Bait and scrape: An approach for assessing biofilm microbial communities on organic media used for gas-phase biofiltration

Jason P. Oliver, Kevin A. Janni, Jonathan S. Schilling

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Gas-phase biofilters offer effective pollution control for agricultural effluents, but a better understanding of microbial communities responsible for capture and degradation is needed to improve process control. In this study, we developed a wood bait and optimized microbial biofilm sampling for monitoring microbial biomarkers (microbial C, ergosterol, DNA) in a full-scale biofilter. Results demonstrated that targeting biofilm dynamics required removing the biofilm from the wood substrates prior to biomarker extraction. We identified a sampling threshold for these biofilms of ≥100 mg for accurate and low variability biomarker measurement, a threshold that can inform analyses in other systems or using other approaches (i.e. DNA sequencing). Using this approach in a full-scale biofilter revealed that the fungal contribution (as ergosterol) to total microbial biomass was greatest in the most desiccation-prone area of the biofilter. This observation is in-line with results from previous lab-scale studies and could be due, in part, to connectivity between fungal hyphae growing in biofilms and the wood baits, shown by confocal microscopy. This work provides a targeted sampling strategy for microbial biofilms in gas-phase biofiltration, adaptable to other pollution control bioreactors and that can be used to study microbial community dynamics in full-scale systems.

Original languageEnglish (US)
Pages (from-to)50-57
Number of pages8
JournalEcological Engineering
StatePublished - Jun 1 2016

Bibliographical note

Funding Information:
Funding for this project was provided by grants from the United States Department of Agriculture , National Institute of Food and Agriculture , Agriculture and Food Research Initiative ( USDA/2010-85112-20520 & USDA/2012-69002-19880 ) and the USDA NIFA Mcintire Stennis Project #MIN-12-074 at the University of Minnesota. The authors wish to gratefully acknowledge Brian Hetchler and Larry Jacobsen for their biofilter design, installation and field work expertise, members of the Schilling laboratory for assistance with sample processing, the United States Forest Service Laboratory in Grand Rapids, MN for use of laboratory equipment and the staff of the University of Minnesota Imaging Center for confocal microscopy assistance.

Publisher Copyright:
© 2016.


  • Biofilm
  • Biofilter
  • Biomarker
  • Fungi
  • Microbial biomass
  • Wood


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