Abstract
Flow cytometry is a promising tool used to identify the phenotypic features of bacterial communities in aquatic ecosystems by measuring the physical and chemical properties of cells based on their light scattering behavior and fluorescence. Compared to molecular or culture-based approaches, flow cytometry is suitable for the online monitoring of microbial water quality because of its relatively simple sample preparation process, rapid analysis time, and high-resolution phenotypic data. Advanced statistical techniques (e.g., denoising and binning) can be utilized to successfully calculate phenotypic diversity by processing the scatter data obtained from flow cytometry. These phenotypic diversities were well correlated with taxonomic-based diversity computed using next-generation 16S RNA gene sequencing. The protocol provided in this paper should be a useful guide for a fast and reliable flow cytometric monitoring of bacterial phenotypic diversity in aquatic ecosystems.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Buzatu, D.A., Moskal, T.J., Williams, A.J., Cooper, W.M., Mattes, W.B., and Wilkes, J.G. 2014. An integrated flow cytometry-based system for real-time, high sensitivity bacterial detection and identification. PLoS ONE 9, e94254.
Collier, S.A., Deng, L., Adam, E.A., Benedict, K.M., Beshearse, E.M., Blackstock, A.J., Bruce, B.B., Derado, G., Edens, C., Fullerton, K.E., et al. 2021. Estimate of burden and direct healthcare cost of infectious waterborne disease in the United States. Emerg. Infect. Dis. 27, 140–149.
Frossard, A., Hammes, F., and Gessner, M.O. 2016. Flow cytometric assessment of bacterial abundance in soils, sediments and sludge. Front. Microbiol. 7, 903.
Gillespie, S., Lipphaus, P., Green, J., Parsons, S., Weir, P., Juskowiak, K., Jefferson, B., Jarvis, P., and Nocker, A. 2014. Assessing microbiological water quality in drinking water distribution systems with disinfectant residual using flow cytometry. Water Res. 65, 224–234.
Hong, J.K., Kim, S.B., Lyou, E.S., and Lee, T.K. 2021. Microbial phenomics linking the phenotype to function: The potential of Raman spectroscopy. J. Microbiol. 59, 249–258.
Jelinek, T., Bezdekova, R., Zatopkova, M., Burgos, L., Simicek, M., Sevcikova, T., Paiva, B., and Hajek, R. 2017. Current applications of multiparameter flow cytometry in plasma cell disorders. Blood Cancer J. 7, e617.
Kim, J., Darlington, A., Salvador, M., Utrilla, J., and Jiménez, J.I. 2020. Trade-offs between gene expression, growth and phenotypic diversity in microbial populations. Curr. Opin. Biotechnol. 62, 29–37.
Krediet, C.J., DeNofrio, J.C., Caruso, C., Burriesci, M.S., Cella, K., and Pringle, J.R. 2015. Rapid, precise, and accurate counts of Symbiodinium cells using the guava flow cytometer, and a comparison to other methods. PLoS ONE 10, e0135725.
Kret, E., Kiecak, A., Malina, G., Nijenhuis, I., and Postawa, A. 2015. Identification of TCE and PCE sorption and biodegradation parameters in a sandy aquifer for fate and transport modelling: batch and column studies. Environ. Sci. Pollut. Res. 22, 9877–9888.
Leight, A.K., Crump, B.C., and Hood, R.R. 2018. Assessment of fecal indicator Bacteria and potential pathogen co-occurrence at a shellfish growing area. Front. Microbiol. 9, 384.
Li, L., Mendis, N., Trigui, H., Oliver, J.D., and Faucher, S.P. 2014. The importance of the viable but non-culturable state in human bacterial pathogens. Front. Microbiol. 5, 258.
Nurliyana, M.R., Sahdan, M.Z., Wibowo, K.M., Muslihati, A., Saim, H., Ahmad, S.A., Sari, Y., and Mansor, Z. 2018. The detection method of Escherichia coli in water resources: a review. J. Phys. Conf. Ser. 995, 012065.
Oksanen, J., Blanchet, F.G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P.R., O’Hara, R.B., Simpson, G.L., Solymos, P., et al. 2020. vegan: Community Ecology Package. R package version 2.5-6. 2019. https://CRAN.R-project.org/package=vegan.
Picot, J., Guerin, C.L., Le Van Kim, C., and Boulanger, C.M. 2012. Flow cytometry: retrospective, fundamentals and recent instrumentation. Cytotechnology 64, 109–130.
Props, R., Monsieurs, P., Mysara, M., Clement, L., and Boon, N. 2016. Measuring the biodiversity of microbial communities by flow cytometry. Methods Ecol. Evol. 7, 1376–1385.
Props, R., Schmidt, M.L., Heyse, J., Vanderploeg, H.A., Boon, N., and Denef, V.J. 2018. Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels. Environ. Microbiol. 20, 521–534.
Ramírez-Castillo, F.Y., Loera-Muro, A., Jacques, M., Garneau, P., Avelar-González, F.J., Harel, J., and Guerrero-Barrera, A.L. 2015. Waterborne pathogens: detection methods and challenges. Pathogens 4, 307–334.
Rockey, N., Bischel, H.N., Kohn, T., Pecson, B., and Wigginton, K.R. 2019. The utility of flow cytometry for potable reuse. Curr. Opin. Biotechnol. 57, 42–49.
Sadler, M.C., Senouillet, J., Kuenzi, S., Grasso, L., and Watson, D.C. 2020. Computational surveillance of microbial water quality with online flow cytometry. Front. Water 2, 45.
Shrestha, A. and Dorevitch, S. 2019. Evaluation of rapid qPCR method for quantification of E. coli at non-point source impacted Lake Michigan beaches. Water Res. 156, 395–403.
Stroo, H.F. and Ward, C.H. 2010 In situ Remediation of Chlorinated Solvent Plumes. Springer, New York, USA.
Tan, B., Ng, C., Nshimyimana, J.P., Loh, L.L., Gin, K.Y., and Thompson, J.R. 2015. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. Front. Microbiol. 6, 1027.
Acknowledgements
This project was conducted with support from the Korea Ministry of Environment (MOE) GAIA program (20200024-80003) and the “Research Program for Agricultural Science & Technology Development (Project No. PJ0141942021)” of the National Institute of Agricultural Sciences, Rural Development Administration, Republic of Korea. This study was also supported by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry (IPET) through the Strategic Initiative for Microbiomes in Agriculture and Food, Ministry of Agriculture, Food and Rural Affairs (Project No. 918014-4).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
The authors declare no conflict of interest.
Rights and permissions
About this article
Cite this article
Hong, JK., Kim, S.B., Ahn, S.H. et al. Flow cytometric monitoring of the bacterial phenotypic diversity in aquatic ecosystems. J Microbiol. 59, 879–885 (2021). https://doi.org/10.1007/s12275-021-1443-7
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12275-021-1443-7