Editing Ecosystem (section)

==Processes==
[[File:River gambia Niokolokoba National Park.gif|thumb|[[Rainforest]] ecosystems are rich in [[biodiversity]]. This is the [[Gambia River]] in [[Senegal]]'s [[Niokolo-Koba National Park]].]]
[[File:Baja California Desert.jpg|thumb|[[Flora]] of [[Baja California desert]], [[Cataviña]] region, [[Mexico]]]]

=== External and internal factors ===
Ecosystems are controlled by both external and internal factors. External factors, also called state factors, control the overall structure of an ecosystem and the way things work within it, but are not themselves influenced by the ecosystem. On broad geographic scales, [[climate]] is the factor that "most strongly determines ecosystem processes and structure".<ref name="Chapin-2011a">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Chapter 1: The Ecosystem Concept|oclc=755081405}}</ref>{{rp|14}} Climate determines the [[biome]] in which the ecosystem is embedded. Rainfall patterns and seasonal temperatures influence photosynthesis and thereby determine the amount of energy available to the ecosystem.<ref name="Chapin-2011d" />{{rp|145}}

[[Parent material]] determines the nature of the soil in an ecosystem, and influences the supply of mineral nutrients. [[Topography]] also controls ecosystem processes by affecting things like [[microclimate]], soil development and the movement of water through a system. For example, ecosystems can be quite different if situated in a small depression on the landscape, versus one present on an adjacent steep hillside.<ref name="Chapin-2011b">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Chapter 2: Earth's Climate System|oclc=755081405}}</ref>{{rp|39}}<ref name="Chapin-2011c">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Chapter 3: Geology, Soils, and Sediments|oclc=755081405}}</ref>{{rp|66}}

Other external factors that play an important role in ecosystem functioning include time and potential [[biota (ecology)|biota]], the organisms that are present in a region and could potentially occupy a particular site. Ecosystems in similar environments that are located in different parts of the world can end up doing things very differently simply because they have different pools of species present.<ref name="Chapin-2011j">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Chapter 11: Species Effects on Ecosystem Processes|oclc=755081405}}</ref>{{rp|321}} The [[introduced species|introduction of non-native species]] can cause substantial shifts in ecosystem function.<ref>{{Cite journal|last1=Simberloff|first1=Daniel|last2=Martin|first2=Jean-Louis|last3=Genovesi|first3=Piero|last4=Maris|first4=Virginie|last5=Wardle|first5=David A.|last6=Aronson|first6=James|last7=Courchamp|first7=Franck|last8=Galil|first8=Bella|last9=García-Berthou|first9=Emili|date=2013|title=Impacts of biological invasions: what's what and the way forward|journal=Trends in Ecology & Evolution|volume=28|issue=1|pages=58–66|doi=10.1016/j.tree.2012.07.013|pmid=22889499|bibcode=2013TEcoE..28...58S |issn=0169-5347|hdl=10261/67376|hdl-access=free}}</ref>

Unlike external factors, internal factors in ecosystems not only control ecosystem processes but are also controlled by them.<ref name="Chapin-2011a" />{{rp|16}} While the [[Resource (biology)|resource]] inputs are generally controlled by external processes like climate and parent material, the availability of these resources within the ecosystem is controlled by internal factors like decomposition, root competition or shading.<ref>{{Cite web|date=2018-07-17|title=46.1A: Ecosystem Dynamics|url=https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/46%3A_Ecosystems/46.1%3A__Ecology_of_Ecosystems/46.1A%3A_Ecosystem_Dynamics|access-date=2021-08-02|website=Biology LibreTexts|language=en|archive-date=2021-08-02|archive-url=https://web.archive.org/web/20210802144400/https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book:_General_Biology_(Boundless)/46:_Ecosystems/46.1:__Ecology_of_Ecosystems/46.1A:_Ecosystem_Dynamics|url-status=live}}{{open access}}[[File:CC-BY icon.svg|50px]] Text was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/  Creative Commons Attribution 4.0 International License] {{Webarchive|url=https://web.archive.org/web/20171016050101/https://creativecommons.org/licenses/by/4.0/ |date=2017-10-16 }}.</ref> Other factors like disturbance, succession or the types of species present are also internal factors.

===Primary production===
[[File:Seawifs global biosphere.jpg|upright=1.8|thumb|Global oceanic and terrestrial phototroph abundance, from September 1997 to August 2000. As an estimate of [[autotroph]] biomass, it is only a rough indicator of primary production potential and not an actual estimate of it.]]
{{main|Primary production}}
Primary production is the production of [[organic matter]] from inorganic carbon sources. This mainly occurs through [[photosynthesis]]. The energy incorporated through this process supports life on earth, while the carbon makes up much of the organic matter in living and dead biomass, [[soil carbon]] and [[fossil fuel]]s. It also drives the [[carbon cycle]], which influences global [[climate]] via the [[greenhouse effect]].

Through the process of photosynthesis, plants capture energy from light and use it to combine [[carbon dioxide]] and water to produce [[carbohydrate]]s and [[oxygen]]. The photosynthesis carried out by all the plants in an ecosystem is called the gross primary production (GPP).<ref name="Chapin-2011d">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Chapter 5: Carbon Inputs to Ecosystems|oclc=755081405}}</ref>{{rp|124}} About half of the gross GPP is respired by plants in order to provide the energy that supports their growth and maintenance.<ref name="Chapin-2011e">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Chapter 6: Plant Carbon Budgets|oclc=755081405}}</ref>{{rp|157}} The remainder, that portion of GPP that is not used up by respiration, is known as the [[net primary production]] (NPP).<ref name="Chapin-2011e" />{{rp|157}} Total photosynthesis is limited by a range of environmental factors. These include the amount of light available, the amount of [[leaf]] area a plant has to capture light (shading by other plants is a major limitation of photosynthesis), the rate at which carbon dioxide can be supplied to the [[chloroplast]]s to support photosynthesis, the availability of water, and the availability of suitable temperatures for carrying out photosynthesis.<ref name="Chapin-2011d" />{{rp|155}}

===Energy flow===

{{main|Energy flow (ecology)}}
{{See also|Food web|Trophic level}}
[[Energy]] and [[carbon]] enter ecosystems through photosynthesis, are incorporated into living tissue, transferred to other organisms that feed on the living and dead plant matter, and eventually released through respiration.<ref name="Chapin-2011e" />{{rp|157}} The carbon and energy incorporated into plant tissues (net primary production) is either consumed by animals while the plant is alive, or it remains uneaten when the plant tissue dies and becomes [[detritus]]. In [[terrestrial ecosystem]]s, the vast majority of the net primary production ends up being broken down by [[decomposition|decomposers]]. The remainder is consumed by animals while still alive and enters the plant-based trophic system. After plants and animals die, the organic matter contained in them enters the detritus-based trophic system.<ref name="Chapin-2011i">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Chapter 10: Trophic Dynamics|oclc=755081405}}</ref>

[[Ecosystem respiration]] is the sum of [[Cellular respiration|respiration]] by all living organisms (plants, animals, and decomposers) in the ecosystem.<ref>{{Cite journal|last1=Yvon-Durocher|first1=Gabriel|last2=Caffrey|first2=Jane M.|last3=Cescatti|first3=Alessandro|last4=Dossena|first4=Matteo|last5=Giorgio|first5=Paul del|last6=Gasol|first6=Josep M.|last7=Montoya|first7=José M.|last8=Pumpanen|first8=Jukka|last9=Staehr|first9=Peter A.|date=2012|title=Reconciling the temperature dependence of respiration across timescales and ecosystem types|journal=Nature|language=En|volume=487|issue=7408|pages=472–476|bibcode=2012Natur.487..472Y|doi=10.1038/nature11205|issn=0028-0836|pmid=22722862|s2cid=4422427}}</ref> [[Net ecosystem production]] is the difference between [[Primary production|gross primary production]] (GPP) and ecosystem respiration.<ref name="Lovett-2006">{{Cite journal|last1=Lovett|first1=Gary M.|last2=Cole|first2=Jonathan J.|last3=Pace|first3=Michael L.|date=2006|title=Is Net Ecosystem Production Equal to Ecosystem Carbon Accumulation?|journal=Ecosystems|language=en|volume=9|issue=1|pages=152–155|doi=10.1007/s10021-005-0036-3|bibcode=2006Ecosy...9..152L |issn=1435-0629|s2cid=5890190}}</ref> In the absence of disturbance, net ecosystem production is equivalent to the net carbon accumulation in the ecosystem.

Energy can also be released from an ecosystem through disturbances such as [[wildfire]] or transferred to other ecosystems (e.g., from a forest to a stream to a lake) by [[erosion]].

In [[aquatic ecosystem|aquatic systems]], the proportion of plant biomass that gets consumed by [[herbivore]]s is much higher than in terrestrial systems.<ref name="Chapin-2011i" /> In trophic systems, photosynthetic organisms are the primary producers. The organisms that consume their tissues are called primary consumers or [[secondary production|secondary producers]]—[[herbivores]]. Organisms which feed on [[microbe]]s ([[bacteria]] and [[fungi]]) are termed [[microbivore]]s. Animals that feed on primary consumers—[[carnivore]]s—are secondary consumers. Each of these constitutes a trophic level.<ref name="Chapin-2011i" />

The sequence of consumption—from plant to herbivore, to carnivore—forms a [[food chain]]. Real systems are much more complex than this—organisms will generally feed on more than one form of food, and may feed at more than one trophic level. Carnivores may capture some prey that is part of a plant-based trophic system and others that are part of a detritus-based trophic system (a bird that feeds both on herbivorous grasshoppers and earthworms, which consume detritus). Real systems, with all these complexities, form [[food web]]s rather than food chains which present a number of common, non random properties in the topology of their network.<ref>{{cite journal |last1=Briand |first1=F. |last2=Cohen |first2=J.E. |title=Community food webs have scale-invariant structure |journal=Nature |date=19 January 1984 |volume=307 |issue=5948 |pages=264–267|doi=10.1038/307264a0 |bibcode=1984Natur.307..264B |s2cid=4319708 }}</ref>

===Decomposition===
{{See also|Decomposition}}
[[File:Decomposition stages.jpg|thumb|upright=3.0|Sequence of a decomposing pig carcass over time]]
The carbon and nutrients in [[soil organic matter|dead organic matter]] are broken down by a group of processes known as decomposition. This releases nutrients that can then be re-used for plant and microbial production and returns carbon dioxide to the atmosphere (or water) where it can be used for photosynthesis. In the absence of decomposition, the dead organic matter would accumulate in an ecosystem, and nutrients and atmospheric carbon dioxide would be depleted.<ref name="Chapin-2011f" />{{rp|183}}

Decomposition processes can be separated into three categories—[[leaching (agriculture)|leaching]], fragmentation and chemical alteration of dead material. As water moves through dead organic matter, it dissolves and carries with it the water-soluble components. These are then taken up by organisms in the soil, react with mineral soil, or are transported beyond the confines of the ecosystem (and are considered lost to it).<ref name="Chapin-2011h">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Chapter 9: Nutrient cycling|oclc=755081405}}</ref>{{rp|271–280}} Newly shed leaves and newly dead animals have high concentrations of water-soluble components and include [[sugar]]s, [[amino acid]]s and mineral nutrients. Leaching is more important in wet environments and less important in dry ones.<ref name="Chapin-2011c" />{{rp|69–77}}

Fragmentation processes break organic material into smaller pieces, exposing new surfaces for colonization by microbes. Freshly shed [[leaf litter]] may be inaccessible due to an outer layer of [[plant cuticle|cuticle]] or [[Bark (botany)|bark]], and [[protoplasm|cell contents]] are protected by a [[cell wall]]. Newly dead animals may be covered by an [[exoskeleton]]. Fragmentation processes, which break through these protective layers, accelerate the rate of microbial decomposition.<ref name="Chapin-2011f">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Chapter 7: Decomposition and Ecosystem Carbon Budgets|oclc=755081405}}</ref>{{rp|184}} Animals fragment detritus as they hunt for food, as does passage through the gut. [[Freeze-thaw cycle]]s and cycles of wetting and drying also fragment dead material.<ref name="Chapin-2011f" />{{rp|186}}

The chemical alteration of the dead organic matter is primarily achieved through bacterial and fungal action. Fungal [[hypha]]e produce enzymes that can break through the tough outer structures surrounding dead plant material. They also produce enzymes that break down [[lignin]], which allows them access to both cell contents and the nitrogen in the lignin. Fungi can transfer carbon and nitrogen through their hyphal networks and thus, unlike bacteria, are not dependent solely on locally available resources.<ref name="Chapin-2011f" />{{rp|186}}

==== Decomposition rates ====
Decomposition rates vary among ecosystems.<ref name="Ochoa-Hueso-2019">{{cite journal |last1=Ochoa-Hueso |first1=R |last2=Delgado-Baquerizo |first2=M |last3=King |first3=PTA |last4=Benham |first4=M |last5=Arca |first5=V |last6=Power |first6=SA |title=Ecosystem type and resource quality are more important than global change drivers in regulating early stages of litter decomposition |journal=Soil Biology and Biochemistry |date=February 2019 |volume=129 |pages=144–152 |doi=10.1016/j.soilbio.2018.11.009 |bibcode=2019SBiBi.129..144O |s2cid=92606851 |hdl=10261/336676 |hdl-access=free }}</ref> The rate of decomposition is governed by three sets of factors—the physical environment (temperature, moisture, and soil properties), the quantity and quality of the dead material available to decomposers, and the nature of the microbial community itself.<ref name="Chapin-2011f" />{{rp|194}} Temperature controls the rate of microbial respiration; the higher the temperature, the faster the microbial decomposition occurs. Temperature also affects soil moisture, which affects decomposition. Freeze-thaw cycles also affect decomposition—freezing temperatures kill soil microorganisms, which allows leaching to play a more important role in moving nutrients around. This can be especially important as the soil thaws in the spring, creating a pulse of nutrients that become available.<ref name="Chapin-2011h" />{{rp|280}}

Decomposition rates are low under very wet or very dry conditions. Decomposition rates are highest in wet, moist conditions with adequate levels of oxygen. Wet soils tend to become deficient in oxygen (this is especially true in [[wetland]]s), which slows microbial growth. In dry soils, decomposition slows as well, but bacteria continue to grow (albeit at a slower rate) even after soils become too dry to support plant growth.<ref name="Chapin-2011f" />{{rp|200}}

=== Dynamics and resilience ===
{{Further|Resistance (ecology)|Ecological resilience}}

Ecosystems are dynamic entities. They are subject to periodic disturbances and are always in the process of recovering from past disturbances.<ref name="Chapin-2011k" />{{rp|347}} When a [[perturbation (biology)|perturbation]] occurs, an ecosystem responds by moving away from its initial state. The tendency of an ecosystem to remain close to its equilibrium state, despite that disturbance, is termed its [[resistance (ecology)|resistance]]. The capacity of a system to absorb disturbance and reorganize while undergoing change so as to retain essentially the same function, structure, identity, and feedbacks is termed its [[ecological resilience]].<ref>{{Cite book|title=Principles of ecosystem stewardship: resilience-based natural resource management in a changing world|date=2009|publisher=Springer|editor-first1=F. Stuart III |editor-last1=Chapin |editor-first2=Gary P. |editor-last2=Kofinas |editor-first3=Carl |editor-last3=Folke |editor-first4=Melissa C. |editor-last4=Chapin|isbn=978-0-387-73033-2|edition=1st|location=New York|oclc=432702920}}</ref><ref>{{Cite journal|last1=Walker|first1=Brian|last2=Holling|first2=C. S.|last3=Carpenter|first3=Stephen R.|last4=Kinzig|first4=Ann P.|date=2004|title=Resilience, Adaptability and Transformability in Social-ecological Systems|url=http://www.ecologyandsociety.org/vol9/iss2/art5/|journal=Ecology and Society|language=en|volume=9|issue=2|pages=art5|doi=10.5751/ES-00650-090205 |doi-access=free |issn=1708-3087|hdl=10535/3282|hdl-access=free|access-date=2021-07-23|archive-date=2019-05-17|archive-url=https://web.archive.org/web/20190517073955/https://www.ecologyandsociety.org/vol9/iss2/art5/|url-status=live}}</ref> Resilience thinking also includes humanity as an integral part of the [[biosphere]] where we are dependent on [[ecosystem services]] for our survival and must build and maintain their natural capacities to withstand shocks and disturbances.<ref>{{Cite web|last=Simonsen|first=S.H. |publisher=Stockholm Resilience Centre |title=Applying Resilience Thinking|url=https://whatisresilience.org/wp-content/uploads/2016/04/Applying_resilience_thinking.pdf|url-status=live|archive-url=https://web.archive.org/web/20171215163627/http://whatisresilience.org:80/wp-content/uploads/2016/04/Applying_resilience_thinking.pdf |archive-date=2017-12-15 }}</ref> Time plays a central role over a wide range, for example, in the slow development of soil from bare rock and the faster [[ecological succession|recovery of a community from disturbance]].<ref name="Chapin-2011e" />{{rp|67}}

[[Disturbance (ecology)|Disturbance]] also plays an important role in ecological processes. [[F. Stuart Chapin III|F. Stuart Chapin]] and coauthors define disturbance as "a relatively discrete event in time that removes plant biomass".<ref name="Chapin-2011k">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Chapter 12: Temporal Dynamics|oclc=755081405}}</ref>{{rp|346}} This can range from [[herbivore]] outbreaks, treefalls, fires, hurricanes, floods, [[Glacial motion|glacial advances]], to [[Types of volcanic eruptions|volcanic eruptions]]. Such disturbances can cause large changes in plant, animal and microbe populations, as well as soil organic matter content. Disturbance is followed by succession, a "directional change in ecosystem structure and functioning resulting from biotically driven changes in resource supply."<ref name="Chapin-2011m">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Glossary|oclc=755081405}}</ref>{{rp|470}}

The frequency and severity of disturbance determine the way it affects ecosystem function. A major disturbance like a volcanic eruption or [[Glacier|glacial]] advance and retreat leave behind soils that lack plants, animals or organic matter. Ecosystems that experience such disturbances undergo [[primary succession]]. A less severe disturbance like forest fires, hurricanes or cultivation result in [[secondary succession]] and a faster recovery.<ref name="Chapin-2011k" />{{rp|348}} More severe and more frequent disturbance result in longer recovery times.

From one year to another, ecosystems experience variation in their biotic and abiotic environments. A [[drought]], a colder than usual winter, and a pest outbreak all are short-term variability in environmental conditions. Animal populations vary from year to year, building up during resource-rich periods and crashing as they overshoot their food supply. Longer-term changes also shape ecosystem processes. For example, the forests of eastern North America still show legacies of [[Agriculture|cultivation]] which ceased in 1850 when large areas were reverted to forests.<ref name="Chapin-2011k" />{{rp|340}} Another example is the [[methane]] production in eastern [[Siberia]]n lakes that is controlled by [[organic matter]] which accumulated during the [[Pleistocene]].<ref>{{Cite journal|last1=Walter|first1=K. M.|last2=Zimov|first2=S. A.|last3=Chanton|first3=J. P.|last4=Verbyla|first4=D.|last5=Chapin|first5=F. S.|date=2006|title=Methane bubbling from Siberian thaw lakes as a positive feedback to climate warming|url=http://faculty.jsd.claremont.edu/emorhardt/159/pdfs/2007/Walter%20et%20al.%202006.pdf |journal=Nature|language=en|volume=443|issue=7107|pages=71–75|doi=10.1038/nature05040|pmid=16957728|bibcode=2006Natur.443...71W|s2cid=4415304 |s2cid-access=free |issn=0028-0836|access-date=2021-08-16|archive-date=Nov 23, 2011 |archive-url=https://web.archive.org/web/20111123193233/http://faculty.jsd.claremont.edu/emorhardt/159/pdfs/2007/Walter%20et%20al.%202006.pdf |url-status=dead }}</ref>

{{clear}}
[[File:Panorama presa las niñas mogan gran canaria.jpg|thumb|upright=4.1|center|{{center|1=A [[freshwater]] lake in [[Gran Canaria]], an [[island]] of the [[Canary Islands]]. Clear boundaries make lakes convenient to study using an [[ecosystem approach]].}}]]

===Nutrient cycling===
{{See also|Nutrient cycle|Biogeochemical cycle|Nitrogen cycle}}
[[File:Nitrogen Cycle.jpg|thumb|right|upright=1.8|Biological nitrogen cycling]]
Ecosystems continually exchange energy and carbon with the wider [[environment (systems)|environment]]. Mineral nutrients, on the other hand, are mostly cycled back and forth between plants, animals, microbes and the soil. Most nitrogen enters ecosystems through biological [[nitrogen fixation]], is deposited through precipitation, dust, gases or is applied as [[fertilizer]].<ref name="Chapin-2011h" />{{rp|266}} Most [[terrestrial ecosystems]] are nitrogen-limited in the short term making [[Nitrogen cycle|nitrogen cycling]] an important control on ecosystem production.<ref name="Chapin-2011h" />{{rp|289}} Over the long term, phosphorus availability can also be critical.<ref>{{Cite journal|last1=Vitousek|first1=P.|last2=Porder|first2=S.|date=2010|title=Terrestrial phosphorus limitation: mechanisms, implications, and nitrogen–phosphorus interactions|journal=Ecological Applications|volume=20|issue=1|pages=5–15|doi=10.1890/08-0127.1|pmid=20349827|bibcode=2010EcoAp..20....5V |doi-access=free}}</ref>

Macronutrients which are required by all plants in large quantities include the primary nutrients (which are most limiting as they are used in largest amounts): Nitrogen, phosphorus, potassium.<ref name="Chapin-2011g">{{Cite book|last=Chapin|first=F. Stuart III|title=Principles of terrestrial ecosystem ecology|date=2011|publisher=Springer|others=P. A. Matson, Peter Morrison Vitousek, Melissa C. Chapin|isbn=978-1-4419-9504-9|edition=2nd|location=New York|chapter=Chapter 8: Plant Nutrient Use|oclc=755081405}}</ref>{{rp|231}} Secondary major nutrients (less often limiting) include: Calcium, magnesium, sulfur. [[Micronutrient]]s required by all plants in small quantities include boron, chloride, copper, iron, manganese, molybdenum, zinc. Finally, there are also beneficial nutrients which may be required by certain plants or by plants under specific environmental conditions: aluminum, cobalt, iodine, nickel, selenium, silicon, sodium, vanadium.<ref name="Chapin-2011g" />{{rp|231}}

Until modern times, nitrogen fixation was the major source of nitrogen for ecosystems. Nitrogen-fixing bacteria either live [[symbiosis|symbiotically]] with plants or live freely in the soil. The energetic cost is high for plants that support nitrogen-fixing symbionts—as much as 25% of gross primary production when measured in controlled conditions. Many members of the [[legume]] plant family support nitrogen-fixing symbionts. Some [[cyanobacteria]] are also capable of nitrogen fixation. These are [[phototroph]]s, which carry out photosynthesis. Like other nitrogen-fixing bacteria, they can either be free-living or have symbiotic relationships with plants.<ref name="Chapin-2011k" />{{rp|360}} Other sources of nitrogen include [[acid deposition]] produced through the combustion of fossil fuels, [[ammonia]] gas which evaporates from agricultural fields which have had fertilizers applied to them, and dust.<ref name="Chapin-2011h" />{{rp|270}} Anthropogenic nitrogen inputs account for about 80% of all nitrogen fluxes in ecosystems.<ref name="Chapin-2011h" />{{rp|270}}

When plant tissues are shed or are eaten, the nitrogen in those tissues becomes available to animals and microbes. Microbial decomposition releases nitrogen compounds from dead organic matter in the soil, where plants, fungi, and bacteria compete for it. Some soil bacteria use organic nitrogen-containing compounds as a source of carbon, and release [[ammonium]] ions into the soil. This process is known as [[ammonification|nitrogen mineralization]]. Others convert ammonium to [[nitrite]] and [[nitrate]] ions, a process known as [[nitrification]]. [[Nitric oxide]] and [[nitrous oxide]] are also produced during nitrification.<ref name="Chapin-2011h" />{{rp|277}} Under nitrogen-rich and oxygen-poor conditions, nitrates and nitrites are converted to [[nitrogen|nitrogen gas]], a process known as [[denitrification]].<ref name="Chapin-2011h" />{{rp|281}}

Mycorrhizal fungi which are symbiotic with plant roots, use carbohydrates supplied by the plants and in return transfer phosphorus and nitrogen compounds back to the plant roots.<ref>{{Cite journal|last=Bolan|first=N.S.|date=1991|title=A critical review on the role of mycorrhizal fungi in the uptake of phosphorus by plants|journal=Plant and Soil|volume=134|issue=2|pages=189–207|doi=10.1007/BF00012037|bibcode=1991PlSoi.134..189B |s2cid=44215263}}</ref><ref name="Hestrin-2019" /> This is an important pathway of organic nitrogen transfer from dead organic matter to plants. This mechanism may contribute to more than 70 Tg of annually assimilated plant nitrogen, thereby playing a critical role in global nutrient cycling and ecosystem function.<ref name="Hestrin-2019">{{Cite journal|last1=Hestrin|first1=R.|last2=Hammer|first2=E.C.|last3=Mueller|first3=C.W.|date=2019|title=Synergies between mycorrhizal fungi and soil microbial communities increase plant nitrogen acquisition|journal=Commun Biol|volume=2|page=233|doi=10.1038/s42003-019-0481-8|pmid=31263777|pmc=6588552}}</ref>

Phosphorus enters ecosystems through [[weathering]]. As ecosystems age this supply diminishes, making phosphorus-limitation more common in older landscapes (especially in the tropics).<ref name="Chapin-2011h" />{{rp|287–290}} Calcium and sulfur are also produced by weathering, but acid deposition is an important source of sulfur in many ecosystems. Although magnesium and manganese are produced by weathering, exchanges between soil organic matter and living cells account for a significant portion of ecosystem fluxes. Potassium is primarily cycled between living cells and soil organic matter.<ref name="Chapin-2011h" />{{rp|291}}

===Function and biodiversity===
{{Main|Biodiversity}}{{See also|Ecosystem diversity}}
[[File:View of loch lomond.JPG|thumb|[[Loch Lomond]] in [[Scotland]] forms a relatively isolated ecosystem. The fish community of this lake has remained stable over a long period until a number of [[introduced species|introductions]] in the 1970s restructured its [[food web]].<ref>{{cite journal | last=Adams | first=C.E. | title=The fish community of Loch Lomond, Scotland: its history and rapidly changing status | journal=Hydrobiologia | year=1994 | volume=290 | issue=1–3 | pages=91–102 | doi=10.1007/BF00008956 | s2cid=6894397 | doi-access=free | bibcode=1994HyBio.290...91A }}</ref>]]
[[File:Spiny Forest Ifaty Madagascar.jpg|thumb|Spiny forest at Ifaty, [[Madagascar]], featuring various ''[[Adansonia]]'' (baobab) species, ''[[Alluaudia procera]]'' (Madagascar ocotillo) and other vegetation]]
[[Biodiversity]] plays an important role in ecosystem functioning.<ref name="Schulze-2005">{{cite book |last=Schulze |first=Ernst-Detlef |author2=Erwin Beck |author3=Klaus Müller-Hohenstein  |title=Plant Ecology |publisher=Springer |location=Berlin |year=2005 |isbn=978-3-540-20833-4}}</ref>{{rp|449–453}} Ecosystem processes are driven by the species in an ecosystem, the nature of the individual species, and the relative abundance of organisms among these species. Ecosystem processes are the net effect of the actions of individual organisms as they interact with their environment. [[Theoretical ecology|Ecological theory]] suggests that in order to coexist, species must have some level of [[limiting similarity]]—they must be different from one another in some fundamental way, otherwise, one species would [[competitive exclusion|competitively exclude]] the other.<ref name="Schoener-2009">{{cite book|last=Schoener|first=Thomas W.|title=The Princeton Guide to Ecology|url=https://archive.org/details/princetonguideto00levi|url-access=limited|editor=Simon A. Levin|editor-link=Simon A. Levin|publisher=Princeton University Press|location=Princeton|year=2009|pages=[https://archive.org/details/princetonguideto00levi/page/n16 2]–13|chapter=Ecological Niche|isbn=978-0-691-12839-9}}</ref> Despite this, the cumulative effect of additional species in an ecosystem is not linear: additional species may enhance nitrogen retention, for example. However, beyond some level of species richness,<ref name="Chapin-2011j" />{{rp|331}} additional species may have little additive effect unless they differ substantially from species already present.<ref name="Chapin-2011j" />{{rp|324}} This is the case for example for [[Introduced species|exotic species]].<ref name="Chapin-2011j" />{{rp|321}}

The addition (or loss) of species that are ecologically similar to those already present in an ecosystem tends to only have a small effect on ecosystem function. Ecologically distinct species, on the other hand, have a much larger effect. Similarly, dominant species have a large effect on ecosystem function, while rare species tend to have a small effect. [[Keystone species]] tend to have an effect on ecosystem function that is disproportionate to their abundance in an ecosystem.<ref name="Chapin-2011j" />{{rp|324}}

An [[ecosystem engineer]] is any [[organism]] that creates, significantly modifies, maintains or destroys a [[Habitat (ecology)|habitat]].<ref>{{Cite journal|last1=Jones|first1=Clive G.|last2=Lawton|first2=John H.|last3=Shachak|first3=Moshe|date=1994|title=Organisms as Ecosystem Engineers|journal=Oikos|volume=69|issue=3|pages=373–386|doi=10.2307/3545850|issn=0030-1299|jstor=3545850|bibcode=1994Oikos..69..373J }}</ref>