JILSA  Vol.5 No.1 , February 2013
Genetic Optimization of Artificial Neural Networks to Forecast Virioplankton Abundance from Cytometric Data

Since viruses are able to influence the trophic status and community structure they should be accessed and accounted in ecosystem functioning and management models. So, this work met a set of biological, chemical and physical time series in order to explore the correlations with marine virioplankton community across different trophic gradients. The case studied is the Arraial do Cabo upwelling system, northeast of Rio de Janeiro State in Southeast coast of Brazil. The main goal is to evolve three type of artificial neural network (ANN) by genetic algorithm (GA) optimization to predict virioplankton abundance and dynamic. The input variables range from the abundance of phytoplankton, bacterioplankton and its ratios acquired by one in situ and another ex situ flow cytometers. These data were collected with weekly frequency from August 2006 to June 2007. Our results show viruses being highly correlated to their host, and that GA provided an efficient method of optimizing ANN architectures to predict the virioplankton abundance. The RBF-NN model presented the best performance to an accuracy of 97% for any period in the year. A discussion and ecological interpretations about the system behavior is also provided.

Cite this paper
G. Pereira, M. Oliveira and N. Ebecken, "Genetic Optimization of Artificial Neural Networks to Forecast Virioplankton Abundance from Cytometric Data," Journal of Intelligent Learning Systems and Applications, Vol. 5 No. 1, 2013, pp. 57-66. doi: 10.4236/jilsa.2013.51007.
[1]   C. P. D. Brussaard, S. W. Wilhelm, F. Thingstad, M. G. Weinbauer, G. Bratbak, M. Heldal, S. A. Kimmance, M. Middelboe, K. Nagasaki, J. H. Paul, D. C. Schroeder, C. A. Suttle, Vaqué and D. K. E. Wommack, “Global-Scale Processes with a Nanoscale Drive: The Role of Marine Viruses,” The ISME Journal, Vol. 2, 2008, pp. 1-4.

[2]   C. A. Suttle, “Marine Viruses: Major Players in the Global Ecosystem,” Nature, Vol. 5, No. 8, 2007, pp. 801812.

[3]   D. Lindell, J. D. Jaffe, M. L. Coleman, M. E. Futschik, I. M. Axmann, T. Rector, G. Kettler, M. B. Sullivan, R. Steen, W. R. Hess, G. M. Church and S. M. Chisholm, “Genome-Wide Expression Dynamics of a Marine Virus and Host Reveal Features of Co-Evolution,” Nature, Vol. 449, No. 7158, 2007, pp. 83-86. doi:10.1038/nature06130

[4]   N. Jiao, Y. Zhao, T. W. Luo and X. Wang, “Natural and Anthropogenic Forcing on the Dynamics of Virioplankton in the Yangtze River Estuary,” Journal of Marine Biology Association United Kingdom, Vol. 86, No. 3, 2006, pp. 543-550. doi:10.1017/S0025315406013452

[5]   J. P. Payet and C. A. Suttle, “Physical and Biological Correlates of Virus Dynamics in the Southern Beaufort Sea and Amundsen Gulf,” Journal of Marine Systems, Vol. 74, No. 3-4, 2007, pp. 933-945. doi:10.1016/j.jmarsys.2007.11.002

[6]   J. L. Clasen, S. M. Brigden, J. P. Payet and C. A. Suttle, “Evidence That Viral Abundance across Oceans and Lakes Is Driven by Different Biological Factors,” Freshwater Biology, Vol. 53, No. 6, 2008, pp. 1090-1100. doi:10.1111/j.1365-2427.2008.01992.x

[7]   G. C. Pereira, A. Granato, A. R. Figueiredo and N. F. F. Ebecken, “Virioplankton Abundance in Trophic Gradients of an Upwelling Field,” Brazilian Journal of Microbiology, Vol. 40, No. 4, 2009, pp. 857-865. doi:10.1590/S1517-83822009000400017

[8]   O. Bergh, K. Y. B?rsheim, G. Bratbak and M. Heldal, “High Abundance of Viruses Found in Aquatic Environments,” Nature, Vol. 340, 1989, pp. 467-468. doi:10.1038/340467a0

[9]   R. T. Noble and J. A. Fuhrman, “Use of SYBR Green I for Rapid Epifluorescence Counts of Marine Viruses and Bacteria,” Aquatic Microbial Ecology, Vol. 14, No. 2, 1998, pp. 113-118. doi:10.3354/ame014113

[10]   D. Marie, C. P. D. Brussaard, R. Thyrhaug, G. Bratbak and D. Vaulot, “Enumeration of Marine Viruses in Culture and Natural Samples by Flow Cytometry,” Applied and Environmental Microbiology, Vol. 65, No. 1, 1999, pp. 45-52.

[11]   Y. Bettarel, T. Sine-Nagano, C. Amblard and H. Laveran, “A Comparison of Methods for Counting Viruses in Aquatic Systems,” Applied and Environmental Microbiology, Vol. 66, No. 6, 2000, pp. 2283-2289. doi:10.1128/AEM.66.6.2283-2289.2000

[12]   M. M. Ferris, C. L. Stoffel, T. T. Maurer and K. L. Rowlen, “Quantitative Intercomparison of Transmission Electron Microscopy, Flow Cytometry, and Epifluorescence Microscopy for Nanometric Particle Analysis,” Analytical Biochemistry, Vol. 304, No. 2, 2002, pp. 249-256. doi:10.1006/abio.2002.5616

[13]   C. Courties, A. Vaquer, M. Tousselier, M. J. ChretiennotDinet, J. Neveux, C. Machado and H. Claustre, “Smallest Eukaryotic Organism,” Nature, Vol. 370, No. 255, 1994. p. 255.

[14]   M. Yanada, T. Yokokawa, C. H. Lee, H. Tanaka, I. Kudo and Y. Maita, “Seasonal Variation of Two Different Heterotrophic Bacterial Assemblages in Subarctic Coastal Seawater,” Marine Ecology Progress Series, Vol. 204, 2000, pp. 289-292. doi:10.3354/meps204289

[15]   E. S. Lindstr?m, T. Weisse and P. Sadler, “Enumeration of Small Ciliates in Culture by Flow Cytometry and Nucleic Acid Staining,” Journal Microbiological Methods, Vol. 49, No. 2, 2002, pp. 173-182. doi:10.1016/S0167-7012(01)00366-9

[16]   J. M. Rose, D. A. Caron, M. E. Sieracki and N. Poulton, “Counting Heterotrophic Nanoplanktonic Protists in Cultures and Aquatic Communities by Flow Cytometry,” Aquatic Microbial Ecology, Vol. 34, No. 3, 2004, pp. 263-277. doi:10.3354/ame034263

[17]   G. B. J. Dubelaar and P. L. Gerritzen, “CytoBuoy: A Step Forward towards Using Flow Cytometry in Operational Oceanography,” Scientia Marina, Vol. 64, No. 2, 2000, pp. 255-265.

[18]   R. J. Olson, A. Shalapyonok and H. M. Sosik, “An Automated Submersible Floe Cytometer for Analyzing Pico and Nanoplankton: FlowCytobot,” Deep-Sea Research I, Vol. 50, No. 2, 2003, pp. 301-315. doi:10.1016/S0967-0637(03)00003-7

[19]   R. Danovaro, A. Dellanno, A. Trucco, M. Serresi and S. Vanucci, “Determination of Viruses in Marine Sediments,” Applied and Environmental Microbiology, Vol. 67, No. 3, 2001, pp. 1384-1387. doi:10.1128/AEM.67.3.1384-1387.2001

[20]   I. Hewson and J. A. Fuhrman, “Viriobenthos Production and Virioplankton Sorptive Scavenging by Suspended Sediment Particles in Coastal and Pelagic Waters,” Microbiological Ecology, Vol. 46, No. 3, 2003, pp. 337-347. doi:10.1007/s00248-002-1041-0

[21]   M. S. Schwalbach, I. Hewson and J. A. Fuhrman, “Viral Effects on Bacterial Community Composition in Marine Plankton Microcosms,” Aquatic Microbial Ecology, Vol. 34, No. 2, 2004, pp. 117-127. doi:10.3354/ame034117

[22]   D. Prangishvili, P. Forterre and R. A. Garrett, “Viruses of the Archaea: A unifying view,” Nature Reviews Microbiology, Vol. 4, No. 11, 2006, pp. 837-48. doi:10.1038/nrmicro1527

[23]   A. C Baudoux and C. P. Brussaard, “Characterization of Different Viruses Infecting the Marine Harmful Algal Bloom Species Phaeocystis globosa,” Virology, Vol. 341, No. 1, 2005, pp. 80-90. doi:10.1016/j.virol.2005.07.002

[24]   Y. Takao, K. Nagasaki, K. Mise, T. Okuno and D. Honda, “Isolation and Characterization of a Novel Single-Stranded RNA Virus Infectious to a Marine Fungoid Protist, Schizochytrium sp. (Thraustochytriaceae, Labyrinthulea),” Applied and Environmental Microbiology, Vol. 71, No. 8, 2004, pp. 4516-4522. doi:10.1128/AEM.71.8.4516-4522.2005

[25]   M. G. Fischer, M. J. Allen, W. H. Wilson and C. A. Suttle, “Giant Virus with a Remarkable Complement of Genes Infects Marine Zooplankton,” Proceedings National Academy Science, Vol. 107, No. 45, 2010, pp. 19508-19513. doi:10.1073/pnas.1007615107

[26]   J. Zhuang, G. Cai, Q. Lin, Z. Wu and L. Xie, “A Bacteriophage-Related Chimeric Marine Infecting Abalone,” PloS ONE, Vol.5, No. 11, 2010, pp. 1-12. doi:10.1371/journal.pone.0013850

[27]   A. Vardi, B. A. S. Van Mooy, H. F. Fredricks, K. J. Popendorf, J. E. Ossolinski, L. Haramaty and K. D. Bidle, “Viral Glycosphingolipids Induce Lytic Infection and Cell Death in Marine Phytoplankton,” Science, Vol. 326, No. 5954, 2009, pp. 861-865. doi:10.1126/science.1177322

[28]   A. Long, L. D. McDaniel, J. Mobberley and J. H. Paul, “Comparison of Lysogeny (Prophage Induction) in Heterotrophic Bacterial and Synechococcus Populations in the Gulf of Mexico and Mississippi River Plume,” The ISME Journal, Vol. 2, 2008, pp. 132-144. doi:10.1038/ismej.2007.102

[29]   D. Coombs, M. A. Gilchrist, J. Percus and A. S. Perelson, “Optimal Viral Production,” Bulletin of Mathematical Biology, Vol. 65, No. 6, 2003, pp. 1003-1023. doi:10.1016/S0092-8240(03)00056-9

[30]   K. E. Wommack and R. R. Colwell, “Virioplankton: Viruses in Aquatic Ecosystems,” Microbiology and Molecular Biology, Vol. 64, No. 1, 2000, pp. 69-114. doi:10.1128/MMBR.64.1.69-114.2000

[31]   M. Middelboe, “Bacterial Growth Rate and Virus-Host Dynamics,” Microbial Ecology, Vol. 40, No. 2, 2000, pp. 114124.

[32]   S. Haykin, “Neural Networks,” Prentice Hall, Upper Saddle River, 1999

[33]   M. Scardi, “Artificial Neural Network as Empirical Models of Phytoplankton Production,” Marine Ecological Progress Series, Vol. 139, 1996, pp. 289-299. doi:10.3354/meps139289

[34]   R. S. Woodd-Walkers, K. S. Kingston and C. P. Gallienne, “Using Neural Networks to Predict Surface Zooplankton Biomass along a 50?N to 50?S Transect of the Atlantic,” Journal of Plankton Research, Vol. 23, No. 8, 2001, pp. 875-888. doi:10.1093/plankt/23.8.875

[35]   G. Brion, C. Viswanathan, T. R. Neelakantan, S. Lingireddy, R. Girones, D. Lees, A. Allard and A. Vantarakis, “Artificial Neural Network Prediction of Viruses in Shellfish,” Applied and Environmental Microbiology, Vol. 71, No. 9, 2005, pp. 5244-5253. doi:10.1128/AEM.71.9.5244-5253.2005

[36]   J. D. Olden, N. L. Poff and B. P. Bledsoe, “Incorporating Ecological Knowledge into Ecoinformatics: An Example of Modeling Hierarchically Structured Aquatic Communities with Neural Network,” Ecological Informatics, Vol. 1, No. 1, 2006, pp. 33-42. doi:10.1016/j.ecoinf.2005.08.003

[37]   Tae-Soo, I. S. Kawak and Y. S. Park, “Patterns Recognition of Long-Term Ecological Data in Community Changes by Using Artificial Neural Network: Benthic Macroinvertebates and Chironomids in a Polluted Stream,” Korean Journal Ecology, Vol. 23, No. 2, 2000, pp. 89-100.

[38]   S. Malek, A. SalleH and M. S. Baba, “Analysis of Selected Algal Growth (Pyrrophyta) in Tropical Lake Using Kohonen Self Organizing Feature Map (SOM) and Its Prediction Using Rule Based Systems,” International Conference and Workshop on Emerging Trends on Technology, Mumbai, 26-27 February 2010, pp. 761-764. doi:10.1145/1741906.1742083

[39]   G. C. Pereira and N. F. F. Ebecken, “Combining in Situ Flow Cytometry and artificial Neural Networks for Aquatic Systems Monitoring,” Expert Systems with Applications, Vol. 38, No. 8, 2011, pp. 9626-9632. doi:10.1016/j.eswa.2011.01.140

[40]   G. Yen and H. Lu, “Hierarchical Genetic Algorithm for near Optimal Feedforward Neural Network Design,” International Journal Neural Systems, Vol. 12, No. 1, 2002, pp. 31-43.

[41]   Z.-Y. Xing, Y. Zhang, Y. Qin, L.-M. Jia and Y.-Y. Wu, “A Hierarchical Genetic Algorithm Based RBF Neural Network Approach for Modelling of Electrohydraulic System,” ICROS-SICE International Joint Conference, Fukuoka International Congress Center-Japan, 18-21 August 2009.

[42]   R. Ghorbani, Q. Wu and G. G. Wang, “Nearly Optimal Neural Network Stabilization of Bipedal Standing Using Genetic Algorithm,” Engineering Applications of Arti?cial Intelligence, Vol. 20, No. 4, 2007, pp. 473-480. doi:10.1016/j.engappai.2006.09.007

[43]   S. H. Ling and F. H. F. Leung, “An Improved Genetic Algorithm with Average-Bound Crossover and Wavelet Mutation Operations,” Soft Computing, Vol. 11, No. 1, 2007, pp. 7-31. doi:10.1007/s00500-006-0049-7

[44]   N. ?ztürk, “Use of Genetic Algorithm to Design Optimal Neural Network Structure,” Engineering Computations, Vol. 20, No. 8, 2003, pp. 979-997. doi:10.1108/02644400310502982

[45]   S. H. Ling, “A New Neural Network Structure: Node-toNode-Link Neural Network,” Journal of Intelligence Learning Systems and Application, Vol. 2, No. 1, 2010, pp. 1-11. doi:10.4236/jilsa.2010.21001

[46]   S. H. Ling and H. K. Lam, “Playing Tic-Tac-Toe Using Genetic Neural Network with Double Transfer Functions,” Journal of Intelligence Learning Systems and Application, Vol. 3, No. 1, 2011, pp. 37-44. doi:10.4236/jilsa.2011.31005

[47]   F. H .F. Leung, H. K. Lam, S. H. Ling and P. K. S. Tam, “Tuning of the Structure and Parameters of Neural Network Using an Improved Genetic Algorithm,” IEEE Transactions on Neural Networks, Vol. 14, No. 1, 2003, pp. 79-88. doi:10.1109/TNN.2002.804317

[48]   S. A. Gaeta, J. A. Lorenzetti, L. B. Miranda, S. M. M. Susimi-Ribeiro, M. Pompeu and C. E. S. Araújo, “The Vitória Eddy and Its Relation to the Phytoplankton Biomass and Primary Production during the Austral Fall of 1995,” Archive Fishery Marine Research, Vol. 47, No. 2-3, 1999, pp. 253-270.

[49]   G. C. Pereira, R. Coutinho and N. F. F. Ebecken, “Data Mining for Environmental Analysis and Diagnostic: A Case Study of Upwelling Ecosystem of Arraial do Cabo,” Brazilian Journal of Oceanography, Vol. 65, No. 1, 2008, pp. 1-12. doi:10.1590/S1679-87592008000100001

[50]   M. Guenther, E. Gonzalez-Rodriguez, W. F. Carvalho, C. E. Rezende, G. Mugrabe and J. L. Valentin, “Plankton Trophic Structure and Particulate Organic Carbon Production during a Coastal Downwelling-Upwelling Cycle,” Marine Ecololy Progress Series, Vol. 363, 2008, pp. 109-119. doi:10.3354/meps07458

[51]   SCOR, “Protocols for the Joint Global Ocean Flux Study (JGOFS) Core Measurements,” Scientific Committee on Ocean Research, International Council of Scientific Unions 9170, Bergen, 1996.

[52]   C. P. D. Brussaard, “Optimization of Procedures for Counting Viruses by Flow Cytometry,” Applied and Environmental Microbiology, Vol. 70, No. 3, 2004, pp. 1506-1513. doi:10.1128/AEM.70.3.1506-1513.2004

[53]   M. Kearns, “A Bound on the Error of Cross Validation Using the Approximation and Estimation Rates, with Consequences for the Training-Test Split,” AT&T Research, Murray Hill, 1996, pp. 183-189.

[54]   D. E. Rumelhart, G. E. Hinton and R. J. Williams, “Learning Representations by Back-Propagation Error,” Nature, Vol. 323, 1986, pp. 533-536. doi:10.1038/323533a0

[55]   M. D. Buhmann, “Radial Basis Functions: Theory and Implementations,” Cambridge University Press, Cambridge, 2003. doi:10.1017/CBO9780511543241

[56]   D. F. Specht, “A General Regression Neural Network,” IEEE Transactions on Neural Networks, Vol. 2, 1991, pp. 568-1989. doi:10.1109/72.97934

[57]   L. Rutkowski, “Generalized Regression Neural Network in Time-Varying Environment,” IEEE Transactions on Neural Networks, Vol. 15, No. 3, 2004, pp. 576-596. doi:10.1109/TNN.2004.826127

[58]   J. H. Holland, “Adaptation in Natural and Artificial Systems,” University of Michigan Press, Ann Abor, 1975.

[59]   D. E. Goldberg, “Genetic Algorithm in Search, Optimization, and Machine Learning,” Addison-Wesley, New York, 1989.

[60]   G. Salzmann, “Light Scatter: Detection and Usage,” Current Protocols in Cytometry, No. 9, 1999. doi:10.1002/0471142956

[61]   J. C. Cury, F. V. Araujo, S. A. Coelho-Souza, R. S. Peixoto, J. A. L. Oliveira, H. F. Santos, A. M. R. Dávila and A. S. Rosado, “Microbial Diversity of a Brazilian Coastal Region Influenced by an Upwelling System and Anthropogenic Activity,” PloS ONE, Vol. 6, No. 1, 2011, pp. 1-13. doi:10.1371/journal.pone.0016553

[62]   J. C. Auguet, H. Montanie, D. Delmas, H. J. Hartmann, and V. Huet, “Dynamic of Virioplankton Abundance and Its Enviromental Control in the Charente Estuary (France),” Microbial Ecology, Vol. 50, No. 3, 2005, pp. 1-13. doi:10.1007/s00248-005-0183-2

[63]   S. J. Williamson, L. A. Houchin, L. Daniel and J. H. Paul, “Seasonal Variation in Lysogeny as Described by Prophage Induction in Tampa Bay, Florida,” Applied and Environmental Microbiology, Vol. 68, No. 9, 2002, pp. 4307-4314. doi:10.1128/AEM.68.9.4307-4314.2002

[64]   A. Barreto, H. Barbosa and N. F. F. Ebecken, “Growing Compact RBF Networks Using a Genetic Algorithm,” Proceedings of the 7th Brazilian Symposium on Neural Networks, S?o Luís, 11-14 November 2002.

[65]   A. Conty, F. Garcia-Criado and E. Bécares, “Changes in Bacterial and Ciliate Densities with Trophic Status in Mediterranean Shallow Lakes,” Hydrobiologia, Vol. 584, No. 1, 2007, pp. 327-335. doi:10.1007/s10750-007-0585-x

[66]   M. G. Weinbauer, D. Fuks and P. Peduzzi, “Distribution of Viruses and Dissolved DNA along a Coastal Trophic Gradient in the Northern Adriatic Sea,” Applied and Environmental Microbiology, Vol. 59, No. 12, 1993, pp. 4074-4082.

[67]   M. Breitbart, B. Felts, S. Kelley, J. M. Mahaffy, J. Nulton, P. Salomon and F. Rohwer, “Diversity and Population Structure of a Near-Shore Marine-Sediment Viral Community,” Proceedings of the Royal Society B: Biological Sciences, Vol. 271, No. 1539, 2003, pp. 565-574.

[68]   M. G. Weinbauer, “Ecology of Procaryotic Viruses,” FEMS Microbiology Reviews, Vol. 28, No. 2, 2004, pp. 127-181. doi:10.1016/j.femsre.2003.08.001

[69]   K. Nagasaki, Y. Shirai, Y. Tomaru, K. Nishida and S. Pietrokovski, “Algal Viruses with Distinct Intraspecies Host Specificities Include Identical Intein Elements,” Applied and Environmental Microbiology, Vol. 71, No. 7, 2005, pp. 3599-3607. doi:10.1128/AEM.71.7.3599-3607.2005

[70]   L. McDaniel and J. H. Paul, “Effect of Nutrient Addition and Environmental Factors on Prophage Induction in Natural Populations of Marine Synechococcus Species,” Applied and Environmental Microbiology, Vol. 71, No. 2, 2005, pp. 842-850. doi:10.1128/AEM.71.2.842-850.2005

[71]   K. D. Bidle, L. Haramaty, J. Barcelos e Ramos and P. Falkowski, “Viral Activation and Recruitment of Metacaspases in the Unicellular Coccolithophore, Emiliania huxleyi,” Proceedings National Academy Science, Vol. 104, No. 14, 2007, pp. 6049-6054. doi:10.1073/pnas.0701240104