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Ecology and physiology of methylotrophic bacteria

Ecology and physiology of methylotrophic bacteria


Several research questions arising in the context of soil, rhizosphere and phyllosphere microbiology are addressed by focusing on a specific functional guild within the microbial communities: the methylotrophic microorganisms. These are characterized by their ability to use one-carbon compounds such as methanol or methane as source of carbon and energy. Methylotrophic microorganisms occur quite widespread in nature; they are common in soils, aquatic ecosystems, air, sediments and dust. Noteworthy is their consistent occurrence in association with plants. In particular diverse strains of the methylotrophic genus Methylobacterium are found in the phyllosphere of essentially all land plants. The key characteristics of this alphaproteobacterial genus are a facultative methylotrophic lifestyle and pink pigmentation (Figure 4). It appears likely that the successful plant colonization of Methylobacteriumstrains is linked to the utilization of plant-released methanol. Due to the consistent colonization of plants by this bacterial genus, it serves as a good model to study plant colonization strategies by microorganisms and adaptations to life in the phyllosphere.

 

Methylobacterium

Figure 4: Soybean leaf imprint on a mineral salt medium agar plate supplemented with methanol as sole carbon source results in the development of colonies with pink pigmented bacteria of the genus Methylobacterium (left). Diverse members of this genus have been successfully isolated from plant leaves, characterized and used for in-depth studies.

 

A specific subgroup of methylotrophic bacteria are methanotrophic bacteria, which are defined by their ability to use methane as carbon and energy source. Methanotrophic bacteria represent the only biological sink for the greenhouse gas methane and are important players in the global methane cycle. They are frequently found at oxic/anoxic interfaces, e. g. in the rhizosphere of rice plants growing under flooded conditions, where they consume substantial amounts of the methane that is produced in the anoxic rice paddy. Moreover, methanotrophic bacteria are found in upland soils, where they oxidize atmospheric methane. Besides the well-known genera of methanotrophic bacteria, uncultivated representatives appear to play an important role in different soil ecosystems and the rice rhizosphere (Figure 5). Obtaining more information about the distribution and physiology of cultivated and uncultivated methanotrophs in soil and rhizosphere ecosystems is our research goal.

 

Methanotrophe Stammbaum

Figure 5: Diversity of methanotrophic bacteria as reflected by a phylogenetic tree based on pmoA, the gene encoding the active site subunit of the particulate methane monooxygenase. Selected sequences of evolutionary related moonooxygenases (amoA, hmoA) are included in this tree. Branches highlighted in red represent lineages of uncultivated groups of (potential) methanotrophic bacteria. Nomenclature of groups is in accordance with the review article of Knief (2015). 

Selected publications:

Knief, C. (2019) Diversity of methane-cycling microorganisms in soils and their relation to oxygen. In: Methylotrophs and methylotroph communities. Editor: L. Chistoserdova. Caister Academic Press, Poole, U.K. P. 23 – 56.

Dedysh, S.N., Knief, C. (2018) Diversity and phylogeny of described aerobic methanotrophs. In: Methane biocatalysis: paving the way to sustainability. Editors: Marina Kalyuzhnaya, Xin-Hui Xing, Springer, Cham, Switzerland. p. 17 – 42.

Frindte, K., Maarastawi, S.A., Lipski, A., Hamacher, J., Knief, C. (2017) Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai. Int. J. Syst. Evol. Microbiol. 67: 4507-4514.

Frindte, K., Kalyuzhnaya, M.G., Bringel, F., Dunfield, P.F., Jetten, M.S.M., Khmelenina, V.N., Klotz, M.G., Murrell, J.C., Op den Camp, H.J.M., Sakai, Y., Semrau, J.D., Shapiro, N., DiSpirito, A.A., Stein, L.Y., Svenning, M.M., Trotsenko, Y.A., Vuilleumier, S., Woyke, T., Knief, C. (2017) Draft genome sequences of two gammaproteobacterial methanotrophs isolated from rice ecosystems. Genome Announc. 5:e00526-17.

Knief, C. (2015) Diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoA as molecular marker. Front. Microbiol. 6: 1346

Knief, C., Dengler, V., Bodelier, P. L. E., Vorholt, J. A. (2012) Characterization of Methylobacterium strains isolated from the phyllosphere and description of Methylobacterium longum sp. nov. Antonie van Leeuwenhoek 101: 169-183.

Knief, C., Frances, L., Vorholt, J. A. (2010) Competitiveness of diverse Methylobacterium strains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1. Microb. Ecol. 60: 440-452.

Knief, C., Ramette, A., Frances, L., Alonso-Blanco, C., Vorholt, J. A. (2010) Site and plant species are important determinants of the Methylobacteriumcommunity composition in the phyllosphere. ISME J. 4: 719-728.

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