Comparative genomics and physiology of the genus Methanohalophilus , a prevalent methanogen in hydraulically fractured shale

The marine cyanobacterium Prochlorococcus is the smallest and most abundant photosynthetic organism on Earth. In this Review, we summarize our understanding of the diversity of this remarkable phototroph and describe its role in ocean ecosystems. We discuss the importance of interactions of Prochlorococcus with the physical environment, with phages and with heterotrophs in shaping the ecology and evolution of this group. In light of recent studies, we have come to view Prochlorococcus as a 'federation' of diverse cells that sustains its broad distribution, stability and abundance in the oceans via extensive genomic and phenotypic diversity. Thus, it is proving to be a useful model system for elucidating the forces that shape microbial populations and ecosystems.

Background Genetic studies are increasingly based on short noisy next generation scanners. Typically complete DNA sequences are assembled by matching short NextGen sequences against reference genomes. Despite considerable algorithmic gains since the turn of the millennium, matching both single ended and paired end strings to a reference remains computationally demanding. Further tailoring Bioinformatics tools to each new task or scanner remains highly skilled and labour intensive. With this in mind, we recently demonstrated a genetic programming based automated technique which generated a version of the state-of-the-art alignment tool Bowtie2 which was considerably faster on short sequences produced by a scanner at the Broad Institute and released as part of The Thousand Genome Project. Results Bowtie2 G P and the original Bowtie2 release were compared on bioplanet’s GCAT synthetic benchmarks. Bowtie2 G P enhancements were also applied to the latest Bowtie2 release (2.2.3, 29 May 2014) and retained both the GP and the manually introduced improvements. Conclusions On both singled ended and paired-end synthetic next generation DNA sequence GCAT benchmarks Bowtie2GP runs up to 45% faster than Bowtie2. The lost in accuracy can be as little as 0.2–0.5% but up to 2.5% for longer sequences.

Bacteria and their viruses (phages) undergo rapid coevolution in test tubes, but the relevance to natural environments is unclear. By using a "mark-recapture" approach, we showed rapid coevolution of bacteria and phages in a soil community. Unlike coevolution in vitro, which is characterized by increases in infectivity and resistance through time (arms race dynamics), coevolution in soil resulted in hosts more resistant to their contemporary than past and future parasites (fluctuating selection dynamics). Fluctuating selection dynamics, which can potentially continue indefinitely, can be explained by fitness costs constraining the evolution of high levels of resistance in soil. These results suggest that rapid coevolution between bacteria and phage is likely to play a key role in structuring natural microbial communities.