title: Exploration and prediction of interactions between methanotrophs and heterotrophs.
abstract: Methanotrophs can form the basis of a methane-driven food web on which heterotrophic microorganisms can feed. In return, these heterotrophs can stimulate growth of methanotrophs in co-culture by providing growth additives. However, only a few specific interactions are currently known. We incubated nine methanotrophs with 25 heterotrophic strains in a pairwise miniaturized co-cultivation setup. Through principal component analysis and k-means clustering, methanotrophs and heterotrophs could be grouped according to their interaction behaviour, suggesting strain-dependent methanotroph-heterotroph complementarity. Co-cultivation significantly enhanced the growth parameters of three methanotrophs. This was most pronounced for Methylomonas sp. M5, with a threefold increase in maximum density and a fourfold increase in maximum increase in density in co-culture with Cupriavidus taiwanensis LMG 19424. In contrast, co-cultivation with Methylobacterium radiotolerans LMG 2269 and Pseudomonas aeruginosa LMG 12228 inhibited growth of most methanotrophs. Functional genomic analysis suggested the importance of vitamin metabolism for co-cultivation success. The generated data set was then successfully exploited as a proof-of-principle for predictive modelling of co-culture responses based on other interactions of the same heterotrophs and methanotrophs, yielding values of the area under the receiver operating characteristic curve of 0.73 upon 50% missing values for the maximum increase in density parameter. As such, these modelling-based tools were shown to hold great promise in reducing the amount of data that needs to be generated when conducting large co-cultivation studies.
authors.affiliation: KERMIT, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Gent, Belgium. Electronic address: Michiel.Stock@ugent.be.
authors.forename: Michiel
authors.initials: M
authors.lastname: Stock
authors.forename: Sven
authors.initials: S
authors.lastname: Hoefman
authors.forename: Frederiek-Maarten
authors.initials: FM
authors.lastname: Kerckhof
authors.forename: Nico
authors.initials: N
authors.lastname: Boon
authors.forename: Paul
authors.initials: P
authors.lastname: De Vos
authors.forename: Bernard
authors.initials: B
authors.lastname: De Baets
authors.forename: Kim
authors.initials: K
authors.lastname: Heylen
authors.forename: Willem
authors.initials: W
authors.lastname: Waegeman
mesh_terms: D001419:Bacteria / Q000254:growth & development* / Q000378:metabolism*; D002244:Carbon / Q000378:metabolism; D004734:Energy Metabolism; D052836:Heterotrophic Processes; D008697:Methane / Q000378:metabolism*; D056265:Microbial Interactions; D009584:Nitrogen / Q000378:metabolism
chemical_list: D002244:Carbon; D009584:Nitrogen; D008697:Methane
keywords: Methanotroph; Microbial interaction; Predictive modelling