Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing

Abstract New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes o...

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Autores principales:	Krithika Arumugam, Irina Bessarab, Mindia A. S. Haryono, Xianghui Liu, Rogelio E. Zuniga–Montanez, Samarpita Roy, Guanglei Qiu, Daniela I. Drautz–Moses, Ying Yu Law, Stefan Wuertz, Federico M. Lauro, Daniel H. Huson, Rohan B. H. Williams
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Microbial ecology QR100-130
Acceso en línea:	https://doaj.org/article/0e7f1b54b39d45908d7c06e60e12a27c
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spelling	oai:doaj.org-article:0e7f1b54b39d45908d7c06e60e12a27c2021-12-02T11:39:44ZRecovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing10.1038/s41522-021-00196-62055-5008https://doaj.org/article/0e7f1b54b39d45908d7c06e60e12a27c2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41522-021-00196-6https://doaj.org/toc/2055-5008Abstract New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas, and Micropruina, Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.Krithika ArumugamIrina BessarabMindia A. S. HaryonoXianghui LiuRogelio E. Zuniga–MontanezSamarpita RoyGuanglei QiuDaniela I. Drautz–MosesYing Yu LawStefan WuertzFederico M. LauroDaniel H. HusonRohan B. H. WilliamsNature PortfolioarticleMicrobial ecologyQR100-130ENnpj Biofilms and Microbiomes, Vol 7, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbial ecology QR100-130
spellingShingle	Microbial ecology QR100-130 Krithika Arumugam Irina Bessarab Mindia A. S. Haryono Xianghui Liu Rogelio E. Zuniga–Montanez Samarpita Roy Guanglei Qiu Daniela I. Drautz–Moses Ying Yu Law Stefan Wuertz Federico M. Lauro Daniel H. Huson Rohan B. H. Williams Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing
description	Abstract New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas, and Micropruina, Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.
format	article
author	Krithika Arumugam Irina Bessarab Mindia A. S. Haryono Xianghui Liu Rogelio E. Zuniga–Montanez Samarpita Roy Guanglei Qiu Daniela I. Drautz–Moses Ying Yu Law Stefan Wuertz Federico M. Lauro Daniel H. Huson Rohan B. H. Williams
author_facet	Krithika Arumugam Irina Bessarab Mindia A. S. Haryono Xianghui Liu Rogelio E. Zuniga–Montanez Samarpita Roy Guanglei Qiu Daniela I. Drautz–Moses Ying Yu Law Stefan Wuertz Federico M. Lauro Daniel H. Huson Rohan B. H. Williams
author_sort	Krithika Arumugam
title	Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing
title_short	Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing
title_full	Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing
title_fullStr	Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing
title_full_unstemmed	Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing
title_sort	recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/0e7f1b54b39d45908d7c06e60e12a27c
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Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing

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