Editing Limnology (section)

===Chemical properties===
The chemical composition of water in aquatic ecosystems is influenced by natural characteristics and processes including [[precipitation]], underlying [[soil]] and [[bedrock]] in the [[drainage basin]], [[erosion]], [[evaporation]], and [[sedimentation]].<ref name="limnology book"/> All bodies of water have a certain composition of both [[Organic compound|organic]] and [[Inorganic compound|inorganic]] elements and compounds. Biological reactions also affect the chemical properties of water. In addition to natural processes, human activities strongly influence the chemical composition of aquatic systems and their water quality.<ref name="water quality book" />

''Allochthonous'' sources of carbon or nutrients come from outside the aquatic system (such as plant and soil material).  Carbon sources from within the system, such as algae and the microbial breakdown of aquatic particulate [[organic carbon]], are ''autochthonous''. In aquatic food webs, the portion of biomass derived from allochthonous material is then named "allochthony".<ref>Grosbois, G., del Giorgio, P.A. & Rautio, M. (2017). [http://onlinelibrary.wiley.com/wol1/doi/10.1111/fwb.12879/full ''Zooplankton allochthony is spatially heterogeneous in a boreal lake'']. Freshwat. Biol., 62, 474-490</ref> In streams and small lakes, allochthonous sources of carbon are dominant while in large lakes and the ocean, autochthonous sources dominate.<ref>Eby, G.N., 2004, Principles of Environmental Geochemistry: Thomson Brooks/Cole, Pacific Grove, CA., 514 pp.</ref>

==== Oxygen and carbon dioxide ====
[[Oxygen saturation|Dissolved oxygen]] and dissolved [[carbon dioxide]] are often discussed together due their coupled role in [[Cellular respiration|respiration]] and [[photosynthesis]]. Dissolved oxygen concentrations can be altered by physical, chemical, and biological processes and reaction. Physical processes including wind mixing can increase dissolved oxygen concentrations, particularly in surface waters of aquatic ecosystems. Because dissolved oxygen solubility is linked to water temperatures, changes in temperature affect dissolved oxygen concentrations as warmer water has a lower capacity to "hold" oxygen as colder water.<ref name=":0">{{Cite book|title=Freshwater ecology : concepts and environmental applications of limnology|last=Dodds|first=Walter K.|date=2010|publisher=Academic Press|others=Whiles, Matt R.|isbn=9780123747242|edition= 2nd|location=Burlington, MA|oclc=784140625}}{{page needed|date=December 2020}}</ref> Biologically, both photosynthesis and aerobic respiration affect dissolved oxygen concentrations.<ref name="water quality book"/> Photosynthesis by [[Autotroph|autotrophic organisms]], such as [[phytoplankton]] and aquatic [[algae]], increases dissolved oxygen concentrations while simultaneously reducing carbon dioxide concentrations, since carbon dioxide is taken up during photosynthesis.<ref name=":0" /> All [[aerobic organism]]s in the aquatic environment take up dissolved oxygen during aerobic respiration, while carbon dioxide is released as a byproduct of this reaction. Because photosynthesis is light-limited, both photosynthesis and respiration occur during the [[daylight]] hours, while only respiration occurs during [[Night|dark]] hours or in dark portions of an ecosystem. The balance between dissolved oxygen production and consumption is calculated as the [[Lake metabolism|aquatic metabolism rate]].<ref>{{cite journal |last1=Cole |first1=Jonathan J. |last2=Caraco |first2=Nina F. |title=Carbon in catchments: connecting terrestrial carbon losses with aquatic metabolism |journal=Marine and Freshwater Research |date=2001 |volume=52 |issue=1 |pages=101 |doi=10.1071/mf00084 |bibcode=2001MFRes..52..101C |s2cid=11143190 }}</ref>
[[File:Lake metabolism cross section.png|thumb|upright=2.2|Lake cross-sectional diagram of the factors influencing lake metabolic rates and concentration of dissolved gases within lakes. Processes in gold text consume oxygen and produce carbon dioxide while processes in green text produce oxygen and consume carbon dioxide.]]
Vertical changes in the concentrations of dissolved oxygen are affected by both wind mixing of surface waters and the balance between photosynthesis and respiration of [[organic matter]]. These vertical changes, known as profiles, are based on similar principles as thermal stratification and light penetration. As light availability decreases deeper in the water column, photosynthesis rates also decrease, and less dissolved oxygen is produced. This means that dissolved oxygen concentrations generally decrease as you move deeper into the body of water because of photosynthesis is not replenishing dissolved oxygen that is being taken up through respiration.<ref name="water quality book" /> During periods of thermal stratification, water density gradients prevent oxygen-rich surface waters from mixing with deeper waters. Prolonged periods of stratification can result in the depletion of bottom-water dissolved oxygen; when dissolved oxygen concentrations are below 2 milligrams per liter, waters are considered [[Hypoxia (environmental)|hypoxic]].<ref name=":0" /> When dissolved oxygen concentrations are approximately 0 milligrams per liter, conditions are [[Anoxic waters|anoxic]]. Both hypoxic and anoxic waters reduce available habitat for organisms that respire oxygen, and contribute to changes in other chemical reactions in the water.<ref name=":0" />

==== Nitrogen ====
[[Nitrogen]] is a nutrient central for the function of aquatic ecosystems. Nitrogen is generally present as a [[gas|dissolved gas]] ([[Nitrogen gas|N<sub>2</sub>]]) in aquatic ecosystems, however due to the high energy requirement of utilising N<sub>2</sub> most organisms tend not to use it.<ref name=":3">{{Citation |last1=Dodds |first1=Walter K. |title=Nitrogen, Sulfur, Phosphorus, and Other Nutrients |date=2010 |work=Freshwater Ecology |pages=345–373 |url=https://linkinghub.elsevier.com/retrieve/pii/B9780123747242000143 |access-date=2025-04-24 |publisher=Elsevier |language=en |doi=10.1016/b978-0-12-374724-2.00014-3 |isbn=978-0-12-374724-2 |last2=Whiles |first2=Matt R.|url-access=subscription }}</ref> Therefore, most water quality studies tend to focus on [[nitrate]], [[nitrite]] and [[ammonia]] levels.<ref name="limnology book"/><ref name=":3" /> Most of these dissolved nitrogen compounds follow a seasonal pattern with greater concentrations in the [[Autumn|fall]] and [[winter]] months compared to the [[Spring (season)|spring]] and [[summer]].<ref name="limnology book"/> 

==== Phosphorus ====
Another important nutrient in aquatic systems is [[phosphorus]]. Phosphorus has a different role in aquatic ecosystems as it is a limiting factor in the growth of phytoplankton because of generally low concentrations in the water.<ref name="limnology book" /> Dissolved phosphorus is also crucial to all living things, is often very limiting to primary productivity in freshwater, and has its own distinctive ecosystem [[Phosphorus cycle|cycling]].<ref name="water quality book" />