Friday, February 02, 2007

 

Metagenomics: Investigating the invisible life in our environment

A new comparative metagenomics method provides insights into the evolution of the smallest beings on Earth

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 [1], 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 lifestyles," Bork says. "This tells us that it is not easy to enter 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.

Source: European Molecular Biology Laboratory PR 2 February 2007

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Based on the Science paper:

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

C. von Mering, P. Hugenholtz, J. Raes, S. G. Tringe, T. Doerks, L. J. Jensen, N. Ward, P. Bork
Published online February 1 2007; 10.1126/science.1133420 (Science Express Reports)

The taxonomic composition of environmental communities is an important indicator of their ecology and function. Here, we use a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative and accurate picture of community composition than traditional rRNA-based approaches using polymerase chain reaction (PCR). By mapping marker genes from four diverse environmental data sets onto a reference species phylogeny, we show that certain communities evolve faster than others, determine preferred habitats for entire microbial clades, and provide evidence that such habitat preferences are often remarkably stable over time.

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[1] See:

Metagenomics: the science of biological diversity
By K. J. Shelswell

Shelswell, K. J. (2006). Metagenomics: the science of biological diversity. The Science Creative Quarterly, 2. Retrieved February 2, 2007 from http://www.scq.ubc.ca/?p=509.

For approximately 4.5 billion years, the Earth has been evolving from a barren volcanic landscape into the vibrant globe full of life that it is today. The first forms of life, small microorganisms, have been found in fossils from 3.5 billion years ago. Around 1.5 billion years ago, motile microorganisms emerged allowing life to migrate to different environments with different environmental conditions like increased exposure to ultraviolet radiation or higher temperatures. Microorganisms began to evolve with the changing environmental conditions of the planet.

These new environmental conditions, acting as selective pressures, drove the evolutionary process. They forced new species of organisms to evolve that were better suited to survival under particular environmental pressures. The evolution of new species generates biological diversity, which is represented by the number of different species in an environment. Over time, the evolutionary process has led to the development of more complex life forms such as trees, fish, and humans. A simple example of biological diversity is a comparison between a human and a monkey...

And the PLoS Computational Biology paper:

Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
Kevin Chen, Lior Pachter

The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

Citation: Chen K, Pachter L (2005) Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. PLoS Comput Biol 1(2): e24 doi:10.1371/journal.pcbi.0010024

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Recent posts include:

"Horizontal gene transfer adds to speed and complexity of evolution"

"Shotgun sequencing finds nanoorganisms"

"Cooperation among Micro-organisms"

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