Abstract
Ships’ ballast water (BW) commonly moves macroorganisms and microorganisms across the world’s oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships’ BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world’s oceans.
Similar content being viewed by others
References
Caron DA, Countway PD, Jones AC, Kim DY, Schnetzer A (2012) Marine protistan diversity. Annu Rev Mar Sci 4:467–493
Caron DA (2013) Towards a molecular taxonomy for Protists: benefits, risks, and applications in plankton ecology. J Eukaryot Microbiol 60:407–413
Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR et al (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102–112
Baas Becking LGM (1934) Geobiologie: of inleiding tot de milieukunde. W.P. Van Stockum and Zoon, The Hague, the Netherlands
Dolan JR (2005) Biogeography of aquatic microbes. Aquat Microb Ecol 41:39–48
Gollasch S (2002) The importance of ship hull fouling as a vector of species introductions into the north Sea. Biofouling 18:105–121
Davidson IC, Brown CW, Sytsma MD, Ruiz GM (2009) The role of containerships as transfer mechanisms of marine biofouling species. Biofouling 25:645–655
Ruiz GM, Rawlings TK, Dobbs FC, Drake LA, Mullady T, Huq A, Colwell RR (2000) Global spread of microorganisms by ships. Nat 408:49–50
Carlton JT (1985) Transoceanic and interoceanic dispersal of coastal marine organisms: the biology of ballast water. Oceanogr Mar Biol Ann Rev 23:313–317
Coutts ADM, Dodgshun TJ (2007) The nature and extent of organisms in vessel sea-chests: a protected mechanism for marine bioinvasions. Mar Pollut Bull 54:875–886
United Nations Conference on Trade Development (2012), http://unctad.org/en/pages/Statistics.aspx
Miller AW, Minton MS, Ruiz GM (2011) Geographic limitations and regional differences in ships’ ballast water management to reduce marine invasions in the contiguous United States. Bioscience 61:880–887
Hallegraeff GM, Bolch CJ (1991) Transport of toxic dinoflagellate cysts via ships’ ballast water. Mar Pollut Bull 22:27–30
Steichen JL, Schulze A, Brinkmeyer R, Quigg A (2014) All aboard! A biological survey of ballast water onboard vessels spanning the North Atlantic Ocean. Mar Pollut Bull 87:201–210
Hallegraeff GM (1998) Transport of toxic dinoflagellates via ships’ ballast water: bioeconomic risk assessment and efficacy of possible ballast water management strategies. Mar Ecol Prog Ser 168:297–309
Hallegraeff GM, Bolch CJ (1992) Transport of diatom and dinoflagellate resting spores in ships’ ballast water: implications for plankton biogeography and aquaculture. J Plankton Res 14:1067–1084
McCarthy SA, Khambaty FM (1994) International dissemination of epidemic Vibrio cholerae by cargo ship ballast and other nonpotable waters. Appl Environ Microbiol 60:2597–2601
Aguirre-Macedo ML, Vidal-Martinez VM, Aguirre-Macedo ML, Vidal-Martinez VM, Herrera-Silveira JA, Valdés-Lozano DS, Herrera-Rodríguez M, Olvera-Novoa MA (2008) Ballast water as a vector of coral pathogens in the Gulf of Mexico: The case of the Cayo Arcas coral reef. Mar Poll Bull 56:1570–1577
Galil BS, Hulsmann N (1997) Protist transport via ballast water—biological classification of ballast tanks by food web interactions. Eur J Protistol 33:244–253
Galil BS, Hulsmann N (2001) The effects of freshwater flushing on marine heterotrophic protists—implications for ballast water management. Mar Poll Bull 42:1082–1086
Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JR, Bowser SS, Brugerolle G, Fensome RA, Fredericq S et al (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 52:399–451
National Ballast Information Clearinghouse (2008) http://invasions.si.edu/nbic/search.html.
Bråte J, Logares R, Berney C, Ree DK, Klaveness D, Jakobsen KS, Shalchian-Tabrizi K (2010) Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA. ISME J 4:1144–1153
Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM (2009) A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE 4, e6372
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Method 7:335–336
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinform 26:2460–2461
Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Method 10:996–998
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinform 27:2194–2200
Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, de Vargas C, Decelle J et al (2013) The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acid Res 41:D597–D604
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267
Nguyen NH, Smith D, Peay K, Kennedy P (2015) Parsing ecological signal from noise in next generation amplicon sequencing. New Phytol 205:1389–1393
Kermarrec L, Franc A, Rimet F, Chaumeil P, Humbert JF, Bouchez A (2013) Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms. Mol Ecol Resour 13:607–619
Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Micobiol 67:4399. doi:10.1128/AEM.67.10.4399-4406.2001
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl Acid Res 30:3059–3066
Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9:286–298
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest2: more models, new heuristics and parallel computing. Nat Method 9(8):772. doi:10.1038/nmeth.2109
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinform 19:1572–1574
Lindeque PK, Parry HE, Harmer RA, Somerfield PJ, Atkinson A (2013) Next generation sequencing reveals the hidden diversity of zooplankton assemblages. PLoS ONE 8, e81327
Kim Y, Gim Aw T, Teal TK, Rose JB (2015) Metagenomic investigation of viral communities in ballast water. Environ Sci Technol 49:8396–8407
Zhan A, He S, Brown EA, Chain FJJ, Therriault TW, Abbott CL, Heath DD, Cristescu ME, MacIsaac HJ (2014) Reproducibility of pyrosequencing data for biodiversity assessment in complex communities. Methods Ecol Evol 5:881–890
Dejean T, Valentini A, Duparc A, Pellier-Cuit S, Pompanon F, Taberlet P, Miaud C (2011) Persistence of environmental DNA in freshwater ecosystems. PLoS ONE 6, e23398
Zaiko A, Martinez JL, Ardura A, Clusa L, Borrell YJ, Samuiloviene A, Roca A, Garcia-Vazquez E (2015) Detecting nuisance species using NGST: methodology shortcomings and possible application in ballast water monitoring. Mar Environ Res. doi:10.1016/j.marenvres.2015.07.002
Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR, Amaral-Zettler L, Guillou L (2014) Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS ONE 6, e18169
Zhan A, Hulák M, Sylvester F, Huang X, Adebayo AA, Abbott CL, Adamowicz SJ, Heath DD, Cristescu ME, MacIsaac HJ (2013) High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Mar Environ Res 4:558–565
Lafferty KD, Dobson AP, Kuris AM (2006) Parasites dominate food web links. Proc Natl Acad Sci 103:11211–11216
Kuris AM, Hechinger RF, Shaw JC, Whitney KL, Aguirre-Macedo L, Boch CA, Dobson AP, Dunham EJ, Fredensborg BL, Huspeni TC et al (2008) Ecosystem energetic implications of parasite and free-living biomass in three estuaries. Nat 454:515–518
Hudson P (2005) Parasites, diversity, and the ecosystem. In: Frédéric T, Renaud F, Guegan JF (eds) Parasitism and ecosystems. Oxford University Press, New York, pp 1–52
Møller AP (2005) Parasitism and the regulation of host populations. In: Frédéric T, Renaud F, Guegan JF (eds) Parasitism and ecosystems. Oxford University Press, New York, pp 43–53
Hudson PJ, Dobson AP, Lafferty KD (2006) Is a healthy ecosystem one that is rich in parasites? Trends Ecol Evol 21:381–385
Harvell CD, Kim K, Burkholder JM, Colwell RR, Epstein PR, Grimes DJ, Hofmann EE, Lipp EK, Osterhaus A, Overstreet RM et al (1999) Emerging marine diseases—climate links and anthropogenic factors. Sci 285:1505–1510
Ward JR, Lafferty KD (2004) The elusive baseline of marine disease: are diseases in ocean ecosystems increasing? PLoS Biol 2, e120
Lafferty KD, Kuris AM (2005) Parasitism and environmental disturbances. In: Frédéric T, Renaud F, Guegan JF (eds) Parasitism and ecosystems. Oxford University Press, New York, pp 113–123
Harvell D, Aronson R, Baron N, Connell J, Dobson A, Ellner S, Gerber L, Kim K, Kuris AM, McCallum H et al (2004) The rising tide of ocean diseases: unsolved problems and research priorities. Front Ecol Environ 2:375–382
Padilla DK, Williams SL (2004) Beyond ballast water: aquarium and ornamental trades as sources of invasive species in aquatic ecosystems. Front Ecol Environ 2:131–138
Hines PM (2001) Problems of applying risk analysis to aquatic organisms. Proceedings of the International Conference on Risk Analysis in Aquatic Animal Health, Paris
Korringa P, Lambert L (1951) Quelques observations sur la fréquence de Mytilicola intestinalis steuer (Copepoda parasita) dans les moules du littoral méditerranéen français. Revue Des Travaux de l’Institut Des Pêches Maritimes 17:15–29
Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, Massana R, Scanlan DJ, Worden AZ (2008) Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol 10:3349–3365
Coats DW (1999) Parasitic life styles of marine dinoflagellates. J Eukaryot Microbiol 46:402–409
Glockling SL, Marshall WL, Gleason FH (2013) Phylogenetic interpretations and ecological potentials of the Mesomycetozoea (Ichthyosporea). Fungal Ecol 6:237–247
Raghukumar S, Damare VS (2011) Increasing evidence for the role of Labyrinthulomycetes in marine ecosystems. Bot Mar 54:3–11
Leander CA, Porter D (2001) The Labyrinthulomycota is comprised of three distinct lineages. Mycol 93:459–464
Muehlstein LK, Porter D, Short FT (1991) Labyrinthula zosterae sp. nov., the causative agent of wasting disease of eelgrass, Zostera marina. Mycol 83:180–191
Ragan MA, MacCallum GS, Murphy CA, Cannone JJ, Gutell RR, McGladdery SE et al (2000) Protistan parasite QPX of hard-shell clam Mercenaria mercenaria is a member of Labyrinthulomycota. Dis Aquat Orgs 42:185–190
Burge CA, Kim CJS, Lyles JM, Harvell CD (2013) Special Issue Oceans and Humans Health: the ecology of marine opportunists. Microb Ecol 65:869–879
Bower SM (1987) Labyrinthuloides haliotidis n. sp. (Protozoa: Labyrinthomorpha), a pathogenic parasite of small juvenile abalone in a British Columbia mariculture facility. Can J Zool 65:1996–2007
Van Bressem MF, Raga JA, Guardo GD, Jepson PD, Duignan PJ, Siebert U, Barrett T, de Oliveira Santos MC, Moreno IB, Siciliano S et al (2009) Emerging infectious diseases in cetaceans worldwide and the possible role of environmental stressors. Dis Aqu Org 86:143–157
Holt RD, Dobson AP, Begon M, Bowers RG, Schauber EM (2003) Parasite establishment in host communities. Ecol Lett 6:837–842
Taraschewski H (2006) Hosts and parasites as aliens. J Helminthol 80:99–128
Litchman E (2010) Invisible invaders: non-pathogenic invasive microbes in aquatic and terrestrial ecosystems: invasive microbes. Ecol Lett 13:1560–1572
Acknowledgments
The crews of the various cargo ships, the facilities within the Ports of Baltimore and Hampton Roads, and agents T. Parker Host and Capes Shipping Agencies enabled vessel and tank access. Rebecca Dikow assisted with interpreting some phylogenetic analyses and access to computers. Rebecca Dikow, Carly Woltz, and three anonymous reviewers provided useful feedback on the content of this manuscript. Taylor and Joel Callicrate assisted with file formatting. Nancy Rotzel McInerney provided logistical support at CCEG. We thank Roche-454 for providing a GS Junior to CCEG, and assistance with protocols. This project was funded by the Center for Conservation and Evolutionary Genetics and a Smithsonian Institution Next Generation Sequencing Small Grant. Sample collection was supported by funding from the US Coast Guard. Pagenkopp Lohan was funded by a Smithsonian MarineGEO Postdoctoral Fellowship.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
ESM 1
(PDF 744 kb)
Rights and permissions
About this article
Cite this article
Pagenkopp Lohan, K.M., Fleischer, R.C., Carney, K.J. et al. Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships’ Ballast Water: Implications for Biogeography and Infectious Diseases. Microb Ecol 71, 530–542 (2016). https://doi.org/10.1007/s00248-015-0684-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00248-015-0684-6