Comparative genomics analyses indicate differential methylated amine utilization trait within members of the genus Gemmobacter.

Eileen Kröber,Ricardo Kruger,Daniela Wischer,Julianna Peixoto,Deepak Kumaresan,Lewis Spurgin,Mark R Cunningham

doi:10.1111/1758-2229.12927

Abstract

Methylated amines are ubiquitous in the environment and play a role in regulating the earth's climate via a set of complex biological and chemical reactions. Microbial degradation of these compounds is thought to be a major sink. Recently we isolated a facultative methylotroph, Gemmobacter sp. LW-1, an isolate from the unique environment Movile Cave, Romania, which is capable of methylated amine utilization as a carbon source. Here, using a comparative genomics approach, we investigate how widespread methylated amine utilization is within members of the bacterial genus Gemmobacter. Seven genomes of different Gemmobacter species isolated from diverse environments, such as activated sludge, fresh water, sulphuric cave waters (Movile Cave) and the marine environment were available from the public repositories and used for the analysis. Our results indicate that methylamine utilization is a distinctive feature of selected members of the genus Gemmobacter, namely G. aquatilis, G. lutimaris, G. sp. HYN0069, G. caeni and G. sp. LW-1 have the genetic potential while others (G. megaterium and G. nectariphilus) have not.

Highlights

Methylated amines (MAs) are ubiquitous in the environment with a variety of natural and anthropogenic sources including the oceans, vegetation, sediments and organicrich soils, animal husbandry, food industry, pesticides, sewage and automobiles, to mention only a few (Schade and Crutzen, 1995; Latypova et al, 2010; Ge et al, 2011)
Phylogenomic analysis based on single copy marker genes specific to members within Alphaproteobacteria revealed that G. sp LW1, G. caeni and G. lutimaris clustered together and along with G. aquatilis and G. sp HYN0069 were closely related to Rhodobacter sphaeroides 2.4.1 whereas G. megabacterium and G. nectariphilus to Paracoccus denitrificans (Fig. 1B & Table S5 for genome taxonomy classification)
LW-1, G. lutimaris and G. caeni are capable of generating energy from complete oxidation of methylated amines via the H4F-dependent pathway using either the NMG pathway or the direct MMA oxidation pathway

Summary

Introduction

Methylated amines (MAs) are ubiquitous in the environment with a variety of natural and anthropogenic sources including the oceans, vegetation, sediments and organicrich soils, animal husbandry, food industry, pesticides, sewage and automobiles, to mention only a few (Schade and Crutzen, 1995; Latypova et al, 2010; Ge et al, 2011). Microbial metabolism of methylated amines involves both aerobic and anaerobic microorganisms, for example some methanogenic archaea such as Methanosarcina and Methanomicrobium can use MAs to produce methane (Burke et al, 1998; Liu and Whitman, 2008; Lyimo et al, 2009) while Gram-positive and Gram-negative methylotrophic bacteria can use MAs as carbon and nitrogen source (Chen et al, 2010a). Recent studies have reported the detection and activity of aerobic methylotrophic bacteria that utilize MAs in a variety of natural and engineered environments (Chen et al, 2009; Chistoserdova et al, 2009; Chistoserdova, 2011; Ge et al, 2011; Wischer et al, 2015) and could play a major role in global C and N budgets

Methods

Results

Conclusion