BIOLOGY 5801
Microbial
Ecology
Microbial
Ecology Reading List
[numbers = required reading for each week of the semester]
[* = suggested additional reading]
Microbial Evolution and Biodiversity
Amann, R., W. Ludwig, K.-H. Schleifer. 1994. Identification of uncultured bacteria: a
challenging task for molecular taxonomists. ASM News 60:360-365.
Bintrim, S. B., T. J. Donohue, J. Handelsman, G. P. Roberts, and R. M. Goodman. 1997.
Molecular phylogeny of Archaea from soil. Proc. Natl. Acad. Sci. 94:277-282.
4 DeLong, E. F., K. Y. Wu, B. B. Prezelin, and R. V. M. Jovine. 1994. High abundance of
Archaea in Antarctic marine picoplankton. Nature 371:695-697.*
Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity of
Sargasso Sea bacterioplankton. Nature 345:60-62.
MacGregor, B. J., D. P. Moser, E. W. Alm., K. H. Nealson, and D. A. Stahl. 1997.
Crenarchaeota in Lake Michigan sediment. Appl. Environ. Microbiol. 63:1178-1181.
Stackebrandt, E. and B. M. Goebel. 1994. Taxonomic note: A place for DNA-DNA
reassociation and 16S rRNA sequence analysis in the present species definition in
bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
2 Stahl, D. A. 1993. The natural history of microorganisms. ASM News 59:609-613.*
Woese, C. E. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271. *
Methods to Study Microbial Biodiversity
3 Amann, R. I., et al. 1995. Phylogenetic identification and in situ detection of individual microbial
cells without cultivation. Microbiol. Rev. 59:143-169.*
Bratbak, G. 1985. Bacterial biovolume and biomass estimations. Appl. Environ. Microbiol.
49:1488-1493.
Choi, J. W., E. B. Sherr, and B. F. Sherr. 1996. Relation between presence-absence of a visible
nucleoid and metabolic activity in bacterioplankton cells. Limnol. Oceanogr. 41:1161-1168.
DeBruijn, F. J. 1992. Use of repetitive (repetitive extragenic palindromic and enterobacterial
repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint
the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl. Environ.
Microbiol. 58:2180-2187.
Doddema, H. J., and G. D. Vogels. 1978. Improved identification of methanogenic bacteria by
fluorescence microscopy. Appl. Environ. Microbiol. 36:752-754.
Eirich, L., G. D. Vogels, and R. S. Wolfe. 1979. Distribution of coenzyme F420 and properties
of its hydrolytic fragments. J. Bacteriol. 140:20-27.
Ellery, W. N., and M. H. Schleyer. 1984. Comparison of homogenization and ultrasonication as
techniques in extracting attached sedimentary bacteria. Mar. Ecol. Prog. Ser. 15:247-250.
Fallon, R. D., S. Y. Newell, and C. S. Hopkinson. 1983. Bacterial production in marine
sediments: will cell-specific measures agree with whole-system metabolism? Mar. Ecol.
Prog. Ser. 11:119-127.
Garland, J. L., and A. L. Mills. Classification and characterization of heterotrophic microbial
communities on the basis of patterns of community-level sole-carbon-source utilization.
Appl. Environ. Microbiol. 57:2351-2359.
Hazen, T. C., and L. Jimenez. 1988. Enumeration and identification of bacteria from
environmental samples using nucleic acid probes. Microbiol. Sci. 5:340-343.*
Lee, S., and J. A. Fuhrman. 1990. DNA hybridization to compare species compositions of
natural bacterioplankton assemblages. Appl. Environ. Microbiol. 56:739-746.
8 Lewis, D. L., and D. K. Gattie. 1991. The ecology of quiescent microbes. ASM News 57:27-32. *
Nagata, T. 1986. Carbon and nitrogen content of natural planktonic bacteria. Appl. Environ.
Microbiol. 52:28-32.
Nagata, T., and . Watanabe. 1990. Carbon- and nitrogen-to-volume ratios of bacterioplankton
grown under different nutritional conditions. Appl. Environ. Microbiol. 56:1303-1309.
Newell, S. Y. 1992. Estimating fungal biomass and productivity in decomposing litter. Pp.
521-561 In The Fungal Community (G. C. Carroll and D. T Wicklow, eds.). Marcel Cekker,
Inc., New York.
Newell, S.Y., R. D. Fallon, and P. S. Tabor. 1986. Direct microscopy of natural assemblages.
Pp. 1-47 In Bacteria in Nature, Vol. 2 (J. S. Poindexter, ed.). Plenum Publishing Corp.
7 Staley, J. T., and A. Konopka. 1985. Measurement of in situ activities of nonphotosynthetic
microorganisms in aquatic and terrestrial habitats. Ann. Rev. Microbiol. 39:321-346.
Turley, C. M., And D. J. Hughes. 1992. Effects of storage on direct estimates of bacterial
numbers of preserved seawater samples. Deep-Sea Res. 39:375-394.
Zweifel, U. L., and A. Hagström. 1995. Total counts of marine bacteria include a large fraction
of non-nucleoid-containing bacteria (ghosts). Appl. Environ. Microbiol. 61:2180-2185.*
Microbial Populations
Button, D. K., F. Schut, P. Quang, R. Martin, and B. R. Robertson. 1993. Viability and isolation
of marine bacteria by dilution culture: theory, procedures, and initial results. Appl. Environ.
Microbiol. 59:881-891.
11 Cole, J. J., S. Findlay, and M. L. Pace. 1988. Bacterial production in fresh and saltwater
ecosystems: a cross-system overview. Mar. Ecol. Progr. Ser. 43:1-10.*
8 Costerton, J. W., Z. Lewandowski, D. DeBreer, D. Caldwell, K. Korber, and G. James. 1994.
Biofilms, the customized microniche. J. Bacteriol. 176:2137-2142.*
Covney, M. F., and R. G Wetzel. 1988. Experimental evaluation of conversion factors for the
[3H]thymidine incorporation assay of bacterial secondary productivity. Appl. Environ.
Microbiol. 54:2018-2026.
del Giorgio, P. A., and G. Scarborough. 1995. Increase 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. Plankton Res. 17:1905-1924.
Fahnenstiel, G. L., L. Sicko-Goad, D. Scavia, and E. F. Stoermer. 1986. Importance of
picoplankton in Lake Superior. Can. J. Fish. Aquat. Sci. 43:235-240.
Fahnenstiel, G. L., and H. J. Carrick. 1992. Phototrophic picoplankton in Lakes Huron and
Michigan: abundance, distribution, composition, and contribution to biomass and production.
Can. J. Fish. Aquat. Sci. 49:378-388.
Fenchel. T. 1986. The ecology of heterotrophic microflagellates. Adv. Microb. Ecol. 9:57-97.
Ferguson, R. L., E. N. Buckley, and A. V. Palumbo. 1984. Response of marine bacterioplankton
to differential filtration and confinement. Appl. Environ. Microbiol. 47:49-55.
Herndl. G. J., G. Muller-Niklas, and J. Frick. 1993. Major role of ultraviolet-B in controlling
bacterioplankton growth in the surface layer of the ocean. Nature 361:717-719.
Kaplan, L. S., T. L. Bott, and J. K. Bielicki. 1992. Assessment of [3H]thymidine incroporation
into DNA as a method to determine bacterial productivity in stream bed sediments. Appl.
Environ. Microbiol. 58:3614-3621.
Karner, M., and J. A. Fuhrman. 1997. Determination of active marine bacterioplankton: a
comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining. Appl.
Environ. Microbiol. 63:1208-1213.
Kirchman, D., H. Ducklow, and R. Mitchell. 1982. Estimates of bacterial growth from changes
in uptake rates and biomass. Appl. Environ. Microbiol. 44:1296-1307.
Kirchman, D. L., E. K'Nees, and R. Hodson. 1985. Leucine incorporation and its potential as a
measure of protein synthesis by bacteria in natural aquatic systems. Appl. Environ. Microbiol.
49:599-607.
Moran, M. A., and R. E. Hodson. 1990. Bacterial production on humic and nonhumic
components of dissolved organic carbon. Limnol. Oceanogr. 35:1744-1756.
Munawar, M., et al. 1978. Relative importance of nannoplankton in Lake Superior
phytoplankton biomass and community metabolism. J. Great Lakes Res. 4:462-480.
Newell, S. Y., and R. R. Christian. 1981. Frequency of dividing cells as an estimator of bacterial
productivity. Appl. Environ. Microbiol. 42:23-31.
Novitsky, J. A. 1987. Microbial growth rates and biomass production in a marine sediment:
evidence for a very active by mostly nongrowing community. Appl. Environ. Microbiol.
53:2368-2372.
11 Pace, M. L. 1988. Bacterial mortality and the fate of bacterial production. Hydrobiology
159:41-49.*
Pedros-Alio, C. 1989. Toward an autecology of bacterioplankton. Pp. 297-336 In Plankton
Ecology, Succession if Plankton Communities (U. Sommer, ed.). Springer Verlag, Berlin.
Pedros-Alio, C., and T. D. Brock. 1983. The importance of attachment to particles for
planktonic bacteria. Arch. Hydrobiol. 98:354-379.
8 Peterson, B. J. 1980. Aquatic primary productivity and the 14C-CO2 method: A history of the
productivity problem. Ann. Rev. Ecol. Syst. 11:359-385.*
Poindexter. J. S. 1981. Oligotrophy: Fast and famine existence Adv. Microb. Ecol. 5:63-89. *
Pomeroy, L. R., and D. Deibel. 1986. Temperature regulation of bacterial activity during the
spring bloom in Newfoundland coastal waters. Science 233:359-361.*
Pomeroy, L. R., W. J. Wiebe, D. Deibel, R. J. Thompson, G. T. Rowe, and J. D. Pakulski. 1991.
Bacterial responses to temperature and substrate concentration during the Newfoundland
spring bloom. Mar. Ecol. Progr. Ser. 75:143-159.
Purcell, E. M. 1977. Life at low Reynolds number. Am. J. Phys. 45:3-11.*
Robarts, R. D. 1987. Effect of rainstorms on heterotrophic bacterial activity in a hypertrophic
African lake. Hydrobiologia 148:281-286.
Roszak, D. B., and R. E. Colwell. 1987. Survival strategies of bacteria in the natural
environment. Microbiol. Rev. 51:365-379.*
Schramm, A., L. H. Larsen, N. P. Revsbech, N. B. Ramsing, R. Amann, and K-H. Schleifer.
1996. Structure and function of a nitrifying biofilm as determined by in situ hybridization
and the use of microelectrodes. Appl. Environ. Microbiol. 62:461-4647.
Schut, F., D. J. DeVries, J. C. Gottschal, B. R. Robertson, W. Harder, R. A. Prins, and D. K.
Button. 1993. Isolation of typical marine bacteria by dilution culture: growth, maintenance,
and characteristics of isolates under laboratory conditions. Appl. Environ. Microbiol.
59:2150-2160.
Servais, P., G. Billen, and J. V. Rego. 1985. Rate of bacterial mortality in aquatic environments.
Appl. Environ. Microbiol. 49:1448-1454.
Simon, M., and F. Azam. 1989. Protein content and protein synthesis rates of planktonic marine
bacteria. Mar. Ecol. Progr. Ser. 51:201-213.*
Stockner, J. G., M. E. Klut, and W. P. Cochlan. 1990. Leaky filters: a warning to aquatic
ecologists. Can. J. Fish. Aquat. Sci. 47:16-23.
Wiebe, W. J., W. M. Sheldon, Jr., and L. R. Pomeroy. 1992. Bacterial growth in the cold:
Evidence for an enhanced substrate requirement. Appl. Environ. Microbiol. 58;359-364.
Population Interactions
Bird, D. F., and J. Kalff. 1986. Bacterial grazing by planktonic lake algae. Science 231:493-495. *
Caron, D. A., P. G. Davis, L. P. Madin, and J. McN. Sieburth. 1982. Heterotrophic bacteria and
bacterivorous protozoa in oceanic macroaggregates. Science 218:795-797.
Cotner, J. B., Jr., and R. G. Wetzel. 1992. Uptake of dissolved inorganic and organic
phosphorus compounds by phytoplankton and bacterioplankton. Limnol. Oceanogr.
37:232-243. *
Fredrickson, A. G., and G. Stephanopoulos. 1981. Microbial competition. Science 213:972-979.
15 Grimes, D. J. 1991. Ecology of estuarine bacteria capable of causing human disease: a review.
Estuaries 14:345-360.*
Maranger, R., and D. F. Bird. 1995. Viral abundance in aquatic systems: a comparison between
marine and fresh waters. Mar. Ecol. Prog. Ser. 121:217-226.
12 Pace, M L., and E. Funke. 1991. Regulation of planktonic microbial communities by nutrients
and herbivores. Ecology 72:904-914.*
Proctor, L., and J. Fuhrman. 1990. Viral mortality of marine bacteria and cyanobacteria.
Nature 343: 60-62.*
Sanders, R. W., D. A. Caron, and U-G. Berninger. 1992. Relationships between bacteria and
heterotrophic nanoplankton in marine and fresh waters: an inter-ecosystem comparison.
Mar. Ecol. Prog. Ser. 86:1-14.
Sherr, B. F., E. B. Sherr, and J. McDaniel. 1992. Effect of protistan grazing on the frequency of
dividing cells in bacterioplankton assemblages. Appl. Environ. Microbiol. 58:2381-2385. *
Shortreed, K. S., and J. G. Stockner. 1990. Effect of nutrient additions on distribution and
density of pico-, nano-, and microphytoplankton in an oligotrophic lake with a seasonal
hypolimnetic chlorophyll maximum. Can. J. Fish. Aquat. Sci. 47:262-273.
13 Suttle, C., A. Chan, and M. Cotrell. 1994. The significance of viruses to mortality in aquatic
microbial communities. Microb. Ecol. 28:237-243.
Weinbauer, M. G., and C. A. Suttle. 1996. Potential significance of lysogeny to bacteriophage
production and bacterial mortality in coastal waters of the Gulf of Mexico. Appl. Environ.
Microbiol. 62:4374-4380.
White, P. A., J. Kalff, J. B. Rasmussen, and J. M. Gasol. 1991. The effect of temperature and
algal biomass on bacterial production and specific growth rate in freshwater and marine
habitats. 21:99-118.
Wilcox, R. M., and J. A. Fuhrman. 1994. Bacterial viruses in coastal seawater: lytic rather than
lysogenic production. Mar. Ecol. Prog. Ser. 114:35-45.
Microbial Communities
Azam, F., T. Fenchel, J. G. Field, J. S. Gray, L. A. Meyer-Reil, and F. Thingstad. 1983. The
ecological role of water-column microbes in the sea. Mar. Ecol. Prog. Ser. 10:257-263.
Bratbak, G., F. Thingstad, and M. Heldal. 1994. Viruses and the microbial loop. Microb. Ecol.
28:209-221.*
13 Coleman, D. C. 1994. The microbial loop concept as used in terrestrial soil ecology studies.
Microb. Ecol. 28:245-250.*
Decho, A. W. 1990. Microbial exopolymer secretions in ocean environments: their role(s) in
food webs and marine processes. Oceanogr. Mar. Biol. Ann. Rev. 28:73-153.
Ferris, M. J., and D. M. Ward. 1997. Seasonal distributions of dominant 16S rRNA-defined
populations in a hot spring microbial mat examined by denaturing gradient gel eletrophoresis.
Appl. Environ. Microbiol. 63:1375-1381.
Gilbert, G. S., J. L. Parke, and M. K. Clayton. 1993. Effects of an introduced bacterium on
bacterial communities on roots. Ecology 74:840-854.*
Gold, T. 1992. The deep, hot biosphere. Proc. Natl. Acad. Sci, USA 89:6045-6049.*
Jannasch, H. W., and C. O. Wirsen. 1977. Microbial life in the deep sea. Sci. Amer. 236:42-52.
Johnston, C. G., and J. R. Vestal. 1991. Photosynthetic carbon incorporation and turnover in
antarctic cryptoendolithic microbial communities: Are they the slowest-growing communities
on Earth? Appl. Environ. Microbiol. 57:2308-2311.*
Krumholz, L. R., J. P. McKinley, G. A. Ulrich, and J. M Suflita. 1997. Confined subsurface
microbial communities in Cretaceous rock. Nature 386:64-66.
Lewis, D. L., and D. K. Gattie. 1990. Effects of cellular aggregation on the ecology of
microorganisms. ASM News 56:263-268.
MacGregor, B. J., D. P. Moser, E. W. Alm, K. H. Nealson, and D. A. Stahl. 1997.
Crenarchaeota in Lake Michigan sediment. Appl. Environ. Microbiol. 63:1178-1181.
Maki, J. S. 1993. The air-water interface as an extreme environment, p. 409-439. In T. E. Ford
(ed.), Aquatic microbiology. Blackwell.
Moyer, C. L., F. C. Dobbs, and D. M. Karl. 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. 60:871-879.
Norkrans, B. 1980. Surface microlayers in aquatic environments. Adv. Microb. Ecol. 4:51-85.
14 Paerl, H. W., and J. L. Pickney. 1996. A mini-review of microbial consortia: their roles in
aquatic production and biogeochemical cycling. Microb. Ecol. 31:225-247. *
Pick, F. R., and D. A. Caron. 1987. Picoplankton and nanoplankton biomass in Lake Ontario:
relative contribution of phototrophic and heterotrophic communities. Can. J. Fish. Aquat.
Sci. 44:2164-2172.
Schallenberg, M., and J. Kalff. 1993. The ecology of sediment bacteria in lakes and comparisons
with other aquatic systems. Ecology 74:919-934.
Serban, M. S., T. C. Kane, and B. K. Kinkle. 1996. A chemoautotrophically based cave
ecosystem. Science 272:1953-1955.
Sherr, E. B., and B. Sherr. 1991. Planktonic microbes: Tiny cells at the base of the ocean's
food webs. Trends Ecol. Evol. 6:50-54.
Stetter, K. O. 1995. Microbial life in hyperthrmal environments. ASM News 61:285-290.
14 Stevens, T. O., and J. P. McKinley. 1995. Lithoautotrohpic microbial ecoystems in deep basalt
aquifers. Science 270:450-454.
Thingstad, T. F., M. Heldal, G. Bratbak, and I. Dundas. 1993. Are viruses important partners in
pelagic food webs? TREE 8:209-213.
Wainright, S. C. 1990. Sediment-to-water fluxes of particulate material and microbes by
resuspension and their contribution to the planktonic food web. Mar. Ecol. Prog. Ser.
62:271-281.
[Also see Vol. 28 (1994) of the journal Microbial Ecology. It was a special issue dedicated to
the the microbial loop hypothesis.]
Microbial Roles in Ecosystem Function & Maintenance
Benner, R., et al. 1986. Biogeochemical cycling of lignocellulosic carbon in marine and
freshwater ecosystems: Relative contributions of procaryotes and eucaryotes. Limnol.
Oceanogr. 31:89-100.
Bratbak, G., M. Heldal, S. Norland, and T. F. Thingstad. 1990. Viruses as partners in spring
bloom microbial trophodynamics. Appl. Environ. Microbiol. 56:1400-1405.
Carlton, R. G., G. S. Walker, M. J. Klug, and R. G. Wetzel. 1989. Relative values of oxygen,
nitrate, and sulfate to terminal microbial processes in the sediments of Lake Superior. J.
Great Lakes Res. 15:133-140.
Ducklow, H. W., et al. 1986. Bacterioplankton: A sink for carbon in a coastal marine plankton
community. Science 232:865-867.*
Fenchel, T. M., and B. B. Jørgensen. 1977. Detritus food chains of aquatic ecosystems: The
role of bacteria. Adv. Microb. Ecol. 1-58.
Fossing, H., et al. 1995. Concentration and transport of nitrate by the mat-forming sulphur
bacterium Thioploca. Nature 374:713-715.*
Gardner, W. S., et al. 1989. Organic nitrogen mineralization and substrate limitation of bacteria
in lake Michigan. Limnol. Oceanogr. 34:478-485.
Nealson, K. H., and C. R. Myers. 1992. Microbial reduction of manganese and iron: new
approaches to carbon cycling. Appl. Environ. Microbiol. 58:439-443.
Scavia, D., and G. A. Laird. 1987. Bacterioplankton in Lake Michigan: Dynamics, controls, and
significance to carbon flux. Limnol. Oceanogr. 32:1017-1033.
Tortell, P. D., M. T. Maldonado, and N. M. Price. 1996. The role of heterotrophic bacteria in
iron-limited ocean ecoystems. Nature 383:330-332.
Wetzel, R. G. 1995. Death, detritus, and energy flow in aquatic ecosystems. Freshwater Biol.
33:83-89.
Biotechnology Aspects of Microbial Ecology
Ford, T. E. 1993. The microbial ecology of water distribution and outfall systems. Pp.
455-482 in Aquatic Microbiology, An Ecological Approach, T. E. Ford (ed). Blackwell
Scientific Publications, Boston, MA.
Gonzalez, J. M., J. Iriberri, L. Egea, and I. Barcina. 1992. Characterization of culturability,
protistan grazing, and death of enteric bacteria in aquatic ecosystems. Appl. Environ.
Microbiol. 58:998-1004.
Lappin-Scott, H. M., et al. 1988. Nutrient resuscitation and growth of starved cells in sandstone
cores: A novel approach to enhanced oil recovery. Appl. Environ. Microbiol. 54:1373-1382.
Smith, J. J., J. P. Howington, and G. A. McFetters. 1994. Survival, physiological response, and
recovery of enteric bacteria exposed to a polar marine environment. Appl. Environ.
Microbiol. 60:2977-2984. *
McFeters, G. A., and D. G. Stuart. 1972. Survival of coliform bacteria in natural waters: field
and laboratory studies with membrane-filter chambers. Appl. Microbiol. 24:805-811.
Shaw, J. J., F. Dane, D. Geiger, and J. W. Kloepper. 1992. Use of bioluminescence for
detection of genetically engineered microorganisms released into the environment. Appl.
Environ. Microbiol. 58:267-273.