Characterization of Aquatic Biofilms with Flow Cytometry

Abstract

Biofilms are dynamic consortia of microorganism that play a key role in freshwater ecosystems. By changing their community structure, biofilms respond quickly to environmental changes and can be thus used as indicators of water quality. Currently, biofilm assessment is mostly based on integrative and functional endpoints, such as photosynthetic or respiratory activity, which do not provide information on the biofilm community structure. Flow cytometry and computational visualization offer an alternative, sensitive, and easy-to-use method for assessment of the community composition, particularly of the photoautotrophic part of freshwater biofilms. It requires only basic sample preparation, after which the entire sample is run through the flow cytometer. The single-cell optical and fluorescent information is used for computational visualization and biological interpretation. Its main advantages over other methods are the speed of analysis and the high-information-content nature. Flow cytometry provides information on several cellular and biofilm traits in a single measurement: particle size, density, pigment content, abiotic content in the biofilm, and coarse taxonomic information. However, it does not provide information on biofilm composition on the species level. We see high potential in the use of the method for environmental monitoring of aquatic ecosystems and as an initial biofilm evaluation step that informs downstream detailed investigations by complementary and more detailed methods.

Evaluation of Phototrophic Stream Biofilms Under Stress: Comparing Traditional and Novel Ecotoxicological Endpoints After Exposure to Diuron

“…Although this, and our previous studies have demonstrated the potential of the new methods, more studies are needed to see whether they work equally well in a variety of environmental conditions. We have so far shown that FC-CS can be a good indicator of changes in biofilms under temperature ( Sgier et al, 2016 ) and chemical stress, and that it can be evaluated in a relatively short amount of time once set up ( Sgier et al, 2018 ). However, missing are studies that would measure FC-CS across a gradient of chemical concentration of different chemicals to see what the limits of sensitivity are.…”

“…To facilitate the interpretation of the viSNE maps and the defined subpopulation, FC data of reference species (16 diatoms, 8 green algae, 6 cyanobacteria, and 1 red algae species, Supplementary Table S6 ) were projected on the viSNE map. For a more detailed description of the procedure, see ( Sgier et al, 2016 , 2018 ).…”

“…Recently, new biofilm characterization methods have been developed that can simultaneously measure both functional and structural features. Members of our laboratory have, in particular, focused on characterization of freshwater biofilms based on flow cytometry derived community structure (FC-CS) ( Sgier et al, 2016 , 2018 ) and liquid chromatography coupled to organic carbon and nitrogen detection (LC-OCD-OND) for characterization of extracellular (polymeric) substances (EPS) present in biofilms ( Stewart et al, 2013 ; Kroll et al, 2014 ). Both methods measure multiple features of biofilms.…”

Integrating periphyton and surfacewater–groundwatermethods to understand lake ecosystem processes

“…Fatty acid content can vary with environmental conditions. Kelly and Scheibling (2012), Taipale et al (2013), Galloway and Winder (2015), Galloway et al (2015) particle size, particle density, biovolume, pigments, and rough taxonomy at one time (Sgier et al 2018). While the initial calibration and machine training can be time intensive, once mastered, the procedure can lead to fast results.…”

Updates on the applications of flow cytometry in microbiology

“…Culture base techniques used for the analysis of microbiological samples are time consuming; they are not able to detect non-culturable microorganisms and they do not provide real-time information on the physiological status of the organism in situ [9]. FCM is largely used in food industry for optimization and monitoring of microbial industrial processes [10,11], for the detection of microbial contaminants in food products [12] and also it has applications in environmental research [13]. But although in clinical laboratories the application of the flow cytometric technique is well established in hematology and the use of this method in routine clinical microbiology is still rare [14].…”