Curriculum Vitae
April 2005 – to Present
PhD Student
supervised by Prof. Dr. J. H. J. Leveau Dr. W. de Boer and Prof. Dr. J. A. van Veen.
The project is part of the Ecogenomics research program (http://www.ecogenomics.eu, http://www.ecogenomics.nl) and it is carried out at the Centre for terrestrial Ecology of the NIOO-KNAW.
Projects
PhD project: “Genomic Analysis of Bacterial Mycophagy"
Collimonas bacteria have been described in 2004 as a novel genus unique in its property of growing at the expense of living hyphae of different fungi. The complete genome sequence of Collimonas fungivorans Ter331 (Fig. 1) constitutes the basis for this project and it is studied for identifying the key genes used by this bacterium in its attack to fungi.
 Fig. 1 C. fungivorans Ter331 circular chromosome (~5.2 MBp)
Main experiments performed within the project:
¨ Sequence, Evolution, and Ecology of pTer331 Plasmid
The sequence of the plasmid pTer331, isolated from C. fungivorans Ter331, was annotated and studied (Fig. 2). This cryptic, conjugative plasmid codes for genes needed for its maintenance, self replication and transfer. We tested the contribution of pTer331 to Collimonas phenotypic traits and we found no evidence that functions related to mycophagy could be located on the plasmid. Being a broad-host-range plasmid with mobilizing and retromobilizing activity its presence could benefit the bacterial populations by favoring gene transfer, chromosomal rearrangements and bacterial evolution.
 Fig. 2 Genetic map of plasmid pTer331 (~40.5 KBp)
¨ Expression Microarrays
A dual culture plate assay was set up to confront the bacterium C. fungivorans and the fungus Aspergillus niger. The changes in the transcriptional profile, induced in each organism as a consequence of the presence of the other, were studied by isolating mRNA from both organisms and comparing the confrontation plate mRNA with mRNA extracted form control plates, where each organism was plated singly (Fig. 3).
The transcription profiles were analyzed by mean of expression microarrays. The experiment pointed out the set of genes triggered in each organism as a result of the presence of the other (Fig. 4), and confirmed the existence of an antagonistic interaction between the two organisms.
 Fig. 3 The picture represents the set up of the assay. On the confrontation plate (central) the fungus is plated in the center on top of a polycarbonate membrane, while the bacterium is plated in two line on its side. On the control plates each organism is plated singly (left plate, fungus; right plate, bacterium).
 Fig4 Heat map of a subset of genes differentially expressed in C. fungivorans when it is grown in the presence of A. niger (conf) and when it is grown singly (ctrl) (high gene expression=yellow, low gene expression=blue). The experiment was performed twice, at two different time points during the experiment. As it is shown by the figure, the genes differentially induced change with time point.
¨
¨ Microarray-based Comparative Genomic Hybridization
The genomic content of several Collimonas belonging to different species was juxtaposed using a microarray-based genome comparison. The ratio of the hybridization intensity of the test to the reference was used to detect potential differences in the genome content of the tested strains and the genome content of the reference strain C. fungivorans Ter331 (Fig. 5). The aim of this experiment was to identify a core of conserved genes, common to all the tested Collimonas species, and a set of genes specific to the reference and to some, but not all, of the other strains. The common Collimonas genes confer to the genus its general properties, while the second kind of genes could possibly be linked to more specific properties, such as the adaptation of certain Collimonas species to a determined ecological niche.
 Fig. 5 Graph showing log2 ratios of hybridized probes plotted as a function of their location on the chromosome, using C. fungivorans Ter6 as the test strain. Probes showing a log2 ratio of around zero correspond to areas where the test and the reference probably share the same sequence, probes with negative log2 ratios indicate potential gene deletions and probes with positive log2 ratios indicate potential gene duplications. On the right side of the panel are highlighted in blue the probes corresponding to plasmid pTer331
Selected Publications
F. Mela, K. Fritsche, H. Boersma, J.D. van Elsas, D. Bartels, F. Meyer, W. de Boer, J.A. van Veen and J.H.J. Leveau, 2008. Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS Microbiology Ecology: 66: 45-62
Mela, F., Fritsche, K., de Boer, W., van Veen, J. A. & Leveau, J. H. J. Comparative genomics of mycophagy. In preparation
Mela, F., Fritsche, K., de Boer, W., van Veen, J. A. & Leveau, J. H. J. Expression profile of the antagonistic interaction of Collimonas fungivorans and Aspergillus niger. In preparation
| 
