Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing.

Katharina Willenbücher,Patrice Ramm,Julia Gätcke,Jimena Barrero Canosa,Andreas Schlüter,Ulrich Szewzyk,Tobias Busche,Liren Huang,Daniel Wibberg,Irena Maus,Christian Brandt,Marius Conrady

doi:10.3390/microorganisms10020368

Abstract

The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering process of the microbial network. In this study, an enriched fraction of virus-like particles was extracted from a mesophilic biogas reactor and sequenced on the Illumina MiSeq and Nanopore GridION sequencing platforms. Metagenome data analysis resulted in identifying 375 metagenome-assembled viral genomes (MAVGs). Two-thirds of the classified sequences were only assigned to the superkingdom Viruses and the remaining third to the family Siphoviridae, followed by Myoviridae, Podoviridae, Tectiviridae, and Inoviridae. The metavirome showed a close relationship to the phage genomes that infect members of the classes Clostridia and Bacilli. Using publicly available biogas metagenomic data, a fragment recruitment approach showed the widespread distribution of the MAVGs studied in other biogas microbiomes. In particular, phage sequences from mesophilic microbiomes were highly similar to the phage sequences of this study. Accordingly, the virus particle enrichment approach and metavirome sequencing provided additional genome sequence information for novel virome members, thus expanding the current knowledge of viral genetic diversity in biogas reactors.

Highlights

Bacteriophages or phages, viruses that infect Bacteria and Archaea, are increasingly being recognized as the most abundant biological entities on earth, with an estimated amount of 1031 particles on our planet [1,2]
After a subsequent rest period of about 6 months including stirring under mesophilic conditions, the whole reactor content was removed from the continuous stirred tank reactor (CSTR) and particles >5 mm were separated by a food mill
Many of the environments in which phages interact with their bacterial hosts are anaerobic. Some of these scenarios are of importance regarding biotechnological applications, such as energy recovery by the anaerobic digestion of biomass

Summary

Introduction

Bacteriophages or phages, viruses that infect Bacteria and Archaea, are increasingly being recognized as the most abundant biological entities on earth, with an estimated amount of 1031 particles on our planet [1,2]. They play a critical role in shaping microbial diversity and composition. Bacteriophages encode “auxiliary metabolic genes” (AMGs) that may provide new genetic traits to their hosts and/or alter bacterial metabolism [6,7,8,9] They may affect the performance of the host and its surrounding community. The prevalence of virus/phage sequences varies between 0.1 and 1% of the entire biogas microbiome [17,18]

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