Relative Diversity and Community Structure of Ciliates in Stream Biofilms According to Molecular and Microscopy Methods

Abstract

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.Heterotrophic microeukaryotes such as ciliates are thought to be of considerable importance in aquatic ecosystems, as they are major predators of bacteria and constitute a nutritional resource for other protozoa, invertebrates, and probably fish larvae (9,22,36,52,62,63,71). In addition, protozoan bacterivory contributes to enhanced decomposition of leaf detritus-a vital nutrient resource in streams-by increasing turnover of bacterial populations through predation (57). It is not well understood, however, how ciliate diversity and community structure in streams are affected by changing environmental conditions, or how ciliate communities affect other stream biota and processes. The effects of various physical, chemical, and biological factors on freshwater protozoan communities have been considered by a number of studies, but most of these have focused upon planktonic organisms in lentic habitats (for example, see references 2, 11, and 44). However, the complex microbial communities in biofilms have been recognized as important contributors to critical ecological processes, such as auxotrophic primary ...

A comparison of bacterial, ciliate and macroinvertebrate indicators of stream ecological health

“…Adopting a similar approach, Stein et al (2010) analysed the fauna and bacteria within groundwater aquifers revealing that both communities responded to the environmental impacts occurring on the surface of the land. Similar to bacterial communities, only limited evidence has so far been provided to support the possibility that communities of ciliated protozoa have the potential to provide viable assessments of freshwater ecological health (Dopheide et al 2009). Indeed, prior to Dopheide et al (2008), research in this field was significantly hampered by a lack of knowledge regarding the appropriate ciliate-specific PCR primers with which to characterise the structure and composition of these diverse microbial communities.…”

“…Nevertheless, the analysis of microbial communities may provide a useful alternative measure of ecosystem health since (1) microorganisms are ubiquitous and require little sampling effort, (2) there is minimal site disturbance associated with collecting small volumes of sediment, biofilm or water for microbial community analysis, (3) the rapid life cycle of microorganisms means they may be rapid indicators of environmental change and (4) numerous methods are now available with which to characterise the genetic diversity of aquatic microbial communities using rapid community DNA fingerprinting techniques such as denaturing gradient gel electrophoresis (DGGE; Lyautey et al 2003), terminal restriction fragment length polymorphism (T-RFLP; Dopheide et al 2009) and automated ribosomal intergenic spacer analysis (ARISA; Jones et al 2007). For example, Lear et al (2009a) recently used ARISA to characterise bacterial communities within stream biofilms and identified that these communities could provide a more sensitive indicator of ecological health than macroinvertebrates within highly impacted streams.…”

Changes in eukaryotic microbial communities of vernal pools along an urban–rural land use gradient

“…It is more common that microbial communities change in their taxonomic composition with human impacts, which has been consistently documented in scientific literature (e.g. Cody et al 2000, Dorigo et al 2002, Cousins et al 2003, Duarte et al 2004, Duong et al 2007, Borin et al 2009, Dopheide et al 2009). We also found that the community composition of eukaryotic microbes in vernal pools was related to the percent of each subwatershed that was urban area.…”

“…Urbanization may be increasing habitat heterogeneity in vernal pools, in both space and time, resulting in higher levels of diversity. Studies of stream bacterial (Cody et al 2000) and ciliate (Dopheide et al 2009) communities also found higher richness and diversity at sites more impacted by human activity. It is plausible that in urbanized watersheds, increased nutrient runoff and changes in water chemistry following storm events create greater temporal heterogeneity in aquatic habitats, leading to increases in overall microbial diversity.…”

“…Such urban-rural gradients are interesting settings to ask basic ecological questions, test theories, and contribute to ecosystem management (McDonnell & Pickett 1990). Our study specifically addressed whether the eukaryotic microbial community was altered by changes in watershed land use, since there is conflicting evidence on whether urbanization affects the richness and diversity of eukaryotic microorganisms negatively (Jumpponen & Jones 2009), positively (Dopheide et al 2009), or has no effect (Cousins et al 2003, Duong et al 2007). We also sought to determine if and how the composition of the eukaryotic microbial community was affected by urbanization.…”