Acuña S, Deng DF, Lehman P, Teh SJ: Sublethal dietary effects of Microcystis on Sacramento splittail, Pogonichthys macrolepidotus . Aquat Toxicol 2012, 110–111: 1-8.
Article
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Evol 1990, 215: 403-410.
Google Scholar
American Public Health Association: Standard Methods of Water and Wastewater. American Public Health Association, American Water Works Association, Water Environment Federation publication. 18th edition. Washington D.C: APHA; 1992.
Google Scholar
Baxa DV, Kurobe T, Ger KA, Lehman PW, Teh SJ: Estimating the abundance of toxic Microcystis in the San Francisco Estuary using quantitative real-time PCR. Harmful Algae 2010, 9: 342-349. 10.1016/j.hal.2010.01.001
Article
Google Scholar
Betournay S, Marsh AC, Donello N, Stiller JW: Selective recovery of microalgae from diverse habitats using “Phyto-specific” 16S rDNA primers. J Phycol 2007, 43: 609-613. 10.1111/j.1529-8817.2007.00350.x
Article
Google Scholar
Casamatta DA, Johansen JR, Vis ML, Broadwater ST: Molecular and morphological characterization of ten polar and near-polar strains within the Oscillatoriales (cyanobacteria). J Phycol 2005, 41: 421-435. 10.1111/j.1529-8817.2005.04062.x
Article
Google Scholar
Castle JW, Rogers JH: Hypothesis for the role of toxin-producing algae in Phanerozoic mass extinctions based on evidence from the geologic record and modern environments. Environ Geosci 2009, 16: 1-23. 10.1306/eg.08110808003
Article
Google Scholar
Cheng C, Zaichao Z, Aizhong D, Jiayan W, Jingfa X, Yujiao S: Bar-coded pyrosequencing reveals the bacterial community during Microcystis water Bloom in Guanting Reservoir, Beijing. Procedia Eng 2011, 18: 341-346.
Article
Google Scholar
Cloern JE, Dufford R: Phytoplankton community ecology: principles applied in San Francisco Bay. Mar Ecol-Prog Ser 2005, 285: 11-28.
Article
Google Scholar
Darriba D, Taboada GL, Doallo R, Posada D: jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 2012, 30: 772.
Article
Google Scholar
Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A: Geneious v5.0.3. 2011. Available from http://www.geneious.com
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32: 1792-1797. 10.1093/nar/gkh340
Article
Google Scholar
Edgar RC: Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26: 2460-2461. 10.1093/bioinformatics/btq461
Article
Google Scholar
Edwards U, Rogall T, Blocker H, Emde M, Bottger EC: Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nuc Aci Res 1989, 17: 7843-7853. 10.1093/nar/17.19.7843
Article
Google Scholar
Engene N, Choi H, Esquenazi E, Rottacker EC, Ellisman MH, Dorrestein PC, Gerwick WH: Underestimated biodiversity as a major explanation for the perceived rich secondary metabolite capacity of the cyanobacterial genus Lyngbya . Env Microbiol 2011, 13: 1601-1610. 10.1111/j.1462-2920.2011.02472.x
Article
Google Scholar
Ezhilarasi A, Anand N: Phylogenetic analysis of Anabaena spp. (Cyanobacteria) using sequences of 16S rRNA Gene. Aust J Basic Appl Sci 2009, 3: 4026-4031.
Google Scholar
Fetscher AE, Busse L, Ode PR: Standard operating procedures for collecting stream algae samples and associated physical habitat and chemical data for ambient bioassessments in California. California State Water Resources Control Board Surface Water Ambient Monitoring Program (SWAMP) Bioassessment SOP 002; 2009. . updated May 2010 http://swamp.mpsl.mlml.calstate.edu/wp-content/uploads/2010/06/SWAMP_SOP_Algae_Field_Collection_050110.pdf
Google Scholar
Ger KA, Teh SJ, Baxa DV, Lesmeister SA, Goldman CR: The effects of dietary Microcystis aeruginosa and microcystin on the copepods of the upper San Francisco Estuary. Freshwater Biol 2010, 55: 1548-1559. 10.1111/j.1365-2427.2009.02367.x
Article
Google Scholar
Goldstein JJ, Tolsdorf TN: An economic analysis of potential water quality improvement in Clear Lake. U.S: Department of Agriculture Soil Conservation Service; 1994:1-42.
Google Scholar
Gugger M, Lyra C, Henriksen P, Coute A, Humbert JF, Sivonen K: Phylogenetic comparison of the cyanobacterial genera Anabaena and Aphanizomenon . Int J Syst Evol Microbiol 2002, 52: 1867-1880. 10.1099/ijs.0.02270-0
Google Scholar
Guiry MD, Guiry GM: AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. 2012. (searched on 29 October 2012) http://www.algaebase.org
Google Scholar
Hebert PD, Ratnasingham S, deWaard JR: Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Bio Soc 2003, 7: S96-99.
Article
Google Scholar
Horne AJ: The ecology of Clear Lake phytoplankton. Lakeport Clear Lake Algal Research Unit; 1975:1-116.
Google Scholar
Janda JM, Abbott SL: 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 2007, 45: 2761-2764. 10.1128/JCM.01228-07
Article
Google Scholar
Jassby AD: Phytoplankton in the upper San Francisco Estuary: recent biomass trends, their causes and their trophic significance. San Fran Est Watershed Sci 2008, 6: 1-24.
Google Scholar
Jones AC, Monroe EA, Podell S, Hess WR, Klages S, Esquenazi E, Niessen S, Hoover H, Rothmann M, Lasken RS, Yates JR, Reinhardt R, Kube M, Burkart MD, Allen EE, Dorrestein PC, Gerwick WH, Gerwick L: Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula . Proc Natl Acad Sci U S A 2011, 108: 8815-8820. 10.1073/pnas.1101137108
Article
Google Scholar
Jüttner F, Watson SB: Biochemical and ecological control of geosmin and 2-methylisoborneol in source waters. Appl Env Microbiol 2007, 73: 4395-4406. 10.1128/AEM.02250-06
Article
Google Scholar
Karlson B, Cusack C, Bresnan E:Microscopic and molecular methods for quantitative phytoplankton analysis. Intergov Oceanograph Commission of UNESCO. (IOC Manuals and Guides, no. 55.). 2010. [http://hab.ioc-unesco.org/index.php?option=com_oe&task=viewDocumentRecord&docID=5440]
Google Scholar
Khan HA, Arif IA, Shobrak M: DNA Barcodes of Arabian partridge and Philby’s Rock partridge: Implications for phylogeny and species identification. Evol Bioinform 2010, 5: 151-158.
Article
Google Scholar
Kochzius M, Seidel C, Antoniou A, Botla SK, Campo D, Cariani A, Vazquez EG, Hauschild J, Hervet C, Hjörleifsdottir S, Hreggvidsson G, Kappel K, Landi M, Magoulas A, Marteinsson V, Nölte M, Planes S, Tinti F, Turan C, Venugopal MN, Weber H, Blohm D: Identifying fishes through DNA barcodes and microarrays. PLoS ONE 2010, 5: e12620. 10.1371/journal.pone.0012620
Article
Google Scholar
Komárek J: Planktic oscillatorialean cyanoprokaryotes. Hydrobiologia 2003, 502: 367-382.
Article
Google Scholar
Komárek J, Zapomělová E, Šmarda J, Kopecký J, Rejmánková E, Woodhouse J, Neilan BA, Komárková J: Polyphasic evaluation of Limnoraphis robusta , a water-bloom forming cyanobacterium from Lake Atitlán, Guatemala, with a description of Limnoraphis gen. nov. Fottea 2013, 13: 39-52.
Article
Google Scholar
Lehman PW, Boyer G, Hall C, Waller S, Gehrts K: Distribution and toxicity of a new colonial Microcystis aeruginosa bloom in the San Francisco Bay Estuary, California. Hydrobiologia 2005, 541: 87-99. 10.1007/s10750-004-4670-0
Article
Google Scholar
Lehman PW, Boyer G, Satchwell M, Waller S: The influence of environmental conditions on the seasonal variation of Microcystis cell density and microcystins concentration in San Francisco Estuary. Hydrobiologia 2008, 600: 187-204. 10.1007/s10750-007-9231-x
Article
Google Scholar
Lehman PW, Teh SJ, Boyer GL, Nobriga ML, Bass E, Hogle C: Initial Impacts of Microcystis aeruginosa blooms on the aquatic food web in the San Francisco Estuary. Hydrobiologia 2010, 637: 229-248. 10.1007/s10750-009-9999-y
Article
Google Scholar
Lehtimäki J, Lyra C, Suomalainen S, Sundman P, Rouhiainen L, Paulin L, Salkinoja-Salonen M, Sivonen K: Characterization of Nodularia strains, cyanobacteria from brackish waters, by genotypic and phenotypic methods. Int J Syst Evol Microbiol 2000, 50: 1043-1053. 10.1099/00207713-50-3-1043
Article
Google Scholar
Lepere C, Wilmotte A, Meyer B: Molecular diversity of Microcystis strains (Cyanophyceae, Chroococcales) based on 16S rRNA sequences. Syst Geogr Plants 2000, 70: 275-283. 10.2307/3668646
Article
Google Scholar
Lin S, Zhang H, Hou Y, Zhuang Y, Miranda L: High-level diversity of dinoflagellates in the natural environment, revealed by assessment of mitochondrial cox1 and cob genes for dinoflagellate DNA barcoding. Appl Env Microbiol 2009, 75: 1279-1290. 10.1128/AEM.01578-08
Article
Google Scholar
Litaker WR, Vandersea WM, Kibler RS, Reece SK, Stokes AN, Lutzoni MF, Yonish AB, West AM, Black NDM, Tester AP: Recognizing dinoflagellate species using ITS rDNA sequences. J Phycol 2007, 43: 344-355. 10.1111/j.1529-8817.2007.00320.x
Article
Google Scholar
Lopes VR, Ramos V, Martins A, Sousa M, Welker M, Antunes A, Vasconcelos VM: Phylogenetic, chemical and morphological diversity of cyanobacteria from Portuguese temperate estuaries. Mar Env Res 2012, 73: 7-16.
Article
Google Scholar
Lopez-Legentil S, Song B, Bosch M, Pawlik JR, Turon X: Cyanobacterial diversity and a new acaryochloris-like symbiont from Bahamian sea-squirts. PLoS One 2011, 6: e23938. 10.1371/journal.pone.0023938
Article
Google Scholar
Lyra C, Suomalainen S, Gugger M, Vezie C, Sundman P, Paulin L, Sivonen K: Molecular characterization of planktic cyanobacteria of Anabaena , Aphanizomenon , Microcystis and Planktothrix genera. Int J Syst Evol Microbiol 2001, 51: 513-526.
Article
Google Scholar
Mankiewicz J, Tarczynska M, Walter Z, Zalewski M: Natural toxins from cyanobacteria. Acta Biol Cracov Bot 2003, 45: 9-20.
Google Scholar
Mioni CE, Kudela RM: Algal toxins bioassessment - Clear Lake, July/August 2010. Final report for Lake County, April 2011. The University of California, Santa Cruz: Institute of Marine Sciences; 2011. (accessed May 2, 2012) http://www.swrcb.ca.gov/rwqcb5/water_issues/basin_plans/tr_living_rivers_council.pdf
Google Scholar
Mioni CE, Kudela RM, Baxa DV: Harmful cyanobacteria blooms and their toxins in Clear Lake and the Delta (California). Final Report, Project #: 10-058-150. Surface Water Ambient Monitoring Program (SWAMP), prepared for the Central Valley Quality Control Board; 2012. (accessed May 2, 2012) http://www.co.lake.ca.us/Assets/WaterResources/Algae/2011+Cyanobacteria+Report.pdf
Google Scholar
Moniz MB, Kaczmarska I: Barcoding of diatoms: nuclear encoded ITS revisited. Protist 2010, 161: 7-34. 10.1016/j.protis.2009.07.001
Article
Google Scholar
Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O’Brien SJ: Molecular phylogenetics and the origins of placental mammals. Nature 2001, 409: 614-618. 10.1038/35054550
Article
Google Scholar
Neilan BA, Jacobs J, Del Dot T, Blackall LL, Hawkins PR, Cox PT, Goodman AE: rDNA sequences and evolutionary relationships among toxic and nontoxic cyanobacteria of the genus Microcystis. Int J Syst Bacteriol 1997, 47: 693-697. 10.1099/00207713-47-3-693
Article
Google Scholar
Osswald J, Rellan S, Carvalho AP, Gago A, Vasconcelos V: Acute effects of an anatoxin-a producing cyanobacterium on juvenile fish Cyprinus carpio L . Toxicon 2007, 49: 693-698. 10.1016/j.toxicon.2006.11.010
Article
Google Scholar
Palinska KA, Liesack W, Rhiel E, Krumbein WE: Phenotype variability of identical genotypes: the need for a combined approach in cyanobacterial taxonomy demonstrated on Merismopedia -like isolates. Arch Microbiol 1996, 166: 224-233. 10.1007/s002030050378
Article
Google Scholar
Puschner B, Pratt C, Tor ER: Treatment and diagnosis of a dog with fulminant neurological deterioration due to anatoxin-a intoxication. J Vet Emergency and Crit Care 2010, 20: 518-522. 10.1111/j.1476-4431.2010.00578.x
Article
Google Scholar
Rajaniemi P, Hrouzek P, Kastovská K, Willame R, Rantala A, Hoffmann L, Komárek J, Sivonen K: Phylogenetic and morphological evaluation of the genera Anabaena , Aphanizomenon , Trichormus and Nostoc (Nostocales, Cyanobacteria). Int J Syst Evol Microbiol 2005, 55: 11-26. 10.1099/ijs.0.63276-0
Article
Google Scholar
Rejmánková E, Komárek J, Dix M, Komárková J, Girón N: Cyanobacterial blooms in Lake Atitlan, Guatemala. Limnologica 2011, 41: 296-302. 10.1016/j.limno.2010.12.003
Article
Google Scholar
Richerson PJ, Suchanek TH, Why SJ: The causes and control of algal blooms in Clear Lake. Final report, July 28, 1994. California: Clean Lake Diagnostic/Feasibility Study for Clear Lake; 1994:1-182.
Google Scholar
Robertson BR, Tezuka N, Watanabe MM: Phylogenetic analyses of Synechococcus strains (cyanobacteria) using sequences of 16S rDNA and part of the phycocyanin operon reveal multiple evolutionary lines and reflect phycobilin content. Int J Syst Evol Microbiol 2001, 51: 861-871. 10.1099/00207713-51-3-861
Article
Google Scholar
Ronquist F, Teslenko M, Van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP: MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 2012, 61: 539-542. 10.1093/sysbio/sys029
Article
Google Scholar
SanMauro D, Vences M, Alcobendas M, Zardoya R, Meyer A: Initial diversification of living amphibians predated the breakup of Pangaea. Am Nat 2005, 165: 590-599. 10.1086/429523
Article
Google Scholar
Sivonen K, Jones G: Cyanobacterial toxins. In Toxic cyanobacteria in water: a guide to their public health consequences, monitoring and management. Edited by: Chorus I, Bartram J. London: Spon Press; 1999:41-111.
Google Scholar
Smith JL, Boyer GL, Zimba PV: A review of cyanobacterial odorous and bioactive metabolites: Impacts and management alternatives in aquaculture. Aquaculture 2008, 280: 5-20. 10.1016/j.aquaculture.2008.05.007
Article
Google Scholar
Sommer T, Armor C, Baxter R, Breuer R, Brown L, Chotkowski M, Culberson S, Feyrer F, Gingras M, Herbold B, Kimmerer W, Mueller-Solger A, Nobriga M, Souza K: The collapse of pelagic fishes in the upper San Francisco Estuary. Fisheries 2007, 32: 270-277. 10.1577/1548-8446(2007)32[270:TCOPFI]2.0.CO;2
Article
Google Scholar
Spier C, Koski T, Graham J, Hanlon J, Brunell M, Borglin S, Stringfellow W: Distribution of Microcystis and microcystin in the southern reach of the Sacramento San Joaquin Delta. Final report, January 2010. Program: University of the Pacific Ecological Engineering Research; 2010:1-38.
Google Scholar
Stackebrandt E, Goebel BM: Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in Bacteriology. Int J Syst Evol Microbiol 1994, 44: 846-849.
Article
Google Scholar
Urbach E, Vergin KL, Young L, Morse A, Larson GL, Giovannoni SJ: Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake. Limnol Oceanogr 2001, 46: 557-572. 10.4319/lo.2001.46.3.0557
Article
Google Scholar
Wacklin P, Hoffmann L, Komárek J: Nomenclatural validation of the genetically revised cyanobacterial genus Dolichospermum (RALFS ex BORNET et FLAHAULT) comb. nova. Fottea 2009, 9: 59-64.
Article
Google Scholar
Winder M, Reuter J, Schladow G: Clear Lake historical data analysis.s Clear Lake final report for Lake County. Davis: University of California; 2010:pp 1-51.
Google Scholar
Zehr JP, Mellon MT, Hiorns WD: Phylogeny of cyanobacterial nif H genes: evolutionary implications and potential applications to natural assemblages. Microbiology 1997, 143: 1443-1450. 10.1099/00221287-143-4-1443
Article
Google Scholar