Open Access Highly Accessed Research article

Characterization of structures in biofilms formed by a Pseudomonas fluorescens isolated from soil

Marc M Baum1*, Aleksandra Kainović1, Teresa O'Keeffe1, Ragini Pandita1, Kent McDonald2, Siva Wu3 and Paul Webster3

Author affiliations

1 Department of Chemistry, Oak Crest Institute of Science, 2275 E. Foothill Blvd, Pasadena, CA 91107, USA

2 Electron Microscope Lab, 26 Giannini Hall, University of California, Berkeley, Berkeley, CA 94720, USA

3 Ahmanson Advanced EM & Imaging Center, House Ear Research Institute, 2100 W. 3rd Street, Los Angeles, CA 90057, USA

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Citation and License

BMC Microbiology 2009, 9:103  doi:10.1186/1471-2180-9-103

Published: 21 May 2009



Microbial biofilms represent an incompletely understood, but fundamental mode of bacterial growth. These sessile communities typically consist of stratified, morphologically-distinct layers of extracellular material, where numerous metabolic processes occur simultaneously in close proximity. Limited reports on environmental isolates have revealed highly ordered, three-dimensional organization of the extracellular matrix, which may hold important implications for biofilm physiology in vivo.


A Pseudomonas spp. isolated from a natural soil environment produced flocculent, nonmucoidal biofilms in vitro with unique structural features. These mature biofilms were made up of numerous viable bacteria, even after extended culture, and contained up to 50% of proteins and accumulated 3% (by dry weight) calcium, suggesting an important role for the divalent metal in biofilm formation. Ultrastructurally, the mature biofilms contained structural motifs consisting of dense, fibrillary clusters, nanofibers, and ordered, honeycomb-like chambers enveloped in thin sheets.


Mature biofilms contained living bacteria and were structurally, chemically, and physiologically heterogeneous. The principal architectural elements observed by electron microscopy may represent useful morphological clues for identifying bacterial biofilms in vivo. The complexity and reproducibility of the structural motifs observed in bacterial biofilms appear to be the result of organized assembly, suggesting that this environmental isolate may possess ecological advantages in its natural habitat.