title: Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities.
abstract: Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, "Candidatus Accumulibacter phosphatis." The analysis sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of A. phosphatis in this habitat, its lifestyle outside EBPR and probable cultivation requirements. Comparison of the same species from different EBPR sludges highlights recent evolutionary dynamics in the A. phosphatis genome that could be linked to mechanisms for environmental adaptation. In spite of an apparent lack of phylogenetic overlap in the flanking communities of the two sludges studied, common functional themes were found, at least one of them complementary to the inferred metabolism of the dominant organism. The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems.
authors.affiliation: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
authors.forename: Héctor
authors.initials: H
authors.lastname: García Martín
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.forename: Victor
authors.initials: V
authors.lastname: Kunin
authors.forename: Falk
authors.initials: F
authors.lastname: Warnecke
authors.forename: Kerrie W
authors.initials: KW
authors.lastname: Barry
authors.forename: Alice C
authors.initials: AC
authors.lastname: McHardy
authors.forename: Christine
authors.initials: C
authors.lastname: Yeates
authors.forename: Shaomei
authors.initials: S
authors.lastname: He
authors.forename: Asaf A
authors.initials: AA
authors.lastname: Salamov
authors.forename: Ernest
authors.initials: E
authors.lastname: Szeto
authors.forename: Eileen
authors.initials: E
authors.lastname: Dalin
authors.forename: Nik H
authors.initials: NH
authors.lastname: Putnam
authors.forename: Harris J
authors.initials: HJ
authors.lastname: Shapiro
authors.forename: Jasmyn L
authors.initials: JL
authors.lastname: Pangilinan
authors.forename: Isidore
authors.initials: I
authors.lastname: Rigoutsos
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.forename: Linda Louise
authors.initials: LL
authors.lastname: Blackall
authors.forename: Katherine D
authors.initials: KD
authors.lastname: McMahon
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
mesh_terms: D000220:Adaptation, Biological; D020562:Betaproteobacteria / Q000235:genetics* / Q000378:metabolism*; D016680:Genome, Bacterial; D010758:Phosphorus / Q000302:isolation & purification / Q000378:metabolism*; D012722:Sewage / Q000382:microbiology*; D014865:Waste Disposal, Fluid
chemical_list: D012722:Sewage; D010758:Phosphorus