Shearing of biofilms enables selective layer based microbial sampling and analysis

Lu, Yang., Slater, Frances, Bello-Mendoza, Ricardo and Batstone, Damien J. (2013) Shearing of biofilms enables selective layer based microbial sampling and analysis. Biotechnology and Bioengineering, 110 10: 2600-2605. doi:10.1002/bit.24947

Author Lu, Yang.
Slater, Frances
Bello-Mendoza, Ricardo
Batstone, Damien J.
Title Shearing of biofilms enables selective layer based microbial sampling and analysis
Journal name Biotechnology and Bioengineering   Check publisher's open access policy
ISSN 0006-3592
Publication date 2013-01-01
Year available 2013
Sub-type Article (original research)
DOI 10.1002/bit.24947
Open Access Status Not yet assessed
Volume 110
Issue 10
Start page 2600
End page 2605
Total pages 6
Place of publication Hoboken, NJ United States
Publisher John Wiley and Sons Inc.
Language eng
Subject 2402 Applied Microbiology and Biotechnology
1502 Banking, Finance and Investment
1305 Biotechnology
Abstract Granules are large, self-supporting biofilms that form naturally in high-rate anaerobic treatment systems and are extremely important to reactor functionality. Granules exhibit functional and phylogenetic layering, interesting to both scientists and technologists. Until now, it has only been possible to analyze layering through sectioning and microscopic analysis with fluorescent in situ hybridization, or to analyze the whole granule through DNA extraction and microbial community profiling methods. This means different functional and spatial layers cannot be analyzed separately, including next generation sequencing techniques, such as pyrotag sequencing. In this work, we describe a method to remove microbes selectively from successive spatial layers through hydraulic shearing and demonstrate its application on anaerobic granules of three different types (VFA-, carbohydrate-, protein-fed) in size ranges 0.6-2mm. Outer layers in particular could be selectively sheared as confirmed by FISH. TRFLP was used as an example bulk DNA method on selectively sheared fractions. A shift in dominant population was found from presumptive acidogens (such as Bacteroidetes and Anaerolinea) in outer layers to syntrophs (such as Syntrophomonas and Geobacter) in inner layers, with progressive changes through the depth. The strength of the shear-bulk molecular method over FISH was that a deeper phylogenetic profile could be obtained, even with TRFLP, and that prior knowledge of the community is not required. Biotechnol.
Keyword Anaerobic granule
Granule layer
Shear stress
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
Advanced Water Management Centre Publications
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