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Metagenomic analysis of phosphorus removing sludge communities

  • Author(s): Garcia Martin, Hector
  • Ivanova, Natalia
  • Kunin, Victor
  • Warnecke, Falk
  • Barry, Kerrie
  • McHardy, Alice C.
  • Yeates, Christine
  • He, Shaomei
  • Salamov, Asaf
  • Szeto, Ernest
  • Dalin, Eileen
  • Putnam, Nik
  • Shapiro, Harris J.
  • Pangilinan, Jasmyn L.
  • Rigoutsos, Isidore
  • Kyrpides, Nikos C.
  • Blackall, Linda Louise
  • McMahon, Katherine D.
  • Hugenholtz, Philip
  • et al.
Abstract

Enhanced Biological Phosphorus Removal (EBPR) is not well understood at the metabolic level despite being one of the best-studied microbially-mediated industrial processes due to its ecological and economic relevance. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, "Candidatus Accumulibacter phosphatis." This analysis resolves 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.

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