DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Integrated Omic Analyses Provide Evidence that a “ Candidatus Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions

Journal Article · · mSystems
 [1]; ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [1];
  1. Department of Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
  2. Department of Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA, Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA

“ Candidatus Accumulibacter phosphatis” is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, microaerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our report provides strong genomics-based evidence not only that “ Ca . Accumulibacter phosphatis” is the main organism contributing to phosphorus removal under microaerobic conditions but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.

Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1490902
Journal Information:
mSystems, Journal Name: mSystems Journal Issue: 1 Vol. 4; ISSN 2379-5077
Publisher:
American Society for MicrobiologyCopyright Statement
Country of Publication:
United States
Language:
English

References (98)

Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway inEscherichia coli under microaerobic growth conditions journal January 2005
Simultaneous nitrification, denitrification, and phosphorus removal from nutrient-rich industrial wastewater using granular sludge journal June 2008
The RegB/RegA two-component regulatory system controls synthesis of photosynthesis and respiratory electron transfer components in Rhodobacter capsulatus journal May 2001
Aerobic denitrification — old wine in new bottles? journal November 1984
Aerobic Denitrifiers Isolated from Diverse Natural and Managed Ecosystems journal February 2000
Microbiology and biochemistry of the enhanced biological phosphate removal process journal November 1998
Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs journal December 2003
Metabolic behavior of denitrifying phosphate-accumulating organisms under nitrate and nitrite electron acceptor conditions journal January 2001
Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape journal September 2016
Identification and validation of suitable reference genes for quantitative expression of xylA and xylE genes in Pseudomonas putida mt-2 journal February 2009
Bacterial sensors of oxygen journal April 2009
Denitrifying phosphorus removal: Linking the process performance with the microbial community structure journal November 2007
Incorporating microbial ecology into the metabolic modelling of polyphosphate accumulating organisms and glycogen accumulating organisms journal September 2010
Monitoring associations between clade-level variation, overall community structure and ecosystem function in enhanced biological phosphorus removal (EBPR) systems using terminal-restriction fragment length polymorphism (T-RFLP) journal September 2010
Population dynamics of bacteria involved in enhanced biological phosphorus removal in Danish wastewater treatment plants journal March 2013
The impact of aeration on the competition between polyphosphate accumulating organisms and glycogen accumulating organisms journal December 2014
Treating low carbon/nitrogen (C/N) wastewater in simultaneous nitrification-endogenous denitrification and phosphorous removal (SNDPR) systems by strengthening anaerobic intracellular carbon storage journal June 2015
Accumulibacter clades Type I and II performing kinetically different glycogen-accumulating organisms metabolisms for anaerobic substrate uptake journal October 2015
Candidatus Accumulibacter phosphatis clades enriched under cyclic anaerobic and microaerobic conditions simultaneously use different electron acceptors journal October 2016
Denitrification of nitrate and nitrite by ‘Candidatus Accumulibacter phosphatis’ clade IC journal November 2016
Non-denitrifying polyphosphate accumulating organisms obviate requirement for anaerobic condition journal March 2017
Cooperation between Candidatus Competibacter and Candidatus Accumulibacter clade I, in denitrification and phosphate removal processes journal September 2017
Pilot plant demonstration of stable and efficient high rate biological nutrient removal with low dissolved oxygen conditions journal September 2017
The Diheme Cytochrome c 4 from Vibrio cholerae Is a Natural Electron Donor to the Respiratory cbb 3 Oxygen Reductase journal September 2010
Genome Reconstruction and Gene Expression of “ Candidatus Accumulibacter phosphatis” Clade IB Performing Biological Phosphorus Removal journal August 2014
‘Candidatus Accumulibacter’ gene expression in response to dynamic EBPR conditions journal August 2010
Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal journal July 2013
Deep-sea hydrothermal vent Epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (Nap) journal January 2014
Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis journal November 2015
Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria journal April 2016
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities journal September 2006
Mapping and quantifying mammalian transcriptomes by RNA-Seq journal May 2008
QIIME allows analysis of high-throughput community sequencing data journal April 2010
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life journal September 2017
Dominant and novel clades of Candidatus Accumulibacter phosphatis in 18 globally distributed full-scale wastewater treatment plants journal July 2015
Nitrate and periplasmic nitrate reductases journal January 2014
Competition between Escherichia coli strains expressing either a periplasmic or a membrane-bound nitrate reductase: does Nap confer a selective advantage during nitrate-limited growth? journal November 1999
Cascade regulation of the two CRP/FNR‐related transcriptional regulators (ANR and DNR) and the denitrification enzymes in Pseudomonas aeruginosa journal September 1997
Regulation of Pseudomonas aeruginosa hemF and hemN by the dual action of the redox response regulators Anr and Dnr journal August 1998
A novel NO-responding regulator controls the reduction of nitric oxide in Ralstonia eutropha journal November 2000
Regulation of expression of terminal oxidases in Paracoccus denitrificans : Regulation of expression of terminal oxidases journal April 2001
Genomic insights that advance the species definition for prokaryotes journal February 2005
Shifting the genomic gold standard for the prokaryotic species definition journal October 2009
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample journal June 2010
Bacterial Adaptation of Respiration from Oxic to Microoxic and Anoxic Conditions: Redox Control journal April 2012
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models journal August 2006
FIMO: scanning for occurrences of a given motif journal February 2011
UCHIME improves sensitivity and speed of chimera detection journal June 2011
FLASH: fast length adjustment of short reads to improve genome assemblies journal September 2011
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data journal October 2012
HTSeq--a Python framework to work with high-throughput sequencing data journal September 2014
Structure and mechanism of the aberrant ba3-cytochrome c oxidase from Thermus thermophilus journal April 2000
MEME: discovering and analyzing DNA and protein sequence motifs journal July 2006
GenBank journal November 2015
Microbial species delineation using whole genome sequences journal July 2015
Transcriptional control of several aerobically induced cytochrome structural genes in Rhodobacter sphaeroides journal October 1997
Bacterial respiration: a flexible process for a changing environment journal March 2000
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes journal May 2015
metaSPAdes: a new versatile metagenomic assembler journal March 2017
Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates: Primer design exploiting extension bias in PCR journal September 2013
Expanding our view of genomic diversity in C andidatus  Accumulibacter clades : Metabolic plasticity in Accumulibacter clades journal August 2014
Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm: Meta-omics of floccular and granular biofilms journal October 2015
Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite-sensitive transcription repressor: NsrR regulation of NirK expression in N. europaea journal July 2004
Microbial distribution of Accumulibacter spp. and Competibacter spp. in aerobic granules from a lab-scale biological nutrient removal system journal February 2008
Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal: Environmental distribution of Accumulibacter journal July 2008
Metatranscriptomic array analysis of ‘Candidatus Accumulibacter phosphatis’-enriched enhanced biological phosphorus removal sludge: Metatranscriptomic array analysis of EBPR sludge journal February 2010
Confirmation of ‘aerobic denitrification’ in batch cultures, using gas chromatography and 15N mass spectrometry journal October 1995
Microbiology of ‘Candidatus Accumulibacter’ in activated sludge: Microbiology of ‘Candidatus Accumulibacter’ journal February 2011
Denitrification capabilities of two biological phosphorus removal sludges dominated by different ‘ Candidatus Accumulibacter’ clades journal December 2009
Nitrate/oxygen co-sensing by an NreA/NreB sensor complex of Staphylococcus carnosus : NreA function in journal December 2013
Genome-Wide Mapping of in Vivo Protein-DNA Interactions journal June 2007
"Candidatus Accumulibacter" Population Structure in Enhanced Biological Phosphorus Removal Sludges as Revealed by Polyphosphate Kinase Genes journal August 2007
Characterization of the Denitrification-Associated Phosphorus Uptake Properties of “Candidatus Accumulibacter phosphatis” Clades in Sludge Subjected to Enhanced Biological Phosphorus Removal journal January 2013
Involvement of Rhodocyclus-Related Organisms in Phosphorus Removal in Full-Scale Wastewater Treatment Plants journal June 2002
Contributions of [4Fe-4S]-FNR and Integration Host Factor to fnr Transcriptional Regulation journal February 2007
Oxygen Reactivity of Both Respiratory Oxidases in Campylobacter jejuni: the cydAB Genes Encode a Cyanide-Resistant, Low-Affinity Oxidase That Is Not of the Cytochrome bd Type journal December 2006
The Periplasmic Nitrate Reductase Nap Is Required for Anaerobic Growth and Involved in Redox Control of Magnetite Biomineralization in Magnetospirillum gryphiswaldense journal June 2012
Transcriptome Dynamics during the Transition from Anaerobic Photosynthesis to Aerobic Respiration in Rhodobacter sphaeroides 2.4.1 journal October 2007
Oxygen Regulation of the ccoN Gene Encoding a Component of the cbb3 Oxidase inRhodobacter sphaeroides 2.4.1T: Involvement of the FnrL Protein journal April 1998
Terminal Oxidases of Bacillus subtilis Strain 168: One Quinol Oxidase, Cytochrome aa3 or Cytochrome bd, Is Required for Aerobic Growth journal December 2000
Mobile Cytochrome c2 and Membrane-Anchored Cytochrome cy Are Both Efficient Electron Donors to the cbb3- and aa3-Type Cytochrome c Oxidases during Respiratory Growth of Rhodobacter sphaeroides journal March 2001
Coordination of Ubiquinol Oxidase and Cytochrome cbb3 Oxidase Expression by Multiple Regulators in Rhodobacter capsulatus journal May 2002
Genome-Wide Expression Analysis Indicates that FNR of Escherichia coli K-12 Regulates a Large Number of Genes of Unknown Function journal January 2005
Epigenetic Gene Regulation in the Bacterial World journal September 2006
A high-affinity cbb3-type cytochrome oxidase terminates the symbiosis-specific respiratory chain of Bradyrhizobium japonicum. journal March 1996
Metabolic pathways for the whole community journal January 2014
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm journal August 2014
Quantifying similarity between motifs journal January 2007
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment journal October 2015
LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads journal August 2015
Aerobic Denitrification of Pseudomonas putida AD-21 at Different C/N Ratios journal November 2008
Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding journal June 2013
Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups journal October 2013
Long-term operation of a reactor enriched in Accumulibacter clade I DPAOs: performance with nitrate, nitrite and oxygen journal January 2011
The Microbial Database for Danish wastewater treatment plants with nutrient removal (MiDas-DK) – a tool for understanding activated sludge population dynamics and community stability journal June 2013
Taking Advantage of Aerated-Anoxic Operation in a Full-Scale University of Cape Town Process journal June 2006
Anvi’o: an advanced analysis and visualization platform for ‘omics data journal January 2015
PhyloSift: phylogenetic analysis of genomes and metagenomes journal January 2014