Only a short time period is given to investigate the microbial composition of the water pond at the Zulauf AG in Schinznach. Therefor selected methods must be applied.
To estimate the number of bacteria one possibility would be to use flow cytometry. It’s a modern software-based method which uses conductivity and optical measurements to sort and count cells in a fluid medium. The main advantage is the rapidness and the low costs (Lavergne, Beaugeard, Dupuy, Courties, & Agogué, 2014). Another more simpler method for counting bacteria and fungi would be to plate the sample to a petri dish and count the forming cultures (Lazarova & Manem, 1995). The plating method needs a certain incubation time and is therefore slower than flow cytometry but can be performed with simpler equipment and in the time given.
Other key factors to describe the microbial community is the diversity as well as to assess specific groups of microorganisms. Most literature describes molecular methods such as RNA sequencing or measuring the phospholipid-derived fatty acids (PFLA). Another, not molecular based, method to differ between microorganism is to observe their appearance when cultivated on a petri dish. When bacteria were spread individually on a growing medium (i.e. Agar) they start to form new colonies. The different organism units can then be distinguished by their morphology. For example Serratia marcescens can be determined by its reddish colour (Sanders, 2012), Streptococcus pneumoniae colonies were smooth in appearance (‘Bacterial Colony Morphology and Identification of Bacteria - Page 2’, n.d.) and colonies of bacteria with flagella are less compact due to their ability to move.
Further different growth-mediums can give information about the variety of abundant microorganism, either by changing colour when a specific type of bacteria is present or by allowing only a selected group of bacteria to grow (i.e. gram positive, gram negative, Staphylococcus and Microccus) (Port & Cepaitis, 2015).
The condition of the microbial community gives information about their environment. Different bacteria were promoted by parameters such as pH, water temperature and oxygen content. Moreover, the presence of pesticides also causes a shift in the microbial community and therefore a conclusion can be drawn whether what sort of pesticides are available (Widenfalk, 2005).
Bacterial Colony Morphology and Identification of Bacteria - Page 2. (n.d.). Retrieved 22 April 2018, from http://www.scienceprofonline.com/microbiology/bacterial-colony-morphology-identification-unknown-bacteria-2.html
Lavergne, C., Beaugeard, L., Dupuy, C., Courties, C., & Agogué, H. (2014). An efficient and rapid method for the enumeration of heterotrophic prokaryotes in coastal sediments by flow cytometry. Journal of Microbiological Methods, 105, 31–38. https://doi.org/10.1016/j.mimet.2014.07.002
Lazarova, V., & Manem, J. (1995). Biofilm characterization and activity analysis in water and wasterwater treatment. Center of Internation Research for Water and Environment (CIRSEE).
Observing microbes – Observing bacteria in a petri dish. (n.d.). Retrieved 22 April 2018, from http://microbiologyonline.org/teachers/observing-microbes/observing-bacteria-in-a-petri-dish
Port, T., & Cepaitis, A. (2015). Differential and Selective Bacterial Growth Media. Retrieved 15 April 2018, from http://www.scienceprofonline.org/microbiology/differential-selective-bacterial-growth-media.html
Sanders, E. R. (2012). Aseptic Laboratory Techniques: Plating Methods. Journal of Visualized Experiments : JoVE, (63). https://doi.org/10.3791/3064
Widenfalk, A. (2005). Interactions between pesticides and microorganisms in freshwater sediments: toxic effects and implications for bioavailability: Doctoral thesis. Swedish University of Agricultural Sciences.
To estimate the number of bacteria one possibility would be to use flow cytometry. It’s a modern software-based method which uses conductivity and optical measurements to sort and count cells in a fluid medium. The main advantage is the rapidness and the low costs (Lavergne, Beaugeard, Dupuy, Courties, & Agogué, 2014). Another more simpler method for counting bacteria and fungi would be to plate the sample to a petri dish and count the forming cultures (Lazarova & Manem, 1995). The plating method needs a certain incubation time and is therefore slower than flow cytometry but can be performed with simpler equipment and in the time given.
Other key factors to describe the microbial community is the diversity as well as to assess specific groups of microorganisms. Most literature describes molecular methods such as RNA sequencing or measuring the phospholipid-derived fatty acids (PFLA). Another, not molecular based, method to differ between microorganism is to observe their appearance when cultivated on a petri dish. When bacteria were spread individually on a growing medium (i.e. Agar) they start to form new colonies. The different organism units can then be distinguished by their morphology. For example Serratia marcescens can be determined by its reddish colour (Sanders, 2012), Streptococcus pneumoniae colonies were smooth in appearance (‘Bacterial Colony Morphology and Identification of Bacteria - Page 2’, n.d.) and colonies of bacteria with flagella are less compact due to their ability to move.
Possible morphology of bacteria colonies
Further different growth-mediums can give information about the variety of abundant microorganism, either by changing colour when a specific type of bacteria is present or by allowing only a selected group of bacteria to grow (i.e. gram positive, gram negative, Staphylococcus and Microccus) (Port & Cepaitis, 2015).
The condition of the microbial community gives information about their environment. Different bacteria were promoted by parameters such as pH, water temperature and oxygen content. Moreover, the presence of pesticides also causes a shift in the microbial community and therefore a conclusion can be drawn whether what sort of pesticides are available (Widenfalk, 2005).
Bacterial Colony Morphology and Identification of Bacteria - Page 2. (n.d.). Retrieved 22 April 2018, from http://www.scienceprofonline.com/microbiology/bacterial-colony-morphology-identification-unknown-bacteria-2.html
Lavergne, C., Beaugeard, L., Dupuy, C., Courties, C., & Agogué, H. (2014). An efficient and rapid method for the enumeration of heterotrophic prokaryotes in coastal sediments by flow cytometry. Journal of Microbiological Methods, 105, 31–38. https://doi.org/10.1016/j.mimet.2014.07.002
Lazarova, V., & Manem, J. (1995). Biofilm characterization and activity analysis in water and wasterwater treatment. Center of Internation Research for Water and Environment (CIRSEE).
Observing microbes – Observing bacteria in a petri dish. (n.d.). Retrieved 22 April 2018, from http://microbiologyonline.org/teachers/observing-microbes/observing-bacteria-in-a-petri-dish
Port, T., & Cepaitis, A. (2015). Differential and Selective Bacterial Growth Media. Retrieved 15 April 2018, from http://www.scienceprofonline.org/microbiology/differential-selective-bacterial-growth-media.html
Sanders, E. R. (2012). Aseptic Laboratory Techniques: Plating Methods. Journal of Visualized Experiments : JoVE, (63). https://doi.org/10.3791/3064
Widenfalk, A. (2005). Interactions between pesticides and microorganisms in freshwater sediments: toxic effects and implications for bioavailability: Doctoral thesis. Swedish University of Agricultural Sciences.
Hi Tobias,
AntwortenLöschenYou have been rather vague in the description of possible techniques. I am aware that the possibilities are quite large, but providing a practical example, would have helped greatly.
Hi Tobias,
LöschenIn case you are not finished yet you can disregard my comment above. In case you were finished you have time to brush it up a little. ;)
Dieser Kommentar wurde vom Autor entfernt.
AntwortenLöschenHi Tobias
LöschenI also think that we should do a plate count in combination with other groups, e.g. environmental chemistry, to determine whether there is a correlation between possible pollution and the number of microorganisms in the rainwater pond.
The overview of the different microorganism forms will also be useful for a determination. With this and the selective media we can certainly make good statements about the composition of sediment microorganisms.
Best regards
Adrian
Hey Tobias
AntwortenLöschenThe flow cytometry method sounds interesting. Do you know if it's available in the ZHAW?
To describe the microbila comunity i think the culture growing on petri dish method could be a simple and doable. Is it possible to make this experiment within one week?
Also I'd be interested, if this method works for fungi too.
Best,
Stefanie
Hi Tobias,
AntwortenLöschenThis is now a bit more detailed. Did you have any specific microorganism in mind (as key-species, or indicator species) or did you just want to search for random microorganism? It would have been interesting to see which media you would have suggested for the plating methods.
Flow Cell Cytometry would be nice but well you had the lecture, unfortunately it is not that easy to set up, and then we don't have one available to us.
As a general rule, try to use actual scientific literature and not web-sites as a reference, as web-sites are not a really reliable source of knowledge.
Hi Tobias
AntwortenLöschenSpecific media would have been nice, especially if they aim to distinguish different organisms. Probably we can solve some issues like that in the next days.
Theo