Genomic features in relation to trophic strategy

A review of: Lauro, FM. McDougald, D. Thomas, T. et al (2009) The genomic basis of trophic strategy in marine bacteria. Proceedings of the National Academy of Sciences, Vol. 106 (37) 155527-33.

The marine environment is known for being one of the largest on the planet, but it is also one of the most productive. It is saturated with microorganisms, and it is the bacteria (along with Archaea), which play important roles in biogeochemical processes and are responsible for cycling the largest pool of organic carbon on the planet. As well as being one of the largest environments it is also one of the harshest with conditions varying dramatically and ranging from nutrient rich (copiotrophic) to nutrient poor (oligotrophic).

This study investigates two types of marine bacteria which have adapted to the selective pressures of these extreme conditions, photobacterium angustum S14 (copiotroph) and sphingopyxis alaskensis RB2256 (oligotroph). The aim of the study was to show that the trophic strategy behind these marine bacteria was reflected in their genomics, by sequencing their genomes to understand the molecular basis behind their adaptations. This information would be invaluable as it will allow for ecological characteristics of unculturable microorganisms to be determined.

To ensure that there was a stronger basis than just the comparison of the two bacteria, the genetic markers derived were validated by searching for 32 additional genome sequences which represented relating species. In total 43 genetic markers were accurately identified which predict trophic strategy. These were also consistent with physiological adaptations for enhancing microbial reproduction under specific nutrient regimes.

The comparisons between the two bacteria allowed a set of discriminative genomic features of trophic lifestyles to be defined. Genomic markers were applied to a clustering method along with 92 additional genomes of marine bacteria, which made it possible to detect more subtle variations in trophic strategy across the full range of genomes used. A model was produced which was able to predict the trophic strategy of an organism from genomic data. This was tested using genomic sequences with metagenomic datasets to allow for the trophic strategies of dominant micro-organisms in whole environmental samples to be derived. Even after reducing the number of core characteristics in the study there was little effect on the predicted outcomes indicating that this model is robust and will be a useful application to a wide range of data sets.

The importance of sequencing the genome of an organism is something of common knowledge; this paper shows the implications of sequencing in understanding bacterial evolution. It can show how bacteria have evolved to inhabit different niches and may indicate previously unknown relationships in communities. It could be used to predict how bacteria will cope or adapt to changes, this could be an important tool for ecotoxicologists.