AMD biofilms: Using model communities to study microbial evolution and ecological complexity in nature

Vincent J. Denef, Ryan S. Mueller, Jillian F. Banfield

Research output: Contribution to journalReview ArticleResearchpeer-review

69 Citations (Scopus)

Abstract

Similar to virtually all components of natural environments, microbial systems are inherently complex and dynamic. Advances in cultivation-independent molecular methods have provided a route to study microbial consortia in their natural surroundings and to begin resolving the community structure, dominant metabolic processes and inter-organism interactions. However, the utility of these methods generally scales inversely with community complexity. By applying genomics-enabled methods to the study of natural microbial communities with reduced levels of species richness, a relatively comprehensive understanding of the metabolic networks and evolutionary processes within these communities can be attained. In such well-defined model systems, it is also possible to link emergent ecological patterns to their molecular and evolutionary underpinnings, facilitating construction of predictive ecosystem models. In this study, we review over a decade of research on one such systemacid mine drainage biofilm communities. We discuss the value and limitations of tractable model microbial communities in developing molecular methods for microbial ecology and in uncovering principles that may explain behavior in more complex systems.

Original languageEnglish
Pages (from-to)599-610
Number of pages12
JournalThe ISME Journal
Volume4
Issue number5
DOIs
Publication statusPublished - May 2010
Externally publishedYes

Keywords

  • Community proteogenomics
  • CRISPR
  • Geomicrobiology
  • Population genomics
  • Recombination
  • Virus-microbe interactions

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