The freshwater habitat is filled with various kinds of plants and animals which make the flora and fauna of the system. These organisms interact and are found in different parts of freshwater ecosystem.
Autotrophic organisms are producers which produce organic compounds from inorganic material. Algae employ solar energy to produce biomass from carbon dioxide and are the most significant autotrophic organisms in aquatic environments. Chemosynthetic bacteria are found in benthic marine ecosystems. These organisms are capable to feed on hydrogen sulfide in water which comes from volcanic vents. Great concentrations of animals which feed on the bacteria are found around volcanic vents. Several species have the higher density than water that must make them sink and end up in benthos. To combat this, phytoplankton have developed density changing mechanisms, by making vacuoles and gas vesicles or by varying shapes to induce drag, slowing their descent. A very sophisticated adaptation used by the small number of species is a tail-like flagella which can adjust vertical position and permit movement in any direction. Phytoplankton can also keep their presence in water column by being circulated in Langmuir rotations. Periphytic algae, on the other hand, are attached to a substrate. In lakes and ponds, they can cover all benthic surfaces.
Both kinds of plankton are significant as food sources and as oxygen providers. Plants, or macrophytes, in freshwater systems live in both benthic and pelagic zones and can be grouped according to the manner of growth:
1) Emergent macrophytes = rooted in substrate but with leaves and flowers extending into air,
2) Floating-leaved macrophytes = rooted in the substrate but with floating leaves,
3) Submerged macrophytes = not rooted in substrate and floating under the surface and
4) Free-floating macrophytes = not rooted in the substrate and floating on the surface.
These different forms of macrophytes usually take place in various areas of the benthic zone, with emergent vegetation nearest the shoreline, then floating leaved macrophytes, followed by submersed vegetation. Free-floating macrophytes can take place anywhere on the system's surface. Aquatic plants are more buoyant than their terrestrial counterpart as freshwater has the higher density than air. This makes structural rigidity insignificant in lakes and ponds (except in aerial stems and leaves). Therefore, leaves and stems of most aquatic plants utilize less energy to create and maintain woody tissue, investing energy in fast growth instead. To contend with stresses induced by wind and waves, plants should be both flexible and tough. Light is the most significant factor controlling distribution of submerged aquatic plants. Macrophytes are sources of food, oxygen, and habitat structure in benthic zone, but can't penetrate the depths of the euphotic zone and therefore are not found there.
Heterotrophic organisms consume autotrophic organisms and use the organic compounds in their bodies as energy sources and as raw materials to make their own biomass. Euryhaline organisms are salt tolerant and can survive in marine ecosystems, whereas stenohaline or salt intolerant species can only live in freshwater environments.
Water striders are predatory insects that depend on surface tension to walk on top of water. They live on surface of ponds, marshes, and other quiet waters. They can move very rapidly, up to 1.5 m/s. Zooplankton are small animals suspended in the water column. Similar to phytoplankton, these species have developed mechanisms which keep them from sinking to deeper waters, comprising drag-inducing body forms and active flicking of appendages like antennae or spines. Remaining in water column may have its benefits in terms of feeding, but this zone's lack of refugia leaves zooplankton susceptible to predation.
Vertebrate taxa inhabit freshwater systems as well. These comprise amphibians (like salamanders and frogs), reptiles (like turtles, snakes, and alligators), and the large number of waterfowl species. Most of these vertebrates spend part of their time in terrestrial habitats and therefore are not directly affected by abiotic factors in lake or pond. Several fish species are significant as consumers and as prey species to larger vertebrates.
Fishes have a range of physiological tolerances which are dependent on which species they belong to. They have various lethal temperatures, dissolved oxygen requirements, and spawning requirements which are based on activity levels and behaviors. As fishes are highly mobile, they are able to deal with inappropriate abiotic factors in one zone by just moving to another. A detrital feeder in profundal zone, for instance, which finds oxygen concentration has dropped very low, may feed closer to the benthic zone. The fish might also change its residence during various parts of its life history: hatching in the sediment nest, then moving to weedy benthic zone to develop in the protected environment with food resources, and lastly into pelagic zone as an adult.
Under certain conditions bacteria can colonize freshwaters infrequently making large rafts of filamentous mats called as sewage fungus - generally Sphaerotilus natans. Presence of such organisms is almost always the indicator of extreme organic pollution and would be anticipated to be matched with low dissolved oxygen concentrations and high BOD vales.
E. coli bacteria have been usually found in recreational waters and their presence is utilized to point presence of recent fecal contamination, but E. coli presence may not be indicative of human waste. E. coli are harbored in all warm-blooded animals: birds and mammals alike. E. coli bacteria have also been found in fish and turtles. Sand also harbors E. coli bacteria and few strains of E. coli have become naturalized. Few geographic areas may support exclusive populations of E. coli and on the contrary, few E. coli strains are cosmopolitan. Bacteria are present in all regions of freshwaters may be free-living or commensals. Free-living forms are related with decomposing organic material, biofilm on surfaces of rocks and plants, suspended in water column, and in the sediments of benthic and profundal zones. Other forms are also related with guts of lentic animals as parasites or in commensal relationships. Bacteria play the significant role in system metabolism by nutrient recycling.
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