Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event


The Pacific oyster, Crassostrea gigas, is a key commercial species that is cultivated globally. In recent years, disease outbreaks have heavily impacted C. gigas stocks worldwide, with many losses incurred during summer. A number of infectious agents have been associated with these summer mortality events, including viruses (particularly Ostreid herpesvirus 1, OsHV-1) and bacteria; however, cases where no known aetiological agent can be identified are common. In this study, we examined the microbiome of disease-affected and disease-unaffected C. gigas during a 2013–2014 summer mortality event in Port Stephens (Australia) where known oyster pathogens including OsHV-1 were not detected. The adductor muscle microbiomes of 70 C. gigas samples across 12 study sites in the Port Stephens estuary were characterised using 16S rRNA (V1–V3 region) amplicon sequencing, with the aim of comparing the influence of spatial location and disease state on the oyster microbiome. Spatial location was found to be a significant determinant of the disease-affected oyster microbiome. Furthermore, microbiome comparisons between disease states identified a significant increase in rare operational taxonomic units (OTUs) belonging to Vibrio harveyi and an unidentified member of the Vibrio genus in the disease-affected microbiome. This is indicative of a potential role of Vibrio species in oyster disease and supportive of previous culture-based examination of this mortality event.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4


  1. 1.

    Friedman CS, Estes RM, Stokes NA, Burge CA, Hargove JS, Barber BJ, Elston RA, Burreson EM, Reece KS (2005) Herpes virus in juvenile Pacific oysters Crassostrea gigas from Tomales Bay, California, coincides with summer mortality episodes. Dis Aquat Org 63:33–41.

    Article  PubMed  Google Scholar 

  2. 2.

    Soletchnik P, Lambert C, Costil K (2005) Summer mortality of Crassostrea gigas (Thunberg) in relation to environmental rearing conditions. J Shellfish Res 24:197–207

    Article  Google Scholar 

  3. 3.

    Burge CA, Judah LR, Conquest LL, Griffin FJ, Cheney DP, Suhrbier A, Vadopalas B, Olin PG, Renault T, Friedman CS (2007) Summer seed mortality of the Pacific oyster, Crassostrea gigas Thunberg grown in Tomales Bay, California, USA: the influence of oyster stock, planting time, pathogens, and environmental stressors. J Shellfish Res 26:163–172.[163:SSMOTP]2.0.CO;2

  4. 4.

    Soletchnik P, Ropert M, Mazurié J, Gildas Fleury P, Le Coz F (2007) Relationships between oyster mortality patterns and environmental data from monitoring databases along the coasts of France. Aquaculture 271:384–400.

    Article  Google Scholar 

  5. 5.

    Watermann BT, Herlyn M, Daehne B, Bergmann S, Meemken M, Kolodzey H (2008) Pathology and mass mortality of Pacific oysters, Crassostrea gigas (Thunberg), in 2005 at the east Frisian coast, Germany. J Fish Dis 31:621–630.

    Article  CAS  PubMed  Google Scholar 

  6. 6.

    Mortensen S, Strand A, Bodvin T, Alfjorden A, Skar CK, Jelmert A, Aspán A, Sælemyr L, Naustvoll LJ, Albretsen J (2016) Summer mortalities and detection of ostreid herpesvirus microvariant in Pacific oyster Crassostrea gigas in Sweden and Norway. Dis Aquat Org 117:171–176.

    Article  PubMed  Google Scholar 

  7. 7.

    Garnier M, Labreuche Y, Garcia C, Robert M, Nicolas JL (2007) Evidence for the involvement of pathogenic bacteria in summer mortalities of the pacific oyster Crassostrea gigas. Microb Ecol 53:187–196.

    Article  CAS  PubMed  Google Scholar 

  8. 8.

    Malham SK, Cotter E, O'Keeffe S, Lynch S, Culloty SC, King JW, Latchford JW, Beaumont AR (2009) Summer mortality of the Pacific oyster, Crassostrea gigas, in the Irish Sea: the influence of temperature and nutrients on health and survival. Aquaculture 287:128–138.

    Article  CAS  Google Scholar 

  9. 9.

    Segarra A, Pepin JF, Arzul I, Morga B, Faury N, Renault T (2010) Detection and description of a particular Ostreid herpesvirus 1 genotype associated with massive mortality outbreaks of Pacific oysters, Crassostrea gigas, in France in 2008. Virus Res 153:92–99.

    Article  CAS  PubMed  Google Scholar 

  10. 10.

    Jenkins C, Hick P, Gabor M, Spiers Z, Fell SA, Gu X, Read A, Go J, Dove M, O'Connor W, Kirkland PD, Frances J (2013) Identification and characterisation of an ostreid herpesvirus-1 microvariant (OsHV-1 micro-var) in Crassostrea gigas (Pacific oysters) in Australia. Dis Aquat Org 105:109–126.

    Article  CAS  PubMed  Google Scholar 

  11. 11.

    Petton B, Pernet F, Robert R, Boudry P (2013) Temperature influence on pathogen transmission and subsequent mortalities in juvenile Pacific oysters Crassostrea gigas. Aquac Environ Interact 3:257–273

    Article  Google Scholar 

  12. 12.

    Renault T, Bouquet AL, Maurice J-T, Lupo C, Blachier P (2014) Ostreid herpesvirus 1 infection among Pacific oyster (Crassostrea gigas) spat: relevance of water temperature to virus replication and circulation prior to the onset of mortality. Appl Environ Microbiol 80:5419–5426.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Jeffries VE (1982) Three Vibrio strains pathogenic to larvae of Crassostrea gigas and Ostrea edulis. Aquaculture 29:201–226.

    Article  Google Scholar 

  14. 14.

    Waechter M, Le Roux F, Nicolas JL, Marissal E, Berthe F (2002) Characterisation of Crassostrea gigas spat pathogenic bacteria. C R Biol 325:231–238.

    Article  CAS  PubMed  Google Scholar 

  15. 15.

    Pernet F, Barret J, Le Gall P, Corporeau C, Dégremont L, Lagarde F, Pépin JF, Keck N (2012) Mass mortalities of Pacific oysters Crassostrea gigas reflect infectious diseases and vary with farming practices in the Mediterranean Thau lagoon, France. Aquac Environ Interact 2:215–237.

    Article  Google Scholar 

  16. 16.

    Petton B, Bruto M, James A, Labreuche Y, Alunno-Bruscia M, Le Roux F (2015) Crassostrea gigas mortality in France: the usual suspect, a herpes virus, may not be the killer in this polymicrobial opportunistic disease. Front. Microbiol. 6. doi:

  17. 17.

    Go J, Deutscher A, Spiers Z, Dahle K, Kirkland P, Jenkins C (2017) An investigation into mass mortalities of unknown aetiology in Pacific oysters, Crassostrea gigas, in port Stephens, new South Wales, Australia. Dis Aquat Org 125:227–242.

    Article  CAS  PubMed  Google Scholar 

  18. 18.

    Lipovsky VP, Chew KK (1972) Mortality of Pacific oysters (Crassostrea gigas): the influence of temperature and enriched seawater on oyster survival. Proc Nat Shellfish Ass:72–82

  19. 19.

    Mori K (1979) Effects of artificial eutrophication on the metabolism of the Japanese oyster Crassostrea gigas. Mar Biol 53:361–369.

    Article  Google Scholar 

  20. 20.

    Cotter E, Malham SK, O'Keeffe S, Lynch SA, Latchford JW, King JW, Beaumont AR, Culloty SC (2010) Summer mortality of the Pacific oyster, Crassostrea gigas, in the Irish Sea: the influence of growth, biochemistry and gametogenesis. Aquaculture 303:8–21.

    Article  Google Scholar 

  21. 21.

    Samain JF, Dégremont L, Soletchnik P, Haure J, Bédier E, Ropert M, Moal J, Huvet A, Bacca H, Van Wormhoudt A, Delaporte M, Costil K, Pouvreau S, Lambert C, Boulo V, Soudant P, Nicolas JL, Le Roux F, Renault T, Gagnaire B, Geret F, Boutet I, Burgeot T, Boudry P (2007) Genetically based resistance to summer mortality in the Pacific oyster (Crassostrea gigas) and its relationship with physiological, immunological characteristics and infection processes. Aquaculture 268:227–243.

    Article  Google Scholar 

  22. 22.

    Segarra A, Mauduit F, Faury N, Trancart S, Dégremont L, Tourbiez D, Haffner P, Barbosa-Solomieu V, Pépin J-F, Travers M-A, Renault T (2014) Dual transcriptomics of virus-host interactions: comparing two Pacific oyster families presenting contrasted susceptibility to ostreid herpesvirus 1. BMC Genomics 15:1–13.

    Article  Google Scholar 

  23. 23.

    Dégremont L, Tanguy G, Delphine T, Jean-François P (2013) Is horizontal transmission of the Ostreid herpesvirus OsHV-1 in Crassostrea gigas affected by unselected or selected survival status in adults to juveniles? Aquaculture 408–409:51–57.

    Article  Google Scholar 

  24. 24.

    Dégremont L (2011) Evidence of herpesvirus (OsHV-1) resistance in juvenile Crassostrea gigas selected for high resistance to the summer mortality phenomenon. Aquaculture 317:94–98.

    Article  Google Scholar 

  25. 25.

    Lang RP, Langdon C, Taris N, Camara M (2010) Use of laboratory assays to predict subsequent growth and survival of Pacific oyster (Crassostrea gigas) families planted in coastal waters. Aquaculture 306:68–79.

  26. 26.

    Wegner KM, Volkenborn N, Peter H, Eiler A (2013) Disturbance induced decoupling between host genetics and composition of the associated microbiome. BMC Microbiol 13:252.

    Article  PubMed  PubMed Central  Google Scholar 

  27. 27.

    Lokmer A, Wegner KM (2015) Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection. ISME J 9:670–682.

    Article  CAS  PubMed  Google Scholar 

  28. 28.

    Lokmer A, Kuenzel S, Baines JF, Wegner KM (2016) The role of tissue-specific microbiota in initial establishment success of Pacific oysters. Environ Microbiol 18:970–987.

    Article  CAS  PubMed  Google Scholar 

  29. 29.

    Trabal N, Mazon-Suastegui JM, Vazquez-Juarez R, Asencio-Valle F, Morales-Bojorquez E, Romero J (2012) Molecular analysis of bacterial microbiota associated with oysters (Crassostrea gigas and Crassostrea corteziensis) in different growth phases at two cultivation sites. Microb Ecol 64:555–569.

    Article  CAS  PubMed  Google Scholar 

  30. 30.

    Trabal Fernández N, Mazón-Suástegui JM, Vázquez-Juárez R, Ascencio-Valle F, Romero J (2014) Changes in the composition and diversity of the bacterial microbiota associated with oysters (Crassostrea corteziensis, Crassostrea gigas and Crassostrea sikamea) during commercial production. FEMS Microbiol Ecol 88:69–83.

    Article  CAS  PubMed  Google Scholar 

  31. 31.

    Lemire A, Goudenege D, Versigny T, Petton B, Calteau A, Labreuche Y, Le Roux F (2015) Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters. ISME J 9:1523–1531.

    Article  PubMed  Google Scholar 

  32. 32.

    Roy PS, Williams RJ, Jones AR, Yassini I, Gibbs PJ, Coates B, West RJ, Scanes PR, Hudson JP, Nichol S (2001) Structure and function of south-east Australian estuaries. Estuar Coast Shelf Sci 53:351–384.

    Article  Google Scholar 

  33. 33.

    Australian Bureau of Statistics (2016) Port Stephens census data (Statistical area). Accessed 1 May 2018

  34. 34.

    Earth Tech Engineering Pty Ltd (2008) Tilligerry creek management plan. Accessed 6 November 2017

  35. 35.

    Lokmer A, Goedknegt MA, Thieltges DW, Fiorentino D, Kuenzel S, Baines JF, Wegner KM (2016) Spatial and temporal dynamics of Pacific oyster hemolymph microbiota across multiple scales. Front Microbiol 7:1367.

    Article  PubMed  PubMed Central  Google Scholar 

  36. 36.

    Vezzulli L, Stagnaro L, Grande C, Tassistro G, Canesi L, Pruzzo C (2017) Comparative 16SrDNA gene-based microbiota profiles of the Pacific oyster (Crassostrea gigas) and the Mediterranean mussel (Mytilus galloprovincialis) from a shellfish farm (Ligurian Sea, Italy). Microb Ecol 75:495–504.

    Article  CAS  PubMed  Google Scholar 

  37. 37.

    Gagnaire B, Duchemin M, Auffret M, Thomas-Guyon H, Renault T (2008) Comparison of hemocyte parameters in the pericardial cavity and the adductor muscle sinus in the Pacific oyster, Crassostrea gigas using two types of flow cytometers. Aquat Living Resour 21:39–43.

    Article  Google Scholar 

  38. 38.

    Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley and Sons, New York, pp 115–175

    Google Scholar 

  39. 39.

    Turner S, Pryer KM, Miao VP, Palmer JD (1999) Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol 46:327–338

    Article  CAS  PubMed  Google Scholar 

  40. 40.

    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461.

    Article  CAS  Google Scholar 

  42. 42.

    McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610–618.

    Article  CAS  PubMed  Google Scholar 

  43. 43.

    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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Hammer Ø, Harper DAT, Ryan PD (2001) Past: Paleontological statistics software package for education and data analysis. Palaeontol Electron 4:XIX–XXX

    Google Scholar 

  45. 45.

    Fernandez-Piquer J, Bowman JP, Ross T, Tamplin ML (2012) Molecular analysis of the bacterial communities in the live Pacific oyster (Crassostrea gigas) and the influence of postharvest temperature on its structure. J Appl Microbiol 112:1134–1143.

    Article  CAS  PubMed  Google Scholar 

  46. 46.

    Green TJ, Barnes AC (2010) Bacterial diversity of the digestive gland of Sydney rock oysters, Saccostrea glomerata infected with the paramyxean parasite, Marteilia sydneyi. J Appl Microbiol 109:613–622.

    CAS  Article  PubMed  Google Scholar 

  47. 47.

    Thurber RV, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, Angly F, Dinsdale E, Kelly L, Rohwer F (2009) Metagenomic analysis of stressed coral holobionts. Environ Microbiol 11:2148–2163.

    Article  CAS  Google Scholar 

  48. 48.

    Saulnier D, de Decker S, Haffner P, Cobret L, Robert M, Garcia C (2010) A large-scale epidemiological study to identify bacteria pathogenic to Pacific oyster Crassostrea gigas and correlation between virulence and metalloprotease-like activity. Microb Ecol 59:787–798.

    Article  PubMed  Google Scholar 

  49. 49.

    Newton RJ, VandeWalle JL, Borchardt MA, Gorelick MH, McLellan SL (2011) Lachnospiraceae and Bacteroidales alternative fecal indicators reveal chronic human sewage contamination in an Urban Harbor. Appl Environ Microbiol 77:6972–6981.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Ueki A, Akasaka H, Suzuki D, Ueki K (2006) Paludibacter propionicigenes gen. Nov., sp. nov., a novel strictly anaerobic, gram-negative, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil in Japan. Int J Syst Evol Microbiol 56:39–44.

    Article  CAS  PubMed  Google Scholar 

  51. 51.

    Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI (2005) Host-bacterial mutualism in the human intestine. Science 307:1915–1920.

    Article  CAS  PubMed  Google Scholar 

  52. 52.

    Kreader CA (1995) Design and evaluation of Bacteroides DNA probes for the specific detection of human fecal pollution. Appl Environ Microbiol 61:1171–1179

    CAS  PubMed  PubMed Central  Google Scholar 

Download references


We would like to acknowledge the New South Wales Department of Primary Industries for their assistance in collecting and processing the oyster samples, as well as their continued support over the length of the project. This research was supported by an Australian Research Council Linkage Project LP160101785 and partly funded by Ausgem, a research partnership initiated between the University of Technology Sydney and the New South Wales Department of Primary Industries.

Author information



Corresponding author

Correspondence to Maurizio Labbate.

Electronic Supplementary Material


(DOCX 655 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

King, W.L., Jenkins, C., Go, J. et al. Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event. Microb Ecol 77, 502–512 (2019).

Download citation


  • Crassostrea gigas
  • Mortality
  • Oyster
  • Microbiome
  • Summer mortality