Phytoplankton, bacterioplankton and virioplankton structure and function across the southern Great Barrier Reef shelf

Journal of Marine Systems

Volumn 142, Issue , 2015, Pages 25-39

  Alongi, Daniel M ^a   Patten, Nicole L ^b   McKinnon, David ^a   Köstner, Nicole ^a   Bourne, David G ^a   Brinkman, Richard ^a  

^a AUSTRALIAN INSTITUTE OF MARINE SCIENCE   (Australia)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Bacterioplankton; Diazotrophs; Great Barrier Reef; Phytoplankton; Plankton; Virioplankton

Indexed keywords

PLANKTON;

BACTERIOPLANKTONS; DIAZOTROPHS; GREAT BARRIER REEF; VIRIOPLANKTON;

PHYTOPLANKTON;

BACTERIOPLANKTON; BIOMASS; MARINE SEDIMENT; PHYTOPLANKTON; PRIMARY PRODUCTION; PRINCIPAL COMPONENT ANALYSIS; VIRUS; WATER CHEMISTRY; WATER COLUMN;

AUSTRALIA; CORAL SEA; GREAT BARRIER REEF; QUEENSLAND;

EID: 84908180844     PISSN: 09247963     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmarsys.2014.09.010     Document Type: Article

References (66)

1. Alongi D.M., McKinnon D.A. The cycling and fate of terrestrially-derived sediment and nutrients in the coastal zone of the Great Barrier Reef. Mar. Pollut. Bull. 2005, 51:239-253.
2. Alongi D.M., Trott L.A., Møhl M. Strong tidal currents and labile organic matter stimulate benthic decomposition and carbonate fluxes on the southern Great Barrier Reef shelf. Cont. Shelf Res. 2011, 31:1384-1395.
3. Andutta F.P., Ridd P.V., Wolanski E. Dynamics of hypersaline coastal waters in the Great Barrier Reef. Estuar. Coast. Shelf Sci. 2011, 94:299-305.
4. Bar-Zeev E., Berman-Frank I., Stambler N., Domínguez, Zohary T., Capuzzo E., Meeder E., Suggett D.J., Iluz D., Dishon G., Berman T. Transparent exopolymer particles (TEP) link phytoplankton and bacterial production in the Gulf of Aqaba. Aquat. Microb. Ecol. 2009, 56:217-225.
5. Bell R.T. Estimating production of heterotrophic bacterioplankton via incorporation of tritiated thymidine. Handbook of Methods in Aquatic Microbial Ecology 1993, 495-503. CRC Press, Boca Raton. P.F. Kemp, B.F. Sherr, J.J. Cole (Eds.).
6. 14C production and other rate terms during the JGOFS Equatorial Pacific experiment. Deep-Sea Res. I 1999, 46:637-654.
7. Bertilsson S., Berglund O., Karl D.M., Chisholm S.W. Elemental composition of marine Prochlorococcus and Synechococcus: implications for the ecological stoichiometry of the sea. Limnol. Oceanogr. 2003, 48:1721-1731.
8. Bhaskar P.V., Bhosle N.B. Bacterial production, glucosidase activity and particle-associated carbohydrates in Dona Paula Bay, west coast of India. Estuar. Coast. Shelf Sci. 2008, 80:413-424.
9. Bong C.W., Lee C.W. The contribution of heterotrophic nanoflagellates grazing towards bacterial mortality in tropical waters: comparing estuaries and coastal ecosystems. Mar. Freshw. Res. 2011, 62:414-420.
10. Bourne D.G., Webster N.S. Coral reef bacterial communities. The Prokaryotes - Prokaryotic Communities and Ecophysiology 2013, 165-187. Springer-Verlag, Heidelberg. E. Rosenberg (Ed.).
11. Bourne D.G., Dennis P.G., Uthicke S., Soo R.M., Tyson G.W., Webster N.S. Coral reef invertebrate microbiomes correlate with the presence of photosymbionts. ISME J. 2013, 10.1038/ismej.2012.172.
12. Bouvy M., Combe M., Bettarel Y., Dupuy C., Rochelle-Newell E., Charpy L. Uncoupled viral and bacterial distributions in coral reef waters of Tuamotu Archipelago (French Polynesia). Mar. Pollut. Bull. 2012, 65:5-6. (515).
13. Bragg L., Stone G., Imelfort M., Hugenholtz P., Tyson G.W. Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat. Methods 2012, 9:425-426.
14. Breitbart M., Middelboe M., Rohwer F. Marine viruses: community dynamics, diversity and impact on microbial processes. Microbial Ecology of the Oceans 2008, 443-480. Wiley-Blackwell, New Jersey. D.L. Kirchman (Ed.).
15. Brinkman R., Wolanski E., Deleersnijder, McAllister F., Skirving W. Oceanic inflow from the Coral Sea into the Great Barrier Reef. Estuar. Coast. Shelf Sci. 2001, 54:655-668.
16. Brussaard C.P.D. Optimization of procedures for counting viruses by flow cytometry. Appl. Environ. Microbiol. 2004, 70:1506-1513.
17. Burns K., Brinkman D. Organic biomarkers describe the major carbon inputs and cycling of organic matter in the southern Great Barrier Reef region. Estuar. Coast. Shelf Sci. 2011, 93:132-141.
18. Calvo-Díaz A., Móan X.A.G. Empirical leucine-to-carbon conversion factors for estimating heterotrophic bacterial production: seasonality and predictability in a temperate coastal ecosystem. Appl. Environ. Microbiol. 2009, 75:3216-3221.
19. Caporaso J.G., Kuczynski J., Stombaugh J., et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 2010, 7:335-336.
20. Crosbie N.D., Furnas M.J. Abundance, distribution and flow-cytometric characterization of picophytoprokaryotes populations in the central (17°S) and southern (20°S) shelf waters of the Great Barrier Reef. J. Plankton Res. 2001, 23:809-828.
21. DeSantis T.Z., Hugenholtz P., Larsen N., et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 2006, 72:5069-5072.
22. Ducklow H.W. Bacterial production and biomass in the oceans. Microbial Ecology of the Oceans 2000, 85-120. Wiley and Sons, New York. D.L. Kirchman (Ed.).
23. Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194.
24. Fitzwater S.E., Knauer G.A., Martin J.H. Metal contamination and its effect on primary production measurements. Limnol. Oceanogr. 1982, 27:544-551.
25. Fuhrman J., Hewson I. Plankton viruses. Encyclopedia of Ocean Sciences 2009, 13-20. Academic Press, London. 2nd edition. J.H. Steele, S.A. Thorpe, K.K. Turekian (Eds.).
26. Fukuda R., Ogawa H., Nagata T., Koike I. Direct determination of carbon and nitrogen contents of natural bacterial assemblages in marine environments. Appl. Environ. Microbiol. 1998, 64:3352-3358.
27. Furnas M.J., Mitchell A.W., Skuza M. Nitrogen and phosphorus budgets for the central Great Barrier Reef. Research Report No. 36 1995, Great Barrier Reef Marine Park Authority, Townsville.
28. Furnas M.J., Alongi D.M., McKinnon D., Trott L., Skuza M. Regional-scale nitrogen and phosphorus budgets for the northern (14°S) and central (17°S) Great Barrier Reef shelf ecosystem. Cont. Shelf Res. 2011, 31:1967-1990.
29. Green R.H. Sampling Design and Statistical Methods for Environmental Biologists 1979, Wiley and Sons, New York.
30. Hammer O., Harper D.A.T., Ryan P. Past: paleontological statistics software package for education and data analysis. Palaeontol. Electron. 2001, 4:1-9.
31. Hewson I., Moisander P.H., Morrison A.E., Zehr J.P. Diazotrophic bacterioplankton in a coral reef lagoon: phylogeny, diel nitrogenase expression and response to phosphate enrichment. ISME J. 2007, 1:78-91.
32. Hopley D. Coral reef growth on the shelf margin of the Great Barrier Reef with special reference to the Pompey Complex. J. Coast. Res. 2006, 22:150-158.
33. Hopley D., Smithers S.G., Parnell K.E. The Geomorphology of the Great Barrier Reef: Development, Diversity and Change 2007, Cambridge University Press, Cambridge.
34. Jolliffe I.T. Principal Component Analysis 1986, Springer-Verlag, New York.
35. Kirchman D.L. Measuring bacterial biomass production and growth rates from leucine incorporation in natural aquatic environments. Marine Microbiology, Methods in Microbiology 2001, vol. 30:227-238. Academic Press, San Diego.
36. Lee C.W., Bong C.W. Bacterial abundance and production, and their relation to primary production in tropical coastal waters of Peninsular Malaysia. Mar. Freshw. Res. 2008, 59:10-21.
37. Lee C.W., Bong C.W., Hii Y.S. Temporal variation of bacterial respiration and growth efficiency in tropical coastal waters. Appl. Environ. Microbiol. 2009, 75:7594-7601.
38. Legendre L., Rivkin R.B. Planktonic food webs: microbial hub approach. Mar. Ecol. Prog. Ser. 2008, 365:289-309.
39. Lema K.A., Willis B.L., Bourne D.G. Corals form characteristic associations with symbiotic nitrogen-fixing bacteria. Appl. Environ. Microbiol. 2012, 78:3136-3144.
40. Lema K.A., Willis B.L., Bourne D.G. Amplicon pyrosequencing reveals spatial and temporal consistency in diazotroph assemblages of the Acropora millepora microbiome. Environ. Microbiol. 2014, 10.1111/1462-2920-12366.
41. Meekan M.G., Carleton J.H., Steinberg C.R., McKinnon A.D., Brinkman R.M., Doherty P.J., Halford A.R., Talbot S., Mason L. Turbulent mixing and mesoscale distributions of late stage larval fishes on the NW Shelf of Western Australia. Fish. Oceanogr. 2006, 15:44-59.
42. Morán X.A.G., Fernández E., Pérez V. Size-fractionated primary production, bacterial production and net community production in subtropical and tropical domains of the oligotrophic NE Atlantic in autumn. Mar. Ecol. Prog. Ser. 2004, 274:17-29.
43. Motulsky H. Intuitive Biostatistics 2010, Oxford University Press, New York. 2nd edition.
44. Mulholland M.R., Rocha A.M., Boneillo G.E. Incorporation of leucine and thymidine by estuarine phytoplankton: implications for bacterial productivity estimates. Estuar. Coast. 2011, 34:310-325.
45. NCSS User's Guide IV 2007, NCSS, Kaysville, Utah, USA.
46. Ogbebo F.E., Ochs C. Bacterioplankton and phytoplankton production rates compared at different levels of solar ultraviolet radiation and limiting nutrient ratios. J. Plankton Res. 2008, 30:1271-1284.
47. Parsons T.R., Maita Y., Lalli C.M. A Manual of Chemical and Biological Methods for Seawater Analysis 1984, Pergamon Press, Oxford.
48. Patten N.L., Mitchell J.G., Middelboe M., Eyre B.D., Seuront L., Harrison P.L., Glud R.N. Bacterial and viral dynamics during a mass coral spawning period on the Great Barrier Reef. Aquat. Microb. Ecol. 2008, 50:209-220.
49. Payet J.P., McMinds R., Burkepile D., Vega Thurber R. Unprecedented evidence for high viral abundance and lytic evidence in coral reef watrers of the South Pacific Ocean. Front. Microbiol. 2014, 5:493. 10.3389/fmicb.2014.00493.
50. Pitcher C.R., Doherty P.J., Anderson T.J. Seabed environments, habitats and biological assemblages. The Great Barrier Reef: Biology, Environment and Management 2009, 551-558. Springer, Dordrecht. P. Hutchings, M. Kingsford, O. Hoegh-Guldberg (Eds.).
51. Ram A.S.P., Nair S., Chandramohan D. Bacterial growth efficiency in the tropical estuarine and coastal waters of Goa, southwest Coast of India. Microb. Ecol. 2003, 45:88-96.
52. Ranasinghe R., Pattiaratchi C. Circulation and mixing characteristics of a seasonally-open tidal inlet: a field study. Mar. Freshw. Res. 1999, 50:281-290.
53. Riemann L., Nielsen T.G., Kragh T., Richardson K., Parner H., Jakobsen H.H., Munk P. Distribution and production of plankton communities in the subtropical convergence zone of the Sargasso Sea. I. Phytoplankton and bacterioplankton. Mar. Ecol. Prog. Ser. 2011, 426:57-70.
54. Scavia D. On the role of bacteria in secondary production. Limnol. Oceanogr. 1988, 33:1220-1224.
55. Schauer C., Massana R., Pedros-Alio C. Spatial differences in bacterioplankton composition along the Catalan coast (NW Mediterranean) assessed by molecular finger-printing. FEMS Microbiol. Ecol. 2000, 33:51-59.
56. Schloss P.D., Westcott S.L., Ryabin T., et al. Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
57. Seymour J.R., Patten N., Bourne D.G., Mitchell J.G. Spatial dynamics of virus-like particles and heterotrophic bacteria within a shallow coral reef system. Mar. Ecol. Prog. Ser. 2005, 288:1-8.
58. Simpson J.H., Hunter J.R. Fronts in the Irish Sea. Nature 1974, 250:404-406.
59. Sorokin Y.I., Sorokin P.Y. Analysis of plankton in the southern Great Barrier Reef: abundance and roles in trophodynamics. J. Mar. Biol. Assoc. U. K. 2009, 89:235-241.
60. Steindler L., Schwalbach M.S., Smith D.P., Chan F., Giovannoni S.J. Energy starved Candidatus Pelagibacter ubique substitutes light-mediated ATP production for endogenous carbon respiration. PLoS One 2011, 6:e19725.
61. Steward G.F., Fandino L.B., Hollibaugh J.T., Whitledge T.E., Azam F. Microbial biomass and viral infections of heterotrophic prokaryotes in the sub-surface layer of the central Arctic Ocean. Deep-Sea Res. 2007, 54:1744-1757.
62. Strayer D. On the limits to secondary production. Limnol. Oceanogr. 1988, 33:1217-1220.
63. Strom S.L. Microbial ecology of ocean biogeochemistry: a community perspective. Science 2008, 320:1043-1045.
64. Wolanski E. Physical Oceanographic Processes of the Great Barrier Reef 1994, CRC Press, Boca Raton.
65. Zehr J.P., McReynolds L.A. Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl. Environ. Microbiol. 1989, 55:2522-2526.
66. Zehr J.P., Jenkins B.D., Short S.M., Steward G.F. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ. Microbiol. 2003, 5:539-554.