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Url last accessed 2006-04-06</ref> It is particularly concerned with the [[biogeochemistry|cycling of nutrients]], soil aggregate formation and soil [[biodiversity]].<ref>{{Cite web |title=Soil Ecology {{!}} Crop and Soil Sciences {{!}} NC State University |url=https://cals.ncsu.edu/crop-and-soil-sciences/soil-ecology/#:~:text=Soil%20ecology%20is%20the%20study,for%20delivering%20essential%20ecosystem%20services. |access-date=2024-11-13 |website=cals.ncsu.edu |language=en}}</ref> == Overview == [[Soil]] is made up of a multitude of [[soil physics|physical]], [[soil chemistry|chemical]], and [[soil biology|biological]] entities, with many interactions occurring among them. It is a heterogenous mixture of minerals and organic matter with variations in moisture, temperature and nutrients. Soil supports a wide range of living organisms and is an essential component of terrestrial ecology. ==Features of the ecosystem== *[[Moisture]] is a significant limiting factor in terrestrial ecosystems and majorly in the soil.<ref>{{Cite journal |last1=Orth |first1=Rene |last2=Denissen |first2=Jasper M.C. |last3=Li |first3=Wantong |last4=Oh |first4=Sungmin |date=2023-05-15 |title=Increasing water limitation of global ecosystems in a changing climate |journal=Egu General Assembly Conference Abstracts |url=https://meetingorganizer.copernicus.org/EGU23/EGU23-1422.html |access-date=2024-11-13 |doi=10.5194/egusphere-egu23-1422|doi-access=free |bibcode=2023EGUGA..25.1422O }}</ref> Soil organisms are constantly confronted with the problem of [[dehydration]].<ref>{{Citation |last=Chipman |first=Ariel D. |title=Terrestrialization |date=2024-05-31 |work=Organismic Animal Biology |pages=133–136 |url=https://academic.oup.com/book/56289/chapter/445243977 |access-date=2024-11-14 |edition=1 |publisher=Oxford University PressOxford |language=en |doi=10.1093/oso/9780192893581.003.0022 |isbn=978-0-19-289358-1}}</ref> Soil microbial communities experience shifts in the diversity and composition during dehydration and rehydration cycles.<ref>{{Cite journal |last1=Šťovíček |first1=Adam |last2=Kim |first2=Minsu |last3=Or |first3=Dani |last4=Gillor |first4=Osnat |date=2017-04-06 |title=Microbial community response to hydration-desiccation cycles in desert soil |journal=Scientific Reports |language=en |volume=7 |issue=1 |page=45735 |doi=10.1038/srep45735 |issn=2045-2322 |pmc=5382909 |pmid=28383531|bibcode=2017NatSR...745735S }}</ref> Soil moisture affects carbon cycling a phenomenon known as Birch effect.<ref>{{Cite journal |last1=Liang |first1=Guopeng |last2=Reed |first2=Sasha C. |last3=Stark |first3=John M. |last4=Waring |first4=Bonnie G. |date=October 2023 |title=Unraveling mechanisms underlying effects of wetting–drying cycles on soil respiration in a dryland |url=https://link.springer.com/10.1007/s10533-023-01085-0 |journal=Biogeochemistry |language=en |volume=166 |issue=1 |pages=23–37 |doi=10.1007/s10533-023-01085-0 |bibcode=2023Biogc.166...23L |issn=0168-2563|doi-access=free }}</ref><ref>{{Cite journal |last1=Singh |first1=Shikha |last2=Mayes |first2=Melanie A. |last3=Kivlin |first3=Stephanie N. |last4=Jagadamma |first4=Sindhu |date=2023-04-01 |title=How the Birch effect differs in mechanisms and magnitudes due to soil texture |url=https://linkinghub.elsevier.com/retrieve/pii/S0038071723000354 |journal=Soil Biology and Biochemistry |volume=179 |pages=108973 |doi=10.1016/j.soilbio.2023.108973 |bibcode=2023SBiBi.17908973S |issn=0038-0717}}</ref> *Temperature variations in soil are influenced by factors such as seasonality, environmental conditions, vegetation, and soil composition.<ref>{{Citation |last=Atesmen |first=M. Kemal |title=Seasonally Averaged Temperature Fluctuation Penetrations into The Ground |date=2023-06-15 |work=Case Studies in Transient Heat Transfer With Sensitivities to Governing Variables |pages=187–193 |url=https://asmedigitalcollection.asme.org/ebooks/book/297/chapter/27392070/Seasonally-Averaged-Temperature-Fluctuation |access-date=2024-11-14 |publisher=ASME |language=en |doi=10.1115/1.886786_ch20 |isbn=978-0-7918-8678-6}}</ref><ref>{{Cite journal |last=Kulish |first=T |date=2022-06-01 |title=Spatial variation of soil temperature fields in a urban park |url=https://iopscience.iop.org/article/10.1088/1755-1315/1049/1/012056 |journal=IOP Conference Series: Earth and Environmental Science |volume=1049 |issue=1 |pages=012056 |doi=10.1088/1755-1315/1049/1/012056 |bibcode=2022E&ES.1049a2056K |issn=1755-1307|doi-access=free }}</ref> Soil temperature also varies with depth; upper soil layers are majorly influence by air temperature, while soil temperature fluctuations decrease with depth.<ref>{{Cite journal |last1=Bourletsikas |first1=Athanassios |last2=Proutsos |first2=Nikolaos |last3=Michopoulos |first3=Panagiotis |last4=Argyrokastritis |first4=Ioannis |date=2023-04-14 |title=Temporal Variations in Temperature and Moisture Soil Profiles in a Mediterranean Maquis Forest in Greece |journal=Hydrology |language=en |volume=10 |issue=4 |pages=93 |doi=10.3390/hydrology10040093 |doi-access=free |issn=2306-5338}}</ref><ref>{{Cite journal |last1=Bulgakov |first1=Volodymyr |last2=Pascuzzi |first2=Simone |last3=Adamchuk |first3=Valerii |last4=Gadzalo |first4=Jaroslav |last5=Nadykto |first5=Volodymyr |last6=Olt |first6=Jüri |last7=Nowak |first7=Janusz |last8=Kaminskiy |first8=Viktor |date=2022-03-23 |title=Dynamics of Temperature Variation in Soil under Fallow Tillage at Different Depths |journal=Agriculture |language=en |volume=12 |issue=4 |pages=450 |doi=10.3390/agriculture12040450 |doi-access=free |issn=2077-0472}}</ref> Soil temperature influences biological and biochemical processes in soil, playing an important role in microbial and enzymatic activities, mineralization and organic matter decomposition. <ref>{{Citation |last1=Sharma |first1=Pradeep K. |title=Soil Temperature and Plant Growth |date=2023 |work=Soil Physical Environment and Plant Growth: Evaluation and Management |pages=175–204 |editor-last=Sharma |editor-first=Pradeep K. |url=https://link.springer.com/chapter/10.1007/978-3-031-28057-3_7 |access-date=2024-11-16 |place=Cham |publisher=Springer International Publishing |language=en |doi=10.1007/978-3-031-28057-3_7 |isbn=978-3-031-28057-3 |last2=Kumar |first2=Sandeep |editor2-last=Kumar |editor2-first=Sandeep}}</ref> *Air is vital for respiration in soil organisms and in plant growth. <ref name=":1">{{Citation |last1=Novák |first1=Viliam |title=Soil Air and Its Dynamics |date=2019 |work=Applied Soil Hydrology |volume=32 |pages=293–301 |url=http://link.springer.com/10.1007/978-3-030-01806-1_19 |access-date=2024-11-14 |place=Cham |publisher=Springer International Publishing |doi=10.1007/978-3-030-01806-1_19 |isbn=978-3-030-01805-4 |last2=Hlaváčiková |first2=Hana}}</ref> Both wind and atmospheric pressure play critical roles in soil aeration.<ref>{{Cite journal |last1=Maier |first1=Martin |last2=Osterholt |first2=Laurin |last3=Schindler |first3=Dirk |date=2022-03-28 |title=Blowing in the wind: a review of wind and air- pressure-related effects on soil gas transport&#160; |journal=Egu General Assembly Conference Abstracts |url=https://meetingorganizer.copernicus.org/EGU22/EGU22-8713.html |access-date=2024-11-14 |doi=10.5194/egusphere-egu22-8713|doi-access=free |bibcode=2022EGUGA..24.8713M }}</ref> In addition, convection and diffusion and influence the rates of soil aeration<ref name=":1" /> *Soil structure refers to the size, shape and arrangement of solid particles in soil. <ref>{{Cite journal |last=Letey |first=J |date=1991 |title=The study of soil structure - Science or art |url=http://www.publish.csiro.au/?paper=SR9910699 |journal=Soil Research |language=en |volume=29 |issue=6 |pages=699 |doi=10.1071/SR9910699 |issn=1838-675X}}</ref> Factors such as climate, vegetation and organisms influence the complex arrangement of particles in the soil <ref>{{Citation |last=Hillel |first=Daniel |title=Soil Structure and Aggregation |date=1980 |work=Fundamentals of Soil Physics |pages=93–119 |url=https://linkinghub.elsevier.com/retrieve/pii/B978008091870950011X |access-date=2024-11-17 |publisher=Elsevier |language=en |doi=10.1016/b978-0-08-091870-9.50011-x |isbn=978-0-08-091870-9}}</ref> Structural features of the soil include macroporosity and pore sieze which are also affected by minerals and soil organic matter.<ref>{{Cite journal |last=Leuther |first=Frederic |date=2023-05-15 |title=Soil structure – a dynamic soil property which effects multiple soil functions |journal=Egu General Assembly Conference Abstracts |url=https://meetingorganizer.copernicus.org/EGU23/EGU23-15721.html |access-date=2024-11-17 |doi=10.5194/egusphere-egu23-15721|doi-access=free |bibcode=2023EGUGA..2515721L }}</ref> *Land, unlike the ocean, is not continuous; there are important geographical barriers to free movement. *The nature of the substrate, although important in water is especially vital in terrestrial environment. Soil, not air, is the source of highly variable nutrients; it is a highly developed ecological subsystem. ==Soil fauna== Soil fauna is crucial to [[soil formation]], litter decomposition, [[nutrient cycling]], biotic regulation, and for promoting [[plant growth]]. Yet soil organisms remain underrepresented in studies on soil processes and in existing modeling exercises. This is a consequence of assuming that much below ground diversity is ecologically redundant and that [[soil food web]]s exhibit a higher degree of [[omnivory]]. However, evidence is accumulating on the strong influence of [[Abiotic component|abiotic filters]], such as temperature, moisture and [[soil pH]], as well as soil habitat characteristics in controlling their spatial and temporal patterns.<ref name=Briones2018 /> Soils are complex systems and their complexity resides in their heterogeneous nature: a mixture of air, water, minerals, organic compounds, and living organisms. The spatial variation, both horizontal and vertical, of all these constituents is related to soil forming agents varying from micro to macro scales.<ref>{{cite journal |doi = 10.1016/j.ecolmodel.2004.04.006|title = Assessment of soil spatial variability at multiple scales|year = 2005|last1 = Lin|first1 = Hangsheng|last2 = Wheeler|first2 = Dan|last3 = Bell|first3 = Jay|last4 = Wilding|first4 = Larry|journal = Ecological Modelling|volume = 182|issue = 3–4|pages = 271–290| bibcode=2005EcMod.182..271L }}</ref> Consequently, the horizontal patchy distribution of soil properties (soil temperature, moisture, pH, litter/nutrient availability, etc.) also drives the patchiness of the soil organisms across the landscape,<ref>{{Cite book|url=https://books.google.com/books?id=w_o0obAFdLQC&pg=PA136|title = Soil Ecology and Ecosystem Services|isbn = 978-0-19-957592-3|last1 = Wall|first1 = Diana H.|date = 14 June 2012| publisher=OUP Oxford }}</ref> and has been one of the main arguments for explaining the great diversity observed in soil communities.<ref name=Nielsen2010 /> Because soils also show vertical stratification of their elemental constituents along the [[soil profile]] as result of [[microclimate]], [[soil texture]], and resource quantity and quality differing between soil horizons, soil communities also change in abundance and structure with soil depth.<ref>{{cite journal |doi = 10.1111/j.0030-1299.2007.15748.x|title = Temporal and spatial variability in soil food web structure|year = 2007|last1 = Berg|first1 = Matty P.|last2 = Bengtsson|first2 = Janne|journal = Oikos|volume = 116|issue = 11|pages = 1789–1804| bibcode=2007Oikos.116.1789B }}</ref><ref name=Briones2018 /> The majority of these organisms are [[Aerobic organism|aerobic]], so the amount of [[Pore space in soil|porous space]], pore-size distribution, surface area, and oxygen levels are crucial to their life cycles and activities. The smallest creatures (microbes) use the [[micropores]] filled with air to grow, whereas other bigger animals require bigger spaces, [[macropores]], or the water film surrounding the soil particles to move in search for food. Therefore, soil textural properties together with the depth of the [[water table]] are also important factors regulating their diversity, population sizes, and their vertical stratification. Ultimately, the structure of the soil communities strongly depends not only on the natural soil forming factors but also on human activities (agriculture, forestry, urbanization) and determines the shape of landscapes in terms of healthy or contaminated, pristine or degraded soils.<ref name=Briones2018 /> ===Macrofauna=== [[File:Soil fauna, climatic gradients and soil heterogeneity.jpg|thumb|upright=2| {{center|'''Soil macrofauna, climatic gradients and soil heterogeneity'''{{hsp}}<ref name=Briones2018>{{cite journal |doi = 10.3389/fenvs.2018.00149|doi-access = free|title = The Serendipitous Value of Soil Fauna in Ecosystem Functioning: The Unexplained Explained|year = 2018|last1 = Briones|first1 = Maria J. I.|journal = Frontiers in Environmental Science|volume = 6}} [[File:CC-BY icon.svg|50px]] Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].</ref>}} Historical factors, such as climate and soil [[parent material]]s, shape landscapes above and below ground, but the regional/local abiotic conditions constraint biological activities. These operate at different spatial and temporal scales and can switch on and off different organisms at different microsites resulting in a hot moment in a particular hotspot. As a result, [[trophic cascade]]s can occur up and down the [[food web]].<br />Soil invertebrates are shown. Ellipses indicate hot (red) or cold spots (blue), with the curved arrows giving some examples of the factors that could switch on/off a hot moment and the straight black arrows (continuous black line = on, dashed = off) showing the implications for soil processes along the soil profile. In the boxes, the main ecosystem characteristics are listed.]] Since all these drivers of biodiversity changes also operate above ground, it is thought that there must be some concordance of mechanisms regulating the spatial patterns and structure of both above and below ground communities. In support of this, a small-scale field study revealed that the relationships between [[environmental heterogeneity]] and [[species richness]] might be a general property of ecological communities.<ref name=Nielsen2010>{{cite journal |doi = 10.1371/journal.pone.0011567|doi-access = free|title = The Enigma of Soil Animal Species Diversity Revisited: The Role of Small-Scale Heterogeneity|year = 2010|last1 = Nielsen|first1 = Uffe N.|last2 = Osler|first2 = Graham H. R.|last3 = Campbell|first3 = Colin D.|last4 = Neilson|first4 = Roy|last5 = Burslem|first5 = David F. R. P.|last6 = Van Der Wal|first6 = René|journal = PLOS ONE|volume = 5|issue = 7|pages = e11567|pmid = 20644639|pmc = 2903492|bibcode = 2010PLoSO...511567N}}</ref> In contrast, the molecular examination of 17,516 environmental 18S rRNA gene sequences representing 20 [[Phylum|phyla]] of soil animals covering a range of [[biome]]s and latitudes around the world indicated otherwise, and the main conclusion from this study was that below-ground animal diversity may be inversely related to above-ground biodiversity.<ref>{{cite journal |doi = 10.1073/pnas.1103824108|title = Molecular study of worldwide distribution and diversity of soil animals|year = 2011|last1 = Wu|first1 = T.|last2 = Ayres|first2 = E.|last3 = Bardgett|first3 = R. D.|last4 = Wall|first4 = D. H.|last5 = Garey|first5 = J. R.|journal = Proceedings of the National Academy of Sciences|volume = 108|issue = 43|pages = 17720–17725|pmid = 22006309|pmc = 3203765|bibcode = 2011PNAS..10817720W| doi-access=free }}</ref><ref name=Briones2018 /> The lack of distinct [[Latitudinal gradients in species diversity|latitudinal gradients]] in [[soil biodiversity]] contrasts with those clear global patterns observed for plants above ground and has led to the assumption that they are indeed controlled by different factors.<ref name=Bardgett2014>{{cite journal |doi = 10.1038/nature13855|title = Belowground biodiversity and ecosystem functioning|year = 2014|last1 = Bardgett|first1 = Richard D.|last2 = Van Der Putten|first2 = Wim H.|journal = Nature|volume = 515|issue = 7528|pages = 505–511|pmid = 25428498|bibcode = 2014Natur.515..505B|s2cid = 4456564}}</ref> For example, in 2007 Lozupone and Knight found salinity was the major environmental determinant of bacterial diversity composition across the globe, rather than extremes of temperature, pH, or other physical and chemical factors.<ref>{{cite journal |doi = 10.1111/j.0030-1299.2007.15748.x|title = Temporal and spatial variability in soil food web structure|year = 2007|last1 = Berg|first1 = Matty P.|last2 = Bengtsson|first2 = Janne|journal = Oikos|volume = 116|issue = 11|pages = 1789–1804| bibcode=2007Oikos.116.1789B }}</ref> In another global scale study in 2014, Tedersoo ''et al''. concluded [[fungal]] richness is causally unrelated to plant diversity and is better explained by climatic factors, followed by [[edaphic]] and spatial patterns.<ref>{{cite journal |doi = 10.1126/science.1256688|title = Global diversity and geography of soil fungi|year = 2014|last1 = Tedersoo|first1 = Leho|last2 = Bahram|first2 = Mohammad|last3 = Põlme|first3 = Sergei|last4 = Kõljalg|first4 = Urmas|last5 = Yorou|first5 = Nourou S.|last6 = Wijesundera|first6 = Ravi|last7 = Ruiz|first7 = Luis Villarreal|last8 = Vasco-Palacios|first8 = Aída M.|last9 = Thu|first9 = Pham Quang|last10 = Suija|first10 = Ave|last11 = Smith|first11 = Matthew E.|last12 = Sharp|first12 = Cathy|last13 = Saluveer|first13 = Erki|last14 = Saitta|first14 = Alessandro|last15 = Rosas|first15 = Miguel|last16 = Riit|first16 = Taavi|last17 = Ratkowsky|first17 = David|last18 = Pritsch|first18 = Karin|last19 = Põldmaa|first19 = Kadri|last20 = Piepenbring|first20 = Meike|last21 = Phosri|first21 = Cherdchai|last22 = Peterson|first22 = Marko|last23 = Parts|first23 = Kaarin|last24 = Pärtel|first24 = Kadri|last25 = Otsing|first25 = Eveli|last26 = Nouhra|first26 = Eduardo|last27 = Njouonkou|first27 = André L.|last28 = Nilsson|first28 = R. Henrik|last29 = Morgado|first29 = Luis N.|last30 = Mayor|first30 = Jordan|journal = Science|volume = 346|issue = 6213|pmid = 25430773| hdl=11336/20627 |s2cid = 206559506|url = https://e-space.mmu.ac.uk/606982/1/LehoFungiFinal.pdf|display-authors = 1}}</ref> Global patterns of the distribution of macroscopic organisms are far poorer documented. However, the little evidence available appears to indicate that, at large scales, soil metazoans respond to altitudinal, latitudinal or area gradients in the same way as those described for above-ground organisms.<ref>{{cite journal |doi = 10.1111/j.1466-8238.2009.00517.x|title = Macroecological patterns in soil communities|year = 2010|last1 = Decaëns|first1 = Thibaud|journal = Global Ecology and Biogeography|volume = 19|issue = 3|pages = 287–302|doi-access = free| bibcode=2010GloEB..19..287D }}</ref> In contrast, at local scales, the great diversity of microhabitats commonly found in soils provides the required niche portioning to create hot spots of diversity in just a gram of soil.<ref name=Bardgett2014 /><ref name=Briones2018 /> Spatial patterns of soil biodiversity are difficult to explain, and its potential linkages to many soil processes and the overall ecosystem functioning are debated. For example, while some studies have found that reductions in the abundance and presence of soil organisms results in the decline of multiple ecosystem functions,<ref>{{cite journal |doi = 10.1073/pnas.1320054111|title = Soil biodiversity and soil community composition determine ecosystem multifunctionality|year = 2014|last1 = Wagg|first1 = C.|last2 = Bender|first2 = S. F.|last3 = Widmer|first3 = F.|last4 = Van Der Heijden|first4 = M. G. A.|journal = Proceedings of the National Academy of Sciences|volume = 111|issue = 14|pages = 5266–5270|pmid = 24639507|pmc = 3986181|bibcode = 2014PNAS..111.5266W| doi-access=free }}</ref> others concluded that above-ground plant diversity alone is a better predictor of ecosystem multi-functionality than soil biodiversity.<ref>{{cite journal |doi = 10.1038/ncomms9159|title = The links between ecosystem multifunctionality and above- and belowground biodiversity are mediated by climate|year = 2015|last1 = Jing|first1 = Xin|last2 = Sanders|first2 = Nathan J.|last3 = Shi|first3 = Yu|last4 = Chu|first4 = Haiyan|last5 = Classen|first5 = Aimée T.|last6 = Zhao|first6 = Ke|last7 = Chen|first7 = Litong|last8 = Shi|first8 = Yue|last9 = Jiang|first9 = Youxu|last10 = He|first10 = Jin-Sheng|journal = Nature Communications|volume = 6|page = 8159|pmid = 26328906| pmc=4569729 |bibcode = 2015NatCo...6.8159J|s2cid = 10933025}}</ref> Soil organisms exhibit a wide array of feeding preferences, life-cycles and survival strategies and they interact within complex food webs.<ref>{{cite journal |doi = 10.3389/fenvs.2014.00007|doi-access = free|title = Soil fauna and soil functions: A jigsaw puzzle|year = 2014|last1 = Briones|first1 = Marãa Jesãºs I.|journal = Frontiers in Environmental Science|volume = 2}}</ref> Consequently, [[species richness]] ''per se'' has very little influence on soil processes and functional dissimilarity can have stronger impacts on ecosystem functioning.<ref>{{cite journal |doi = 10.1126/science.1101865|title = Biodiversity Effects on Soil Processes Explained by Interspecific Functional Dissimilarity|year = 2004|last1 = Heemsbergen|first1 = D. A.|last2 = Berg|first2 = M. P.|last3 = Loreau|first3 = M.|last4 = Van Hal|first4 = J. R.|last5 = Faber|first5 = J. H.|last6 = Verhoef|first6 = H. A.|journal = Science|volume = 306|issue = 5698|pages = 1019–1020|pmid = 15528441|bibcode = 2004Sci...306.1019H|s2cid = 39362502}}</ref> Therefore, besides the difficulties in linking above and below ground diversities at different spatial scales, gaining a better understanding of the biotic effects on ecosystem processes might require incorporating a great number of components together with several multi-trophic levels{{hsp}}<ref>{{cite journal |doi = 10.1038/nature09492|title = Bottom-up effects of plant diversity on multitrophic interactions in a biodiversity experiment|year = 2010|last1 = Scherber|first1 = Christoph|last2 = Eisenhauer|first2 = Nico|last3 = Weisser|first3 = Wolfgang W.|last4 = Schmid|first4 = Bernhard|last5 = Voigt|first5 = Winfried|last6 = Fischer|first6 = Markus|last7 = Schulze|first7 = Ernst-Detlef|last8 = Roscher|first8 = Christiane|last9 = Weigelt|first9 = Alexandra|last10 = Allan|first10 = Eric|last11 = Beßler|first11 = Holger|last12 = Bonkowski|first12 = Michael|last13 = Buchmann|first13 = Nina|last14 = Buscot|first14 = François|last15 = Clement|first15 = Lars W.|last16 = Ebeling|first16 = Anne|last17 = Engels|first17 = Christof|last18 = Halle|first18 = Stefan|last19 = Kertscher|first19 = Ilona|last20 = Klein|first20 = Alexandra-Maria|last21 = Koller|first21 = Robert|last22 = König|first22 = Stephan|last23 = Kowalski|first23 = Esther|last24 = Kummer|first24 = Volker|last25 = Kuu|first25 = Annely|last26 = Lange|first26 = Markus|last27 = Lauterbach|first27 = Dirk|last28 = Middelhoff|first28 = Cornelius|last29 = Migunova|first29 = Varvara D.|last30 = Milcu|first30 = Alexandru|journal = Nature|volume = 468|issue = 7323|pages = 553–556|pmid = 20981010|bibcode = 2010Natur.468..553S|s2cid = 4304004|url = https://www.zora.uzh.ch/id/eprint/39737/4/Scherber_etal_Nature10.pdf|display-authors = 1}}</ref> as well as the much less considered non-trophic interactions such as [[phoresy]], passive consumption.<ref>{{cite journal |doi = 10.1086/523945|title = Nontrophic Interactions, Biodiversity, and Ecosystem Functioning: An Interaction Web Model|year = 2008|last1 = Goudard|first1 = Alexandra|last2 = Loreau|first2 = Michel|journal = The American Naturalist|volume = 171|issue = 1|pages = 91–106|pmid = 18171154|s2cid = 5120077}}</ref>) In addition, if soil systems are indeed self-organized, and soil organisms concentrate their activities within a selected set of discrete scales with some form of overall coordination,<ref>{{cite journal |doi = 10.1097/SS.0000000000000155|title = Ecosystem Engineers in a Self-organized Soil|year = 2016|last1 = Lavelle|first1 = Patrick|last2 = Spain|first2 = Alister|last3 = Blouin|first3 = Manuel|last4 = Brown|first4 = George|last5 = Decaëns|first5 = Thibaud|last6 = Grimaldi|first6 = Michel|last7 = Jiménez|first7 = Juan José|last8 = McKey|first8 = Doyle|last9 = Mathieu|first9 = Jérôme|last10 = Velasquez|first10 = Elena|last11 = Zangerlé|first11 = Anne|journal = Soil Science|volume = 181|issue = 3/4|pages = 91–109|bibcode = 2016SoilS.181...91L|s2cid = 102056683}}</ref> there is no need for looking for external factors controlling the assemblages of soil constituents. Instead we might just need to recognize the unexpected and that the linkages between above and below ground diversity and soil processes are difficult to predict.<ref name=Briones2018 /> {{clear}} ===Microfauna=== Recent advances are emerging from studying sub-organism level responses using [[environmental DNA]]{{hsp}}<ref>{{cite journal |doi = 10.1016/j.biocon.2014.11.019|title = Environmental DNA – an emerging tool in conservation for monitoring past and present biodiversity|year = 2015|last1 = Thomsen|first1 = Philip Francis|last2 = Willerslev|first2 = Eske|journal = Biological Conservation|volume = 183|pages = 4–18| s2cid=27384537 |doi-access = free| bibcode=2015BCons.183....4T }}</ref> and various [[omics]] approaches, such as [[metagenomics]], [[metatranscriptomics]], [[proteomics]] and [[proteogenomics]], are rapidly advancing, at least for the microbial world.<ref>{{cite journal |doi = 10.6092/issn.2281-4485/4541|year = 2014|last1 = Nannipieri|first1 = Paolo|title = Soil as a Biological System and Omics Approaches|journal = EQA - International Journal of Environmental Quality|volume = 13|pages = 61–66}}</ref> [[Metaphenomics]] has been proposed recently as a better way to encompass the omics and the environmental constraints.<ref>{{cite journal |doi = 10.1016/j.mib.2018.01.013|title = The soil microbiome — from metagenomics to metaphenomics|year = 2018|last1 = Jansson|first1 = Janet K.|last2 = Hofmockel|first2 = Kirsten S.|journal = Current Opinion in Microbiology|volume = 43|pages = 162–168|pmid = 29454931| s2cid=3377418 |doi-access = free}}</ref><ref name=Briones2018 /> === Soil microbes === {{Main article|Soil microbiology}} Soil harbors many microbes: bacteria, archaea, protist, fungi and viruses.<ref>{{Cite journal |last=Nannipieri |first=Paolo |date=2014-12-01 |title=Soil as a Biological System and Omics Approaches |url=http://eqa.unibo.it/article/view/4541 |journal=EQA - International Journal of Environmental Quality |volume=13 |language=en |pages=61–66 Pages |doi=10.6092/ISSN.2281-4485/4541}}</ref> A majority of these microbes have not been cultured and remain undescribed.<ref>{{Cite journal |last=Fierer |first=Noah |date=2017-08-21 |title=Embracing the unknown: disentangling the complexities of the soil microbiome |url=https://www.nature.com/articles/nrmicro.2017.87 |journal=Nature Reviews Microbiology |language=en |volume=15 |issue=10 |pages=579–590 |doi=10.1038/nrmicro.2017.87 |pmid=28824177 |issn=1740-1534 |via=Springer Nature}}</ref> Development of next generation sequencing technologies open up the avenue to investigate microbial diversity in soil. <ref>{{Cite journal |last1=Chaudhary |first1=Dhiraj Kumar |last2=Khulan |first2=Altankhuu |last3=Kim |first3=Jaisoo |date=2019-04-30 |title=Development of a novel cultivation technique for uncultured soil bacteria |journal=Scientific Reports |language=en |volume=9 |issue=1 |page=6666 |doi=10.1038/s41598-019-43182-x |pmid=31040339 |pmc=6491550 |bibcode=2019NatSR...9.6666C |issn=2045-2322}}</ref> One feature of soil microbes is spatial separation which influences microbe to microbe interactions and ecosystem functioning in the soil habitat. <ref>{{Cite journal |last1=Cao |first1=Tingting |last2=Kong |first2=Xiangshi |last3=He |first3=Weihua |last4=Chen |first4=Yunru |last5=Fang |first5=You |last6=Li |first6=Qiang |last7=Chen |first7=Qi |last8=Luo |first8=Yunchao |last9=Tian |first9=Xingjun |date=2022-09-01 |title=Spatiotemporal characteristics of enzymatic hotspots in subtropical forests: In situ evidence from 2D zymography images |url=https://linkinghub.elsevier.com/retrieve/pii/S0341816222003514 |journal=CATENA |volume=216 |pages=106365 |doi=10.1016/j.catena.2022.106365 |bibcode=2022Caten.21606365C |issn=0341-8162}}</ref> Microorganisms in soil are found to be concentrated in specific sites called 'hot spots' which is characterized by an abundance of resources such as moisture or nutrients. <ref>{{Cite journal |last1=Kuzyakov |first1=Yakov |last2=Blagodatskaya |first2=Evgenia |date=2015-04-01 |title=Microbial hotspots and hot moments in soil: Concept & review |url=https://linkinghub.elsevier.com/retrieve/pii/S0038071715000449 |journal=Soil Biology and Biochemistry |volume=83 |pages=184–199 |doi=10.1016/j.soilbio.2015.01.025 |bibcode=2015SBiBi..83..184K |issn=0038-0717}}</ref> An example is the [[rhizosphere]], and areas with accumulated organic matter such as the detritusphere.<ref name=":0">{{Cite journal |last1=Sieradzki |first1=Ella T. |last2=Nuccio |first2=Erin E. |last3=Pett-Ridge |first3=Jennifer |last4=Firestone |first4=Mary K. |date=2023-10-26 |editor-last=Makhalanyane |editor-first=Thulani P. |title=Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development |journal=mSystems |language=en |volume=8 |issue=5 |pages=e0031523 |doi=10.1128/msystems.00315-23 |issn=2379-5077 |pmc=10654102 |pmid=37754554}}</ref> These areas are characterized by the presence of decaying root litter and exudates released from plant roots which regulates the availability of carbon and nitrogen and in consequence modulate microbial processes. <ref name=":0" /> Apart from labile organic carbon, spatial separation of microbes in soil may be influenced by other environmental factors such as temperature and moisture. <ref>{{Citation |last1=Tiedje |first1=J. M. |title=Soil teeming with life: new frontiers for soil science. |date=2000-12-11 |work=Sustainable management of soil organic matter |pages=393–425 |url=http://dx.doi.org/10.1079/9780851994659.0393 |access-date=2024-11-10 |place=UK |publisher=CABI Publishing |isbn=978-0-85199-465-9 |last2=Cho |first2=J. C. |last3=Murray |first3=A. |last4=Treves |first4=D. |last5=Xia |first5=B. |last6=Zhou |first6=J.|doi=10.1079/9780851994659.0393 }}</ref> Other abiotic factors like pH and mineral nutrient composition may also influence the distribution of microorganisms in soil. <ref>{{Cite journal |last1=Zhalnina |first1=Kateryna |last2=Dias |first2=Raquel |last3=de Quadros |first3=Patricia Dörr |last4=Davis-Richardson |first4=Austin |last5=Camargo |first5=Flavio A. O. |last6=Clark |first6=Ian M. |last7=McGrath |first7=Steve P. |last8=Hirsch |first8=Penny R. |last9=Triplett |first9=Eric W. |date=2014-11-14 |title=Soil pH Determines Microbial Diversity and Composition in the Park Grass Experiment |url=http://dx.doi.org/10.1007/s00248-014-0530-2 |journal=Microbial Ecology |volume=69 |issue=2 |pages=395–406 |doi=10.1007/s00248-014-0530-2 |pmid=25395291 |issn=0095-3628}}</ref> Variability of these factors make soil a dynamic system. <ref>{{Cite journal |last1=Nannipieri |first1=P. |last2=Ascher |first2=J. |last3=Ceccherini |first3=M. T. |last4=Landi |first4=L. |last5=Pietramellara |first5=G. |last6=Renella |first6=G. |date=January 2017 |title=Microbial diversity and soil functions |url=http://dx.doi.org/10.1111/ejss.4_12398 |journal=European Journal of Soil Science |volume=68 |issue=1 |pages=12–26 |doi=10.1111/ejss.4_12398 |bibcode=2017EuJSS..68...12N |issn=1351-0754}}</ref> Interactions between members of the soil microhabitat takes place via chemical signaling which is mediated by soluble metabolites and volatile organic compounds, in addition to extracellular polysaccharides. <ref>{{Cite journal |last1=Cao |first1=Tingting |last2=Luo |first2=Yunchao |last3=Shi |first3=Man |last4=Tian |first4=Xingjun |last5=Kuzyakov |first5=Yakov |date=2024-01-01 |title=Microbial interactions for nutrient acquisition in soil: Miners, scavengers, and carriers |url=https://linkinghub.elsevier.com/retrieve/pii/S0038071723002778 |journal=Soil Biology and Biochemistry |volume=188 |pages=109215 |doi=10.1016/j.soilbio.2023.109215 |bibcode=2024SBiBi.18809215C |issn=0038-0717}}</ref> Chemical signals enable microbes to interact, for example bacterial peptidoglycans stimulate growth of ''Candida albicans''.<ref>{{Cite journal |last1=Cugini |first1=Carla |last2=Calfee |first2=M. Worth |last3=Farrow |first3=John M. |last4=Morales |first4=Diana K. |last5=Pesci |first5=Everett C. |last6=Hogan |first6=Deborah A. |date=2007-07-19 |title=Farnesol, a common sesquiterpene, inhibits PQS production in <i>Pseudomonas aeruginosa</i> |url=http://dx.doi.org/10.1111/j.1365-2958.2007.05840.x |journal=Molecular Microbiology |volume=65 |issue=4 |pages=896–906 |doi=10.1111/j.1365-2958.2007.05840.x |pmid=17640272 |issn=0950-382X}}</ref> Reciprocally, ''C. albicans'' production of [[farnesol]] modulates the expression of virulence genes and influences bacterial quorum sensing. <ref>{{Cite journal |last1=Cugini |first1=Carla |last2=Morales |first2=Diana K. |last3=Hogan |first3=Deborah A. |date=2010 |title=Candida albicans-produced farnesol stimulates Pseudomonas quinolone signal production in LasR-defective Pseudomonas aeruginosa strains |journal=Microbiology |volume=156 |issue=10 |pages=3096–3107 |doi=10.1099/mic.0.037911-0 |doi-access=free |issn=1465-2080 |pmc=3068698 |pmid=20656785}}</ref> Trophic interactions by microbes in the same environment is driven by molecular communication.<ref>{{Cite journal |last1=Zelezniak |first1=Aleksej |last2=Andrejev |first2=Sergej |last3=Ponomarova |first3=Olga |last4=Mende |first4=Daniel R. |last5=Bork |first5=Peer |last6=Patil |first6=Kiran Raosaheb |date=2015-05-19 |title=Metabolic dependencies drive species co-occurrence in diverse microbial communities |journal=Proceedings of the National Academy of Sciences |language=en |volume=112 |issue=20 |pages=6449–6454 |doi=10.1073/pnas.1421834112 |doi-access=free |issn=0027-8424 |pmc=4443341 |pmid=25941371|bibcode=2015PNAS..112.6449Z }}</ref> Microbes may also exchange metabolites to support each other's growth, e.g., the release of extracellular enzymes by ectomycorrhiza decomposes organic matter and releases nutrients which then benefits other members of the population, in exchange organic acids from bacteria stimulate fungal growth <ref>{{Cite journal |last1=Olsson |first1=PÃ¥l Axel |last2=Wallander |first2=HÃ¥kan |date=October 1998 |title=Interactions between ectomycorrhizal fungi and the bacterial community in soils amended with various primary minerals |url=https://academic.oup.com/femsec/article-lookup/doi/10.1111/j.1574-6941.1998.tb00537.x |journal=FEMS Microbiology Ecology |language=en |volume=27 |issue=2 |pages=195–205 |doi=10.1111/j.1574-6941.1998.tb00537.x}}</ref> These examples of trophic interactions especially metabolite dependencies drive species interactions and are important in the assembly of soil microbial communities. <ref>{{Cite journal |last1=Zelezniak |first1=Aleksej |last2=Andrejev |first2=Sergej |last3=Ponomarova |first3=Olga |last4=Mende |first4=Daniel R. |last5=Bork |first5=Peer |last6=Patil |first6=Kiran Raosaheb |date=2015-05-19 |title=Metabolic dependencies drive species co-occurrence in diverse microbial communities |journal=Proceedings of the National Academy of Sciences |language=en |volume=112 |issue=20 |pages=6449–6454 |doi=10.1073/pnas.1421834112 |doi-access=free |issn=0027-8424 |pmc=4443341 |pmid=25941371|bibcode=2015PNAS..112.6449Z }}</ref> == Soil food web == {{main|soil food web}} Diverse organisms make up the soil [[food web]]. They range in size from one-celled [[bacteria]], [[algae]], [[fungi]], and [[protozoa]], to more complex [[nematode]]s and micro-[[arthropod]]s, to the visible [[earthworm]]s, [[insect]]s, small [[vertebrate]]s, and [[plant]]s. As these organisms eat, grow, and move through the soil, they make it possible to have clean water, clean air, healthy plants, and moderated water flow. There are many ways that the soil food web is an integral part of landscape processes. [[Soil life|Soil organisms]] decompose organic compounds, including [[manure]], plant residues, and [[pesticide]]s, preventing them from entering water and becoming pollutants. They sequester nitrogen and other nutrients that might otherwise enter groundwater, and they fix nitrogen from the atmosphere, making it available to plants. Many organisms enhance soil aggregation and [[porosity]], thus increasing [[Infiltration (hydrology)|infiltration]] and reducing [[surface runoff]]. Soil organisms prey on crop pests and are food for above-ground animals. == Research == Research interests span many aspects of soil ecology and [[microbiology]], Fundamentally, researchers are interested in understanding the interplay among [[microorganisms]], [[fauna]], and plants, the [[biogeochemical]] processes they carry out, and the physical environment in which their activities take place, and applying this knowledge to address environmental problems. Example research projects are to examine the [[biogeochemistry]] and microbial ecology of [[septic drain field]] soils used to treat domestic [[wastewater]], the role of [[anecic]] [[earthworm]]s in controlling the movement of water and [[nitrogen cycle]] in [[agricultural soil science|agricultural soils]], and the assessment of soil quality in turf production.<ref>[http://www.uri.edu/cels/nrs/seml/ Laboratory of Soil Ecology and Microbiology]. Url last accessed 2006-04-18</ref> Of particular interest {{As of|2006|lc=on}} is to understand the roles and functions of [[arbuscular mycorrhiza|arbuscular]] [[mycorrhizal fungi]] in natural ecosystems. The effect of [[Terra preta|anthropic soil conditions]] on arbuscular mycorrhizal fungi, and the production of [[glomalin]] by arbuscular mycorrhizal fungi are both of particular interest due to their roles in [[Carbon sequestration|sequestering atmospheric carbon dioxide]]. == References == {{reflist|2}} == Bibliography == {{refbegin|2}} * {{cite book|author=Adl, M.S.|editor-first1=S. M |editor-last1=Adl |year=2003|title=The Ecology of Soil Decomposition|publisher=CABI, UK|doi=10.1079/9780851996615.0000|isbn=978-0851996615}} * {{cite book|author1=Coleman, D.C. |author2=D.A. Crorsley, Jr. |name-list-style=amp |year=2004|title=Fundamentals of Soil Ecology|edition=2nd|publisher=Academic Press|isbn=978-0121797263}} * Killham, 1994, Soil Ecology, Cambridge University Press * Metting, 1993,Soil Microbial Ecology, Marcel Dekker {{refend}} == External links == * {{cite web|url=https://www.soilecologysociety.com/|title=Soil Ecology Society|publisher=rutgers.edu|accessdate=2016-05-02}} * {{cite web|author=Floor, J. Anthoni|year=2000|url=http://www.seafriends.org.nz/enviro/soil/ecology.htm|title=Soil Ecology|accessdate=2016-05-02}} * {{cite web|url=http://www.esa.org/soilecology2/|title=Soil Ecology Section| publisher=Ecological Society of America|accessdate=2016-05-02}} * Yahoo! [https://web.archive.org/web/20060420042508/http://dir.yahoo.com/Science/Ecology/Soil_Ecology/ Soil Ecology Directory]. 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