The effects of stream substratum texture on interstitial conditions and bacterial biofilms: Methodological strategies

Unravelling the drivers of aquatic communities using disparate organismal groups and different taxonomic levels

“…For example, bacterial communities have been shown to be influenced by environmental factors (Horner-Devine et al, 2004;Beisner et al, 2006;Van der Gucht et al, 2007;Besemer et al, 2009;Newton et al, 2011;Adams et al, 2014), past environmental conditions (Andersson et al, 2014), substratum texture (Mueller et al, 2013b) and biotic interactions (Newton et al, 2011;Eigemann et al, 2013;Berga et al, 2015), and they seem to lack the effect of geographic distance when environmental heterogeneity is controlled for (Horner-Devine et al, 2004). Our results largely support the importance of local environmental conditions as water chemistry variables explained a relatively large proportion of variation in bacterial community structure at the three taxonomic levels we studied.…”

“…These facts indicate that bacterial sampling procedures need to be refined before comprehensive use of bacteria in bioassessment. As the texture of the substratum can affect bacterial biofilms, special attention should also be given to the selection of a suitable sampling substratum (Mueller et al, 2013b). In addition, although being a fast, flexible method, we are not entirely certain that the BLAST method (Altschul et al, 1990) is the best one to be used when aiming to compare different taxonomic resolutions.…”

Alteration of physico-chemical and microbial properties in freshwater substrates by burrowing invertebrates

“…In order to reduce such impact, standardized samples of interstital water (from 5 cm substratum depth) were taken on experiment days 0, 10 and 20 using the installed control valve. The sampled interstitial water was subsequently filtered through 0.22 m CME membrane filters (Carl Roth GmbH & Co. KG, Karlsruhe, Germany) following the methodology by Mueller et al (2013) who verified the validity of this method for charactization of microbial communities. Nevertheless, the sessile bacterial community (adherent on substratum particles) has not been completely disregarded since in every sample of interstitial water a small amount of substratum was present.…”

“…Nevertheless, the sessile bacterial community (adherent on substratum particles) has not been completely disregarded since in every sample of interstitial water a small amount of substratum was present. Filters with adherent bacterial biomass and substratum were transferred to sterile Petri dishes and frozen immediately at −20 • C. Since Mueller et al (2013) showed that technical replicates produce highly similar results, emphasis was put on including a high number of nine biological replicates per treatment. Membrane filters were cut into pieces (0.5 cm 2 ) using a sterile scalpel for DNA-isolation from each filter as described in Mueller et al (2013).…”

The effect of light intensity and shear stress on microbial biostabilization and the community composition of natural biofilms

“…This is due to their high economic importance, whether they are regarded as beneficial, eg, in the context of bioremediation, 1,2 or as adverse, eg, by biofouling [3][4][5] or colmation of riverine sediments. 6 Most studies have focused on one of two fundamental perspectives: the impact of environmental conditions on the development and characteristics of biofilms, or "performance", eg, the rate of nutrient cycling or contaminant retention of the biofilm system. Thereby, the influence of different environmental factors has been investigated in view of the biofilm structure, impact of important environmental conditions, such as light or nutrient availability, upon biofilm systems is constantly increasing to unravel different feedback loops between biofilm and environment.…”