Microbial community response during the iron fertilization experiment LOHAFEX

Applied and Environmental Microbiology

Volumn 78, Issue 24, 2012, Pages 8803-8812

  Thiele, Stefan ^a   Fuchs, Bernhard M ^a   Ramaiah, Nagappa ^b   Amanna, Rudolf ^a,b  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b NATIONAL INSTITUTE OF OCEANOGRAPHY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; ALGAL BLOOMS; ARCHAEA; ARCHAEAL; ATLANTIC OCEAN; CELL NUMBER; FLUORESCENCE IN SITU HYBRIDIZATION; GAMMAPROTEOBACTERIA; GRAZING PRESSURE; IRON FERTILIZATION; MICROBIAL COMMUNITIES; MICROBIAL PRODUCTION; PHYTOPLANKTON BLOOM; PYROSEQUENCING; ROSEOBACTERS; SEQUENCE NUMBER; WATERBODIES;

AMINO ACIDS; CHLOROPHYLL; FLUORESCENCE MICROSCOPY; IRON; MICROORGANISMS; PHYTOPLANKTON; RNA;

EXPERIMENTS;

ARCHAEAL DNA; ARCHAEAL RNA; BACTERIAL DNA; BACTERIAL RNA; FERTILIZER; IRON; RIBOSOME DNA; RNA 16S; SEA WATER;

ALGAL BLOOM; CATALYSIS; FERTILIZATION (REPRODUCTION); GRAZING PRESSURE; IRON; MICROBIAL COMMUNITY; PHYTOPLANKTON;

ARCHAEON; ARTICLE; ATLANTIC OCEAN; BACTERIUM; BIOTA; CHEMISTRY; CLASSIFICATION; GENETICS; IN SITU HYBRIDIZATION; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; RNA GENE;

ARCHAEA; ATLANTIC OCEAN; BACTERIA; BIOTA; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; FERTILIZERS; GENES, RRNA; IN SITU HYBRIDIZATION; IRON; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEAWATER;

ATLANTIC OCEAN; ATLANTIC OCEAN (SOUTH);

ALGAE; ARCHAEA; BACTERIA (MICROORGANISMS); GAMMAPROTEOBACTERIA; PHAEOCYSTIS; ROSEOBACTER;

EID: 84871017138     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01814-12     Document Type: Article

References (68)

1. Alderkamp AC, Sintes E, Herndl GJ. 2006. Abundance and activity of major groups of prokaryotic plankton in the coastal North Sea during spring and summer. Aquat. Microb. Ecol. 45:237-246.
2. Amann RI, et al. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
3. Arrieta JM, Weinbauer MG, Lute C, Herndl GJ. 2004. Response of bacterioplankton to iron fertilization in the southern ocean. Limnol. Oceanogr. 49:799-808.
4. Buchan A, Gonzalez JM, Moran MA. 2005. Overview of the marine Roseobacter lineage. Appl. Environ. Microbiol. 71:5665-5677.
5. Coale KH, et al. 2004. Southern Ocean iron enrichment experiment: carbon cycling in high-and low-Si waters. Science 304:408-414.
6. Cochlan WP. 2001. The heterotrophic bacterial response during a mesoscale iron enrichment experiment (IronEx II) in the eastern equatorial Pacific Ocean. Limnol. Oceanogr. 46:428-435.
7. Cottrell MT, Kirchman D. 2000. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low-and high-molecular-weight dissolved organic matter. Appl. Environ. Microbiol. 66:1692-1697.
8. 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.
9. Debaar HJW, Dejong JTM. 2001. Distributions, sources and sinks of iron in seawater, p 123-253. In Turner D, Hunter KA (ed), The biogeochemistry of iron in seawater. Wiley, New York, NY.
10. Ducklow HW, Steinberg DK, Buessler KO. 2001. Upper ocean carbon export and the biological pump. Oceanography 14:50-58.
11. Dupont CL, et al. 2011. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J. 6:1186-1199.
12. Eilers H, et al. 2001. Isolation of novel pelagic bacteria from the German Bight and their seasonal contributions to surface picoplankton. Appl. Environ. Microbiol. 67:5134-5142.
13. Fenchel T. 1986. The ecology of heterotrophic microflagellates. Adv. Microb. Ecol. 9:57-97.
14. Frette L, Winding A, Kroer N. 2010. Genetic and metabolic diversity of Arctic bacterioplankton during the post-spring phytoplankton bloom in Disko Bay, western Greenland. Aquat. Microb. Ecol. 60:29-41.
15. Frias-Lopez J, Thompson A, Waldbauer J, Chisholm SW. 2009. Use of stable isotope-labeled cells to identify active grazers of picocyanobacteria in ocean surface waters. Environ. Microbiol. 11:512-525.
16. Fuchs BM, Glöckner FO, Wulf J, Amann R. 2000. Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 66:3603-3607.
17. Fuhrman JA, Azam F. 1980. Bacterioplankton secondary production estimates for coastal waters of British Columbia, Antarctica, and California. Appl. Environ. Microbiol. 39:1085-1095.
18. Giovannoni SJ, et al. 2005. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1242-1245.
19. Gomez-Pereira PR, et al. 2010. Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean. ISME J. 4:472-487.
20. Gómez-Pereira PR, et al. 2012. Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean. Environ. Microbiol. 14:52-66.
21. Hall JA, Safi K. 2001. The impact of in situ Fe fertilisation on the microbial food web in the Southern Ocean. Deep Sea Res. Part II Top. Stud. Oceanogr. 48:2591-2613.
22. Herlemann DP, et al. 2011. Transitions in bacterial communities along the 2000-km salinity gradient of the Baltic Sea. ISME J. 5:1571-1579.
23. Kirchman D, K'nees 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.
24. Kirchman DL, Hoch MP. 1988. Bacterial production in the Delaware Bay estuary estimated from thymidine and leucine incorporation rates. Mar. Ecol. Prog. Ser. 45:169-178.
25. Kirchman DL, Yu L, Cottrell MT. 2003. Diversity and abundance of uncultured Cytophaga-like bacteria in the Delaware Estuary. Appl. Environ. Microbiol. 69:6587-6596.
26. Labrenz M, et al. 1998. Antarctobacter heliothermus gen. nov., sp. nov., a budding bacterium from hypersaline and heliothermal Ekho Lake. Int. J. Syst. Evol. Microbiol. 48:1363-1372.
27. Lamy D, et al. 2009. Temporal changes of major bacterial groups and bacterial heterotrophic activity during a Phaeocystis globosa bloom in the eastern English Channel. Aquat. Microb. Ecol. 58:95-107.
28. Lochte K, Bjørnsen PK, Giesenhagen H, Weber A. 1997. Bacterial standing stock and production and their relation to phytoplankton in the Southern Ocean. Deep Sea Res. Part II Top. Stud. Oceanogr. 44:321-340.
29. Ludwig W, et al. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
30. Makarenkov V, Legendre P. 2002. Nonlinear redundancy analysis and canonical correspondence analysis based on polynomial regression. Ecology 83:1146-1161.
31. Malmstrom RR, Cottrell MT, Elifantz H, Kirchman DL. 2005. Biomass production and assimilation of dissolved organic matter by SAR11 bacteria in the Northwest Atlantic Ocean. Appl. Environ. Microbiol. 71:2979-2986.
32. Malmstrom RR, Kiene RP, Cottrell MT, Kirchman DL. 2004. Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate and amino acid uptake in the North Atlantic Ocean. Appl. Environ. Microbiol. 70:4129-4135.
33. 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.
34. Manz W, Amann R, Ludwig W, Vancanneyt M, Schleifer K-H. 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.
35. Manz W, Amann R, Ludwig W, Wagner M, Schleifer K-H. 1992. Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst. Appl. Microbiol. 15:593-600.
36. Martin JH. 1990. Glacial-interglacial CO2 change: the iron hypothesis. Paleoceanography 5:1-13.
37. Martin JH, et al. 1994. Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean. Nature 371:123-129.
38. Mary I, et al. 2006. Seasonal dynamics of bacterioplankton community structure at a coastal station in the western English Channel. Aquat. Microb. Ecol. 42:119-126.
39. Massana R, Murray AE, Preston CM, DeLong EF. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 63:50-56.
40. Morris RM, et al. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806-810.
41. Neef A. 1997. Anwendung der in situ-Einzelzell-Identifizierung von Bakterien zur Populationsanalyse in komplexen mikrobiellen Biozönosen. Technische Universität München, Lehrstuhl für Mikrobiologie, Munich, Germany.
42. Obernosterer I, et al. 2008. Rapid bacterial mineralization of organic carbon produced during a phytoplankton bloom induced by natural iron fertilization in the Southern Ocean. Deep Sea Res. Part II Top. Stud. Oceanogr. 55:777-789.
43. Oliver JL, Barber RT, Smith WO, Ducklow HW. 2004. The heterotrophic bacterial response during the Southern Ocean Iron Experiment (SOFeX). Limnol. Oceangr. 49:2129-2140.
44. 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.
45. Pernthaler J. 2005. Predation on prokaryotes in the water column and its ecological implications. Nat. Rev. Microbiol. 3:537-546.
46. Pernthaler J, Amann R. 2005. Fate of heterotrophic microbes in pelagic habitats: focus on populations. Microbiol. Mol. Biol. Rev. 69:440-461.
47. Pernthaler J, Pernthaler A, Amann R. 2003. Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization. Appl. Environ. Microbiol. 69:2631-2637.
48. Pinhassi J, et al. 1999. Coupling between bacterioplankton species composition, population dynamics, and organic matter degradation. Aquat. Microb. Ecol. 17:13-26.
49. Pinhassi J, et al. 2004. Changes in bacterioplankton composition under different phytoplankton regimens. Appl. Environ. Microbiol. 70:6753-6766.
50. Pruesse E, et al. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35:7188-7196.
51. Puddu A, et al. 2003. Bacterial uptake of DOM released from P-limited phytoplankton. FEMS Microbiol. Ecol. 46:257-268.
52. Rappe MS, Connon SA, Vergin KL, Giovannoni SJ. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630-633.
53. Rooney-Varga JN, et al. 2005. Links between phytoplankton and bacterial community dynamics in a coastal marine environment. Microb. Ecol. 49:163-175.
54. Schattenhofer M, et al. 2011. Phylogenetic characterisation of picoplanktonic populations with high and low nucleic acid content in the North Atlantic Ocean. Syst. Appl. Microbiol. 34:470-475.
55. Simon M, Glöckner F, 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.
56. Smetacek V, et al. 2012. Deep carbon export from a Southern Ocean iron-fertilized diatom bloom. Nature 487:313-319.
57. Teeling H, et al. 2012. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336: 608-611.
58. Thiele S, Fuchs BM, Amann RI. 2011. Identification of microorganisms using the ribosomalRNAapproach and fluorescence in situ hybridization, p 171-189. In Wilderer P (ed), Treatise on water science. Elsevier, Oxford, United Kingdom.
59. Thingstad TF. 2000. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol. Oceangr. 45:1320-1328.
60. Tortell PD, Maldonado MT, Price NM. 1996. The role of heterotrophic bacteria in iron-limited ocean ecosystems. Nature 383:330-332.
61. Wallner G, Amann R, Beisker W. 1993. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14:136-143.
62. West NJ, Obernosterer I, Zemb O, Lebaron P. 2008. Major differences of bacterial diversity and activity inside and outside of a natural ironfertilized phytoplankton bloom in the Southern Ocean. Environ. Microbiol. 10:738-756.
63. Wiltshire KH, Manly BFJ. 2004. The warming trend at Helgoland Roads, North Sea: phytoplankton response. Helgol. Mar. Res. 58:269-273.
64. Zhou J, Bruns M, Tiedje J. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.
65. Zhou J, et al. 2011. Reproducibility and quantitation of amplicon sequencing-based detection. ISME J. 5:1303-1313.
66. Zubkov MV, et al. 2001. Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphoniopropionate in an algal bloom in the North Sea. Environ. Microbiol. 3:304-311.
67. Zubkov MV, Fuchs BM, Burkill PH, Amann R. 2001. Comparison of cellular and biomass specific activities of dominant bacterioplankton groups in stratified waters of the Celtic Sea. Appl. Environ. Microbiol. 67:5210-5218.
68. Zubkov MV, Burkill PH, Topping JN. 2007. Flow cytometric enumeration of DNA-stained oceanic planktonic protists. J. Plankton Res. 29:79-86.