Abstract
Bacteria play a pivotal role in engineered systems such as wastewater treatment plants. Obtaining genomes of the bacteria provides the genetic potential of the system and also allows studies of in situ functions through transcriptomics and proteomics. Hence, it enables correlations of operational parameters with functions of specific bacteria within the ecosystems in order to decipher principles that might be used to control and predict ecosystem performance.
The main bottleneck in obtaining genomes from the environment is that the vast majority of bacteria are not readily cultured. Metagenomics, the sequencing of bulk genomic DNA from environmental samples, has the potential to provide genomes of this uncultured majority. However, so far only few bacterial genomes have been obtained from metagenomic data.
In this study we present a new approach to obtain individual genomes from metagenomes. We deeply sequenced two metagenomes from the same environmental sample, but using two independent DNA extraction methods, which resulted in different population abundances. This allowed sequence-composition independent binning of numerous high quality draft genomes from both high and low abundant members of the community. The assembled genomes include many of the process-critical bacteria involved in wastewater treatment, such as Competibacter, Tetrasphaera and TM7.
The approach is not limited to different extraction methods, but can be applied to any treatment that results in different relative abundance of the bacteria, including time-series. Using more than two metagenomes increases the binning resolution and hence the number of genomes that can be extracted.
We are currently at a tipping point in microbial ecology – in the future it will be fast, cheap and easy to obtain genomes directly from the environment. We can only begin to grasp the impact of having genomes available for the full tree of life on the development of environmental biotechnology.
The main bottleneck in obtaining genomes from the environment is that the vast majority of bacteria are not readily cultured. Metagenomics, the sequencing of bulk genomic DNA from environmental samples, has the potential to provide genomes of this uncultured majority. However, so far only few bacterial genomes have been obtained from metagenomic data.
In this study we present a new approach to obtain individual genomes from metagenomes. We deeply sequenced two metagenomes from the same environmental sample, but using two independent DNA extraction methods, which resulted in different population abundances. This allowed sequence-composition independent binning of numerous high quality draft genomes from both high and low abundant members of the community. The assembled genomes include many of the process-critical bacteria involved in wastewater treatment, such as Competibacter, Tetrasphaera and TM7.
The approach is not limited to different extraction methods, but can be applied to any treatment that results in different relative abundance of the bacteria, including time-series. Using more than two metagenomes increases the binning resolution and hence the number of genomes that can be extracted.
We are currently at a tipping point in microbial ecology – in the future it will be fast, cheap and easy to obtain genomes directly from the environment. We can only begin to grasp the impact of having genomes available for the full tree of life on the development of environmental biotechnology.
| Originalsprog | Engelsk |
|---|---|
| Publikationsdato | 2013 |
| Status | Udgivet - 2013 |
| Begivenhed | 2nd International Water Research Conference: WaterRes2013 - Singapore, Singapore Varighed: 20 jan. 2013 → 23 jan. 2013 Konferencens nummer: 2 |
Konference
| Konference | 2nd International Water Research Conference |
|---|---|
| Nummer | 2 |
| Land/Område | Singapore |
| By | Singapore |
| Periode | 20/01/2013 → 23/01/2013 |