9. Microbial Carbon Cycling in Pelagic Ecosystems: Microbial Methods for Ecosystem Scientists
149
Porter, K.G.; Feig, Y.S. The use of DAPI for identifying
and counting the microflora. Limnol. Oceanogr.
25:943-948; 1980.
Porter, K.G.; Sherr, E.B.; Sherr, B.P.; Pace, M.; Sanders,
R.W. Protozoa in planktonic food webs. J. Protozool.
32:409-415; 1985.
Psenner, R. Determination of size and morphology of
aquatic bacteria by automated image analysis. In:
Kemp, P.P.; Sherr, B.P.; Sherr, E.B.; Cole, J.J., eds.
Handbook of Methods in Aquatic Microbial Ecology.
Ann Arbor, MI: Lewis; 1993:339-345.
Rich, J.H.; Ducklow, H.; Kirchman, D.L. Concentrations
and uptake of neutral monosaccharides along 140
0
W
in the equatorial Pacific: Contribution of glucose to
heterotrophic bacterial activity and the DOM flux.
Limnol. Oceanogr. 41:595-604; 1996.
Robarts, R.D.; Zohary, T. Fact or fiction-Bacterial
growth rates and production as determined by [methyl
3H]-thymidine? Adv. Microb. Ecol. 13:371-425;
1993.
Robertson, B.R.; Button, D.K. Characterizing aquatic
bacteria according to population, cell size, and apparent DNA content by flow cytometry. Cytometry
10:70-76; 1989.
Rodriguez, G.G.; Phipps, D.; Ishiguro, K.; Ridgeway,
H.P. Use of a fluorescent redox probe for direct visualization of actively respiring bacteria. Appl. Environ.
Microbiol. 58:1801-1808; 1992.
Roland, F; Cole J.J. Regulation of bacterial growth efficiency in a large turbid estuary. Aquat. Microb. Ecol.
20:31-38; 1999.
Roszak, D.B.; Colwell, R. Survival strategies of bacteria
in the natural environment. Microbiol. Rev. 51:365379; 1997.
Sanders, R.w.; Caron, D.A.; Berninger, U.-G. Relationships between bacteria and heterotrophic nanoplankton in marine and freshwaters: An inter-ecosystem
comparison. Mar. Ecol. Prog. Ser. 86:1-14; 1992.
Sarmiento, 1.L.; Slater, R.D.; Fasham, J.R.; Ducklow,
H.W.; Toggweiler, J.R.; Evans, G.T. A seasonal threedimensional ecosystem model of nitrogen cycling in
the north Atlantic euphotic zone. Global Biogeochem.
Cycl. 7:417-450; 1993.
Scavia, D. On the role of bacteria in secondary production. Lirnnol. Oceanogr. 33:1220-1224; 1988.
Sherr, E.B.; Sherr, B.P. Temporal offset in oceanic production and respiration implied by seasonal changes
in atmospheric oxygen: the role of heterotrophic microbes. Aquat. Microb. Ecol. 11:91-100; 1996.
Sieracki, M.E.; Johnson, P.W.; Webb, K.L. Detection,
enumeration and sizing of planktonic bacteria by
image-analyzed epiflourescence microscopy. Appl.
Environ. Microbiol. 49:799-814; 1989.
Simon, M.; Azam, P. Protein content and protein synthesis rates of planktonic marine bacteria. Mar. Ecol.
Prog. Ser. 51:201-213; 1989.
Simon, M.; Cho, B.C.; Azam, P. Significance of bacterial
biomass in lakes and the ocean: Comparison to phytoplankton biomass and biogeochemical implications.
Mar. Ecol. Prog. Ser. 86:103-110; 1992.
Sinsabaugh, R.L.; Findlay, S.; Franchini, P.; Fischer, D.
Enzymatic analysis of riverine bacterioplankton production. Lirnnol. Oceanogr. 42:29-38; 1997.
Smith, D.C.; Azam, P. A simple economical method for
measuring bacterial protein synthesis rates in seawater
using tritiated leucine. Mar. Microb. Food Webs
6:107-114; 1993.
Smith, E.M. Coherence of microbial respiration rate and
cell-specific bacterial activity in a coastal planktonic
community. Aquat. Microb. Ecol. 16:27-35; 1998.
Strayer, D.L. On the limits to secondary production. Limnol. Oceanogr. 33:1217-1220; 1988.
Suzuki, M.; Sherr, E.B.; Sherr, B.P. DAPI direct counting
underestimates bacterial abundance and average cell
size compared to AO direct count. Limnol. Oceanogr.
38:1566-1569; 1993.
Thingstad, T.P.; Lignell, R. Theoretical models for the
control of bacterial growth rate, abundance, diversity
and carbon demand. Aquat. Microb. Ecol. 13:19-27;
1997.
Toolan, T.; Wehr, J.D.; Findlay, S. Inorganic phosphorus
stimulation of bacterioplankton production in a mesoeutrophic lake. Appl. Environ. Microbiol. 57:20742078; 1991.
Turley, C.M. Direct estimates of bacterial numbers in
seawater samples without incurring cell loss due to
sample storage. In: Kemp, P.P'; Sherr, B.P.; Sherr,
E.B.; Cole, J.J., eds. Handbook of Methods in Aquatic
Microbial Ecology. Ann Arbor, MI: Lewis; 1993:143148.
Turley, C.M.; Hughes, DJ. Effects of storage on direct
estimates of bacterial numbers of preserved seawater
samples. Deep Sea Res. 39:375-382; 1992.
Valino, J.1.; Hopkinson, C.S.; Hobbie, J.E. Modeling
bacterial utilization of dissolved organic matter: Optimization replaces Monod growth kinetics. Limnol.
Oceanogr. 41:1591-1609; 1997.
Vaque, D.; Pace, M.L. Grazing on bacteria by flagellates
and cladocerans in lakes of contrasting food-web
structure. 1. Plank. Res. 14:307-321; 1992.
Vezina, A.; Pace, M.L. An inverse model analysis of
planktonic food webs in experimental lakes. Can. J.
Fish. Aquat. Sci. 51:2034-2044; 1994.
Vezina, A.P.; Platt, T. Food web dynamics in the ocean.
I. Best estimates of flow networks using inverse models. Mar. Ecol. Prog. Ser. 42:269-284; 1988.
Waiser, M.J.; Robarts, R.D. Microbial nutrient limitation
in prairie saline lakes with high sulfate concentrations.
Limnol. Oceanogr. 40:566-574; 1995.
Wallner, G.; Spring, S.; Beisker, W.; Amman, R.
Flow sorting of microorganisms for molecular
149
Porter, K.G.; Feig, Y.S. The use of DAPI for identifying
and counting the microflora. Limnol. Oceanogr.
25:943-948; 1980.
Porter, K.G.; Sherr, E.B.; Sherr, B.P.; Pace, M.; Sanders,
R.W. Protozoa in planktonic food webs. J. Protozool.
32:409-415; 1985.
Psenner, R. Determination of size and morphology of
aquatic bacteria by automated image analysis. In:
Kemp, P.P.; Sherr, B.P.; Sherr, E.B.; Cole, J.J., eds.
Handbook of Methods in Aquatic Microbial Ecology.
Ann Arbor, MI: Lewis; 1993:339-345.
Rich, J.H.; Ducklow, H.; Kirchman, D.L. Concentrations
and uptake of neutral monosaccharides along 140
0
W
in the equatorial Pacific: Contribution of glucose to
heterotrophic bacterial activity and the DOM flux.
Limnol. Oceanogr. 41:595-604; 1996.
Robarts, R.D.; Zohary, T. Fact or fiction-Bacterial
growth rates and production as determined by [methyl
3H]-thymidine? Adv. Microb. Ecol. 13:371-425;
1993.
Robertson, B.R.; Button, D.K. Characterizing aquatic
bacteria according to population, cell size, and apparent DNA content by flow cytometry. Cytometry
10:70-76; 1989.
Rodriguez, G.G.; Phipps, D.; Ishiguro, K.; Ridgeway,
H.P. Use of a fluorescent redox probe for direct visualization of actively respiring bacteria. Appl. Environ.
Microbiol. 58:1801-1808; 1992.
Roland, F; Cole J.J. Regulation of bacterial growth efficiency in a large turbid estuary. Aquat. Microb. Ecol.
20:31-38; 1999.
Roszak, D.B.; Colwell, R. Survival strategies of bacteria
in the natural environment. Microbiol. Rev. 51:365379; 1997.
Sanders, R.w.; Caron, D.A.; Berninger, U.-G. Relationships between bacteria and heterotrophic nanoplankton in marine and freshwaters: An inter-ecosystem
comparison. Mar. Ecol. Prog. Ser. 86:1-14; 1992.
Sarmiento, 1.L.; Slater, R.D.; Fasham, J.R.; Ducklow,
H.W.; Toggweiler, J.R.; Evans, G.T. A seasonal threedimensional ecosystem model of nitrogen cycling in
the north Atlantic euphotic zone. Global Biogeochem.
Cycl. 7:417-450; 1993.
Scavia, D. On the role of bacteria in secondary production. Lirnnol. Oceanogr. 33:1220-1224; 1988.
Sherr, E.B.; Sherr, B.P. Temporal offset in oceanic production and respiration implied by seasonal changes
in atmospheric oxygen: the role of heterotrophic microbes. Aquat. Microb. Ecol. 11:91-100; 1996.
Sieracki, M.E.; Johnson, P.W.; Webb, K.L. Detection,
enumeration and sizing of planktonic bacteria by
image-analyzed epiflourescence microscopy. Appl.
Environ. Microbiol. 49:799-814; 1989.
Simon, M.; Azam, P. Protein content and protein synthesis rates of planktonic marine bacteria. Mar. Ecol.
Prog. Ser. 51:201-213; 1989.
Simon, M.; Cho, B.C.; Azam, P. Significance of bacterial
biomass in lakes and the ocean: Comparison to phytoplankton biomass and biogeochemical implications.
Mar. Ecol. Prog. Ser. 86:103-110; 1992.
Sinsabaugh, R.L.; Findlay, S.; Franchini, P.; Fischer, D.
Enzymatic analysis of riverine bacterioplankton production. Lirnnol. Oceanogr. 42:29-38; 1997.
Smith, D.C.; Azam, P. A simple economical method for
measuring bacterial protein synthesis rates in seawater
using tritiated leucine. Mar. Microb. Food Webs
6:107-114; 1993.
Smith, E.M. Coherence of microbial respiration rate and
cell-specific bacterial activity in a coastal planktonic
community. Aquat. Microb. Ecol. 16:27-35; 1998.
Strayer, D.L. On the limits to secondary production. Limnol. Oceanogr. 33:1217-1220; 1988.
Suzuki, M.; Sherr, E.B.; Sherr, B.P. DAPI direct counting
underestimates bacterial abundance and average cell
size compared to AO direct count. Limnol. Oceanogr.
38:1566-1569; 1993.
Thingstad, T.P.; Lignell, R. Theoretical models for the
control of bacterial growth rate, abundance, diversity
and carbon demand. Aquat. Microb. Ecol. 13:19-27;
1997.
Toolan, T.; Wehr, J.D.; Findlay, S. Inorganic phosphorus
stimulation of bacterioplankton production in a mesoeutrophic lake. Appl. Environ. Microbiol. 57:20742078; 1991.
Turley, C.M. Direct estimates of bacterial numbers in
seawater samples without incurring cell loss due to
sample storage. In: Kemp, P.P'; Sherr, B.P.; Sherr,
E.B.; Cole, J.J., eds. Handbook of Methods in Aquatic
Microbial Ecology. Ann Arbor, MI: Lewis; 1993:143148.
Turley, C.M.; Hughes, DJ. Effects of storage on direct
estimates of bacterial numbers of preserved seawater
samples. Deep Sea Res. 39:375-382; 1992.
Valino, J.1.; Hopkinson, C.S.; Hobbie, J.E. Modeling
bacterial utilization of dissolved organic matter: Optimization replaces Monod growth kinetics. Limnol.
Oceanogr. 41:1591-1609; 1997.
Vaque, D.; Pace, M.L. Grazing on bacteria by flagellates
and cladocerans in lakes of contrasting food-web
structure. 1. Plank. Res. 14:307-321; 1992.
Vezina, A.; Pace, M.L. An inverse model analysis of
planktonic food webs in experimental lakes. Can. J.
Fish. Aquat. Sci. 51:2034-2044; 1994.
Vezina, A.P.; Platt, T. Food web dynamics in the ocean.
I. Best estimates of flow networks using inverse models. Mar. Ecol. Prog. Ser. 42:269-284; 1988.
Waiser, M.J.; Robarts, R.D. Microbial nutrient limitation
in prairie saline lakes with high sulfate concentrations.
Limnol. Oceanogr. 40:566-574; 1995.
Wallner, G.; Spring, S.; Beisker, W.; Amman, R.
Flow sorting of microorganisms for molecular