Testing a Microarray to Detect and Monitor Toxic Microalgae in Arcachon Bay in France
Abstract
:1. Introduction
2. Experimental Section
2.1. Field Sampling
Sample name | Sample date | Volume filtered (L) | Total RNA extracted (µg) | DoL |
---|---|---|---|---|
1A | 24/07/2011 | 3.3 | 7.46 | 2.2 |
2A | 08/08/2011 | 3.0 | 9.48 | 2.0 |
3A | 22/08/2011 | 3.3 | 9.52 | 1.9 |
4A | 04/10/2011 | 3.25 | 10.66 | 2.2 |
6A | 20/10/2011 | 3.3 | 13.82 | 2.2 |
2.2. RNA Extraction
2.3. RNA Labeling and Fragmentation
2.4. Microarray Design
Probe Name | Targeted Taxon | Gene |
---|---|---|
Controls | ||
DunGS02_25_dT | Dunaliella spp. | 18S |
DunGS05_25_dT | Dunaliella spp. | 18S |
Higher group-level probes | ||
EukS_328_25_dT | Eukaryotes | 18S |
EukS_1209_25_dT | Eukaryotes | 18S |
HeteroS01_25_dT | Heterokonta | 18S |
PrymS01_25_dT | Prymnesiophyta | 18S |
Class-level probes | ||
PrymS03_25_dT | Prymnesiophyceae | 18S |
DinoB_25_dT | Dinophyceae (incl. Apicomplexa) | 18S |
DinoE12_25_dT | Dinophyceae (incl. Apicomplexa) | 18S |
Clade-level probes | ||
DphyexacutaFS01_25_dT | Dinophysiaceae (Dinophysis + Phalacroma) | 18S |
DphyFS02_25_dT | Dinophysiaceae (Dinophysis + Phalacroma) | 18S |
PdeliD02_25_dT | P. delicatissima all clades | 28S |
Clade 01new_25_dT | Prymnesium B1 clade | 18S |
Clade01old_25_dT | Prymnesium | 18S |
ProroPKD01_25_dT | Prorocentrum planktonic clade | 28S |
ProroFPS01 | Prorocentrum planktonic clade | 18S |
ProroFBS02_25_dT | Prorocentrum benthic clade | 18S |
ProroFBS01 | Prorocentrum benthic clade | 18S |
Genus-level probes | ||
PsnGS01_25_dT | Pseudo-nitzschia | 18S |
PsnGS02_25_dT | Pseudo-nitzschia + Fragilariopsis | 18S |
PSN+FRAGS02-25new_dT | Pseudo-nitzschia + Fragilariopsis | 18S |
PSN no pungens_25_dT | Pseudo-nitzschia no pungens | 18S |
PSN + some Frags_25_dT | Pseudo-nitzschia + some Fragilariopsis | 18S |
KareGD01_25_dT | Karenia | 28S |
AlexGD01_25_dT | Alexandrium | 28S |
DphyGD01_25_dT | Dinophysis in part | 28S |
DphyGD02_25_dT | Dinophysis | 28S |
PschGS01_25_dT | Pseudochattonella (genus) | 18S |
PschGS04_25_dT | Pseudochattonella (genus) | 18S |
PschG05_25_dT | Pseudochattonella (genus) | 18S |
DphyGS01_25_dT | Dinophysis genus sensu stricto | 18S |
DphyGS02_25_dT | Dinophysis genus sensu stricto | 18S |
DphyGS03_25_dT | all Dinophysis and Phalacroma | 18S |
DphyGS04_25_dT | all Dinophysis | 18s |
KargeD01_25_dT | Karlodinium genus | 28S |
AzaGD01_dT | Azadinium genus | 28S |
AzaGD03_dT | Azadinium genus | 28S |
AzaGS01_dT | Azadinium genus | 18S |
AzaGS02_dT | Azadinium genus | 18S |
Species-level probes | ||
AtamaS01_25_dT | Alexandrium NA,WE,TA, species complex | 18S |
AminuS01_25_dT | Alexandrium minutum | 18S |
ATNA_D01_25_dT | A. tamarense (North America) | 28S |
ATNA_D02_25_dT | A. tamarense (North America) | 28S |
ATTA _D01_25_dT | A. tamarense (Temperate Asian) | 28S |
AostD01 _25_dT | A. ostenfeldii | 28S |
AostS02 _25_dT | A. ostenfeldii | 18S |
CpolyS01_25_dT | Chrysochromulina polylepis | 18S |
PparvD01_25_dT | Prymnesium parvum | 28S |
Prymparv01_25_dT | Prymnesium parvum | 18S |
KbreD03_25_dT | Karenia mikimotoi and brevis | 28S |
KbreD04_25_dT | K. mikimotoi and brevis | 28S |
KmikiD01_25_dT | K. mikimotoi | 28S |
KbreD05_25 | K. brevis | 28S |
LSKbre0548A25_dT | K. mikimotoi and brevis | 28S |
KmGcS06_25_dT | K. mikimotoi, Gymnodinium catenatum, cf. Chatonella sp. | 18S |
KbreD03c_25_dT | Competitor K. mikimotoi and brevis | 18S |
KbreD04_25c_dT | Competitor K. mikimotoi and brevis | 28S |
SSKbre1448A25_dT | K. brevis | 18S |
SSKbre1448A25c_dT | K. brevis | 18S |
LSKBre0548A25c_dT | K. brevis | 28S |
SSGcat0826A27_dT | Gymnodinium catenatum | 18S |
LSGcat0270A24_dT | G. catenatum | 28S |
GcateS01_25_dT | G. catenatum | 18S |
KveneD01_25_dT | Karlodinium veneficum | 28S |
KveneD02_25_dT | Karlodinium veneficum | 28S |
KveneD03_25_dT | Karlodinium veneficum | 28S |
KveneD04_25_dT | Karlodinium veneficum | 28S |
KveneD05_25_dT | Karlodinium veneficum | 28S |
KveneD06_25_dT | Karlodinium veneficum | 28 |
PlimaS01_25_dT | Prorocentrum lima | 18S |
PlimaFD01_2_dT5 | P. lima | 28S |
PmicaD02_25_dT | P. micans | 28S |
PminiD01_25_dT | P. minimum | 28S |
PmacuS01 | P. maculosum and belizeanum | 18S |
PmacuD01 | P. maculosum | 28S |
PmacuD02 | P. maculosum | 28S |
PrathD01 | P. rathymum and mexicanum | 28S |
PrathD02 | P. rathymum and mexicanum | 28S |
DacumiD02_25_dT | Dinophysis acuminata, dens and sacculus | 28S |
DacutaD02_25_dT | Dinophysis acuta and fortii | 28S |
DacumiS01_25_dT | Dinophysis acuminata | 18S |
DacutaS01_25_dT | Dinophysis acuta | 18S |
DnorvS01_25_dT | Dinophysis norvegica | 18S |
PausserD01_25_dT | Pseudo-nitzschia australis and seriata | 28S |
PmulausD01_25_dT | P. australis and multistriata | 28S |
PcaserausD02_25_dT | P. australis, seriata, deli2 | 28S |
PcaserausD03_25_dT | P. australis, seriata, calliantha | 28S |
PfraucalD02_25_dT | P. fraudulenta, subfraudulenta, calliantha | 28S |
PcaciD01_25_dT | P. caciantha | 28S |
PcaciD02_25_dT | P. caciantha | 28S |
PcaciD04_25_dT | P. caciantha | 28S |
Pcal1D01_25_dT | P. calliantha | 28S |
PmanD01_25_dT | P. manii | 28S |
Pman2D02_25_dT | P. manii | 28S |
Pman2D03_25_dT | P. manii | 28S |
Pman2D05_25_dT | P. manii | 28S |
Pdel4D01_25_dT | P. cf. delicatissima Clade4 | 28S |
Pdel4D02_25_dT | P. cf. delicatissima Clade4 | 28S |
Pdel3B_25_dT | P. delicatissima clade 3 + micropora | 28S |
Pdel3A_25_dT | P. delicatissima clade 3 + micropora | 28S |
CompPdel3_25_dT | Competitor Pdel3A | 28S |
Pdel1D01_25_dT | P. delicatissima Clade1 | 28S |
Pcaldel2D01_25_dT | P. delicatissima Clade2 | 28S |
PcaldelD03_25_dT | P. delicatissima Clade2 and calliantha | 28S |
Pdel4D03_25_dT | P. delicatissima Clade4 | 28S |
PgalaD01_25_dT | P. galaxiae | 28S |
PgalaD02_25_dT | P. galaxiae | 28S |
PgalaD04_25_dT | P. galaxiae | 28S |
PmultS01_25_dT | P. multiseries | 18S |
PmultD02_25_dT | P. multiseries | 28S |
PmultcalD01_25_dT | P. multiseries and calliantha | 28S |
PmultcalD03_25_dT | P. multiseries and calliantha | 28S |
PmultcalD04_25_dT | P. multiseries and calliantha | 28S |
PcalfrauD04_25_dT | P. fraudulenta and multistriata | 28S |
PmulaD03_25_dT | P. multistriata | 28S |
PmulacalD02_25_dT | P. multistriata and calliantha | 28S |
PpdeD01_25_dT | P. pseudodelicatissima and cuspidata | 28S |
PpdeD02_25_dT | P. pseudodelicatissima and cuspidata | 28S |
PpungcalS01_25_dT | P. pungens and calliantha | 18S |
PpungcalD02_25_dT | P. pungens and calliantha | 28S |
PpungcalD04_25_dT | P. pungens and calliantha | 28S |
PsercalD01_25_dT | P. seriata and calliantha | 28S |
CtoxS05_25_dT | cf. Chatonella sp. | 18S |
CtoxiS07_25_dT | cf. Chatonella sp. | 18S |
CtoxiS09_25_dT | cf. Chatonella sp. | 18S |
PfarD01_25_dT | Pseudochattonella farcimen | 28S |
PverD01_25_dT | Pseudochattonella verruculosa | 28S |
SSHaka0193A25_dT | Heterosigma akashiwo | 18S |
SSHaka0200A25_dT | H. akashiwo | 18S |
LSHaka0544A25b_dT | H. akashiwo | 28S |
LSHaka0268A25_dT | H. akashiwo | 28S |
LSHaka0544A25c_dT | H. akashiwo | 28S |
LSHaka0548A25_dT | H. akashiwo | 28S |
LSHaka0329A25_dT | H. akashiwo | 28S |
LSHaka0358A24_dT | H. akashiwo | 28S |
2.6. Microarray Hybridization
2.7. Data Analysis
3. Results and Discussion
3.1. Species Composition during Sampling Period Based on Cell Counts
Species | 1A | 2A | 3A | 4A | 6A |
---|---|---|---|---|---|
Cryptomonadales | 50.700 | 331.500 | 181.400 | 194.100 | 36.400 |
Chaetoceros spp. | 59.000 | 1.841.200 | 629.100 | 4.400 | 40.600 |
Asterionellopsis glacialis | 19.000 | 32.400 | 0 | 27.800 | 446.400 |
Nitzschia spp. | 1.200 | 400 | 600 | 11.000 | 73.200 |
Species | 1A | 2A | 3A | 4A | 6A |
---|---|---|---|---|---|
Pseudo-nitzschia spp. | 30,200 | 7,000 | 0 | 0 | 800 |
Pseudo-nitzschia multistriata | 0 | 0 | 400 | 1,700 | 40,600 |
Prorocentrum minimum, balticum, cordatum | 0 | 400 | 0 | 400 | 0 |
Heterosigma akashiwo | 0 | 0 | 0 | 600 | 400 |
Alexandrium spp. | 20 | 0 | 0 | 0 | 0 |
Dinophysis caudata | 0 | 0 | 0 | 0 | 30 |
3.2. Relations between Microarray Signal, Cell Counts and Detection of Toxins
3.2.1. Pseudo-nitzschia and ASP Toxins
STX | Okadaic Acid, DTXS | Domoic Acid | ||||
---|---|---|---|---|---|---|
(PSP) | (DSP) | (ASP) | ||||
Sampling Date | Multi SPR | ELISA | Multi SPR | ELISA | Multi SPR | ELISA |
24.07.2011 | − | − | − | − | − | − |
08.08.2011 | − | − | − | + | − | − |
22.08.2011 | − | + | − | + | − | − |
04.10.2011 | − | + | − | + | − | + |
20.10.2011 | + | + | − | + | − | + |
3.2.2. Dinophysis and Prorocentrum and DSP Toxins
3.2.3. Alexandrium and PSP Toxins
3.2.4. Heterosigma akashiwo
3.2.5. Species Unfound by Cell Counts but Identified with Microarray and Hierarchy File
Fish Killing Species
Azaspiracid Shellfish Poisoning (AZP) Toxins Producer
Other PSP Toxins
4. Conclusions
Acknowledgments
Appendix
* Alexandrium | 20 | 0 | 0 | 0 | 0 |
* Dinophysis caudata | 0 | 0 | 0 | 0 | 30 |
Dinophysis tripos | 20 | 0 | 0 | 0 | 0 |
Gymnodiniaceae | 0 | 400 | 3,800 | 1,800 | |
Katodinium | 100 | 0 | 0 | 0 | 0 |
Gyrodinium | 0 | 100 | 100 | 200 | 200 |
Gyrodinium spirale | 0 | 200 | 0 | 100 | 0 |
Prorocentrum micans | 0 | 100 | 0 | 0 | 0 |
* Prorocentrum minimum + balticum + cordatum | 0 | 400 | 0 | 400 | 0 |
Prorocentrum triestinum | 0 | 0 | 200 | 800 | 400 |
Protoperidinium | 0 | 200 | 0 | 800 | 600 |
Protoperidinium bipes | 0 | 400 | 5,400 | 600 | 0 |
Protoperidinium steinii + pyriforme | 0 | 0 | 100 | 0 | 0 |
Protoperidinium diabolus | 0 | 0 | 200 | 0 | 0 |
Heterocapsa niei | 0 | 100 | 1000 | 0 | 0 |
Gonyaulax | 0 | 0 | 100 | 0 | 0 |
Scrippsiella + Ensiculifera + Pentapharsodinium + Bysmatrum | 0 | 200 | 2,600 | 1,000 | 1,800 |
Torodinium | 0 | 0 | 100 | 100 | 200 |
Amphidinium | 0 | 0 | 0 | 200 | 0 |
Heterocapsa triquetra | 0 | 0 | 200 | 0 | 0 |
Peridiniales | 400 | 0 | 0 | 1,200 | 1,000 |
Peridiniaceae | 0 | 0 | 1,400 | 0 | 0 |
Peridinium quinquecorne | 0 | 400 | 3,200 | 0 | 0 |
Euglena | 1A | 2A | 3A | 4A | 6A |
Euglenaceae | 0 | 600 | 400 | 0 | 0 |
Eutreptiaceae | 0 | 0 | 0 | 2,200 | 0 |
Eutreptiella | 2,400 | 5,000 | 4,000 | 0 | 3,600 |
Cryptomonads | 1A | 2A | 3A | 4A | 6A |
Cryptomonadales | 50,700 | 331,500 | 181,400 | 194,100 | 36,400 |
Diatoms | 1A | 2A | 3A | 4A | 6A |
Centrales | 0 | 0 | 0 | 0 | 400 |
Rhizosolenia imbricata + styliformis | 0 | 100 | 0 | 0 | 0 |
Rhizosolenia setigera + pungens | 0 | 0 | 0 | 600 | 1000 |
Proboscia alata | 0 | 100 | 0 | 0 | 0 |
Corethron | 0 | 0 | 0 | 100 | 0 |
Paralia sulcata | 600 | 0 | 0 | 400 | 0 |
Thalassiosira | 0 | 0 | 0 | 2,400 | 7,000 |
Thalassiosira rotula | 0 | 0 | 0 | 0 | 400 |
Corethron | 0 | 0 | 0 | 0 | 1,200 |
Chaetoceros | 56,200 | 1,821,400 | 627,900 | 0 | 13,400 |
Chaetoceros decipiens | 2,800 | 19,800 | 1,200 | 3,200 | 6,800 |
Chaetoceros curvisetus + debilis + pseudocurvisetus | 0 | 0 | 0 | 1200 | 19,800 |
Chaetoceros danicus | 0 | 0 | 0 | 0 | 600 |
Lithodesmium | 200 | 5,300 | 7,000 | 3,600 | 6,800 |
Leptocylindrus danicus | 6,200 | 1,600 | 0 | 3,800 | 12,200 |
Leptocylindrus minimus | 0 | 4,800 | 0 | 0 | 6200 |
Cerataulina pelagica | 400 | 1,000 | 5,400 | 2,800 | |
Dactyliosolen fragilissimus | 1,000 | 4,600 | 1200 | 1,000 | 4,400 |
Guinardia striata | 1,100 | 0 | 0 | 0 | 1,800 |
Guinardia flaccida | 100 | 0 | 0 | 0 | 0 |
Guinardia delicatula | 0 | 0 | 0 | 0 | 1,400 |
Skeletonema costatum | 0 | 3,600 | 500 | 0 | 1,000 |
Odontella regia | 0 | 0 | 0 | 0 | 600 |
Biddulphia alternans | 0 | 0 | 0 | 0 | 600 |
Eucampia zodiacus | 0 | 0 | 0 | 0 | 1,400 |
Hemiaulus | 400 | 1,100 | 0 | 0 | 0 |
Lauderia | 400 | 0 | 0 | 0 | 0 |
Pennales | 3,800 | 600 | 200 | 2,000 | 4,200 |
* Pseudo-nitzschia large width, seriata complex (australis + fraudulenta + seriata + subpacifica) | 30,200 | 200 | 0 | 0 | 0 |
* Pseudo-nitzschia narrow width, delicatissima complex (calliantha + delicatissima + pseudodelicatissima) | 0 | 6,800 | 0 | 0 | 0 |
* Pseudo-nitzschi, slender group, seriata complex (multiseries + pungens) | 0 | 0 | 0 | 0 | 800 |
* Pseudo-nitzschia sigmoid group (multistriata) | 0 | 0 | 400 | 1,700 | 40,600 |
Thalassionema nitzschioides | 0 | 2,200 | 0 | 1,200 | 12,600 |
Pleurosigma + Gyrosigma | 0 | 0 | 100 | 600 | 600 |
Nitzschia | 0 | 0 | 0 | 1,1000 | 72,800 |
Nitzschia longissima | 1200 | 400 | 600 | 0 | 400 |
Cylindrotheca closterium | 6,600 | 16,400 | 25,350 | 0 | 2,600 |
Asterionellopsis glacialis | 19,000 | 32,400 | 0 | 2,7800 | 446,400 |
Licmophora | 0 | 0 | 0 | 100 | 0 |
Cocconeis | 0 | 0 | 0 | 400 | 200 |
Heterokonts | 1A | 2A | 3A | 4A | 6A |
*Heterosigma akashiwo | 0 | 0 | 0 | 600 | 400 |
Dictyocha | 0 | 0 | 100 | 400 | 200 |
1A (24.07.2011) | 2A (08.08.2011) | 3A (22.08.2011) | 4A (04.10.2011) | 6A (20.10.2011) | ||||||
---|---|---|---|---|---|---|---|---|---|---|
TI | STDEV | TI | STDEV | TI | STDEV | TI | STDEV | TI | STDEV | |
PSN + some Frags_25_dT | 571,661 | 283,278 | 462,375 | 261,002 | 376,328 | 136,949 | 328,723 | 64,836 | 1,234,899 | 246,612 |
PSN+FRAGS02-25new_dT | 570,012 | 278,217 | 483,590 | 235,672 | 374,378 | 107,819 | 328,689 | 73,975 | 1,236,907 | 237,510 |
PsnGS02_25_dT | 366,160 | 122,407 | 269,644 | 59,512 | 176,231 | 40,406 | 154,926 | 102,545 | 527,093 | 47,698 |
PmulacalD02_25_dT | 201,918 | 30,724 | 189,923 | 53,609 | 35,294 | 18,226 | 35,985 | 14,234 | 253,037 | 27,753 |
PmulaD03_25_dT | 66,635 | 5,760 | 71,895 | 9,951 | 37,380 | 15,172 | 18,590 | 10,183 | 212,033 | 22,236 |
PmulausD01_25_dT | 240,310 | 36,151 | 168,879 | 19,588 | 154,874 | 31,009 | 181,673 | 30,966 | 784,727 | 91,653 |
ProroFPS01 | 169,269 | 31,916 | 160,601 | 35,392 | 58,362 | 14,735 | 78,983 | 19,111 | ||
ProroFBS01 | 113,540 | 137,560 | 67,434 | 189,17 | ||||||
PrathD01 | 108,027 | 8,344 | ||||||||
PbeliS01 | 60,137 | 58,069 | 21,412 | 24,719 | ||||||
AlexGD01_25_dT | 477,054 | 82,900 | 555,744 | 276,647 | 270,780 | 352,356 | 154,715 | 37,017 | 389,966 | 29,238 |
PschGS01_25_dT | 63,769 | 9,284 | ||||||||
PschGS04_25_dT | 547,515 | 98,442 | ||||||||
PschGS05_25_dT | 47,371 | 12,185 | ||||||||
PverD01_25_dT | 70,207 | 10,052 | ||||||||
PfarD01_25_dT | 51,096 | 8,260 | ||||||||
PrymS01_25_dT | 1,062,712 | 223,123 | 1,208,456 | 400,071 | 1,285,690 | 372,848 | 1,592,062 | 501,853 | 1,127,413 | 97,605 |
PrymS03_25_dT | 184,896 | 64,536 | 262,141 | 132,584 | 204,940 | 51,019 | 231,062 | 63,987 | 285,495 | 49,415 |
Clade01old_25_dT | 935,860 | 146,759 | 707,441 | 135,777 | 487,530 | 194,120 | 521,791 | 172,448 | 353,814 | 29,352 |
Clade 01new25_dt | 217,043 | 82,294 | 293,107 | 86,528 | 141,925 | 34,971 | ||||
CpolyS01_25_dT | 112,327 | 9,400 | 122,730 | 29,900 | ||||||
PparvD01_25_dT | 133,275 | 251,500 | ||||||||
KargeD01_25_dT | 138,096 | 195,135 | 90,368 | 92,796 | 17,867 | 11,278 |
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Kegel, J.U.; Del Amo, Y.; Costes, L.; Medlin, L.K. Testing a Microarray to Detect and Monitor Toxic Microalgae in Arcachon Bay in France. Microarrays 2013, 2, 1-23. https://doi.org/10.3390/microarrays2010001
Kegel JU, Del Amo Y, Costes L, Medlin LK. Testing a Microarray to Detect and Monitor Toxic Microalgae in Arcachon Bay in France. Microarrays. 2013; 2(1):1-23. https://doi.org/10.3390/microarrays2010001
Chicago/Turabian StyleKegel, Jessica U., Yolanda Del Amo, Laurence Costes, and Linda K. Medlin. 2013. "Testing a Microarray to Detect and Monitor Toxic Microalgae in Arcachon Bay in France" Microarrays 2, no. 1: 1-23. https://doi.org/10.3390/microarrays2010001