Influence of Amazon and Orinoco offshore surface water plumes on oligotrophic bacterioplankton diversity in the west tropical Atlantic

Aquatic Microbial Ecology

Volumn 43, Issue 1, 2006, Pages 11-22

  Hewson, Ian ^a,b   Capone, Douglas G ^a   Steele, Joshua A ^a   Fuhrman, Jed A ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Amazon; ARISA; Bacteria; Biogeography; Resource

Indexed keywords

BACTERIA (MICROORGANISMS); OTUS;

EID: 33744961963     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame043011     Document Type: Article

References (82)

1. Acinas SG, Rodriguez-Valera F, Pedrós-Alió C (1997) Spatial and temporal variation in marine bacterioplankton diversity as shown by RFLP fingerprinting of PCR amplified 16S rDNA. FEMS Microbiol Ecol 24:27-40
2. Acinas SG, Klepac-Ceraj V, Hunt DE, Pharino C, Ceraj I, Distel DL, Polz MF (2004) Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430:551-554
3. Amon RMW, Benner R (1996a) Bacterial utilization of different size classes of dissolved organic matter. Limnol Oceanogr 41:41-51
4. Amon RMW, Benner R (1996b) Photochemical and microbial consumption of dissolved organic carbon and dissolved oxygen in the Amazon River system. Geochim Cosmochim Acta 60:1783-1792
5. Amon RMW, Benner R (1998) Seasonal patterns of bacterial abundance and production in the Mississippi River plume and their importance for the fate of enhanced primary production. Microb Ecol 35:289-300
6. Aucour AM, Tao FX, Moreira-Turcq P, Seyler P, Sheppard S, Benedetti MF (2003) The Amazon River: behavior of metals (Fe, Al, Mn) and dissolved organic matter in the initial mixing at the Rio Negros/Solimoes confluence. Chem Geol 197:271-285
7. Avaniss-Aghajani E, Jones K, Chapman D, Brunk C (1994) A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. Biotechniques 17:144-149
8. Azam F (1998) Microbial control of oceanic carbon flux: the plot thickens. Science 280:694
9. Azam F, Fenchel T, Field JG, Gray JS, Meyer-Reil LA, Thingstad F (1983) The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser 10:257-263
10. Beja O, Aravind L, Koonin EV, Suzuki MT and 8 others (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902-1906
11. Brown MV, Schwalbach MS, Hewson I, Fuhrman JA (2005) Coupling 16S-ITS rDNA clone libraries and ARISA to show marine microbial diversity: development and application to a time series. Environ Microbiol 7:1466-1479
12. Buckling A, Kassen R, Bell G, Rainey PB (2000) Disturbance and diversity in experimental microcosms. Nature 408:961-964
13. Cardinale BJ, Palmer MA, Collins SL (2002) Species diversity enhances ecosystem functioning through interspecific facilitation. Nature 415:426-429
14. Choi KH, Dobbs FC, Cowen RK (2001) Short-term temporal and spatial dynamics of bacterioplankton near Barbados in the Caribbean Sea. Aquat Microb Ecol 25:43-53
15. Connell JH (1978) Diversity in tropical rainforests and coral reefs. Science 199:1304-1310
16. Crosby LD, Criddle CS (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34:790-802
17. Crump BC, Amrmbrust EV, Baross JA (1999) Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary and the adjacent coastal ocean. Appl Environ Microbiol 65:3192-3204
18. Currie DJ (1991) Energy and large-scale patterns of animal-and plant-species richness. Am Nat 137:27-49
19. De Long EF (2002) Microbial population genomics and ecology. Curr Opin Microbiol 5:520-524
20. Del Vecchio R, Subramaniam A (2004) Influence of the Amazon River on the surface optical properties of the western tropical North Atlantic Ocean. J Geophys Res 109:C11001, doi:11010.11029/12004JC002503
21. DeMaster DJ, Smith WO Jr, Nelson DM, Aller JY (1996) Biogeochemical processes in Amazon shelf waters: chemical distributions and uptake rates of silicon, carbon and nitrogen. Coast Shelf Res 16:617-643
22. Farjalla VF, Esteves FA, Bozelli RL, Roland F (2002) Nutrient limitation of bacterial production in clear water Amazonian ecosystems. Hydrobiol 489:197-205
23. Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65:4630-4836
24. Flagg CN, Gordon RL, McDowell S (1986) Hydrographic and current observations on the continental slope and shelf in the Western Equatorial Atlantic. J Phys Oceanogr 16:1412-1429
25. Fuhrman JA (1992) Bacterioplankton roles in cycling of organic matter: The Microbial food web. In: Falkowski PG, Woodhead AD (eds) Primary productivity and Biogeochemical Cycles in the Sea. Plenum Press, New York
26. Fuhrman JA, Azam F (1980) Bacterioplankton secondary production estimates for coastal waters of British Columbia, Antarctica, and California. Appl Environ Microbiol 39:1085-1095
27. Fuhrman JA, Azam F (1982) Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters: Evaluation and field results. Mar Biol 66:109
28. Fuhrman JA, Ouverney CC (1998) Marine microbial diversity studied via 16S rRNA sequences: cloning results from coastal waters and counting of native archaea with fluorescent single cell probes. Aquat Ecol 32:3-15
29. Fuhrman JA, Suttle CA (1993) Viruses in marine planktonic systems. Oceanogr 6:51-63
30. Fuhrman JA, Comeau DE, Hagström Å, Chan AM (1988) Extraction of DNA suitable for molecular biological studies from natural planktonic microorganisms. Appl Environ Microbiol 54:1426-1429
31. Fuhrman JA, Sleeter TD, Carlson CA, Proctor LM (1989) Dominance of bacterial biomass in the sargasso sea and its ecological implications. Mar Ecol Prog Ser 57:207-217
32. Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356:148-149
33. Giovannoni SJ, Rappe M (2000) Evolution, diversity and molecular ecology of marine prokaryotes. In: Kirchman DL (ed) Microbial Ecology of the Oceans. Wiley-Liss, New York, p 47-84
34. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63
35. Givnish TJ (1999) On the causes of gradients in tropical tree diversity. J Ecol 87:193-210
36. Goni GJ, Johns WE (2001) A census of North Brazil Current rings observed from TOPEX/POSEIDON altimetry: 1992-1998. Geophys Res Lett 28:1-4
37. Hansell DA, Ducklow HW (2003) Bacterioplankton distribution and production in the bathypelagic ocean: Directly coupled to particulate organic carbon export? Limnol Oceanogr 48:150-156
38. Hellweger FL, Gordon AL (2002) Tracing Amazon River water into the Caribbean Sea. J Mar Res 60:537-549
39. Hewson I, Fuhrman JA (2004) Bacterioplankton species richness and diversity along an estuarine gradient in Moreton Bay, Australia. Appl Environ Microbiol 70:3425-3433
40. Hewson I, Fuhrman JA (2006) Improved strategy for comparing microbial assemblage fingerprints. Microb Ecol 51:147-153
41. Hewson I, Vargo GA, Fuhrman JA (2003) Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: effects of virus infection, containment and nutrient enrichment. Microb Ecol 46:322-336
42. Hewson I, Steele JA, Capone DG, Fuhrman JA (2006) Temporal and spatial scales of variation in bacterioplankton assemblages of oligotrophic surface waters. Mar Ecol Prog Ser 311:67-77
43. Hollibaugh JT, Wong PS, Murrell MC (2000) Similarity of particle-associated and free-living bacterial communities in northern San Francisco Bay, California. Aquat Microb Ecol 21:103-109
44. Horner-Devine MC, Leibold MA, Smith VH, Bohannan BJM (2003) Bacterial diversity patterns along a gradient of primary productivity. Ecol Lett 6:613-622
45. Janzen DH (1970) Herbivores and the number of tree species in tropical forests. Am Nat 104:501-528
46. Jochem FJ (2003) Photo- and heterotrophic pico- and nanoplankton in the Mississippi River plume: distribution and grazing activity. J Plankton Res 25:1201-1214
47. Kassen R, Buckling A, Bell G, Rainey PB (2000) Diversity peaks at intermediate productivity in a laboratory microcosm. Nature 406:508-512
48. Kirchman D, Knees E, Hodson R (1985) Leucine incorporation and its potential as a measure of protein-synthesis by bacteria in natural aquatic systems. Appl Environ Microbiol 49:599-607
49. Klappenbach JL, Dunbar JM, Schmidt TM (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66:1328-1333
50. Kolber ZS, Plumley FG, Lang AS, Beatty JT and 6 others (2001) Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292:2492-2495
51. Kondoh M (2001) Unifying the relationships of species richness to productivity and disturbance. Proc R Soc Lond B Biol Sci 268:269-271
52. Kuypers MMM, Lavik G, Woebken D, Schmid M, Fuchs BM, Amann R, Jorgensen BB, Jetten MSM (2005) Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc Natl Acad Sci USA 102:6478-6483
53. Legendre P, Legendre L (1998) Numerical ecology. Elsevier, Amsterdam
54. Lerman A (1980) Controls on river water composition and mass balance of river systems. In: Martin JM (ed) River inputs to ocean systems. Wiley & Sons, Chichester, p 1-4
55. Leuders T, Friedrich MW (2003) Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69:320-326
56. Long RA, Azam F (2001) Antagonistic interactions among marine pelagic bacteria. Appl Environ Microbiol 67:4975-4983
57. Moeseneder MM, Winter C, Herndl GJ (2001) Horizontal and vertical complexity of attached and free-living bacteria of the eastern Mediterranean Sea, determined by 16S rDNA and 16S rRNA fingerprints. Limnol Oceanogr 46:95-107
58. Morris RM, Rappé M, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ (2002) SAR11 clade dominated ocean surface bacterioplankton communities. Nature 420:806-810
59. Mulder CPH, Uliassi DD, Doak DF (2001) Physical stress and diversity-productivity relationships: the role of positive interactions. Proc Natl Acad Sci USA 98:6704-6708
60. Nittrouer CA, DeMaster DJ (1996) The Amazon shelf setting: tropical, energetic, and influenced by a large river. Cont Shelf Res 16:553-573
61. Noble RT, Fuhrman JA (1998) Use of SYBR Green I rapid epifluoresence counts of marine viruses and bacteria. Aquat Microb Ecol 14:113-118
62. Palenik B, Brahamsha B, Larimer FW, Land M and 11 others (2003) The genome of the motile marine Synechococcus. Nature 424:1037-1042
63. Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724-3730
64. Polz MF, Harbison C, Cavanaugh CM (1999) Diversity and heterogeneity of epibiotic bacterial communities on the marine nematode Eubostrichus dianae. Appl Environ Microbiol 65:4271-4275
65. Riemann L, Middelboe M (2002) Stability of bacterial and viral community compositions in Danish coastal waters as depicted by DNA fingerprinting techniques. Aquat Microb Ecol 27:219-232
66. Ryther JH, Menzel DW, Corwin N (1967) Influence of the Amazon River outflow on the ecology of the western tropical Atlantic. J Mar Res 25:69-82
67. Schmidt TM, DeLong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S ribosomal-RNA gene cloning and sequencing. J Bacteriol 173:4371-4378
68. Šimek K, Pernthaler J, Weinbauer MG, Hornák K, Dolan JR, Nedoma J, Masín M, Amann R (2001) Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir. Appl Environ Microbiol 67:2723-2733
69. Simon M, Azam F (1989) Protein content and protein synthesis rates of planktonic marine bacteria. Mar Ecol Prog Ser 51:201-213
70. Sokal RR, Rohlf FJ (1995) Biometry. The principles and practice of statistics in biological research. Freeman, New York
71. Stepanauskas R, Moran MA, Bergamaschi BA, Hollibaugh JT (2003) Covariance of bacterioplankton composition and environmental variables in a temperate delta system. Aquat Microb Ecol 31:85-98
72. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625-630
73. Suzuki MT, Rappé M, Giovannoni SJ (1998) Kinetic bias in estimates of picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl Environ Microbiol 64:4522-4529
74. Thingstad TF, Lignell R (1997) A theoretical approach to the question of how trophic interactions control carbon demand, growth rate, abundance and diversity. Aquat Microb Ecol 13:19-27
75. Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity - magnitude, dynamics and controlling factors. Science 296:1064-1066
76. Troussellier M, Schafer H, Batailler N, Bernard L, and 5 others (2002) Bacterial activity and genetic richness along an estuarine gradient (Rhone River plume, France). Aquat Microb Ecol 28:13-24
77. Venter JC, Remington K, Heidelberg JF, Halpern AL and 19 others (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74
78. Waide R (1999) The relationship between productivity and species richness. Annu Rev Ecol Syst 30:257-300
79. Wawrik B, Paul JH, Campbell D, Griffin D, Houchin LA, Fuentes-Ortega A, Muller-Karger F (2003) Vertical structure of the phytoplankton community associated with a coastal plume in the Gulf of Mexico. Mar Ecol Prog Ser 251:87-101
80. Whittaker RH (1952) A study of summer foliage insect communities in the Great Smoky Mountains. Ecol Monogr 22:1-44
81. Zehr JP, Ward BB (2002) Nitrogen cycling in the ocean: new perspectives on processes and paradigms. Appl Environ Microbiol 68:1015-1024
82. Zehr JP, Carpenter EJ, Villareal TA (2000) New perspectives on nitrogen-fixing microorganisms in tropical and subtropical oceans. Trends Microbiol 8:68-73