Changes in bacterial activity and community structure in response to dissolved organic matter in the Hudson River, New York

Aquatic Microbial Ecology

Volumn 35, Issue 3, 2004, Pages 243-257

  Kirchman, David L ^a   Dittel, Ana I ^a   Findlay, Stuart E G ^b   Fischer, David ^b  

^a UNIVERSITY OF DELAWARE   (United States)

^b CARY INSTITUTE OF ECOSYSTEM STUDIES   (United States)

Author keywords

Bacteria; Bacterial production; Community structure; Dissolved organic carbon; Extracellular enzymes; Fluorescence in situ hybridization; Hudson River

Indexed keywords

BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; CYTOPHAGA; GAMMAPROTEOBACTERIA; PROTEOBACTERIA;

EID: 4143075890     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame035243     Document Type: Article

References (62)

1. Amann RI, Krumholz L, Stahl DA (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172:762-770
2. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
3. Amon RMW, Benner R (1994) Rapid cycling of high-molecular-weight dissolved organic matter in the ocean. Nature 369:549-552
4. Amon R, Benner R (1996) Bacterial utilization of different size classes of dissolved organic matter. Limnol Oceanogr 41: 41-51
5. Arnosti C (2003) Microbial extracellular enzymes and their role in dissolved organic matter cycling. In: Findlay SEG, Sinsabaugh RL (eds) Aquatic ecosystems: interactivity of dissolved organic matter. Academic Press, San Diego, p 315-342
6. Beardsley C, Pernthaler J, Wosniok W, Amann R (2003) Are readily culturable bacteria in coastal North Sea waters suppressed by selective grazing mortality? Appl Environ Microbiol 69:2624-2630
7. Benner R (2002) Chemical composition and reactivity. In: Hansell DA, Carlson CA (eds) Biogeochemistry of marine dissolved organic matter. Academic Press, New York, p 59-90
8. Benner R (2003) Molecular indicators of bioavailability of dissolved organic matter. In: Findlay SEG, Sinsabaugh RL (eds) Aquatic ecosystems: interactivity of dissolved organic matter. Academic Press, San Diego, p 121-137
9. Cole JJ, Carpenter SR, Kitchell JF, Pace ML (2002) Pathways of organic carbon utilization in small lakes: results from a whole-lake C-13 addition and coupled model. Limnol Oceanogr 47:1664-1675
10. Cotner JB, Ammerman JW, Peele ER, Bentzen E (1997) Phosphorus-limited bacterioplankton growth in the Sargasso Sea. Aquat Microb Ecol 13:141-149
11. Cotner JB, Johengen TH, Biddanda BA (2000) Intense winter heterotrophic production stimulated by benthic resuspension. Limnol Oceanogr 45:1672-1676
12. Cottrell MT, Kirchman DL (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
13. Cottrell MT, 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
14. Cottrell MT, Kirchman DL (2004) Phylogenetic composition and size structure of thymidine and leucine-active heterotrophic bacteria in the Delaware estuary. Aquat Microb Ecol 34:139-149
15. Covert JS, Moran MA (2001) Molecular characterization of estuarine bacterial communities that use high- and low-molecular weight fractions of dissolved organic carbon. Aquat Microb Ecol 25:127-139
16. Davey KE, Kirby RR, Turley CM, Weightman AJ, Fry JC (2001) Depth variation of bacterial extracellular enzyme activity and population diversity in the northeastern North Atlantic Ocean. Deep-Sea Res II 48:1003-1017
17. del Giorgio PA, Bouvier TC (2002) Linking the physiologic and phylogenetic successions in free-living bacterial communities along an estuarine salinity gradient. Limnol Oceanogr 47:471-486
18. del Giorgio PA, Davis J (2003) Patterns in dissolved organic matter lability and consumption across aquatic ecosystems. In: Findlay SEG, Sinsabaugh RL (eds) Aquatic ecosystems: interactivity of dissolved organic matter. Academic Press, San Diego, p 399-424
19. DeLong EF, Franks DG, Alldredge AL (1993) Phylogenetic diversity of aggregate-attached versus free-living marine bacterial assemblages. Limnol Oceanogr 38:924-934
20. Eilers H, Pernthaler J, Amann R (2000a) Succession of pelagic marine bacteria during enrichment: a close look at cultivation-induced shifts. Appl Environ Microbiol 66:4634-4640
21. Eilers H, Pernthaler J, Glöckner FO, Amann R (2000b) Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl Environ Microbiol 66:3044-3051
22. 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 contributions to surface picoplankton. Appl Environ Microbiol 67:5134-5142
23. Fandino LB, Riemann L, Steward GF, Long RA, Azam F (2001) Variations in bacterial community structure during a dinoflagellate bloom analyzed by DGGE and 16S rDNA sequencing. Aquat Microb Ecol 23:119-130
24. Findlay SEG (2003) Bacterial response to variation in dissolved organic matter. In: Findlay SEG, Sinsabaugh RL (eds) Aquatic ecosystems: interactivity of dissolved organic matter. Academic Press, San Diego, p 363-379
25. Findlay S, Pace ML, Lints D, Cole JJ, Caraco NF, Peierls B (1991) Weak coupling of bacterial and algal production in a heterotrophic ecosystem - the Hudson River Estuary. Limnol Oceanogr 36:268-278
26. Findlay S, Pace M, Fischer D (1996) Spatial and temporal variability in the lower food web of the tidal freshwater Hudson River. Estuaries 19:866-873
27. Findlay S, Sinsabaugh RL, Fischer DT, Franchini P (1998) Sources of dissolved organic carbon supporting planktonic bacterial production in the tidal freshwater Hudson River. Ecosystems 1:227-239
28. Findlay SEG, Sinsabaugh RL, Sobczak WV, Hoostal M (2003) Metabolic and structural response of hyporheic microbial communities to variations in supply of dissolved organic matter. Limnol Oceanogr 48:1608-1617
29. Fuhrman JA (2000) Impact of viruses on bacterial processes. In: Kirchman DL (ed) Microbial ecology of the oceans. Wiley-Liss, New York, p 327-350
30. Gasol JM, Comerma M, Garcia JC, Armengol J, Casamayor EO, Kojecka P, Šimek K (2002) A transplant experiment to identify the factors controlling bacterial abundance, activity, production, and community composition in a eutrophic canyon-shaped reservoir. Limnol Oceanogr 47:62-77
31. Giovannoni SJ, Rappé MS (2000) Evolution, diversity and molecular ecology of marine prokaryotes. In: Kirchman DL (ed) Microbial ecology of the ocean. Wiley Interscience, New York, p 47-84
32. 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
33. Glöckner FO, Zaichikov E, Belkova N, Denissova L, Pernthaler J, Pernthaler A, Amann R (2000) Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl Environ Microbiol 66: 5053-5065
34. Horner-Devine MC, Leibold MA, Smith VH, Bohannan BJM (2003) Bacterial diversity patterns along a gradient of primary production. Ecol Lett 6:613-622
35. Karner M, Fuhrman JA (1997) Determination of active marine bacterioplankton: a comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining. Appl Environ Microbiol 63:1208-1213
36. Karner MB, DeLong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507-510
37. Kirchman DL (2001) Measuring bacterial biomass production and growth rates from leucine incorporation in natural aquatic environments. In: Paul JH (ed) Marine microbiology, Vol. 30. Academic Press, San Diego
38. Kirchman DL (2002) The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microb Ecol 39:91-100
39. Malmstrom RR, Kiene RP, Kirchman DL (2004) Identification and enumeration of bacteria assimilating dimethylsulfoniopropionate (DMSP) in the North Atlantic and Gulf of Mexico. Limnol Oceanogr 49:597-606
40. 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
41. 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
42. Martinez J, Smith DC, Steward GF, Azam F (1996) Variability in ectohydrolytic enzyme activities of pelagic marine bacteria and its significance for substrate processing in the sea. Aquat Microb Ecol 10:223-230
43. McKnight DM, Boyer EW, Westerhoff PK, Doran PT, Kulbe T, Andersen DT (2001) Spectrofluorometric characterization of aquatic fulvic acid for determination of precursor organic material and general structural properties. Limnol Oceanogr 46:38-48
44. Morris RM, Rappé MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806-810
45. Mulholland PJ, Fellows CS, Tank JL, Grimm NB and 9 others (2001) Inter-biome comparison of factors controllling stream metabolism. Freshw Biol 46:1503-1517
46. Muylaert K, Van der Gucht K, Vloemans N, De Meester L, Gillis M, Vyverman W (2002) Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes. Appl Environ Microbiol 68:4740-4750
47. Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhock 73:127-141
48. Pakulski JD, Coffin RB, Kelley CA, Holder SL, Downer R, Aas P, Lyons MM, Jeffrey WH (1996) Iron stimulation of Antarctic bacteria. Nature 383:133-134
49. Pernthaler J, Posch T, Simek K, Vrba J and 5 others (2001) Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture. Appl Environ Microbiol 67:2145-2155
50. Pomeroy LR, Wiebe WJ (2001) Temperature and substrates as interactive limiting factors for marine heterotrophic bacteria. Aquat Microb Ecol 23:187-204
51. Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369-394
52. 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
53. Roland F, Cole JJ (1999) Regulation of bacterial growth efficiency in a large turbid estuary. Aquat Microb Ecol 20: 31-38
54. Rossello-Mora R, Thamdrup B, Schafer H, Weller R, Amann R (1999) The response of the microbial community of marine sediments to organic carbon input under anaerobic conditions. Syst Appl Microbiol 22:237-248
55. Šimek K, Vrba J, Pernthaler J, Posch T, Hartman P, Nedoma J, Psenner R (1997) Morphological and compositional shifts in an experimental bacterial community influenced by protists with contrasting feeding modes. Appl Environ Microbiol 63:587-595
56. Šimek K, Hornak K, Masin M, Christaki U, Nedoma J, Weinbauer MG, Dolan JR (2003) Comparing the effects of resource enrichment and grazing on a bacterioplankton community of a meso-eutrophic reservoir. Aquat Microb Ecol 31:123-135
57. Sinsabaugh RL, Findlay SEG (2003) Dissolved organic matter: out of the black box and into the mainstream. In: Findlay SEG, Sinsabaugh RL (eds) Aquatic ecosystems: interactivity of dissolved organic matter. Academic Press, San Diego, p 497-498
58. 3H-leucine. Mar Microb Food Webs 6:107-114
59. Suzuki MT (1999) Effect of protistan bacterivory on coastal bacterioplankton diversity. Aquat Microb Ecol 20:261-272
60. van Hannen EJ, Mooij W, van Agterveld MP, Gons HJ, Laanbroek HJ (1999) Detritus-dependent development of the microbial community in an experimental system: Qualitative analysis by denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:2478-2484
61. Wetzel RG (2001) Limnology: lake and river ecosystems. Academic Press, San Diego
62. Zarda B, Hahn D, Chatzinotas A, Schonhuber W, Neef A, Amann RI, Zeyer J (1997) Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch Microbiol 168:185-192