Multilevel analysis of the bacterial diversity along the environmental gradient Río de la Plata-South Atlantic Ocean

Aquatic Microbial Ecology

Volumn 61, Issue 1, 2010, Pages 57-72

  Alonso, Cecilia ^a   Gómez Pereira, Paola ^b   Ramette, Alban ^b   Ortega, Leonardo ^c   Fuchs, Bernhard M ^b   Amann, Rudolf ^b  

^a INSTITUTO DE INVESTIGACIONES BIOLÓGICAS CLEMENTE ESTABLE   (Uruguay)

^b MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^c Direccion Nacional de Recursos Acuaticos   (Uruguay)

Author keywords

ARISA; Bacteria; Cloning; Diversity; Estuary; FISH; R o de la Plata

Indexed keywords

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; BETAPROTEOBACTERIA; GAMMAPROTEOBACTERIA; OTUS; PLANCTOMYCETES;

EID: 77957605901     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame01439     Document Type: Article

References (79)

1. Abell GCJ, Bowman JP (2005a) Colonization and community dynamics of class Flavobacteria on diatom detritus in experimental mesocosms based on Southern Ocean seawater. FEMS Microbiol Ecol 53:379-391
2. Abell GCJ, Bowman JP (2005b) Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean. FEMS Microbiol Ecol 51:265-277
3. Acha EM, Mianzan H, Guerrero R, Carreto J, Giberto D, Montoya N, Carignan M (2008) An overview of physical and ecological processes in the Rio de la Plata Estuary. Cont Shelf Res 28:1579-1588
4. Alonso C, Pernthaler J (2006) Roseobacter and SAR11 dominate microbial glucose uptake in coastal North Sea waters. Environ Microbiol 8:2022-2030
5. Alonso C, Zeder M, Piccini C, Conde D, Pernthaler J (2009) Ecophysiological differences of betaproteobacterial populations in two hydrochemically distinct compartments of a subtropical lagoon. Environ Microbiol 11:867-876
6. Alonso-Saez L, Gasol JM (2007) Seasonal variations in the contributions of different bacterial groups to the uptake of low-molecular-weight compounds in northwestern Mediterranean coastal waters. Appl Environ Microbiol 73: 3528-3535
7. Alonso-Sáez L, Balagué V, Sà EL, Sánchez O and others (2007) Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH. FEMS Microbiol Ecol 60:98-112
8. Anton J, Rossello-Mora R, Rodriguez-Valera F, Amann R (2000) Extremely halophilic bacteria in crystallizer ponds from solar salterns. Appl Environ Microbiol 66:3052-3057
9. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72:5734-5741
10. Barberán A, Casamayor EO (2010) Global phylogenetic community structure and â-diversity patterns in surface bacterioplankton metacommunities. Aquat Microb Ecol 59:1-10
11. 2 fluxes in the Patagonian shelf. J Geophys Res 110:C07003 doi: 10.1029/2004JC002488 (Pubitemid 41320250)
12. Bisbal GA (1995) The Southeast South American shelf large marine ecosystem: evolution and components. Mar Policy 19:21-38
13. Boltovskoy D, Gibbons MJ, Hutchings L, Biinet D (1990) General biological features of South Atlantic. In: Boltovskoy D (ed) Zooplankton. Backhyus Publishers, Leiden, p 1-42
14. Bouvier TC, del Giorgio PA (2002) Compositional changes in free-living bacterial communities along a salinity gradient in two temperate estuaries. Limnol Oceanogr 47: 453-470
15. Brown MV, Schwalbach MS, Hewson I, Fuhrman JA (2005) Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environ Microbiol 7:1466-1479
16. Calliari D, Brugnoli E, Ferrari G, Vizziano D (2009) Phytoplankton distribution and production along a wide environmental gradient in the South-West Atlantic off Uruguay. Hydrobiologia 620:47-61
17. Cardinale M, Brusetti L, Quatrini P, Borin S and others (2004) Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl Environ Microbiol 70:6147-6156
18. Carreto JI, Montoya NG, Benavides HR, Guerrero R, Carignan MO (2003) Characterization of spring phytoplankton communities in the Río de La Plata maritime front using pigment signatures and cell microscopy. Mar Biol 143: 1013-1027
19. Clarke KR, Gorley RN (2006) PRIMER v6: user manual/tutorial. PRIMER-E, Plymouth
20. Clarke KR, Somerfield PJ, Gorley RN (2008) Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage. J Exp Mar Biol Ecol 366:56-69
21. CottrellMT, Kirchman DL (2003) Contribution of major bacterial groups to bacterial biomass production (thymidine and leucine incorporation) in the Delaware estuary. Limnol Oceanogr 48:168-178
22. Crump BC, Armbrust 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
23. Crump BC, Hopkinson CS, Sogin ML, Hobbie JE (2004) Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Appl Environ Microbiol 70:1494-1505
24. Daims H, Bruhl A, Amann R, Schleifer KH, Wagner M (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22: 434-444
25. DeLong EF, Franks DG, Alldredge AL (1993) Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol Oceanogr 38:924-934
26. Eaton AD, Clesceri LS, Rice EW, Greenberg AE, Franson MAH (eds) (2005) Standard methods for the examination of water and wastewater: centennial edition. American Public Health Association, Washington, DC
27. Eilers H, Pernthaler J, Glöckner FO, Amann R (2000) Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl Environ Microbiol 66:3044-3051
28. Eilers H, Pernthaler J, Peplies J, Glöckner FO, Gerdts G, Amann R (2001) Isolation of novel pelagic bacteria from the German Bight and their seasonal contribution to surface picoplankton. Appl Environ Microbiol 67:5134-5142
29. Fandino LB, Riemann L, Steward GF, Azam F (2005) Population dynamics of Cytophaga-Flavobacteria during marine phytoplankton blooms analyzed by real-time quantitative PCR. Aquat Microb Ecol 40:251-257
30. 2 survey. Oceanography (Wash DC) 14:18-32
31. Framiñan MB, Brown OB (1996) Study of the Río de la Plata turbidity front, Part I: spatial and temporal distribution. Cont Shelf Res 16:1259-1282
32. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461-2470
33. Glöckner FO, Fuchs BM, Amann R (1999) Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65:3721-3726
34. Gomez-Pereira PR, Fuchs BM, Alonso C, Oliver M, van Beusekom J, Amann R (2010) Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean. ISME J 4:472-487
35. González JM, Simo R, Massana R, Covert JS, Casamayor EO, Pedros-Alio C, Moran MA (2000) Bacterial community structure associated with a dimethylsulfoniopropionateproducing North Atlantic algal bloom. Appl Environ Microbiol 66:4237-4246
36. Grossart HP, Levold F, Allgaier M, Simon M, Brinkhoff T (2005) Marine diatom species harbour distinct bacterial communities. Environ Microbiol 7:860-873
37. Guerrero RA, Acha EM, Framiñan MB, Lasta CA (1997) Physical oceanography of the Río de la Plata estuary, Argentina. Cont Shelf Res 17:727-742
38. Hahn MW, Pöckl M, Wu QL (2005) Low intraspecific diversity in a Polynucleobacter subcluster population numerically dominating bacterioplankton of a freshwater pond. Appl Environ Microbiol 71:4539-4547
39. Hewson I, Fuhrman JA (2004) Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Appl Environ Microbiol 70: 3425-3433
40. 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 21:103-114
41. Jeffrey SW, Humphrey GF (1975) New spectrophotometric equations for determining chlorophylls a, b, c1 and c2 in higher plants, algae and natural phytoplankton. Biochem Physiol Pflanz 167:191-194
42. Kirchman DL, Yu LY, Cottrell MT (2003) Diversity and abundance of uncultured Cytophaga-like bacteria in the Delaware Estuary. Appl Environ Microbiol 69:6587-6596
43. Kirchman DL, Dittel AI, Malmstrom RR, Cottrell MT (2005) Biogeography of major bacterial groups in the Delaware estuary. Limnol Oceanogr 50:1697-1706
44. Koroleff F (1976) Determination of ammonia. In: Grasshoft K (ed) Methods of seawater analysis. Verlag Chemie, New York, NY p 126-133
45. Legendre P, Gallagher ED (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129:271-280
46. Legendre P, Legendre L (1998) Numerical ecology, 2nd English edn. Elsevier Science, Amsterdam
47. Lorenzen CJ (1967) Determination of chlorophyll and pheopigments: spectrophotometric equations. Limnol Oceanogr 12:343-346
48. Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104:11436-11440
49. Ludwig W, Strunk O, Westram R, Richter L and others (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363-1371
50. Malmstrom RR, Straza TRA, Cottrell MT, Kirchman DL (2007) Diversity, abundance, and biomass production of bacterial groups in the western Arctic Ocean. Aquat Microb Ecol 47:45-55
51. Manz W, Amann R, Ludwig W, Wagner M, Schleifer KH (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst Appl Microbiol 15:593-600
52. Manz W, Amann R, Ludwig W, Vancanneyt M, Schleifer KH (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum Cytophaga-Flavobacter-Bacteroides in the natural environment. Microbiology 142:1097-1106
53. Martinez CM, Retta S (2001) Caracterizacion de las areas de cria de la corvina (Micropogonias furnieri) en la zona costera uruguaya. In: Vizziano D, Puig P, Mesones C, Nagy G (eds) El Rio de la Plata. Investigacion para la gestion del Ambiente, los recursos pesqueros y la pesqueria en el frente salino. Programa Ecoplata, Montevideo, p 141-148
54. Martiny JBH, Bohannan BJM, Brown JH, Colwell RK and others (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102-112
55. Moran MA, González JM, Kiene RP (2003) Linking a bacterial taxon to sulfur cycling in the sea: studies of the marine Roseobacter group. Geomicrobiol J 20:375-388
56. Morris RM, Rappe MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806-810
57. Murphy J, Riley JP (1962) A modified single solution method for the determination of phosphate in natural waters. Anal Chim Acta 27:31-36
58. Murray AE, Hollibaugh JT, Orrego C (1996) Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl Environ Microbiol 62:2676-2680
59. Muyzer G, Teske A, Wirsen CO, Jannasch HW (1995) Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164:165-172
60. Nagy G, Gómez M, López C, Perdomo A (2002) Distribution patterns of nutrients and symptoms of eutrophication in the Río de la Plata Estuary System. Hydrobiologia 475-476:125-139
61. Neef A (1997) Anwendung der in situ-Einzelzell-Identifizierung von Bakterien zur Populationsanalyse in komplexen mikrobiellen Biozönosen. PhD thesis, Technical University Munich
62. Neef A, Amann R, Schlesner H, Schleifer KH (1998) Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144:3257-3266
63. O'Sullivan LA, Fuller KE, Thomas EM, Turley CM, Fry JC, Weightman AJ (2004) Distribution and culturability of the uncultivated 'AGG58 cluster' of Bacteroidetes phylum in aquatic environments. FEMS Microbiol Ecol 47:359-370
64. Pernthaler A, Pernthaler J, Amann R (2002) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68:3094-3101
65. Piccini C, Conde D, Alonso C, Sommaruga R, Pernthaler J (2006) Blooms of single bacterial species in a coastal lagoon of the Southwestern Atlantic Ocean. Appl Environ Microbiol 72:6560-6568
66. Pinhassi J, Berman T (2003) Differential growth response of colony-forming alpha- and gamma-proteobacteria in dilution culture and nutrient addition experiments from Lake Kinneret (Israel), the eastern Mediterranean Sea, and the Gulf of Eilat. Appl Environ Microbiol 69:199-211
67. Pinhassi J, Sala MM, Havskum H, Peters F, Guadayol O, Malits A, Marrase CL (2004) Changes in bacterioplankton composition under different phytoplankton regimens. Appl Environ Microbiol 70:6753-6766
68. Pommier T, Canbäck B, Riemann L, Boström KH, Simu K, Lundberg P, Tunlid A, Hagström Å (2007) Global patterns of diversity and community structure in marine bacterioplankton. Mol Ecol 16:867-880
69. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188-7196
70. Ramette A (2007) Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 62:142-160
71. Ramette A (2009) Quantitative community fingerprinting methods for estimating the abundance of operational taxonomic units in natural microbial communities. Appl Environ Microbiol 75:2495-2505
72. Riemann L, Steward GF, Azam F (2000) Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl Environ Microbiol 66:578-587
73. Riemann L, Leitet C, Pommier T, Simu K, Holmfeldt K, Larsson U, Hagstrom A (2008) The native bacterioplankton community in the central Baltic Sea is influenced by freshwater bacterial species. Appl Environ Microbiol 74: 503-515
74. Roller C, Wagner M, Amann R, Ludwig W, Schleifer KH (1994) In situ probing of Gram-positive bacteria with high DNA G+C content using 23S rRNA-targeted oligonucleotides. Microbiology 140:2849-2858
75. Schattenhofer M, Fuchs BM, Amann R, Zubkov MV, Tarran GA, Pernthaler J (2009) Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean. Environ Microbiol 11:2078-2093
76. Selje N, Simon M (2003) Composition and dynamics of particle- associated and free-living bacterial communities in the Weser estuary, Germany. Aquat Microb Ecol 30: 221-237
77. Simek K, Pernthaler J, Weinbauer M, Hornak K and others (2001) Changes in bacterial community composition, dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir. Appl Environ Microbiol 67:2723-2733
78. Simon M, Glöckner FO, Amann R (1999) Different community structure and temperature optima of heterotrophic picoplankton in various regions of the Southern Ocean. Aquat Microb Ecol 18:275-284
79. Simonato F, Gómez-Pereira PR, Fuchs BM, Amann R (2010) Bacterioplankton diversity and community composition in the Southern Lagoon of Venice. Syst Appl Microbiol 33: 128-138