Abstract
Organic matter is mainly present in the top 20–30 cm of most soil profiles and is essentially an array of organic macromolecules consisting principally of combinations of carbon, oxygen, hydrogen, nitrogen, phosphorus and sulphur. Soil organic matter is commonly measured as the quantity of organic carbon. The global pool of organic carbon in soil to a depth of 1 m has been estimated at 1,200–1,550 Pg (2 m: 2,370–2,450 Pg), and as such is significantly greater than either the biological-biota (560 Pg) or atmospheric (760 Pg) carbon pools (Baldock 2007). Almost all organic matter in soil is directly and indirectly derived from plants via photosynthesis. Thus atmospheric carbon dioxide is transformed by reduction into simple and complex organic carbon compounds, which in combination with key nutrients enable the plant to function and grow. Carbon dioxide is released directly from plants by respiration, but most of the fixed carbon is retained and ultimately transferred to the soil ecosystem via a combination of spatially distinct pathways over a variety of timescales. The most important pathways are the direct addition of senes-cent material as above-ground and below-ground detritus, return of ingested plant matter in animal faeces, and exudation of soluble organic compounds from roots (Howarth 2007).
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsNotes
- 1.
Resistance, the degree to which microbial composition remains unchanged following disturbance.
- 2.
Resilience, the rate at which microbial composition returns to its original composition after the disturbance.
- 3.
Functional redundancy, the ability of one microbial group to carry out a process at the same rate as another under the same environmental conditions (according to Allison and Martiny 2008).
References
Aira M, Sampedro L, Monroy F, Dominguez J (2008) Detritivorous earthworms directly modify the structure, thus altering the functioning of a microdecomposer food web. Soil Biol Biochem 40:2511–2516
Alami Y, Achouak W, Marol C, Heulin T (2000) Rhizosphere soil aggregation and plant growth promotion of sunflowers by an exopolysaccharide-producing Rhizobium sp. strain isolated from sunflower roots. Appl Environ Microbiol 66:3393–3398
Allison SD, Martiny JBH (2008) Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci 105:11512–11519
Allison SD, Hanson CA, Treseder KK (2007a) Nitrogen fertilization reduces diversity and alters community structure of active fungi in boreal ecosystems. Soil Biol Biochem 39:1878–1887
Allison VJ, Condron LM, Peltzer DA, Richardson SJ, Turner BL (2007b) Changes in enzyme activities and soil microbial community composition along carbon and nutrient gradients at the Franz Josef chronosequence, New Zealand. Soil Biol Biochem 39:1770–1781
Almendros G, Tinoco P, González-Vila FJ, Lüdemann HD, Sanz J, Velasco F (2001) 13C-NMR of forest soil lipids. Soil Sci 166:186–196
Anderson J (1995) Soil organisms as engineers: microsite modulation of macroscale processes. In: Jones C, Lawton J (eds) Linking species and ecosystems. Chapman Hall, London, pp 94–106
Antibus RK, Lauber C, Sinsabaugh RL, Zak DR (2006) Responses of Bradford-reactive soil protein to experimental nitrogen addition in three forest communities in northern lower Michigan. Plant Soil 288:173–187
Appuhn A, Scheller E, Joergensen RG (2006) Relationships between microbial indices in roots and silt loam soils forming a gradient in soil organic matter. Soil Biol Biochem 38:2557–2564
Badalucco L, Gelsomino A, Dell’orco S, Grego S, Nannipieri P (1992) Biochemical characterization of soil organic compounds extracted by 0.5 M K2SO4 before and after chloroform fumigation. Soil Biol Biochem 24:569–578
Bahri H, Dignac MF, Rumpel C, Rasse DP, Chenu C, Mariotti A (2006) Lignin turnover kinetics in an agricultural soil is monomer specific. Soil Biol Biochem 38:1977–1988
Bailey VL, Smith JL, Bolton H Jr (2002) Fungal-to-bacterial ratios in soils investigated for enhanced C sequestration. Soil Biol Biochem 34:997–1007
Bais H, Weir T, Perry L, Gilroy S, Vivanco J (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:233–266
Baldock J (2007) Composition and cycling of organic carbon in soil. In: Marschner P, Rengel Z (eds) Nutrient cycling in terrestrial ecosystems. Springer, Berlin, Germany, pp 1–36
Baldock JA, Oades JM, Vassallo AM, Wilson MA (1989) Incorporation of uniformly labelled 13C-glucose carbon into the organic fraction of a soil. Carbon balance and CP/MAS 13C NMR measurements. Aust J Soil Res 27:725–746
Balser TC, Firestone MK (2005) Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest. Biogeochemistry 73:395–415
Barea J (1997) Mycorrhiza/bacteria interactions on plant growth promotion. In: Ogoshi A, Kobayashi K, Homma Y, Kodama F, Kondo N, Akino S (eds) Plant growth-promoting rhizobacteria – present status and future prospects. Proceedings of the 4th international workshop on plant growth-promoting rhizobacteria, 5–10 October 1997, Sapporo, Japan. OECD, Paris
Barea JM, Andrade G, Bianciotto V, Dowling D, Lohrke S, Bonfante P et al (1998) Impact on arbuscular mycorrhiza formation of Pseudomonas strains used as inoculants for biocontrol of soil-borne fungal plant pathogens. Appl Environ Microbiol 64:2304–2307
Barea JM, Azcón R, Azcón-Aguilar C (2002) Mycorrhizosphere interactions to improve plant fitness and soil quality. Anton Leeuw Int J G 81:343–351
Bärlocher F, Corkum M (2003) Nutrient enrichment overwhelms diversity effects in leaf decomposition by stream fungi. Oikos 101:247–252
Bastian F, Bouziri L, Nicolardot B, Ranjard L (2009) Impact of wheat straw decomposition on successional patterns of soil microbial community structure. Soil Biol Biochem 41:262–275
Bastida F, Kandeler E, Moreno JL, Ros M, García C, Hernández T (2008) Application of fresh and composted organic wastes modifies structure, size and activity of soil microbial community under semiarid climate. Appl Soil Ecol 40:318–329
Bausenwein U, Gattinger A, Langer U, Embacher A, Hartmann HP, Sommer M et al (2008) Exploring soil microbial communities and soil organic matter: variability and interactions in arable soils under minimum tillage practice. Appl Soil Ecol 40:67–77
Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK (2005) The contribution of species richness and composition to bacterial services. Nature 436:1157–1160
Berg B, Matzner E (1997) Effect of N deposition on decomposition of plant litter and soil organic matter in forest systems. Environ Rev 5:1–25
Billings SA, Ziegler SE (2005) Linking microbial activity and soil organic matter transformations in forest soils under elevated CO2. Glob Change Biol 11:203–212
Billings SA, Ziegler SE (2008) Altered patterns of soil carbon substrate usage and heterotrophic respiration in a pine forest with elevated CO2 and N fertilization. Glob Change Biol 14:1025–1036
Bossuyt H, Six J, Hendrix P (2004) Rapid incorporation of fresh residue-derived carbon into newly formed microaggregates within earthworm casts. Eur J Soil Sci 55:393–399
Bossuyt H, Six J, Hendrix P (2005) Protection of soil carbon by microaggregates within earthworm casts. Soil Biol Biochem 37:251–258
Bragazza L, Freeman C, Jones T, Rydin H, Limpens J, Fenner N et al (2006) Atmospheric nitrogen deposition promotes carbon loss from peat bogs. Proc Natl Acad Sci USA 103:19386–19389
Brant JB, Sulzman EW, Myrold DD (2006) Microbial community utilization of added carbon substrates in response to long-term carbon input manipulation. Soil Biol Biochem 38:2219–2232
Broughton LC, Gross KL (2000) Patterns of diversity in plant and soil microbial communities along a productivity gradient in a Michigan old-field. Oecologia 125:420–427
Brown G (1995) How do earthworms affect microfloral and faunal community diversity? Plant Soil 170:209–231
Brown G, Doube B (2004) Functional interactions between earthworms, microorganisms, organic matter and plants. Earthworm ecology, 2nd edn. London, CRC Press, pp 213–239
Brown G, Barois P, Lavelle P (2000) Regulation of sol organic matter dynamics and microbial activity in the drilosphere and the role of interactions with other edaphic functional domains. Eur J Soil Biol 36:177–198
Bünemann E, Condron L (2007) Phosphorus and sulphur cycling in terrestrial ecosystems. In: Marschner P, Rengel Z (eds) Nutrient cycling in terrestrial ecosystems. Springer, Berlin, Germany, pp 65–92
Bünemann EK, Bossio DA, Smithson PC, Frossard E, Oberson A (2004) Microbial community composition and substrate use in a highly weathered soil as affected by crop rotation and P fertilization. Soil Biol Biochem 36:889–901
Buyer JS, Drinkwater LE (1997) Comparison of substrate utilization assay and fatty acid analysis of soil microbial communities. J Microbiol Meth 30:3–11
Carletti P, Vendramin E, Pizzeghello D, Concheri G, Zanella A, Nardi S et al (2009) Soil humic compounds and microbial communities in six spruce forests as function of parent material, slope aspect and stand age. Plant Soil 315:47–65
Carney KM, Matson PA (2005) Plant communities, soil microorganisms, and soil carbon cycling: does altering the world belowground matter to ecosystem functioning? Ecosystems 8:928–940
Carreiro MM, Sinsabaugh RL, Repert DA, Parkhurst DF (2000) Microbial enzyme shifts explain litter decay responses to simulated nitrogen deposition. Ecology 81:2359–2365
Catovsky S, Bradford MA, Hector A (2002) Biodiversity and ecosystem productivity: implications for carbon storage. Oikos 97:443–448
Chabbi A, Rumpel C (2009) Organic matter dynamics in agro-ecosystems – The knowledge gaps: guest editors’ introduction. Eur J Soil Sci 60:153–157
Chander K, Ulrich E, Jörgensen RG, Klein T (2002) Decomposition of 14C labelled wheat straw in repeatedly fumigated and non-fumigated soils with different levels of heavy metal contamination. Biol Fert Soils 35:86–91
Chu H, Lin X, Fujii T, Morimoto S, Yagi K, Hu J et al (2007) Soil microbial biomass, dehydrogenase activity, bacterial community structure in response to long-term fertilizer management. Soil Biol Biochem 39:2971–2976
Cleveland CC, Townsend AR (2006) Nutrient additions to a tropical rain forest drive substantial soil carbon dioxide losses to the atmosphere. Proc Natl Acad Sci USA 103:10316–10321
Clinton PW, Newman RH, Allen RB (1995) Immobilization of 15N in forest litter studies by 15N CPMAS NMR spectroscopy. Eur J Soil Sci 46:551–556
Coleman D, Wall D (2007) Fauna: the engine for microbial activity and transport. In: Paul E (ed) Soil microbiology, ecology, and biochemistry. Academic Press, Amsterdam, The Netherlands, pp 163–194
Conn CE, Day FP (1996) Response of root and cotton strip decay to nitrogen amendment along a barrier island dune chronosequence. Can J Bot 74:276–284
Cookson WR, Abaye DA, Marschner P, Murphy DV, Stockdale EA, Goulding KWT (2005) The contribution of soil organic matter fractions to carbon and nitrogen mineralization and microbial community size and structure. Soil Biol Biochem 37:1726–1737
Coq S, Barthes B, Oliver R, Rabary B, Blanchart E (2007) Earthworm activity affects soil aggregation and organic matter dynamics according to the quality and localization of crop residues – An experimental study (Madagascar). Soil Biol Biochem 39:2119–2128
Couteaux MM, Bottner P, Berg B (1995) Litter decomposition climate and litter quality. Trend Ecol Evol 10:63–66
Craine JM, Morrow C, Fierer N (2007) Microbial nitrogen limitation increases decomposition. Ecology 88:2105–2113
Cruz AF, Hamel C, Hanson K, Selles F, Zentner RP (2009) Thirty-seven years of soil nitrogen and phosphorus fertility management shapes the structure and function of the soil microbial community in a Brown Chernozem. Plant Soil 315:173–184
Dakora FD, Phillips DA (2002) Root exudates as mediators of mineral acquisition in low-nutrient environments. Plant Soil 245:35–47
Dang CK, Chauvet E, Gessner MO (2005) Magnitude and variability of process rates in fungal diversity-litter decomposition relationships. Ecol Lett 8:1129–1137
Darwin C (1881) The formation of vegetable mould through the action of worms, with observations on their habit. In: Ridely M (ed) The essential Darwin. Allen and Unwin, London, pp 237–256
Deacon J (1985) Decomposition of filter paper cellulose by thermophilic fungi acting singly, in combination, and in sequence. T Brit Mycol Soc 85:663–669
Degens BP (1998) Decreases in microbial functional diversity do not result in corresponding changes in decomposition under different moisture conditions. Soil Biol Biochem 30:1989–2000
Dijkstra FA, Hobbie SE, Knops JMH, Reich PB (2004) Nitrogen deposition and plant species interact to influence soil carbon stabilization. Ecol Lett 7:1192–1198
Don A, Steinberg B, Schöning I, Pritsch K, Joschko M, Gleixner G (2008) Organic carbon sequestration in earthworm burrows. Soil Biol Biochem 40:1803–1812
Downs MR, Nadelhoffer KJ, Melillo JM, Aber JD (1996) Immobilization of a 15N-labeled nitrate addition by decomposing forest litter. Oecologia 105:141–150
Duarte S, Pascoal C, Cássio F, Bärlocher F (2006) Aquatic hyphomycete diversity and identity affect leaf litter decomposition in microcosms. Oecologia 147:658–666
Dukes JS, Field CB (2000) Diverse mechanisms for CO2 effects on grassland litter decomposition. Glob Change Biol 6:145–154
Edwards C (2000) Soil invertebrate controls and microbial interactions in nutrient and organic matter dynamics in natural and agroecosystems. In: Coleman D, Hendrix P (eds) Invertebrates as webmasters in ecosystems. CAB International, Wallingford, UK, pp 141–159
Edwards IP, Cripliver JL, Gillespie AR, Johnsen KH, Scholler M, Turco RF (2004) Nitrogen availability alters macrofungal basidiomycete community structure in optimally fertilized loblolly pine forests. New Phytol 162:755–770
Ekschmitt K, Griffiths BS (1998) Soil biodiversity and its implications for ecosystem functioning in a heterogeneous and variable environment. Appl Soil Ecol 10:201–215
Ekschmitt K, Klein A, Pieper B, Wolters V (2001) Biodiversity and functioning of ecological communities – why is diversity important in some cases and unimportant in others? J Plant Nutr Soil Sci 164:239–246
Ekschmitt K, Liu M, Vetter S, Fox O, Wolters V (2005) Strategies used by soil biota to overcome soil organic matter stability – Why is dead organic matter left over in the soil? Geoderma 128:167–176
Engelking B, Flessa H, Joergensen RG (2007) Microbial use of maize cellulose and sugarcane sucrose monitored by changes in the 13C/12C ratio. Soil Biol Biochem 39:1888–1896
Enríquez S, Duarte CM, Sand-Jensen K (1993) Patterns in decomposition rates among photosynthetic organisms: the importance of detritus C:N:P content. Oecologia 94:457–471
Feng X, Simpson AJ, Wilson KP, Dudley Williams D, Simpson MJ (2008) Increased cuticular carbon sequestration and lignin oxidation in response to soil warming. Nature Geosci 1:836–839
Fierer N, Craine JM, McLauchlan K, Schimel JP (2005) Litter quality and the temperature sensitivity of decomposition. Ecology 86:320–326
Fog K (1988) The effect of added nitrogen on the rate of decomposition of organic matter. Biol Rev Camb Philos Soc 63:433–462
Fontaine S, Barot S (2005) Size and functional diversity of microbe populations control plant persistence and long-term soil carbon accumulation. Ecol Lett 8:1075–1087
Fontaine S, Bardoux G, Abbadie L, Mariotti A (2004) Carbon input to soil may decrease soil carbon content. Ecol Lett 7:314–320
Fontaine S, Barot S, Barré P, Bdioui N, Mary B, Rumpel C (2007) Stability of organic carbon in deep soil layers controlled by fresh carbon supply. Nature 450:277–280
Fonte S, Winsome T, Six J (2009) Earthworm populations in relation to soil organic matter dynamics and management in California tomato cropping systems. Appl Soil Ecol 41:206–214
Franklin O, Högberg P, Ekblad A, Ågren GI (2003) Pine forest floor carbon accumulation in response to N and PK additions: bomb 14C modelling and respiration studies. Ecosystems 6:644–658
Frey S, Elliott E, Paustian K (1999) Bacterial and fungal abundance and biomass in conventional and no-tillage agroecosystems along two climatic gradients. Soil Biol Biochem 31:573–585
Gallo M, Amonette R, Lauber C, Sinsabaugh RL, Zak DR (2004) Microbial community structure and oxidative enzyme activity in nitrogen-amended north temperate forest soils. Microb Ecol 48:218–229
Galloway JN, Dentener FJ, Capone DG, Boyer EW, Howarth RW, Seitzinger SP et al (2004) Nitrogen cycles: past, present, and future. Biogeochemistry 70:153–226
Garcia-Pausas J, Casals P, Camarero L, Huguet C, Thompson R, Sebastià M-T et al (2008) Factors regulating carbon mineralization in the surface and subsurface soils of Pyrenean mountain grasslands. Soil Biol Biochem 40:2803–2810
Gattinger A, Höfle MG, Schloter M, Embacher A, Böhme F, Munch JC et al (2007) Traditional cattle manure application determines abundance, diversity and activity of methanogenic Archaea in arable European soil. Environ Microbiol 9:612–624
Glaser B, Millar N, Blum H (2006) Sequestration and turnover of bacterial- and fungal-derived carbon in a temperate grassland soil under long-term elevated atmospheric pCO2. Glob Change Biol 12:1521–1531
González-Pérez JA, González-Vila FJ, González-Vázquez R, Arias ME, Rodríguez J, Knicker H (2008) Use of multiple biogeochemical parameters to monitor the recovery of soils after forest fires. Org Geochem 39:940–944
Grayston SJ, Vaughan D, Jones D (1996) Rhizosphere carbon flow in trees, in comparison with annual plants: the importance of root exudation and its impact on microbial activity and nutrient availability. Appl Soil Ecol 5:29
Griffiths BS, Ritz K, Bardgett RD, Cook R, Christensen S, Ekelund F et al (2000) Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship. Oikos 90:279–294
Griffiths BS, Ritz K, Wheatley R, Kuan HL, Boag B, Christensen S et al (2001) An examination of the biodiversity-ecosystem function relationship in arable soil microbial communities. Soil Biol Biochem 33:1713–1722
Gunapala N, Scow KM (1998) Dynamics of soil microbial biomass and activity in conventional and organic farming systems. Soil Biol Biochem 30:805–816
Hagedorn F, Spinnler D, Siegwolf R (2003) Increased N deposition retards mineralization of old soil organic matter. Soil Biol Biochem 35:1683–1692
Haider K, Frederick LR, Flaig W (1965) Reactions between amino acid compounds and phenols during oxidation. Plant Soil 22:49–64
Hamilton EW III, Frank DA (2001) Can plants stimulate soil microbes and their own nutrient supply? Evidence from a grazing tolerant grass. Ecology 82:2397–2402
Hättenschwiler S, Tiunov AV, Scheu S (2005) Biodiversity and litter decomposition in terrestrial ecosystems. Annu Rev Ecol Evol Syst 36:191–218
He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG et al (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9:2364–2374
He JZ, Zheng Y, Chen CR, He YQ, Zhang LM (2008) Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches. J Soil Sediments 8:349–358
Heal OW, Flanagan PW, French DD, Maclean SF (1981) Decomposition and accumulation of organic matter in tundra. In: Bliss LC, Heal OW, Moore JJ (eds) Tundra ecosystems: a comparative analysis. Cambridge University Press, Cambridge, UK, pp 587–634
Hedlund K, Öhrn MS (2000) Tritrophic interactions in a soil community enhance decomposition rates. Oikos 88:585–591
Hendrix PF, Parmelee RW, Crossley DA Jr, Coleman DC, Odum EP, Groffman PM (1986) Detritus food webs in conventional and no-tillage agroecosystems. Bioscience 36:374–380
Hessen DO, Ågren GI, Anderson TR, Elser JJ, De Ruiter PC (2004) Carbon sequestration in ecosystems: the role of stoichiometry. Ecology 85:1179–1192
Hobbie SE, Vitousek PM (2000) Nutrient limitation of decomposition in Hawaiian forests. Ecology 81:1867–1877
Hopkins DW, Gregorich EG (2005) Carbon as a substrate for soil organisms. In: Bardgett RD, Usher MB, Hopkins DW (eds) Biological diversity and function in soils. Cambridge University Press, Cambridge, UK, pp 57–79
Howarth W (2007) Carbon cycling and formation of organic matter. In: Paul EA (ed) Soil microbiology, ecology, and biochemistry, 3rd edn. Academic Press, Amsterdam, The Netherlands, pp 303–340
Hutsch B, Augustin J, Merbach W (2002) Plant rhizodeposition – an important source for carbon turnover in soils. J Plant Nutr Soil Sci 165:397–407
Janzen HH (2004) Carbon cycling in earth systems–a soil science perspective. Agr Ecosys Environ 104:399–417
Janzen RA, Dormaar JF, McGill WB (1995) A community-level concept of controls on decomposition processes: decomposition of barley straw by Phanerochaete chrysosporium or Phlebia radiata in pure or mixed culture. Soil Biol Biochem 27:173–179
Jastrow JD, Amonette JE, Bailey VL (2007) Mechanisms controlling soil carbon turnover and their potential application for enhancing carbon sequestration. Climatic Change 80:5–23
Jiang L (2007) Negative selection effects suppress relationships between bacterial diversity and ecosystem functioning. Ecology 88:1075–1085
Jiang L, Pu Z, Nemergut DR (2008) On the importance of the negative selection effect for the relationship between biodiversity and ecosystem functioning. Oikos 117:488–493
Joergensen RG, Wichern F (2008) Quantitative assessment of the fungal contribution to microbial tissue in soil. Soil Biol Biochem 40:2977–2991
Johnson D, Booth R, Whiteley A, Bailey M, Read D, Grime J et al (2003) Plant community composition affects the biomass, activity and diversity of microorganisms in limestone grassland soil. Eur J Soil Sci 54:671–677
Johnston AE, Poulton PR, Coleman K, Donald LS (2009) Soil organic matter: its importance in sustainable agriculture and carbon dioxide fluxes. Adv Agron 101:1–57
Jolivet C, Angers DA, Chantigny MH, Andreux F, Arrouays D (2006) Carbohydrate dynamics in particle-size fractions of sandy spodosols following forest conversion to maize cropping. Soil Biol Biochem 38:2834–2842
Jones HL, Worrall JJ (1995) Fungal biomass in decayed wood. Mycologia 87:459–466
Kelleher BP, Simpson AJ (2006) Humic substances in soils: are they really chemically distinct? Environ Sci Technol 40:4605–4611
Kelley KR, Stevenson FJ (1996) Organic forms of N in soil. In: Piccolo A (ed) Humic substances in terrestrial ecosystems. Elsevier, Amsterdam, The Netherlands, pp 407–427
Kemmitt SJ, Lanyon CV, Waite IS, Wen Q, Addiscott TM, Bird NRA et al (2008) Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass–a new perspective. Soil Biol Biochem 40:61–73
Kennedy A (2005) Rhizosphere. In: Sylvia D, Fuhrmann J, Hartel P, Zuberer D (eds) Principles and applications of soil microbiology, 2nd edn. Pearson Prentice Hall, Upper Saddle River, NJ, pp 242–262
Kim J-S, Dungan R, Crowley D (2008) Microarray analysis of bacterial diversity and distribution in aggregates from a desert agricultural soil. Biol Fert Soils 44:1003–1011
Kindler R, Miltner A, Richnow HH, Kästner M (2006) Fate of gram-negative bacterial biomass in soil – Mineralization and contribution to SOM. Soil Biol Biochem 38:2860–2870
Kindler R, Miltner A, Thullner M, Richnow HH, Kästner M (2009) Fate of bacterial biomass derived fatty acids in soil and their contribution to soil organic matter. Org Geochem 40:29–37
Knicker H, Lüdemann HD (1995) N-15 and C-13 CPMAS and solution NMR studies of N-15 enriched plant material during 600 days of microbial degradation. Org Geochem 23:329–341
Knicker H, Almendros G, González-Vila FJ, Martin F, Lüdemann HD (1996) 13C- and 15N-NMR spectroscopic examination of the transformation of organic nitrogen in plant biomass during thermal treatment. Soil Biol Biochem 28:1053–1060
Kögel-Knabner I (2002) The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter. Soil Biol Biochem 34:139–162
Kramer C, Gleixner G (2008) Soil organic matter in soil depth profiles: distinct carbon preferences of microbial groups during carbon transformation. Soil Biol Biochem 40:425–433
Kubartová A, Moukoumi J, Béguiristain T, Ranger J, Berthelin J (2007) Microbial diversity during cellulose decomposition in different forest stands: I. Microbial communities and environmental conditions. Microb Ecol 54:393–405
Lattaud C, Locati S, Mora P, Rouland C, Lavelle P (1998) The diversity of digestive systems in tropical geophagous earthworms. Appl Soil Ecol 9:189–195
Lattaud C, Mora P, MH G, Locati S, Rouland C (1999) Enzymatic digestive capabilities in geophagous earthworms – origin and activities of cellulolytic enzymes. Pedobiologia 43:842–850
Lavelle P, Gilot C (1994) Priming effect of macroorganisms on soil microflora: a key process of soil function? In: Ritz K, Dighton J, Giller K (eds) Beyond the biomass. Wiley, Chichester, UK, pp 173–180
Lehmann J (2007) Bio-energy in the black. Front Ecol Environ 5:381–387
Liang C, Fujinuma R, Wei L, Balser TC (2007) Tree species-specific effects on soil microbial residues in an upper Michigan old-growth forest system. Forestry 80:65–72
Loreau M, Naeem S, Inchausti P, Bengtsson J, Grime JP, Hector A et al (2001) Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294:804–808
Lorenz K, Lal R, Preston CM, Nierop KGJ (2007) Strengthening the soil organic carbon pool by increasing contributions from recalcitrant aliphatic bio(macro)molecules. Geoderma 142:1–10
Luengo JM, García B, Sandoval A, Naharro G, Olivera ER (2003) Bioplastics from microorganisms. Curr Opin Microbiol 6:251–260
Mack MC, Schuur EAG, Bret-Harte MS, Shaver GR, Chapin FS III (2004) Ecosystem carbon storage in arctic tundra reduced by long-term nutrient fertilization. Nature 431:440–443
Marinissen J, Hillenaar S (1997) Earthworm-induced distribution of organic matter in macroaggregates from differently managed arable fields. Soil Biol Biochem 29:391–395
Marschner P, Yang CH, Lieberei R, Crowley DE (2001) Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem 33:1437–1445
McGrady-Steed J, Harris PM, Morin PJ (1997) Biodiversity regulates ecosystem predictability. Nature 390:162–165
McGroddy ME, Silver WL, De Oliveira Jr RC (2004) The effect of phosphorus availability on decomposition dynamics in a seasonal lowland Amazonian forest. Ecosystems 7:172–179
McGuire AD, Joyce LA, Kicklighter DW, Melillo JM, Esser G, Vorosmarty CJ (1993) Productivity response of climax temperate forests to elevated temperature and carbon dioxide: a North American comparison between two global models. Climatic Change 24:287–310
McLean MA, Parkinson D (2000) Field evidence of the effects of the epigeic earthworm Dendrobaena octaedra on the microfungal community in pine forest floor. Soil Biol Biochem 32:1671–1681
McNeill A, Unkovich M (2007) The nitrogen cycle in terrestrial ecosystems. In: Marschner P, Rengel Z (eds) Nutrient cycling in terrestrial ecosystems. Springer, Berlin, Germany, pp 37–64
Mead DJ, Preston CM (1994) Distribution and retranslocation of 15N in lodgepole pine over eight growing seasons. Tree Physiol 14:389–402
Mead DJ, Chang SX, Preston CM (2008) Recovery of 15N-urea 10 years after application to a Douglas-fir pole stand in coastal British Columbia. For Ecol Manage 256:694–701
Melillo JM, Aber JD, Muratore JF (1982) Nitrogen and lignin control of hardwood leaf litter decomposition dynamics. Ecology 63:621–626
Michel K, Matzner E (2002) Nitrogen content of forest floor Oa layers affects carbon pathways and nitrogen mineralization. Soil Biol Biochem 34:1807–1813
Mikutta R, Schaumann GE, Gildemeister D, Bonneville S, Kramer MG, Chorover J et al (2009) Biogeochemistry of mineral-organic associations across a long-term mineralogical soil gradient (0.3–4100 kyr), Hawaiian Islands. Geochim Cosmochim Acta 73:2034–2060
Moore JC, McCann K, Setälä H, De Ruiter PC (2003) Top-down is bottom-up: does predation in the rhizosphere regulate aboveground dynamics? Ecology 84:846–857
Moorhead DL, Sinsabaugh RL (2006) A theoretical model of litter decay and microbial interaction. Ecol Monogr 76:151–174
Mummey D, Matthias C, Six J (2006) Endogeic earthworms differentially influence bacterial communities associated with different soil aggregate size fractions. Soil Biol Biochem 38:1608–1614
Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and functions. Eur J Soil Sci 54:655–670
Neff JC, Townsend AR, Gleixner G, Lehman SJ, Turnbull J, Bowman WD (2002) Variable effects of nitrogen additions on the stability and turnover of soil carbon. Nature 419:915–917
Nelson PN, Baldock JA (2005) Estimating the molecular composition of a diverse range of natural organic materials from solid-state 13C NMR and elemental analyses. Biogeochemistry 72:1–34
Nemergut DR, Townsend AR, Sattin SR, Freeman KR, Fierer N, Neff JC et al (2008) The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling. Environ Microbiol 10:3093–3105
Neumann G (2007) Root exudates and nutrient cycling. In: Marschner P, Rengel Z (eds) Nutrient cycling in terrestrial ecosystems. Springer, Berlin, Germany, pp 123–157
Nierop KGJ (1998) Origin of aliphatic compounds in a forest soil. Org Geochem 29:1009–1016
Noguez A, Escalante A, Forney LJ, Nava-Medoza M, Rosas I, Souza V et al (2008) Soil aggregates in a tropical deciduous forest: effects on C and N dynamics, and microbial communities as determined by t-RFLPs. Biogeochemistry 89:209–220
Nömmik H, Vahtras K (1982) Retention and fixation of ammonium and ammonia in soils. In: Stevenson FJ (ed) Nitrogen in agricultural soils. Agronomy Society of America, Madison, WI, pp 123–161
Nunan N, Wu K, Young I, Crawford I, Ritz K (2003) Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil. FEMS Microbiol Ecol 44:203–215
Olsson P, Linder S, Giesler R, Högberg P (2005) Fertilization of boreal forest reduces both autotrophic and heterotrophic soil respiration. Glob Change Biol 11:1745–1753
Orwin KH, Wardle DA, Greenfield LG (2006) Ecological consequences of carbon substrate identity and diversity in a laboratory study. Ecology 87:580–593
Otto A, Shunthirasingham C, Simpson MJ (2005) A comparison of plant and microbial biomarkers in grassland soils from the Prairie Ecozone of Canada. Org Geochem 36:425–448
Parton W, Schimel D, Cole C, Ojima D (1987) Analysis of factors controlling soil organic-matter levels in great-plains grasslands. Soil Sci Soc Am J 51:1173–1179
Paterson E, Gebbing T, Abel C, Sim A, Telfer G (2007) Rhizodeposition shapes rhizosphere microbial community structure in organic soil. New Phytol 173:600–610
Paterson E, Osler G, Dawson LA, Gebbing T, Sim A, Ord B (2008a) Labile and recalcitrant plant fractions are utilised by distinct microbial communities in soil: independent of the presence of roots and mycorrhizal fungi. Soil Biol Biochem 40:1103–1113
Paterson E, Thornton B, Midwood AJ, Osborne SM, Sim A, Millard P (2008b) Atmospheric CO2 enrichment and nutrient additions to planted soil increase mineralisation of soil organic matter, but do not alter microbial utilisation of plant- and soil C-sources. Soil Biol Biochem 40:2434–2440
Plassart P, Akpa Vinceslas M, Gangneux C, Mercier A, Barray S, Laval K (2008) Molecular and functional responses of soil microbial communities under grassland restoration. Agr Ecosys Environ 127:286–293
Postgate J (1998) Nitrogen fixation, 3rd edn. Cambridge University Press, Cambridge, UK
Powell J, Klironomos J (2007) The ecology of plant-microbial mutualisms. In: Paul EA (ed) Soil microbiology, ecology, and biochemistry, 3rd edn. Academic Press, Amsterdam, The Netherlands, pp 257–282
Prescott CE (1995) Does nitrogen availability control rates of litter decomposition in forests? Plant Soil 168–169:83–88
Reed HE, Martiny JBH (2007) Testing the functional significance of microbial composition in natural communities. FEMS Microbiol Ecol 62:161–170
Resh SC, Binkley D, Parrotta JA (2002) Greater soil carbon sequestration under nitrogen-fixing trees compared with Eucalyptus species. Ecosystems 5:217–231
Rillig MC (2004) Arbuscular mycorrhizae and terrestrial ecosystem processes. Ecol Lett 7:740–754
Rillig MC, Caldwell BA, Wösten HAB, Sollins P (2007) Role of proteins in soil carbon and nitrogen storage: controls on persistence. Biogeochemistry 85:25–44
Robinson C, Dighton J, Frankland J, Coward P (1993) Nutrient and carbon dioxide release by interacting species of straw-decomposing fungi. Plant Soil 151:139–142
Ros M, Pascual JA, Garcia C, Hernandez MT, Insam H (2006) Hydrolase activities, microbial biomass and bacterial community in a soil after long-term amendment with different composts. Soil Biol Biochem 38:3443–3452
Saiya-Cork KR, Sinsabaugh RL, Zak DR (2002) The effects of long term nitrogen deposition on extracellular enzyme activity in an Acer saccharum forest soil. Soil Biol Biochem 34:1309–1315
Sampedro L, Dominguez J (2008) Stable isotope natural abundance (d13C and d15N) of the earthworm Eisenia fetida and other soil fauna living in two different vermicomposting environments. Appl Soil Ecol 38:91–99
Sampedro L, Whalon J (2007) Changes in fatty acid profiles through the digestive tract of the earthworm Lumbricus terrestris L. Appl Soil Ecol 35:226–236
Schimel JP, Gulledge J (1998) Microbial community structure and global trace gases. Glob Change Biol 4:745–758
Schindler FV, Mercer EJ, Rice JA (2007) Chemical characteristics of glomalin-related soil protein (GRSP) extracted from soils of varying organic matter content. Soil Biol Biochem 39:320–329
Schulze E-D, Mooney HA (1993) Biodiversity and ecosystem function. Springer, Berlin, Germany
Schutter M, Dick R (2002) Microbial community profiles and activities among aggregates of winter fallow and cover-cropped soil. Soil Sci Soc Am J 66:142–153
Schwartz E, Adair KL, Schuur EA (2007) Bacterial community structure correlates with decomposition parameters along a Hawaiian precipitation gradient. Soil Biol Biochem 39:2164–2167
Scow KM (1997) Interrelationships between soil microbial communities and carbon flow in agroecosystems. In: Jackson LE (ed) Ecology in agriculture. Academic Press, New York, pp 367–416
Setälä H, McLean M (2004) Decomposition rate of organic substrates in relation to the species diversity of soil saprophytic fungi. Oecologia 139:98–107
Shaw C, Pawluk S (1986) Faecal microbiology of Octolasion tyrtaeum, Aporrectodea turgida and Lumbricus terrestris and its relation to the carbon budgets of three artificial soils. Pedobiologia 29:377–389
Simpson AJ, Simpson MJ, Smith E, Kelleher BP (2007a) Microbially derived inputs to soil organic matter: are current estimates too low? Environ Sci Technol 41:8070–8076
Simpson AJ, Song G, Smith E, Lam B, Novotny EH, Hayes MHB (2007b) Unraveling the structural components of soil humin by use of solution-state Nuclear Magnetic Resonance spectroscopy. Environ Sci Technol 41:876–883
Simpson MJ, Otto A, Feng X (2008) Comparison of solid-state carbon-13 nuclear magnetic resonance and organic matter biomarkers for assessing soil organic matter degradation. Soil Sci Soc Am J 72:268–276
Singh G, Mukerji K (2006) Root exudates as determinant of rhizospheric microbial diversity. In: Mukerji K, Manoharachary C, Singh J (eds) Microbial activity in the rhizosphere. Springer, Berlin, Germany, pp 39–53
Six J, Elliott E, Paustian K (2000) Soil macroaggregate turnover and microaggregate formation: a mechanism for C sequestration under no-tillage agriculture. Soil Biol Biochem 32:2099–2103
Six J, Conant R, Paul EA, Paustian K (2002) Stabilization mechanisms for soil organic matter: implications for C-saturation of soils. Plant Soil 241:155–176
Six J, Bossuyt H, Degryze S, Denef K (2004) A history of research on the link between (micro)aggregates soil biota, and soil organic matter dynamics. Soil Till Res 79:7–31
Six J, Frey SD, Thiet RK, Batten KM (2006) Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Sci Soc Am J 70:555–569
Sjöberg G, Knicker H, Nilsson SI, Berggren D (2004) Impact of long-term N fertilization on the structural composition of spruce litter and mor humus. Soil Biol Biochem 36:609–618
Smith JL, Paul EA (1990) The significance of soil microbial biomass estimations. In: Bollag J-M, Stotzky G (eds) Soil biochemistry. Marcel Dekker, New York, pp 357–393
Sollins P, Homann P, Caldwell BA (1996) Stabilization and destabilization of soil organic matter: mechanisms and controls. Geoderma 74:65–105
Stevenson F (1985) Geochemistry of soil humic substances. In: Aiken G, McKnight D, Wershaw R, MacCarthy P (eds) Humic substances in soil, sediment, and water. Wiley, New York, pp 13–52
Stevenson F (1994) Humus chemistry: genesis, composition, reactions. Wiley, New York
Sutton R, Sposito G (2005) Molecular structure in soil humic substances: the new view. Environ Sci Technol 39:9009–9015
Swift MJ, Heal OW, Anderson JM (1979) Decomposition in terrestrial ecosystems. Studies in ecology. Blackwell Scientific, Oxford, UK
Sylvia D (2005) Mycorrhizal symbioses. In: Sylvia D, Fuhrmann J, Hartel P, Zuberer D (eds) Principles and applications of soil microbiology, 2nd edn. Pearson Prentice Hall, Upper Saddle River, NJ, pp 263–282
Timonen S, Marschner P (2006) Mycorrhizosphere concept. In: Mukerji K, Manoharachary C, Singh J (eds) Microbial activity in the rhizosphere. Springer, Berlin, Germany, pp 155–172
Tiunov AV, Scheu S (2005) Facilitative interactions rather than resource partitioning drive diversity-functioning relationships in laboratory fungal communities. Ecol Lett 8:618–625
Tiwari S, Mishra R (1993) Fungal abundance and diversity in earthworm casts and in uningested soil. Biol Fert Soils 16:131–134
Toljander YK, Lindahl BD, Holmer L, Högberg NOS (2006) Environmental fluctuations facilitate species co-existence and increase decomposition in communities of wood decay fungi. Oecologia 148:625–631
Treseder KK (2008) Nitrogen additions and microbial biomass: a meta-analysis of ecosystem studies. Ecol Lett 11:1111–1120
Treton C, Chauvet E, Charcosset JY (2004) Competitive interaction between two aquatic hyphomycete species and increase in leaf litter breakdown. Microb Ecol 48:439–446
Tsavkelova EA, Klimova SY, Cherdyntseva TA, Netrusov AI (2006) Microbial producers of plant growth stimulators and their practical use: a review. Appl Biochem Microbiol 42:117–126
Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255:571–586
Vitousek PM (2004) Nutrient cycling and limitation: Hawai’i as a model system. Princeton University Press, Princeton, NJ
Vitousek PM, Howarth RW (1991) Nitrogen limitation on land and in the sea: how can it occur? Biogeochemistry 13:87–115
Vitousek PM, Aber JD, Howarth RW, Likens GE, Matson PA, Schindler DW et al (1997) Human alteration of the global nitrogen cycle: sources and consequences. Ecol Appl 7:737–750
von Lützow M, Kögel-Knabner I, Ekschmitt K, Flessa H, Guggenberger G, Matzner E et al (2007) SOM fractionation methods: relevance to functional pools and to stabilization mechanisms. Soil Biol Biochem 39:2183–2207
Waldrop MP, Balser TC, Firestone MK (2000) Linking microbial community composition to function in a tropical soil. Soil Biol Biochem 32:1837–1846
Wardle DA (2002) Communities and ecosystems – linking the aboveground and belowground components. Princeton University Press, Princeton, NJ
Wardle DA (2005) How plant communities influence decomposer communities. In: Bardgett RD, Usher MB, Hopkins DW (eds) Biological diversity and function in soils. Cambridge University Press, Cambridge, UK, pp 119–138
Wardle DA, Nilsson M-C, Zackrisson O (2008) Fire-derived charcoal causes loss of forest humus. Science 320:629
Watkinson SC, Davison EM, Bramah J (1981) The effect of nitrogen availability on growth and cellulolysis by Serpula lacrimans. New Phytol 89:295–305
Webster EA, Chudek JA, Hopkins DW (2000) Carbon transformations during decomposition of different components of plant leaves in soil. Soil Biol Biochem 32:301–314
Wells JM, Boddy L, Donnelly DP (1998) Wood decay and phosphorus translocation by the cord-forming basidiomycete Phanerochaete velutina: the significance of local nutrient supply. New Phytol 138:607–617
Wertz S, Degrange V, Prosser JI, Poly F, Commeaux C, Freitag T et al (2006) Maintenance of soil functioning following erosion of microbial diversity. Environ Microbiol 8:2162–2169
White P, Rice C (2009) Tillage effects on microbial and carbon dynamics during plant residue decomposition. Soil Sci Soc Am J 73:138–145
Wohl DL, Arora S, Gladstone JR (2004) Functional redundancy supports biodiversity and ecosystem function in a closed and constant environment. Ecology 85:1534–1540
Wolf D, Wagner G (2005) Carbon transformations and soil organic matter formation. In: Sylvia D, Fuhrmann J, Hartel P, Zuberer D (eds) Principles and applications of soil microbiology. Pearson Prentice Hall, Upper Saddle River, NJ, pp 285–332
Wolter C, Scheu S (1999) Changes in bacterial numbers and hyphal lengths during the gut passage through Lumbricus terrestris (Lumbricidae, Oligochaeta). Pedobiologia 43:891–900
Zech W, Kögel-Knabner I (1994) Patterns and regulation of organic matter transformation in soils: litter decomposition and humification. In: Schulze E-D (ed) Flux control in biological systems: from enzymes to populations and ecosystems. Academic Press, San Diego, CA, pp 35–73
Zhang X, He H, Amelung W (2007) A GC/MS method for the assessment of 15N and 13C incorporation into soil amino acid enantiomers. Soil Biol Biochem 39:2785–2796
Zhong WH, Cai ZC (2007) Long-term effects of inorganic fertilizers on microbial biomass and community functional diversity in a paddy soil derived from quaternary red clay. Appl Soil Ecol 36:84–91
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media B.V.
About this chapter
Cite this chapter
Condron, L., Stark, C., O’Callaghan, M., Clinton, P., Huang, Z. (2010). The Role of Microbial Communities in the Formation and Decomposition of Soil Organic Matter. In: Dixon, G., Tilston, E. (eds) Soil Microbiology and Sustainable Crop Production. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-9479-7_4
Download citation
DOI: https://doi.org/10.1007/978-90-481-9479-7_4
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-90-481-9478-0
Online ISBN: 978-90-481-9479-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)