Recent advances in understanding the ecophysiology of enhanced biological phosphorus removal

Roy, Samarpita; Qiu, Guanglei; Zuniga-Montanez, Rogelio; Williams, Rohan B.H.; Wuertz, Stefan

doi:10.1016/j.copbio.2021.01.011

Cited by 58 publications

(21 citation statements)

References 62 publications

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“…Accumulibacter” was equally well detected at the genus-level with primers targeting the V1 to V3 and V4 variable regions of the 16S rRNA gene ( 29 ). This is also in accordance with what was recently observed by Roy et al ( 38 ). However, there may be clear differences in how good amplicons from different variable regions are at resolving the species-level diversity within specific genera ( 27 ).…”

Section: Resultssupporting

confidence: 94%

“…Accumulibacter was equally well detected at the genus-level with primers targeting the V1-V3 and V4 variable regions of the 16S rRNA gene (26). This is also in accordance to what was recently observed by Roy et al, (65). However, there may be clear differences in how good amplicons from different variable regions are in resolving the species-level diversity within specific genera (24) We therefore used the MiDAS4 reference database to determine the ecosystemspecific theoretical taxonomic resolution provided by amplicons targeting different variable regions of the 16S rRNA gene (Figure S5A).…”

Section: Geographic Distribution Of Ca Accumulibacter Populations In ...supporting

confidence: 84%

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Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “CandidatusAccumulibacter”

et al. 2022

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“ Candidatus Accumulibacter” is the most studied PAO, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing approaches. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages.

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Section: Resultssupporting

confidence: 94%

Section: Geographic Distribution Of Ca Accumulibacter Populations In ...supporting

confidence: 84%

Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “CandidatusAccumulibacter”

et al. 2022

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“…Accumulibacter was equally well detected at the genus-level with primers targeting the V1-V3 and V4 variable regions of the 16S rRNA gene (26). This is also in accordance to what was recently observed by Roy et al, (65). However, there may be clear differences in how good amplicons from different variable regions are in resolving the species-level diversity within specific genera (24) We therefore used the MiDAS4 reference database to determine the ecosystem-specific theoretical taxonomic resolution provided by amplicons targeting different variable regions of the 16S rRNA gene ( Figure S5A) .…”

Section: Resultssupporting

confidence: 94%

Re-evaluation of the phylogenetic diversity and global distribution of the genusCandidatusAccumulibacter

Petriglieri

Singleton

Kondrotaite

et al. 2021

Preprint

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Candidatus Accumulibacter was the first microorganism identified as a polyphosphate-accumulating organism (PAO), important for phosphorus removal from wastewater. This genus is diverse, and the current phylogeny and taxonomic framework appears complicated, with the majority of publicly available genomes classified as Candidatus Accumulibacter phosphatis, despite notable phylogenetic divergence. The ppk1 marker gene allows for a finer scale differentiation into different types and clades, nevertheless taxonomic assignments remain confusing and inconsistent across studies. Therefore, a comprehensive re-evaluation is needed to establish a common understanding of this genus, both in terms of naming and basic conserved physiological traits. Here, we provide this re-assessment using a comparison of genome, ppk1, and 16S rRNA gene-based approaches from comprehensive datasets. We identified 15 novel species, along with the well-known Ca. A. phosphatis, Ca. A. deltensis and Ca. A. aalborgensis. To compare the species in situ, we designed new species-specific FISH probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey, Ca. Accumulibacter species were widespread in WWTPs with phosphorus removal, indicating the process design as a major driver for their abundance. Genome mining for PAO related pathways and FISH-Raman microspectroscopy confirmed the potential for the PAO metabolism in all Ca. Accumulibacter species, with detection in situ of the typical PAO storage polymers. Genome annotation further revealed fine-scale differences in the nitrate/nitrite reduction pathways. This provides insights into the niche differentiation of these lineages, potentially explaining their coexistence in the same ecosystem while contributing to overall phosphorus and nitrogen removal.

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“…All continuous flow enhanced biological phosphorus removal wastewater treatment plants (EBPR) operate by passing the biomass continuously between anaerobic and aerobic reactors, a plant configuration considered essential for removing phosphorus (P) microbiologically by advantaging selectively the populations involved in its removal ( Seviour and McIlroy, 2008 ; Stokholm-Bjerregaard et al, 2017 ; Nielsen et al, 2019 ; Roy et al, 2021 ). One popular but not universally accepted explanation as to why EBPR plants often perform badly is that the polyphosphate-accumulating organisms (PAO) are out-competed in the EBPR anaerobic “feed” stage by other bacteria known collectively as the glycogen-accumulating organisms (GAO) ( Cech and Hartman, 1993 ; Liu et al, 1996 ; Law et al, 2016 ; Nielsen et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics of Members of the Genus Defluviicoccus With Insights Into Their Ecophysiological Importance

et al. 2022

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Members of the genus Defluviicoccus occur often at high abundances in activated sludge wastewater treatment plants designed to remove phosphorus, where biomass is subjected to alternating anaerobic feed/aerobic famine conditions, believed to favor the proliferation of organisms like Ca. Accumulibacter and other phosphate-accumulating organisms (PAO), and Defluviicoccus. All have a capacity to assimilate readily metabolizable substrates and store them intracellularly during the anaerobic feed stage so that under the subsequent famine aerobic stage, these can be used to synthesize polyphosphate reserves by the PAO and glycogen by Defluviicoccus. Consequently, Defluviicoccus is described as a glycogen-accumulating organism or GAO. Because they share a similar anaerobic phenotype, it has been proposed that at high Defluviicoccus abundance, the PAO are out-competed for assimilable metabolites anaerobically, and hence aerobic P removal capacity is reduced. Several Defluviicoccus whole genome sequences have been published (Ca. Defluviicoccus tetraformis, Defluviicoccus GAO-HK, and Ca. Defluviicoccus seviourii). The available genomic data of these suggest marked metabolic differences between them, some of which have ecophysiological implications. Here, we describe the whole genome sequence of the type strain Defluviicoccus vanusT, the only cultured member of this genus, and a detailed comparative re-examination of all extant Defluviicoccus genomes. Each, with one exception, which appears not to be a member of this genus, contains the genes expected of GAO members, in possessing multiple copies of those for glycogen biosynthesis and catabolism, and anaerobic polyhydroxyalkanoate (PHA) synthesis. Both 16S rRNA and genome sequence data suggest that the current recognition of four clades is insufficient to embrace their phylogenetic biodiversity, but do not support the view that they should be re-classified into families other than their existing location in the Rhodospirillaceae. As expected, considerable variations were seen in the presence and numbers of genes encoding properties associated with key substrate assimilation and metabolic pathways. Two genomes also carried the pit gene for synthesis of the low-affinity phosphate transport protein, pit, considered by many to distinguish all PAO from GAO. The data re-emphasize the risks associated with extrapolating the data generated from a single Defluviicoccus population to embrace all members of that genus.

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Recent advances in understanding the ecophysiology of enhanced biological phosphorus removal

Cited by 58 publications

References 62 publications

Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “CandidatusAccumulibacter”

Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “CandidatusAccumulibacter”

Re-evaluation of the phylogenetic diversity and global distribution of the genusCandidatusAccumulibacter

Comparative Genomics of Members of the Genus Defluviicoccus With Insights Into Their Ecophysiological Importance

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