“Candidatus Accumulibacter delftensis”: A clade IC novel polyphosphate-accumulating organism without denitrifying activity on nitrate

Rubio-Rincón, F.J.; Weissbrodt, David G.; López-Vázquez, Carlos M.; Welles, Laurens; Abbas, Ben; Albertsen, Mads; Nielsen, Per Halkjær; Loosdrecht, Mark C.M. van; Brdjanović, Damir

doi:10.1016/j.watres.2019.03.053

Cited by 80 publications

(37 citation statements)

References 60 publications

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“…Additionally, the Accumulibacter lineage exhibits specific trait variation within individual ppk1-defined clades for specific traits, such as denitrification capabilities. For example, differences among clade IC strains with respect to anoxic nitrate reduction coupled to phosphorus uptake suggests that the ability to carry out each sequential step in denitrification could be strain-specific (14,17,(26)(27)(28). The persistence of several phylogenetically distinct clades within the Accumulibacter lineage in both full-scale wastewater treatment plants and lab-scale enrichment bioreactors suggests that different clades may inhabit distinct ecological niches (17,29).…”

Section: For Example Genetically Diverse Ecotypes Of the Marine Cyanmentioning

confidence: 99%

Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics

McDaniel

Moya-Flores

Beach

et al. 2020

Preprint

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Microbial communities in their natural habitats consist of closely related populations that may exhibit phenotypic differences and inhabit distinct niches. However, connecting genetic diversity to ecological properties remains a challenge in microbial ecology due to the lack of pure cultures across the microbial tree of life. ‘Candidatus Accumulibacter phosphatis’ is a polyphosphate-accumulating organism that contributes to the Enhanced Biological Phosphorus Removal (EBPR) biotechnological process for removing excess phosphorus from wastewater and preventing eutrophication from downstream receiving waters. Distinct Accumulibacter clades often co-exist in full-scale wastewater treatment plants and lab-scale enrichment bioreactors, and have been hypothesized to inhabit distinct ecological niches. However, since individual strains of the Accumulibacter lineage have not been isolated in pure culture to date, these predictions have been made solely on genome-based comparisons and enrichments with varying strain composition. Here, we used genome-resolved metagenomics and metatranscriptomics to explore the activity of co-existing Accumulibacter clades in an engineered bioreactor environment. We obtained four high-quality genomes of Accumulibacter strains that were present in the bioreactor ecosystem, one of which is a completely contiguous draft genome scaffolded with long reads. We identified core and accessory genes to investigate how gene expression patterns differ among the dominating strains. Using this approach, we were able to identify putative pathways and functions that may differ between Accumulibacter clades and provide key functional insights into this biotechnologically significant microbial lineage.IMPORTANCE‘Candidatus Accumulibacter phosphatis’ is a model polyphosphate accumulating organism that has been studied using genome-resolved metagenomics, metatranscriptomics, and metaproteomics to understand the EBPR process. Within the Accumulibacter lineage, several similar but diverging clades are defined by the polyphosphate kinase (ppk1) locus sequence identity. These clades are predicted to have key functional differences in acetate uptake rates, phage defense mechanisms, and nitrogen cycling capabilities. However, such hypotheses have largely been made based on gene-content comparisons of sequenced Accumulibacter genomes, some of which were obtained from different systems. Here, we performed time-series genome-resolved metatranscriptomics to explore gene expression patterns of co-existing Accumulibacter clades in the same bioreactor ecosystem. Our work provides an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.

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Section: For Example Genetically Diverse Ecotypes Of the Marine Cyanmentioning

confidence: 99%

Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics

McDaniel

Moya-Flores

Beach

et al. 2020

Preprint

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“…Flowers, He, Yilmaz, Noguera, and McMahon () using a laboratory‐scale reactor found that clade IA was able to take up P while using nitrate, but clade IIA could not. Other studies indicated that clade I was not capable of using nitrate as electron acceptor for anoxic phosphate uptake (Rubio‐Rincón, Lopez‐Vazquez, Welles, Loosdrecht, & Brdjanovic, ; Rubio‐Rincón et al, ). Zeng, Zhang, Fan, Guo, and Peng () studied abundance of the same five clades used in this study in EBPR full‐scale plants in China and found that while all five clades were present, clade IIC was the dominant in all processes (>80% of all clades) and clade IA accounted for the smallest portion (less than 0.5%).…”

Section: Resultsmentioning

confidence: 97%

Impact of solid residence time (SRT) on functionally relevant microbial populations and performance in full‐scale enhanced biological phosphorus removal (EBPR) systems

Onnis‐Hayden

Majed

et al. 2019

Water Environment Research

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Investigations of the impact of solid residence time (SRT) on microbial ecology and performance of enhanced biological phosphorus removal (EBPR) process in full‐scale systems have been scarce due to the challenges in isolating and examining the SRT from other complex plant‐specific factors. This study performed a comprehensive evaluation of the influence of SRT on polyphosphate‐accumulating organisms (PAOs) and glycogen‐accumulating organisms (GAOs) dynamics and on P removal performance at Clark County Water Reclamation District Facility in Las Vegas, USA. Five parallel treatment trains with separated clarifiers were operated with five different SRTs ranging from 6 to 40 days. Microbial community analysis using multiple molecular and Raman techniques suggested that the relative abundances and diversity of PAOs and GAOs in EBPR systems are highly affected by the SRT. The resultant EBPR system stability and performance can be potentially controlled and optimized by manipulating the system SRT, and shorter SRT (<10 days) seems to be preferred. Practitioner points Phosphorus removal performance and kinetics are highly affected by the operational solid residence time (SRT), with lower and more stable effluent P level achieved at SRT < 10 days. Excessive long SRTs above that needed for nitrification may harm EBPR performance; additionally, excessive long SRT may favor GAOs to dominate over PAOs and thus further reducing efficient use of rbCOD for EBPR. Microbial population abundance and diversity, especially those functionally relevant PAOs and GAOs, can impact the P removal performances, and they are highly dependent on the operational solid residence time. EBPR performance can be potentially controlled and optimized by manipulating the system SRT, and shorter SRT (≤10 days) seems to be preferred at the influent rbCOD/P ratio and environmental conditions as in the plant studied.

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“…Various metagenome-assembled genomes (MAGs) of “ Ca . Accumulibacter” available in public repositories and surveyed in literature (Rubio-Rincón et al 2019) were used to predict their potential to produce NulOs and their possible diversity. The prediction was focused on the NulO synthase (NAB-2), the enzyme that condenses a 6-carbon intermediate with phosphoenolpyruvate to yield a 9-carbon α-keto acid.…”

Section: Resultsmentioning

confidence: 99%

“…Different near-complete draft metagenome-assembled genomes (MAGs) of “ Ca . Accumulibacter” (Rubio-Rincón et al 2019) were used to get the amino acid sequences of nonulosonic acid synthases (NAB-2), i.e. the most conserved enzymes of the biosynthetic pathway, which condensates a 6-carbon intermediate with pyruvate to produce a 9-carbon α-keto acid (Fig.…”

Section: Methodsmentioning

confidence: 99%

“…Accumulibacter" has been identified as the dominant organisms responsible for EBPR (Zilles et al 2002). This microorganism has been well studied in the past decades: different genomic, proteomic, metabolic and modelling studies are available (Oehmen et al 2010;Barr et al 2016;Oyserman et al 2016;Guedes da Silva et al 2018;Guedes da Silva et al 2019;Rubio-Rincón et al 2019). However, most of the studies overlook the extracellular matrix.…”

Section: Nonulosonic Acids and The Ebpr Processmentioning

confidence: 99%

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Production of nonulosonic acids in the extracellular polymeric substances of “CandidatusAccumulibacter phosphatis”

Tomás-Martínez

Kleikamp

Neu

et al. 2020

Preprint

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Nonulosonic acids (NulOs) are a family of acidic carbohydrates with a nine-carbon backbone, which include different related structures, such as sialic acids. They have mainly been studied for their relevance in animal cells and pathogenic bacteria. Recently, sialic acids have been discovered as important compound in the extracellular matrix of virtually all microbial life and in Candidatus Accumulibacter phosphatis, a well-studied polyphosphate-accumulating organism, in particular. Here, bioaggregates highly enriched with these bacteria (approx. 95% based on proteomic data) were used to study the production of NulOs in an enrichment of this microorganism. Fluorescence lectin-binding analysis, enzymatic quantification, and mass spectrometry were used to analyze the different NulOs present, showing a wide distribution and variety of these carbohydrates, such as sialic acids and bacterial NulOs, in the bioaggregates. Phylogenetic analysis confirmed the potential of Ca. Accumulibacter to produce different types of NulOs. Proteomic analysis showed the ability of Ca. Accumulibacter to reutilize and reincorporate these carbohydrates. This investigation points out the importance of diverse NulOs in non-pathogenic bacteria, which are normally overlooked. Sialic acids and other NulOs should be further investigated for their role in the ecology of Ca. Accumulibacter in particular, and biofilms in general.

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“Candidatus Accumulibacter delftensis”: A clade IC novel polyphosphate-accumulating organism without denitrifying activity on nitrate

Cited by 80 publications

References 60 publications

Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics

Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics

Impact of solid residence time (SRT) on functionally relevant microbial populations and performance in full‐scale enhanced biological phosphorus removal (EBPR) systems

Production of nonulosonic acids in the extracellular polymeric substances of “CandidatusAccumulibacter phosphatis”

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