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.

Coffee break biogeosciences – using truffle dogs for science!

Coffee break biogeosciences –  using truffle dogs for science!

Coffee break biogeosciences, your bi-weekly biogeoscience cake to accompany your coffee…

Do you remember your last scientific conference? Did you also find the scientific coffee break discussion as interesting as the scientific talks? If yes, these short blog posts will allow you to keep the interesting coffee break discussions going as we´ll give you on a bi-weekly basis your scientific biogeoscience cake to accompany your coffee…

Mushrooms are considered perfect bio-indicators of environmental pollution. For instance, some forest mushrooms can accumulate high levels of radioactivity if the soil is contaminated with radioactive nuclides like caesium-137 (137Cs) and 90-strontium (90Sr). In a recent paper published in Biogeosciences (Büntgen et al., 2016), an open access journal of the European Geoscience Union, Swiss and German researchers analyzed truffles collected at different spots in central Europe and found that they contained insignificant amounts of 137Cs, hence being fit for human consumption.

In 1986, the Chernobyl nuclear disaster in Ukraine released substantial quantities of radioactive particles, especially 137Cs. Transported by winds and deposited by heavy rainfall, 137Cs polluted large parts of the European continent, leaving much of the continent’s topsoil layers still radioactively contaminated 30 years later. To date it remained unclear whether truffles accumulate radioactivity at a harmful level comparable to other fungal species. The researchers collected with the help of trained dogs Burgundy truffles in several natural habitats and plantations in Switzerland, Germany, France and Italy. The collected truffles contained negligible amounts of radioactivity, with 137Cs values ranging below the detection limit of 2 becquerels per kilogram (Bq kg -1). This is far below the tolerance value of 600 Bq kg-1, meaning the truffles are safe for consumption, at least in the areas the researchers sampled from. Therefore, if you´re having a headache after eating truffles in your local Italian restaurant, don´t blame the truffles but rather suspect the waiter, who overcharged you for a plate of pasta with fungi (on top of the bottle of Chianti wine).

Büntgen, U., Jäggi, M., Stobbe, U., Tegel, W., Sproll, L., Eikenberg, J., and Egli, S.: All-clear for gourmets: truffles not radioactive, Biogeosciences, 13, 1145-1147, doi:10.5194/bg-13-1145-2016, 2016.

Sky-scraping Biogeoscience at 325m above the Amazonian rainforest

Sky-scraping Biogeoscience at 325m above the Amazonian rainforest

“The outcome of this project will help us to understand the Amazonian forest system before we all destroy it completely”

The Amazon Rainforest in South America represents the Earth´s largest rainforest, housing at least 10% of the world´s known biodiversity and consisting of more than 350 billion individual trees. Besides its large diversity in floral and faunal species, the Amazonian biome has an important impact on the global atmosphere. It produces half of the global atmospheric oxygen via photosynthesis and evaporates vast amounts of water into the atmosphere influencing the climate worldwide.  Nevertheless, this unique biome is under constant human threat as deforestation has continued in the last decades and only begun to dwindle since 2004.

There is a need to better understand the key roles the Amazon biome plays on a local, regional, and global scale. To do this a German-Brazilian joint project was initiated in 2008 and coordinated by the Max Planck Institute for Chemistry, the Max Planck Institute for Biogeochemistry, the Brazilian National Institute of Amazonian Research, Instituto Nacional de Pesquisas da Amazônia (INPA), and the University of the State of Amazonas and the Universidade do Estado do Amazonas(UEA).  The core of the project was to build the Amazonian Tall Tower Observatory (ATTO) right in the heart of the Amazonian rainforest. Thereby allowing researchers to measure greenhouse (e.g. CO2 , CH4, and N2O) and trace gases along with volatile organic compounds and ozone (for understanding aerosol formation) far away from anthropogenic influences. Moreover, they will use the tower-based measurements to assess turbulence and transport processes up to the lower atmospheric boundary layer and to validate and develop different type of models on vegetation, atmospheric boundary layer processes and ecosystem-atmosphere gas exchange. During a short interview for this blog post Jürgen Kesselmeier, from the Max-Planck-Institute for Chemistry in Mainz and the German coordinator of the project, said “Data from the ATTO project will reflect biosphere/atmosphere exchange and effects on cloud development over a forested area related to a transport distance of several hundred kilometers.” While tall towers, such as the the 302 m high Zotino Tall tower observatory (ZOTTO) in the Siberian Taiga, have been used in the past for greenhouse gas and aerosol monitoring before, this project aimed to erect one of the highest towers in one of the most ecologically important terrestrial biomes of the world.

Morning at ATTO_BennerS

Morning view from the ATTO tower over the Amazonian rainforest (credit: Susanne Benner/Max Planck Institute for Chemistry).



ATTO from the botton_combined

Reaching 325 meters into the sky above the Amazonian rainforest, the ATTO is the tallest tower in South America even taller than the Eiffel Tower. Photo on the left shows the tower base (credit: Susanne Benner, Max Planck Institute for Chemistry). Photo on the right shows the tower top (credit: Jürgen Kesselmeier/ Max Planck Institute for Chemistry).


A site was selected 150 km northeast of Manaus, Brazil (see map), at Sebastiao do Uatuma in Amazonas state, to allow for measurements with minimal human perturbation in a location with easy accessibility to facilitate research and educational activities. Construction of the 142 ton, 325m tall (331m with lightning rod) tower in the heart of the Amazonian rainforest, took 30 workers around 4 months to complete and was a logistical and constructional feat. A new road had to be build, allowing transport of the 15 000 tower components to the construction site. At the site, all the different tower elements had to be lifted and assembled using 24 000 screws and bolts and 26 km of steel cable was needed to safely anchor the tower to the rainforest ground. Meteorological and micrometeorological data at the site have been collected since 2012 using two 80m high towers. The 325m high tower was officially inaugurated last August and in the coming months the tower will be equipped with a wide array of instruments before the actual measurements will start by the end of 2016.



The location of the ATTO tower, 150 km northeast of Manaus, Brazil at Sebastiao do Uatuma in Amazonas state and right in the heart of the Amazonian rainforest (credit: Andreae et al. 2015, Atm. Chem. Phys.)


Finally, an important question is whether data from the ATTO tower can help to convince policymakers to stop deforestation of the Amazonian rainforest. “As the outcome of the ATTO project will highlight the role of the Amazonian rainforest in the relationship between global change, carbon cycle, trace gasses and aerosols and clouds, it will make the needs of this biome visible and strongly support its protection, ” says Jürgen Kesselmeier. In short, the outcome of this project will help us to understand the Amazonian forest system before we all destroy it completely. The ATTO project already attracted the interests of the media and in the future, all scientists involved in the project will start disseminating their results. Therefore, it can be expected that in the coming years, we´ll hear much more about this scientific sky-scraper and its role in saving the planet´s green lungs.



Construction of the 325m tall ATTO tower was not for the faint-hearted. In the picture on the left, taken at 130m height, you can see Jürgen Kesselmeier from the Max-Planck Insitute of Chemistry, Mainz and German coordinator of the ATTO project together with two construction workers. On the right you can see construction workers assembling the tower at 150m height (credit: Jürgen Kesselmeier, Max Planck Institute for Chemistry).



Andreae et al. (2015) The Amazon Tall Tower Observatory (ATTO): overview of pilot measurements on ecosystem ecology, meteorology, trace gases, and aerosols. Atmos. Chem. Phys., 15, 10723-10776

For more information on the project and an impressive movie of the construction, visit:

For an overview of the different type of measurements performed during the ATTO project, visit:


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,

Welcome to the multi-faceted world of biogeosciences

Welcome to the multi-faceted world of biogeosciences

“From marine micro-organisms to mountain ecosystems”

Welcome to the official blog of the Biogeosciences (BG) Division of the European Geoscience Union! This blog is run by biogeoscience enthusiasts with very different backgrounds, ranging from plantecophysiology over geology to geomicrobiology. Therefore we think that the variety of posts, will make this blog interesting for all interested in biogeosciences.

We bio‐geoscientists perform research on the processes in and interactions among the Earth’s atmosphere, biosphere, hydrosphere, and geosphere. At first sight, our research might seem very broad and indefinite, but due to the multi‐faceted and interdisciplinary nature of biogeoscientific research, we can provide the scientific basis for understanding the role of ecosystem processes in some of today’smost pressing environmental issues: including, (but not limited to) climate change, deforestation,eutrophication of lakes and rivers, and the effect of sea level rise on coastal and estuarine ecosystems. In addition to all of that, biogeoscientific research informs our understanding of the biogenic signatures found within rocks from early Earth, and areas of our planet which are highly inhospitable.

Benthic foraminifers Mediterranean

Benthic foraminifers recovered from Mediterranean sediments of Neogene age (credit: Aleix Cortina)

Our first blog entry will be on the timing of the closure of the Panama Isthmus which had an important impact on the Great American Biotic Interchange‐ also known as GABIA. Our second blog posts will be on the European Consortium for Ocean Research and Drilling (ECORD) Summer school “Ocean Crust Processes: magma, faults , fluxes, and life” which was recently held in Bremen Germany. Our third post will be on the Amazonian Tall Tower Observatory (Atto) in the Brazilian rain forest which was inaugurated last month and will be used to measure greenhouse gases, aerosol particles, cloud properties, boundary‐layer processes, far away from human influences. In a later stage we foresee blog contributions from scientists with a wide range of biogeoscientific backgrounds. If you would like to write a blog entry about your research, please get in touch with the editor, especially if you are an early career scientist! We welcome all contributions that fit broadly within the topic of Biogeosciences.


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