title: Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal.
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.
authors.affiliation: Department of Earth and Planetary Sciences, University of California at Berkeley, Berkeley, CA 94720, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Wilmes
authors.forename: Anders F
authors.initials: AF
authors.lastname: Andersson
authors.forename: Mark G
authors.initials: MG
authors.lastname: Lefsrud
authors.forename: Margaret
authors.initials: M
authors.lastname: Wexler
authors.forename: Manesh
authors.initials: M
authors.lastname: Shah
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
authors.forename: Philip L
authors.initials: PL
authors.lastname: Bond
authors.forename: Nathan C
authors.initials: NC
authors.lastname: VerBerkmoes
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
mesh_terms: D000332:Aerobiosis; D000693:Anaerobiosis; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D001426:Bacterial Proteins / Q000032:analysis / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005227:Fatty Acids / Q000378:metabolism; D014644:Genetic Variation; D006038:Glyoxylates / Q000378:metabolism; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000378:metabolism; D010758:Phosphorus / Q000378:metabolism*; D020543:Proteome / Q000032:analysis* / Q000235:genetics*; D012722:Sewage / Q000382:microbiology*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D005227:Fatty Acids; D006038:Glyoxylates; D020543:Proteome; D012722:Sewage; D010758:Phosphorus; C031150:glyoxylic acid; D009584:Nitrogen