Aquatic microbiology for ecosystem scientists: New and recycled paradigms in ecological microbiology

Ecosystems

Volumn 2, Issue 3, 1999, Pages 215-225

  Cole, Jonathan J ^a  

^a CARY INSTITUTE OF ECOSYSTEM STUDIES   (United States)

Author keywords

Aquatic microbiology; Ecosystems; Microbial ecology; Review

Indexed keywords

EID: 0032805446     PISSN: 14329840     EISSN: None     Source Type: Journal    
DOI: 10.1007/s100219900069     Document Type: Review

References (105)

1. Baines SBB, Pace ML. 1991. The production of dissolved organic matter by phytoplankton and its importance to bacteria: Patterns across marine and freshwater systems. Limnol Oceanogr 36:1078-1090.
2. Bird DF, Kalff J. 1984. Empirical relationships between bacterial abundance and chlorophyll concentration in fresh and marine waters. Can J Fish Aquat Sci 41:1015-1023.
3. Bormann FH Likens GE. 1979. Pattern and process in a forested ecosystem. Springer-Verlag. NY.
4. Brock TD. 1979. Biology of microorganisms, Ed. 3. Prentice-Hall, New Jersey.
5. Bjornsen, P.K. 1986. Bacterioplanklon growth yield in continuous sea water culture. Mar Ecol Prog Ser 30:191-196.
6. Buck KR, Chavez FP, Campbell L. 1996. Basin-wide distributions of living carbon components and the inverted trophic pyramid of the central gyre of the North Atlantic Ocean, summer 1993. Aq Microb Ecol 10:283-298.
7. 2 models. In: Joint meeting of the American Society of Limnology and Oceanography and the Ecological Society of America. St. Louis, MO. June 1998.
8. Cho BC, Azam F. 1990. Biogeochemical significance of bacterial biomass in the ocean's euphotic zone. Mar Ecol Prog Ser 63:253-259.
9. Chrzanowski TH, Kyle M. 1996. Ratios of carbon nitrogen and phosphorus in Psuedomonas fluorescens as a model for bacterial element ratios and nutrient regeneration. Aq Microb Ecol 10:115-122.
10. Chrzanowski TH, Kyle M, Elser JJ, Sterner RW. 1996. Element ratios and growth dynamics of bacteria in oligotrophic Canadian Shield lakes. Aq Microb Ecol 11:119-125.
11. Chrzanowski TH, Simek K. 1990. Prey-size selection by freshwater flagellated protozoa. Limnol Oceanogr 35: 1429-1436
12. Choi JW, Sherr EB, Sherr BF. 1996. Relation between presence-absence of a visible nucleoid and metabolic activity in bacterioplankton cells. Limnol Oceanogr 41:1161-1168.
13. Cole JJ. 1982. Interactions between bacteria and algae in aquatic ecosystems. Ann Rev Ecol Syst 13:291-314.
14. Cole JJ, Caraco NF. 1993. The pelagic microbial food webs of oligotrophic lakes. P.101-112. In: Ford T, editor. Aquatic microbiology. Blackwell, New York.
15. 6. Limnol Oceanogr 43:647-656.
16. Cole JJ, Pace ML. 1995. Why measure bacterial production? A reply to the comment by Jahnke and Craven. Limnol Oceanogr 40:441-444.
17. Cole JJ, Likens GE, Strayer DL. 1982. Photosynthetically produced dissolved organic carbon: An important carbon source for planktonic bacteria. Limnol Oceanogr 27:1080-1090.
18. Cole JJ, Findlay S, Pace ML. 1988. Bacterial production in fresh and saltwater ecosystems: A cross-system overview. Mar Ecol Prog Ser 43:1-10.
19. Cole JJ, Caraco NF, Strayer CL, Ochs C, Nolan S. 1989. A detailed organic carbon budget as an ecosystem-level calibration of bacterial respiration in an oligotrophic lake during midsummer. Limnol Oceanogr 34:286-296.
20. Cole JJ, Caraco NF, Kling GW, Kratz TK. 1994. Carbon dioxide supersaturation in the surface waters of lakes. Science 265: 1568-1570.
21. Daley RJ, Hobbie JE. 1975. Direct counts of aquatic bacteria by a modified epifluorescence technique. Limnol Oceanogr 20:875-886.
22. Daneri G, Riemann B, Williams, PJLeB. 1994. In situ bacterial production and growth yield measured by thymicine, leucine and fractioned dark oxygen uptake. J Plank Res 16:105-113.
23. del Giorgio PA, Peters RH. 1994. Patterns in planktonic P:R ratios in lakes: Influence of lake trophy and dissolves organic C. Limnol Oceanogr 39:772-787.
24. del Giorgio PA, Scarborough G. 1995. Increases in the proportion of metabolically active bacteria along gradients of enrichment in freshwater and marine plankton: Implications for estimates of bacterial growth and production rates. J Plank Res 17:1905-1924.
25. del Giorgio PA, Gasol JM. 1995. Biomass distribution in freshwater plankton communities. Am Nat 146:135-152.
26. del Giorgio PA, Bird D, Prairie YT, Planas D. 1996 a. Flow cytometric determinations of bacterial abundance in lake plankton with the green nucleic acid stain SYTO 13. Limnol Oceanogr 41:783-789.
27. del Giorgio PA, Gasol JM, Vaque D, Mura P, Agusti S, Duarte CM. 1996 b. Bacterioplankton community structure: Protists control net production and the proportion of active bacteria in a coastal marine community. Limnol Oceanogr 41:1169-1179.
28. del Giorgio PA, Cole JJ, Cimbleris A. 1997. Respiration rates in bacteria exceed phytoplankton production in unproductive aquatic systems. Nature 385:148-151.
29. del Giorgio PA, Cole JJ, Caraco NF, Peters RH. 1999. Linking planktonic biomass structure to plankton metabolism and net gas flux in northern temperate lakes. Ecology 80:1422-1431.
30. Dillon PJ, Molot LA. 1997. Dissolved organic and inorganic carbon mass balances in central Ontario lakes. Biogeochemistry 36:29-42.
31. 2 balance of unproductive aquatic ecosystems. Science 281:234-236.
32. Ducklow HW, Carlson CA. 1992. Oceanic bacterial production. Adv Microb Ecol 12:113-181.
33. Elser JJ, Stabler LB, and Hassett RP. 1995. Nutrient limitation of bacterial growth and rates of bacterivory in lakes and oceans: a comparative study. Aq Microb Ecol 9:105-110.
34. Finlay BJ, Maberly SC, Cooper JI. 1997. Microbial diversity and ecosystem function. Okios 80:209-213
35. Findlay S, Pace ML, Lints D, Cole JJ, Caraco NF, Peierls F. 1991. Weak coupling of bacterial and algal production in a heterotrophic ecosystem, the Hudson estuary. Limnol Oceanogr 36:268-278.
36. Ford, TE (ed.). 1993. Aquatic microbiology - p.101-112. Blackwell, New York.
37. Fuhrman JA, Davis AA. 1997. Widespread and novel bacteria from the deep sea as shown by 16S rRNA gene sequences. Mar Ecol Prog Ser 150:275-285.
38. Fuhrman JA, Azam F. 1980. Bacterioplankton secondary production estimates for coastal waters of British Columbia, Antarctica and California. Appl Environ Microbiol 39:1085-1095.
39. Fuhrman JA, Azam F. 1982. Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters: Evaluation and field results. Mar Biol 66:109-120.
40. Fuhrman JA, Sleeter TD, Carlson CA, Proctor LM. 1989. Dominance of bacterial biomass in the Sargasso Sea and its ecological implications. Mar Ecol Prog Ser 57:207-217.
41. Gasol JM, del Giorgio PA, Massana R, Duarte CM. 1996. Active versus unactive bacteria: Size-dependence in a coastal marine plankton community. Mar Ecol Prog Ser 128:91-97.
42. Geider RJ. 1997. Photosynthesis or planktonic respiration. Nature 388:132.
43. Geller A. 1985. Light-induced conversion ol refractory, high molecular weight lake water constituents. Schweiz Z Hydrol 47:21-26.
44. Geller A. 1986. Comparison of mechanisms enhancing biodegradability of refractory lake water constituents. Limnol Oceanogr 31:755-764.
45. Gonzalez JM, Sherr EB, Sherr BF. 1993. Differential feeding by marine flagellates on growing versus starving and on motile versus nonmotile bacterial prey. Mar Ecol Prog Ser 102:257-267.
46. Graneli W, Lindell M, Tranvik L. 1996. Photo-oxidative production of dissolved inorganic carbon in lakes of different humic content. Limnol Oceanogr 41:698-706.
47. Herndl GJ, Kaltenbock E, Muller-Niklas G. 1993. Dialysis bag incubation as a nonradiolabeling technique to estimate bacterioplankton production in situ. P.553-556. In: Kemp PF, Sherr BF, Sherr EB, Cole JJ [eds.], Handbook of methods in aquatic microbial ecology. Lewis Publishers, Boca Raton, FL.
48. Hobbie JE, Cole JJ. 1984. Response of a detrital foodweb to eutrophication. Bull Mar Sci 35:357-363.
49. Hobbie JE, Daley RJ, Jasper S. 1977. Use of nuclepore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol 22:1225-1228.
50. 2 and dissolved organic carbon in Northern Wisconsin lakes. J Environ Qual 25:1442-1445.
51. Howarth RW, Marino R, Garritt R, Sherman D. 1992. Ecosystem respiration and organic carbon processing in a large, tidally influenced river: the Hudson River. Biogeochem 16:83-102.
52. Howarth RW, Schneider R, Swaney D. 1996. Metabolism and organic carbon fluxes in the tidal freshwater Hudson River. Estuaries 19:848-865.
53. Jahnke RA, Craven DB. 1995. Quantifying the role of heterotrophic bacteria in the carbon cycle: A need for respiration rate measurements. Limnol Oceanogr 40:436-441.
54. Jannasch HW, Jones GE. 1959. Bacterial populations in sea water as determined by different methods of enumeration. Limnol Oceanogr 4:128-139.
55. Jepras RI, Pearson SC, Paul FE, Wilkinson MJ. 1995. Development of a robust flow cytometric assay for determining numbers of viable bacteria. Appl Environ Microbiol 61:2696-2701.
56. Karentz D, Bothwell ML, Coffin RB, Hanson A, Herndl GJ, Kilham SS, Lesser MP, Lindell M, Moeller RE, Morris DP, Neale PJ, Sanders RW, Weiler CS, Wetzel RG. 1994. Impact of UV-B radiation on pelagic freshwater ecosystems: Report of working group on bacteria and phytoplankton. Ergebnisse der Limnologie 43:31-69.
57. 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.
58. Kaiser E, Herndl GJ. 1997. Rapid recovery of marine bacterioplankton activity after inhibition by UV radiation in coastal waters. Appl Environ Microbiol 63:4026-4031.
59. Kemp PF, Sherr BF, Cole JJ. 1993. Handbook of methods in Aquatic microbial ecology, Lewis Publishers, Boca Raton, FL.
60. Kieber DJ, McDaniel J, Mopper K. 1989. Photochemical source of biological substrates in sea water: Implications for carbon cycling. Nature 341:637-639.
61. Kinner NE, Harvey RW, Blakesless K, Novarino G, Meeker LD. 1998. Size-selective predation on groundwater bacteria by nannoflagellates in an organic-contaminated aquifer. Appl Environ Microbiol 64:618-625.
62. Kirchman DL, Ducklow HW. 1993. Estimating conversion factors for the Thymidine and Leucine methods for measuring bacterial production. P.513-517. In: Kemp PF, Sherr BF, Sherr EB, Cole JJ, [eds.], Handbook of methods in aquatic microbial ecology. : Lewis Publishers, Boca Raton, FL.
63. Kirchman DL, 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 49:599-605.
64. Kirk, JTO. 1994. Optics of UV-B radiation in natural waters. Arch Hydrobiol Beih Ergebn Limnol 43:1-16.
65. Kling GW, Kipphut GW, Miller MC. 1991. Arctic lakes and streams as gas conduits to the atmosphere: Implications for tundra carbon budgets. Science 251:298-301.
66. Kratz TK, Schindler J, Hope D, Riera JL, Bowser CJ. 1997. Average annual carbon dioxide concentrations in eight neighboring lakes in northern Wisconsin. Verb Int Verein Limnol 26:335-338.
67. Larsson U, Hagstrom A. 1979. Phytoplankton exudate release as an energy source for the growth of pelagic bacteria. Mar Biol 52:199-206.
68. Lindell MJ, Graneli W, Tranvik LJ. 1995. Enhanced bacterial growth in response to photochemical transformation of dissolved organic matter. Limnol Oceanogr 40:195-199.
69. Lindell MJ, Graneli HW, Tranvik LJ. 1996. Effects of sunlight on bacterial growth in lakes of different humic content. Aquat Microb Ecol 11:135-141.
70. McConnaughey TA, LaBaugh JW, Rosenberry DO, Striegl RG, Reddy MM, Schuster PF, Carter V. 1994. Carbon budget for a groundwater-fed lake: Calcification supports summer photosynthesis. Limnol Oceanogr 39:1319-1332.
71. McFeters GA, Yu FP, Pyle H, Stewart PS. 1995. Physiological assessment of bacteria using fluorochromes. J Microbiol Methods 21:1-13.
72. 13C and d 15N) of Zooplankton species. p.53-61. In: Simon, M, Gude H, Weisse T, [eds.], Aquatic Microbial Ecology. E Schweizerbart'she Verlagsbuchhandlung, Konstanz, Germany.
73. Molot LA, Dillon PJ. 1997. Photolytic regulation of dissolved organic carbon in northern lakes. Global Biogeochem Cycles 11:357-366.
74. Mopper K, Zhou X, Kieber RJ, Kieber DJ, Sikorski RJ, Jones RD. 1991. Photochemical degradation of dissolved organic carbon and its impact on the oceanic carbon cycle. Nature 353:60-62.
75. Moran MA, Zepp G. 1997. Role of photoreactions in the formation of biologically labile compounds from dissolved organic matter. Limnol Oceanogr 42:1307-1316.
76. Morris DP, Hargreaves BR. 1997. The role of photochemical degradation of dissolved organic carbon in regulating UV transparency of three lakes on the Pocono Plateau. Limnol Oceanogr 42:239-249.
77. Mura MP, Agusti S, del Giorgio PA, Gasol JM, Vaque D, Duarte CM. 1996. Loss-controlled phytoplankton production in nutrient-poor littoral waters of the NW Mediterranean: In situ experimental evidence. Mar Ecol Prog Ser 130:213-219.
78. Pace ML. 1988. Bacterial mortality and the fate of bacterial production. Hydrobiol 159:41-50.
79. Pace ML, Cole JJ. 1996. Regulation of bacteria by resources and predation tested in whole lake experiments. Limnol Oceanogr 41:1448-1460.
80. Pace ML, Funke E. 1991. Regulation of planktonic microbial communities by nutrients and herbivores. Ecol 72:904-914.
81. Peterson BJ, Hobbie JE, Haney JF. 1978. Daphnia grazing on natural bacteria. Limnol Oceanogr 23:1039-1044.
82. Polis GA, Anderson WB, Holt RD. 1997. Toward an integration of landscape and food web ecology: The dynamics of spatially subsidized food webs. Ann Rev Ecol Syst 28:289-316.
83. Porter KG, Feig YS. 1980. The use of DAPI for identifying and counting the microflora. Limnol Oceanogr 25:943-948.
84. Reche I, Pace ML, Cole JJ. 1998. Interactions of pho obleaching and mineral nutrients in determining bacterial growth on colored dissolved organic carbon. Microb Ecol 36:270-280.
85. Rodriguez GG, Phipps D, Ishiguro K, Ridgeway HF. 1992. Use of a fluorescent redox probe for direct visualization of actively respiring bacteria. Appl Environ Microbiol 58:1801-1808.
86. Roland F, Cole JJ. 1999. Prediction of bacterial growth efficiency in a riverine ecosystem. Verh Int Ver Limnol (IN PRESS).
87. Sherr BF, Sherr EB. 1988. Role of microbes in pelagic food webs: A revised concept. Limnol Oceanogr 33:1225-1226.
88. Sherr BF, Sherr EB, del Giorgio PA. 1998. Estimating abundance and single-cell characteristics of actively respiring bacteria via the redox dye CTC. Aq Microb Ecol (In Press).
89. Sherr BF, Sherr EB, McDaniel J. 1992. Effect of protistan grazing on the frequency of dividing cells in bacterioplankton assemblages. Appl Environ Microbiol 58:2381-2385.
90. Simek K, Chrzanowski TH. 1992. Direct and indirect evidence of size-selective grazing on pelagic bacteria by freshwater nannoflagellates. Appl Environ Microbiol 58:3715-3720.
91. Simon M, Cho BC, Azam F. 1992. Significance of bacterial biomass in lakes and the ocean: comparison to phytoplankton biomass and biogeochemical implications. Mar Ecol Prog Ser 86:103-110.
92. Smith DC, Azam F. 1993. A simple economical method for measuring bacterial protein synthesis rates in seawater using tritiated leucine. Mar Microb Food Webs 6:107-114.
93. Sondergaard M, Scheirup HH. 1982. Release of extracellular organic carbon during a diatom bloom in Lake Mosso: Molecular weight fractionation. Freshwat Biol 12:313-320
94. Sterner RW, Chrzanowski TH, Elser JJ, George NB. 1995. Sources of nitrogen and phosphorus supporting the growth of bacterio-and phytoplankton in oligotrophic Canadian Shield lakes. Limnol Oceanogr 40:242-249.
95. Stevenson LH. 1978. A case for bacterial dormancy in aquatic systems. Microb Ecol 4:127-133.
96. Stewart AJ, Wetzel RG. 1982. Influence of dissolved humic materials on carbon assimilation and alkaline phosphatase activity in natural algal-bacterial assemblages. Freshwat Biol 12:369-380.
97. Strayer DL. 1988. On the limits to secondary production. Limnol Oceanogr 33:1217-1220.
98. Tiedje JM, Zhou J-Z. 1996. Analysis of non-culturable bacteria. p. 53-65. In: Hall GS [ed.], Methods for the examination of organismal diversity in soils and sediments. CAB International, New York.
99. Tranvik LJ. 1992. Allochthonous dissolved organic matter as an energy source for pelagic bacteria and the concept of the microbial loop. Hydrobiol 229:107-114.
100. Vaque D, Pace ML. 1992. Grazing on bacteria by flagellates and cladocerans in lakes of contrasting food-web structure. J Plank Res 14:307-321.
101. nd Edition. Saunder College Publishing.
102. Wetzel RG, Rich PH, Miler MC, Allen HL. 1972. Metabolism of dissolved and particulate detrital carbon in a temperate hard water lake. Mem Ist Ital Idrobiol 29 Suppl: 185-243.
103. Wetzel RG, Hatcher PG, Blanchi TS. 1995. Natural photolysis by ultraviolet irradiance of recalcitrant dissolved organic matter to simple substrates for rapid bacterial metabolism. Limnol Oceanogr 40:1369-1380.
104. Williams, PJLeB. 1998. The balance of plankton respiration and photosynthesis in the open ocean. Nature 394: 55-57.
105. Zweifel UL, Hagstrom A. 1995. Total counts of marine bacteria include a large fraction of non-nucleoid-containing bacteria (ghosts). Appl Environ Microbiol 61:2180-2185.