Ancient bird preen glands uncovered!

The following is a news piece from UCD that features my latest paper on fossil preen (uropygial) glands and associated lipids preserved in a 48-million-year-old Eocene bird. Links to other media coverage are feature below this news piece.

Researchers have shown that a well-preserved preen gland in a 48-million-year-old bird fossil contains its original fat molecules.

The fossil is from the famous Messel locality in Germany, well known to preserve birds, mammals, fish, reptiles, insects and leaves with exceptional details, including stomach contents and original colour.

“Animal soft tissue fossils are rare discoveries but, when found, provide exquisite insight into past biological diversity and fossil formation – that is why Messel is so special” said Dr. Shane O’Reilly, UCD geochemist and lead author on the study.

The study came about after co-author Gerald Mayr – an ornithologist from the Senckenberg Natural History Museum who has studied birdfossils from Messel for over two decades –  and the Messel field crew unearthed a bird fossil that appeared to contain intact preen glands.

The preen gland, also called the uropygial gland, is an important gland in modern birds that produces a waxy oil birds use for waterproofing and maintaining the health of their feathers.

Dr. Mayr and his colleague, Dr. Jakob Vinther – a palaeobiologist from the University of Bristol and also co-author on the study – had been waiting for such a find for a number of years.

“Usually, only melanin is preserved in these sorts of fossils; all the keratin and other proteins are lost” said Dr. Vinther.

“Previously collected fossils have all been transferred to a plate of resin and covered in varnish, which would complicate any analysis of the organic composition of the glands” he added.

Jakob and Gerald quickly contacted Professor Roger Summons, a geochemist in MIT and global expert in studying molecular fossils in petroleum and sedimentary rocks, to look at chemical composition of the wax material.

“I was a postdoctoral researcher working with Roger and jumped at the opportunity to get involved” said Dr. O’Reilly.

“For decades, organic geochemists have been studying molecular fossils in petroleum and sedimentary rocks and making important discoveries about the history of life on Earth. Surprisingly, we have paid relatively little attention to preservation of organic molecules in vertebrate bone fossils and soft tissues fossil” said Dr. O’Reilly.

Using a technique called mass spectrometry to look at the chemical composition of a tiny amount of the fossil wax, the geochemist found distinct fat, or lipid, molecules preserved within the gland that were very different to the surround sediment and other parts of the fossil.

“By studying the fossils within the fossil, and picking out the molecules coming from the algae and plants that made up the sediment, we could clearly see that a portion of the original waxy molecules that make up preen oil were preserved in the fossil gland” said Dr. O’Reilly.

“Finding the intact preen glands and the fat molecules within them is a milestone in our understanding of fossil formation as it shows that fat molecules can preserve well and are important for preservation of certain animal soft tissues” he added.

When asked about what next, Dr. O’Reilly said: “This research raises exciting new questions and research directions. How far back in time can we find fossil preen glands? What other fat-rich animal tissues are preserved at the molecular level? Did feathered dinosaurs also engage in preening?”



‘Preservation of uropygial gland lipids in a 48-million-year-old bird’ by S. O’Reilly, R. Summons, G. Mayr and J. Vinther in Proceedings of the Royal Society B


Sven Tränkner, Gerald Mayr, Sonja Wedmann, Michael Ackermann


Shane O’Reilly,


Additional media coverage of this research:

Nature Research Highlights

Discover Magazine

Science Daily

MIT news


Land and soil mismanagement in Ireland: Problems and Solutions

Soil is a dynamic living substance vital for life on Earth. It is also one of our most diverse ecosystems, with numerous studies showing how thousands of different microbial species can live in one single gram of soil.

Soil is also the most fundamental requirement for agriculture and has been feeding global populations since the dawn of agricultural practices about 10,000 years ago. Soil takes thousands of years to form, yet it can be degraded in an instant due to gross mismanagement by humankind.

There is ample historical evidence that civilisations mismanaging their soils collapsed as a result. It is also clear that we are also currently facing a global soil crisis and urgent action is needed if we wish to avoid disaster in the near future.

This global soil crisis has resulted from radical land use change and poor agricultural practices and the consequences are widespread – soil erosion, desertification, accumulation of salinity, nutrient loss and pollution.

Soil degradation has now affected about one-third of global land area. The UN’s Food and Agriculture Organisation (FAO) estimates that about one per cent of the global land area is degraded each year.

In total, it is estimated that 33 per cent of arable land has been lost to soil erosion or pollution. At this rate, and with current practices and population growth, the world’s topsoil could be gone withing decades.

Why is soil organic carbon important?

Organic molecules are the building blocks of life. Generally, the most important factor that determines healthy or good quality soil is organic matter.

The word ‘organic’ here describes the molecules of carbon that bond together, often containing hydrogen, oxygen and nitrogen. In soil, the majority of organic matter is composed of an insoluble residue from plants and microorganism exudates – a fluid discharged from cells – and their decaying remains. Or as it is more commonly known – humus.

Despite normally making up less than 5 per cent of soil by weight, soil organic carbon supplies essential nutrients for agricultural and biological productivity and helps maintain soil structure and water content.

Loss of soil organic carbon has been caused by desertification, deforestation, soil erosion and intensive crop production. Globally it is estimated that between 50 and 70 per cent of the world’s cultivated soils have now lost their original carbon stock.

The consequences of this include substantial decreases in soil quality and biodiversity and changes to the physical properties of soil. While excessive amounts of soil organic carbon are being eroded, leached or respired to the atmosphere, they are not being replaced by sufficient amounts of new organic carbon.

Carbon Cycle

Soil is also one of the largest pools of carbon on Earth and a major component of the global carbon cycle. There is three times more carbon in the soil than in the atmosphere, and over four times more than in all land plants combined.

Substantial land use change across the globe, together with historical and modern day agricultural practices, has caused widespread loss of soil carbon to the atmosphere as carbon dioxide. This is second only to fossil fuels as a source of carbon dioxide fueling anthropogenic climate change.

Therefore, strategies to minimise soil degradation and restore soil health will have a double impact, both reducing carbon dioxide loss and increasing carbon dioxide uptake and sequestration in plants and soil. But are we doing enough to lessen our impact on our soil?

Land and soil mismanagement in Ireland

While lauded for our lush green landscape, we have witnessed and been responsible for large scale impacts on our soil dating back hundreds of years. For example, both deforestation in the 18th century and famine and depopulation in the 19th century brought about wholesale changes on our island.

More recently, increases in pastoral grassland and the spread of urban areas have had major impacts on our soil. Arguably the most critical issue in Ireland relates to the loss of peatlands.

Globally, peatlands only cover only around two or three per cent of land surface but store up to 30 per cent of total soil carbon making peatlands vitally important carbon sinks. They also support unique biodiversity.

Peatlands are an important wetland ecosystem, accounting for 15 per cent of Ireland’s land area. We, in fact, hold eight per cent of the world’s blanket bogs on our small island.

Unfortunately, only about 21 per cent of our peatlands is in relatively intact conditions, with turf-cutting, industrial peat extraction, commercial afforestation and urban development taking its toll on our bogs.

In addition to stresses faced by peatlands in northern temperate locations such as Ireland, tropical peatlands are also being destroyed by the likes of the spread of palm oil plantations.

Stop Treating Soil like Dirt

It is clear that maintaining our soils is fundamentally tied to protecting our economy, food, health, biodiversity and climate. So what can we do to protect and restore our soil?

There are a number of sustainable management strategies that can be used to restore the organic content of soil, including manuring, no-tillage, conservation tillage, rotating crops, cover cropping and agroforestry.

Numerous studies have shown that sustainable agriculture can match or exceed productivity and profit and increase soil organic carbon, while also reducing environmental impacts. Unfortunately, only a fraction of global agriculture uses sustainable techniques at present.

Currently, we have EU legislation to protect water and air, but, despite its importance and the recognised global crisis we have on our hands, we do not have an EU Directive dedicated to protecting our soils. Without legislation, we have little chance of addressing soil degradation.

People4Soil is a campaign run by the Environmental Pillar that aims to change this by using a European Citizen’s Initiative petition to call on the European Commission to pass a dedicated Soil Directive.

Read about the People4Soil campaign and sign the petition here.

A version of this article appeared in the Green News on May 27th 2017.

The Paris Climate Agreement & recent news

Below is a short video summarizing the 2015 Paris Climate Conference Agreement (also known as COP21 – ‘Conference of Parties 21’), which was approved almost a year ago. This is the first global climate deal since the Kyoto Protocol, and aims to limit global average temperature changes to within 2°C climate change, and to combat the unavoidable impacts on people and the Earth. It follows on from Kyoto Protocol and its Doha Amendament, (which ends in 2020) that suffered from limited overall participation.

The Paris Agreement was ratified on 4th October this year by the EU, thereby reaching the threshold of countries needed to come into force. It officially came into force on 4th November. The agreement will encompasses continued reduction of emissions (relative to 1990 levels), increased investment and transitioning to renewable energy technology, increased energy efficiency and ensuring energy security.

Despite concerns of the US support for the Paris Agreement, the EU announced it is driving ahead and announced this week it will reveal plans to eliminate subsidies on power generation by coal, gas and peat, according to a report yesterday in the Financial Times. A recent article in the Huffington Post, explored the options the Trump Presidency has in withdrawing from the Paris commitments, and also what diplomatic and legal risks may be involved for the US on doing so. The article ends on an optimistic note “no matter the reluctance of Trump’s administration to take further action to reduce greenhouse gas emissions, the civil society is already moving forward”

Recent UCD news piece

Below is a reproduced UCD news piece that first appeared here on UCD School of Earth Sciences.


Geobiology and Molecular Fossils

Geobiology is the study of the interactions and interrelationships between the physical Earth and biology, especially the ‘unseen’ microbial majority. As a multidisciplinary and highly integrated discipline Geobiology is relatively young, but the types of questions it addresses have been puzzling scientists for generations – How did life arise and diversify on early Earth? How has biology affected global physical and chemical processes throughout Earth’s history and today? What are the major triggers that drive evolution and diversification of life? These questions are some of the most fundamentally important scientific questions that we can hope to answer.

In September, an exciting yet controversial paper in Nature reported new physical and chemical evidence for microbial life preserved in the Isua Greenstone Belt, and if correct extends the evidence of life from 3500 Ma to 3700 Ma! The preserved laminated microbial mat structures that accrete to form stromatolites. These rocks, with other reported examples, are the scant remains of extensive shallow marine, carbonate-producing environments from Archean Earth. However, while relatively rare, modern examples such as those in The Bahamas and Turks and Caicos provide an important alternative to understanding life and environments on early Earth. In July, a team of geologists, sedimentologists, microbiologists, geochemists and historians from Caltech, Harvard, MIT, Dartmouth College and UC Berkeley gathered on Little Ambergris Cay in the Turks and Caicos Islands to study some of the best modern analogs for these ancient settings and hotspots for early life. This was funded by the Agouron Institute.


Aerial View of Little Ambergris Cay microbial mats and ooiltic sands offshore (Image Credit: Agouron Team)


Shane sampling dense microbial mats on Little Ambergris Cay, Turks & Caicos. (Image Credit: Agouron Team)


MIT and UCD Postdoctoral Fellow, Dr. Shane O’Reilly, was a member of the team. Shane is an organic and isotope biogeochemist, whereby he studies biomolecules and their relict geomolecules, or molecular fossils, in rocks, sediment and soil. These molecules (often called biomarkers) provide a window into the complex molecular world of organic matter. Organic matter is essentially the currency of life and amazingly certain organic molecules can be preserved over tens to hundreds of millions of years. In addition to fueling our global industrial economy, these molecular fossils provide important insight into past life and environments. For more information on molecular fossils, check out this recent public lecture Shane gave as part of the NOVA PBS CaféSci Boston, and the accompanying MIT News piece.


The basic principle of organic geochemistry and molecular fossils


Together with microbial mats, non-skeletal carbonate grains called ooids were common on Proterozoic and Archean Earth. These concentrically-layered accretionary grains have puzzled scientists for over a century, but a recent paper published by Shane in the journal Geobiology, indicates that the organic matter that is ubiquitous within ooids is derived from microbial biofilms that were once growing on grain surfaces. This has important implications for understanding the role of organic matter and microbes in ooid formation on early Earth. The intricate balance between physical, chemical and biological factors that are involved in ooid formation remain to be fully elucidated, and is one of the principle aims of the Agouron trip to the Turks and Caicos.



The results from microbial mat and ooid studies from the Turks and Caicos trip will be presented in four abstracts at the upcoming American Geophysical Union Fall Meeting in San Francisco in mid-December. This will be within a session celebrating ‘15 Years of Geobiology’. If the first 15 years of Geobiology are anything to go by, then the next 15 will be worth paying very close attention to!


The ‘gassy’ global seafloor

Methane is a potent greenhouse gas with a multitude of biological as well as non-biological sources. It is also one of the main targets for NASA and European/Russian missions on Mars. One of the most exciting recent advances in understanding Earth’s methane cycle has been the recognition that methane seepage from marine seabed is globally widespread. The primary sink of this methane, which prevents the vast majority of it being released into the water and into the atmosphere, is consumption in sediment by ‘methanothrophic’ archaea. These archaea often work together with sulfate reducing bacteria to consume the methane and produce calcium carbonate rock and sulfide. An important reservoir of methane are gas hydrates, which exist of solid methane/water complexes under specific temperature/pressure conditions in marine sediments.

Check out the abundant shallow methane seepage environments on Dublin’s doorstep, just a few kilometres into the Irish Sea by these papers I authored and co-authored;

O’Reilly et al. (2014) Marine Geology

Van Landeghem et al. (2015) Geo-Marine Letters

Also check out these cool videos from the E/V Nautilus on the East coast of North America.


Recent paper in Geobiology



Here is a link to my recent paper from the Summons Lab where I use molecular fossil lipids bound within ooid grains to try to reconstruct microbial taxa and processes that are associated with ooid formation. Ooids were common carbonate sands in Precambrian Earth and have puzzled and intrigued geologists for well over a hundred years. This paper makes significant advances and opens up a number of interesting questions and researching directions! Feel free to get in touch if you want more info or want to share some ideas.