title: On the reproducibility of microcosm experiments - different community composition in parallel phototrophic biofilm microcosms.
abstract: Phototrophic biofilms were cultivated simultaneously using the same inoculum in three identical flow-lane microcosms located in different laboratories. The growth rates of the biofilms were similar in the different microcosms, but denaturing gradient gel electrophoresis (DGGE) analysis of both 16S and 18S rRNA gene fragments showed that the communities developed differently in terms of species richness and community composition. One microcosm was dominated by Microcoleus and Phormidium species, the second microcosm was dominated by Synechocystis and Phormidium species, and the third microcosm was dominated by Microcoleus- and Planktothrix- affiliated species. No clear effect of light intensity on the cyanobacterial community composition was observed. In addition, DGGE profiles obtained from the cultivated biofilms showed a low resemblance with the profiles derived from the inoculum. These findings demonstrate that validation of reproducibility is essential for the use of microcosm systems in microbial ecology studies.
authors.affiliation: Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
authors.forename: Guus
authors.initials: G
authors.lastname: Roeselers
authors.forename: Barbara
authors.initials: B
authors.lastname: Zippel
authors.forename: Marc
authors.initials: M
authors.lastname: Staal
authors.forename: Mark
authors.initials: M
authors.lastname: van Loosdrecht
authors.forename: Gerard
authors.initials: G
authors.lastname: Muyzer
mesh_terms: D018441:Biofilms / Q000254:growth & development*; D016000:Cluster Analysis; D000458:Cyanobacteria / Q000145:classification* / Q000235:genetics / Q000502:physiology*; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D008027:Light; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S