High phylogenetic diversity in a marine-snow-associated bacterial assemblage

Aquatic Microbial Ecology

Volumn 14, Issue 3, 1998, Pages 261-269

  Rath, Johannes ^a   Wu, Ke Ying ^b   Herndl, Gerhard J ^c   DeLong, Edward F ^d  

^a UNIVERSITY OF VIENNA   (Austria)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

^d MONTEREY BAY AQUARIUM RESEARCH INSTITUTE   (United States)

Author keywords

Adriatic sea; Bacteria; Diversity; Particles

Indexed keywords

BACTERIA (MICROORGANISMS); BACTEROIDES; CYTOPHAGA; EPSILONPROTEOBACTERIA; FLAVOBACTERIA; PLANCTOMYCES; POSIBACTERIA; PROTEOBACTERIA;

EID: 0542442094     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame014261     Document Type: Article

References (54)

1. Alldredge AL, Cohen Y (1987) Can microscale chemical patches persist in the sea? Microelectrode study of marine snow, fecal pellets. Science 235:689-691
2. Alldredge A, Silver M (1988) Characteristics, dynamics and significance of marine snow. Prog Oceanogr 20:41-82
3. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59(1):142-169
4. Bidle KD, Fletcher M (1995) Comparison of free-living and particle-associated bacterial communities in the Chesapeake Bay by stable low-molecular-weight RNA analysis. Appl Environ Microbiol 61(3):944-952
5. Bochdansky A, Herndl GJ (1992a) Ecology of amorphous aggregations (marine snow) in the Northern Adriatic Sea. III. Zooplankton interactions with marine snow. Mar Ecol Prog Ser 87:135-146
6. Bochdansky AB, Herndl GJ (1992b) Ecology of amorphous aggregations (marine snow) in the Northern Adriatic Sea. V. Role of fecal pellets in marine snow, Mar Ecol Prog Ser 89:297-303
7. Borneman J, Skroch PW, O'Sullivan KM, Palus JA, Rumjanek NG, Jansen JL, Nienhuis J, Triplett EW (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62:1935-1943
8. Caron DA, Davis PG, Madin LP, Sieburth JM (1986) Enrichment of microbial populations in macroaggregates (marine snow) from surface waters of the North Atlantic. J Mar Res 44:543-565
9. Cutter GA, Krahforst CF (1988) Sulfide in surface waters of the western Atlantic Ocean. Geophys Res Lett 15:1393-1396
10. Davis CL (1989) Uptake and incorporation of thymidine by bacterial isolates from an upwelling environment. Appl Environ Microbiol 55:1267-1272
11. Decho AW (1990) Microbial exopolymer secretions in ocean environments: their role(s) in food webs and marine processes. Oceanogr Mar Biol Annu Rev 28:73-153
12. Degobbis D, Fonad-Umani S, Franco P, Malej A, Precali R, Smodlaka N (1995) Changes in the nothern Adriatic ecosystem and the hypertrophic appearance of gelatinous aggregates. Sci Total Environ 165:43-58
13. DeLong EF (1992) Archea in coastal marine environments. Proc Natl Acad Sci 89:5685-5689
14. DeLong EF, Franks DG, Alldredge AL (1993) Phylogenetic diversity of aggregate-attached vs free-living marine bacterial assemblages, Limnol Oceanogr 38:924-934
15. DeLong EF, Wu KY, Prezelin BB, Jovine RVM (1994) High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695-697
16. DeSoete G (1983) A least squares algorithm for fitting additive trees to proximity data. Psychometrika 48:621-626
17. Devereux R, Mundfrom GW (1994) A phylogenetic tree of 16S rRNA sequences from sulfate reducing bacteria in a sandy marine sediment. Appl Environ Microbiol 60:3437-3439
18. Felsenstein J (1989) PHYLIP-phylogeny inference package. Cladistics 5:164-166
19. Fuhrman JA, McCallum KM, Davis AA (1993) Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Ocean. Appl Envrion Microbiol 59:1294-1302
20. Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356:148-149
21. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-65
22. Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40:237-264
23. Herndl GJ (1992) Marine snow in the Northern Adriatic Sea: possible causes and consequences for a shallow ecosystem. Mar Microb Food Webs 6:140-172
24. Herndl GJ, Bochdansky AB, Kaltenböck E, Müller-Niklas G (1993) Marine snow in the northern Adriatic Sea: major role of microbes in the metabolism of marine snow. Biologia Marina, suppl. 1:1-12
25. Höfle MG, Brettar I (1995) Taxonomic diversity and metabolic activity of microbial communities in the water column of the central Baltic Sea. Limnol Oceanogr 40:868-874
26. Kaltenböck E, Herndl GJ (1992) Ecology of amorphous aggregations (marine snow) in the Northern Adriatic Sea. IV. Dissolved nutrients and the autotrophic community associated with marine snow. Mar Ecol Prog Ser 87:147-159
27. Karl DM, Tilbrook BD (1994) Production and transport of methane in oceanic participate organic matter, Nature 368:732-734
28. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematic. Wiley, New York, p 115-175
29. Liesack W, Stackebrandt E (1992) Occurence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174:5072-5078
30. Liesack W, Weyland H, Stackebrandt E (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb Ecol 21:191-198
31. Maidak BL, Larsen NL, McCaughey MJ, Overbeek R, Olsen GJ, Fogel K, Blandy J, Woese CR (1994) The ribosomal database project. Nucleic Acids Res 22:3485-3487
32. Moyer CL, Dobbs FC, Karl DM (1994) Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl Environ Microbiol 69:871-879
33. Moyer CL, Tiedje JM, Dobbs FC, Karl DM (1996) A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl Environ Microbiol 62:2501-2507
34. Müller-Niklas G, Schuster S, Kaltenböck E, Herndl GJ (1994) Organic content and bacterial metabolism in amorphous aggregations of the northern Adriatic Sea, Limnol Oceanogr 39:58-68
35. Mullins TD, Britschgi TB, Krest RL, Giovannoni SJ (1995) Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol Oceanogr 40:148-158
36. Novitsky JA (1990) Evidence for sedimenting particles as the origin of the microbial community in a coastal marine sediment. Mar Ecol Prog Ser 60:161-167
37. Paerl HW (1984) Alteration of microbial metabolic activities in association with detritus. Bull Mar Sci 35:393-408
38. Paerl HW, Pruffert LE (1987) Oxygen-poor microzones as potential sites of microbial nitrogen fixation in nitrogen-depleted aerobic marine waters. Appl Environ Microbiol 53:1078-1087
39. Painting SJ, Lucas MI, Muir DG (1989) Fluctuations in heterotrophic bacterial community structure, activity and production in response to development and decay of phytoplankton in a microcosm. Mar Ecol Prog Ser 53:129-141
40. Rath J, Herndl GJ (1994) Characteristics and diversity of β-D-glucosidase (EC 3,2,1,21) activity in marine snow. Appl Envrion Microbiol 60:807-813
41. Reysenbach AL, Giver LJ, Wickham SG, Pace NR (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58:3417-3418
42. Robinson-Cox JF, Bateson MM, Ward DM (1995) Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Appl Environ Microbiol 61:1240-1245
43. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning - a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York
44. Schmidt TM, DeLong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173(14):4371-4378
45. Shanks AL, Reeder ML (1993) Reducing microzones and sulfide production in marine snow. Mar Ecol Prog Ser 96:43-47
46. Sieburth JM (1991) Methane and hydrogen sulfide in the pycnocline: a result of tight coupling of photosynthetic and 'benthic' processes in stratified waters, In: Rogers JE, Whitman WB (eds) Microbial production and consumption of greenhouse gases: methane, nitrogen oxides, and halomethanes. American Society for Microbiology, Washington, DC, p 147-174
47. Smith MT, Overbeek R, Woese CR, Gilbert W, Gillevet PM (1994) The genetic data envrionment and expandable GUI for multiple sequence analysis. CABIOS 10:671-675
48. Stein J, Marsh TL, Wu KY, Shizuya H, DeLong EF (1996) Characterization of uncultivated marine prokaryotes: isolation and analysis of rRNA and protein encoding genes from a planktonic marine Crenarchaeote. J Bacteriol 178:591-599
49. Suzuki M, Giovannoni SJ (1996) Mechanisms of bias in the amplification of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625-630
50. Torsvik V, Salte K, Sorheim R, Goksoyr J (1990) Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl Environ Microbiol. 56:776-781
51. Urbach E, Robertson DL, Chisholm SW (1992) Multiple evolutionary origins of prochlorophytes within the cyanobacterial radiation. Nature 355:267-270
52. Wang GCY, Wang Y (1996) The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA from different bacterial species. Microbiology 142:1107-1114
53. Weiss P, Schweitzer B, Amann R, Simon M (1996) identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow). Appl Environ Microbiol 62:1998-2005
54. Winding A (1992) (3H) Thymidine incorporation to estimate growth rates of anaerobic bacterial strains, Appl Environ Microbiol 58:2660-2662