Combined eukaryotic and bacterial community fingerprinting of natural freshwater biofilms using automated ribosomal intergenic spacer analysis

Abstract

Biofilms are complex communities playing an important role in aquatic ecosystems. Automated ribosomal intergenic spacer analysis (ARISA) has been used successfully to explore biofilm bacterial diversity. However, a gap remains to be filled as regards its application to biofilm eukaryotic populations. The aim of this study is to use ARISA to detect eukaryotic population shifts in biofilm. We designed a new set of primers to focus specifically on the ITS1-5.8S-ITS2 region of diatoms and tested it on natural biofilms. Additionally, we tested universal primers, used previously to perform ARISA on fungal communities. Cloning and sequencing showed that the universal primer set amplified various eukaryotes, whereas the new set was diatom specific. The new set amplified a wider variety of diatoms. Therefore, the universal set is appropriate to study the general eukaryotic population shifts in biofilms, whereas the new set is more appropriate to study diatoms specifically. We used both primer sets, along with a bacterial set, to study the population shifts in natural river biofilms. Principal component analysis of the ARISA fingerprints revealed seasonal shifts that did not coincide for bacterial and eukaryotic communities. Therefore, the use of both eukaryotic and bacterial primers provides a useful insight to assess microbial succession in biofilms.

Impact of an urban multi-metal contamination gradient: Metal bioaccumulation and tolerance of river biofilms collected in different seasons

“…At each sampling date, biofilm dry weights (DWs), ash-free dry weights (AFDWs) and chlorophyll a (Chl-a) concentrations were measured in triplicate as in Fechner et al (2010b).…”

Low exposure levels of urban metals induce heterotrophic community tolerance: a microcosm validation

“…Aliquots of biofilm suspension were assigned to various analyses in terms of biomass, metal accumulation and tolerance acquisition. Periphyton dry weight (DW), ash-free dry weight (AFDW) and chlorophyll a concentration were determined as in Fechner et al (2010b). To perform ARISA, aliquots of 50 ml of each periphyton suspension (biofilms from the microcosms at the end of the three experiments and river biofilm at the beginning of each experiment) were centrifuged for 15 min at 10,0009g, and 4°C.…”

“…DNA amplification and ARISA fingerprinting were performed as in Fechner et al (2010b). Briefly, primers ITSF/ ITSReub (Cardinale et al 2004) were used for amplification of bacterial 16S-23S intergenic spacers and primers 2234C/3126T (Ranjard et al 2001) were used for amplification of eukaryotic ITS1-5.8S-ITS2 regions.…”

“…These modifications can be assessed by the use of indicators like biofilm biomass, species richness or the abundance of particular taxa (Blanck 2002). More recently, modifications of community structure have been identified using fingerprinting techniques like DGGE (Dorigo et al 2010), or ARISA (Fechner et al 2010b).…”

Analysis of phytoplankton distribution and community structure in the German Bight with respect to the different size classes

“…Fingerprinting techniques provide information on general changes in the phytoplankton community (Knefelkamp, 2009;Wolf et al, 2013), although they are not suitable for an absolute assessment of biodiversity (Bent et al, 2007). The ARISA (automated ribosomal intergenic spacer analysis) approach used in this study has been often applied for prokaryotic communities (e.g., Danovaro et al, 2006;Kovacs et al, 2010), but has also been used for eukaryotes (Fechner et al, 2010;Wolf et al, 2013). In contrast, DNA-microarrays can provide taxon-specific information about the phytoplankton community in a sample (Kochzius et al, 2007;Metfies and Medlin, 2005).…”