A mesocosm is an experimental tool that brings a small part of the natural environment under controlled conditions. In this way mesocosms provide a link between observational field studies that take place in natural environments, but without replication, and controlled laboratory experiments that may take place under somewhat unnatural conditions.
When pursuing a laboratory experiment, the experimenter cannot account for every possible factor that would normally occur in the original environment. Mesocosms circumvent this problem as the experiment is performed in the natural environment, but in an enclosure that is small enough that key variables can be brought under control. Mesocosms have been used to evaluate how organisms or communities might react to environmental change, through deliberate manipulation of environmental variables, such as increased temperature, carbon dioxide or pH levels.
The advantage to mesocosm studies provides us with what we already know and what possible influential factors will produce a positive or negative reaction of our subject areas of interest. Manipulating something can give us an idea as to what to expect if something were to occur in that ecosystem or environment. For indoor mesocosms, growth chambers allow us to control the experiment. You can place plants in a growth chamber and manipulate the air, temperature, heat and light distribution and observe the effects when exposed to different amounts of each factor.
Using growth chambers for a laboratory experiment is sometimes a disadvantage due to the limited amount of space.  Another disadvantage to using mesocosms is not adequately imitating the environment, causing the organism to avoid giving off a certain reaction versus its natural behavior in its original environment.
[A] Mazzeo and colleagues examined the eating habits of Hoplias malabaricus fish when exposed to different amounts of phytoplankton, zooplankton, and competition. Three months prior to conducting the experiment, they maintained an average precipitation, air temperature, and overall subtropical environment. Using 12 units, they filled them with aquifer water, sand and plants and kept them in isolation until the environment became suitable for phytoplankton to emerge. After careful preparation, Mazzeo et al. began the experiment dividing those units into categories of a control (zooplankton and phytoplankton) and 3 experiments: (Jenynsia multidentata with zooplankton and phytoplankton), (juvenile Hoplias malabaricus with zooplankton and phytoplankton), and (Large Hoplias malabaricus, Jenynsia multidentata, zooplankton, and phytoplankton) and observed biomass differences within different conditions.
[B] Flanagan and McCauley tested the effects of climate warming on carbon dioxide concentration on shallow ponds by creating an eight-cylinder shaped in situ mesocosms. They divided it into four controls and four experiments on University of Calgary's campus pond. Those mesocosms contained openings underneath and were submerged at the same depth as the pond. By carefully sustaining the sediments and temperature from any changes, the production of zooplankton and algae were successful. After manipulation (pumping heat into water), they measured the sediments at the bottom of the pond for carbon dioxide concentration. After collecting data and analyzing it, Flanagan and McCauley concluded that due to the warming of the environment in the pond, carbon dioxide from the pond will increase into the surroundings, in turn, decreasing the amount of carbon dioxide within the sediments, indirectly modifying the carbon cycle of that ecosystem.
[C] Mesocosms are useful for studying the fate of pollutants in marine environments as well as providing the ability to conduct controlled manipulative experiments that could not be undertaken in natural marine environments. Since 1976, the Marine Ecosystems Research Laboratory (MERL) at the University of Rhode Island has been conducting pollution studies and experimental marine ecological studies using mesocosm tanks drawing water from nearby Narragansett Bay.
Example publications of scientific studies using the MERL mesocosms include:
- Hinga, K.R., M.E.Q. Pilson, R.F. Lee, J.W. Farrington, K. Tjessem and A.C. Davis. 1980. Biogeochemistry of benzanthracene in an enclosed marine ecosystem. Environmental Science and Technology 14:1136-1143.
- Hunt, C.D. and S.L. Smith. 1982. Controlled marine ecosystems- A tool for studying stable trace metal cycles: Long-term response and variability. pp. 123–135 In: G.D. Grice and M.R. Reeves, (eds.) Marine Mesocosms: Biological and Chemical Research in Experimental Ecosystems. Springer Verlag, New York.
- Donaghay, P.L. 1984. Utility of mesocosms to assess marine pollution. pp. 589–620 In: H.H. White, (ed). Concepts in Marine Pollution Measurements. Maryland Sea Grant College, College Park, Maryland.
- Doering, P.H., C.A. Oviatt, and J.R. Reilly 1986. The effects of the filter feeding clam Mercenaria mercenaria on carbon cycling in experimental marine mesocosms. Journal of Marine Research 44:839-861.
- Oviatt, C.A., D.T. Rudnick, A.A. Keller, P.A. Sampou, and G.T. Almquist. 1986. A comparison of system oxygen and carbon dioxide and C-14 measurements of metabolism in estuarine mesocosms. Marine Ecology Progress Series 28:57-67.
- Nowicki, B.L. and C.A. Oviatt. 1990. Are estuaries traps for anthropogenic nutrients? Evidence from estuarine mesocosms. Marine Ecology Progress Series 66:131-146.
- Doering, P.H., C.A. Oviatt, B.L. Nowicki, E.G. Klos and L.W. Reed. 1995. Phosphorus and nitrogen limitation of primary production in a simulated estuarine gradient. Limnology and Oceanography. 124:271-287.
- Peitros, J.M. and M.A. Rice. 2003. The impacts of aquacultured oysters, Crassostrea virginica (Gmelin, 1791) on water quality and sedimentation: results of a mesocosm study. Aquaculture 220:407-422.
- "MESOCOSM". Retrieved 18 July 2011.
- Sala, Jackson, Mooney, Howarth, O.E., R.B., H.A., R.W. (2000). Methods in Ecosystem Science. New York: Springer-Verlag. p. 353.
- Kennedy, A.D. (1995a). "Temperature Effects of Passive Greenhouse Apparatus in High Latitude Climate Change Experiments". Funct.Ecol. 9: 340–350.
- Kennedy, A.D. (1995b). "Simulated Climate Change: Are Passive Greenhouses a Valid Microcosm for Testing the Biological Effects of Environmental Perturbations?". Global Change Biology 1: 29–42. doi:10.1111/j.1365-2486.1995.tb00004.x.
- Dudzik, M.; Harte, Jassby, Lapan, Levy, Rees (1979). "Some Considerations in the Design of Aquatic Microcosms for Plankton Studies". Int. J. Environ.Studies 13: 125–130.
- Mazzeo, Ne'stor; Iglesias,C., Teixeira-de Mello,F., Borthagaray, A., Fosalba, C., Ballabio, R., Larrea, D., Vilches, J., Garc'ia,S, Pacheco, J.P., Jeppesen, E. (May 2010). "Trophic Cascade Effects of Hoplias malbaricus (Characiformes, Erythrinidae) in Subtropical Lakes Food Webs: A Mesocosm Approach". Hydrobiologia 644 (1): 325.
- Flanagan, Kyla; McCauley (2010). "Edward". Aquatic Ecology 44 (4): 749–759.
- "The Marine Ecosystem Research Laboratory". University of Rhode Island. Retrieved 12 July 2011.
- Klos, E (1989). "Diving techniques in marine mesocosms". In: Lang, MA; Jaap, WC (ed). Diving for Science…1989. Proceedings of the American Academy of Underwater Sciences annual scientific diving symposium 28 September - 1 October 1989 Wood Hole Oceanographic Institution, Woods Hole, Massachusetts, USA. Retrieved 2013-04-27.