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4/06/2015
1
Development and standardisation of the PhytoxigeneTM
CyanoDTec Test: A rapid molecular assay for the routine monitoring and differentiation of toxin producing
cyanobacterial blooms
Authors: Mark Van Asten1,2, Jason N Woodhouse2, Leonardo Pinheiro3 , Kerry R Emslie3 and Brett A Neilan2
1 Diagnostic Technology Pty Ltd2 School of Biotechnology and Biomolecular Sciences, UNSW Australia
3 National Measurement Institute (NMI), Australia
2015 Water Microbiology Conference: May 18‐22, Chapel Hill, NC
Toxin Species Distribution and challenge
• Cyanobacteria can be readily differentiated into three phylogenetically distinct orders
– Nostocales
– Oscillatorales
– Chroococales
• For each of the major cyanobacterial toxins, biosynthetic pathways can be found in representatives from each order
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Specialised Metabolite Biosynthesis
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3 2
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Module 1(PKS)
Module 2(PKS)
Module 3(PKS)
Module 4(PKS)
Module 5(NRPS)
Module 6(NRPS)
Module 7(NRPS)
+ substrate 3
+ substrate 2
+ substrate 4
+ substrate 5
+ substrate 6
+ substrate 7
cyclisation
cyclised compound
Substrate: amino acidsSubstrate: carboxyacyl‐CoA
Non‐Ribosomal Peptide Synthetase (NRPS)Polyketide synthase (PKS)
Enzyme: protein that acts as a biological catalystModule: set of catalytic centres that facilitates a set of unique reactionsDomain: individual catalytic centre that facilitates a distinct reaction
Discovery of CyanotoxinGene Clusters
• Microcystin• Tillett et al, 2000
• Nodularin• Moffitt and Neilan, 2004
• Cylindrospermopsin• Mihali et al, 2008
• Saxitoxin• Kellmann et al, 2008
Neilan Laboratory of Microbial & Molecular Diversity
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Microcystin Biosynthesis
Microcystin biosynthesis
• Microcystins are a class of cyclic hepapetidesfeaturing the Adda (PKS) side chain– Variations can be introduced by presence/absence of tailoring enzymes (ie mcyL)
– Variations can also be introduced by the relaxed specificity of the mcyB1 (Leu) and mcyC (Arg) adenylation domains
• Microcystin‐LR (Leu/Arg)
• Microcystin‐RR (Arg/Arg)
• Microcystin‐YR (Tyr/Arg)
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4
~ 4.5 kb
mcyH I F E J D G A B C atn1
Microcystis aeruginosa PCC7806
dnaN G F E D A B C uma1-6mcy J-H
Anabaena sp. 90
Planktothrix agardhii CYA126
mcyT D E G H A B C J ORF1
Nodularia spumigena NSOR10
ORF6-8 I H G F E D C A B ORF1-5
KEY:Nonribosomal peptide synthetase(NRPS) genes
Polyketide synthase (PKS) genes
Tailoring genes
Putative transposases
flanking genes
microcystin gene clusters
Species Strain Hepatoxic Hepatoxin Other Cyanotoxins OriginChroococcalesMicrocystis aeruginosa PCC7806 + microcystin - The NetherlandsMicrocystis aeruginosa PCC7005 + microcystin - ScotlandMicrocystis sp. UTEX 2667 + microcystin - United StatesMicrocystis sp. UTEX 2664 + microcystin - United StatesMicrocystis viridis NIES 102 + microcystin - JapanMicrocystis wesenbergii NIES 107 + microcystin - JapanMicrocystis aeruginosa HUB53 - - - GermanyMicrocystis aeruginosa UWOCC C1 - - - United StatesMicrocystis aeruginosa UWOCC C4 - - United StatesMicrocystis aeruginosa UWOCC P3 - - United StatesMicrocystis sp. UWOCC Bauld B - - - AustraliaSynechocystis sp. PCC6803 - - - United States
NostocalesAnabaena sp. strain 202A2 + microcystin - FinlandAnabaena circinalis NIES 19 - - saxitoxin EnglandCylindrospermopsis sp. strain T3 - - cylindropermopsis AustraliaNodularia harveyana PCC7804 + nodularin FranceNodularia harveyana PCC73104 - - - CanadaNodularia spumigena NROS 10 + nodularia - FinlandNodularia spumigena. BY1 + nodularia - Baltic SeaNodularia spumigena. HEM + nodularia - Baltic SeaNostoc sp. strain 152 + microcystin - JapanNostoc sp. PCC7120 - - - United StatesNostoc sp. PCC73120 - - - Australia
OscillatorialesLyngbya sp. BAN 01 - - n/a AustraliaOscillatoria sp. strain18R + microcystin - FinlandOscillatoria sp. strain 195 + microcystin - FinlandPhormidium tenue - - - n/a JapanPhormidium sp. isolate 2-26b + microcystin n/a United StatesPhormidium sp. isolate 1-6c + microcystin n/a United StatesPhormidium sp. isolate 4-19b + microcystin n/a United States
Detection of cyclic peptide hepatotoxins in three orders of cyanobacteria (Chroococcales, Nostocales, Oscillatoriales)
AMT gene of the microcystin and nodularin synthetases (mcyE, ndaF)
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180000 2000 4000 6000 8000 10000 12000 14000 16000
sxtAsxtB sxtD sxtE sxtF sxtG sxtH sxtIJ sxtK sxtL sxtM sxtNsxtC sxtN
Saxitoxin production in Cynobacteria
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Cylindrospermopsis
Anabaena
From gene to toxin...microcystin
HOMe
HNH
O
H
Me
N
O
H N
MeCOOHH
O CH2
NH
O
NH
MeH
H
HN
OCOOHH
MeH
O
HN
NH
NH2HN
H
O
Me
Me
GK DHIJ
Me H Me
CF B1 A1GP EP A2 B2EK
1 23
4
5
6
7
PK1
PK2-4
T T T
The Phytoxigene test is based on simple paradigm; Like any biological product, toxins have a genetic pathway, if the gene is present then toxin can be produced
Conversely if gene not present, no toxin can be produced
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Challenges of cyanobacteria monitoring include:Identification of cyanobacteria, is it toxic or non‐toxic?
Is there a potential to become Toxic?
Warragamba Dam August 2007
Understanding the biological process for toxin production and the gene sequences responsible enables the
development of standardised molecular tests for the;
• Detection of toxin producing cyanobacteria, irrespective of species and order
• Monitoring and measurement to allow for specific targets and guidelines
• Quantification of the potential for a toxic event
• Predictive surveillance tool to add to the monitoring process, pre and post bloom
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Development of CyanoDTec: A rapid molecular assay for the routine
monitoring of toxic cyanobacterial blooms
Key role of NMI• Develop primary measurement methods, reference
materials and infrastructure to allow traceable measurements to be performed across all areas of
science.
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Certified Reference Material
• Homogeneous and stable‐ subsamples, time
• Specified properties – define the measurement
• Fit for purpose – context, accuracy needed
• Authoritative body – independent, qualified
• Property values – numbers
• Uncertainty‐ confidence interval (accuracy)
• Traceability ‐ units
• Characterised by carrying out measurements using two or more independent reference methods.
• ISO Guide 34:2009, General requirements for the competence of reference material producers.
AN
Nn
n, amount of substance (mole)
Calibrant: dNMP reference materials
N, number of moleculesNA, Avogadro’s constant (6.0221479 x 1023)
No calibrant
Isotope dilution mass spectrometry (IDMS)Weighing
Digital PCRCounting
NMI methods used for DNA quantification
dAMP dGMP
TMP
dCMP
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Quantification of CyanoDTec DNA Reference Material
Independent test run 1 2 3 4PCR Assay sxtA cyrA 16S rRNA mcyEThreshold setting Auto Auto Auto Manual
Replicate 1 1.39E+09 1.41E+09 1.37E+09 1.39E+09Replicate 2 1.46E+09 1.37E+09 1.38E+09 1.35E+09Replicate 3 1.45E+09 1.40E+09 1.39E+09 1.39E+09Replicate 4 1.47E+09 1.37E+09 1.38E+09 1.39E+09Replicate 5 1.40E+09 1.42E+09 1.34E+09 1.38E+09Replicate 6 1.33E+09 1.43E+09 1.37E+09 1.37E+09Replicate 7 1.35E+09 1.41E+09 1.37E+09 1.38E+09Replicate 8
Data for technical replicatesNumber of technical replicates 7 7 7 7Concentration copies/µL 1.41E+09 1.40E+09 1.37E+09 1.38E+09Standard deviation (SD) copies/µL 5.58E+07 2.48E+07 1.62E+07 1.36E+07Relative standard deviation (RSD) % 3.97 1.77 1.18 0.99Grand Mean concentration copies/µL 1.39E+09Expanded Uncertainty copies/µL 4.30E+07Relative expanded uncertainty % 3.1
16S rRNA sxtA cyrA mcyE/nadF
Quantification by digital PCR confirms 1:1 copy number ratio for the four cyanobacteria target sequences
Preparation of CyanoDTec DNA RM working standards
Batch of DNA standards at approximate concentrations of 0, 20, 200, 2000 and 20,000 copies per µL in each vial
Sample NA011 dilution
NA012 dilution
NA013 dilution
NA014 dilution
NA015 dilution
Threshold setting Auto Auto Auto Auto Auto
Replicate 1
copies/µL
0.00E+00 1.97E+01 1.89E+02 1.96E+03 1.97E+04
Replicate 2 0.00E+00 2.16E+01 2.00E+02 1.93E+03 1.95E+04
Replicate 3 0.00E+00 2.07E+01 1.99E+02 2.01E+03 1.96E+04
Replicate 4 0.00E+00 1.96E+01 1.87E+02 1.96E+03 1.98E+04
Replicate 5 0.00E+00 1.85E+01 1.99E+02 2.04E+03 1.99E+04
Number of technical replicates 5 5 5 5 5
Concentration copies/µL 0.00E+00 2.00E+01 1.95E+02 1.98E+03 1.97E+04
Standard deviation (SD) copies/µL 0.00E+00 1.16E+00 6.44E+00 4.58E+01 1.36E+02
Relative standard deviation (RSD) % 0.00 5.82 3.30 2.32 0.69
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Amplification plots of reference material
16S rRNA target assays using BioGX 8 master mix
y = -3.3561x + 38.296
R2 = 0.9992
0
5
10
15
20
25
30
35
40
0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0log DNA RM copy number
Ct
va
lue
s
sxtA target assays using BioGX 8 master mix
y = -3.4412x + 39.939
R2 = 0.9966
0
5
10
15
20
25
30
35
40
0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0log DNA RM copy number
Ct
valu
es
cyrA target assays using BioGX 8 master mix
y = -3.3627x + 40.468
R2 = 0.9956
0
5
10
15
20
25
30
35
40
0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0log DNA RM copy number
Ct
valu
es
mcyE target assays using BioGX 8 master mix
y = -3.3278x + 41.358
R2 = 0.9912
0
5
10
15
20
25
30
35
40
0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0log DNA RM copy number
Ct
valu
es
16S rRNA
sxtA cyrA mcyE
Amplification efficiencies of 95 to 99%
Highly accurate Reference Materials (CyanoNAS) have been produced to verify and/or validate methodologies for detecting toxin producing cyanobacteria using DNA‐based technology.
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CyanoDTec Test Specifics• Simultaneously identifies and quantifies the presence of
total cyanobacteria along with 3 genes responsible for 4 different toxin production;
– Cyanobacteria species, 16S rRNA gene
– Microcystin & Nodularin, mcyE gene
– Cylindrospermopsin, cyrA gene
– Saxitoxin, sxtA gene
• Test completed within 3 hours
• Scalable
• Cost effective
• Specific, no gene no toxin
CyanoDTecMethodology
• Prepare Sample (std extraction protocols)
• Re‐hydrolyse bead/enzyme mix in kit
• Add 5ul of sample to 20ul of enzyme mix into reaction rube
• Run PCR
• TOTAL time 2‐3 hours
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Assay Design and Setupparallel or sequential options
Sample/Standards/Controls
Internal Amplification Control/ 16S rRNA
Toxin Gene Targetsmcy/nda, cyr, sxt
Total Cyanobacteria Assay Toxin gene Assay
Quantifies total Cyanobacteria, determines if dilution is needed or if toxin gene test required
Quantifies and identifies the presence of a toxin gene specific to microcystin, nodularin, cylindrospermopsin and saxitoxinin cyanobacteria
• standardised cyanobacterial toxin gene assay
• Improves understanding and insights of bloom
– Dynamics
– Toxic capacity/potential
• Offers direct relationship between gene level and toxin capacity and production for water management and establishment of toxin gene level guidelines
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ACKNOWLEDGEMENTS
• Lee Bowling
National Measurement Institute, Department of Industry
Brett Neilan
Jason Woodhouse
Yvette Gaweda
Leo Pinheiro
Kerry Emlsie
Cheryl Lim