Cultivation and quantitative proteomic analyses of acidophilic microbial communities

Christopher P. Belnap, Chongle Pan, Nathan C. Verberkmoes, Mary E. Power, Nagiza F. Samatova, Rudolf L. Carver, Robert L. Hettich, Jillian F. Banfield

Research output: Contribution to journalArticlepeer-review

59 Scopus citations

Abstract

Acid mine drainage (AMD), an extreme environment characterized by low pH and high metal concentrations, can support dense acidophilic microbial biofilm communities that rely on chemoautotrophic production based on iron oxidation. Field determined production rates indicate that, despite the extreme conditions, these communities are sufficiently well adapted to their habitats to achieve primary production rates comparable to those of microbial communities occurring in some non-extreme environments. To enable laboratory studies of growth, production and ecology of AMD microbial communities, a culturing system was designed to reproduce natural biofilms, including organisms recalcitrant to cultivation. A comprehensive metabolic labeling-based quantitative proteomic analysis was used to verify that natural and laboratory communities were comparable at the functional level. Results confirmed that the composition and core metabolic activities of laboratory-grown communities were similar to a natural community, including the presence of active, low abundance bacteria and archaea that have not yet been isolated. However, laboratory growth rates were slow compared with natural communities, and this correlated with increased abundance of stress response proteins for the dominant bacteria in laboratory communities. Modification of cultivation conditions reduced the abundance of stress response proteins and increased laboratory community growth rates. The research presented here represents the first description of the application of a metabolic labeling-based quantitative proteomic analysis at the community level and resulted in a model microbial community system ideal for testing physiological and ecological hypotheses.

Original languageEnglish
Pages (from-to)520-530
Number of pages11
JournalISME Journal
Volume4
Issue number4
DOIs
StatePublished - Apr 2010

Funding

Mr Ted Arman (President, Iron Mountain Mines) and Dr Richard Sugarek are thanked for site access and other assistance. We also thank Mike Zach, Andy Thompson and Becca Ryals for technical assistance. Vincent Denef and Paul Wilmes are thanked for helpful discussions. This research was supported by the US Department of Energy Genomics: GTL and ASCR programs, the NSF Biocom-plexity Program and the NASA Astrobiology Institute.

Keywords

  • Acid mine drainage
  • Biofilm
  • Proteomics

Fingerprint

Dive into the research topics of 'Cultivation and quantitative proteomic analyses of acidophilic microbial communities'. Together they form a unique fingerprint.

Cite this