1. ¹Department of Earth and Planetary Sciences, University of California at Berkeley, Berkeley, USA
2. ²Bioresource Engineering, McGill University, Ste-Anne-de-Bellevue, Canada
3. ³School of Biological Sciences, University of East Anglia, Norwich, UK
4. ⁴Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, USA
5. ⁵Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, USA
6. ⁶Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, USA
7. ⁷Advanced Wastewater Management Center, University of Queensland, St Lucia, Queensland, Australia
8. ⁸Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, USA

Correspondence: JF Banfield, Department of Earth and Planetary Sciences, Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA 94720, USA. E-mail: jbanfield@berkeley.edu; PL Bond, Advanced Wastewater Management Center, University of Queensland, St Lucia, Queensland 4072, Australia. E-mail: phil.bond@uq.edu.au

Received 18 January 2008; Revised 25 March 2008; Accepted 25 March 2008; Published online 1 May 2008.

Abstract

Enhanced biological phosphorus removal (EBPR) selects for polyphosphate accumulating microorganisms to achieve phosphate removal from wastewater. We used high-resolution community proteomics to identify key metabolic pathways in 'Candidatus Accumulibacter phosphatis' (A. phosphatis)-mediated EBPR and to evaluate the contributions of co-existing strains within the dominant population. Overall, 702 proteins from the A. phosphatis population were identified. Results highlight the importance of denitrification, fatty acid cycling and the glyoxylate bypass in EBPR. Strong similarity in protein profiles under anaerobic and aerobic conditions was uncovered (only 3% of A. phosphatis-associated proteins exhibited statistically significant abundance differences). By comprehensive genome-wide alignment of 13 930 orthologous proteins, we uncovered substantial differences in protein abundance for enzyme variants involved in both core-metabolism and EBPR-specific pathways among the A. phosphatis population. These findings suggest an essential role for genetic diversity in maintaining the stable performance of EBPR systems and, hence, demonstrate the power of integrated cultivation-independent genomics and proteomics for the analysis of complex biotechnological systems.