Environmental Microbiology Laboratory
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School of Biological Sciences,
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The Research Group
Associate Professor Gillian Lewis (Group Leader)
Dr Gavin Lear (Post Doctoral Research Fellow)
Yimin Dong (Research and Teaching Technician)
Andrew Dopheide (Research Technician)
Sarveshni Pillay (Administration Assistant)
Kelly Roberts (PhD Student: Bacterial biofilm in streams)
Vidya Washington (PhD Student: Biofilm formation by key bacterial species )
Pierre Ancion (PhD Student: Biofilm manipulation to support stream restoration )
Jo Smith (PhD Student: A Novel Mn depositing stream bacteria)
Joanne Hewitt ( PhD Student : Human Adenovirus: a Surrogate for the presence of enteric viruses in food and water based ae ESR Porirua)
Anne-Marie Perchec (MSc Student : Is there an environmental clade of Escherichia coli?)
Biofilm Research
Stream biofilms are the focus of our current research. This work focuses on the structure, function and ecological roles of these complex communities.
See the stream biofilm website at www.streambiofilm.org.nz
Current and ongoing projects
- Relationship between bacterial community diversity and functional diversity in stream biofilms
- Influence of light and flow regimes on bacterial communities in stream biofilms.
- Microbial biofilms for enhancement of stormwater treatment systems.
- Microbial biofilms for monitoring the ecological health of streams.
- The importance of rare bacteria in mixed communities.
- Stream microbial food webs
Past, Completed Projects
- Distribution, persistence and fate of human viruses in aquatic systems.
- Contaminants of Oyster farms by microbial pathogens and indicators.
- Source distribution and implications of microbial contamination of beaches.
- Microbiological components and activity in reducing contaminants in stormwater treatment systems
- Alternative microbial indicators and water quality.
- Virus transfer to the air by bubble bursting.
- Bacterial resuspension from sediments: implications for water quality.
- Microbial assemblages in wetlands receiving wastewater.
- The influence of bacterial viruses on the bacterial population dynamics in wastewater treatment systems
- Human viruses in New Zealand Rivers.
- Microbial intervention to reduce methane emissions from waste treatment systems.
Recent Publications
Lear, G., Niyogi, D., Harding, J., Dong, Y., Lewis, GD (2009) Biofilm bacterial community structure in streams affected by acid mine drainage. Applied and Environmental Microbiology 75 (11) 3455-3460.Lear, G., Boothroyd, IKG., Turner, SJ., Roberts, K., Lewis, GD (2009) A comparison of bacterial and benthic invertebrate community assemblages as indicators of ecological health within freshwater streams. Freshwater Biology 54: 1532-1543.
Lear, G., Turner, SJ., Lewis GD (2009) Effect of light regimes on the utilisation of an exogenous carbon source by biofilm bacterial communities. Aquatic Ecology 43: 207-220.
Lear, G., Lewis, GD (2009) Impact of land use on bacterial communities within stream biofilms. Ecological Indicators 9: 848-855.
Lear, G., Lewis, GD (2009) Nested Automated Ribosomal Intergenic Spacer Analysis: A rapid and accurate method for comparison of bacterial community composition. Journal of Rapid Methods and Automation in Microbiology 17: 257-270.
Lear, G., Anderson, MJ., Smith, JP., Boxen, K., Lewis, GD (2008) Spatial and temporal heterogeneity of the bacterial communities in stream epilithic biofilms. FEMS Microbiology Ecology. 65 (3): 463-473
Dopheide, A., Lear, G., Stott, R., Lewis, GD (2008) Molecular characterisation of ciliate diversity in stream biofilms. Applied and Environmental Microbiology 74(6):1740-1747 (and journal front cover)
Love Your Biofilm -
LoveYourBiofilm.pdf (235kB)
(235k PDF) Biofilm in Streams -
BiofilmsInStreams.pdf (73kB)
(74k PDF)
Recent Significant Reports
Lewis GD, G. Lear and P-Y Ancion. 2009. Stormwater changes bacterial communities and ecological function in streams. Proceedings NZWWA 6th South Pacific Stormwater Conference, 29th April - 1st May 2009, Auckland, New Zealand
Lewis GD: Enteric Zoonoses Pathogens Outside The Host: Transmission Persistence. Distribution Detection And Risk Potential: Report Of Enteric Zoonoses Steering Committee Workshop 30 April Wellington. pp 12
Recent Conference Presentations
G.D. Lewis, G. Lear, I K.M Roberts.K.G. Boothroyd, A. Dopheide, Enhancing Ecosystem Services in your stream? It’s the little things that count. New Zealand Freshwater Sciences Society Annual Conference New Plymouth 24 -27 November 2008
Boothroyd,IKG, Colley E, Lewis GD. Restoring Streams: Colonisation of Biofilm and Macrobenthic invertebrate communities on surfaces in streams. New Zealand Freshwater Sciences Society Annual Conference New Plymouth 24 -27 November 2008
Lewis G D, G Lear, S.Turner, I Boothroyd, R Stott, K Roberts, P Ancion, A Dopheide, v. Washington, J Smith, D Knight: Bacteria the invisible Powerhouse of stream ecosystem function. New Zealand Microbiology Society Annual Conference: Christchurch 18 - 21 November 2008. Key Note Address
Lewis G D, G Lear, S.Turner, I Boothroyd, R Stott, K Roberts, P Ancion, A Dopheide, v. Washington, J Smith, D Knight: Stream Restoration: Getting the microbial ecology right. 12th International Symposium on Microbial Ecology: ISME12, Cairns, Australia, August 17-22 2008 (poster).
Dopheide A , G Lear, R Stott, G D Lewis: Ciliate Diversity in Stream Biofilms revealed by group-specific PCR primers. 12th International Symposium on Microbial Ecology: ISME12, Cairns, Australia, August 17-22 2008
Roberts K, G Lear, S. Turner, G D Lewis: What drives bacterial community structure in stream biofilms? 12th International Symposium on Microbial Ecology: ISME12, Cairns, Australia, August 17-22 2008
Washington V, S Villas-Boas, GD Lewis: Metabolomics as a novel approach to study mixed species biofilms of stream bacteria exhibiting mutualistic and antagonistic responses: 12th International Symposium on Microbial Ecology: ISME12, Cairns, Australia, August 17-22 2008
Smith J, GD Lewis: Unusual Bacterially mediated manganese-based structures within biofilms from urban streams. 12th International Symposium on Microbial Ecology: ISME12, Cairns, Australia, August 17-22 2008
Ancion P, G Lear, Lewis G D: Effects of Storm water metal contaminats on microbial communities in stream biofilm revealed by Automated Ribosomal Intergenic Spacer Analysis (ARISA): 12th International Symposium on Microbial Ecology: ISME12, Cairns, Australia, August 17-22 2008
Lear G, J Smith, K Roberts, I Boothroyd, GD Lewis: Use of whole-community bacterial indicators to monitor ecological health, function and variability within freshwater stream biofilms. 12th International Symposium on Microbial Ecology: ISME12, Cairns, Australia, August 17-22 2008
