Viral and bacterial abundance and production in the Western Pacific Ocean and the relation to other oceanic realms

FEMS Microbiology Ecology

Volumn 79, Issue 2, 2012, Pages 359-370

  Rowe, Janet M ^a,c   Debruyn, Jennifer M ^a   Poorvin, Leo ^a   Lecleir, Gary R ^a   Johnson, Zackary I ^b   Zinser, Erik R ^a   Wilhelm, Steven W ^a  

^a UNIVERSITY OF TENNESSEE   (United States)

^b DUKE UNIVERSITY   (United States)

^c UNIVERSITY OF NEBRASKA   (United States)

Author keywords

Marine viruses; Microbial ecology; Spatial diversity

Indexed keywords

SEA WATER;

ABUNDANCE; BACTERIUM; BIOLOGICAL PRODUCTION; COMMUNITY STRUCTURE; ECOZONE; ENVIRONMENTAL GRADIENT; MARINE ECOSYSTEM; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; SEAWATER; SPATIAL VARIATION; TEMPERATURE EFFECT; TRANSECT; VIRUS; WARM POOL;

ALPHAPROTEOBACTERIA; ARTICLE; BACTERIUM; CHEMISTRY; CLASSIFICATION; ECOLOGY; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIOLOGY; PACIFIC OCEAN; VIROLOGY; VIRUS;

ALPHAPROTEOBACTERIA; BACTERIA; ECOLOGY; PACIFIC OCEAN; SEAWATER; VIRUSES;

ATLANTIC OCEAN; PACIFIC OCEAN; PACIFIC OCEAN (WEST);

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 84855280632     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2011.01223.x     Document Type: Article

References (57)

1. Angly FE, Felts B, Salamon P et al. (2006) The marine viromes of four oceanic regions. PLoS Biol 4: e368.
2. Baldwin AJ, Moss JA, Pakulski JD, Catala P, Joux F & Jeffrey WH (2005) Microbial diversity in a Pacific Ocean transect from the Arctic to Antarctic circles. Aquat Microb Ecol 41: 91-102.
3. Boland GJ, Melzer MS, Hopkin A, Higgins V & Nassuth A (2004) Climate change and plant diseases in Ontario. Can J Plant Pathol 26: 335-350.
4. Brussaard CPD, Kuipers B & Veldhuis MJW (2005) A mesocosm study of Phaeocystis globosa population dynamics - 1. Regulatory role of viruses in bloom. Harmful Algae 4: 859-874.
5. Brussaard CPD, Wilhelm SW, Thingstad F et al. (2008) Global scale processes with a nanoscale drive - from viral genes to oceanic biogeochemical cycles. ISME J 2: 575-578.
6. Church MJ, Ducklow HW & Karl DM (2004) Light dependence of [3H]leucine incorporation in the oligotropihc North Pacific Ocean. Appl Environ Microbiol 70: 4079-4087.
7. Cole JR, Chai B, Farris RJ et al. (2007) The Ribosomal Database Project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35: D169-D172.
8. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh TL, Barrity GM & Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
9. Fuhrman JA (1992) Bacterioplankton roles in cycling of organic matter: the microbial food web. Primary Productivity and Biogeochemical Cycles in the Sea (Falkowski PG & Woodhead A, eds), pp. 361-384. Plenum, New York, NY.
10. Goddard L & Dilley M (2005) El Nino: catastrophe or opportunity. J Clim 18: 651-655.
11. Halpert MS & Ropelewski CF (1992) Surface-temperature patterns associated with the Southern Oscillation. J Clim 5: 577-593.
12. Hamady M, Walker JJ, Harris JK, Gold NJ & Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods 5: 235-237.
13. Hewson I & Fuhrman JA (2007) Covariation of viral parameters with bacterial assemblage richness and diversity in the water column and sediments. Deep Sea Res Part 1 Oceanogr Res Pap 54: 811-830.
14. Hobbie JE, Daley RJ & Jasper S (1977) Use of nuclepore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol 33: 1225-1228.
15. Huse SM, Huber JA, Morrison HG, Sogin ML & Mark Welch D (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143.
16. Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA & Sogin ML (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4: e1000255.
17. Hynes AM, Chappell PD, Dyhrman ST, Doney SC & Webb EA (2009) Cross-basin comparison of phosphorus stress and nitrogen fixation in Trichodesmium. Limnol Oceanogr 54: 1438-1448.
18. Jiang SC & Paul JH (1994) Seasonal and diel abundance of viruses and occurrence of lysogeny/bacteriocinogeny in the marine environment. Mar Ecol Prog Ser 104: 163-172.
19. Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EMS & Chisholm SW (2006) Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311: 1737-1740.
20. Johnson ZI, Shyam R, Ritchie AE, Mioni C, Lance VP, Murray JW & Zinser ER (2010) The effect of iron- and light-limitation on phytoplankton communities of deep chlorophyll maxima of the western Pacific Ocean. J Mar Res 68: 283-308.
21. Kirchman DL (2001) Measuring bacterial biomass production and growth rates from leucine incorporation in natural aquatic environments. Methods Microbiol 30: 227-236.
22. Lee SH & Fuhrman JA (1987) Relationships between biovolume and biomass of naturally derived marine bacterioplankton. Appl Environ Microbiol 53: 1298-1303.
23. Lindell D, Sullivan MB, Johnson ZI, Tolonen AC, Rohwer F & Chisholm SW (2004) Transfer of photosynthesis genes to and from Prochlorococcus viruses. P Natl Acad Sci USA 101: 11013-11018.
24. Lozupone C, Hamady M & Knight R (2006) UniFract - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7: 371.
25. Marie D, Partensky F, Jacquet S & Vaulot D (1997) Enumeration and cell cycle analysis of natural populations of marine picoplankton by flow cytometry using the nucleic acid stain SYBR Green I. Appl Environ Microbiol 63: 186-193.
26. McPhaden MJ, Zebiak SE & Glantz MH (2006) ENSO as an integrating concept in earth science. Science 314: 1740-1745.
27. Middelboe M & Jörgensen NOG (2006) Viral lysis of bacteria: an important source of dissolved amino acids and cell wall compounds. J Mar Biol Assoc UK 86: 605-612.
28. Middelboe M, Jörgensen NOG & Kroer N (1996) Effects of viruses on nutrient turnover and growth efficiency of noninfected marine bacterioplankton. Appl Environ Micorbiol 62: 1991-1997.
29. Murray AG & Jackson GA (1992) Viral dynamics: a model of the effects of size, shape, motion and abundance of single-celled planktonic organisms and other particles. Mar Ecol Prog Ser 89: 103-116.
30. Noble RT & Fuhrman JA (1998) Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat Microb Ecol 14: 113-118.
31. Noble RT & Fuhrman JA (2000) Rapid virus production and removal as measured with fluorescently labeled viruses as tracers. Appl Environ Microbiol 66: 3790-3797.
32. Pace ML, del Giorgio P, Fisher D, Condon R & Malcom H (2004) Estimates of bacterial production using the leucine incorporation method are influenced by differences in protein retention of microcentrifuge tubes. Limnol Oceanogr Methods 2: 55-61.
33. Poorvin L, Rinta-Kanto JM, Hutchins DA & Wilhelm SW (2004) Viral release of Fe and its bioavailability to marine plankton. Limnol Oceanogr 49: 1734-1741.
34. Rinta-Kanto JM, Ouellette AJA, Boyer GL, Twiss MR, Bridgeman TB & Wilheim SW (2005) Quantification of toxic Microcystis spp. during the 2003 and 2004 blooms in western Lake Erie using quantitative real-time PCR. Environ Sci Technol 39: 4198-4205.
35. Rowe JM, Saxton MA, Cottrell MT et al. (2008) Constraints on viral production in the Sargasso Sea and North Atlantic. Aquat Microb Ecol 52: 233-244.
36. Steinberg DK, Carlson CA, Bates NR, Johnson RJ, Michaels AF & Knap AH (2001) Overview of the US JGOFS Bermuda Atlantic Time-series Study (BATS): a decade-scale look at ocean biology and biogeochemistry. Deep Sea Res Part 2 Top Stud Oceanogr 48: 1405-1447.
37. Suttle CA & Chan AM (1993) Marine cyanophages infecting oceanic and coastal strains of Synechococcus - abundance, morphology, cross-infectivity and growth characteristics. Mar Ecol Prog Ser 92: 99-109.
38. Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
39. Thingstad TF & Lignell R (1997) Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat Microb Ecol 13: 19-27.
40. Vaulot D, Courties C & Partensky F (1989) A simple method to preserve oceanic phytoplankton for flow cytometric analyses. Cytometry 10: 629-635.
41. Wang CL & Enfield DB (2001) The tropical western hemisphere warm pool. Geophys Res Lett 28: 1635-1638.
42. Weinbauer MG & Suttle CA (1996) Potential significance of lysogeny to bacteriophage production and bacterial mortality in coastal waters of the Gulf of Mexico. Appl Environ Microbiol 62: 4374-4380.
43. Weinbauer MG, Winter C & Höfle MG (2002) Reconsidering transmission electron microscopy based estimates of viral infection of bacterioplankton using conversion factors derived from natural communities. Aquat Microb Ecol 27: 103-110.
44. Weinbauer MG, Rowe JM & Wilhelm SW (2010) Determining rates of virus production in aquatic systems by the virus reduction approach. Manual of Aquatic Viral Ecology (Wilhelm SW, Weinbauer MG & Suttle CA, eds), pp. 1-8. ASLO, Waco, TX.
45. Welschmeyer NA (1994) Fluorometric analysis of chlorophyll a in the presence of chlorophyll b and pheopigments. Limnol Oceanogr 39: 1985-1992.
46. Wen K, Ortmann AC & Suttle CA (2004) Accurate estimation of viral abundance by epifluorescence microscopy. Appl Environ Microbiol 70: 3862-3867.
47. Wilhelm SW & Matteson AR (2008) Freshwater and marine virioplankton: a brief overview of commonalities and differences. Freshw Biol 53: 1076-1089.
48. Wilhelm SW & Poorvin L (2001) Quantification of algal viruses in marine samples. Methods Microbiol vol. 30, Marine Microbiology (Paul JH, ed), pp. 53-66. Academic Press, London, UK.
49. Wilhelm SW & Suttle CA (1999) Viruses and nutrient cycles in the sea. Bioscience 49: 781-788.
50. Wilhelm SW, Weinbauer MG, Suttle CA & Jeffrey WH (1998) The role of sunlight in the removal and repair of viruses in the sea. Limnol Oceanogr 43: 586-592.
51. Wilhelm SW, Brigden SM & Suttle CA (2002) A dilution technique for the direct measurement of viral production: a comparison in stratified and tidally mixed coastal waters. Microb Ecol 43: 168-173.
52. Wilhelm SW, Jeffrey WH, Dean AL, Meador J, Pakulski JD & Mitchell DL (2003) UV radiation induced DNA damage in marine viruses along a latitudinal gradient in the southeastern Pacific Ocean. Aquat Microb Ecol 31: 1-8.
53. Wilson WH, Francis I, Ryan K & Davy SK (2001) Temperature induction of viruses in symbiotic dinoflagellates. Aquat Microb Ecol 25: 99-102.
54. Winter C, Herndl GJ & Weinbauer MG (2004) Diel cycles in viral infection of bacterioplankton in the North Sea. Aquat Microb Ecol 35: 207-216.
55. Winter C, Moeseneder MM, Herndl GJ & Weinbauer MG (2008) Relationship of geographic distance, depth, temperature, and viruses with prokaryotic communities in the eastern Tropical Atlantic ocean. Microb Ecol 56: 383-389.
56. Wommack KE & Colwell RR (2000) Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev 64: 69-114.
57. Wommack KE, Hill RT, Kessel M, Russek-Cohen E & Colwell RR (1992) Distribution of viruses in the Chesapeake Bay. Appl Environ Microbiol 58: 2965-2970.