Labrys methylaminiphilus sp. nov., a novel facultatively methylotrophic bacterium from a freshwater lake sediment

Abstract

A new bacterial isolate from a methylamine enrichment culture is described, representing a novel species of facultatively methylotrophic bacteria. The non-motile bacterium is Gram-negative, replicates by budding and does not form endospores. The isolate utilizes methylated amines, as well as a variety of monosaccharides, disaccharides, amino acids, organic acids, aromatic compounds and alcohols as substrates, but does not utilize methanol. Growth factors are not required, although yeast extract stimulates growth. The major components of the fatty acid profile are C 18 : 1 v7c, C 19 : 0 cyclo and C 16 : 0 . The dominant cellular phospholipids are phosphatidyl acid, phosphatidylcholine and phosphatidylethanolamine. The G+C content of the DNA is 65?7±0?3 mol%. 16S rRNA gene-based phylogenetic analysis revealed that the novel isolate belongs to the a-Proteobacteria and is closely related to the only representative of the genus Labrys, Labrys monachus (97?4 % sequence similarity). However, the level of DNA-DNA relatedness with L. monachus is less than 3 %, justifying the placement of this isolate into a novel species of the genus Labrys. The name Labrys methylaminiphilus sp. nov. is proposed (type strain JLW10 T =ATCC BAA-1080 T =DSM 16812 T ).Methylotrophs are a group of bacteria capable of metabolizing compounds containing no carbon-carbon bonds as sole sources of carbon and energy. These bacteria are ubiquitous in the biosphere and have been isolated from a wide variety of natural habitats including plants, soils and freshwater and marine sediments (Anthony, 1982). Methylotrophs play an important role in biogeochemical cycling and possess a potential for use in bioremediation (Pol et al., 1994; De Marco et al., 2004). We are studying a specific habitat that is rich in methylotrophic activity: the sediment of Lake Washington at a depth of about 60 m (Kuivila et al., 1988;Costello & Lidstrom, 1999). Until recently, research at this site has focused primarily on methanotroph populations (Auman et al., 2000;Costello & Lidstrom, 1999) and no survey of broader methylotroph presence has been conducted. This study focused on enrichment, isolation and taxonomic description of methylamine-utilizing bacteria from Lake Washington sediment. One of these isolates, a novel facultative methylotroph, is described. Sediment samples were collected on 21 July 2003, off the RV Clifford Barnes from a 63 m-deep site in Lake Washington, Seattle, WA, USA (47 u 38?0759 N 122 u 15?9939 W) using a box core that allowed collection of undisturbed sediment. Sediment cores were taken to a depth of approximately 20 cm and subsectioned into layers approximately 1?5 cm thick. Samples were transported to the laboratory on ice and used immediately. One millilitre samples of the upper 1?0 cm of the sediment cores were inoculated into 250 ml flasks containing 50 ml 0?26 salts medium (Harder et al., 1973) supplemented with 0?01 % methylamine (w/v) and were incubated for 6-8 days at room temperature with shaking (125 r.p.m.). In subsequent enrichments, ...

Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil

“…Isolates of this family possess xoxF-like genes (Beck et al, 2015). The only methylotrophic species reported to date is Labrys methylaminiphilus that utilizes methylamine and several monosaccharides, but not methanol (Miller et al, 2005). However, also L. monachus can utilize methanol to a certain extent (Miller et al, 2005).…”

“…The only methylotrophic species reported to date is Labrys methylaminiphilus that utilizes methylamine and several monosaccharides, but not methanol (Miller et al, 2005). However, also L. monachus can utilize methanol to a certain extent (Miller et al, 2005). Thus, the genus Labrys might comprise hitherto unknown methanol utilizers.…”

Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates

“…Alphaproteobacterial methane‐oxidizing methylotrophs have been previously described from Lake Washington, all classified within the family Methylocystaceae (Auman et al ., ). A novel type of an alphaproteobacterial methylotroph, Labrys methylaminiphilus was also previously characterized (Miller et al ., ), classified within the family Xanthobacteraceae (Lee et al ., ). We recently cultivated a broader variety of alphaproteobacterial methylotrophs from the same study site, using a variety of enrichment conditions (http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12736/suppinfo).…”

Methylotrophy in a Lake: from Metagenomics to Single-Organism Physiology

“…Many methylotrophic bacteria are available in culture, including a number of isolates from Lake Washington (3,20,21,23,28,35). These organisms provide useful models for studying the distinguishing features of methylotrophic metabolism (1,33).…”