Systems Biology for Ecology: From Molecules to Ecosystems

• Published in: Advances in ecological research Vol. 43; pp. 87 - 149
• Main Authors: Purdy, Kevin J, Hurd, Paul J, Moya-Larano, Jordi, Trimmer, Mark, Oakley, Brian B, Woodward, Guy
• Format: Journal Article
• Language: English
• Published: 01.01.2010
• ISSN: 0065-2504
• DOI: 10.1016/B978-0-12-385005-8.00003-4

Ecology stands on the edge of a true paradigm shift, fuelled by a recent technological revolution in our ability to measure both taxonomic and functional biodiversity via the application of metagenomics and transcriptomics. The advent of 'next generation sequencing' (NGS) in molecular biology is rapidly opening the black box of microbial ecology, providing us with some of the first glimpses of a previously hidden world. This is now enabling microbial ecology to become firmly embedded as a core subdiscipline within ecology, and to test general theories about biodiversity, biogeography and ecosystem functioning using a combination of molecular and more traditional techniques. In addition, NGS offers a means of not only measuring the abundance and diversity of the main drivers of many of the planet's key biogeochemical processes, but also of linking the microscopic and macroscopic worlds that have, until now, been largely studied in isolation. We provide a detailed review of the rise of NGS, as well as highlighting areas that offer special promise for addressing general ecological questions across a range of levels of organisation, from individuals to ecosystems: essentially, how a 'systems biology for ecology' might be developed. We consider the current limitations and future prospects for NGS, and also how it offers potential economic benefits, for instance via bioprospecting the environment for commercially valuable genes and their products within the metagenome of natural ecosystems.