Assessing microbial growth of six pure cultures grown anaerobically using optical density, ATP measurements, DNA concentrations and 16S rRNA targeted qPCR to compare commonly used techniques in lab and industry settings

Brown, D.; Turner, R. J.

doi:10.1101/2021.10.05.463247

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bioRxiv · 10.1101/2021.10.05.463247

Assessing microbial growth of six pure cultures grown anaerobically using optical density, ATP measurements, DNA concentrations and 16S rRNA targeted qPCR to compare commonly used techniques in lab and industry settings

Brown, D.·Turner, R. J.

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Abstract

This is a paper focusing on the comparison of growth curves using field relevant testing methods and moving away from colony counts. Challenges exist to explore antimicrobial growth of fastidious strains, poorly culturable bacterial and bacterial communities of environmental interest. Thus, various approaches have been explored to follow bacteria growth that can be an efficient surrogate for classical optical density or colony forming unit measurements. Here we tested optical density, ATP assays, DNA concentrations and 16S rRNA qPCR as means to monitor pure culture growth of six different species including Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica. Optical density is and excellent, rapid monitoring method of pure culture planktonic cells but cannot be applied to environmental or complex samples. ATP assays provide rapid results but conversions to cell counts may be misleading for different species. DNA concentration is a very reliable technique which can be used for any sample type and provides genetic materials for downstream applications. qPCR of the 16S rRNA gene is a widely applicable technique for monitoring microbial cell concentrations but is susceptible to variation between replicates. DNA concentrations were found to correlate the best with the other three assays and provides the advantages of rapid extraction, consistency between replicates and potential for downstream analysis, DNA concentrations is determined to be the best universal monitoring method for complex environmental samples.

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Brown, D., Turner, R. J.. 2021-10-05. Assessing microbial growth of six pure cultures grown anaerobically using optical density, ATP measurements, DNA concentrations and 16S rRNA targeted qPCR to compare commonly used techniques in lab and industry settings. https://doi.org/10.1101/2021.10.05.463247

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