Comparative Genomics and Mutational Analysis Reveals a Novel XoxF-Utilizing Methylotroph in the Roseobacter Group Isolated From the Marine Environment.

Alexandra M. Howat,Yin Chen,Joanna L. Dixon,Anne-Kristin Kaster,J. C. Murrell,Carolina Grob,John Vollmers,Jonathan D. Todd,Martin Taubert

doi:10.3389/fmicb.2018.00766

Abstract

The Roseobacter group comprises a significant group of marine bacteria which are involved in global carbon and sulfur cycles. Some members are methylotrophs, using one-carbon compounds as a carbon and energy source. It has recently been shown that methylotrophs generally require a rare earth element when using the methanol dehydrogenase enzyme XoxF for growth on methanol. Addition of lanthanum to methanol enrichments of coastal seawater facilitated the isolation of a novel methylotroph in the Roseobacter group: Marinibacterium anthonyi strain La 6. Mutation of xoxF5 revealed the essential nature of this gene during growth on methanol and ethanol. Physiological characterization demonstrated the metabolic versatility of this strain. Genome sequencing revealed that strain La 6 has the largest genome of all Roseobacter group members sequenced to date, at 7.18 Mbp. Multilocus sequence analysis (MLSA) showed that whilst it displays the highest core gene sequence similarity with subgroup 1 of the Roseobacter group, it shares very little of its pangenome, suggesting unique genetic adaptations. This research revealed that the addition of lanthanides to isolation procedures was key to cultivating novel XoxF-utilizing methylotrophs from the marine environment, whilst genome sequencing and MLSA provided insights into their potential genetic adaptations and relationship to the wider community.

Highlights

Previous research has shown that methanol in the oceans can reach concentrations of up to 420 nM (Williams et al, 2004; Kameyama et al, 2010; Beale et al, 2011, 2013; Dixon et al, 2011, 2013a; Read et al, 2012)
The model methylotroph Methylobacterium extorquens contains both xoxF and mxaF genes, and work on this bacterium showed that it expressed XoxF instead of MxaF when lanthanide concentrations were higher than 100 nM (Vu et al, 2016)
By adding lanthanides to methanol seawater enrichments, we isolated a novel member of the Roseobacter clade that can use methanol as a carbon and energy source

Summary

Introduction

Previous research has shown that methanol in the oceans can reach concentrations of up to 420 nM (Williams et al, 2004; Kameyama et al, 2010; Beale et al, 2011, 2013; Dixon et al, 2011, 2013a; Read et al, 2012). A second type of methanol dehydrogenase (XoxF) encoded by a homolog of mxaF, xoxF, has been discovered in many methylotrophs (Chistoserdova and Lidstrom, 1997; Giovannoni et al, 2008; Chistoserdova, 2011; Keltjens et al, 2014). With five clades (named xoxF1-5) and often multiple gene copies present, it is generally difficult to examine the exact role in methylotrophs of MDH enzymes encoded by xoxF (Chistoserdova, 2011; Keltjens et al, 2014)

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Conclusion