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Fishing for DNA – A drilling core reveals the history of an entire ecosystem

Prof. Dr. Michael Hofreiter. Photo: Karla Fritze.
Photo :
Prof. Dr. Michael Hofreiter. Photo: Karla Fritze.

How wild horses and chickens were bred thousands of years ago, which species were closely related to the long-extinct European straight-tusked elephant, and even whether cave bears used the same winter quarters every year – molecular biologist Michael Hofreiter knows it all. He “hunts” long-extinct animals by analyzing so-called ancient DNA that has, for instance, been extracted from archaeological skeletons. He is currently working with evolutionary biologists and geoscientists on a method for reconstructing the development of an entire ecosystem over thousands of years. To do this, they go “fishing” for DNA in a drilling core – on a very large scale.

Strictly speaking, Michael Hofreiter is a gatherer. The Schleich figurines on his office desk give it away. “These are models of some of the animal species I have researched,” Hofreiter explains. They include sharks, small horses, mammoths, and Macrauchenia patachonica, the “long-necked llama” Charles Darwin referred to as the “strangest animal ever discovered”. But Hofreiter did not hunt them: Most of them have been extinct for thousands of years. He finds the few traces that remain of them in well-preserved skeletons, sediment layers, or permafrost soil. As soon as samples are retrieved, Hofreiter and his team begin their molecular biological search. In what are often heavily decayed DNA remains, they look for sections or unique markers that allow individual species to be identified. “Just as a box of cereal is identified at the checkout by a barcode, so too can an organism be identified by a specific DNA sequence,” the researcher explains. To do this, the unique DNA section of the respective species is synthesized, its double helix separated by heat, and half of it is applied to slides – in large quantities. With this DNA “fishing pole”, the researchers go “fishing” in the sample for the relevant, complementary strand. If it is there, it will “stick”. Next, the order of its building blocks – the so-called DNA sequence – is determined and only after this barcoding is complete, the researcher can interpret all genetic information obtained and compare it, for instance, to that of related, modern species. The disadvantage is that you have to know roughly what you are looking for – which organism, or at least which group of organisms.

Instead of 96 DNA sequences, 6 billion can be analyzed at once

Standing in the laboratory, analyzing DNA for days on end – this is also how Hofreiter’s career as a molecular biologist began. Gene sequencing was still in its infancy not so long ago. “Back then I sequenced radioactively,” he says with a laugh. “At first, you could analyze 96 DNA sections at a time.” Today, high performance sequencers can do 6 billion sequences per run – in about 24 hours. Next Generation Sequencing (NGS) is the name of the process that revolutionized working with genetic material. In the laboratory of Hofreiter’s research team sits a black box that looks like a conventional printer. In fact, it is a small sequencer that can do “only” some 400 million sequences per run – more than enough to keep the researchers busy for weeks. Their main task is analyzing bioinformatic data. “NGS allows us to sequence vast quantities of DNA,” Hofreiter explains. “The method is also very well suited for old DNA, since it allows us to analyze the remaining sections, which are often very short.”

New technological developments like NGS enable molecular biologists to not only search samples for individual organisms but also to analyze large quantities of DNA simultaneously. Metabarcoding is the method with which experts analyze a sample’s so-called environmental DNA, with many different genetic traces. This, too, requires “fishing”, as Hofreiter explains: “The complete sequencing of such a wild mix of DNA would take forever.” That is why in metabarcoding short and less specific sequences – that may be typical of several species – are synthesized and used as “fishing poles”. This allows researchers to isolate genetic material of the species they are interested in and identify them more precisely later by identifying species-specific DNA sections. An entire ecosystem can, then, be described in its diversity, which could lead to major research advancements in biodiversity in particular.

Bit by bit, the drilling core is searched for old DNA

Michael Hofreiter has joined forces with evolutionary biologist Prof. Dr. Ralph Tiedemann and geoscientist Prof. Dr. Martin Trauth from Potsdam in order to reconstruct through metabarcoding the diversity and the development of an ecosystem over a long period – and not just anywhere. In fact, they go where old DNA is very hard to find: in the tropical regions of East Africa. “The hotter the weather, the lower the chances of finding old DNA,” the researcher explains. Because the genetic material is better preserved in deeper deposits, the researchers are planning to extract the DNA from a drilling core. This is absolutely a pilot project, so the methods for analyzing the sediments have yet to be found. And while initial random tests using conventional methods were not able to detect old DNA, NGS allowed the researchers to make a discovery: “We produced some million sequences and compared them with databases – and actually detected ancient DNA,” the biologist explains. “In low concentrations but enough to work with.”

The idea underlying the project is as simple as it is unusual: With the help of metabarcoding the researchers can “fish” the sediment samples of the drilling core for the DNA of numerous species. As “bait” they synthesize the unique marker gene sections of the species they hope to find and, as Hofreiter explains, not just any species: “On the one hand, we are on the lookout for species we assume lived in East Africa about 100,000 or 200,000 years ago.” This could be determined to some extent by looking at the current distribution of species. The researchers, though, are on the lookout for specific organisms whose existence says more about the ecosystem they were living in. “We are looking for organisms that are ecological indicators of, for instance, salt content, oxygen concentration, temperature, and other features.” These analyses are then made with samples taken from different sections of the drilling core – and, thus, from different periods.

Data say a lot about the connection between climate change and species development 

The project is a good example of how geoscientists and biologists can intensify their collaboration – and practically benefit from each other. After all, it is a novelty that biologists can search drilling cores for ancient DNA and that geoscientists can gain insight into climatic development by identifying genetic material. 

For the pilot project, the researchers are now designing marker genes for “only” several dozen species and are analyzing the environmental DNA of only a dozen sediment samples. This should suffice to test their method. “If we are successful, we will apply for a full project,” Hofreiter says. If this happens, the researchers would literally take the drilling core apart and “fish” hundreds of samples for several hundred species. 

“This would allow us to draw conclusions about the connection between climate change and species development and understand, for instance, which species lived under what climatic conditions and adapted and which ones went extinct,” Hofreiter explains. “In fact, we could even make predictions: Some 120,000 years ago it was so warm that hippos swam in the River Thames. If temperatures rise again, we might see them swimming under Tower Bridge one day,” he says with a smile.

In genetics, barcoding refers to a method by which a DNA sample is identified as belonging to a particular species. A certain, species-specific sequence of base pairs is used for identification – like a barcode on a product label.

The project

DNA Metabarcoding of phyto- and zooplankton in East African lake sediments as proxies for past environmental perturbation 
Participants: Professor Dr. Michael Hofreiter, Professor Dr. Ralph Tiedemann, apl. Professor Dr. Martin Trauth
Funding: German Research Foundation (DFG)
Duration: 2016–2018

The researcher

Prof. Dr. Michael Hofreiter studied biology in Munich and earned his PhD at Leipzig University in 2002. Until 2010 he worked at the Max Planck Institute for Evolutionary Anthropology in Leipzig. He held a professorship at the University of York from 2009 to 2013, when he was appointed Professor of General Zoology/Evolutionary Adaptive Genomics at the University of Potsdam.
Universität Potsdam
Institut für Biochemie und Biologie
Karl-Liebknecht-Str. 24–25
14476 Potsdam
Email to: michael.hofreiteruni-potsdamde

This research is linked to the research initiative NEXUS: Earth Surface Dynamics, which clusters approaches from various scientific disciplines in the Berlin-Brandenburg area within the overarching theme of Earth surface dynamics. The University of Potsdam, along with its partnering institutions the Helmholtz-Centre Potsdam - German Research Centre for Geosciences (GFZ), the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI) and partners from the Potsdam Institute for Climate Impact Research (PIK), the Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science (MfN) and the Technische Universität Berlin (TUB) therefore combines the outstanding expertise from geo-, bio-, climate and data sciences.  

Text: Matthias Zimmermann
Translation: Monika Wilke
Online published by: Marieke Bäumer
Contact us: onlineredaktionuni-potsdamde 

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