Review of - Rodriguez-Brito, B., Li, L., Wegley, L., Furlan, M., Angly, F., Breitbart, M., et al. (2010). Viral and microbial community dynamics in four aquatic environments. The ISME Journal, 1-13. doi: 10.1038/ismej.2010.1.
Regarded by Forest Rohwer as “the best paper of 2010...but no-one understands it”. Rodriguez-Brito et al, (2010) set out to investigate the potential merit of macroecological models of predator-prey interactions in microbial ecology following previous proposals of Lotka-Volterra type models for viral and microbe population fluctuations in aquatic systems.
This paper represents the first large-scale time series study of microbial and viral community dynamics at a DNA level over several environments. Viral and microbial communities, from environments ranging from 0 – 30% salinity, were monitored with metagenomics at both level of species and fine-grain level of strains.
The macroecological models on test here, for any reader with an ecology background, are at least familiar. Referred to as “kill-the-winner”, the current working model for microbial communities is very similar to the intermediate disturbance hypothesis in both marine and terrestrial ecology – viruses will rapidly reduce the population of the most abundant microbial species, preventing the community being dominated by the best competitors. The support for the paradigm from previous small scale studies of viral/host pair interactions is explained in the introduction, which may lull the reader into a false sense of security that they understand what is to follow.
Exactly what does follow, as noted by Rohwer, without a thorough knowledge of virology may seem somewhat impenetrable. Confusion arising from the sheer number of specialist statistical analysis applied is confounded where information on the analyses themselves is only available in supplementary methods. It must be acknowledged however that the authors do, at least, clearly explain the ecological functions observed and tested in the analyses.
Within the results section non-specialist readers again may find themselves overwhelmed by the sheer mass of data presented. However, the “Conclusions from...” and “Caveats” for each both coarse, and fine-grain analysis sections are very useful, providing a concise, bite-size presentation of results in ecological terms and a honest, considered evaluation of the reliability and confidence the authors have placed in the analyses. The presentation of results in ecological terms allows the reader to engage with the overall findings, and, once feeling slightly braver, gain more understanding from the extensive displays of results in the figures and associated descriptions.
The discussion is delivered in a remarkably clear and concise manner, although still contains at least one stumbling block for readers to fall over. The authors reveal that not only were suggestion of a “kill-the-winner” model supported, counter arguments of microbial communities remaining biologically stable were also supported in all four of the studied environments. This may, for some readers, be the proverbial nail in the coffin of their understanding of microbial ecology...until Figure 6. Here, at the end of the paper a single figure communicates what maybe a critical proposal for the modelling for microbial communities. Taxonomically and metabolically stable ecosystems, where microbial taxa and phage taxa coexist stably over time, are observed, but only at species level. At the underlying strain level, dynamic cycling of microbial strains and viral genotypes are observed, revealing a “kill-the-winner” dynamic is indeed operating, although not at the expected level of species.
Every reader is likely to take a different opinion to this study, most likely dependant on how their level of understanding before beginning reading. However, it may be suggested that if nothing else is gained from this study all ecologists and microbiologists alike must concede that the processes underpinning microbial community ecology are vastly understudied and understood. Only through studies of this nature will the functioning of these organisms become clearer. But Forest Rohwer was definitely right....no-one understands it. And he was one of the authors.
Posted by Ross Bullimore, March 2011
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