All posts by Andy

Viruses Inhibit CO2 Fixation in the Most Abundant Phototrophs on Earth

This week, we published a paper in Current Biology, titled “Viruses Inhibit CO2Fixation in the Most Abundant Phototrophs on Earth”. The paper is a product of work done by Rich Puxty in the course of his Phd thesis under the supervision ofDave Scanlan, Dave Evans and myself. During his postgraduate research, Rich was looking into the effect of cyanophage infection on host photosynthesis and carbon fixation, using a model system of marine cyanophages S-PM2 and S-RSM4, with their host cyanobacterium Synechococcus WH7803.

Cyanophages are a group of viruses that specifically infect cyanobacteria –  photoautotrophic bacteria  which  utilise light energy to  synthesize sugars and drive metabolic processes. The two most interesting phyla of marine cyanobacteria are Synechococcus and Prochlorococcus. They are widespread in the global oceans and play an important role in the fixation of CO2 and production of oxygen. It has been known for two decades that cyanophages infect cyanobacteria and for over a decade we have known that cyanophages carry genes that can maintain the photosynthetic apparatus of their host.

Our latest published research has shown that whilst photosynthesis is maintained during infection, CO2 fixation is not, thus effectively decoupling CO2 fixation from photosynthesis. If we use these findings with the current data for the number of infected marine cyanobacterial cells per day, the abundance of cyanobacteria and the data from model system of S-PM2/S-RSM4 and WH7803 ,  we can extrapolate that up to 5.39 petagram (1015 grams) of carbon per year is lost to viral-induced inhibition of marine CO2 fixation. Just to put this number in some perspective, that ~ 10% of total marine primary production. More importantly, this huge impact that viruses have on global carbon fixation has not been taken into account in all of the global models and we are hoping that our research will allow us to get a far more accurate picture about global carbon balances.
Another surprising finding in this work was difference in “fitness ” between cyanophages S-PM2 and S-RSM4. These phages contain a number of auxiliary metabolic genes (AMGs) – genes which are suspected to participate in bacterial metabolic processes of the infected host. Our assumption was that since AMGs are supposed to provide the cyanophage with more metabolites required for successful infection cycle, and thus with selective advantage, the phage which carries more AMGs, would possess greater “fitness”.

By using  infection physiological parameters – burst size (number of phage particles produced per cell) and latent period (time from initial attachment to production of new phage particles), we discovered that surprisingly the phage which contained fewer putative AMGs – S-PM2, had both a larger burst size and a shorter latent period, suggesting selective advantage over AMG-replete S-RSM4.

Puxty, RJ., Millard, AD., Evans, DJ., Scanlan, DJ., Viruses inhibit CO2 fixation in the most abundant phototrophs on Earth. Current Biology. doi: 10.1016/j.cub.2016.04.036. http://dx.doi.org/10.1016/j.cub.2016.04.036

More comments on this work in the general press can be found here

ScienceNews 

Bacteriophage Genome assembly

Recently, we published a paper in PeerJ titled “Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes “. The work on this problem started several years ago, when I was actively encouraged (forced) to write a blog post on the Warwick Microbiology and Infection Unit blog (http://blogs.warwick.ac.uk/microbialunderground/). At the time, I looked at some basic parameters that influenced the assembly of bacterial genomes and showed how above a certain coverage there was no benefit in increasing sequencing depth alone. 

Given my interested in bacteriophage genomes and some work we were doing on sequencing multiple phage genomes, I started to look at the amount of sequence coverage required to successfully assemble bacteriophage genomes.  Combined with a throwaway comment on a grant review I received saying that  “it won’t work anyway, as most phage genomes cannot be assembled”, I had enough motivation to start looking at this in far more detail, largely out of frustration and the wish to prove the reviewer wrong.

Using in silico modelling of ~2000 complete phage genomes from ENA (some later got removed as the initial assemblies contained too many ambiguous bases), we investigated how increasing the depth of coverage and insert size affected the assembly of phage genomes when using SPAdes as an assembly algorithm. We demonstrated that the majority of bacteriophage genomes could be assembled without errors and went on to test this in vitro, by the sequencing of some novel phage genomes.

The resulting paper was submitted to PeerJ, where I experienced, for the first time, open peer review, as two of the four reviewers signed their reviews. An interesting observation from the review was that the two signed reviews provided the most useful critique by far. The feedback from the reviewers undoubtedly improved the manuscript by requesting that we further test our hypothesis using additional two assemblyalgorithms (Ray & Velvet), using a variety of sequencing depths and insert sizes.

As a result, after completing ~ 75,000 phage assemblies with a range of insert sizes, sequencing depths and assembly algorithms,we demonstrated that:

  • The majority of phage genomes (>98 %) can be completely assembled at 30x coverage
  • Multiple phages can be combined in a single sequencing library
  • the sequenced phage genomes from combined libraries can be completely reconstructed.

For full details, check out the paper:
Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes.
Rihtman B, Meaden S, Clokie MR, Koskella B, Millard AD.
PeerJ. 2016 Jun 1;4:e2055. doi: 10.7717/peerj.2055. eCollection 2016.