiteit Amsterdam, has been measuring carbon fluxes at the site since 2003. This year I took on the reigns of these measurements, a long way from my home country of New Zealand, and it was more challenging than I expected…


Our long-term record of CO2 fluxes from the Kylalyk site in Arctic Siberia, one of just a handful of such “lookout posts” in the vulnerable Arctic (photo credit: Luca Belelli Marchesini).


During my interview for this position, I was asked to respond to a riddle:

“You are in the field with a team of Russians, they have been drinking vodka and are very drunk. An emergency arises, and you need to get everyone to safety. What do you do?”

Whilst carefully refraining from explaining that if everyone else was drinking vodka, I probably would have been too, I managed to find an answer that must have been acceptable because I got the job. This question was just a taster for the unique encounters you can experience while doing fieldwork in new and wonderful places.

Siberian Russia is not the most culturally divergent place from what I am accustomed to, and I’m sure there are many readers who have been to more wild regions and eaten more outrageous cuisine. But I wanted to share some of my experiences for those of you who may have to follow a similar path involving cultural and culinary experiences that you might otherwise not seek out in your daily life.

I’m not a big fan of fish, for instance, certainly not raw fish. Raw fish happens to be the go-to protein dish in this part of Siberia. A particular treat is the Indigirka Salad, cubes of frozen raw fish and onions – the ultimate challenge for any breath freshener.

I was also to enjoy boiled tongue (I’m not sure whose) in creamy, custard-like sauce, and soup made primarily from cow stomach and entrails. It smelt as bad as it sounds, something like a cross between cow burps and a pig’s fart, and the meat looked exceptionally disturbing.


Cow stomach soup: best served not at all (photo credit: Joshua Dean).

Cow stomach soup: best served not at all (photo credit: Joshua F. Dean).


Out at the field site I would eat plenty more frozen fish, but cut directly from the fish itself and dipped in instant noodle flavouring. This was quite tasty if you ate it fast enough not to notice the texture of raw fish melting in your mouth. I would also drink fermented horse milk, and eat jelly made from bone marrow. A cube of the latter is enough to make you see your breakfast again under the right circumstances, unless you have vodka to wash it down.

My advice here? Don’t be afraid to try new things, but don’t be afraid to say no if it tastes like an unwashed cow’s anus and vomiting isn’t high on your agenda for the day.

Taking a sled ride behind a snowmobile as we headed into the remote and snowy Arctic was also an amazing experience, but after an hour of riding in a sled with no suspension, the majority of your bones will eventually turn into a fine powder, as shown here.

During our stay in the field we celebrated Koningsdag, the Dutch King’s Birthday (27th April – also my birthday, though I didn’t convince anyone that I was royalty), by flying a Dutch flag over a small piece of the Russian Arctic (this was not meant as an act of geopolitical aggression).



Definitely not conquering the Russian Arctic, Joshua Dean on the left, Han Dolman on the right, with the (not yet working) eddy covariance tower in the background (photo credit: Joshua F. Dean).


At the site, setting up the eddy covariance tower proved to be relatively straight forward. However, we first found that we weren’t collecting data from the sonic anemometer (measuring wind speed and direction in three-dimensions). It turns out we hadn’t turned it on (duh!) leading to the discovery that the solar panels and batteries weren’t working. Some MacGyver-like electrical combos later and we had the system up and running. Success! But a good example of how inventive you have to be to fix things when backup gear is literally half a world away.

Back in Yakutsk we relaxed with a banya (a Russian Sauna), which includes plenty of beer, hanging out naked with your boss, and a thorough birch branch whipping by a 60-something Russian professor.

The generosity of our Russian hosts was unsurpassed. While the food certainly pushed some of my culinary boundaries, I’m pretty sure our hosts found my myriad reactions to their food and drink highly amusing. I look forward to visiting again in the summer for more fieldwork, and to strengthen the bond of social and scientific collaboration that started with a mouthful of cow guts.

Reference: Zona, D. et al. (2016) Cold season emissions dominate the Arctic tundra methane budget. Proceedings of the National Academy of Sciences 113(1):40-45.

Dr. Joshua F. Dean from the VU University Amsterdam wrote this blogpost. He is a postdoctoral researcher who explores the carbon cycle in the Arctic and temperate peatlands to determine methane and carbon dioxide feedbacks under a warming climate. His work involves experimental approaches, modelling, and direct and indirect measurements of carbon dioxide and methane emissions from freshwater environments, with fieldwork campaigns throughout the Arctic and northern hemisphere peatlands.

Digging up bones for science – looking into 48 million years old blood vessel-like structures

Digging up bones for science – looking into 48 million years old blood vessel-like structures

The Messel Pit is a worldwide famous fossil site recognized by UNESCO as a World Natural Heritage Site because of the exceptional preservation, as well as the diversity of its fossils from the early-middle Eocene (~48 Ma). The Messel Pit, located in an old Quarry in Germany near Frankfurt am Main , includes fossils from vertebrates (turtles, crocodiles, mammals, birds, lizards, among others), invertebrates (insects), and plants. The vertebrates are preserved in articulation, often with associated ‘‘soft ’’ tissues such as hair, scales or feathers, and even occasionally in situ stomach contents. Despite of the exceptional macroscopic (complete skeletons) preservation of Messel Pit vertebrates, the internal preservation of bones has been almost completely unexplored, leaving unresolved questions as for example if such exceptional preservation also occurs at microscopic and molecular level, allowing the recovery of bone proteins and even DNA.

A new research topic was started at the Senckenberg Museum in Frankfurt, focused on examining the preservation of blood vessels and bone cells-like (called osteocytes) from some of the Messel pit vertebrates. Osteocytes are remarkably important for understanding evolution since they are the most abundant cells forming bones in all vertebrates on Earth. After analysing very small pieces of fossil bones (less than 1 cm2), beautiful osteocytes-like and blood-vessels-like from two species of turtles, one mammal species, and one crocodile were discovered. It thus indicated that the exquisite preservation of Messel Pit vertebrates occurs at both macro (skeletons) and micro (cells-like) scales.


Step by step illustration of osteocytes-like cell analysis. Top-left (fragments less than 1 cm3 of bone from Messel pit vertebrates were taken for analysis). Middle-left (all the mineral phase of the bone are removed, leaving after only the osteocytes and blood vessels-like microstructures). Bottom-left (osteocytes and blood-vessels-like are observed and photographed using a light-transmitted microscope. Bottom-right (osteocytes are also observed under Field Emission Scanning Electron Microscope, to explore in detail their textures and physical properties) (Credit: Edwin Cadena, Senckenberg museum)

However, work on these bone osteocytes and blood vessels-like microstructures is not quite complete. It is also interesting to establish if there are any remains of their original molecular composition (proteins or even DNA) after 48 millions years of being trapped inside the rocks. Preliminary results show that osteocytes-like and blood vessels-like exhibit important amount of iron (Fe) in their composition, contrasting with bone remains and collagen fibrils-like that lack iron. Although no proteins or DNA remains have been found yet in the Messel Pit fossil vertebrates, the occurrence of iron is a good signal because iron has also been found in similar microstructures of dinosaurs bones from USA, in which proteins are truly preserved.


Analysis of the elemental composition of one of the osteocytes-like cells from a fossil turtle from Messel Pit, using a Phenom Pro X Scanning Electron Microscope. Red dots on the osteocytes indicate different spots that were analysed for compositional elements, as shown for example for spot 2, indicating a high content of iron (Fe), Carbon (C), and Oxygen (O2) (Credit: Edwin Cadena, Senckenberg museum).


At this point, it is clear that further research is needed for establishing the original biomolecular composition (amino acids and proteins) of fossil cells or soft tissue. If bone proteins – or even DNA- are preserved in Messel Pit fossils that could shed light on understanding evolutionary relationships, as well as the mode and rate of evolution at molecular levels, which is crucial for explaining different lineages of extant vertebrate animals, including us.



For further details, see Cadena (2016).

Reference:Cadena, E.A. 2016. Microscopical and elemental FESEM and Phenom ProX-SEM-EDS analysis of osteocyte- and blood vessel-like microstructures obtained from fossil vertebrates of the Eocene Messel Pit, Germany. PeerJ 4:e1618; DOI 10.7717/peerj.1618


Dr. Edwin Cadena wrote this blogpost. He got a grant from the Alexander Von Humboldt foundation to perform his research on osteocytes from fossilized (in)vertebrates at the Messel Pit.

Insights into the ocean crust and deep biosphere – ECORD Summer School 2015

Insights into the ocean crust and deep biosphere – ECORD Summer School 2015

Summer time as an early career geochemist can mean many things, to some it is vacation time, to others it is field season, and yet for others it is time to enroll in a summer school. ECORD, the European Consortium for Ocean Drilling, offers at least one summer school a year. If you work with foraminifera you may be familiar with the Urbino Summer School in Paleoclimatology, sorry to disappoint, but this post is on another summer school that ECORD offered this year.

The participants of the ECORD Summer School 2015. Image credit: Volker Diekamp

The participants of the ECORD Summer School 2015 (credit: Volker Diekamp).

The ECORD Summer School on Ocean crust processes: magma, faults, fluxes, and life in Bremen, Germany took place from August 31-September 11. It was the second time this course was offered, and the first was in 2009. The MARUM houses the Bremen Core Repository. This repository is for cores drilled by the Deep Sea Drilling Project (DSDP), Ocean Drilling Program (ODP), the Integrated Ocean Drilling Program (IODP) and International Ocean Discovery Program (IODP) in the Atlantic Ocean, the Mediterranean and Black Seas and the Arctic Ocean. Being located in the MARUM offered the unique opportunity to not only hear lectures about specific expeditions and cores, but view the cores themselves. We also got to see some of the German remotely operated  (ROVs) and autonomous underwater vehicle (AUVs) along with the MeBo and MeBo 200, two seafloor rock drills, which were developed by the MARUM.

The “and life” portion of the ECORD course was naturally on the deep biosphere as it applies to ocean ridges and spreading zones.  While life may have appeared almost as an afterthought in the course title it was given an entire day onto itself in the 10 day program. Further, it was a frequently mentioned topic throughout. As you may know the deep biosphere is a relatively poorly understood and poorly studied area of the global biosphere. When talking about the ocean crust and life it is always easy to just focus on well known hydrothermal vent fields such as TAG, and ignore any life that may exist outside of a vent environment. This course did neither. One of the highlights from a biogeosciences perspective was the presentation of Prof. Dr. Gretchen Fuhr-Green on the ECORD Mission Specific Platform expedition 357 to Atlantis Massif which is in process now. Expedition 357 looks at serpentinization and life using two seafloor rock drills, the MARUM’s MeBo, and the British Geological Survey’s Rock Drill. It focuses on the microbial communities found in serpentinized rocks, and how they might impact or influence the process of serpentinization. Her presentation featured quite a lot of information about the planning of expedition, along with a detailed explanation of how mission specific platforms work. Both of which are important knowledge to any ESCs who may consider proposing an IODP expedition in the future.

Another highlight was the final full day of the summer school. This was the “biology” day. Speakers Dr. Magnus Ivarsson and Dr. Benedicte Menez told us all about how microimaging techniques can be used to image and study the deep biosphere. Additionally Dr. Menez presented how microbiological techniques can be used to examine and identify the microbial communities found in hard rock. After, Prof. Wolfgang Bach taught a practical on modeling hydrothermal reactions and bioenergetics. All of these are very useful for someone who studies deep life and/or rocks that deep life may act on.

I study geomicrobiology and the deep biosphere as it pertains to ocean basalts which is why such a course would have been relevant for me even if “life” wasn’t tacked onto the end of the title. However, the biogeosciences are very diverse field of Earth Sciences, which can span from biology in soils, to trees, to palaeoclimate, to life on Mars, and etc. So a course like this may not be relevant for everyone. All in all though the ECORD 2015 Bremen Summer School was a fantastic course if you have an interest in either microbial life in hard rocks, or in ocean crustal processes.

The Panamanian Isthmus is not entirely guilty after all!

The Panamanian Isthmus is not entirely guilty after all!


“According to new research, the land bridge connecting Central and South America rose more than 10 million years earlier than originally thought”


Traditionally, closure of the Panama Isthmus has been deemed responsible for the co-occurrence of two major events: The large Pleistocene glaciations and the Great American Biotic Interchange (GABI). Existing evidence indicating a casual relation is controversial, mainly because the difficulty on establishing a precise chronology of closure. Results of a recent publication in Science by Montes and colleagues [1] suggest that closure of the Isthmus was not related to these events. What’s more, these results seem to suggest that the beginning of the major glaciations could actually be the cause of the GABI.

According to this research, closure of the Central American seaway could have happened more than 10 million years (Ma) earlier than originally thought. New evidence relies on cartography, provenance analyses and detrital zircon geochronology. Detrital zircons ages were used to constrain the age of deposition of the host sediment, reconstruct provenance, and, more importantly, characterize source regions. In the northwestern margin of South America, there are several mountain ranges that contain ancient zircons formed under different tectonic settings. However, zircons between 30 and 40 Ma can only be found along the Panamá region. This signature serves as a distinctive Panamanian fingerprint. These Panamanian zircons were found in fluvial and coastal sediments accumulated 15 Ma along the northwestern Colombian region. It is therefore inferred that there were rivers bringing Panamanian rock fragments and crystals from Panama to shallow marine basins of northern South America at that time. A river connecting these two land-masses negates the presence of the Central American seaway. As a result, the flow of deep and intermediate Pacific waters into the Caribbean Sea would be severed. Caribbean-Pacific water exchange could still occur through narrow, shallow, and transient channels that could fragment the emerged land.

Paleogeographic reconstruction of the connection between Central and South America around 13-15 Ma (Modified from Montes et al., 2015-Science)

Paleogeographic reconstruction of the connection between Central and South America around 13-15 Ma (Modified from Montes et al., 2015)

In light of this evidence, it seems that the biotic interchange and the Pleistocene glaciations may need new explanations. One interesting alternative could be that the biotic exchange occurred as a consequence of the onset of the glaciations. Such cold periods typically bring drier conditions and promote the development of savannah-type vegetation corridors in Central and South America. These corridors, along with falling sea-levels results of more ice trapped in continental glaciers, could have finally allowed the massive crossing of mammals. If this is the case, several questions open up. For instance, what triggered the glaciations? Or, when was the onset of the modern thermohaline circulation?

Panamanian rocks outcropping along the Pacora River. These rocks were studied in detail for understanding the origin of the zircons present in sedimentary rocks along the northwestern South America margin. Photo Courtesy: Camilo Montes

Panamanian rocks outcropping along the Pacora River. These rocks were studied in detail for understanding the origin of the zircons present in sedimentary rocks along the northwestern South America margin (credit: Camilo Montes)


[1] Montes et al., (2015). Middle Miocene closure of the Central American Seaway. Science, 348(6231), 226-229. DOI: 10.1126/science.aaa2815,

Diana Ochoa wrote this blog post. Prof. Dr. Camilo Montes, who was the PI of the research leading to these results, edited and verified its scientific content.

Camilo Montes is a professor part of the Geosciences Department at Universidad de los Andes in Colombia,