In a paper appearing in Nature Biotechnology August 17, a collaboration headed by researchers at the University of Washington and the U.S. Department of Energy Joint Genome Institute (DOE JGI) describes a novel approach for extracting single genomes and discerning specific microbial capabilities from mixed community ("metagenomic") sequence data.
For the first time, using an enrichment technique applied to microbial community samples, the research team explored the sediments in Lake Washington, bordering Seattle, WA and characterized biochemical pathways associated with nitrogen cycling and methane utilization, important for understanding methane generation and consumption by microbes. Methane is both a greenhouse gas and a potential energy source.
"Even if you have lots of sequence, for complex communities it still doesn't tell you which organism is responsible for which function," said the paper's senior author Ludmila Chistoserdova, a microbiologist at the University of Washington. "This publication presents an approach, via simplification and targeted metagenomic sequencing, of how you can go after the function in the environment."
Chistoserdova and colleagues study microbes that oxidize single-carbon compounds such as methane, methanol and methylated amines, which are compounds contributing to the greenhouse effect and are part of the global carbon cycle.
"To utilize these single-carbon compounds, organisms employ very specialized metabolism," said Chistoserdova. "We suspect that in the environment, there are novel versions of this metabolism, and possibly completely novel pathways."
Most of the microbes that oxidize single-carbon compounds are unculturable and therefore unknown, as are the vast majority of microbes on Earth. To find species of interest, the researchers sequenced microbial communities from Lake Washington sediment samples, Chistoserdova said, because lake sediment is known to be a site of high methane consumption. However, these sediment samples contained over 5,000 species of microbes performing a complex, interconnected array of biochemical tasks.
To enrich the samples for the microbes of interest, the researchers adapted a technique called stable isotope probing. This is the first time the technique has been used on a microbial community, Chistoserdova said. The researchers used five different single-carbon compounds labeled with a heavy isotope of carbon, and fed each compound to a separate sediment sample. The microbes that could consume the compound incorporated the labeled carbon into their DNA, Chistoserdova said, while organisms that couldn't use the compound did not incorporate the label. The labeled DNA was then separated out and sequenced. In this way, microbial "subsamples" were produced that were highly enriched for organisms that could metabolize methane, methanol, methylated amines, formaldehyde and formate.
The functionally enriched samples contained far fewer microbes than the total sample, Chistoserdova said. The sample that was fed methylated amines was simple enough that the group was able to extract the entire genome of a novel microbe, Methylotenera mobilis, that normally comprises less than half a percent of the community, but appears to be a first responder to methylated amines in the environment. The researchers were able to construct much of M. mobilis' biochemistry, and predict that it is also involved in nitrogen cycling, demonstrating the utility of metagenomic analysis.
The DOE JGI performed the sequencing and assembly of these complex metagenomic data sets. The complexity of the community's sequence samples created new challenges for genome assembly. "It is very important for metagenomic assemblies to rely on high-quality reads," said Alla Lapidus, microbial geneticist at the DOE JGI and co-author on the paper. If some of the sequence is of low quality, she said, it can lead to errors in assembly and gene annotation.
Because of the need for higher quality control, Lapidus said, the DOE JGI developed a new quality control approach that involves a computer tool called LUCY to trim out low-quality sequence in combination with the Paracel Genome Assembler, which appeared to be more appropriate for metagenomic assemblies. This approach was pioneered on the Lake Washington project, Lapidus said, and due to its superior results it is now the standard metagenomic assembly method at the DOE JGI.
"The DOE JGI's unique Integrated Microbial Genomics with Microbiome Samples (IMG/M) [http://img.jgi.doe.gov/m] data management system was used for detailed annotation, and was instrumental for efficient comparative analysis and metabolic reconstruction of the samples," Lapidus said.
Michael Galperin, a microbial geneticist at the National Center for Biotechnology Information at the National Institutes of Health, who was not involved in the study, said in an email that the paper describes "an interesting novel approach" and the results "constitute a significant advance in the emerging discipline of metagenomics."
"I think other people can use the same approach in different environments, as long as they have an enrichment technique," Chistoserdova said. "For us this work is just the beginning, because now we will be using this metagenomic sequence as a scaffold for downstream experiments in our lake."
Further reports about: > Chistoserdova > DOE > Genome > JGI > Lapidus > Methane > Methanol > Sediment > amines > compound > greenhouse effect > metagenomic > metagenomic sequencing > methylated > methylated amines > microbe > microbes > microbial > organism > oxidize single-carbon compounds > single-carbon
Symbiotic bacteria: from hitchhiker to beetle bodyguard
28.04.2017 | Johannes Gutenberg-Universität Mainz
Nose2Brain – Better Therapy for Multiple Sclerosis
28.04.2017 | Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB
More and more automobile companies are focusing on body parts made of carbon fiber reinforced plastics (CFRP). However, manufacturing and repair costs must be further reduced in order to make CFRP more economical in use. Together with the Volkswagen AG and five other partners in the project HolQueSt 3D, the Laser Zentrum Hannover e.V. (LZH) has developed laser processes for the automatic trimming, drilling and repair of three-dimensional components.
Automated manufacturing processes are the basis for ultimately establishing the series production of CFRP components. In the project HolQueSt 3D, the LZH has...
Reflecting the structure of composites found in nature and the ancient world, researchers at the University of Illinois at Urbana-Champaign have synthesized thin carbon nanotube (CNT) textiles that exhibit both high electrical conductivity and a level of toughness that is about fifty times higher than copper films, currently used in electronics.
"The structural robustness of thin metal films has significant importance for the reliable operation of smart skin and flexible electronics including...
The nearby, giant radio galaxy M87 hosts a supermassive black hole (BH) and is well-known for its bright jet dominating the spectrum over ten orders of magnitude in frequency. Due to its proximity, jet prominence, and the large black hole mass, M87 is the best laboratory for investigating the formation, acceleration, and collimation of relativistic jets. A research team led by Silke Britzen from the Max Planck Institute for Radio Astronomy in Bonn, Germany, has found strong indication for turbulent processes connecting the accretion disk and the jet of that galaxy providing insights into the longstanding problem of the origin of astrophysical jets.
Supermassive black holes form some of the most enigmatic phenomena in astrophysics. Their enormous energy output is supposed to be generated by the...
The probability to find a certain number of photons inside a laser pulse usually corresponds to a classical distribution of independent events, the so-called...
Microprocessors based on atomically thin materials hold the promise of the evolution of traditional processors as well as new applications in the field of flexible electronics. Now, a TU Wien research team led by Thomas Müller has made a breakthrough in this field as part of an ongoing research project.
Two-dimensional materials, or 2D materials for short, are extremely versatile, although – or often more precisely because – they are made up of just one or a...
28.04.2017 | Event News
20.04.2017 | Event News
18.04.2017 | Event News
28.04.2017 | Medical Engineering
28.04.2017 | Earth Sciences
28.04.2017 | Life Sciences