Comparison of DNA Extraction Efficiency and Reproducibility of Different Aeration Diffuser Biofilms Using Bead-Beating Protocol

Pitiporn Asvapathanagul; Manel Garrido-Baserba; Betty H. Olson; Hee Deung Park; Deqiang Chen; Diego Rosso

doi:10.1159/000500875

Comparison of DNA Extraction Efficiency and Reproducibility of Different Aeration Diffuser Biofilms Using Bead-Beating Protocol

Pitiporn Asvapathanagul, Manel Garrido-Baserba, Betty H. Olson, Hee Deung Park, Deqiang Chen, Diego Rosso

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

Abstract

An existing bead-beating DNA extraction protocol was employed to compare the DNA extraction recovery and fragment quality of 6 different aeration diffuser biofilms. Escherichia coli, Gordonia amarae, and mixed liquor were used as controls. The fraction of total DNA^biofilm decreased monotonically with increasing number of beat beatings (BB) when the amount of DNA present was sufficient (>4 μg^DNA/cm²), excluding the ceramic disk. While controls required only 2 BBs, 3 out of 5 BBs achieved ≥70% of total DNA (70.3 ± 1.7%) for 5 out of 6 biofilms. Quantitative polymerase chain reaction (PCR) analyses of 353 and 1,505 basepair (bp) amplicons from pure culture extracts showed target copy numbers were not degraded for the first 2 BBs, but the third BB decreased amplicon concentrations by 0.65 and 1.12 log for E. coli, and 0.39 and 0.40 log for G. amarae, respectively. The 353 bp fragment amplification from biofilm samples showed minimal degradation for the first 3 BBs. PCR and gel electrophoresis confirmed integrity of amplified 1,505 bp DNA fragments over the 5 BBs, except in the EDPM (75 mm diameter, tube) diffuser biofilm (4.98 ± 0.62 μg^DNA/cm²). Taken together, this study showed type of diffuser membrane biofilms had no effects on extraction efficiency, but low DNA concentrations reduced extraction performance.

Original language	English
Pages (from-to)	293-303
Number of pages	11
Journal	Journal of Molecular Microbiology and Biotechnology
Volume	28
Issue number	6
DOIs	https://doi.org/10.1159/000500875
Publication status	Published - 2019 Jul 1

Bibliographical note

Funding Information:
This study was funded by Water Environment Research Foundation (WERF Project Number: INFR2R12) and the United States Environmental Protection Agency (EPA-WERF Cooperative Agreement No. CR-83419201). Additionally, the Mentor Appreciation Fund provided by the National Institute of General Medical Sciences of the National Institutes of Health under Award Numbers; UL1GM118979 encouraged the manuscript publication.

Funding Information:
This study was funded by Water Environment Research Foundation (WERF, Project Number: INFR2R12) and the United States Environmental Protection Agency (EPA-WERF Cooperative Agreement No. CR-83419201), with the support of the Irvine Ranch Water District, DC Water, Hampton Roads Sanitation District, Sydney Water, and Southern California Edison. The authors thank David M. Hayden of the Irvine Ranch Water District at the Michelson Water Reclamation Plant for supporting the reactor installation and the sampling campaign and Alice K. Robinson of BKT and Graham W. McCarthy of the Civil and Environmental Engineering Department, University of California, Irvine for their assistant during sampling.

Publisher Copyright:
© 2019 S. Karger AG, Basel. All rights reserved.

Keywords

Aeration
Bead beating
Biofilm
DNA extraction efficiency
Fine-pore diffusers
Fragment length amplification
Wastewater

ASJC Scopus subject areas

Biotechnology
Microbiology
Applied Microbiology and Biotechnology
Molecular Biology

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10.1159/000500875

Cite this

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title = "Comparison of DNA Extraction Efficiency and Reproducibility of Different Aeration Diffuser Biofilms Using Bead-Beating Protocol",

abstract = "An existing bead-beating DNA extraction protocol was employed to compare the DNA extraction recovery and fragment quality of 6 different aeration diffuser biofilms. Escherichia coli, Gordonia amarae, and mixed liquor were used as controls. The fraction of total DNAbiofilm decreased monotonically with increasing number of beat beatings (BB) when the amount of DNA present was sufficient (>4 μgDNA/cm2), excluding the ceramic disk. While controls required only 2 BBs, 3 out of 5 BBs achieved ≥70% of total DNA (70.3 ± 1.7%) for 5 out of 6 biofilms. Quantitative polymerase chain reaction (PCR) analyses of 353 and 1,505 basepair (bp) amplicons from pure culture extracts showed target copy numbers were not degraded for the first 2 BBs, but the third BB decreased amplicon concentrations by 0.65 and 1.12 log for E. coli, and 0.39 and 0.40 log for G. amarae, respectively. The 353 bp fragment amplification from biofilm samples showed minimal degradation for the first 3 BBs. PCR and gel electrophoresis confirmed integrity of amplified 1,505 bp DNA fragments over the 5 BBs, except in the EDPM (75 mm diameter, tube) diffuser biofilm (4.98 ± 0.62 μgDNA/cm2). Taken together, this study showed type of diffuser membrane biofilms had no effects on extraction efficiency, but low DNA concentrations reduced extraction performance.",

keywords = "Aeration, Bead beating, Biofilm, DNA extraction efficiency, Fine-pore diffusers, Fragment length amplification, Wastewater",

author = "Pitiporn Asvapathanagul and Manel Garrido-Baserba and Olson, {Betty H.} and Park, {Hee Deung} and Deqiang Chen and Diego Rosso",

note = "Funding Information: This study was funded by Water Environment Research Foundation (WERF Project Number: INFR2R12) and the United States Environmental Protection Agency (EPA-WERF Cooperative Agreement No. CR-83419201). Additionally, the Mentor Appreciation Fund provided by the National Institute of General Medical Sciences of the National Institutes of Health under Award Numbers; UL1GM118979 encouraged the manuscript publication. Funding Information: This study was funded by Water Environment Research Foundation (WERF, Project Number: INFR2R12) and the United States Environmental Protection Agency (EPA-WERF Cooperative Agreement No. CR-83419201), with the support of the Irvine Ranch Water District, DC Water, Hampton Roads Sanitation District, Sydney Water, and Southern California Edison. The authors thank David M. Hayden of the Irvine Ranch Water District at the Michelson Water Reclamation Plant for supporting the reactor installation and the sampling campaign and Alice K. Robinson of BKT and Graham W. McCarthy of the Civil and Environmental Engineering Department, University of California, Irvine for their assistant during sampling. Publisher Copyright: {\textcopyright} 2019 S. Karger AG, Basel. All rights reserved.",

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AU - Asvapathanagul, Pitiporn

AU - Garrido-Baserba, Manel

AU - Olson, Betty H.

AU - Park, Hee Deung

AU - Chen, Deqiang

AU - Rosso, Diego

N1 - Funding Information: This study was funded by Water Environment Research Foundation (WERF Project Number: INFR2R12) and the United States Environmental Protection Agency (EPA-WERF Cooperative Agreement No. CR-83419201). Additionally, the Mentor Appreciation Fund provided by the National Institute of General Medical Sciences of the National Institutes of Health under Award Numbers; UL1GM118979 encouraged the manuscript publication. Funding Information: This study was funded by Water Environment Research Foundation (WERF, Project Number: INFR2R12) and the United States Environmental Protection Agency (EPA-WERF Cooperative Agreement No. CR-83419201), with the support of the Irvine Ranch Water District, DC Water, Hampton Roads Sanitation District, Sydney Water, and Southern California Edison. The authors thank David M. Hayden of the Irvine Ranch Water District at the Michelson Water Reclamation Plant for supporting the reactor installation and the sampling campaign and Alice K. Robinson of BKT and Graham W. McCarthy of the Civil and Environmental Engineering Department, University of California, Irvine for their assistant during sampling. Publisher Copyright: © 2019 S. Karger AG, Basel. All rights reserved.

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N2 - An existing bead-beating DNA extraction protocol was employed to compare the DNA extraction recovery and fragment quality of 6 different aeration diffuser biofilms. Escherichia coli, Gordonia amarae, and mixed liquor were used as controls. The fraction of total DNAbiofilm decreased monotonically with increasing number of beat beatings (BB) when the amount of DNA present was sufficient (>4 μgDNA/cm2), excluding the ceramic disk. While controls required only 2 BBs, 3 out of 5 BBs achieved ≥70% of total DNA (70.3 ± 1.7%) for 5 out of 6 biofilms. Quantitative polymerase chain reaction (PCR) analyses of 353 and 1,505 basepair (bp) amplicons from pure culture extracts showed target copy numbers were not degraded for the first 2 BBs, but the third BB decreased amplicon concentrations by 0.65 and 1.12 log for E. coli, and 0.39 and 0.40 log for G. amarae, respectively. The 353 bp fragment amplification from biofilm samples showed minimal degradation for the first 3 BBs. PCR and gel electrophoresis confirmed integrity of amplified 1,505 bp DNA fragments over the 5 BBs, except in the EDPM (75 mm diameter, tube) diffuser biofilm (4.98 ± 0.62 μgDNA/cm2). Taken together, this study showed type of diffuser membrane biofilms had no effects on extraction efficiency, but low DNA concentrations reduced extraction performance.

AB - An existing bead-beating DNA extraction protocol was employed to compare the DNA extraction recovery and fragment quality of 6 different aeration diffuser biofilms. Escherichia coli, Gordonia amarae, and mixed liquor were used as controls. The fraction of total DNAbiofilm decreased monotonically with increasing number of beat beatings (BB) when the amount of DNA present was sufficient (>4 μgDNA/cm2), excluding the ceramic disk. While controls required only 2 BBs, 3 out of 5 BBs achieved ≥70% of total DNA (70.3 ± 1.7%) for 5 out of 6 biofilms. Quantitative polymerase chain reaction (PCR) analyses of 353 and 1,505 basepair (bp) amplicons from pure culture extracts showed target copy numbers were not degraded for the first 2 BBs, but the third BB decreased amplicon concentrations by 0.65 and 1.12 log for E. coli, and 0.39 and 0.40 log for G. amarae, respectively. The 353 bp fragment amplification from biofilm samples showed minimal degradation for the first 3 BBs. PCR and gel electrophoresis confirmed integrity of amplified 1,505 bp DNA fragments over the 5 BBs, except in the EDPM (75 mm diameter, tube) diffuser biofilm (4.98 ± 0.62 μgDNA/cm2). Taken together, this study showed type of diffuser membrane biofilms had no effects on extraction efficiency, but low DNA concentrations reduced extraction performance.

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Comparison of DNA Extraction Efficiency and Reproducibility of Different Aeration Diffuser Biofilms Using Bead-Beating Protocol

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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