Stratigraphy, Sedimentology and Palaeontology

Stratigraphy, Sedimentology and Palaeontology

The hard part of life: the secrets of biomineralization

Biomineralization is a fascinating natural process by which living organisms produce hierarchical mineral structures with diverse functions. The “secrets” of biomineralization are explored by the scientists since decades but there are still open questions regarding its function, the regulating mechanisms and why and when biomineralization started.This process occurs through self-organization of organic and inorganic molecules and requires specific ambient conditions. It results in highly structured materials with remarkable physical and chemical properties. Examples are the formation of silicates in algae and diatoms, carbonates in invertebrates and phytoplanktonic algae, and calcium phosphates and carbonates in the hard tissues of vertebrates. The crescent number of works dealing with biomineralization highlights the interest of the scientific community which aims at understanding why, under specific circumstances, the process fails. Here I propose a selection of the latest papers published on this topic.

Coronado et al. (2019) published on Nature Communications the work titled “Impact of ocean acidification on crystallographic vital effect of the coral skeleton” where they have assessed crystallographic parameters of bio-aragonite to study the response of the reefbuilding coral Stylophora pistillata to experimental seawater acidification.

Structural features of Stylophora pistillata cultured at different pH conditions (from Coronado et al. 2019)


Skeletons formed under high pCO2 conditions show systematic crystallographic changes such as better constrained crystal orientation and anisotropic distortions of bio-aragonite lattice parameters due to increased amount of intracrystalline organic matrix and water content.


In the work titled “Terebratulide brachiopod shell biomineralization by mantle epithelial cells” by Roda et al (2019) published in the Journal of Structural Biology the authors wanted to focus on an unknown process in brachiopods: how the mineral is transported from outer mantle epithelium cells to the site of mineralization. So they imaged with TEM and FE-SEM ultrastructural characteristics of outer mantle epithelium cells on Magellania venosa shells to investigate the mineral transport pathways for shell secretion and to assess differences in cellular activity during mineralization.



Tang et al (2019) published in Nature CommunicationSpiculogenesis and biomineralization in early sponge animals” where they  report an early Cambrian sponge that had weakly biomineralized and hexactine-based siliceous spicules with large axial filaments and high organic proportions. This material, along with Ediacaran microfossils containing putative nonbiomineralized axial filaments, suggests that Precambrian sponges may have had weakly biomineralized spicules or lacked them altogether, hence their poor record. This work provides a new search image for Precambrian sponge fossils, which are critical to resolving the origin of sponge spiculogenesis and biomineralization.

Preservation of organic and biosilica structures in Vasispongia delicata (from Tang et al., 2019)



The recipe for making shells, spines, and coral skeletons is not only the same across many modern animal lineages, but is ancient—dating back 550 million years—and evolved independently more than once. This is what is presented in”Biomineralization by particle attachment in early animals ” by Pupa et al (2019) published in PNAS . The authors show that when echinoderms, mollusks, and cnidarians started biomineralizing in the Cambrian (more than 500 million years ago) these three phyla started doing it in precisely the same way: using attachment of amorphous nanoparticles.”

Modern and fossil nacre from 3 molluscan classes, exhibiting irregularly shaped nanoparticles (from Pupa et al. 2019)



Finally, Schoepplera et al (2019) published in PNASCrystal growth kinetics as an architectural constraint on the evolution of molluscan shells” where they  compare the process of ultrastructural morphogenesis of shells from 3 major molluscan classes: A bivalve Unio pictorum, a cephalopod Nautilus pompilius, and a gastropod Haliotis asinina. They demonstrate that the fabrication of these tissues is guided by the organisms by regulating the chemical and physical boundary conditions that control the growth kinetics of the mineral phase. This biomineralization concept is postulated to act as an architectural constraint on the evolution of molluscan shells by defining a morphospace of possible shell ultrastructures that is bounded by the thermodynamics and kinetics of crystal growth.

Structural analysis of the N. pompilius shell using electron microscopy (from Schoepplera et al 2019)


The study of biomineral formation is essential to our understanding of the most fundamental processes in evolution and organisms capability to adapt to environmental changes…so let’s keep investigating the “hard part of life”.

Investigating the climate history of Central Asia in Kashmir/India

As in most arid areas, dust storms are quite common in India. Repeatedly, the wind carries large quantities of dust from the Thar Desert in the south-west into the Asian country, sometimes across long distances. There have also been dust storms in India in the past, making geoarchives of aeolian dust a suitable recorder of the past local climate- and dust history. When the climate was rather warm and humid, thick soils would form in the dust deposits. However, if it was cold and dry, the dust would remain as a loose and grey/ochre sediment called loess. Such dust deposits can accumulate 10s to 100s of meters high, and represent valuable archives of past dust activity, soil formation and also other information on e.g. Earth’s magnetic field in the past.  Prominently, the loess occurring at the Chinese Loess Plateau has been extensively used for reconstructing past monsoon activity.

In the Indian subcontinent, such dust deposits have mainly been reported from northern Pakistan and northern India. From the Kashmir valley >20 m thick loess deposits including palaeosols have been reported, but little data is available. Yet, the age of these deposits is controversially discussed in the literature. Age-analyses derived from carbon isotope measurements (14C dating) suggest a rather young age (~40 ka for the outcrop in the image) and high deposition rates of ~26 cm/ka, while ages calculated via luminescence dating suggest deposits to be older (~120 ka for the outcrop in the image) and generally lower sedimentation rates. Such an inconsistency in dating results is uncommon, and the reason is unclear.

Recently, a field trip by Indian and German scientists visited several outcrops in Kashmir to investigate the spatial homogeneity of the reported dust deposits, and collected sediment samples for generating data for a better understanding of the past environment. We can confirm the statements on the occurrence of large dust deposits in the Kashmir valley of at least around 15 meters in height. In the dust deposits, several grey and brown soils are preserved. Therefore, these deposits indeed represent a valuable archive of the past environment. New dates and sedimentological data are expected to allow for a better understanding of the sediment itself and will place these deposits in a Eurasian perspective.


Exposure of dust sedimentation and soil formation in the Kashmir valley spanning the last ~40 or ~120 ka. The dark horizontal ‘layers’ represent soils, which have formed during humid phases in the dust deposits.


Selected further reading:

Bronger, A., Pant, R.K., Singhvi, A.K., 1987. Pleistocene climatic changes and landscape evolution in the Kashmir Basin, India: Paleopedologic and chronostratigraphic studies. Quat. Res. 27, 167–181.

Dodonov, A.E., Baiguzina, L.L., 1995. Loess stratigraphy of Central Asia: Palaeoclimatic and palaeoenvironmental aspects. Quat. Sci. Rev. 14, 707–720.

Pant, R.K., Dilli, K., 1986. Loess Deposits of Kashmir, Northwest Himalaya, India. Geol. Soc. India 28, 289-297–297.


Slimy Landscapes 2: This time it’s Precambrian

Slimy Landscapes 2: This time it’s Precambrian

Slime is important to the developments of Earth’s landscapes – I have already explored this in a previous post where I learnt how Extracellular Polymeric Substances (EPS), a fancy phrase for a slime produced by organisms, can bind sediments together and making them resistant to erosion. This has impacts on the development of landscapes, from the types of bedforms forming below flows, the rate at which cliffs erode, and the shape deltas take. However, it seems this is just the beginning and the more you dig the greater the influence this slime has had on the planet and its inhabitants.

Let’s go back to the deep ocean, 635 million years ago, where the waters are well oxygenated and full of simple plants and animals. Fast-forward over a hundred million years, beginning 540 million years ago, and there is a sudden explosion in the evolution of life, with ecosystems similar to the present day emerging and the lifeforms becoming my complex. We have travelled from the Ediacaran to the Cambrian and the world has been turned upside down.

I spoke to a couple of researchers at the Energy and Environment Institute, University of Hull, who are researching this sudden change. They work on a project called Worms on Film and both are using art as a way of communicating their research. Catherine Mascord explained to me –

“Before this transition, with nothing to disturb them Precambrian seafloors, including those of the Ediacaran, are generally characterised by prevalent anoxia and sulphur rich sediments. Without animals to break up and disturb the sediment most of the seafloor was blanketed in a thick community of microbes, known as a microbial matground, formed when bacteria and other microorganisms glue themselves and their host sediment together through the secretion of EPS.”

A talented scientist and artist, Catherine uses her talents to communicate her research. This diagram shows the difference between the surface/sub-surface eco-systems of the Ediacaran and the Cambrian.

It was the evolution of burrowing animals, like worms, that initiated the transition from the Ediacaran to the Cambrian, and Catherine’s research is helping us understand this better through a mix of field work and experiments using modern worms.

“We can use modern animals with similar burrowing behaviours as models for ancient animals and use then to help figure out how an animal behaves in Ediacaran-like conditions.”

These worm-like burrowers were key to breaking through the 2-dimensional habitat that was being reinforced by EPS. The sub-surface was barren, de-oxygenated, and lifeless. The emergence of the burrowers broke through this crust and enabled the sub-surface to be oxygenated. I spoke to Jenny James, who is researching the links between climate change and mass-extinctions as part of Worms on Film.

“Marine worms are eco-system engineers; they increase oxygen penetration depth into the sediment allowing microbiota to survive at a greater depth and speeding up the process of nutrient cycling; they also stabilise the sediment by secreting a mucus-like substance (EPS) to line their burrows.”

Although the burrows made by the worms are reinforced, they are not invincible and changes to the planet’s climate can impact on the eco-systems they create. Moving forward in time again to the end of the Permian (252 million years ago) and once again the ocean floor is a barren, 2-dimensional landscape. Rising atmospheric Carbon Dioxide levels at that time caused an acidification of the oceans.

“The knock-on effects on marine ecosystems can often be seen in the fossil record as a rapid decline in biodiversity and even a loss of trace fossils such as burrows and surface trails. The End Permian mass extinction saw a prolonged gap in burrowing animals such as worms and bivalves and because of this, the 3-dimensional benthic habitat became barren and 2-dimensional.”

Also a talented scientist and artist, Jenny sculpted this steampunk representation of a Harbour Ragworm and the Carbon Dioxide so influential to its eco-system.

Jenny is using a particularly resilient species of worm, the Habour Ragworm, to identify whether these patterns seen in the geological record could be repeated due to anthropogenic climate change.

“Similar patterns are beginning to occur today with rapidly declining populations of most vulnerable marine animals such as corals.”

Once again, I am amazed at the impact that small animals, microorganisms, and the mucus they secrete have had in shaping the planet we see today. It seems from the research Catherine and Jenny have showed me, and the results they will produce in the future, that these creatures are not finished shaping our landscapes just yet.

EPS will return in Slimy Landscapes 3.*

*suggestions for titles welcome!

DeepDust ICDP workshop in Norman, Oklahoma, USA discussed drilling the equatorial terrestrial Permian

From microbiology to geophysics – more than 50 international participants of the first DeepDust Workshop covered a wide range of topics. In Oklahoma researchers exchanged views on a possible international drilling project to study the continental geology of the Permian. During a change from the cold to a warm period, large ice masses melted. This may provide interesting insights into current and future climate developments.

After arriving from all around the globe and sharing a joyful ice breaker, the DeepDust workshop started with an introduction to the International Continental Drilling Program (ICDP) including its setup and possible support for projects. This was followed by an introduction to the Permian, highlighting the interest in Permian equatorial terrestrial geoarchives which may partly serve as Mars analogs. The need for a better understanding of this time period and setting was highlighted clearly. The first afternoon was spent with understanding the challenges of different possible drilling areas.

The second day was spent on an excursion where we saw Permian mudstones, including evaporites and siltstones in Oklahoma. The third day was mostly spent discussing key questions and how these may be answered. Discussions included practicalities such as obtaining site survey data and drill planning. The workshop ended with reviewing major objectives and how these may be achieved efficiently regarding, among others, drilling and funding.

Personally, I really enjoyed participating in such an international and focussed workshop. I learned a lot about the Permian, the Geology of Oklahoma and met many enthusiastic colleagues. I am looking forward to continuing pushing the DeepDust project forward.

The workshop participants in front of Permian mudstones in Oklahoma during the workshop field trip.