Next-generation sequencing

"Next-generation", i.e. current generation, sequencing.

High throughput DNA sequencing technologies have developed extensively over the past decade, affecting many fields of biology. In microbial ecology, we aim to understand ecosystems, the communities of organisms they contain, and the complex networks of interactions between them. To do this we need to be able, firstly, to identify what organisms are present in an environment, and then to ask what roles they play and what niche they fill. To this end, the genome of an organism, or its complete genetic make-up, can be a very useful source of information. The genome of an organism can tell you not only what it is, and how it is related to other species, but also their role in ecological processes.

When we study entire ecosystems, one way to access this information is through the metagenome. Where a genome is the complete DNA sequence of an individual organism, the metagenome is the genetic complement of all the organisms in an environment. Most bacteria cannot be grown in the lab in pure cultures. So to get enough DNA from them to be able to sequence it, we have to sample metagenomes, sequence all the DNA that is in there, and then tease apart what we get back to reconstruct genomes of individual species.

High throughput sequencing makes it feasible to get back large amounts of DNA sequence, enough to recover almost the complete genetic information for the abundant microbial populations that are out there in the oceans. These massive amounts of data are generated in collaboration with our partners at the Max Planck-Genome-centre in Cologne, who provide the critical infrastructure, know-how, and generate the sequence data for us.

Once we have the data in hand, we have sizeable high-performance computing resources in house that we use to reconstruct the original DNA sequences. From the reconstructed DNA sequence, we can ask questions about the identity and evolutionary relationships of different populations, their abundance in different locations or at different times, the extent of genetic variation, and we can make predictions about what role these organisms play in their community.

What have we learned from using these sequencing technologies recently?

In our department, we investigate carbon cycling in a variety of different microbial habitats.

In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes

In this study, we recovered genomes from metagenomes and identified clusters of genes known as polysaccharide utilisation loci (PULs) that are used to degrade specific types of polysaccharide structure. We found that the diversity of important polysaccharide food sources for the bacteria was actually fairly limited, in contrast to what might have been expected based on the high complexity of species and functions seen in many other microbial habitats.

Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota

We identified populations of archaea (the ‘third domain’ of life), again from metagenomes, that were abundant at different times of the year in the North Sea. Specifically, one population was more abundant in the summer months, and had bigger genomes, in contrast to the ‘winter’ population. We consider the different ecological niches of these populations to depend in part on the availability of organic matter, which is lower in the winter than in summer, and the smaller genome sizes thus reflect the restrictions of the lean months.

Microbial metal‐sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

Deep-sea hydrothermal vents are locations where the seafloor opens as tectonic plates move apart, releasing geothermally heated water. The water discharged is rich in minerals, which can be deposited to form large chimneys, as well as nutrients, which make them biological hotspots. These areas are not permanently active, however, and in this study, we identified autotrophic bacteria (those that do not need to consume organic matter from other organisms, and instead create their own food and biomass from mineral sources) at inactive chimneys related to those that would be found at actively venting sites. This activity raises the possibility that these processes may be more widespread and longer-lasting than previously assumed.