Characterization of bacterial epibionts on the cyanobacterium Trichodesmium

Aquatic Microbial Ecology

Volumn 67, Issue 1, 2012, Pages 1-14

  Hmelo, L R ^a,b   Van Mooy, B A S ^a   Mincer, T J ^a  

^a WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Cultivation independent; Cyanobacteria; Epibiont; Pelagic microbial community; Trichodesmium

Indexed keywords

ALPHAPROTEOBACTERIA; ARCHAEA; BACTERIA (MICROORGANISMS); CYANOBACTERIA; FLAVOBACTERIA; NEPTUNIA; SPHINGOBACTERIA; TRICHODESMIUM; TRICHODESMIUM THIEBAUTII;

EID: 84866042992     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame01571     Document Type: Article

References (68)

1. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman J (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389-3402 (Pubitemid 27359211)
2. Behrens S, Losekann T, Pett-Ridge J, Weber PK and others (2008) Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS. Appl Environ Microbiol 74:3143-3150 (Pubitemid 351747021)
3. Berman-Frank I, Rosenberg G, Levitan O, Haramaty L, Mari X (2007) Coupling between autocatalytic cell death and transparent exopolymeric particle production in the marine cyanobacterium Trichodesmium. Environ Microbiol 9:1415-1422 (Pubitemid 46763520)
4. Buchan A, Gonzalez JM, Moran MA (2005) Overview of the marine Roseobacter lineage. Appl Environ Microbiol 71:5665-5677 (Pubitemid 41456854)
5. Burke C, Thomas T, Lewis M, Steinberg P, Kjelleberg S (2011) Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis. ISME J 5:590-600
6. Capone DG, Zehr JP, Paerl HW, Bergman B, Carpenter EJ (1997) Trichodesmium, a globally significant marine cyanobacterium. Science 276:1221-1229
7. Carlson CA, Morris R, Parsons R, Treusch AH, Giovannoni SJ, Vergin K (2009) Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea. ISME J 3:283-295
8. Carpenter EJ, Harvey HR, Fry B, Capone DG (1997) Biogeochemical tracers of the marine cyanobacterium Trichodesmium. Deep-Sea Res I 44:27-38
9. Carpenter EJ, Subramaniam A, Capone DG (2004) Biomass and primary productivity of the cyanobacterium Tricho - desmium spp. in the tropical N Atlantic ocean. Deep-Sea Res I 51:173-203 (Pubitemid 38106236)
10. Chao A (1987) Estimating the population size for capturerecapture data with unequal catchability. Biometrics 43:783-791
11. Chao A, Yang M C K (1993) Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika 80:193-201
12. Chisholm S, Olson R, Zettler E, Goericke R (1988) A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334:340-343 (Pubitemid 19317137)
13. Cole JR, Chai B, Marsh TL, Farris RJ and others (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442-443 (Pubitemid 36150424)
14. Dang H, Lovell CR (2000) Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl Environ Microbiol 66:467-475 (Pubitemid 30082728)
15. Dang H, Li T, Chen M, Huang G (2008) Cross-ocean distribution of Rhodobacterales bacteria as primary surface colonizers in temperate coastal marine waters. Appl Environ Microbiol 74:52-60
16. 2-fixing colonial cyanobacterium Tricho - desmium. Science 312:1517-1520 (Pubitemid 43865889)
17. De Long EF, Preston CM, Mincer T, Rich V and others (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311:496-503 (Pubitemid 43157723)
18. Dyhrman ST, Webb EA, Anderson DM, Moffett JW, Waterbury JB (2002) Cell-specific detection of phosphorus stress in Trichodesmium from the western North Atlantic. Limnol Oceanogr 47:1832-1836 (Pubitemid 36016839)
19. Fisher MM, Wilcox LW, Graham LE (1998) Molecular characterization of epiphytic bacterial communities on charophycean green algae. Appl Environ Microbiol 64:4384-4389 (Pubitemid 28538006)
20. Frigaard NU, Martinez A, Mincer TJ, De Long EF (2006) Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439:847-850 (Pubitemid 43255702)
21. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63
22. Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40:237-264
23. Gram L, Grossart HP, Schlingloff A, Kiorboe T (2002) Possible quorum sensing in marine snow bacteria: production of acylated homoserine lactones by Roseobacter strains isolated from marine snow. Appl Environ Microbiol 68:4111-4116 (Pubitemid 34836727)
24. Herbst V, Overbeck J (1978) Metabolic coupling between the alga Oscillatoria redekei and accompanying bacteria. Naturwissenschaften 65:598-599 (Pubitemid 9072863)
25. Hewson I, Govil SR, Capone DG, Carpenter EJ, Fuhrman JA (2004) Evidence of Trichodesmium viral lysis and potential significance for biogeochemical cycling in the oligotrophic ocean. Aquat Microb Ecol 36:1-8 (Pubitemid 39104231)
26. Hewson I, Poretsky RS, Dyhrman ST, Zielinski B and others (2009) Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean. ISME J 3:1286-1300
27. Hmelo L (2010). Microbial interactions associated with biofilms attached to Trichodesmium spp. and detrital particles in the ocean. PhD thesis, Massachusetts Institute of Technology, Woods Hole, MA
28. Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317-2319 (Pubitemid 39341624)
29. 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
30. Karl D, Letelier R, Tupas L, Dore J, Christian J, Hebel D (1997) The role of nitrogen fixation in biogeochemical cycling in the subtropical North Pacific Ocean. Nature 388:533-538 (Pubitemid 27339995)
31. Karner MB, De Long EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507-510 (Pubitemid 32144354)
32. Letelier R, Karl D (1996) Role of Trichodesmium spp. in the productivity of the subtropical North Pacific Ocean. Mar. Ecol Prog Ser 133:263-273
33. Letelier RM, Karl DM (1998) Trichodesmium spp. physiology and nutrient fluxes in the North Pacific subtropical gyre. Aquat Microb Ecol 15:265-276 (Pubitemid 128485357)
34. Ludwig W, Strunk O, Westram R, Richter L and others (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363-1371 (Pubitemid 38854737)
35. Mayali X, Franks P J S, Azam F (2008) Cultivation and ecosystem role of a marine Roseobacter clade-affiliated cluster bacterium. Appl Environ Microbiol 74:2595-2603 (Pubitemid 351632589)
36. Mincer TJ, Church MJ, Taylor LT, Preston C, Karl DM, De Long EF (2007) Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ Microbiol 9:1162-1175 (Pubitemid 46697272)
37. Mohamed NM, Enticknap JJ, Lohr JE, McIntosh SM, Hill RT (2008) Changes in bacterial communities of the marine sponge Mycale laxissima on transfer into aquaculture. Appl Environ Microbiol 74:1209-1222 (Pubitemid 351287093)
38. Morris R, Vergin K, Cho J, Rappé M (2005) Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic Time-series study site. Limnol Oceanogr 50:1687-1696 (Pubitemid 41356448)
39. Nausch M (1996) Microbial activities on Trichodesmium colonies. Mar. Ecol Prog Ser 141:173-181
40. Nicol GW, Schleper C (2006) Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? Trends Microbiol 14:207-212
41. Paerl HW (1982). Interactions with bacteria. In: Carr NG, Whitton BA (eds) The biology of cyanobacteria. University of California Press, Los Angeles, CA, p 441-461
42. 2 fixation. Science 241:442-445 (Pubitemid 19319275)
43. Paerl HW, Gallucci KK (1985) Role of chemotaxis in establishing a specific nitrogen-fixing cyanobacterial-bacterial association. Science 227:647-649 (Pubitemid 15157487)
44. Paerl HW, Bebout BM, Prufert LE (1989) Bacterial associations with marine Oscillatoria sp. (Trichodesmium sp.) populations: ecophysiological implications. J Phycol 25:773-784
45. Pedrós-Alió C (2006) Marine microbial diversity: Can it be determined? Trends Microbiol 14:257-263 (Pubitemid 43825732)
46. Pielou EC (1966) The measurement of diversity in different types of biological collections. J Theor Biol 13:131-144
47. Polz MF, Hunt DE, Preheim SP, Weinreich DM (2006) Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos Trans R Soc Lond B 361:2009-2021 (Pubitemid 44787035)
48. Pommier T, Canback B, Riemann L, Bostrom K and others (2007) Global patterns of diversity and community structure in marine bacterioplankton. Mol Ecol 16:867-880 (Pubitemid 46233106)
49. Roe KL, Barbeau K, Mann EL, Haygood MG (2012) Acquisition of iron by Trichodesmium and associated bacteria in culture. Environ Microbiol 14:1681-1695
50. Sale P (1976) Reef fish lottery. Nat Hist 85:60-65
51. Sapp M, Schwaderer AS, Wiltshire KH, Hoppe HG, Gerdts G, Wichels A (2007) Species-specific bacterial communities in the phycosphere of microalgae? Microb Ecol 53:683-699 (Pubitemid 46763853)
52. Sheridan C, Steinberg D, Kling G (2002) The microbial and metazoan community associated with colonies of Trichodesmium spp.: a quantitative survey. J Plankton Res 24:913-922
53. Siddiqui P, Bergman B, Carpenter E (1992) Filamentous cyanobacterial associates of the marine planktonic cyanobacterium Trichodesmium. Phycologia 31:326-337
54. Simmons TL, Coates RC, Clark BR, Engene N and others (2008) Biosynthetic origin of natural products isolated from marine microorganism-invertebrate assemblages. Proc Natl Acad Sci USA 105:4587-4594 (Pubitemid 351753783)
55. Sohm JA, Webb EA, Capone DG (2011) Emerging patterns of marine nitrogen fixation. Nat Rev Microbiol 9:499-508
56. Stein JL, Marsh TL, Wu KY, Shizuya H, De Long EF (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178:591-599 (Pubitemid 26036628)
57. Stevenson BS, Waterbury JB (2006) Isolation and identification of an epibiotic bacterium associated with heterocystous Anabaena cells. Biol Bull 210:73-77
58. Stihl A, Sommer U, Post AF (2001) Alkaline phosphatase activities among populations of the colony-forming diazo - trophic cyanobacterium Trichodesmium spp. (Cyano - bacteria) in the Red Sea. J Phycol 37:310-317 (Pubitemid 32391880)
59. Sunagawa S, De Santis TZ, Piceno YM, Brodie EL and others (2009) Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J 3:512-521
60. 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 (Pubitemid 26047427)
61. Thompson JR, Marcelino LA, Polz MF (2002) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res 30:2083-2088 (Pubitemid 34537607)
62. Treusch AH, Vergin KL, Finlay LA, Donatz MG and others (2009) Seasonality and vertical structure of microbial communities in an ocean gyre. ISME J 3:1148-1163
63. Tuomainen J, Hietanen S, Kuparinen J, Martikainen PJ, Servomaa K (2006) Community structure of the bacteria associated with Nodularia sp. (Cyanobacteria) aggregates in the Baltic Sea. Microb Ecol 52:513-522 (Pubitemid 44899544)
64. Villareal TA, Carpenter EJ (1990) Diel buoyancy regulation in the marine diazotrophic cyanobacterium Trichodes - mium thiebautii. Limnol Oceanogr 35:1832-1837
65. Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T and others (2009) The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J 4:61-77
66. Ward BB (1985) Light and substrate concentration relationships with marine ammonium assimilation and oxidation rates. Mar. Chem 16:301-316
67. Waterbury JB (1991). The cyanobacteria: isolation, purifi - cation, and identification. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes, 2nd edn. Springer-Verlag, New York, NY, p 2058-2078
68. Yu Y, Breitbart M, McNairnie P, Rohwer F (2006) Fast-GroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics 7:57 doi:10.1186/1471-2105-7-57