Bacterial metabolism of methylated amines and identification of novel methylotrophs in Movile Cave

Abstract

Movile Cave, Romania, is an unusual underground ecosystem that has been sealed off from the outside world for several million years and is sustained by non-phototrophic carbon fixation. Methane and sulfur-oxidising bacteria are the main primary producers, supporting a complex food web that includes bacteria, fungi and cave-adapted invertebrates. A range of methylotrophic bacteria in Movile Cave grow on one-carbon compounds including methylated amines, which are produced via decomposition of organic-rich microbial mats. The role of methylated amines as a carbon and nitrogen source for bacteria in Movile Cave was investigated using a combination of cultivation studies and DNA stable isotope probing (DNA-SIP) using 13 C-monomethylamine (MMA). Two newly developed primer sets targeting the gene for gamma-glutamylmethylamide synthetase (gmaS), the first enzyme of the recently-discovered indirect MMA-oxidation pathway, were applied in functional gene probing. SIP experiments revealed that the obligate methylotroph Methylotenera mobilis is one of the dominant MMA utilisers in the cave. DNA-SIP experiments also showed that a new facultative methylotroph isolated in this study, Catellibacterium sp. LW-1 is probably one of the most active MMA utilisers in Movile Cave. Methylated amines were also used as a nitrogen source by a wide range of non-methylotrophic bacteria in Movile Cave. PCR-based screening of bacterial isolates suggested that the indirect MMA-oxidation pathway involving GMA and N-methylglutamate is widespread among both methylotrophic and non-methylotrophic MMA utilisers from the cave.

Interkingdom Cross-Feeding of Ammonium from Marine Methylamine-Degrading Bacteria to the Diatom Phaeodactylum tricornutum

“…This possibility is supported by culture-independent studies that show the presence of bacterial genera in the phycosphere, which could potentially be capable of methylamine utilization (20). In this respect, the environmental concentrations of MMA and other methylated C 1 compound metabolites have certainly been underestimated because of the fast degradation of such compounds in natural habitats (12,37,49). As our results suggest that interactions of diatoms with MMA-degrading bacteria are profitable in marine environments, it appears to be an attractive hypothesis that diatoms may release molecules to attract methylamine-degrading bacteria.…”

“…The current view is that the MMA dehydrogenase pathway is dominant among bacteria that use MMA also as a carbon source, while those using it as a nitrogen source have mainly the cytosolic NMG pathway (12,15). According to the genome sequence of strain KarMa (unpublished), this bacterium harbors the mau gene cluster for MMA degradation as well as the genes for the NMG pathway.…”

“…Methylamines such as monomethylamine (MMA) are derived from the degradation of proteins and other organic nitrogen compounds and occur ubiquitously in surface waters. Notably, methylamines are also formed during the degradation of osmolytes such as glycine betaine produced by marine organisms (12). Methylamines are C 1 compounds (i.e., compounds containing no carbon-carbon bond), which can be utilized as carbon and energy sources by methylotrophic bacteria (13,14).…”

Methylotrophs in natural habitats: current insights through metagenomics

“…The long-standing question of the activity of this enzyme (Chistoserdova and Lidstrom 1997) has been resolved, by identifying its reliance on lanthanides, as part of its catalytic centre (Hibi et al 2011;Fitriyanto et al 2011;Nakagawa et al 2012;Pol et al 2014). Likewise, the much-celebrated MADH (Davidson 2003) appears to be much less environmentally widespread, compared to the alternative NMG pathway (Latypova et al 2010;Chen et al, 2010;Beck et al 2014Beck et al , 2015Wischer et al 2015). These recent findings set a stage for revisiting methylotrophy as likely a more encompassing and more widespread metabolic feature in the bacterial world than previously thought.…”

“…Communities in another exotic environment, the underground cave ecosystem sealed from the outside world for millions of years and sustained by non-phototrophic carbon fixation, were assessed via methylamine-SIP (Wischer et al 2015). Methylotenera species were determined as the primary methylamine utilizers, closely related to the species from Lake Washington.…”