Abstract
In situ biofilm sampling is a key step for the study of natural biofilms and using methodologies that reflect natural diversity is necessary to guarantee representative sampling. Here, we focalise on the impact of the type of substrata on which biofilms grow on bacterial and fungal communities’ structure. The indirect molecular approach, Denaturing Gel Gradient Electrophoresis (DGGE) of a gene fragment coding for either 16S rRNA or 28S rRNA, for bacteria or fungi respectively, was used to evaluate the variability of microbial community structures among different biofilm substrata: natural (pebbles, live plants, wood and sediment), or artificial (glass, Plexiglas® and sterile wood), in a small river (the Loiret, France). Multivariate statistics, band richness and diversity indexes (Shannon and Simpson) were used to highlight variations in community structure between substrata. Results showed variations of bacterial and fungal diversity between different substrata according to substratum properties/origin (natural or artificial, organic or inorganic) but there was no optimal substratum for sampling, and artificial substrata were not significantly less applicable than natural substrata. Pooling 4 different substrata types allowed a higher bacterial and fungal biodiversity recovery. Point contact sampling may thus gain in robustness by increasing the number of substrata considered. Fungal species richness was similar to the bacterial one on most substrata which suggested they should be more frequently considered in riverine biofilm studies.
Highlights
One of the main difficulties in studying natural aquatic biofilms is the quasi impossibility of growing them in identical conditions ex situ without modifying them, or artificially selecting a number of species
The number of bands in the 16S rRNA Denaturing Gel Gradient Electrophoresis (DGGE) ranged between 10 and 19 bands, the highest numbers being found in the natural sediment and artificial wood samples (Table 1)
Bacterial and fungal diversity Overall the number of different DGGE bands we identified for bacteria and fungi is comparable with previous results (Lyautey et al 2003; Araya et al 2003) as are the results obtained for richness and diversity indexes for bacteria (Lyautey et al 2003)
Summary
One of the main difficulties in studying natural aquatic biofilms is the quasi impossibility of growing them in identical conditions ex situ without modifying them, or artificially selecting a number of species. A few studies have previously sought to test the robustness of artificial substrata for the growing and sampling of algal biofilms, microbial biofilms and other organisms such as diatoms. Branco et al (2010) studied the effects of artificial substrata on algal development and showed that physical structure of the substratum did not affect species richness but did alter the abundance of the macroalgal community. Concerning bacterial communities, there are very few studies measuring the impact of artificial substrata on bacterial biofilms as we mentioned above, they are extensively used for collecting samples (Kröpfl et al 2006; Möhlenhoff et al 2001; Danilov and Ekelund 2001; Rozej et al 2015). Several studies have underlined the importance of fungal communities in riverine biofilms (Baldy et al 1995; Gessner and Chauvet 1994; Golladay and Sinsabaugh 1991)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
