Incorporating microbial ecology into the metabolic modelling of polyphosphate accumulating organisms and glycogen accumulating organisms

Oehmen, Adrian; Carvalho, Gilda; López-Vázquez, Carlos M.; Loosdrecht, M.C.M. van; Reis, Maria A.M.

doi:10.1016/j.watres.2010.06.071

Cited by 145 publications

(94 citation statements)

References 81 publications

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“…Whether the EMP or the ED pathway is utilised has substantial impact on the redox balance of the cell, given the two alternate routes generate three and two moles ATP per mole of glucose-6-phosphate monomer, respectively. Thus, the less energy efficient ED pathway gives predicted higher glycogen utilisation and PHA production under anaerobic conditions (Oehmen et al, 2010). Both genomes analysed here have genes for the complete EMP pathway, whereas the ED pathway was only identified in the C. denitrificans genome.…”

Section: Anaerobic Glycogen Metabolismmentioning

confidence: 84%

“…In other organisms possessing both the ED and EMP pathways, the ED pathway is induced in the presence of specific carbon sources, with the EMP pathway forming the core catabolic route (Conway, 1992), with similar roles for these alternate pathways therefore possible for C. denitrificans. The EMP pathway is included in the current metabolic models for Competibacteraceae, which fit empirical enrichment culture data well (Oehmen et al, 2010). However, evidence at higher temperatures (30 1C) Lopez-Vazquez et al, 2009), albeit inconsistently (Bengtsson, 2009), suggests the operation of the ED pathway in Competibacteraceae enrichments.…”

Section: Anaerobic Glycogen Metabolismmentioning

confidence: 95%

“…However, evidence at higher temperatures (30 1C) Lopez-Vazquez et al, 2009), albeit inconsistently (Bengtsson, 2009), suggests the operation of the ED pathway in Competibacteraceae enrichments. On the basis of these observations it has been suggested that either individual Competibacteraceae species shift their reliance on the EMP to the ED pathway in response to certain conditions (that is, increased temperature) or such conditions select for distinct species with different metabolic potentials for glycogen catabolism pathways (Oehmen et al, 2010). Ultimately, a study using genomics (and perhaps transcriptomics and/or proteomics) analysis of a culture that has demonstrated the stoichiometry of the ED pathway will be required to answer these critical questions, but the data presented here importantly show that different Competibacteraceae species can vary in their genetic potential for glycolytic pathways.…”

Section: Anaerobic Glycogen Metabolismmentioning

confidence: 99%

“…In addition, metabolic models are based on enrichment studies, where the composition of the Competibacter-lineage community is rarely defined. The presence of multiple species in these enrichment cultures may explain apparently conflicting evidence for the metabolism of glycogen, with separate studies suggesting the operation of either the Embden-Meyerhof-Parnas (EMP) or the Entner-Doudoroff (ED) glycolytic pathway (Oehmen et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

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‘Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity

et al. 2013

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The glycogen-accumulating organism (GAO) 'Candidatus Competibacter' (Competibacter) uses aerobically stored glycogen to enable anaerobic carbon uptake, which is subsequently stored as polyhydroxyalkanoates (PHAs). This biphasic metabolism is key for the Competibacter to survive under the cyclic anaerobic-'feast': aerobic-'famine' regime of enhanced biological phosphorus removal (EBPR) wastewater treatment systems. As they do not contribute to phosphorus (P) removal, but compete for resources with the polyphosphate-accumulating organisms (PAO), thought responsible for P removal, their proliferation theoretically reduces the EBPR capacity. In this study, two complete genomes from Competibacter were obtained from laboratory-scale enrichment reactors through metagenomics. Phylogenetic analysis identified the two genomes, 'Candidatus Competibacter denitrificans' and 'Candidatus Contendobacter odensis', as being affiliated with Competibacter-lineage subgroups 1 and 5, respectively. Both have genes for glycogen and PHA cycling and for the metabolism of volatile fatty acids. Marked differences were found in their potential for the Embden-Meyerhof-Parnas and Entner-Doudoroff glycolytic pathways, as well as for denitrification, nitrogen fixation, fermentation, trehalose synthesis and utilisation of glucose and lactate. Genetic comparison of P metabolism pathways with sequenced PAOs revealed the absence of the Pit phosphate transporter in the Competibacter-lineage genomes-identifying a key metabolic difference with the PAO physiology. These genomes are the first from any GAO organism and provide new insights into the complex interaction and niche competition between PAOs and GAOs in EBPR systems.

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Section: Anaerobic Glycogen Metabolismmentioning

confidence: 84%

Section: Anaerobic Glycogen Metabolismmentioning

confidence: 95%

Section: Anaerobic Glycogen Metabolismmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

‘Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity

et al. 2013

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“…Therefore, we sequenced the metagenome of a Clade IA-enriched community to generate a Clade IA reference genome and to better understand ecophysiological and genomic differences between Accumulibacter clades. By developing a greater understanding of the genomic basis underlying hypothesized distinct niches for the clades, we will also be able to provide more accurate models that help to predict the overall performance of EBPR systems (Oehmen et al, 2010c).…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal

et al. 2013

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Members of the genus Candidatus Accumulibacter are important in many wastewater treatment systems performing enhanced biological phosphorus removal (EBPR). The Accumulibacter lineage can be subdivided phylogenetically into multiple clades, and previous work showed that these clades are ecologically distinct. The complete genome of Candidatus Accumulibacter phosphatis strain UW-1, a member of Clade IIA, was previously sequenced. Here, we report a draft genome sequence of Candidatus Accumulibacter spp. strain UW-2, a member of Clade IA, assembled following shotgun metagenomic sequencing of laboratory-scale bioreactor sludge. We estimate the genome to be 80–90% complete. Although the two clades share 16S rRNA sequence identity of >98.0%, we observed a remarkable lack of synteny between the two genomes. We identified 2317 genes shared between the two genomes, with an average nucleotide identity (ANI) of 78.3%, and accounting for 49% of genes in the UW-1 genome. Unlike UW-1, the UW-2 genome seemed to lack genes for nitrogen fixation and carbon fixation. Despite these differences, metabolic genes essential for denitrification and EBPR, including carbon storage polymer and polyphosphate metabolism, were conserved in both genomes. The ANI from genes associated with EBPR was statistically higher than that from genes not associated with EBPR, indicating a high selective pressure in EBPR systems. Further, we identified genomic islands of foreign origins including a near-complete lysogenic phage in the Clade IA genome. Interestingly, Clade IA appeared to be more phage susceptible based on it containing only a single Clustered Regularly Interspaced Short Palindromic Repeats locus as compared with the two found in Clade IIA. Overall, the comparative analysis provided a genetic basis to understand physiological differences and ecological niches of Accumulibacter populations, and highlights the importance of diversity in maintaining system functional resilience.

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Multilevel correlations in the biological phosphorus removal process: From bacterial enrichment to conductivity‐based metabolic batch tests and polyphosphatase assays

Weissbrodt

Maillard

Brovelli

et al. 2014

Biotech & Bioengineering

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Enhanced biological phosphorus removal (EBPR) from wastewater relies on the preferential selection of active polyphosphate-accumulating organisms (PAO) in the underlying bacterial community continuum. Efficient management of the bacterial resource requires understanding of population dynamics as well as availability of bioanalytical methods for rapid and regular assessment of relative abundances of active PAOs and their glycogen-accumulating competitors (GAO). A systems approach was adopted here toward the investigation of multilevel correlations from the EBPR bioprocess to the bacterial community, metabolic, and enzymatic levels. Two anaerobic-aerobic sequencing-batch reactors were operated to enrich activated sludge in PAOs and GAOs affiliating with "Candidati Accumulibacter and Competibacter phosphates", respectively. Bacterial selection was optimized by dynamic control of the organic loading rate and the anaerobic contact time. The distinct core bacteriomes mainly comprised populations related to the classes Betaproteobacteria, Cytophagia, and Chloroflexi in the PAO enrichment and of Gammaproteobacteria, Alphaproteobacteria, Acidobacteria, and Sphingobacteria in the GAO enrichment. An anaerobic metabolic batch test based on electrical conductivity evolution and a polyphosphatase enzymatic assay were developed for rapid and low-cost assessment of the active PAO fraction and dephosphatation potential of activated sludge. Linear correlations were obtained between the PAO fraction, biomass specific rate of conductivity increase under anaerobic conditions, and polyphosphate-hydrolyzing activity of PAO/GAO mixtures. The correlations between PAO/GAO ratios, metabolic activities, and conductivity profiles were confirmed by simulations with a mathematical model developed in the aqueous geochemistry software PHREEQC.

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Incorporating microbial ecology into the metabolic modelling of polyphosphate accumulating organisms and glycogen accumulating organisms

Cited by 145 publications

References 81 publications

‘Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity

‘Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity

Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal

Multilevel correlations in the biological phosphorus removal process: From bacterial enrichment to conductivity‐based metabolic batch tests and polyphosphatase assays

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