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.
Journal Section:
Research Article
References
1.
Asvapathanagul
P
, Huang
Z
, Gedalanga
PB
, Baylor
A
, Olson
BH
. Interaction of operational and physicochemical factors leading to Gordonia amarae-like foaming in an incompletely nitrifying activated sludge plant
. Appl Environ Microbiol
. 2012
Dec
;78
(23
):8165
–75
.
[PubMed]
0099-22402.
Bourrain
M
, Achouak
W
, Urbain
V
, Heulin
T
. DNA extraction from activated sludges
. Curr Microbiol
. 1999
Jun
;38
(6
):315
–9
.
[PubMed]
0343-86513.
Boyle
WC
, Redmon
DT
. Biological fouling of fine bubble diffusers: State-of-Art
. J Environ Eng
. 1983
;109
(5
):991
–1005
. 0733-93724.
Chao
Y
, Guo
F
, Fang
HH
, Zhang
T
. Hydrophobicity of diverse bacterial populations in activated sludge and biofilm revealed by microbial adhesion to hydrocarbons assay and high-throughput sequencing
. Colloids Surf B Biointerfaces
. 2014
Feb
;114
:379
–85
.
[PubMed]
0927-77655.
Cheng
M
, Cook
AE
, Fukushima
T
, Bond
PL
. Evidence of compositional differences between the extracellular and intracellular DNA of a granular sludge biofilm
. Lett Appl Microbiol
. 2011
Jul
;53
(1
):1
–7
.
[PubMed]
0266-82546.
Dominiak
DM
, Nielsen
JL
, Nielsen
PH
. Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms
. Environ Microbiol
. 2011
Mar
;13
(3
):710
–21
.
[PubMed]
1462-29127.
Ferrera
I
, Massana
R
, Balagué
V
, Pedrós-Alió
C
, Sánchez
O
, Mas
J
. Evaluation of DNA extraction methods from complex phototrophic biofilms
. Biofouling
. 2010
Apr
;26
(3
):349
–57
.
[PubMed]
0892-70148.
Ferris
MJ
, Muyzer
G
, Ward
DM
. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community
. Appl Environ Microbiol
. 1996
Feb
;62
(2
):340
–6
.
[PubMed]
0099-22409.
Garrido-Baserba
M
, Asvapathanagul
P
, McCarthy
GW
, Gocke
TE
, Olson
BH
, Park
HD
, et al.. Linking biofilm growth to fouling and aeration performance of fine-pore diffuser in activated sludge
. Water Res
. 2016
Mar
;90
:317
–28
.
[PubMed]
0043-135410.
Garrido-Baserba
M
, Sobhani
R
, Asvapathanagul
P
, McCarthy
GW
, Olson
BH
, Odize
V
, et al.. Modelling the link amongst fine-pore diffuser fouling, oxygen transfer efficiency, and aeration energy intensity
. Water Res
. 2017
Mar
;111
:127
–39
.
[PubMed]
0043-135411.
Ginzinger
DG
. Gene quantification using real-time quantitative PCR: an emerging technology hits the mainstream
. Exp Hematol
. 2002
Jun
;30
(6
):503
–12
.
[PubMed]
0301-472X12.
Guo
F
, Zhang
T
. Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing
. Appl Microbiol Biotechnol
. 2013
May
;97
(10
):4607
–16
.
[PubMed]
0175-759813.
Huang
Z
, Gedalanga
PB
, Asvapathanagul
P
, Olson
BH
. Influence of physicochemical and operational parameters on Nitrobacter and Nitrospira communities in an aerobic activated sludge bioreactor
. Water Res
. 2010
Aug
;44
(15
):4351
–8
.
[PubMed]
0043-135414.
Hwang
C
, Ling
F
, Andersen
GL
, LeChevallier
MW
, Liu
WT
. Evaluation of methods for the extraction of DNA from drinking water distribution system biofilms
. Microbes Environ
. 2012
;27
(1
):9
–18
.
[PubMed]
1342-631115.
Kaliman
A
, Rosso
D
, Leu
SY
, Stenstrom
MK
. Fine-pore aeration diffusers: accelerated membrane ageing studies
. Water Res
. 2008
Jan
;42
(1-2
):467
–75
.
[PubMed]
0043-135416.
Kim
YK
, Boyle
WC
. Mechanisms of fouling in fine-pore diffuser aeration
. J Environ Eng
. 1993
;119
(6
):1119
–38
. 0733-937217.
Lane
DJ
. Nucleic acid techniques in bacterial systematics
. Chichester, West Sussex, UK
: John Wiley & Sons
; 1991
.18.
Leff
LG
, Dana
JR
, McArthur
JV
, Shimkets
LJ
. Comparison of methods of DNA extraction from stream sediments
. Appl Environ Microbiol
. 1995
Mar
;61
(3
):1141
–3
.
[PubMed]
0099-224019.
Miller
DN
, Bryant
JE
, Madsen
EL
, Ghiorse
WC
. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples
. Appl Environ Microbiol
. 1999
Nov
;65
(11
):4715
–24
.
[PubMed]
0099-224020.
Noble
PA
, Park
HD
, Olson
BH
, Asvapathanagul
P
, Hunter
MC
, Garrido-Baserba
M
, et al.. A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time
. Appl Microbiol Biotechnol
. 2016
Jul
;100
(14
):6361
–73
.
[PubMed]
0175-759821.
Palmgren
R
, Nielsen
PH
. Accumulation of DNA in the exopolymeric matrix of activated sludge and bacterial cultures
. Water Sci Technol
. 1996
;34
(5-6
):233
–40
. 0273-122322.
Roberson
EB
, Firestone
MK
. Relationship between desiccation and exopolysaccharide production in a soil Pseudomonas Sp
. Appl Environ Microbiol
. 1992
Apr
;58
(4
):1284
–91
.
[PubMed]
0099-224023.
Rosso
D
, Libra
JA
, Wiehe
W
, Stenstrom
MK
. Membrane properties change in fine-pore aeration diffusers: full-scale variations of transfer efficiency and headloss
. Water Res
. 2008
May
;42
(10-11
):2640
–8
.
[PubMed]
0043-135424.
Rosso
D
, Stenstrom
MK
. Economic implications of fine-pore diffuser aging
. Water Environ Res
. 2006
Aug
;78
(8
):810
–5
.
[PubMed]
1061-430325.
Sambrook
J
, Russell
DW
. Molecular cloning: a laboratory manual
. Cold Spring Harbor, New York, US
: Cold Spring Harbor Laboratory Press
; 2001
.26.
Tchobanoglous
G
, Burton
FL
, Stensel
HD
. Metcalf & Eddy: Wastewater engineering: treatment and reuse
. 4th ed.Boston, Massachusetts, US
: McGraw-Hill
; 2003
.27.
U.S. Environmental Protection Agency
. Office of Research and Development, Center for Environmental Research Information: Design Manual: Fine Pore Aeration Systems
. Cincinnati (OH)
: U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Research Information
; 1989
.28.
Wagner
M
, Amann
R
, Lemmer
H
, Schleifer
KH
. Probing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure
. Appl Environ Microbiol
. 1993
May
;59
(5
):1520
–5
.
[PubMed]
0099-224029.
Wagner
M
, Erhart
R
, Manz
W
, Amann
R
, Lemmer
H
, Wedi
D
, et al.. Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge
. Appl Environ Microbiol
. 1994
Mar
;60
(3
):792
–800
.
[PubMed]
0099-224030.
Wagner
M
, von Hoessle
R
. Biological coating of EPDM-membranes of fine bubble diffusers
. Water Sci Technol
. 2004
;50
(7
):79
–85
.
[PubMed]
0273-122331.
Wolfaardt
GM
, Lawrence
JR
, Headley
JV
, Robarts
RD
, Caldwell
DE
. Microbial exopolymers provide a mechanism for bioaccumulation of contaminants
. Microb Ecol
. 1994
May
;27
(3
):279
–91
.
[PubMed]
0095-362832.
Yu
ZT
, Mohn
WW
. Killing two birds with one stone: simultaneous extraction of DNA and RNA from activated sludge biomass
. Can J Microbiol
. 1999
;45
(3
):269
–72
. 0008-4166© 2019 S. Karger AG, Basel
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