CPHx: Kåre Lehman Nielsen: Metagenomics and metatranscriptomics of complex bacterial communities

Copenhagenomics is just about to get under way and the first speaker is Kåre Lehmann Nielsen from the University of Aalborg, with a talk titled “Metagenomics & metatranscriptomics of complex communities”.  My spell checker is already confused, but I’m certain that the audience won’t be.

I should warn everyone now that if the occasional “ø” sneaks in inappropriately, it’s because I’m using a Danish keyboard, lent to me by CLC bio, and the ø sits exactly where the apostrophe did on my own laptop. (Which, by the way, is still not working.)  However, unlike AGBT, not everyone here seems to have the latest and greatest products from Apple, so this Dell fits right in.

Ok, well with that out of the way, lets get to the talks!

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Metagenomics & metatranscriptomics of complex communities

Complex bacterial systems are a great model system for more complex being.  Only 1% of bacterial can thrive in a monoculture – and those that do don’t behave the same way as when they’re in communities. Thus, investigating communities make much more interesting models, with great potential for future applications.

One great example is in wastewater treatment, where we can use communities to do bio-remediation.  We know the inputs and we know the outputs – and this is currently the worlds largest biotechnology industry.  As water resources become more important, and as photospohrus production becomes more limited, we’re going to have to start to worry about harvesting and re-using this resource. (Phosphorus is also not evenly distributed – and it’s absolutely necessary to do aquaculture.  We may see cartels for it’s production, like we do with oil now.)

Phosphorus can be re-harvested in a two step process, using an anaerobic tank, followed by an aerobic tank. Aacetate is used up in the first, and phosporus is precipitated in the second. [probably simplified]

A pilot project was done on this topic over 4 years.  Many different methods have been used to study the communities of bacteria.  Over 25 full-scale plants, there is a relatively stable community.  (Quantitative FISH used)

Communities are remarkably stable.  Over time, not a lot changes, for any given plant.  It fluctuates, but the core-members does not change.

Models of the various communities and their roles exist.  However, whatøs interesting is understanding why sometimes the system breaks down.  Currently, we can observe it, and we can treat it, but we don’t understand why it happens.

To do this, we can look at the ecosystem using meta-{genomics,proteomics,genomics,transcriptomics}.

Many of the bacteria will not grow on their own, but you can enrich for them, up to 50-60%, which enables many techniques to be applied.  Some examples given using Accumulibacter.  Under anaerobic conditions, it uses Acetate to grow, storing energy for later use.  Not much growth occurs. Under aerobic conditions, the Accumulibacter uses the energy already available, soaking up phosphate and grow biomass, while other bacteria are competing for energy.

A de novo assembly was done, [skipping details].  Most contigs are poor/short – complex communities are difficult to work with.

Top 10 bacteria include things already known and expected. Using the contig assemblies, you can also compare to references, which shows that in each species found, there are huge number of non-reference subspecies.  % identity tapers off, showing more and more distant relatives are present.

Unfortunately, there are only a few reference genomes that are available for wastewater species.

Microbial diversity from FISH and meta genomics.  Actually, it’s poor.  Metagenomic data doesn’t work particularly well, as some types of bacteria are difficult to extract DNA from, and some are hard to quantify [poor references?]

There are a few other interesting things that can bee seen, such as the lack of photosynthesis genes being found, however, you do see surges in other groups such as phosporus metabolism and cell walls and capsuls, to keep them from being washed out.  It makes sense, given the environment, but there’s still a lot more to learn.

Because there is a good ref. genome for Accumulibacter, a lot can be done with this population.  [Some graphs that I can’t do justice to…]  Take home message, there are regions where the reference is well covered, and others where it is less well covered.  Thus, there are some species identical to the reference, but other regions with divergence that are only present in the ref, giving lower coverage.)

No obvious core genes are missing.

Improved extraction methods have been used.  Some new bacteria are shown which do have ref. genomes…. a good improvement. (involved boiling?)

Transcript analysis can be done as well, where references exist.  This allows interesting questions to be asked about the cycles of the bacteria’s lifestyle through the various environments it encounters in the waste water plants.

Running out of time, but has a good example of why this is a great experiment using a NADH oxidase.

There is great value in studying this type of community, both for biotech and for understanding complex community systems.

 

1 thought on “CPHx: Kåre Lehman Nielsen: Metagenomics and metatranscriptomics of complex bacterial communities

  1. Pingback: Copenhagenomics » Recap of Day 1 at CPHx

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