Impact of aquaculture on benthic virus-prokaryote interactions in the Mediterranean Sea

Water Research

Volumn 47, Issue 3, 2013, Pages 1156-1168

  Luna, G M ^a   Corinaldesi, C ^b   Dell'Anno, A ^b   Pusceddu, A ^b   Danovaro, R ^b  

^a INSTITUTE OF MARINE SCIENCES   (Italy)

^b UNIVERSITÀ POLITECNICA DELLE MARCHE   (Italy)

Author keywords

Aquaculture; Marine sediments; Viruses

Indexed keywords

AQUACULTURE; COMPUTER VIRUSES; ECOSYSTEMS; SUBMARINE GEOLOGY; SULFUR COMPOUNDS; VIRUSES;

ASSEMBLAGE COMPOSITION; BACTERIAL DIVERSITY; ENZYMATIC ACTIVITIES; MARINE SEDIMENTS; MEDITERRANEAN SEA; ORGANIC ENRICHMENT; ORGANIC MATTER DECOMPOSITION; POSIDONIA OCEANICA;

SEDIMENTS;

ALKALINE PHOSPHATASE; AMINOPEPTIDASE; BETA GLUCOSIDASE; CARBON; ORGANIC MATTER;

AQUACULTURE; BENTHOS; INTERSPECIFIC INTERACTION; METABOLISM; MICROBIAL COMMUNITY; PROKARYOTE; SEAGRASS; SEDIMENT ANALYSIS; VIRUS;

AQUACULTURE; ARTICLE; BENTHOS; CYPRUS; DELTAPROTEOBACTERIA; ENZYME ACTIVITY; GAMMAPROTEOBACTERIA; GENE SEQUENCE; HABITAT; MEDITERRANEAN SEA; MICROBIAL COMMUNITY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE; SEAGRASS; SEDIMENT; SPAIN; VIRUS INFECTION;

MEDITERRANEAN SEA;

EID: 84872702733     PISSN: 00431354     EISSN: 18792448     Source Type: Journal    
DOI: 10.1016/j.watres.2012.11.036     Document Type: Article

References (58)

1. Anderson M.J. A new method for non-parametric multivariate analysis of variance. Australian Ecology 2001, 26:32-46.
2. Apostolaki E.T., Tsagaraki T., Tsapakis M., Karakassis I. Fish farming impact on sediments and macrofauna associated with seagrass meadows in the Mediterranean. Estuarine Coastal Shelf Sciences 2007, 75:408-416.
3. Asami H., Aida M., Watanabe K. Accelerated sulfur cycle in coastal marine sediment beneath areas of intensive shellfish aquaculture. Applied Environmental Microbiology 2005, 71:2925-2933.
4. Bissett A., Bowman J.P., Burke C. Bacterial diversity in organically-enriched fish farm sediments. FEMS Microbiology Ecology 2006, 55:48-56.
5. Bissett A., Burke C., Cook P.L.M., Bowman J.P. Bacterial community shifts in organically perturbed sediments. Environmental Microbiology 2007, 9:46-60.
6. Bissett A., Bowman J.P., Burke C.M. Flavobacterial response to organic pollution. Aquatic Microbial Ecology 2008, 51:34-43.
7. Bongiorni L., Mirto S., Pusceddu A., Danovaro R. Response of benthic protozoa and thraustochytrid protists to fish farm impact in seagrass (Posidonia oceanica) and soft-bottom sediments. Microbiology Ecology 2005, 50:268-276.
8. Caruso G., Genovese L., Mancuso M., Modica A. Effects of fish farming on microbial enzyme activities and densities: comparison between three Mediterranean sites. Letters in Applied Microbiology 2003, 37:324-328.
9. Chelossi E., Vezzulli L., Milano A., Branzoni M., Fabiano M., Riccardi G., Banat I.M. Antibiotic resistance of benthic bacteria in fish-farm and control sediments of the Western Mediterranean. Aquaculture 2003, 219:83-97.
10. Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G.M., Tiedje J.M. The Ribosomal Database Project, improved alignments and new tools for rRNA analysis. Nucleic Acids Research 2009, 37:D141-D145.
11. Corinaldesi C., Crevatin E., Del Negro P., Marini M., Russo A., Fonda-Umani S., Danovaro R. Large-scale spatial distribution of virioplankton in the Adriatic Sea: testing the trophic state control hypothesis. Applied Environmental Microbiology 2003, 69:2664-2673.
12. Corinaldesi C., Dell'Anno A., Magagnini M., Danovaro R. Viral decay and viral production rates in continental-shelf and deep-sea sediments of the Mediterranean Sea. FEMS Microbiology Ecology 2010, 72:208-218.
13. Danovaro R. Detritus-bacteria-meiofauna interactions in a seagrass bed (Posidonia oceanica) of the NW Mediterranean. Marine Biology 1996, 127:1-13.
14. Danovaro R., Dell'Anno A., Trucco A., Serresi M., Vanucci S. Determination of virus abundance in marine sediments. Applied Environmental Microbiology 2001, 67:1384-1387.
15. Danovaro R., Gambi C., Luna G.M., Mirto S. Sustainable impact of mussel farming in the Adriatic Sea (Mediterranean Sea): evidence from biochemical, microbial and meiofaunal indicators. Marine Pollution Bulletin 2004, 49:325-333.
16. Danovaro R., Luna G.M., Dell'Anno A., Pietrangeli B. Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments. Applied Environmental Microbiology 2006, 72:5982-5989.
17. Danovaro R., Corinaldesi C., Filippini M., Fischer U.R., Gessner M.O., Jacquet S., Magagnini M., Velimirov B. Viriobenthos in freshwater and marine sediments: a review. Freshwater Biology 2008, 53:1186-1213.
18. Danovaro R., Corinaldesi C., Dell'Anno A., Fuhrman J.A., Middelburg J.J., Noble R.T., Suttle C.A. Marine viruses and global climate change. FEMS Microbiological Reviews 2011, 35:993-1034.
19. Dell'Anno A., Danovaro R. Extracellular DNA plays a key role in deep-sea ecosystem functioning. Science 2005, 309:2179.
20. Dell'Anno A., Corinaldesi C., Magagnini M., Danovaro R. Determination of viral production in aquatic sediments using the dilution-based approach. Nature Protocols 2009, 4:1013-1022.
21. Duarte C.M., Holmer M., Olsen Y., Soto D., Marbà N., Guiu J., Black K., Karakassis J. Will the oceans help feed humanity?. BioScience 2009, 59:967-976.
22. FAO - Fisheries and Aquaculture Department The State of World Fisheries and Aquaculture 2010, Food and Agriculture Organization of the United Nations, Rome, 197 pp.
23. Frederiksen M.S., Holmer M., Díaz-Almela E., Marba N., Duarte C.M. Sulfide invasion in the seagrass Posidonia oceanica at Mediterranean fish farms: assessment using stable sulfur isotopes. Marine Ecology Progress Series 2007, 345:93-104.
24. García-Martínez M., López-López A., Calleja M.L., Marbà N., Duarte C.M. Bacterial community dynamics in a seagrass (Posidonia oceanica) meadow sediment. Estuaries and Coasts 2009, 32:276-286.
25. Hewson I., Vargo G.A., Fuhrman J.A. Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: effects of virus infection, containment, and nutrient enrichment. Microbial Ecology 2003, 46:322-336.
26. Hewson I., Fuhrman J.A. Covariation of viral parameters with bacterial assemblage richness and diversity in the water column and sediments. Deep-Sea Research I 2007, 54:811-830.
27. Hoppe H.G. Use of fluorogenic model substrates for extracellular enzyme activity (EEA) measurements of bacteria. Handbook of Methods in Aquatic Microbial Ecology 1993, 509-512. Lewis, London. P.F. Kemp, B.F. Sherr, E.B. Sherr, J.J. Cole (Eds.).
28. Holmer M. Environmental issues of fish farming in offshore waters: perspectives, concerns and research needs. Aquaculture Environment Interactions 2010, 1:57-60.
29. Holmer M., Kristensen E. Impact of fish farming on metabolism and sulfate reduction of underlying sediments. Marine Ecology Progress Series 1992, 80:191-201.
30. Holmer M., Wildish D., Hargrave B. Organic enrichment from marine finfish aquaculture and effects on sediment biogeochemical processes. Handbook of Environmental Chemistry 2005, 5:181-206.
31. Holmer M., Frederiksen M.S. Stimulation of sulphate reduction rates in Mediterranean fish farm sediments inhabited by the seagrass Posidonia oceanica. Biogeochemistry 2007, 85:169-184.
32. Holmer M., Argyrou M., Dalsgaard T., Danovaro R., Diaz-Almela E., Duarte C.M., Frederiksen M., Grau A., Karakassis I., Marbà N., Mirto S., Pérez M., Pusceddu A., Tsapakis M. Effects of fish farm waste on Posidonia oceanica meadows: synthesis and provision of monitoring and management tools. Marine Pollution Bulletin 2008, 56:1618-1629.
33. Karakassis I., Tsapakis M., Hatziyanni E., Papadopoulou K.N., Plaiti W. Impact of cage farming of fish on the seabed in three Mediterranean coastal areas. ICES Journal of Marine Sciences 2000, 57:1462-1471.
34. Karakassis I., Pitta P., Krom M. Contribution of fish farming to the nutrient loading of the Mediterranean. Scientia Marina 2005, 69:313-321.
35. Kawahara N., Shigematsu K., Miyadai T., Kondo R. Comparison of bacterial communities in fish farm sediments along an organic enrichment gradient. Aquaculture 2009, 287:107-113.
36. La Rosa T., Mirto S., Mazzola A., Danovaro R. Differential responses of benthic microbes and meiofauna to fish-farm disturbance in coastal sediments. Environmental Pollution 2001, 112:427-434.
37. La Rosa T., Mirto S., Mazzola A., Maugeri T.L. Benthic microbial indicators of fish farm impact in a coastal area of the Tyrrhenian Sea. Aquaculture 2004, 230:153-167.
38. Luna G.M., Manini E., Danovaro R. Large fraction of dead and inactive bacteria in coastal marine sediments: comparison of protocols for determination and ecological significance. Applied Environmental Microbiology 2002, 68:3509-3513.
39. Luna G.M., Dell'Anno A., Danovaro R. DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments. Environmental Microbiology 2006, 8:308-320.
40. McArdle B.H., Anderson M.J. Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 2001, 82:290-297.
41. Mirto S., La Rosa T., Danovaro R., Mazzola A. Microbial and meiofaunal response to intensive mussel-farm biodeposition in coastal sediments of the Western Mediterranean. Marine Pollution Bulletin 2000, 40:244-252.
42. Mirto S., Bianchelli S., Gambi C., Krzelj M., Pusceddu A., Scopa M., Holmer M., Danovaro R. Fish-farm impact on metazoan meiofauna in the Mediterranean Sea: analysis of regional vs. habitat effects. Marine Environmental Research 2010, 69:38-47.
43. Papageorgiou N., Kalantzi I., Karakassis I. Effects of fish farming on the biological and geochemical properties of muddy and sandy sediments in the Mediterranean Sea. Marine Environmental Research 2010, 69:326-336.
44. Patel A., Noble R.T., Steele J.A., Schwalbach M.S., Hewson I., Fuhrman J.A. Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nature Protocols 2007, 2:269-276.
45. Pitta P., Karakassis I., Tsapakis M., Zivanovic S. Natural vs. mariculture induced variability in nutrients and plankton in the Eastern Mediterranean. Hydrobiologia 1999, 391:181-194.
46. Pusceddu A., Fraschetti S., Mirto S., Holmer M., Danovaro R. Effects of intesive mariculture on sediment biochemistry. Ecological Applications 2007, 17:1366-1378.
47. Qiu X., Wu L., Huang H., McDonel P.E., Palumbo A.V., Tiedje J.M., Zhou J. Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Applied Environmental Microbiology 2001, 67:880-887.
48. Sakami T., Yokoyama H., Ishihi Y. Microbial hydrolytic enzyme activity in the sediment of a net cage aquaculture area. Fisheries Science 2005, 71:271-278.
49. Sarà G., Lo Martire M., Sanfilippo M., Pulicanò G., Cortese G., Mazzola A., Manganaro A., Pusceddu A. Impacts of marine aquaculture at large spatial scales: evidences from N and P catchment loading and phytoplankton biomass. Marine Environmental Research 2011, 71:317-324.
50. Schloss P.D., Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environmental Microbiology 2005, 71:1501-1506.
51. Schneider K., Sher Y., Erez J., van Rijn J. Carbon cycling in a zero-discharge mariculture system. Water Research 2011, 45:2375-2382.
52. Shibata A., Goto Y., Saito H., Kikuchi T., Toda T., Taguchi S. Comparison of SYBR Green I and SYBR Gold stains for enumerating bacteria and viruses by epifluorescence microscopy. Aquatic Microbial Ecology 2006, 43:223-231.
53. Suttle C.A. Marine viruses - major players in the global ecosystem. Nature Reviews in Microbiology 2007, 5:801-812.
54. Torsvik V., Sørheim R., Goksøyr J. Total bacterial diversity in soil and sediment communities - a review. Journal of Industrial Microbiology and Biotechnology 1996, 17:170-178.
55. Vezzulli L., Chelossi E., Riccardi G., Fabiano M. Bacterial community structure and activity in fish farm sediments of the Ligurian sea (Western Mediterranean). Aquaculture International 2002, 10:123-141.
56. Vezzulli L., Moreno M., Marin V., Pezzati E., Bartoli M., Fabiano M. Organic waste impact of capture-based Atlantic bluefin tuna aquaculture at an exposed site in the Mediterranean Sea. Estuarine, Coastal and Shelf Sciences 2008, 78:369-384.
57. Weinbauer M.G. Ecology of prokaryotic viruses. FEMS Microbiology Reviews 2004, 28:127-181.
58. Wen K., Ortmann A.C., Suttle C.A. Accurate estimation of viral abundance by epifluorescence microscopy. Applied and Environmental Microbiology 2004, 70:3862-3867.