Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture.

Lavinia Gambelli,Mike S M Jetten,Laura Van Niftrik,Bas E Dutilh,Rob Mesman,Huub J M Op Den Camp,Simon Guerrero,Geert Cremers

doi:10.3389/fmicb.2016.01740

Abstract

With its capacity for anaerobic methane oxidation and denitrification, the bacterium Methylomirabilis oxyfera plays an important role in natural ecosystems. Its unique physiology can be exploited for more sustainable wastewater treatment technologies. However, operational stability of full-scale bioreactors can experience setbacks due to, for example, bacteriophage blooms. By shaping microbial communities through mortality, horizontal gene transfer, and metabolic reprogramming, bacteriophages are important players in most ecosystems. Here, we analyzed an infected Methylomirabilis sp. bioreactor enrichment culture using (advanced) electron microscopy, viral metagenomics and bioinformatics. Electron micrographs revealed four different viral morphotypes, one of which was observed to infect Methylomirabilis cells. The infected cells contained densely packed ~55 nm icosahedral bacteriophage particles with a putative internal membrane. Various stages of virion assembly were observed. Moreover, during the bacteriophage replication, the host cytoplasmic membrane appeared extremely patchy, which suggests that the bacteriophages may use host bacterial lipids to build their own putative internal membrane. The viral metagenome contained 1.87 million base pairs of assembled viral sequences, from which five putative complete viral genomes were assembled and manually annotated. Using bioinformatics analyses, we could not identify which viral genome belonged to the Methylomirabilis- infecting bacteriophage, in part because the obtained viral genome sequences were novel and unique to this reactor system. Taken together these results show that new bacteriophages can be detected in anaerobic cultivation systems and that the effect of bacteriophages on the microbial community in these systems is a topic for further study.

Highlights

The importance of microorganisms in biogeochemical cycles and global warming is well-known (Falkowski et al, 2008)
The present paper describes the bacteriophage population in a Methylomirabilis bioreactor enrichment culture using electron microscopy, viral metagenomics, and bioinformatics analysis
We investigated the bacteriophage population in a bioreactor containing an enrichment culture of the anaerobic methanotroph Methylomirabilis sp. (Table 1)

Summary

Introduction

The importance of microorganisms in biogeochemical cycles and global warming is well-known (Falkowski et al, 2008). These Gram-negative, rod-shaped bacteria have a polygonal cell shape constituted by several longitudinal ridges running along the cell length and converging in a cap-like structure at the cell poles (Wu et al, 2012) These microorganisms are interesting from a fundamental scientific point of view, but could be important players in natural ecosystems (Deutzmann et al, 2014; Hu et al, 2014) and be implemented in the removal of dissolved methane and ammonium from digester effluents in combination with anaerobic ammonium oxidizing bacteria (Luesken et al, 2011; Shi et al, 2013)

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Results

Conclusion