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Applied and Environmental Microbiology, August 2009, p. 5261-5272, Vol. 75, No. 16
0099-2240/09/$08.00+0     doi:10.1128/AEM.00412-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Relative Diversity and Community Structure of Ciliates in Stream Biofilms According to Molecular and Microscopy Methods{triangledown} ,{dagger}

Andrew Dopheide,1 Gavin Lear,1 Rebecca Stott,2 and Gillian Lewis1*

School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, New Zealand,1 National Institute for Water and Atmospheric Research, P.O. Box 11-115, Hamilton, New Zealand2

Received 18 February 2009/ Accepted 18 June 2009

Ciliates are an important component of aquatic ecosystems, acting as predators of bacteria and protozoa and providing nutrition for organisms at higher trophic levels. Understanding of the diversity and ecological role of ciliates in stream biofilms is limited, however. Ciliate diversity in biofilm samples from four streams subject to different impacts by human activity was assessed using microscopy and terminal restriction fragment length polymorphism (T-RFLP) analysis of 18S rRNA sequences. Analysis of 3' and 5' terminal fragments yielded very similar estimates of ciliate diversity. The diversity detected using microscopy was consistently lower than that suggested by T-RFLP analysis, indicating the existence of genetic diversity not apparent by morphological examination. Microscopy and T-RFLP analyses revealed similar relative trends in diversity between different streams, with the lowest level of biofilm-associated ciliate diversity found in samples from the least-impacted stream and the highest diversity in samples from moderately to highly impacted streams. Multivariate analysis provided evidence of significantly different ciliate communities in biofilm samples from different streams and seasons, particularly between a highly degraded urban stream and less impacted streams. Microscopy and T-RFLP data both suggested the existence of widely distributed, resilient biofilm-associated ciliates as well as ciliate taxa restricted to sites with particular environmental conditions, with cosmopolitan taxa being more abundant than those with restricted distributions. Differences between ciliate assemblages were associated with water quality characteristics typical of urban stream degradation and may be related to factors such as nutrient availability and macroinvertebrate communities. Microscopic and molecular techniques were considered to be useful complementary approaches for investigation of biofilm ciliate communities.

* Corresponding author. Mailing address: School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand. Phone: 64 (9) 373 7599. Fax: 64 (9) 373 7416. E-mail: gd.lewis{at}auckland.ac.nz

{triangledown} Published ahead of print on 26 June 2009.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, August 2009, p. 5261-5272, Vol. 75, No. 16
0099-2240/09/$08.00+0     doi:10.1128/AEM.00412-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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