View source for Earth:Remineralisation

{{Short description|Breakdown of organic matter to simple chemicals by living organisms}}
In [[Chemistry:Biogeochemistry|biogeochemistry]], '''remineralisation''' (or '''remineralization''') refers to the breakdown or transformation of [[Chemistry:Organic matter|organic matter]] (those molecules derived from a biological source) into its simplest [[Chemistry:Inorganic compound|inorganic]] forms. These transformations form a crucial link within [[Earth:Ecosystem|ecosystem]]s as they are responsible for liberating the energy stored in [[Chemistry:Organic compound|organic molecules]] and recycling matter within the system to be reused as [[Earth:Nutrient|nutrient]]s by other organisms.<ref name=":2">{{cite book |title=Ocean Biogeochemical Dynamics |last=Sarmiento |first=Jorge |publisher=Princeton University Press |year=2006 |isbn=978-0-691-01707-5 }}</ref>

Remineralisation is normally viewed as it relates to the cycling of the major biologically important elements such as [[Chemistry:Carbon|carbon]], [[Chemistry:Nitrogen|nitrogen]] and [[Chemistry:Phosphorus|phosphorus]]. While crucial to all ecosystems, the process receives special consideration in [[Earth:Aquatic ecosystem|aquatic]] settings, where it forms a significant link in the biogeochemical dynamics and cycling of aquatic ecosystems.

== Role in biogeochemistry ==

The term "remineralization" is used in several contexts across different disciplines. The term is most commonly used in the [[Medicine:Medicine|medicinal]] and [[Biology:Physiology|physiological]] fields, where it describes the development or redevelopment of mineralized structures in organisms such as [[Medicine:Remineralisation of teeth|teeth]] or bone. In the field of [[Chemistry:Biogeochemistry|biogeochemistry]], however, remineralization is used to describe a link in the chain of elemental cycling within a specific ecosystem. In particular, remineralization represents the point where organic material constructed by living organisms is broken down into basal inorganic components that are not obviously identifiable as having come from an organic source. This differs from the process of [[Medicine:Decomposition|decomposition]] which is a more general descriptor of larger structures degrading to smaller structures.

Biogeochemists study this process across all ecosystems for a variety of reasons. This is done primarily to investigate the flow of material and energy in a given system, which is key to understanding the productivity of that ecosystem along with how it recycles material versus how much is entering the system. Understanding the rates and dynamics of organic matter remineralization in a given system can help in determining how or why some ecosystems might be more productive than others.

=== Remineralization reactions ===
While it is important to note that the process of remineralization is a series of complex biochemical pathways [within microbes], it can often be simplified as a series of one-step processes for ecosystem-level models and calculations. A generic form of these reactions is shown by:

:<chem>{Organic \ Matter} + Oxidant -> {Liberated\ Simple\ Nutrients} + \underset{Carbon~Dioxide}{CO2} + \underset{Water}{H2O}</chem>

The above generic equation starts with two reactants: some piece of organic matter (composed of organic carbon) and an oxidant. Most organic carbon exists in a reduced form which is then oxidized by the oxidant (such as {{chem2|O2}}) into {{CO2|link=yes}} and energy that can be harnessed by the organism. This process generally produces {{CO2}}, water and a collection of simple nutrients like nitrate or phosphate that can then be taken up by other organisms. The above general form, when considering {{chem2|O2}} as the oxidant, is the equation for respiration. In this context specifically, the above equation represents bacterial [[Biology:Respiration (physiology)|respiration]] though the reactants and products are essentially analogous to the short-hand equations used for multi-cellular respiration.

=== Electron acceptor cascade ===
[[File:Electron Acceptor Cascade in marine sediments.png|thumb|Sketch of major electron acceptors in marine sediment porewater based on idealized relative depths]]

The degradation of organic matter through respiration in the modern ocean is facilitated by different electron acceptors, their favorability based on [[Physics:Gibbs free energy|Gibbs free energy law]], and the [[Physics:Laws of thermodynamics|laws of thermodynamics]].<ref>{{cite book |last1=Vernberg |first1=F. John |chapter=Benthic Macrofauna |title=Functional Adaptations of Marine Organisms |editor1-last=Vernberg |editor1-first=F. John |editor2-last=Vernberg |editor2-first=Winona B. |date=1981 |publisher=Academic Press |pages=[https://archive.org/details/functionaladapta0000unse/page/179 179–230] |isbn=978-0-12-718280-3 |chapter-url=https://books.google.com/books?id=-mQhBQAAQBAJ&pg=PA179 |url=https://archive.org/details/functionaladapta0000unse/page/179 }}</ref>  This [[Chemistry:Redox|redox]] chemistry is the basis for life in [[Earth:Deep sea|deep sea]] [[Earth:Sediment|sediment]]s and determines the obtainability of energy to organisms that live there.  From the water interface moving toward deeper sediments, the order of these acceptors is [[Chemistry:Oxygen|oxygen]], [[Chemistry:Nitrate|nitrate]], [[Chemistry:Manganese|manganese]], [[Chemistry:Iron|iron]], and [[Chemistry:Sulfate|sulfate]].  The zonation of these favored acceptors can be seen in Figure 1.  Moving downwards from the surface through the zonation of these deep ocean sediments, acceptors are used and depleted.  Once depleted the next acceptor of lower favorability takes its place.  Thermodynamically, oxygen represents the most favorable electron accepted but is quickly used up in the water sediment interface and {{chem2|O2}} concentrations extends only millimeters to centimeters down into the sediment in most locations of the deep sea.  This favorability indicates an organism's ability to obtain higher energy from the reaction which helps them compete with other organisms.<ref name=":0">{{cite book |title=Anoxia: Evidence for Eukaryote Survival and Paleontological Strategies |url=https://books.google.com/books?id=QW2il1xeUvQC |publisher=Springer Science & Business Media |date=20 October 2011 |isbn=978-94-007-1896-8 |language=en |first1=Alexander |last1=Altenbach |first2=Joan M. |last2=Bernhard |first3=Joseph |last3=Seckbach}}</ref>  In the absence of these acceptors, organic matter can also be degraded through methanogenesis, but the net oxidation of this organic matter is not fully represented by this process. Each pathway and the stoichiometry of its reaction are listed in table 1.<ref name=":0" />

Due to this quick depletion of {{chem2|O2}} in the surface sediments, a majority of microbes use [[Biology:Anaerobic respiration|anaerobic]] pathways to metabolize other oxides such as manganese, iron, and sulfate.<ref>{{cite journal |last=Glud |first=Ronnie |date=2008 |title=Oxygen dynamics of marine sediments |url=ftp://ftp.soest.hawaii.edu/glazer/Chen%20References/8-24-09/Glud%202008.pdf |journal=Marine Biology Research |volume=4 |issue=4 |pages=243–289 |doi= 10.1080/17451000801888726|doi-access=free }}</ref>  It is also important to figure in [[Earth:Bioturbation|bioturbation]] and the constant mixing of this material which can change the relative importance of each respiration pathway.  For the microbial perspective please reference the [[Biology:Electron transport chain|electron transport chain]].

== Remineralisation in sediments ==

=== Reactions ===
[[File:2Reduction reaction energetics.png|thumb|Relative favorability of reduction reactions in marine sediments based on thermodynamic energetics.  Origin of arrows indicate energy associated with half-cell reaction.  Length of arrow indicates an estimate of ΔG for the reaction (Adapted from Libes, 2011).]]
A quarter of all organic material that exits the [[Earth:Photic zone|photic zone]] makes it to the seafloor without being remineralised and 90% of that remaining material is remineralised in sediments itself.<ref name=":2" /> Once in the sediment, organic remineralisation may occur through a variety of reactions.<ref>{{cite book |title=Geochemistry of Marine Sediments |last=Burdige |first=David |publisher=Princeton University Press |year=2006 |isbn=978-0-691-09506-6 }}</ref> The following reactions are the primary ways in which organic matter is remineralised, in them general organic matter (OM) is often represented by the shorthand: {{chem2|(CH2O)106(NH3)16(H3PO4)}}.

==== Aerobic respiration ====
Aerobic respiration is the most preferred remineralisation reaction due to its high energy yield.  Although oxygen is quickly depleted in the sediments and is generally exhausted centimeters from the sediment-water interface.

==== Anaerobic respiration ====
{{main|Biology:Anaerobic respiration}}
In instances in which the environment is suboxic or anoxic, organisms will prefer to utilize [[Biology:Denitrification|denitrification]] to remineralise organic matter as it provides the second largest amount of energy. In depths below where denitrification is favored, reactions such as Manganese Reduction, Iron Reduction, Sulfate Reduction, Methane Reduction (also known as [[Engineering:Methanogenesis|Methanogenesis]]), become favored respectively.  This favorability is governed by Gibbs Free Energy (ΔG). In a water body, sediment seabed, or soil, the sorting of these chemical reactions with depth in order of energy provided is called a [[Biology:Redox gradient|redox gradient]].

{| class="wikitable"
! scope="col" | Respiration type
! colspan="2" scope="col" | Reaction
! scope="col" | '''Δ'''G
|-
! scope="row" | Aerobic
| Oxygen reduction
| <chem>OM + 150O2 -> 106CO2 + 16HNO3 + H3PO4 + 78H2O</chem>
| -29.9
|-
! rowspan="5" scope="row" | Anaerobic
| Denitrification
| <chem>OM + 104HNO3 -> 106CO2 + 60N2 + H3PO4 + 138H2O</chem>
| -28.4
|-
| Manganese reduction
| <chem>OM + 260MnO2 + 174H2O -> 106CO2 + 8N2 + H3PO4 + 260Mn(OH)2</chem>
| -7.2
|-
| Iron reduction
| <chem>OM + 236Fe2O3 + 410H2O -> 106CO2 + 16NH3 + H3PO4 + 472Fe(OH)2</chem>
| -21.0
|-
| Sulfate reduction
| <chem>OM + 59H2SO4 -> 106CO2 + 16NH3 + H3PO4 + 59H2S + 62H2O</chem>
| -6.1
|-
| Methane fermentation ([[Engineering:Methanogenesis|Methanogenesis]])
| <chem>OM + 59H2O -> 47CO2 + 59CH4 + 16NH3 + H3PO4</chem>
| -5.6
|}

=== Redox zonation ===
{{Main article|Biology:Redox gradient}}

Redox zonation refers to how the processes that transfer terminal electrons as a result of organic matter degradation vary depending on time and space.<ref name=":1">{{cite journal |title=Redox zonation: Equilibrium constraints on the Fe(III)/SO4-reduction interface |journal=Geochimica et Cosmochimica Acta |date=1 September 1996 |pages=3169–3175 |volume=60 |issue=17 |doi=10.1016/0016-7037(96)00156-1 |first1=Dieke |last1=Postma |first2=Rasmus |last2=Jakobsen |bibcode=1996GeCoA..60.3169P}}</ref> Certain reactions will be favored over others due to their energy yield as detailed in the energy acceptor cascade detailed above.<ref>{{cite book |title=The Benthic Boundary Layer: Transport Processes and Biogeochemistry |last=Boudreau |first=Bernard |publisher=Oxford University Press |year=2001 |isbn=978-0-19-511881-0 }}</ref> In oxic conditions, in which oxygen is readily available, aerobic respiration will be favored due to its high energy yield. Once the use of oxygen through respiration exceeds the input of oxygen due to bioturbation and diffusion, the environment will become anoxic and organic matter will be broken down via other means, such as denitrification and manganese reduction.<ref>{{cite book |title=Introduction to Marine Biogeochemistry |last=Libes |first=Susan |publisher=Academic Press |year=2009 |isbn=978-0-12-088530-5 }}</ref>

== Remineralisation in the open ocean ==
[[File:Oceanic Food Web.jpg|thumb|Food web showing the flow of carbon in the open ocean|238x238px]]
In most open ocean ecosystems only a small fraction of organic matter reaches the seafloor. Biological activity in the photic zone of most water bodies tends to recycle material so well that only a small fraction of organic matter ever sinks out of that top photosynthetic layer. Remineralisation within this top layer occurs rapidly and due to the higher concentrations of organisms and the availability of light, those remineralised nutrients are often taken up by autotrophs just as rapidly as they are released.

What fraction does escape varies depending on the location of interest. For example, in the North Sea, values of carbon deposition are ~1% of primary production<ref>{{cite journal |last1=Thomas |first1=Helmuth |last2=Bozec |first2=Yann |last3=Elkalay |first3=Khalid |last4=Baar |first4=Hein J. W. de |date=14 May 2004 |title=Enhanced Open Ocean Storage of CO2 from Shelf Sea Pumping |journal=Science |language=en |volume=304 |issue=5673 |pages=1005–1008 |doi=10.1126/science.1095491 |issn=0036-8075 |pmid=15143279 |bibcode=2004Sci...304.1005T|url=https://pure.rug.nl/ws/files/9825939/2004ScienceThomas.pdf |hdl=11370/e821600e-4560-49e8-aeec-18eeb17549e3 |s2cid=129790522 |hdl-access=free }}</ref> while that value is <0.5% in the open oceans on average.<ref>{{cite book |last=De La Rocha |first=C. L. |title=Treatise on Geochemistry |date=2006 |chapter=The Biological Pump |volume=6 |page=625 |editor1-last=Holland |editor1-first=Heinrich D. |editor2-last=Turekian |editor2-first=Karl K. |publisher=Pergamon Press |doi=10.1016/B0-08-043751-6/06107-7 |isbn=978-0-08-043751-4 |bibcode=2003TrGeo...6...83D}}</ref>  Therefore, most of nutrients remain in the water column, recycled by the biota. [[Biology:Heterotroph|Heterotroph]]ic organisms will utilize the materials produced by the [[Biology:Autotroph|autotroph]]ic (and [[Biology:Chemotroph|chemotroph]]ic) organisms and via respiration will remineralise the compounds from the organic form back to inorganic, making them available for primary producers again.

For most areas of the ocean, the highest rates of carbon remineralisation occur at depths between {{convert|100|-|1200|m|ft|abbr=on}} in the water column, decreasing down to about 1,200&nbsp;m where remineralisation rates remain pretty constant at 0.1 μmol kg<sup>−1</sup> yr<sup>−1</sup>.<ref>{{cite journal |last1=Feely |first1=Richard A. |last2=Sabine |first2=Christopher L. |last3=Schlitzer |first3=Reiner |last4=Bullister |first4=John L. |last5=Mecking |first5=Sabine |last6=Greeley |first6=Dana |date=1 February 2004 |title=Oxygen Utilization and Organic Carbon Remineralisation in the Upper Water Column of the Pacific Ocean |journal=Journal of Oceanography |language=en |volume=60 |issue=1 |pages=45–52 |doi=10.1023/B:JOCE.0000038317.01279.aa |s2cid=67846685 |issn=0916-8370}}</ref> As a result of this, the pool of remineralised carbon (which generally takes the form of carbon dioxide) tends to increase in the photic zone.

Most remineralisation is done with [[Chemistry:Dissolved organic carbon|dissolved organic carbon]] (DOC). Studies have shown that it is larger sinking particles that transport matter down to the sea floor<ref>{{cite journal |last1=Karl |first1=David M. |last2=Knauer |first2=George A. |last3=Martin |first3=John H. |date=1 March 1988 |title=Downward flux of particulate organic matter in the ocean: a particle decomposition paradox |bibcode=1988Natur.332..438K |journal=Nature |volume=332 |issue=6163 |pages=438–441 |doi=10.1038/332438a0 |s2cid=4356597 |issn=0028-0836}}</ref> while suspended particles and dissolved organics are mostly consumed by remineralisation.<ref>{{cite journal |last1=Lefévre |first1=D. |last2=Denis |first2=M. |last3=Lambert |first3=C. E. |last4=Miquel |first4=J. -C. |date=1 February 1996 |title=Is DOC the main source of organic matter remineralization in the ocean water column? |journal=Journal of Marine Systems |series=The Coastal Ocean in a Global Change Perspective |volume=7 |issue=2–4 |pages=281–291 |doi=10.1016/0924-7963(95)00003-8 |bibcode=1996JMS.....7..281L}}</ref> This happens in part due to the fact that organisms must typically ingest nutrients smaller than they are, often by orders of magnitude.<ref>{{cite book |url=https://books.google.com/books?id=T5trCQAAQBAJ |title=Biodiversity and Ecosystem Function |last1=Schulze |first1=Ernst-Detlef |last2=Mooney |first2=Harold A. |date=6 December 2012 |publisher=Springer Science & Business Media |isbn=978-3-642-58001-7 |language=en}}</ref> With the microbial community making up 90% of marine biomass,<ref>{{cite web |url=http://www.coml.org/projects/international-census-marine-microbes-icomm |title=International Census of Marine Microbes (ICoMM) |series=Census of Marine Life |website=www.coml.org |access-date=29 February 2016 |url-status=dead |archive-url=https://web.archive.org/web/20160317223727/http://www.coml.org/projects/international-census-marine-microbes-icomm |archive-date=17 March 2016 }}</ref> it is particles smaller than the microbes (on the order of {{10^|-6}}<ref>{{cite web |url=https://www.boundless.com/microbiology/textbooks/boundless-microbiology-textbook/microscopy-3/looking-at-microbes-28/microbe-size-238-4283/ |title=Microbe Size - Boundless Open Textbook |website=Boundless |access-date=29 February 2016}}</ref>) that will be taken up for remineralisation.

== See also ==
* [[Biology:Biological pump|Biological pump]]
* [[Medicine:Decomposition|Decomposition]]
* [[Earth:F-ratio (oceanography)|f-ratio]]
* John D. Hamaker (soil remineralisation)
* [[Biology:Mineralization|Mineralization]]
* [[Chemistry:Mineralization (soil science)|Mineralization (soil science)]]
* [[Chemistry:Immobilization (soil science)|Immobilization (soil science)]]

== References ==
{{reflist}}

[[Category:Oceanography]]

{{Sourceattribution|Remineralisation}}