Comparative Metagenomics of Microbial Communities

“…Genes annotated in the two US sludge assemblies, OZ sludge, acid mine drainage biofilm 15 , soil and three whalefall samples 17 were classified in gene families according to sequence similarity and the relative representation of each family was determined. A sizable fraction of the families believed to be important for survival in the EBPR environment from the metabolic reconstruction were over-represented in the sludge datasets.…”

Section: Gene-centric Analysismentioning

confidence: 99%

“…A gene-centric analysis similar to that described by Tringe et al 15 was used to determine relative representation of gene families between metagenomic datasets. We used the following data sources: US sludge (both Phrap and JAZZ assemblies), OZ sludge, acid mine drainage biofilm 9 , soil and whalefall 15 .…”

Section: Gene-centric Comparative Analysis Of Ebpr Sludges To Other Mmentioning

confidence: 99%

“…We used the following data sources: US sludge (both Phrap and JAZZ assemblies), OZ sludge, acid mine drainage biofilm 9 , soil and whalefall 15 . All samples were sequenced at the JGI, and thus had consistent methods of sample preparation, sequencing methods and assembly.…”

Section: Gene-centric Comparative Analysis Of Ebpr Sludges To Other Mmentioning

confidence: 99%

“…Shotgun sequencing applied directly to environmental samples has recently demonstrated that near complete genomes can be obtained for dominant populations in a community without the need for cultivation [15][16] . Therefore, it was anticipated that a near complete genome could be obtained for A. phosphatis from lab-scale EBPR enrichment cultures, allowing a comprehensive metabolic reconstruction.…”

mentioning

confidence: 99%

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Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

et al. 2006

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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 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. 3Excessive inorganic phosphate (Pi) supply to freshwater negatively affects water quality and ecosystem balance through a process known as eutrophication 1 . Limitations on allowable Pi discharges from municipal and industrial sources via wastewater treatment have proven effective in reducing Pi levels in many waterways 2 . Increasingly stringent Pi limits for effluent wastewater are expected in the future and hence efficient and reliable Pi removal methods are required. Due to the massive quantity of wastewater treated daily (more than 120 billion liters in the US alone 3 ), any improvement in existing methods should have tangible economic and ecological consequences.Enhanced Biological Phosphorus Removal (EBPR) is a treatment process in which microorganisms remove Pi from wastewater by accumulating it inside their cells as polyphosphate. These polyphosphate-accumulating organisms (PAOs) are then allowed to settle in a separate tank (clarifier), leaving the effluent water largely Pi-depleted. EBPR is more economical in the long term 2 and has a lower environmental impact 4 than traditional (chemical) Pi removal 5 , but is prone to unpredictable failures due to loss or reduced activity of microbial populations responsible for Pi removal 6 . This is primarily because the design process is highly empirical due to an incomplete understanding of sludge microbial ecology. Environmental engineers and microbiologists have been studying EBPR since its introduction in municipal wastewater treatment plants over thirty years ago 5 with the goal of making it a more reliable industrial process. Typically, EBPR is studied in lab-scale sequencing batch reactors (SBRs) where the microbial community can be better monitored and perturbed, and PAOs can be enriched to much higher levels than in full scale systems 7 .For th...

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