Ecological theory as a foundation to control pathogenic invasion in aquaculture

ISME Journal

Volumn 8, Issue 12, 2014, Pages 2360-2368

  De Schryver, Peter ^a   Vadstein, Olav ^b  

^a GHENT UNIVERSITY   (Belgium)

^b NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

Author keywords

Aquaculture; Ecological theory; Host microbe; Intestinal; Larviculture; Microbe microbe

Indexed keywords

ANIMALIA;

ANTIINFECTIVE AGENT;

ANIMAL; AQUACULTURE; AQUATIC SPECIES; BIODIVERSITY; ENVIRONMENTAL ASPECTS AND RELATED PHENOMENA; GASTROINTESTINAL TRACT; INFECTION; MICROBIOLOGY; MICROFLORA; VETERINARY;

ANIMALS; ANTI-BACTERIAL AGENTS; AQUACULTURE; AQUATIC ORGANISMS; BIODIVERSITY; ECOLOGICAL AND ENVIRONMENTAL PROCESSES; GASTROINTESTINAL TRACT; INFECTION; MICROBIOTA; WATER MICROBIOLOGY;

EID: 84922463206     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2014.84     Document Type: Review

References (91)

1. Adler PB, HilleRisLambers J, Levine JM. (2007). A niche for neutrality. Ecol Lett 10: 95-104.
2. Andrews JH, Harris JF. (1986). r-and K-selection in microbial ecology. Adv Microb Ecol 9: 99-147.
3. Attramadal KJK, øie G, Størseth TR, Alver MO, Vadstein O, Olsen Y. (2012a). The effects of moderate ozonation or high intensity UV-irradiation on the microbial environment in RAS for marine larvae. Aquaculture 330: 121-129.
4. Attramadal KJK, Salvesen I, Xue RY, øie G, Størseth TR, Vadstein O et al. (2012b). Recirculation as a possible microbial control strategy in the production of marine larvae. Aquacult Eng 46: 27-39.
5. Attramadal KJK, Truong TM, Bakke I, Skjermo J, Olsen Y, Vadstein O. (2014). RAS and microbial maturation as tools for K-selection of microbial communities improve survival in cod larvae. Aquaculture (in press).
6. Bakke I, Skjermo J, Vo TA, Vadstein O. (2013). Live feed is not a major determinant of the microbiota associated with cod larvae (Gadus morhua). Environ Microbiol Rep 5: 537-548.
7. Balvanera P, Kremen C, Martinez-Ramos M. (2005). Applying community structure analysis to ecosystem function: examples from pollination and carbon storage. Ecol Appl 15: 360-375.
8. Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK. (2005). The contribution of species richness and composition to bacterial services. Nature 436: 1157-1160.
9. Benskin CMH, Rhodes G, Pickup RW, Wilson K, Hartley IR. (2010). Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch. Mol Ecol 19: 5531-5544.
10. Bissett A, Richardson AE, Baker G, Wakelin S, Thrall PH. (2010). Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales. Mol Ecol 19: 4315-4327.
11. Bruno JF, Stachowicz JJ, Bertness MD. (2003). Inclusion of facilitation into ecological theory. Trends Ecol Evol 18: 119-125.
12. Cabrol L, Malhautier L. (2011). Integrating microbial ecology in bioprocess understanding: the case of gas biofiltration. Appl Microbiol Biotechnol 90: 837-849.
13. Chapin FS, Zavaleta ES, Eviner VT, Naylor RL, Vitousek PM, Reynolds HL et al. (2000). Consequences of changing biodiversity. Nature 405: 234-242.
14. Chesson P. (2000). Mechanisms of maintenance of species diversity. Annu Rev Ecol Syst 31: 343-366.
15. Cook KL, Garland JL, Layton AC, Dionisi HM, Levine LH, Sayler GS. (2006). Effect of microbial species richness on community stability and community function in a model plant-based wastewater processing system. Microb Ecol 52: 725-737.
16. Costello EK, Stagaman K, Dethlefsen L, Bohannan BJM, Relman DA. (2012). The application of ecological theory toward an understanding of the human microbiome. Science 336: 1255-1262.
17. Curtis TP, Sloan WT. (2004). Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr Opin Microbiol 7: 221-226.
18. De Roy K, Marzorati M, Negroni A, Thas O, Balloi A, Fava F et al. (2013). Environmental conditions and community evenness determine the outcome of biological invasion. Nat Commun 4: 1383.
19. De Schryver P, Defoirdt T, Sorgeloos P. (2014). Early mortality syndrome outbreaks: A microbial management issue in shrimp farming? PLoS Pathog 10: e1003919.
20. Dierckens K, Rekecki A, Laureau S, Sorgeloos P, Boon N, Van den Broeck W et al. (2009). Development of a bacterial challenge test for gnotobiotic sea bass (Dicentrarchus labrax) larvae. Environ Microbiol 11: 526-533.
21. Dillon RJ, Vennard CT, Buckling A, Charnley AK. (2005). Diversity of locust gut bacteria protects against pathogen invasion. Ecol Lett 8: 1291-1298.
22. Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH. (2010). Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J 4: 337-345.
23. Elbal MT, Hernandez MPG, Lozano MT, Agulleiro B. (2004). Development of the digestive tract of gilthead sea bream (Sparus aurata L.). Light and electron microscopic studies. Aquaculture 234: 215-238.
24. Emery SM, Gross KL. (2007). Dominant species identity, not community evenness, regulates invasion in experimental grassland plant communities. Ecology 88: 954-964.
25. Fairbrother JM, Nadeau E, Gyles CL. (2005). Escherichia coli in postweaning diarrhea in pigs: An update on bacterial types, pathogenesis, and prevention strategies. Anim Health Res Rev 6: 17-39.
26. Fargione JE, Tilman D. (2005). Diversity decreases invasion via both sampling and complementarity effects. Ecol Lett 8: 604-611.
27. Fjellheim AJ, Playfoot KJ, Skjermo J, Vadstein O. (2012). Inter-individual variation in the dominant intestinal microbiota of reared Atlantic cod (Gadus morhua L.) larvae. Aquac Res 43: 1499-1508.
28. Forberg T, Vestrum RI, Arukwe A, Vadstein O. (2012). Bacterial composition and activity determines host gene-expression responses in gnotobiotic Atlantic cod (Gadus morhua) larvae. Vet Microbiol 157: 420-427.
29. Gatesoupe FJ. (1999). The use of probiotics in aquaculture. Aquaculture 180: 147-165.
30. Gatesoupe FJ. (2010). Probiotics and other microbial manipulations in fish feeds: prospective health benefits. In: Watson RR, Preedy VR (eds) Bioactive Foods in Promoting Health. Academic Press: Oxford, pp 541-552.
31. Guarner F, Malagelada JR. (2003). Gut flora in health and disease. Lancet 361: 512-519.
32. Gustafson RH, Bowen RE. (1997). Antibiotic use in animal agriculture. J Appl Microbiol 83: 531-541.
33. Hajek A. (2004). Natural Enemies: An Introduction to Biological Control. Cambridge University Press: Cambridge.
34. He T, Xiao ZZ, Liu QH, Ma DY, Xu SH, Xiao YS et al. (2012). Ontogeny of the digestive tract and enzymes in rock bream Oplegnathus fasciatus (Temminck et Schlegel 1844) larvae. Fish Physiol Biochem 38: 297-308.
35. Hillebrand H, Bennett DM, Cadotte MW. (2008). Consequences of dominance: A review of evenness effects on local and regional ecosystem processes. Ecology 89: 1510-1520.
36. Hubbell SP. (2001). The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press: Princeton.
37. Jeraldo P, Sipos M, Chia N, Brulc JM, Dhillon AS, Konkel ME et al. (2012). Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes. Proc Natl Acad Sci USA 109: 9692-9698.
38. Jiang L, Morin PJ. (2004). Productivity gradients cause positive diversity-invasibility relationships in microbial communities. Ecol Lett 7: 1047-1057.
39. Johnson PTJ, Hartson RB, Larson DJ, Sutherland DR. (2008). Diversity and disease: community structure drives parasite transmission and host fitness. Ecol Lett 11: 1017-1026.
40. Kamisaka Y, Rønnestad I. (2011). Reconstructed 3D models of digestive organs of developing Atlantic cod (Gadus morhua) larvae. Mar Biol 158: 233-243.
41. Kennedy TA, Naeem S, Howe KM, Knops JMH, Tilman D, Reich P. (2002). Biodiversity as a barrier to ecological invasion. Nature 417: 636-638.
42. Knops JMH, Tilman D, Haddad NM, Naeem S, Mitchell CE, Haarstad J et al. (1999). Effects of plant species richness on invasion dynamics, disease outbreaks, insect abundances and diversity. Ecol Lett 2: 286-293.
43. Lanzas C, Warnick LD, Ivanek R, Ayscue P, Nydam DV, Grohn YT. (2008). The risk and control of Salmonella outbreaks in calf-raising operations: A mathematical modeling approach. Vet Res 39: 13.
44. Leibold MA, McPeek MA. (2006). Coexistence of the niche and neutral perspectives in community ecology. Ecology 87: 1399-1410.
45. Lemon KP, Armitage GC, Relman DA, Fischbach MA. (2012). Microbiota-targeted herapies: An ecological perspective. Sci Transl Med 4: 137rv5.
46. Levine JM. (2000). Species diversity and biological invasions: relating local process to community pattern. Science 288: 852-854.
47. Little AEF, Robinson CJ, Peterson SB, Raffa KE, Handelsman J. (2008). Rules of engagement: Interspecies interactions that regulate microbial communities. Annu Rev Microbiol 62: 375-401.
48. Losure DA, Wilsey BJ, Moloney KA. (2007). Evenness-invasibility relationships differ between two extinction scenarios in tallgrass prairie. Oikos 116: 87-98.
49. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. (2012). Diversity, stability and resilience of the human gut microbiota. Nature 489: 220-230.
50. MacArthur RH, Wilson EO. (1967). The Theory of Island Biogeography. Princeton University Press: Princeton
51. Marino S, Baxter NT, Huffnagle GB, Petrosino JF, Schloss PD. (2014). Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci USA 111: 439-444.
52. Marques A, Dinh T, Ioakeimidis C, Huys G, Swings J, Verstraete W et al. (2005). Effects of bacteria on Artemia franciscana cultured in different gnotobiotic environments. Appl Environ Microbiol 71: 4307-4317.
53. McCracken VJ, Lorenz RG. (2001). The gastrointestinal ecosystem: A precarious alliance among epithelium, immunity and microbiota. Cell Microbiol 3: 1-11.
54. McGrady-Steed J, Harris PM, Morin PJ. (1997). Biodiversity regulates ecosystem predictability. Nature 390: 162-165.
55. Meiners SJ, Cadenasso ML, Pickett STA. (2004). Beyond biodiversity: Individualistic controls of invasion in a self-assembled community. Ecol Lett 7: 121-126.
56. Mitchell CE, Tilman D, Groth JV. (2002). Effects of grassland plant species diversity, abundance, and composition on foliar fungal disease. Ecology 83: 1713-1726.
57. Naeem S, Thompson LJ, Lawler SP, Lawton JH, Woodfin RM. (1994). Declining biodiversity can alter the performance of ecosystems. Nature 368: 734-737.
58. Ofiteru ID, Lunn M, Curtis TP, Wells GF, Criddle CS, Francis CA et al. (2010). Combined niche and neutral effects in a microbial wastewater treatment community. Proc Natl Acad Sci USA 107: 15345-15350.
59. Pruder GD. (2004). Biosecurity: Application in aquaculture. Aquacult Eng 32: 3-10.
60. Ptacnik R, Solimini AG, Andersen T, Tamminen T, Brettum P, Lepisto L et al. (2008). Diversity predicts stability and resource use efficiency in natural phytoplankton communities. Proc Natl Acad Sci USA 105: 5134-5138.
61. Purvis A, Hector A. (2000). Getting the measure of biodiversity. Nature 405: 212-219.
62. Rawls JF, Mahowald MA, Ley RE, Gordon JI. (2006). Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127: 423-433.
63. Rawls JF, Samuel BS, Gordon JI. (2004). Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci USA 101: 4596-4601.
64. Reitan KI, Natvik CM, Vadstein O. (1998). Drinking rate, uptake of bacteria and microalgae in turbot larvae. J Fish Biol 53: 1145-1154.
65. Ringø E, Olsen RE, Gifstad TO, Dalmo RA, Amlund H, Hemre GI et al. (2010). Prebiotics in aquaculture: A review. Aquacult Nutr 16: 117-136.
66. Robinson CJ, Bohannan BJM, Young VB. (2010a). From structure to function: the ecology of host-associated microbial communities. Microbiol Mol Biol Rev 74: 453-476.
67. Robinson CJ, Schloss P, Ramos Y, Raffa K, Handelsman J. (2010b). Robustness of the bacterial community in the cabbage white butterfly larval midgut. Microb Ecol 59: 199-211.
68. Rogers GB, Hoffman LR, Carroll MP, Bruce KD. (2012). Interpreting infective microbiota: the importance of an ecological perspective. Trends Microbiol 21: 271-276.
69. Shea K, Chesson P. (2002). Community ecology theory as a framework for biological invasions. Trends Ecol Evol 17: 170-176.
70. Silvertown J. (2004). Plant coexistence and the niche. Trends Ecol Evol 19: 605-611.
71. Skjermo J, Vadstein O. (1999). Techniques for microbial control in the intensive rearing of marine larvae. Aquaculture 177: 333-343.
72. Stachowicz JJ, Whitlatch RB, Osman RW. (1999). Species diversity and invasion resistance in a marine ecosystem. Science 286: 1577-1579.
73. Stecher B, Hardt WD. (2008). The role of microbiota in infectious disease. Trends Microbiol 16: 107-114.
74. Summerfelt ST, Sharrer MJ, Tsukuda SM, Gearheart M. (2009). Process requirements for achieving full-flow disinfection of recirculating water using ozonation and UV irradiation. Aquacult Eng 40: 17-27.
75. Suzuki S. (1994). Pathogenicity of Salmonella enteritidis in poultry. Int J Food Microbiol 21: 89-105.
76. Vadstein O. (2000). Strategies for avoiding bacterial infections: beat them or join them. ASM News 66: 446-447.
77. Vadstein O, Bergh O, Gatesoupe FJ, Galindo-Villegas J, Mulero V, Picchietti S et al. (2013). Microbiology and immunology of fish larvae. Rev Aquacult 5: S1-S25.
78. Vadstein O, Mo TA, Bergh ø. (2004). Microbial interactions, prophylaxis and diseases. In: Moksness E, Kjørsvik E, Olsen Y (eds) Culture of Cold-Water Marine Fishes. Blackwell Publishing: Bath, pp 28-72.
79. Vadstein O, øie G, Olsen Y, Salvesen I, Skjermo J, Skjåk-brk G. (1993). A strategy to obtain microbial control during larval development of marine fish. In: Reinertsen H, Dahle LA, Jørgensen L, Tvinnereim K (eds) Fish Farming Technology-Proceedings of the First International Conference on Fish Farming Technology. Balkema: Rotterdam, pp 67-75.
80. Valéry L, Fritz H, Lefeuvre JC, Simberloff D. (2008). In search of a real definition of the biological invasion phenomenon itself. Biol Invasions 10: 1345-1351.
81. van der Wielen P, Keuzenkamp DA, Lipman LJA, van Knapen F, Biesterveld S. (2002). Spatial and temporal variation of the intestinal bacterial community in commercially raised broiler chickens during growth. Microb Ecol 44: 286-293.
82. van Elsas JD, Chiurazzi M, Mallon CA, Elhottova D, Kristufek V, Salles JF. (2012). Microbial diversity determines the invasion of soil by a bacterial pathogen. Proc Natl Acad Sci USA 109: 1159-1164.
83. Vellend M. (2010). Conceptual synthesis in community ecology. Q Rev Biol 85: 183-206.
84. Verschuere L, Rombaut G, Sorgeloos P, Verstraete W. (2000). Probiotic bacteria as biological control agents in aquaculture. Microbiol Mol Biol Rev 64: 655-671.
85. Wennekes PL, Rosindell J, Etienne RS. (2012). The neutral-niche debate: A philosophical perspective. Acta Biotheor 60: 257-271.
86. Wilsey BJ, Polley HW. (2002). Reductions in grassland species evenness increase dicot seedling invasion and spittle bug infestation. Ecol Lett 5: 676-684.
87. Wittebolle L, Marzorati M, Clement L, Balloi A, Daffonchio D, Heylen K et al. (2009). Initial community evenness favours functionality under selective stress. Nature 458: 623-626.
88. Wong SD, Rawls JF. (2012). Intestinal microbiota composition in fishes is influenced by host ecology and environment. Mol Ecol 21: 3100-3102.
89. Yan Q, van der Gast CJ, Yu Y. (2012). Bacterial community assembly and turnover within the intestines of developing zebrafish. PLoS One 7: e30603.
90. Yang R, Xie C, Fan Q, Gao C, Fang L. (2010). Ontogeny of the digestive tract in yellow catfish Pelteobagrus fulvidraco larvae. Aquaculture 302: 112-123.
91. Zambonino-Infante JL, Cahu CL. (2001). Ontogeny of the gastrointestinal tract of marine fish larvae. Comp Biochem Physiol C Toxicol Pharmacol 130: 477-487.