Microorganisms make up more than a third of the Earth’s biomass. They are found in water, on land and even in our bodies, recycling nutrients, influencing the planet’s climate or causing diseases. Still, we know surprisingly little about the smallest beings that colonise Earth.
A new computational method to analyse environmental DNA samples, developed by researchers at the European Molecular Biology Laboratory (EMBL) in Heidelberg, now sheds light on the microbial composition of different habitats, from soil to water. The study, which will be published in this week’s online issue of the journal Science, also reveals that microbes evolve faster in some environments than in others and that they rather rarely change their habitat preferences over time.
Studying microorganisms has proven very difficult in the past, because most naturally occurring types do not grow in the lab. The rapidly growing field of environmental DNA sequencing, called metagenomics, now helps to overcome this problem. Instead of analysing the genome of a specific organism, scientists sequence all the DNA they find in environmental samples, ranging from seawater to soil. They collect vast amounts of sequence fragments, which contain genetic information of thousands of species forming communities that colonise a certain habitat.
“We have developed a new and very precise method to classify the microbial communities that are present in a given sample,” explains Peer Bork, joint coordinator of the Structural and Computational Biology Unit at EMBL. “We first identify informative DNA sequences in a sample and then map them onto the tree of life, a phylogeny of organisms with sequenced genomes, to find out which microbes are present and where yet unknown species fit into taxonomy and evolution.”
In this way, Bork and EMBL alumnus Christian von Mering classified microbial communities present in four very different environments: ocean surface, acidic underground mine water, whale bones from the deep sea and farm soil.
“Most of the DNA we found fits into the evolutionary ancient parts of the tree of life, which means that the organisms are probably not close relatives of the species sequenced and known so far,” says von Mering who carried out the research in Bork’s group. “Our novel method complements current classification attempts based on individual RNA molecules and also has additional unique features . It allows us to gain insight into the evolution of microbes in the context of their habitats.”
Comparing the datasets from different environments, the researchers discovered that microorganisms evolve at different speeds depending on their habitat. While organisms at the ocean surface evolve fairly rapidly, soil microbes only change slowly throughout evolution, perhaps partly due to long dormancy phases during winter.
In collaboration with Phil Hugenholtz and Susannah Green Tringe from the Joint Genome Institute in Walnut Creek, California, Bork and his colleagues also investigated whether habitat preferences of microbes have remained the same throughout evolution. “It turns out that most microbial lineages remain loyal to a certain environment for long periods of time, only very few are able to adapt to different life styles,” Bork says. “This tells us that it is not easy to intrude a new environment and compete with the established communities in it, which contradicts the longstanding belief that every microbe can potentially live everywhere.”
To investigate the invisible life on our planet further, samples of many different environments are being collected and analysed. Metagenomics experiments generating enormous amounts of data and new computational methods extracting meaningful information from it will provide a much better understanding of biodiversity on Earth in future.
Anna-Lynn Wegener | alfa
Upcycling of PET Bottles: New Ideas for Resource Cycles in Germany
25.06.2018 | Fraunhofer-Institut für Betriebsfestigkeit und Systemzuverlässigkeit LBF
Dry landscapes can increase disease transmission
20.06.2018 | Forschungsverbund Berlin e.V.
A new manufacturing technique uses a process similar to newspaper printing to form smoother and more flexible metals for making ultrafast electronic devices.
The low-cost process, developed by Purdue University researchers, combines tools already used in industry for manufacturing metals on a large scale, but uses...
For the first time ever, scientists have determined the cosmic origin of highest-energy neutrinos. A research group led by IceCube scientist Elisa Resconi, spokesperson of the Collaborative Research Center SFB1258 at the Technical University of Munich (TUM), provides an important piece of evidence that the particles detected by the IceCube neutrino telescope at the South Pole originate from a galaxy four billion light-years away from Earth.
To rule out other origins with certainty, the team led by neutrino physicist Elisa Resconi from the Technical University of Munich and multi-wavelength...
For the first time a team of researchers have discovered two different phases of magnetic skyrmions in a single material. Physicists of the Technical Universities of Munich and Dresden and the University of Cologne can now better study and understand the properties of these magnetic structures, which are important for both basic research and applications.
Whirlpools are an everyday experience in a bath tub: When the water is drained a circular vortex is formed. Typically, such whirls are rather stable. Similar...
Physicists working with Roland Wester at the University of Innsbruck have investigated if and how chemical reactions can be influenced by targeted vibrational excitation of the reactants. They were able to demonstrate that excitation with a laser beam does not affect the efficiency of a chemical exchange reaction and that the excited molecular group acts only as a spectator in the reaction.
A frequently used reaction in organic chemistry is nucleophilic substitution. It plays, for example, an important role in in the synthesis of new chemical...
Optical spectroscopy allows investigating the energy structure and dynamic properties of complex quantum systems. Researchers from the University of Würzburg present two new approaches of coherent two-dimensional spectroscopy.
"Put an excitation into the system and observe how it evolves." According to physicist Professor Tobias Brixner, this is the credo of optical spectroscopy....
13.07.2018 | Event News
12.07.2018 | Event News
03.07.2018 | Event News
20.07.2018 | Power and Electrical Engineering
20.07.2018 | Information Technology
20.07.2018 | Materials Sciences