Comparative genomics of members of the genus Defluviicoccus with insights into their ecophysiological importance

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. Accumulibact...

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Main Authors: Bessarab, Irina, Maszenan, Abdul Majid, Haryono, Mindia A. S., Arumugam, Krithika, Saw, Nay Min Min Thaw, Seviour, Robert J., Williams, Rohan B. H.
Other Authors: National University of Singapore
Format: Article
Language:English
Published: 2022
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Online Access:https://hdl.handle.net/10356/163268
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Institution: Nanyang Technological University
Language: English
id sg-ntu-dr.10356-163268
record_format dspace
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Engineering::Environmental engineering
Activated Sludge
Glycogen Accumulating Organisms
spellingShingle Engineering::Environmental engineering
Activated Sludge
Glycogen Accumulating Organisms
Bessarab, Irina
Maszenan, Abdul Majid
Haryono, Mindia A. S.
Arumugam, Krithika
Saw, Nay Min Min Thaw
Seviour, Robert J.
Williams, Rohan B. H.
Comparative genomics of members of the genus Defluviicoccus with insights into their ecophysiological importance
description 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.
author2 National University of Singapore
author_facet National University of Singapore
Bessarab, Irina
Maszenan, Abdul Majid
Haryono, Mindia A. S.
Arumugam, Krithika
Saw, Nay Min Min Thaw
Seviour, Robert J.
Williams, Rohan B. H.
format Article
author Bessarab, Irina
Maszenan, Abdul Majid
Haryono, Mindia A. S.
Arumugam, Krithika
Saw, Nay Min Min Thaw
Seviour, Robert J.
Williams, Rohan B. H.
author_sort Bessarab, Irina
title Comparative genomics of members of the genus Defluviicoccus with insights into their ecophysiological importance
title_short Comparative genomics of members of the genus Defluviicoccus with insights into their ecophysiological importance
title_full Comparative genomics of members of the genus Defluviicoccus with insights into their ecophysiological importance
title_fullStr Comparative genomics of members of the genus Defluviicoccus with insights into their ecophysiological importance
title_full_unstemmed Comparative genomics of members of the genus Defluviicoccus with insights into their ecophysiological importance
title_sort comparative genomics of members of the genus defluviicoccus with insights into their ecophysiological importance
publishDate 2022
url https://hdl.handle.net/10356/163268
_version_ 1751548499251429376
spelling sg-ntu-dr.10356-1632682022-12-03T23:31:21Z Comparative genomics of members of the genus Defluviicoccus with insights into their ecophysiological importance Bessarab, Irina Maszenan, Abdul Majid Haryono, Mindia A. S. Arumugam, Krithika Saw, Nay Min Min Thaw Seviour, Robert J. Williams, Rohan B. H. National University of Singapore Nanyang Environment and Water Research Institute Singapore Centre for Environmental Life Sciences and Engineering (SCELSE) Engineering::Environmental engineering Activated Sludge Glycogen Accumulating Organisms 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. Ministry of Education (MOE) National Research Foundation (NRF) Published version This work was supported by the Singapore National Research Foundation and Ministry of Education under the Research Centre of Excellence Programme. 2022-11-29T08:43:47Z 2022-11-29T08:43:47Z 2022 Journal Article Bessarab, I., Maszenan, A. M., Haryono, M. A. S., Arumugam, K., Saw, N. M. M. T., Seviour, R. J. & Williams, R. B. H. (2022). Comparative genomics of members of the genus Defluviicoccus with insights into their ecophysiological importance. Frontiers in Microbiology, 13, 834906-. https://dx.doi.org/10.3389/fmicb.2022.834906 1664-302X https://hdl.handle.net/10356/163268 10.3389/fmicb.2022.834906 35495637 2-s2.0-85128920348 13 834906 en Frontiers in Microbiology © 2022 Bessarab, Maszenan, Haryono, Arumugam, Saw, Seviour and Williams. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. application/pdf