Abstract
Humans depend upon soil-based ecosystems for many essential activities including agriculture, grazing, and forestry, as well as for other uses such as recreation, mining, drilling, and development. All of these land uses have the potential to affect soil quality and viability. The North American Dust Bowl catastrophe of the early twentieth century focused attention on agricultural soil conservation. Later in the twentieth century, more holistic approaches to ecosystem reclamation and restoration were developed, driven by research documenting the close ties between aboveground and belowground communities of producers, consumers, and decomposers. The important roles of soil microbial communities in soil formation, biogeochemical cycling, nutrient retention, plant–microbe interactions, and soil food webs are now widely recognized as essential to good soil quality, essential ecosystem services, and maintenance of biodiversity. This chapter broadly reviews the progress made toward understanding the effects of various land uses on soil microbial communities, recent developments in our understanding of the roles of soil microbes in facilitating ecosystem reclamation and restoration following anthropogenic degradation, and the implications of these processes for carbon cycling and climate change mitigation.
A nation that destroys its soil destroys itself.
Franklin D. Roosevelt (1937)
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Agnelli A, Ascher J, Corti G et al (2004) Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA. Soil Biol Biochem 36:859–868. https://doi.org/10.1016/j.soilbio.2004.02.004
Aira M, Sampedro L, Monroy F, Domínguez J (2008) Detritivorous earthworms directly modify the structure, thus altering the functioning of a microdecomposer food web. Soil Biol Biochem 40:2511–2516. https://doi.org/10.1016/j.soilbio.2008.06.010
Alele PO, Sheil D, Surget-Groba Y et al (2014) How does conversion of natural tropical rainforest ecosystems affect soil bacterial and fungal communities in the Nile river watershed of Uganda? PLoS One 9:e104818. https://doi.org/10.1371/journal.pone.0104818
Allen MF, Swenson W, Querejeta JI et al (2003) Ecology of mycorrhizae: a conceptual framework for complex interactions among plants and fungi. Annu Rev Phytopathol 41:271–303. https://doi.org/10.1146/annurev.phyto.41.052002.095518
Alletto L, Coquet Y, Benoit P et al (2010) Tillage management effects on pesticide fate in soils. A review. Agron Sustain Dev 30:367–400. https://doi.org/10.1051/agro/2009018
Allison SK (2012) Ecological restoration and environmental change: renewing damaged ecosystems. Routledge, London
Allison SD, Martiny JBH (2008) Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci USA 105:11512–11519. https://doi.org/10.1073/pnas.0801925105
Allison VJ, Miller RM, Jastrow JD et al (2005) Changes in soil microbial community structure in a tallgrass prairie chronosequence. Soil Sci Soc Am J 69:1412–1421
An S-S, Cheng Y, Huang Y-M, Liu D (2013) Effects of revegetation on soil microbial biomass, enzyme activities, and nutrient cycling on the loess plateau in China. Restor Ecol 21:600–607. https://doi.org/10.1111/j.1526-100X.2012.00941.x
An N-H, Lee S-M, Cho J-R et al (2014) Effects of long-term fertilization on microbial diversity in upland soils estimated by biolog ecoplate and DGGE. Korean J Soil Sci Fertil 47:451–456. https://doi.org/10.7745/KJSSF.2014.47.6.451
Anderson JPE, Domsch KH (1978) Mineralization of bacteria and fungi in chloroform-fumigated soils. Soil Biol Biochem 10:207–213. https://doi.org/10.1016/0038-0717(78)90098-6
Anderson T-H, Domsch KH (2010) Soil microbial biomass: the eco-physiological approach. Soil Biol Biochem 42:2039–2043. https://doi.org/10.1016/j.soilbio.2010.06.026
Antonsen H, Olsson PA (2005) Relative importance of burning, mowing and species translocation in the restoration of a former boreal hayfield: responses of plant diversity and the microbial community. J Appl Ecol 42:337–347
Aronson J, Floret C, Le Floc’h E et al (1993) Restoration and rehabilitation of degraded ecosystems in arid and semi-arid lands. I. A view from the South. Restor Ecol 1:8–17. https://doi.org/10.1111/j.1526-100X.1993.tb00004.x
Artz R, Anastasoiu D, Arrouays D et al (2010) European atlas of soil biodiversity, EUR, 130 pp.
Ashby WC (1997) Soil ripping and herbicides enhance tree and shrub restoration on stripmines. Restor Ecol 5:169–177. https://doi.org/10.1046/j.1526-100X.1997.09720.x
Augé RM (2004) Arbuscular mycorrhizae and soil/plant water relations. Can J Soil Sci 84:373–381. https://doi.org/10.4141/S04-002
Averett JM, Klips RA, Nave LE et al (2004) Effects of soil carbon amendment on nitrogen availability and plant growth in an experimental tallgrass prairie restoration. Restor Ecol 12:568–574. https://doi.org/10.1111/j.1061-2971.2004.00284.x
Averill C, Turner BL, Finzi AC (2014) Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage. Nature 505:543–545. https://doi.org/10.1038/nature12901
Ayres E, Wall DH, Bardgett RD (2010) Trophic interactions and their implications for soil carbon fluxes. In: Kutsch WL, Bahn M, Heinemeyer A (eds) Soil carbon dynamics. Cambridge University Press, Cambridge
Azooz RH, Arshad MA, Franzluebbers AJ (1996) Pore size distribution and hydraulic conductivity affected by tillage in northwestern Canada. Soil Sci Soc Am J 60:1197–1201
Babujia LC, Hungria M, Franchini JC, Brookes PC (2010) Microbial biomass and activity at various soil depths in a Brazilian oxisol after two decades of no-tillage and conventional tillage. Soil Biol Biochem 42:2174–2181. https://doi.org/10.1016/j.soilbio.2010.08.013
Badawi N, Johnsen AR, Sørensen J, Aamand J (2013) Centimeter-scale spatial variability in 2-methyl-4-chlorophenoxyacetic acid mineralization increases with depth in agricultural soil. J Environ Qual 42:683–689
Baer SG, Blair JM, Collins SL, Knapp AK (2003) Soil resources regulate productivity and diversity in newly established tallgrass prairie. Ecology 84:724–735. https://doi.org/10.1890/0012-9658(2003)084[0724:SRRPAD]2.0.CO;2
Bailey VL, Peacock AD, Smith JL, Bolton H Jr (2002) Relationships between soil microbial biomass determined by chloroform fumigation–extraction, substrate-induced respiration, and phospholipid fatty acid analysis. Soil Biol Biochem 34:1385–1389. https://doi.org/10.1016/S0038-0717(02)00070-6
Baldrian P, Trögl J, Frouz J et al (2008) Enzyme activities and microbial biomass in topsoil layer during spontaneous succession in spoil heaps after brown coal mining. Soil Biol Biochem 40:2107–2115. https://doi.org/10.1016/j.soilbio.2008.02.019
Balota EL, Colozzi-Filho A, Andrade DS, Dick RP (2003) Microbial biomass in soils under different tillage and crop rotation systems. Biol Fertil Soils 38:15–20. https://doi.org/10.1007/s00374-003-0590-9
Balshi MS, McGuire AD, Duffy P et al (2009) Assessing the response of area burned to changing climate in western boreal North America using a Multivariate Adaptive Regression Splines (MARS) approach. Glob Change Biol 15:578–600. https://doi.org/10.1111/j.1365-2486.2008.01679.x
Banning NC, Gleeson DB, Grigg AH et al (2011) Soil microbial community successional patterns during forest ecosystem restoration. Appl Environ Microbiol 77:6158–6164. https://doi.org/10.1128/AEM.00764-11
Bardgett RD, van der Putten WH (2014) Belowground biodiversity and ecosystem functioning. Nature 515:505–511. https://doi.org/10.1038/nature13855
Bardgett RD, Freeman C, Ostle NJ (2008) Microbial contributions to climate change through carbon cycle feedbacks. ISME J 2:805–814. https://doi.org/10.1038/ismej.2008.58
Baretta D, Santos JCP, Figueiredo SR, Klauberg-Filho O (2005) Effects of native pasture burning and Pinus monoculture on changes in soil biological attributes on the Southern Plateau of Santa Catarina—Brazil. Rev Bras Ciênc Solo 29:715–724. https://doi.org/10.1590/S0100-06832005000500007
Barrios E (2007) Soil biota, ecosystem services and land productivity. Ecol Econ 64:269–285. https://doi.org/10.1016/j.ecolecon.2007.03.004
Bates ST, Clemente JC, Flores GE et al (2013) Global biogeography of highly diverse protistan communities in soil. ISME J 7:652–659. https://doi.org/10.1038/ismej.2012.147
Beare MH, Neely CL, Coleman DC, Hargrove WL (1990) A substrate-induced respiration (SIR) method for measurement of fungal and bacterial biomass on plant residues. Soil Biol Biochem 22:585–594. https://doi.org/10.1016/0038-0717(90)90002-H
Becklin KM, Gamez G, Uelk B et al (2011) Soil fungal effects on floral signals, rewards, and aboveground interactions in an alpine pollination web. Am J Bot 98:1299–1308. https://doi.org/10.3732/ajb.1000450
Becklin KM, Hertweck KL, Jumpponen A (2012) Host identity impacts rhizosphere fungal communities associated with three alpine plant species. Microb Ecol 63:682–693
Beesley L, Moreno-Jiménez E, Gomez-Eyles JL et al (2011) A review of biochars’ potential role in the remediation, revegetation and restoration of contaminated soils. Environ Pollut 159:3269–3282. https://doi.org/10.1016/j.envpol.2011.07.023
Benayas JMR, Newton AC, Diaz A, Bullock JM (2009) Enhancement of biodiversity and ecosystem services by ecological restoration: a meta-analysis. Science 325:1121–1124. https://doi.org/10.1126/science.1172460
Ben-David EA, Zaady E, Sher Y, Nejidat A (2011) Assessment of the spatial distribution of soil microbial communities in patchy arid and semi-arid landscapes of the Negev Desert using combined PLFA and DGGE analyses. FEMS Microbiol Ecol 76:492–503. https://doi.org/10.1111/j.1574-6941.2011.01075.x
Bending GD (2007) What are the mechanisms and specificity of mycorrhization helper bacteria? New Phytol 174:707–710. https://doi.org/10.1111/j.1469-8137.2007.02076.x
Bending GD, Turner MK, Rayns F et al (2004) Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes. Soil Biol Biochem 36:1785–1792
Bennett EM, Carpenter SR, Caraco NF (2001) human impact on erodable phosphorous and eutrophication: a global perspective. Bioscience 51:227–234
Bennett LT, Kasel S, Tibbits J (2008) Non-parametric multivariate comparisons of soil fungal composition: sensitivity to thresholds and indications of structural redundancy in T-RFLP data. Soil Biol Biochem 40:1601–1611. https://doi.org/10.1016/j.soilbio.2008.01.008
Bent SJ, Forney LJ (2008) The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J 2:689–695. https://doi.org/10.1038/ismej.2008.44
Berthrong S, Buckley D, Drinkwater L (2013) Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling. Microb Ecol 66:158–170. https://doi.org/10.1007/s00248-013-0225-0
Bever JD (2002) Negative feedback within a mutualism: host-specific growth of mycorrhizal fungi reduces plant benefit. Proc R Soc Lond B Biol Sci 269:2595–2601. https://doi.org/10.1098/rspb.2002.2162
Bever JD, Schultz PA, Pringle A, Morton JB (2001) Arbuscular mycorrhizal fungi: more diverse than meets the eye, and the ecological tale of why: the high diversity of ecologically distinct species of arbuscular mycorrhizal fungi within a single community has broad implications for plant ecology. Bioscience 51:923–931. https://doi.org/10.1641/0006-3568(2001)051[0923:AMFMDT]2.0.CO;2
Beyerinck MW (1888) Die Bacterien der Papilionaceen-Knöllchen. Botanische Zeitung 46:725–735, 741–750, 757–771, 781–790, 797–804
Beylich A, Oberholzer H-R, Schrader S et al (2010) Evaluation of soil compaction effects on soil biota and soil biological processes in soils. Soil Tillage Res 109:133–143. https://doi.org/10.1016/j.still.2010.05.010
Birkhofer K, Bezemer TM, Bloem J et al (2008) Long-term organic farming fosters below and aboveground biota: implications for soil quality, biological control and productivity. Soil Biol Biochem 40:2297–2308. https://doi.org/10.1016/j.soilbio.2008.05.007
Bishnu A, Saha T, Mazumdar D et al (2008) Assessment of the impact of pesticide residues on microbiological and biochemical parameters of tea garden soils in India. J Environ Sci Health B 43:723–731. https://doi.org/10.1080/03601230802388850
Blagodatskaya E, Kuzyakov Y (2013) Active microorganisms in soil: critical review of estimation criteria and approaches. Soil Biol Biochem 67:192–211. https://doi.org/10.1016/j.soilbio.2013.08.024
Blumenthal DM, Jordan NR, Russelle MP (2003) Soil carbon addition controls weeds and facilitates prairie restoration. Ecol Appl 13:605–615. https://doi.org/10.1890/1051-0761(2003)013[0605:SCACWA]2.0.CO;2
Boerner REJ, Huang J, Hart SC (2009) Impacts of fire and fire surrogate treatments on forest soil properties: a meta-analytical approach. Ecol Appl 19:338–358. https://doi.org/10.1890/07-1767.1
Bonan GB (2008) Forests and climate change: forcings, feedbacks, and the climate benefits of forests. Science 320:1444–1449
Bonfante P, Anca I-A (2009) Plants, mycorrhizal fungi, and bacteria: a network of interactions. Annu Rev Microbiol 63:363–383. https://doi.org/10.1146/annurev.micro.091208.073504
Bonito G, Reynolds H, Robeson MS et al (2014) Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Mol Ecol 23:3356–3370. https://doi.org/10.1111/mec.12821
Bonkowski M (2004) Protozoa and plant growth: the microbial loop in soil revisited. New Phytol 162:617–631. https://doi.org/10.1111/j.1469-8137.2004.01066.x
Brady MV, Hedlund K, Cong RG et al (2015) Valuing supporting soil ecosystem services in agriculture: a natural capital approach. Agron J 107:1809–1821
Brais S, David P, Ouimet R (2000) Impacts of wild fire severity and salvage harvesting on the nutrient balance of jack pine and black spruce boreal stands. For Ecol Manag 137:231–243. https://doi.org/10.1016/S0378-1127(99)00331-X
Briones MJI, Ostle NJ, McNamara NP, Poskitt J (2009) Functional shifts of grassland soil communities in response to soil warming. Soil Biol Biochem 41:315–322. https://doi.org/10.1016/j.soilbio.2008.11.003
Brookes PC, Kragt JF, Powlson DS, Jenkinson DS (1985) Chloroform fumigation and the release of soil nitrogen: the effects of fumigation time and temperature. Soil Biol Biochem 17:831–835. https://doi.org/10.1016/0038-0717(85)90143-9
Buckley DH, Schmidt TM (2001) The structure of microbial communities in soil and the lasting impact of cultivation. Microb Ecol 42:11–21
Buerger S, Spoering A, Gavrish E et al (2012) Microbial scout hypothesis and microbial discovery. Appl Environ Microbiol 78:3229–3233. https://doi.org/10.1128/AEM.07308-11
Bueschl C, Kluger B, Lemmens M et al (2014) A novel stable isotope labelling assisted workflow for improved untargeted LC-HRMS based metabolomics research. Metabolomics 10:754–769. https://doi.org/10.1007/s11306-013-0611-0
Burke MJW, Grime JP (1996) An experimental study of plant community invasibility. Ecology 77:776–790. https://doi.org/10.2307/2265501
Buscot F, Varma A (eds) (2005) Microorganisms in soils: roles in genesis and functions, 1. Aufl. Springer, New York
Busse MD, Beattie SE, Powers RF et al (2006) Microbial community responses in forest mineral soil to compaction, organic matter removal, and vegetation control. Can J For Res 36:577–588. https://doi.org/10.1139/X05-294
Butt KR (2008) Earthworms in soil restoration: lessons learned from United Kingdom case studies of land reclamation. Restor Ecol 16:637–641. https://doi.org/10.1111/j.1526-100X.2008.00483.x
Cabreiro F, Gems D (2013) Worms need microbes too: microbiota, health and aging in Caenorhabditis elegans: the C. elegans-microbe holobiont. EMBO Mol Med 5:1300–1310. https://doi.org/10.1002/emmm.201100972
Caldararo N (2002) Human ecological intervention and the role of forest fires in human ecology. Sci Total Environ 292:141–165. https://doi.org/10.1016/S0048-9697(01)01067-1
Callaham MA, Rhoades CC, Heneghan L (2008) A striking profile: soil ecological knowledge in restoration management and science. Restor Ecol 16:604–607. https://doi.org/10.1111/j.1526-100X.2008.00490.x
Cao X, Ma L, Liang Y et al (2011) Simultaneous immobilization of lead and atrazine in contaminated soils using dairy-manure biochar. Environ Sci Technol 45:4884–4889. https://doi.org/10.1021/es103752u
Carbonetto B, Rascovan N, Álvarez R et al (2014) Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in argentine pampas. PLoS One 9:e99949. https://doi.org/10.1371/journal.pone.0099949
Cardinale M (2014) Scanning a microhabitat: plant-microbe interactions revealed by confocal laser microscopy. Front Microbiol 5:94. https://doi.org/10.3389/fmicb.2014.00094
Cardoso IM, Kuyper TW (2006) Mycorrhizas and tropical soil fertility. Agric Ecosyst Environ 116:72–84. https://doi.org/10.1016/j.agee.2006.03.011
Carter MR (2002) Soil quality for sustainable land management. Agron J 94:38–47
Castro HF, Classen AT, Austin EE et al (2010) Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol 76:999–1007. https://doi.org/10.1128/AEM.02874-09
Cerri CC, Feller C, Chauvel A (1991) Evolução das principais propriedades de um latossolo vermelho escuro após desmatamento e cultivo por doze e cinquenta anos com cana-de-açúcar. Cah ORSTOM Ser Pédol 26:37–50
Chaffron S, Rehrauer H, Pernthaler J, von Mering C (2010) A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res 20:947–959. https://doi.org/10.1101/gr.104521.109
Chang C-H, Szlavecz K, Buyer JS (2016) Species-specific effects of earthworms on microbial communities and the fate of litter-derived carbon. Soil Biol Biochem 100:129–139. https://doi.org/10.1016/j.soilbio.2016.06.004
Chaparro JM, Badri DV, Vivanco JM (2014) Rhizosphere microbiome assemblage is affected by plant development. ISME J 8:790–803. https://doi.org/10.1038/ismej.2013.196
Chapin FS, Walker BH, Hobbs RJ et al (1997) Biotic control over the functioning of ecosystems. Science 277:500–504
Chapin FSI, Matson PA, Mooney HA (2002) Principles of terrestrial ecosystem ecology. Springer, New York
Chaudhry V, Rehman A, Mishra A et al (2012) Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microb Ecol 64:450–460
Chauhan PS, Shagol CC, Yim W-J et al (2011) Use of terminal restriction length polymorphism (T-RFLP) analysis to evaluate uncultivable microbial community structure of soil. Korean J Soil Sci Fertil 44:127–145. https://doi.org/10.7745/KJSSF.2011.44.1.127
Chen T-B, Zheng Y-M, Lei M et al (2005) Assessment of heavy metal pollution in surface soils of urban parks in Beijing, China. Chemosphere 60:542–551. https://doi.org/10.1016/j.chemosphere.2004.12.072
Chen Y, Day SD, Wick AF et al (2013) Changes in soil carbon pools and microbial biomass from urban land development and subsequent post-development soil rehabilitation. Soil Biol Biochem 66:38–44. https://doi.org/10.1016/j.soilbio.2013.06.022
Chhabra S, Brazil D, Morrissey J et al (2013) Characterization of mineral phosphate solubilization traits from a barley rhizosphere soil functional metagenome. Microbiologyopen 2:717–724. https://doi.org/10.1002/mbo3.110
Ciais P, Sabine C (2013) Carbon and other biogeochemical cycles. In: Stocker TF, Qin D, Plattner G-K et al (eds) IPCC, 2013: climate change 2013: the physical science basis. Contribution of working group I to the fifth assessment report of the intergovernmental panel on climate change. Cambridge University Press, Cambridge
Cleland EE, Larios L, Suding KN (2013) Strengthening invasion filters to reassemble native plant communities: soil resources and phenological overlap. Restor Ecol 21:390–398. https://doi.org/10.1111/j.1526-100X.2012.00896.x
Cole JR, Myrold DD, Nakatsu CH, et al (2010) Development of soil metadata standards for international DNA sequence databases. In: 19th World Congress of Soil Science, Soil Solutions for a Changing World, Brisbane
Comerford NB, Franzluebbers AJ, Stromberger ME et al (2013) Assessment and evaluation of soil ecosystem services. Soil Horiz 54:3
Comis D (2002) Glomalin: hiding place for a third of the world’s stored soil carbon. Agric Res 50:4–7
Committee on Metagenomics (2007) The new science of metagenomics: revealing the secrets of our microbial planet. National Academies Press, Washington, DC
Contin M, Jenkinson DS, Brookes PC (2002) Measurement of ATP in soil: correcting for incomplete recovery. Soil Biol Biochem 34:1381–1383. https://doi.org/10.1016/S0038-0717(02)00063-9
Cook FJ, Orchard VA (2008) Relationships between soil respiration and soil moisture. Soil Biol Biochem 40:1013–1018. https://doi.org/10.1016/j.soilbio.2007.12.012
Cookson WR, Murphy DV, Roper MM (2008) Characterizing the relationships between soil organic matter components and microbial function and composition along a tillage disturbance gradient. Soil Biol Biochem 40:763–777. https://doi.org/10.1016/j.soilbio.2007.10.011
Coolon JD, Jones KL, Todd TC et al (2013) Long-term nitrogen amendment alters the diversity and assemblage of soil bacterial communities in tallgrass prairie. PLoS One 8:e67884. https://doi.org/10.1371/journal.pone.0067884
Costanza R, d’Arge R, de Groot R et al (1997) The value of the world’s ecosystem services and natural capital. Nature 387:253–260. https://doi.org/10.1038/387253a0
Costanza R, de Groot R, Sutton P et al (2014) Changes in the global value of ecosystem services. Glob Environ Change Hum Policy Dimens 26:152–158
Cruz-Ruíz A, Cruz-Ruíz E, Vaca R et al (2016) Effects of pumice mining on soil quality. Solid Earth 7:1–9. https://doi.org/10.5194/se-7-1-2016
da C Jesus E, Marsh TL, Tiedje JM, de S Moreira FM (2009) Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME J 3:1004–1011. https://doi.org/10.1038/ismej.2009.47
Davidson EA, Janssens IA (2006) Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature 440:165–173. https://doi.org/10.1038/nature04514
Davis MA, Grime JP, Thompson K (2000) Fluctuating resources in plant communities: a general theory of invasibility. J Ecol 88:528–534. https://doi.org/10.1046/j.1365-2745.2000.00473.x
de Bruijn FJ (2011) Handbook of molecular microbial ecology II: metagenomics in different habitats. Wiley-Blackwell, Hoboken
de Groot R, Brander L, van der Ploeg S et al (2012) Global estimates of the value of ecosystems and their services in monetary units. Ecosyst Serv 1:50–61. https://doi.org/10.1016/j.ecoser.2012.07.005
de Souza RG, da Silva DKA, de Mello CMA et al (2013) Arbuscular mycorrhizal fungi in revegetated mined dunes. Land Degrad Dev 24:147–155. https://doi.org/10.1002/ldr.1113
de Vries FT, Thébault E, Liiri M et al (2013) Soil food web properties explain ecosystem services across European land use systems. Proc Natl Acad Sci USA 110:14296–14301. https://doi.org/10.1073/pnas.1305198110
Dechesne A, Badawi N, Aamand J, Smets BF (2014) Fine scale spatial variability of microbial pesticide degradation in soil: scales, controlling factors, and implications. Front Microbiol 5:667. https://doi.org/10.3389/fmicb.2014.00667
del V Gomez E, Garland JL, Roberts MS (2004) Microbial structural diversity estimated by dilution–extinction of phenotypic traits and T-RFLP analysis along a land-use intensification gradient. FEMS Microbiol Ecol 49:253–259. https://doi.org/10.1016/j.femsec.2004.03.012
Delgado-Baquerizo M, Maestre FT, Reich PB et al (2016) Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun 7:10541. https://doi.org/10.1038/ncomms10541
Delmont TO, Eren AM, Maccario L et al (2015) Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. Front Microbiol 6:358. https://doi.org/10.3389/fmicb.2015.00358
DeLuca TH, Zouhar KL (2000) Effects of selection harvest and prescribed fire on the soil nitrogen status of ponderosa pine forests. For Ecol Manag 138:263–271. https://doi.org/10.1016/S0378-1127(00)00401-1
Denef K, Six J, Merckx R, Paustian K (2004) Carbon sequestration in microaggregates of no-tillage soils with different clay mineralogy. Soil Sci Soc Am J 68:1935. https://doi.org/10.2136/sssaj2004.1935
Deng Y, Jiang Y-H, Yang Y et al (2012) Molecular ecological network analyses. BMC Bioinf 13:113. https://doi.org/10.1186/1471-2105-13-113
Dequiedt S, Saby NPA, Lelievre M et al (2011) Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management. Glob Ecol Biogeogr 20:641–652. https://doi.org/10.1111/j.1466-8238.2010.00628.x
Devine S, Markewitz D, Hendrix P, Coleman D (2014) Soil aggregates and associated organic matter under conventional tillage, no-tillage, and forest succession after three decades. PLoS One 9:e84988. https://doi.org/10.1371/journal.pone.0084988
Dexter AR (2004) Soil physical quality: part I. Theory, effects of soil texture, density, and organic matter, and effects on root growth. Geoderma 120:201–214
Diacono M, Montemurro F (2010) Long-term effects of organic amendments on soil fertility. A review. Agron Sustain Dev 30:401–422. https://doi.org/10.1051/agro/2009040
Díaz S, Demissew S, Carabias J et al (2015) The IPBES conceptual framework—connecting nature and people. Curr Opin Environ Sustain 14:1–16. https://doi.org/10.1016/j.cosust.2014.11.002
Dilly O (2005) Microbial energetics in soils. In: Buscot F, Varma A (eds) Microorganisms in soils: roles in genesis and functions, 1. Aufl. Springer, New York
Dilly O, Nii-Annang S, Schrautzer J et al (2010) Ecosystem manipulation and restoration on the basis of long-term conceptions. In: Müller F, Baessler C, Schubert H, Klotz S (eds) Long-term ecological research. Springer, Netherlands, pp 411–428
Ding G-C, Piceno YM, Heuer H et al (2013) Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem. PLoS One 8:e59497. https://doi.org/10.1371/journal.pone.0059497
Dominati E, Patterson M, Mackay A (2010) A framework for classifying and quantifying the natural capital and ecosystem services of soils. Ecol Econ 69:1858–1868. https://doi.org/10.1016/j.ecolecon.2010.05.002
Doran JW, Zeiss MR (2000) Soil health and sustainability: managing the biotic component of soil quality. Appl Soil Ecol 15:3–11. https://doi.org/10.1016/S0929-1393(00)00067-6
Dorr de Quadros P, Zhalnina K, Davis-Richardson A et al (2012) The effect of tillage system and crop rotation on soil microbial diversity and composition in a subtropical acrisol. Diversity 4:375–395. https://doi.org/10.3390/d4040375
Drijber RA, Doran JW, Parkhurst AM, Lyon DJ (2000) Changes in soil microbial community structure with tillage under long-term wheat-fallow management. Soil Biol Biochem 32:1419–1430
Dudka S, Adriano DC (1997) Environmental impacts of metal ore mining and processing: a review. J Environ Qual 26:590. https://doi.org/10.2134/jeq1997.00472425002600030003x
Duncan DS, Jewell KA, Suen G, Jackson RD (2016) Detection of short-term cropping system-induced changes to soil bacterial communities differs among four molecular characterization methods. Soil Biol Biochem 96:160–168. https://doi.org/10.1016/j.soilbio.2016.02.002
Dungait JAJ, Kemmitt SJ, Michallon L et al (2011) Variable responses of the soil microbial biomass to trace concentrations of 13C-labelled glucose, using 13C-PLFA analysis. Eur J Soil Sci 62:117–126. https://doi.org/10.1111/j.1365-2389.2010.01321.x
Dungait JAJ, Hopkins DW, Gregory AS, Whitmore AP (2012) Soil organic matter turnover is governed by accessibility not recalcitrance. Glob Change Biol 18:1781–1796. https://doi.org/10.1111/j.1365-2486.2012.02665.x
Dykhuizen D (1998) Santa Rosalia revisited: why are there so many species of bacteria? Antonis Van Leeuwenhoek 73:25–33
Egerton-Warburton LM, Johnson NC, Allen EB (2007) Mycorrhizal community dynamics following nitrogen fertilization: a cross-site test in five grasslands. Ecol Monogr 77:527–544. https://doi.org/10.1890/06-1772.1
Ehrenfeld JG (2000) Defining the limits of restoration: the need for realistic goals. Restor Ecol 8:2–9. https://doi.org/10.1046/j.1526-100x.2000.80002.x
Ehrenfeld JG (2003) Effects of exotic plant invasions on soil nutrient cycling processes. Ecosystems 6:503–523. https://doi.org/10.1007/s10021-002-0151-3
Ehrenfeld JG, Toth LA (1997) Restoration ecology and the ecosystem perspective. Restor Ecol 5:307–317. https://doi.org/10.1046/j.1526-100X.1997.00544.x
Ehrenfeld JG, Ravit B, Elgersma K (2005) Feedback in the plant-soil system. Annu Rev Environ Resour 30:75–115. https://doi.org/10.1146/annurev.energy.30.050504.144212
Eisenhauer N, Beßler H, Engels C et al (2010) Plant diversity effects on soil microorganisms support the singular hypothesis. Ecology 91:485–496
Ekelund F, Rønn R, Christensen S (2001) Distribution with depth of protozoa, bacteria and fungi in soil profiles from three Danish forest sites. Soil Biol Biochem 33:475–481. https://doi.org/10.1016/S0038-0717(00)00188-7
Emam T (2016) Local soil, but not commercial AMF inoculum, increases native and non-native grass growth at a mine restoration site. Restor Ecol 24:35–44. https://doi.org/10.1111/rec.12287
Entry JA, Rygiewicz PT, Watrud LS, Donnelly PK (2002) Influence of adverse soil conditions on the formation and function of Arbuscular mycorrhizas. Adv Environ Res 7:123–138. https://doi.org/10.1016/S1093-0191(01)00109-5
Enwall K, Hallin S (2009) Comparison of T-RFLP and DGGE techniques to assess denitrifier community composition in soil. Lett Appl Microbiol 48:145–148. https://doi.org/10.1111/j.1472-765X.2008.02498.x
Epstein SS (ed) (2009) Uncultivated microorganisms, 1. Aufl. Springer, Dordrecht
Erisman JW, Sutton MA, Galloway J et al (2008) How a century of ammonia synthesis changed the world. Nat Geosci 1:636–639. https://doi.org/10.1038/ngeo325
Esperschütz J, Gattinger A, Mäder P et al (2007) Response of soil microbial biomass and community structures to conventional and organic farming systems under identical crop rotations. FEMS Microbiol Ecol 61:26–37. https://doi.org/10.1111/j.1574-6941.2007.00318.x
Eviner VT (2004) Plant traits that influence ecosystem processes vary independently among species. Ecology 85:2215–2229
Eviner VT, Chapin FS III (2003) Functional matrix: a conceptual framework for predicting multiple plant effects on ecosystem processes. Annu Rev Ecol Evol Syst 34:455–485. https://doi.org/10.1146/annurev.ecolsys.34.011802.132342
Eviner VT, Hawkes CV (2008) Embracing variability in the application of plant–soil interactions to the restoration of communities and ecosystems. Restor Ecol 16:713–729. https://doi.org/10.1111/j.1526-100X.2008.00482.x
Faber J, van Wensem J (2012) Elaborations on the use of the ecosystem services concept for application in ecological risk assessment for soils. Sci Total Environ 415:3–8
Fanin N, Bertrand I (2016) Aboveground litter quality is a better predictor than belowground microbial communities when estimating carbon mineralization along a land-use gradient. Soil Biol Biochem 94:48–60. https://doi.org/10.1016/j.soilbio.2015.11.007
Fanin N, Hättenschwiler S, Fromin N (2014) Litter fingerprint on microbial biomass, activity, and community structure in the underlying soil. Plant Soil 379:79–91. https://doi.org/10.1007/s11104-014-2051-7
FAO (1982) World soil charter. www.fap.org/3/T0389E00.htm#Contents
FAO (2015a) Status of the world’s soil resources. FAO. http://www.fao.org/documents/card/en/c/c6814873-efc3-41db-b7d3-2081a10ede50. Accessed 31 May 2016
FAO (2015b) FAO statistical pocketbook 2015. FAO. http://www.fao.org/documents/card/en/c/383d384a-28e6-47b3-a1a2-2496a9e017b2. Accessed 31 May 2016
FAO (2015c) World soil charter. www.fao.org/3/a-mn442e.pdf
FAO/ITPS (2015) Status of the World’s Soil Resources (SWSR) – Main report. Food and Agriculture Organization of the United Nations and Intergovernmental Technical Panel on Soils, Rome
Fashola MO, Ngole-Jeme VM, Babalola OO (2016) Heavy metal pollution from gold mines: environmental effects and bacterial strategies for resistance. Int J Environ Res Public Health 13:E1047
Feeney DS, Crawford JW, Daniell T et al (2006) Three-dimensional microorganization of the soil: root-microbe system. Microb Ecol 52:151–158
Feld L, Hjelmsø MH, Nielsen MS et al (2015) Pesticide side effects in an agricultural soil ecosystem as measured by amoA expression quantification and bacterial diversity changes. PLoS One 10:e0126080. https://doi.org/10.1371/journal.pone.0126080
Feng Y, Motta AC, Reeves DW et al (2003) Soil microbial communities under conventional-till and no-till continuous cotton systems. Soil Biol Biochem 35:1693–1703. https://doi.org/10.1016/j.soilbio.2003.08.016
Ferluga S, Steindler L, Venturi V (2008) N-acyl homoserine lactone quorum sensing in gram-negative rhizobacteria. In: PDP K (ed) Secondary metabolites in soil ecology. Springer, Berlin, pp 69–90
Fernandes MF, Saxena J, Dick RP (2013) Comparison of whole-cell fatty acid (MIDI) or phospholipid fatty acid (PLFA) extractants as biomarkers to profile soil microbial communities. Microb Ecol 66:145–157. https://doi.org/10.1007/s00248-013-0195-2
Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103:626–631. https://doi.org/10.1073/pnas.0507535103
Fierer N, Lauber CL, Ramirez KS et al (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017. https://doi.org/10.1038/ismej.2011.159
Fierer N, Ladau J, Clemente JC et al (2013) Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342:621–624. https://doi.org/10.1126/science.1243768
Finzi AC, Abramoff RZ, Spiller KS et al (2015) Rhizosphere processes are quantitatively important components of terrestrial carbon and nutrient cycles. Glob Change Biol 21:2082–2094. https://doi.org/10.1111/gcb.12816
Fisk MC, Fahey TJ (2001) Microbial biomass and nitrogen cycling responses to fertilization and litter removal in young northern hardwood forests. Biogeochemistry 53:201–223. https://doi.org/10.1023/A:1010693614196
Floch C, Chevremont A-C, Joanico K et al (2011) Indicators of pesticide contamination: soil enzyme compared to functional diversity of bacterial communities via Biolog® Ecoplates. Eur J Soil Biol 47:256–263
Franklin RB, Mills AL (2009) Importance of spatially structured environmental heterogeneity in controlling microbial community composition at small spatial scales in an agricultural field. Soil Biol Biochem 41:1833–1840. https://doi.org/10.1016/j.soilbio.2009.06.003
Franzluebbers AJ (2002) Soil organic matter stratification ratio as an indicator of soil quality. Soil Tillage Res 66:95–106. https://doi.org/10.1016/S0167-1987(02)00018-1
Franzosa EA, Hsu T, Sirota-Madi A et al (2015) Sequencing and beyond: integrating molecular “omics” for microbial community profiling. Nat Rev Microbiol 13:360–372. https://doi.org/10.1038/nrmicro3451
Frey SD, Drijber R, Smith H, Melillo J (2008) Microbial biomass, functional capacity, and community structure after 12 years of soil warming. Soil Biol Biochem 40:2904–2907. https://doi.org/10.1016/j.soilbio.2008.07.020
Frey SD, Lee J, Melillo JM, Six J (2013) The temperature response of soil microbial efficiency and its feedback to climate. Nat Clim Chang 3:395–398. https://doi.org/10.1038/nclimate1796
Frost SM, Stahl PD, Williams SE (2001) Long-term reestablishment of arbuscular mycorrhizal fungi in a drastically disturbed semiarid surface mine soil. Arid Land Res Manag 15:3–12. https://doi.org/10.1080/15324980119429
Frostegård A, Bååth E (1996) The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol Fertil Soils 22:59–65. https://doi.org/10.1007/BF00384433
Frostegård Å, Courtois S, Ramisse V et al (1999) Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol 65:5409–5420
Frostegård Å, Tunlid A, Bååth E (2011) Use and misuse of PLFA measurements in soils. Soil Biol Biochem 43:1621–1625. https://doi.org/10.1016/j.soilbio.2010.11.021
Frouz J (2014) Soil biota and ecosystem development in post mining sites. CRC Press, Boca Raton
Gale WJ, Cambardella CA, Bailey TB (2000) Surface residue- and root-derived carbon in stable and unstable aggregates. Soil Sci Soc Am J 64:196. https://doi.org/10.2136/sssaj2000.641196x
Gaur A, Adholeya A (2004) Prospects of arbuscular mycorrhizal fungi in phytoremediation of heavy metal contaminated soils. Curr Sci 86:528–534
Ghimire R, Norton JB, Stahl PD, Norton U (2014) Soil microbial substrate properties and microbial community responses under irrigated organic and reduced-tillage crop and forage production systems. PLoS One 9:e103901. https://doi.org/10.1371/journal.pone.0103901
Gilbert JA, Jansson JK, Knight R (2014) The earth microbiome project: successes and aspirations. BMC Biol 12:69. https://doi.org/10.1186/s12915-014-0069-1
Giri B, Giang PH, Kumari R et al (2005) Microbial diversity in soils. In: Varma PDA, Buscot PF (eds) Microorganisms in soils: roles in genesis and functions. Springer, Berlin, pp 19–55
Glaser B, Lehmann J, Zech W (2002) Ameliorating physical and chemical properties of highly weathered soils in the tropics with charcoal—a review. Biol Fertil Soils 35:219–230. https://doi.org/10.1007/s00374-002-0466-4
Godbold DL, Hoosbeek MR, Lukac M et al (2006) Mycorrhizal hyphal turnover as a dominant process for carbon input into soil organic matter. Plant Soil 281:15–24. https://doi.org/10.1007/s11104-005-3701-6
Gómez-Brandón M, Lores M, Domínguez J (2012) Species-specific effects of epigeic earthworms on microbial community structure during first stages of decomposition of organic matter. PLoS One 7:1–8. https://doi.org/10.1371/journal.pone.0031895
Gomez-Eyles JL, Yupanqui C, Beckingham B et al (2013) Evaluation of biochars and activated carbons for in situ remediation of sediments impacted with organics, mercury, and methylmercury. Environ Sci Technol 47:13721–13729. https://doi.org/10.1021/es403712q
Goreau TJ (2015) Geotherapy: innovative methods of soil fertility restoration, carbon sequestration and reversing CO2 increase. CRC Press, Boca Raton
Gougoulias C, Clark JM, Shaw LJ (2014) The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems. J Sci Food Agric 94:2362–2371. https://doi.org/10.1002/jsfa.6577
Gould AB, Liberta AE (1981) Effects of topsoil storage during surface mining on the viability of vesicular-arbuscular mycorrhiza. Mycologia 73:914–922. https://doi.org/10.2307/3759802
Graham EB, Wieder WR, Leff JW et al (2014) Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes. Soil Biol Biochem 68:279–282. https://doi.org/10.1016/j.soilbio.2013.08.023
Griffith JA, Price KP, Martinko EA (2001) A multivariate analysis of biophysical parameters of tallgrass prairie among land management practices and years. Environ Monit Assess 68:249–271
Groffman PM, Bohlen PJ (1999) Soil and sediment biodiversity: cross-system comparisons and large-scale effects. Bioscience 49:139–148
Guckert JB, Antworth CP, Nichols PD, White DC (1985) Phospholipid, ester-linked fatty acid profiles as reproducible assays for changes in prokaryotic community structure of estuarine sediments. FEMS Microbiol Ecol 1:147–158. https://doi.org/10.1111/j.1574-6968.1985.tb01143.x
Guggenberger G (2005) Humification and mineralization in soils. In: Buscot F, Varma A (eds) Microorganisms in soils: roles in genesis and functions, 1. Aufl. Springer, New York
Guo LB, Gifford RM (2002) Soil carbon stocks and land use change: a meta analysis. Glob Change Biol 8:345–360. https://doi.org/10.1046/j.1354-1013.2002.00486.x
Guo L-J, Lin S, Liu T-Q et al (2016) Effects of conservation tillage on topsoil microbial metabolic characteristics and organic carbon within aggregates under a rice (Oryza sativa L.) –wheat (Triticum aestivum L.) cropping system in central China. PLoS One 11:e0146145. https://doi.org/10.1371/journal.pone.0146145
Gupta VVSR, Germida JJ (2015) Soil aggregation: influence on microbial biomass and implications for biological processes. Soil Biol Biochem 80:A3–A9. https://doi.org/10.1016/j.soilbio.2014.09.002
Haines-Young R, Potschin M (2013) Common international classification of ecosystem services (CICES): consultation on version 4, Aug–Dec 2012
Haldar S, Sengupta S (2015) Plant-microbe cross-talk in the rhizosphere: insight and biotechnological potential. Open Microbiol J 9:1–7. https://doi.org/10.2174/1874285801509010001
Hamman ST, Burke IC, Knapp EE (2008) Soil nutrients and microbial activity after early and late season prescribed burns in a Sierra Nevada mixed conifer forest. For Ecol Manag 256:367–374. https://doi.org/10.1016/j.foreco.2008.04.030
Hammer EC, Pallon J, Wallander H, Olsson PA (2011) Tit for tat? A mycorrhizal fungus accumulates phosphorus under low plant carbon availability. FEMS Microbiol Ecol 76:236–244. https://doi.org/10.1111/j.1574-6941.2011.01043.x
Harris JA (2003) Measurements of the soil microbial community for estimating the success of restoration. Eur J Soil Sci 54:801. https://doi.org/10.1046/j.1351-0754.2003.0559.x
Harris JA, Birch P, Short KC (1989) Changes in the microbial community and physico-chemical characteristics of topsoils stockpiled during opencast mining. Soil Use Manag 5:161–168. https://doi.org/10.1111/j.1475-2743.1989.tb00778.x
Harris JA, Hobbs RJ, Higgs E, Aronson J (2006) Ecological restoration and global climate change. Restor Ecol 14:170–176. https://doi.org/10.1111/j.1526-100X.2006.00136.x
Hartmann M, Widmer F (2008) Reliability for detecting composition and changes of microbial communities by T-RFLP genetic profiling. FEMS Microbiol Ecol 63:249–260. https://doi.org/10.1111/j.1574-6941.2007.00427.x
He Z, Gentry TJ, Schadt CW et al (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1:67–77. https://doi.org/10.1038/ismej.2007.2
He Z, Deng Y, Van Nostrand JD et al (2010) GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J 4:1167–1179. https://doi.org/10.1038/ismej.2010.46
Heimann M, Reichstein M (2008) Terrestrial ecosystem carbon dynamics and climate feedbacks. Nature 451:289–292. https://doi.org/10.1038/nature06591
Heinze S, Raupp J, Joergensen RG (2010) Effects of fertilizer and spatial heterogeneity in soil pH on microbial biomass indices in a long-term field trial of organic agriculture. Plant Soil 328:203–215. https://doi.org/10.1007/s11104-009-0102-2
Helfrich M, Flessa H, Ludwig B (2010) Modeling carbon dynamics in subsoils using simple models. J Plant Nutr Soil Sci 173:671–677. https://doi.org/10.1002/jpln.200900050
Helgason BL, Walley FL, Germida JJ (2010) Long-term no-till management affects microbial biomass but not community composition in Canadian prairie agroecosytems. Soil Biol Biochem 42:2192–2202. https://doi.org/10.1016/j.soilbio.2010.08.015
Heneghan L, Miller SP, Baer S et al (2008) Integrating soil ecological knowledge into restoration management. Restor Ecol 16:608–617. https://doi.org/10.1111/j.1526-100X.2008.00477.x
Herrera MA, Salamanca CP, Barea JM (1993) Inoculation of woody legumes with selected arbuscular mycorrhizal fungi and rhizobia to recover desertified mediterranean ecosystems. Appl Environ Microbiol 59:129–133
Heuck C, Weig A, Spohn M (2015) Soil microbial biomass C:N:P stoichiometry and microbial use of organic phosphorus. Soil Biol Biochem 85:119–129. https://doi.org/10.1016/j.soilbio.2015.02.029
Holden SR, Treseder KK (2013) A meta-analysis of soil microbial biomass responses to forest disturbances. Terr Microbiol 4:163. https://doi.org/10.3389/fmicb.2013.00163
Holmes WE, Zak DR (1999) Soil microbial control of nitrogen loss following clear-cut harvest in northern hardwood ecosystems. Ecol Appl 9:202–215. https://doi.org/10.1890/1051-0761(1999)009[0202:SMCONL]2.0.CO;2
Horwath WR, Paul EA (1994) Microbial biomass. In: Weaver RW, Angle JS, Bottomley PS (eds) Methods soil anal part 2. SSSA, Madison, pp 753–773. https://doi.org/10.2136/sssabookser5.2.c36
Howe AC, Jansson JK, Malfatti SA et al (2014) Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci USA 111:4904–4909. https://doi.org/10.1073/pnas.1402564111
Huang H, Zhang S, Wu N et al (2009) Influence of Glomus etunicatum/Zea mays mycorrhiza on atrazine degradation, soil phosphatase and dehydrogenase activities, and soil microbial community structure. Soil Biol Biochem 41:726–734. https://doi.org/10.1016/j.soilbio.2009.01.009
Huang X-F, Chaparro JM, Reardon KF et al (2014) Rhizosphere interactions: root exudates, microbes, and microbial communities1. Botany 92:267–275. https://doi.org/10.1139/cjb-2013-0225
Hunt HW, Coleman DC, Ingham ER et al (1987) The detrital food web in a shortgrass prairie. Biol Fertil Soils 3-3. https://doi.org/10.1007/BF00260580
Huyler A, Chappelka AH, Prior SA, Somers GL (2014) Influence of aboveground tree biomass, home age, and yard maintenance on soil carbon levels in residential yards. Urban Ecosyst 17:787–805. https://doi.org/10.1007/s11252-014-0350-7
Ipsilantis I, Samourelis C, Karpouzas DG (2012) The impact of biological pesticides on arbuscular mycorrhizal fungi. Soil Biol Biochem 45:147–155. https://doi.org/10.1016/j.soilbio.2011.08.007
Iqbal Z, Hussain A, Asi MR, Chaudhry JA (2001a) Impact of pesticide applications in cotton agroecosystem and soil bioactivity studies II: nitrification dynamics. Pak J Biol Sci 4:588–592. https://doi.org/10.3923/pjbs.2001.588.592
Iqbal Z, Hussain A, Latif A et al (2001b) Impact of pesticide applications in cotton agroecosystem and soil bioactivity studies I: microbial populations. J Biol Sci 1:640–644. https://doi.org/10.3923/jbs.2001.640.644
Jan B, Sharif M, Khan F (2014) Effect of different fungicides application on wheat yield and soil native status of arbuscular mycorrhizal fungi. Pak J Nutr 13:735–741. https://doi.org/10.3923/pjn.2014.735.741
Jangid K, Williams MA, Franzluebbers AJ et al (2008) Relative impacts of land-use, management intensity and fertilization upon soil microbial community structure in agricultural systems. Soil Biol Biochem 40:2843–2853. https://doi.org/10.1016/j.soilbio.2008.07.030
Jasper DA (2007) Beneficial soil microorganisms of the Jarrah forest and their recovery in bauxite mine restoration in Southwestern Australia. Restor Ecol 15:S74–S84. https://doi.org/10.1111/j.1526-100X.2007.00295.x
Jeffries P, Gianinazzi S, Perotto S et al (2003) The contribution of arbuscular mycorrhizal fungi in sustainable maintenance of plant health and soil fertility. Biol Fertil Soils 37:1–16. https://doi.org/10.1007/s00374-002-0546-5
Jenkinson DS, Brookes PC, Powlson DS (2004) Measuring soil microbial biomass. Soil Biol Biochem 36:5–7. https://doi.org/10.1016/j.soilbio.2003.10.002
Jiang Y, Xiong X, Danska J, Parkinson J (2016) Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. Microbiome 4:2. https://doi.org/10.1186/s40168-015-0146-x
Jim CY (1998) Urban soil characteristics and limitations for landscape planting in Hong Kong. Landsc Urban Plan 40:235–249. https://doi.org/10.1016/S0169-2046(97)00117-5
Joergensen RG, Wu J, Brookes PC (2011) Measuring soil microbial biomass using an automated procedure. Soil Biol Biochem 43:873–876. https://doi.org/10.1016/j.soilbio.2010.09.024
Johnson DW, Curtis PS (2001) Effects of forest management on soil C and N storage: meta analysis. For Ecol Manag 140:227–238. https://doi.org/10.1016/S0378-1127(00)00282-6
Johnson DB, Williamson JC (1994) Conservation of mineral nitrogen in restored soils at opencast coal mine sites: I. Results from field studies of nitrogen transformations following restoration. Eur J Soil Sci 45:311–317. https://doi.org/10.1111/j.1365-2389.1994.tb00514.x
Johnson D, Krsek M, Wellington EMH et al (2005) Soil invertebrates disrupt carbon flow through fungal networks. Science 309:1047–1047
Johnson GA, Davis JG, Qian YL, Doesken KC (2006) Topdressing turf with composted manure improves soil quality and protects water quality. Soil Sci Soc Am J 70:2114–2121. https://doi.org/10.2136/sssaj2005.0287
Johnson DW, Fenn ME, Miller WW, Hunsaker CF (2009) Fire effects on carbon and nitrogen cycling in forests of the Sierra Nevada, chapter 18. Dev Environ Sci 8:405–423. https://doi.org/10.1016/S1474-8177(08)00018-1
Jones SE, Lennon JT (2010) Dormancy contributes to the maintenance of microbial diversity. Proc Natl Acad Sci USA 107:5881–5886. https://doi.org/10.1073/pnas.0912765107
Jørgensen SE, Xu F-L, Costanza R (eds) (2010) Handbook of ecological indicators for assessment of ecosystem health, 2nd edn. CRC Press, Boca Raton
Kaiser EA, Mueller T, Joergensen RG et al (1992) Evaluation of methods to estimate the soil microbial biomass and the relationship with soil texture and organic matter. Soil Biol Biochem 24:675–683. https://doi.org/10.1016/0038-0717(92)90046-Z
Kandeler E, Tscherko D, Spiegel H (1999) Long-term monitoring of microbial biomass, N mineralisation and enzyme activities of a Chernozem under different tillage management. Biol Fertil Soils 28:343–351
Kandeler E, Stemmer M, Gerzabek MH (2005) Role of microorganisms in carbon cycling in soils. In: Buscot F, Varma A (eds) Microorganisms in soils: roles in genesis and functions, 1. Aufl. Springer, New York
Karlen DL, Mausbach MJ, Doran JW et al (1997) Soil quality: a concept, definition, and framework for evaluation (a guest editorial). Soil Sci Soc Am J 61:4. https://doi.org/10.2136/sssaj1997.03615995006100010001x
Karlen DL, Andrews SS, Weinhold BJ, Doran JW (2003) Soil quality: humankind’s foundation for survival a research editorial by conservation professionals. J Soil Water Conserv 58:171–179
Karpouzas DG, Kandeler E, Bru D et al (2014) A tiered assessment approach based on standardized methods to estimate the impact of nicosulfuron on the abundance and function of the soil microbial community. Soil Biol Biochem 75:282–291. https://doi.org/10.1016/j.soilbio.2014.04.022
Kaschuk G, Alberton O, Hungria M (2010) Three decades of soil microbial biomass studies in Brazilian ecosystems: lessons learned about soil quality and indications for improving sustainability. Soil Biol Biochem 42:1–13. https://doi.org/10.1016/j.soilbio.2009.08.020
Kaye JP, McCulley RL, Burke IC (2005) Carbon fluxes, nitrogen cycling, and soil microbial communities in adjacent urban, native and agricultural ecosystems. Glob Change Biol 11:575–587. https://doi.org/10.1111/j.1365-2486.2005.00921.x
Kaye JP, Groffman PM, Grimm NB et al (2006) A distinct urban biogeochemistry? Trends Ecol Evol 21:192–199. https://doi.org/10.1016/j.tree.2005.12.006
Kelly J, Thornton I, Simpson PR (1996) Urban geochemistry: a study of the influence of anthropogenic activity on the heavy metal content of soils in traditionally industrial and non-industrial areas of Britain. Appl Geochem 11:363–370. https://doi.org/10.1016/0883-2927(95)00084-4
Kemmers RH, Bloem J, Faber JH (2013) Nitrogen retention by soil biota; A key role in the rehabilitation of natural grasslands? Restor Ecol 21:431–438. https://doi.org/10.1111/j.1526-100X.2012.00914.x
Kemmitt SJ, Lanyon CV, Waite IS 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. https://doi.org/10.1016/j.soilbio.2007.06.021
Kennedy N, Brodie E, Connolly J, Clipson N (2006) Seasonal influences on fungal community structure in unimproved and improved upland grassland soils. Can J Microbiol 52:689–694. https://doi.org/10.1139/W06-015
Keskin T, Makineci E (2009) Some soil properties on coal mine spoils reclaimed with black locust (Robinia pceudoacacia L.) and umbrella pine (Pinus pinea L.) in Agacli-Istanbul. Environ Monit Assess 159:407. https://doi.org/10.1007/s10661-008-0638-2
Khaitov B, Patiño-Ruiz JD, Pina T, Schausberger P (2015) Interrelated effects of mycorrhiza and free-living nitrogen fixers cascade up to aboveground herbivores. Ecol Evol 5:3756–3768. https://doi.org/10.1002/ece3.1654
Khan MS, Zaidi A, Musarrat J (2009) Microbial strategies for crop improvement, 1. Aufl. Springer, Berlin
Khanna PK, Raison RJ (2013) In situ core methods for estimating soil mineral-N fluxes: re-evaluation based on 25 years of application and experience. Soil Biol Biochem 64:203–210. https://doi.org/10.1016/j.soilbio.2012.09.004
Khodakova AS, Smith RJ, Burgoyne L et al (2014) Random whole metagenomic sequencing for forensic discrimination of soils. PLoS One 9:e104996. https://doi.org/10.1371/journal.pone.0104996
Kibblewhite MG, Ritz K, Swift MJ (2008) Soil health in agricultural systems. Philos Trans R Soc Lond Ser B Biol Sci 363:685–701. https://doi.org/10.1098/rstb.2007.2178
Kimura N (2014) Metagenomic approaches to understanding phylogenetic diversity in quorum sensing. Virulence 5:433–442. https://doi.org/10.4161/viru.27850
Kishchuk BE, Thiffault E, Lorente M et al (2015) Decadal soil and stand response to fire, harvest, and salvage-logging disturbances in the western boreal mixedwood forest of Alberta, Canada1. Can J For Res 45:141–152. https://doi.org/10.1139/cjfr-2014-0148
Knelman JE, Graham EB, Trahan NA et al (2015) Fire severity shapes plant colonization effects on bacterial community structure, microbial biomass, and soil enzyme activity in secondary succession of a burned forest. Soil Biol Biochem 90:161–168. https://doi.org/10.1016/j.soilbio.2015.08.004
Knief C (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci 5:216. https://doi.org/10.3389/fpls.2014.00216
Koerner B, Klopatek J (2002) Anthropogenic and natural CO2 emission sources in an arid urban environment. Environ Pollut 116:S45–S51. https://doi.org/10.1016/S0269-7491(01)00246-9
Koerner BA, Klopatek JM (2010) Carbon fluxes and nitrogen availability along an urban-rural gradient in a desert landscape. Urban Ecosyst 13:1–21. https://doi.org/10.1007/s11252-009-0105-z
Kong AYY, Six J (2010) Tracing root vs. residue carbon into soils from conventional and alternative cropping systems. Soil Sci Soc Am J 74:1201. https://doi.org/10.2136/sssaj2009.0346
Kong AYY, Scow KM, Córdova-Kreylos AL et al (2011) Microbial community composition and carbon cycling within soil microenvironments of conventional, low-input, and organic cropping systems. Soil Biol Biochem 43:20–30. https://doi.org/10.1016/j.soilbio.2010.09.005
Kramer C, Gleixner G (2006) Variable use of plant- and soil-derived carbon by microorganisms in agricultural soils. Soil Biol Biochem 38:3267–3278. https://doi.org/10.1016/j.soilbio.2006.04.006
Krueger-Mangold JM, Sheley RL, Svejcar TJ (2006) Toward ecologically-based invasive plant management on rangeland. Weed Sci 54:597–605. https://doi.org/10.1614/WS-05-049R3.1
Kruse J, Abraham M, Amelung W et al (2015) Innovative methods in soil phosphorus research: a review. J Plant Nutr Soil Sci 178:43–88. https://doi.org/10.1002/jpln.201400327
Kulmatiski A (2011) Changing soils to manage plant communities: activated carbon as a restoration tool in ex-arable fields. Restor Ecol 19:102–110. https://doi.org/10.1111/j.1526-100X.2009.00632.x
Kulmatiski A, Beard KH (2006) Activated carbon as a restoration tool: potential for control of invasive plants in abandoned agricultural fields. Restor Ecol 14:251–257. https://doi.org/10.1111/j.1526-100X.2006.00127.x
Kumar P (ed) (2011) The economics of ecosystems and biodiversity: ecological and economic foundations. Routledge, London
Kumar A, Nayak A, Shukla A et al (2012) Microbial biomass and carbon mineralization in agricultural soils as affected by pesticide addition. Bull Environ Contam Toxicol 88:538–542. https://doi.org/10.1007/s00128-012-0538-6
Kurth F, Zeitler K, Feldhahn L et al (2013) Detection and quantification of a mycorrhization helper bacterium and a mycorrhizal fungus in plant-soil microcosms at different levels of complexity. BMC Microbiol 13:205. https://doi.org/10.1186/1471-2180-13-205
Kuzyakov Y (2002) Review: factors affecting rhizosphere priming effects. J Plant Nutr Soil Sci 165:382
Kuzyakov Y, Blagodatskaya E (2015) Microbial hotspots and hot moments in soil: concept & review. Soil Biol Biochem 83:184–199. https://doi.org/10.1016/j.soilbio.2015.01.025
Laakso J, Setälä H (1999) Sensitivity of primary production to changes in the architecture of belowground food webs. Oikos 87:57–64. https://doi.org/10.2307/3546996
Ladygina N, Hedlund K (2010) Plant species influence microbial diversity and carbon allocation in the rhizosphere. Soil Biol Biochem 42:162–168. https://doi.org/10.1016/j.soilbio.2009.10.009
Laik R, Kumar K, Das DK, Chaturvedi OP (2009) Labile soil organic matter pools in a calciorthent after 18 years of afforestation by different plantations. Appl Soil Ecol 42:71–78. https://doi.org/10.1016/j.apsoil.2009.02.004
Lal R (2004a) Soil carbon sequestration impacts on global climate change and food security. Science 304:1623–1627
Lal R (2004b) Soil carbon sequestration to mitigate climate change. Geoderma 123:1–22. https://doi.org/10.1016/j.geoderma.2004.01.032
Lal R (2014) Soil conservation and ecosystem services. Int Soil Water Conserv Res 2:36–47. https://doi.org/10.1016/S2095-6339(15)30021-6
Lal R, Lorenz K, Hüttl RF et al (2012) Recarbonization of the biosphere: ecosystems and the global carbon cycle. Springer Science & Business Media, Dordrecht
Lamb EG, Kennedy N, Siciliano SD (2011) Effects of plant species richness and evenness on soil microbial community diversity and function. Plant Soil 338:483–495. https://doi.org/10.1007/s11104-010-0560-6
Land M, Hauser L, Jun S-R et al (2015) Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics 15:141–161. https://doi.org/10.1007/s10142-015-0433-4
Lange M, Habekost M, Eisenhauer N et al (2014) Biotic and abiotic properties mediating plant diversity effects on soil microbial communities in an experimental grassland. PLoS One 9:e96182. https://doi.org/10.1371/journal.pone.0096182
Lauber CL, Ramirez KS, Aanderud Z et al (2013) Temporal variability in soil microbial communities across land-use types. ISME J 7:1641–1650. https://doi.org/10.1038/ismej.2013.50
LeCroy C, Masiello CA, Rudgers JA et al (2013) Nitrogen, biochar, and mycorrhizae: alteration of the symbiosis and oxidation of the char surface. Soil Biol Biochem 58:248–254. https://doi.org/10.1016/j.soilbio.2012.11.023
Lee CS, Li X, Shi W et al (2006) Metal contamination in urban, suburban, and country park soils of Hong Kong: a study based on GIS and multivariate statistics. Sci Total Environ 356:45–61. https://doi.org/10.1016/j.scitotenv.2005.03.024
Leff JW, Jones SE, Prober SM et al (2015) Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc Natl Acad Sci USA 112:10967–10972. https://doi.org/10.1073/pnas.1508382112
Lehmann J, Kinyangi J, Solomon D (2007) Organic matter stabilization in soil microaggregates: implications from spatial heterogeneity of organic carbon contents and carbon forms. Biogeochemistry 85:45–57
Lehmann J, Rillig MC, Thies J et al (2011) Biochar effects on soil biota—a review. Soil Biol Biochem 43:1812–1836. https://doi.org/10.1016/j.soilbio.2011.04.022
Lennon JT, Jones SE (2011) Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol 9:119–130. https://doi.org/10.1038/nrmicro2504
Levine JM, Pachepsky E, Kendall BE et al (2006) Plant–soil feedbacks and invasive spread. Ecol Lett 9:1005–1014. https://doi.org/10.1111/j.1461-0248.2006.00949.x
Levine UY, Teal TK, Robertson GP, Schmidt TM (2011) Agriculture’s impact on microbial diversity and associated fluxes of carbon dioxide and methane. ISME J 5:1683–1691. https://doi.org/10.1038/ismej.2011.40
Levy-Booth DJ, Campbell RG, Gulden RH et al (2007) Cycling of extracellular DNA in the soil environment. Soil Biol Biochem 39:2977–2991. https://doi.org/10.1016/j.soilbio.2007.06.020
Lewis DE, White JR, Wafula D et al (2010) Soil functional diversity analysis of a bauxite-mined restoration chronosequence. Microb Ecol 59:710–723
Lewis DE, Chauhan A, White JR et al (2012) Microbial and geochemical assessment of bauxitic un-mined and post-mined chronosequence soils from Mocho Mountains, Jamaica. Microb Ecol 64:738–749
Loeppmann S, Blagodatskaya E, Pausch J, Kuzyakov Y (2016) Substrate quality affects kinetics and catalytic efficiency of exo-enzymes in rhizosphere and detritusphere. Soil Biol Biochem 92:111–118. https://doi.org/10.1016/j.soilbio.2015.09.020
Lorenz K, Lal R (2009) Biogeochemical C and N cycles in urban soils. Environ Int 35:1–8. https://doi.org/10.1016/j.envint.2008.05.006
Lorenz K, Lal R, Shipitalo MJ (2011) Stabilized soil organic carbon pools in subsoils under forest are potential sinks for atmospheric CO2. For Sci 57:19–25
Lovelock CE, Wright SF, Clark DA, Ruess RW (2004) Soil stocks of glomalin produced by arbuscular mycorrhizal fungi across a tropical rain forest landscape. J Ecol 92:278–287. https://doi.org/10.1111/j.0022-0477.2004.00855.x
Lu J, Wilson MJ, Yu J (1997) Effects of trench planting and soil chiselling on soil properties and citrus production in hilly ultisols of China. Soil Tillage Res 43:309–318. https://doi.org/10.1016/S0167-1987(97)00024-X
Luo Y, Durenkamp M, De Nobili M et al (2013) Microbial biomass growth, following incorporation of biochars produced at 350 °C or 700 °C, in a silty-clay loam soil of high and low pH. Soil Biol Biochem 57:513–523. https://doi.org/10.1016/j.soilbio.2012.10.033
Madrid L, Dıaz-Barrientos E, Madrid F (2002) Distribution of heavy metal contents of urban soils in parks of Seville. Chemosphere 49:1301–1308. https://doi.org/10.1016/S0045-6535(02)00530-1
Malik A, Blagodatskaya E, Gleixner G (2013) Soil microbial carbon turnover decreases with increasing molecular size. Soil Biol Biochem 62:115–118. https://doi.org/10.1016/j.soilbio.2013.02.022
Marinari S, Mancinelli R, Campiglia E, Grego S (2006) Chemical and biological indicators of soil quality in organic and conventional farming systems in Central Italy. Ecol Indic 6:701–711
Markowicz A, Woźniak G, Borymski S et al (2015) Links in the functional diversity between soil microorganisms and plant communities during natural succession in coal mine spoil heaps. Ecol Res 30:1005–1014. https://doi.org/10.1007/s11284-015-1301-3
Maron JL, Jefferies RL (2001) Restoring enriched grasslands: effects of mowing on species richness, productivity, and nitrogen retention. Ecol Appl 11:1088–1100. https://doi.org/10.1890/1051-0761(2001)011[1088:REGEOM]2.0.CO;2
Marrs RH (2002) Manipulating the chemical environment of the soil. In: Perrow MR, Davy AJ (eds) Handbook of ecological restoration: volume 1: principles of restoration. Cambridge University Press, Cambridge, pp 155–183
Marschner P (2003) Structure and function of the soil microbial community in a long-term fertilizer experiment. Soil Biol Biochem 35:453–461. https://doi.org/10.1016/S0038-0717(02)00297-3
Marschner P, Crowley D, Rengel Z (2011) Rhizosphere interactions between microorganisms and plants govern iron and phosphorus acquisition along the root axis—model and research methods. Soil Biol Biochem 43:883–894. https://doi.org/10.1016/j.soilbio.2011.01.005
Marshner H (1995) Mineral nutrition of higher plants, 2nd edn. Academic Press, London
Martens R (2001) Estimation of ATP in soil: extraction methods and calculation of extraction efficiency. Soil Biol Biochem 33:973–982. https://doi.org/10.1016/S0038-0717(01)00001-3
Martin-Laurent F, Philippot L, Hallet S et al (2001) DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67:2354–2359. https://doi.org/10.1128/AEM.67.5.2354-2359.2001
Masiello CA, Chen Y, Gao X et al (2013) Biochar and microbial signaling: production conditions determine effects on microbial communication. Environ Sci Technol 47:11496–11503. https://doi.org/10.1021/es401458s
Mathew RP, Feng Y, Githinji L et al (2012) Impact of no-tillage and conventional tillage systems on soil microbial communities. Appl Environ Soil Sci 2012:e548620. https://doi.org/10.1155/2012/548620
McKinley VL, Peacock AD, White DC (2005) Microbial community PLFA and PHB responses to ecosystem restoration in tallgrass prairie soils. Soil Biol Biochem 37:1946–1958. https://doi.org/10.1016/j.soilbio.2005.02.033
McNabb DH (1994) Tillage of compacted haul roads and landings in the boreal forests of Alberta, Canada. For Ecol Manag 66:179–194. https://doi.org/10.1016/0378-1127(94)90156-2
Melero S, Porras JCR, Herencia JF, Madejon E (2006) Chemical and biochemical properties in a silty loam soil under conventional and organic management. Soil Tillage Res 90:162–170
Mendonza HNS, Lima E, Anjos LHC et al (2000) Propriedades químicas e biológicas de solo de tabuleiro cultivado com cana-de-açúcar com e sem queima da palhada. Rev Bras Ciênc Solo 24:201–207
Mergulhão ACES, Burity HA, da Silva FSB et al (2010) Glomalin production and microbial activity in soils impacted by gypsum mining in a Brazilian semiarid area. Am J Agric Biol Sci 5:422–429
Middleton EL, Bever JD (2012) Inoculation with a native soil community advances succession in a grassland restoration. Restor Ecol 20:218–226. https://doi.org/10.1111/j.1526-100X.2010.00752.x
Millenium Ecosystem Assessment (2005) Ecosystems and human well-being: synthesis. Island Press, Washington, DC
Miller RM, Carnes BA, Moorman TB (1985) Factors influencing survival of vesicular-arbuscular mycorrhiza propagules during topsoil storage. J Appl Ecol 22:259–266. https://doi.org/10.2307/2403343
Miltner A, Bombach P, Schmidt-Brücken B, Kästner M (2012) SOM genesis: microbial biomass as a significant source. Biogeochemistry 111:41–55
Montanarella L (2015) The global soil partnership. IOP Conf Ser Earth Environ Sci 25:012001. https://doi.org/10.1088/1755-1315/25/1/012001
Montecchia MS, Tosi M, Soria MA et al (2015) Pyrosequencing reveals changes in soil bacterial communities after conversion of Yungas forests to agriculture. PLoS One 10:e0119426. https://doi.org/10.1371/journal.pone.0119426
Montoya JM, Sole RV (2000) Small world patterns in food webs. ArXivcond-Mat0011195
Morghan KJR, Seastedt TR (1999) Effects of soil nitrogen reduction on nonnative plants in restored grasslands. Restor Ecol 7:51–55. https://doi.org/10.1046/j.1526-100X.1999.07106.x
Morugán-Coronado A, Cerdà A, García-Orenes F (2014) The impact of land use on biological activity of agriculture soils. An State-of-the-Art. In: EGU General Assembly Conference Abstracts. p 2499
Mosier AC, Justice NB, Bowen BP et al (2013) Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics. MBio 4:e00484
Moynahan OS, Zabinski CA, Gannon JE (2002) Microbial community structure and carbon-utilization diversity in a mine tailings revegetation study. Restor Ecol 10:77–87. https://doi.org/10.1046/j.1526-100X.2002.10108.x
Mummey DL, Stahl PD (2003) Spatial and temporal variability of bacterial 16S rDNA-based T-RFLP patterns derived from soil of two Wyoming grassland ecosystems. FEMS Microbiol Ecol 46:113–120. https://doi.org/10.1016/S0168-6496(03)00208-3
Mummey DL, Stahl PD (2004) Analysis of soil whole- and inner-microaggregate bacterial communities. Microb Ecol 48:41–50
Mummey DL, Stahl PD, Buyer JS (2002) Microbial biomarkers as an indicator of ecosystem recovery following surface mine reclamation. Appl Soil Ecol 21:251–259. https://doi.org/10.1016/S0929-1393(02)00090-2
Mummey D, Holben W, Six J, Stahl P (2006) Spatial stratification of soil bacterial populations in aggregates of diverse soils. Microb Ecol 51:404–411
Muñoz-Leoz B, Garbisu C, Antigüedad I, Ruiz-Romera E (2012) Fertilization can modify the non-target effects of pesticides on soil microbial communities. Soil Biol Biochem 48:125–134. https://doi.org/10.1016/j.soilbio.2012.01.021
Murphy CJ, Baggs EM, Morley N et al (2015) Rhizosphere priming can promote mobilisation of N-rich compounds from soil organic matter. Soil Biol Biochem 81:236–243. https://doi.org/10.1016/j.soilbio.2014.11.027
Murugan R, Loges R, Taube F et al (2014) Changes in soil microbial biomass and residual indices as ecological indicators of land use change in temperate permanent grassland. Microb Ecol 67:907–918. https://doi.org/10.1007/s00248-014-0383-8
Nair A, Ngouajio M (2012) Soil microbial biomass, functional microbial diversity, and nematode community structure as affected by cover crops and compost in an organic vegetable production system. Appl Soil Ecol 58:45–55. https://doi.org/10.1016/j.apsoil.2012.03.008
Nannipieri P, Johnson RL, Paul EA (1978) Criteria for measurement of microbial growth and activity in soil. Soil Biol Biochem 10:223–229. https://doi.org/10.1016/0038-0717(78)90100-1
Nardoto GB, da C Bustamante MM (2003) Effects of fire on soil nitrogen dynamics and microbial biomass in savannas of Central Brazil. Pesq Agrop Brasileira 38:955–962. https://doi.org/10.1590/S0100-204X2003000800008
Navarrete AA, Cannavan FS, Taketani RG, Tsai SM (2010) A molecular survey of the diversity of microbial communities in different Amazonian agricultural model systems. Diversity 2:787–809. https://doi.org/10.3390/d2050787
Nave LE, Vance ED, Swanston CW, Curtis PS (2010) Harvest impacts on soil carbon storage in temperate forests. For Ecol Manag 259:857–866
Nawaz MF, Bourrié G, Trolard F (2013) Soil compaction impact and modelling. A review. Agron Sustain Dev 33:291–309. https://doi.org/10.1007/s13593-011-0071-8
Nesme J, Achouak W, Agathos SN et al (2016) Back to the future of soil metagenomics. Front Microbiol 7:73. https://doi.org/10.3389/fmicb.2016.00073
Nguyen DB, Rose MT, Rose TJ et al (2016) Impact of glyphosate on soil microbial biomass and respiration: a meta-analysis. Soil Biol Biochem 92:50–57. https://doi.org/10.1016/j.soilbio.2015.09.014
Nielsen KM, Johnsen PJ, Bensasson D, Daffonchio D (2007) Release and persistence of extracellular DNA in the environment. Environ Biosaf Res 6:37–53. https://doi.org/10.1051/ebr:2007031
Nielsen UN, Ayres E, Wall DH, Bardgett RD (2011) Soil biodiversity and carbon cycling: a review and synthesis of studies examining diversity-function relationships. Eur J Soil Sci 62:105–116. https://doi.org/10.1111/j.1365-2389.2010.01314.x
Noda S, Kitade O, Inoue T et al (2007) Cospeciation in the triplex symbiosis of termite gut protists (Pseudotrichonympha spp.), their hosts, and their bacterial endosymbionts. Mol Ecol 16:1257–1266. https://doi.org/10.1111/j.1365-294X.2006.03219.x
Nunan N, Wu K, Young IM et al (2003) Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil. FEMS Microbiol Ecol 44:203–215. https://doi.org/10.1016/S0168-6496(03)00027-8
Oertel C, Matschullat J, Zurba K et al (2016) Greenhouse gas emissions from soils—a review. Chem Erde—Geochem 76:327–352
Orglazzi A, Bardgett RD, Barrios E (2016) Global soil biodiversity atlas. Publication Office of the European Union, Luxembourg
Pachauri R, Meyer L (eds) (2014) IPCC, 2014: climate change 2014: synthesis report. Contribution of Working Groups I, II and III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. IPCC, Geneva
Palmer MA, Zedler JB, Falk DA (2006) Ecological theory and restoration ecology. In: Foundations of restoration ecology. Island Press, Washington, DC, pp 3–26
Paluch EC, Thomsen MA, Volk TJ (2013) Effects of resident soil fungi and land use history outweigh those of commercial mycorrhizal inocula: testing a restoration strategy in unsterilized soil. Restor Ecol 21:380–389. https://doi.org/10.1111/j.1526-100X.2012.00894.x
Pandey R, Singh B, Nair TVR (2005) Impact of arbuscular-mycorrhizal fungi on phosphorus efficiency of wheat, rye, and triticale. J Plant Nutr 28:1867–1876. https://doi.org/10.1080/01904160500251381
Park S, Ku YK, Seo MJ et al (2006) Principal component analysis and discriminant analysis (PCA–DA) for discriminating profiles of terminal restriction fragment length polymorphism (T-RFLP) in soil bacterial communities. Soil Biol Biochem 38:2344–2349. https://doi.org/10.1016/j.soilbio.2006.02.019
Parolari AJ, Porporato A (2016) Forest soil carbon and nitrogen cycles under biomass harvest: stability, transient response, and feedback. Ecol Model 329:64–76. https://doi.org/10.1016/j.ecolmodel.2016.03.003
Pascual U, Termansen M, Hedlund K et al (2015) On the value of soil biodiversity and ecosystem services. Ecosyst Serv 15:11–18
Pataki DE, Alig RJ, Fung AS et al (2006) Urban ecosystems and the North American carbon cycle. Glob Change Biol 12:2092–2102. https://doi.org/10.1111/j.1365-2486.2006.01242.x
Paul KI, Polglase PJ, O’Connell AM et al (2002) Soil nitrogen availability predictor (SNAP): a simple model for predicting mineralisation of nitrogen in forest soils. Aust J Soil Res 40:1011–1026
Pepper IL, Zerzghi HG, Bengson SA et al (2012) Bacterial populations within copper mine tailings: long-term effects of amendment with Class A biosolids. J Appl Microbiol 113:569–577. https://doi.org/10.1111/j.1365-2672.2012.05374.x
Perez G, Aubert M, Decaëns T et al (2013) Home-field advantage: a matter of interaction between litter biochemistry and decomposer biota. Soil Biol Biochem 67:245–254. https://doi.org/10.1016/j.soilbio.2013.09.004
Perkins LB, Hatfield G (2016) Can commercial soil microbial treatments remediate plant-soil feedbacks to improve restoration seedling performance? Restor Ecol 24:194–201. https://doi.org/10.1111/rec.12302
Pfenning L, Eduardo BDP, Cerri CC (1992) Os métodos da fumigação-incubação e fumigação-extração na estimativa da biomassa microbiana de solos da Amazônia. Rev Bras Ciênc Solo 16:31–37
Philippot L, Germon JC (2005) Contribution of bacteria to initial input and cycling of nitrogen in soils. In: Buscot F, Varma A (eds) Microorganisms in soils: roles in genesis and functions, 1. Aufl. Springer, New York
Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799. https://doi.org/10.1038/nrmicro3109
Piccolo A (2012) Carbon sequestration in agricultural soils: a multidisciplinary approach to innovative methods, 2012th edn. Springer, Berlin
Pietramellara G, Ascher J, Borgogni F et al (2008) Extracellular DNA in soil and sediment: fate and ecological relevance. Biol Fertil Soils 45:219–235. https://doi.org/10.1007/s00374-008-0345-8
Placella SA, Brodie EL, Firestone MK (2012) Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups. Proc Natl Acad Sci USA 109:10931–10936. https://doi.org/10.1073/pnas.1204306109
Plaza C, Courtier-Murias D, Fernández JM et al (2013) Physical, chemical, and biochemical mechanisms of soil organic matter stabilization under conservation tillage systems: a central role for microbes and microbial by-products in C sequestration. Soil Biol Biochem 57:124–134. https://doi.org/10.1016/j.soilbio.2012.07.026
Poncelet DM, Cavender N, Cutright TJ, Senko JM (2014) An assessment of microbial communities associated with surface mining-disturbed overburden. Environ Monit Assess 186:1917–1929. https://doi.org/10.1007/s10661-013-3505-8
Ponge J-F, Pérès G, Guernion M et al (2013) The impact of agricultural practices on soil biota: a regional study. Soil Biol Biochem 67:271–284. https://doi.org/10.1016/j.soilbio.2013.08.026
Potthast K, Hamer U, Makeschin F (2012) Land-use change in a tropical mountain rainforest region of southern Ecuador affects soil microorganisms and nutrient cycling. Biogeochemistry 111:151–167
Pouyat R, Groffman P, Yesilonis I, Hernandez L (2002) Soil carbon pools and fluxes in urban ecosystems. Environ Pollut 116:S107–S118. https://doi.org/10.1016/S0269-7491(01)00263-9
Pouyat RV, Yesilonis ID, Nowak DJ (2006) Carbon storage by urban soils in the United States. J Environ Qual 35:1566–1575. https://doi.org/10.2134/jeq2005.0215
Pouyat RV, Pataki DE, Belt KT et al (2007) Effects of urban land-use change on biogeochemical cycles. In: Canadell JG, Pataki DE, Pitelka LF (eds) Terrestrial ecosystems in a changing world. Springer, Berlin, pp 45–58
Power AG (2010) Ecosystem services and agriculture: tradeoffs and synergies. Philos Trans R Soc Lond Ser B Biol Sci 365:2959–2971. https://doi.org/10.1098/rstb.2010.0143
Pretty JN, Shah P (1997) Making soil and water conservation sustainable: from coercion and control to partnerships and participation. Land Degrad Dev 8:39–58
Prober SM, Thiele KR, Lunt ID, Koen TB (2005) Restoring ecological function in temperate grassy woodlands: manipulating soil nutrients, exotic annuals and native perennial grasses through carbon supplements and spring burns. J Appl Ecol 42:1073–1085. https://doi.org/10.1111/j.1365-2664.2005.01095.x
Prober SM, Leff JW, Bates ST et al (2015) Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide. Ecol Lett 18:85–95. https://doi.org/10.1111/ele.12381
Puget P, Drinkwater LE (2001) Short-term dynamics of root- and Shoot-derived carbon from a leguminous green manure. Soil Sci Soc Am J 65:771. https://doi.org/10.2136/sssaj2001.653771x
Pupin B, da S Freddi O, Nahas E (2009) Microbial alterations of the soil influenced by induced compaction. Rev Bras Ciênc Solo 33:1207–1213. https://doi.org/10.1590/S0100-06832009000500014
Pywell RF, Bullock JM, Roy DB et al (2003) Plant traits as predictors of performance in ecological restoration. J Appl Ecol 40:65–77. https://doi.org/10.1046/j.1365-2664.2003.00762.x
Qian Y, Follett RF (2002) Assessing soil carbon sequestration in turfgrass systems using long-term soil testing data. Agron J 94:930–935. https://doi.org/10.2134/agronj2002.9300
Rastogi G, Osman S, Vaishampayan PA et al (2010) Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library. Microb Ecol 59:94–108
Reeve JR, Schadt CW, Carpenter-Boggs L et al (2010) Effects of soil type and farm management on soil ecological functional genes and microbial activities. ISME J 4:1099–1107. https://doi.org/10.1038/ismej.2010.42
Renshaw CE, Bostick BC, Feng X (2006) Impact of land disturbance on the fate of arsenical pesticides. J Environ Qual 35:61–67. https://doi.org/10.2134/jeq2005.0096
Reuben S, Bhinu VS, Swarup S (2008) Rhizosphere metabolomics: methods and applications. In: PDP K (ed) Secondary metabolites in soil ecology. Springer, Berlin, pp 37–68
Richter BS, Stutz JC (2002) Mycorrhizal inoculation of Big Sacaton: implications for grassland restoration of abandoned agricultural fields. Restor Ecol 10:607–616. https://doi.org/10.1046/j.1526-100X.2002.01041.x
Rinke C, Schwientek P, Sczyrba A et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437. https://doi.org/10.1038/nature12352
Rives CS, Bajwa MI, Liberta AE, Miller RM (1980) Effects of topsoil storage during surface mining on the viability of VA mycorrhiza. Soil Sci 129:253–257
Robinson DA, Hockley N, Cooper DM et al (2013) Natural capital and ecosystem services, developing an appropriate soils framework as a basis for valuation. Soil Biol Biochem 57:1023–1033. https://doi.org/10.1016/j.soilbio.2012.09.008
Robinson DA, Fraser I, Dominati EJ et al (2014) On the value of soil resources in the context of natural capital and ecosystem service delivery. Soil Sci Soc Am J 78:685. https://doi.org/10.2136/sssaj2014.01.0017
Rocca JD, Hall EK, Lennon JT et al (2015) Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed. ISME J 9:1693–1699. https://doi.org/10.1038/ismej.2014.252
Rodrigues JLM, Pellizari VH, Mueller R et al (2013) Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proc Natl Acad Sci USA 110:988–993. https://doi.org/10.1073/pnas.1220608110
Rolli E, Marasco R, Vigani G et al (2015) Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait. Environ Microbiol 17:316–331. https://doi.org/10.1111/1462-2920.12439
Romaní AM, Fischer H, Mille-Lindblom C, Tranvik LJ (2006) Interactions of bacteria and fungi on decomposing litter: differential extracellular enzyme activities. Ecology 87:2559–2569
Rosenzweig N, Bradeen JM, Tu ZJ et al (2013) Rhizosphere bacterial communities associated with long-lived perennial prairie plants vary in diversity, composition, and structure. Can J Microbiol 59:494–502. https://doi.org/10.1139/cjm-2012-0661
Ross DJ (1987) Soil microbial biomass estimated by the fumigation-incubation procedure: seasonal fluctuations and influence of soil moisture content. Soil Biol Biochem 19:397–404. https://doi.org/10.1016/0038-0717(87)90029-0
Rousk J, Brookes PC, Bååth E (2010) Investigating the mechanisms for the opposing pH relationships of fungal and bacterial growth in soil. Soil Biol Biochem 42:926–934. https://doi.org/10.1016/j.soilbio.2010.02.009
Ruiter DP, Neutrel AM, Moore JC (1995) Energetics, patterns of interaction strengths, and stability in real ecosystems. Science 269:1257–1260
Rumpel C, Kögel-Knabner I (2004) Microbial use of lignite compared to recent plant litter as substrates in reclaimed coal mine soils. Soil Biol Biochem 36:67–75. https://doi.org/10.1016/j.soilbio.2003.08.020
Rumpel C, Chabbi A, Marschner B (2012) Carbon storage and sequestration in subsoil horizons: knowledge, gaps and potentials. In: Lal R, Lorenz K, Hüttl RF et al (eds) Recarbonization of the biosphere. Springer, Netherlands, pp 445–464
Sainz MJ, González-Penalta B, Vilariño A (2006) Effects of hexachlorocyclohexane on rhizosphere fungal propagules and root colonization by arbuscular mycorrhizal fungi in Plantago lanceolata. Eur J Soil Sci 57:83–90. https://doi.org/10.1111/j.1365-2389.2005.00775.x
Salomé C, Nunan N, Pouteau V et al (2010) Carbon dynamics in topsoil and in subsoil may be controlled by different regulatory mechanisms. Glob Change Biol 16:416–426. https://doi.org/10.1111/j.1365-2486.2009.01884.x
Sampedro L, Whalen JK (2007) Changes in the fatty acid profiles through the digestive tract of the earthworm Lumbricus terrestris L. Appl Soil Ecol 35:226–236. https://doi.org/10.1016/j.apsoil.2006.04.007
Sanaullah M, Chabbi A, Leifeld J et al (2011) Decomposition and stabilization of root litter in top- and subsoil horizons: what is the difference? Plant Soil 338:127–141. https://doi.org/10.1007/s11104-010-0554-4
Saquing JM, Yu Y-H, Chiu PC (2016) Wood-derived black carbon (biochar) as a microbial electron donor and acceptor. Environ Sci Technol Lett 3:62–66. https://doi.org/10.1021/acs.estlett.5b00354
Saviozzi A, Levi-Minzi R, Cardelli R (2001) A comparison of soil quality in adjacent cultivated, forest and native grassland soils. Plant Soil 233:251–259
Scharfy D, Güsewell S, Gessner MO, Venterink HO (2010) Invasion of Solidago gigantea in contrasting experimental plant communities: effects on soil microbes, nutrients and plant-soil feedbacks. J Ecol 98:1379–1388
Scheuner ET, Makeschin F, Wells ED, Carter PQ (2004) Short-term impacts of harvesting and burning disturbances on physical and chemical characteristics of forest soils in western Newfoundland, Canada. Eur J For Res 123:321–330. https://doi.org/10.1007/s10342-004-0038-2
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. https://doi.org/10.1016/j.soilbio.2006.08.017
Schmidt MWI, Torn MS, Abiven S et al (2011) Persistence of soil organic matter as an ecosystem property. Nature 478:49–56. https://doi.org/10.1038/nature10386
Schmiegelow FKA, Stepnisky DP, Stambaugh CA, Koivula M (2006) Reconciling salvage logging of boreal forests with a natural-disturbance management model. Conserv Biol 20:971–983. https://doi.org/10.1111/j.1523-1739.2006.00496.x
Schnepf A, Roose T, Schweiger P (2008) Impact of growth and uptake patterns of arbuscular mycorrhizal fungi on plant phosphorus uptake—a modelling study. Plant Soil 312:85–99. https://doi.org/10.1007/s11104-008-9749-3
Schübler A, Schwarzott D, Walker C (2001) A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol Res 105:1413–1421. https://doi.org/10.1017/S0953756201005196
Schütte U, Abdo Z, Bent S et al (2008) Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl Microbiol Biotechnol 80:365–380. https://doi.org/10.1007/s00253-008-1565-4
Scullion J, Mohammed ARA (1991) Effects of subsoiling and associated incorporation of fertilizer on soil rehabilitation after opencast mining for coal. J Agric Sci 116:265–273. https://doi.org/10.1017/S0021859600077674
Seabrook L, Mcalpine CA, Bowen ME (2011) Restore, repair or reinvent: options for sustainable landscapes in a changing climate. Landsc Urban Plan 100:407–410. https://doi.org/10.1016/j.landurbplan.2011.02.015
Sengupta A, Dick WA (2015) Bacterial community diversity in soil under two tillage practices as determined by pyrosequencing. Microb Ecol 70:853–859
Seto KC, Güneralp B, Hutyra LR (2012) Global forecasts of urban expansion to 2030 and direct impacts on biodiversity and carbon pools. Proc Natl Acad Sci USA 109:16083–16088. https://doi.org/10.1073/pnas.1211658109
Shackelford N, Hobbs RJ, Burgar JM et al (2013) Primed for change: developing ecological restoration for the 21st century. Restor Ecol 21:297–304. https://doi.org/10.1111/rec.12012
Shade A, Gregory Caporaso J, Handelsman J et al (2013) A meta-analysis of changes in bacterial and archaeal communities with time. ISME J 7:1493–1506. https://doi.org/10.1038/ismej.2013.54
Shange RS, Ankumah RO, Ibekwe AM et al (2012) Distinct soil bacterial communities revealed under a diversely managed agroecosystem. PLoS One 7:e40338. https://doi.org/10.1371/journal.pone.0040338
Sheoran V, Sheoran A, Poonia P (2010) Soil reclamation of abandoned mine land by revegetation: a review. Int J Soil Sediment Water 3:13
Siggins A, Gunnigle E, Abram F (2012) Exploring mixed microbial community functioning: recent advances in metaproteomics. FEMS Microbiol Ecol 80:265–280. https://doi.org/10.1111/j.1574-6941.2011.01284.x
Sindhu SS, Phour M, Choudhary SR, Chaudhary D (2014) Phosphorus cycling: prospects of using rhizosphere microorganisms for improving phosphorus nutrition of plants. In: Parmar N, Singh A (eds) Geomicrobiology and biogeochemistry. Springer, Berlin, pp 199–237
Singer MJ, Ewing S (1999) Soil quality. In: Sumner ME (ed) Handbook of soil science. CRC Press, Boca Raton, pp G271–G298
Singh BK, Bardgett RD, Smith P, Reay DS (2010) Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat Rev Microbiol 8:779–790. https://doi.org/10.1038/nrmicro2439
Singh BP, Cowie AL, Chan KY (2011) Soil health and climate change. Springer Science & Business Media, Dordrecht
Sinsabaugh R, Shah J, Findlay S et al (2015) Scaling microbial biomass, metabolism and resource supply. Biogeochemistry 122:175–190. https://doi.org/10.1007/s10533-014-0058-z
Six J, Paustian K (2014) Aggregate-associated soil organic matter as an ecosystem property and a measurement tool. Soil Biol Biochem 68:A4–A9. https://doi.org/10.1016/j.soilbio.2013.06.014
Six J, Elliott ET, Paustian K (2000) Soil macroaggregate turnover and microaggregate formation: a mechanism for C sequestration under no-tillage agriculture. Soil Biol Biochem 32:2099–2103. https://doi.org/10.1016/S0038-0717(00)00179-6
Six J, Feller C, Denef K et al (2002) Soil organic matter, biota and aggregation in temperate and tropical soils—effects of no-tillage. Agronomie 22:755–775. https://doi.org/10.1051/agro:2002043
Šmejkalová M, Mikanová O, Borůvka L (2003) Effects of heavy metal concentrations on biological activity of soil micro-organisms. Plant Soil Environ 49:321–326
Smith P, Cotrufo MF, Rumpel C et al (2015) Biogeochemical cycles and biodiversity as key drivers of ecosystem services provided by soils. Soil Discuss 2:537–586. https://doi.org/10.5194/soild-2-537-2015
Snyder BA, Hendrix PF (2008) Current and potential roles of soil macroinvertebrates (earthworms, millipedes, and isopods) in ecological restoration. Restor Ecol 16:629–636. https://doi.org/10.1111/j.1526-100X.2008.00484.x
Society for Ecological Restoration International Science & Policy Working Group (2004) The SER International Primer on Ecological Restoration. Society for Ecological Restoration International, Tuscon
Solaiman ZM, Blackwell P, Abbott LK, Storer P (2010) Direct and residual effect of biochar application on mycorrhizal root colonisation, growth and nutrition of wheat. Soil Res 48:546–554. https://doi.org/10.1071/SR10002
Spyrou IM, Karpouzas DG, Menkissoglu-Spiroudi U (2009) Do botanical pesticides alter the structure of the soil microbial community? Microb Ecol 58:715–727
Srinivasulu M, Rangaswamy V (2013) Influence of insecticides alone and in combination with fungicides on enzyme activities in soils. Int J Environ Sci Technol 10:341–350
Staley TE (1999) Soil microbial biomass alterations during the maize silage growing season relative to tillage method. Soil Sci Soc Am J 63:1845–1847
Staley J, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39:321–346. https://doi.org/10.1146/annurev.mi.39.100185.001541
Steenwerth KL, Jackson LE, Calderón FJ et al (2002) Soil microbial community composition and land use history in cultivated and grassland ecosystems of coastal California. Soil Biol Biochem 34:1599–1611. https://doi.org/10.1016/S0038-0717(02)00144-X
Stocker TF, Qin D, Plattner G-K, et al (eds) (2013) IPCC, 2013: climate change 2013: the physical science basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge
Strickland MS, Wickings K, Bradford MA (2012) The fate of glucose, a low molecular weight compound of root exudates, in the belowground foodweb of forests and pastures. Soil Biol Biochem 49:23–29. https://doi.org/10.1016/j.soilbio.2012.02.001
Strukelj M, Brais S, Paré D (2015) Nine-year changes in carbon dynamics following different intensities of harvesting in boreal aspen stands. Eur J For Res 134:737–754. https://doi.org/10.1007/s10342-015-0880-4
Suding KN, Gross KL, Houseman GR (2004a) Alternative states and positive feedbacks in restoration ecology. Trends Ecol Evol 19:46–53. https://doi.org/10.1016/j.tree.2003.10.005
Suding KN, LeJeune KD, Seastedt TR (2004b) Competitive impacts and responses of an invasive weed: dependencies on nitrogen and phosphorus availability. Oecologia 141:526–535. https://doi.org/10.1007/s00442-004-1678-0
Sul WJ, Asuming-Brempong S, Wang Q et al (2013) Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biol Biochem 65:33–38. https://doi.org/10.1016/j.soilbio.2013.05.007
Sun B, Hallett PD, Caul S et al (2011) Distribution of soil carbon and microbial biomass in arable soils under different tillage regimes. Plant Soil 338:17–25. https://doi.org/10.1007/s11104-010-0459-2
Sun B, Wang F, Jiang Y et al (2014) A long-term field experiment of soil transplantation demonstrating the role of contemporary geographic separation in shaping soil microbial community structure. Ecol Evol 4:1073–1087. https://doi.org/10.1002/ece3.1006
Swift MJ, Izac A-MN, van Noordwijk M (2004) Biodiversity and ecosystem services in agricultural landscapes—are we asking the right questions? Agric Ecosyst Environ 104:113–134. https://doi.org/10.1016/j.agee.2004.01.013
Tan X, Chang SX (2007) Soil compaction and forest litter amendment affect carbon and net nitrogen mineralization in a boreal forest soil. Soil Tillage Res 93:77–86. https://doi.org/10.1016/j.still.2006.03.017
Tan X, Chang SX, Kabzems R (2008) Soil compaction and forest floor removal reduced microbial biomass and enzyme activities in a boreal aspen forest soil. Biol Fertil Soils 44:471–479. https://doi.org/10.1007/s00374-007-0229-3
Tarnocai C, Canadell JG, Schuur EAG et al (2009) Soil organic carbon pools in the northern circumpolar permafrost region. Glob Biogeochem Cycles 23:GB2023. https://doi.org/10.1029/2008GB003327
Tedersoo L, Bahram M, Toots M et al (2012) Towards global patterns in the diversity and community structure of ectomycorrhizal fungi. Mol Ecol 21:4160–4170. https://doi.org/10.1111/j.1365-294X.2012.05602.x
Temperton VM, Hobbs RJ, Nuttle T, Halle S (eds) (2004) Assembly rules and restoration ecology: bridging the gap between theory and practice. Island Press, Washington, DC
Templer PH, Mack MC, Chapin FS et al (2012) Sinks for nitrogen inputs in terrestrial ecosystems: a meta-analysis of 15 N tracer field studies. Ecology 93:1816–1829
Thakuria D, Schmidt O, Mac Siúrtáin M et al (2008) Importance of DNA quality in comparative soil microbial community structure analyses. Soil Biol Biochem 40:1390–1403. https://doi.org/10.1016/j.soilbio.2007.12.027
Thomas D, Middleton N (1997) World atlas of desertification, 2nd edn. Routledge, London
Tiedje JM, Cho JC, Murray A et al (2001) Soil teeming with life: new frontiers for soil science. In: Rees RM, Ball BC, Watson CA (eds) Sustainable management of soil organic matter. CAB International, Wallingford, pp 393–425. https://doi.org/10.1079/9780851994659.0393
Tischer A, Blagodatskaya E, Hamer U (2015) Microbial community structure and resource availability drive the catalytic efficiency of soil enzymes under land-use change conditions. Soil Biol Biochem 89:226–237. https://doi.org/10.1016/j.soilbio.2015.07.011
Tisdall JM, Oades JM (1982) Organic matter and water-stable aggregates in soils. J Soil Sci 33:141–163. https://doi.org/10.1111/j.1365-2389.1982.tb01755.x
Tiunov AV (2007) Stable isotopes of carbon and nitrogen in soil ecological studies. Biol Bull 34:395–407. https://doi.org/10.1134/S1062359007040127
Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296:1064–1066
Trojan MD, Linden DR (1998) Macroporosity and hydraulic properties of earthworm-affected soils as influenced by tillage and residue management. Soil Sci Soc Am J 62:1687–1692
Tu Q, Yu H, He Z et al (2014) GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Mol Ecol Resour 14(5):914–928. https://doi.org/10.1111/1755-0998.12239
Turner TR, Ramakrishnan K, Walshaw J et al (2013) Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME J 7:2248–2258. https://doi.org/10.1038/ismej.2013.119
United Nations (2014) System of environmental-economic accounting 2012. The World Bank
Upchurch R, Chiu C-Y, Everett K et al (2008) Differences in the composition and diversity of bacterial communities from agricultural and forest soils. Soil Biol Biochem 40:1294–1305. https://doi.org/10.1016/j.soilbio.2007.06.027
Ushio M, Kitayama K, Balser TC (2010) Tree species-mediated spatial patchiness of the composition of microbial community and physicochemical properties in the topsoils of a tropical montane forest. Soil Biol Biochem 42:1588–1595. https://doi.org/10.1016/j.soilbio.2010.05.035
Vacher CA, Loch RJ, Raine SR (2003) Effect of polyacrylamide additions on infiltration and erosion of disturbed lands. Soil Res 41:1509–1520. https://doi.org/10.1071/sr02114
van der Heijden MGA, Klironomos JN, Ursic M et al (1998) Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396:69–72. https://doi.org/10.1038/23932
Vance ED, Brookes PC, Jenkinson DS (1987) An extraction method for measuring soil microbial biomass C. Soil Biol Biochem 19:703–707. https://doi.org/10.1016/0038-0717(87)90052-6
Vargas Gil S, Becker A, Oddino C et al (2009) Field trial assessment of biological, chemical, and physical responses of soil to tillage intensity, fertilization, and grazing. Environ Manag 44:378–386. https://doi.org/10.1007/s00267-009-9319-3
Verastegui Y, Cheng J, Engel K et al (2014) Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities. mBio 5:e01157–e01114. https://doi.org/10.1128/mBio.01157-14
Verbruggen E, Röling WFM, Gamper HA et al (2010) Positive effects of organic farming on below-ground mutualists: large-scale comparison of mycorrhizal fungal communities in agricultural soils. New Phytol 186:968–979
Vestal JR, White DC (1989) Lipid analysis in microbial ecology. Bioscience 39:535–541. https://doi.org/10.2307/1310976
Vinton MA, Goergen EM (2006) Plant–soil feedbacks contribute to the persistence of Bromus inermis in tallgrass prairie. Ecosystems 9:967–976. https://doi.org/10.1007/s10021-005-0107-5
Vitousek PM, Matson PA (1985) Disturbance, nitrogen availability, and nitrogen losses in an intensively managed loblolly pine plantation. Ecology 66:1360–1376. https://doi.org/10.2307/1939189
Vitousek PM, Gosz JR, Grier CC et al (1982) A comparative analysis of potential nitrification and nitrate mobility in forest ecosystems. Ecol Monogr 52:155–177. https://doi.org/10.2307/1942609
Vries FT, Manning P, Tallowin JRB et al (2012) Abiotic drivers and plant traits explain landscape-scale patterns in soil microbial communities. Ecol Lett 15:1230–1239. https://doi.org/10.1111/j.1461-0248.2012.01844.x
Wakelin SA, Macdonald LM, Rogers SL et al (2008) Habitat selective factors influencing the structural composition and functional capacity of microbial communities in agricultural soils. Soil Biol Biochem 40:803–813
Walker RF, McLaughlin SB, West DC (2004) Establishment of sweet birch on surface mine spoil as influenced by mycorrhizal inoculation and fertility. Restor Ecol 12:8–19. https://doi.org/10.1111/j.1061-2971.2004.00255.x
Wall DH, Adams G, Parsons AN (2001) Soil biodiversity. In: Chapin FS, Sala OE, Huber-Sannwald E (eds) Global biodiversity in a changing environment: scenarios for the 21st century. Springer, New York
Wall DH, Bradford MA, St. John MG et al (2008) Global decomposition experiment shows soil animal impacts on decomposition are climate-dependent. Glob Change Biol 14:2661–2677. https://doi.org/10.1111/j.1365-2486.2008.01672.x
Wallenstein MD, Hall EK (2012) A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning. Biogeochemistry 109:35–47. https://doi.org/10.1007/s10533-011-9641-8
Wan S, Hui D, Luo Y (2001) Fire effects on nitrogen pools and dynamics in terrestrial ecosystems: a meta-analysis. Ecol Appl 11:1349–1365. https://doi.org/10.2307/3060925
Wander MM, Yang X (2000) Influence of tillage on the dynamics of loose-and occluded-particulate and humified organic matter fractions. Soil Biol Biochem 32:1151–1160
Wander MM, Bidart MG, Aref S (1998) Tillage impacts on depth distribution of total and particulate organic matter in three Illinois soils. Soil Sci Soc Am J 62:1704. https://doi.org/10.2136/sssaj1998.03615995006200060031x
Wang S, Fu B (2013) Trade-offs between forest ecosystem services. For Policy Econ 26:145–146
Wang Q, Zhong M, Wang S (2012) A meta-analysis on the response of microbial biomass, dissolved organic matter, respiration, and N mineralization in mineral soil to fire in forest ecosystems. For Ecol Manag 271:91–97. https://doi.org/10.1016/j.foreco.2012.02.006
Wang C, Lu H, Dong D et al (2013) Insight into the effects of biochar on manure composting: evidence supporting the relationship between N2O emission and denitrifying community. Environ Sci Technol 47:7341–7349. https://doi.org/10.1021/es305293h
Wang J-T, Zheng Y-M, Hu H-W et al (2016) Coupling of soil prokaryotic diversity and plant diversity across latitudinal forest ecosystems. Sci Rep 6:19561. https://doi.org/10.1038/srep19561
Wardle DA (1992) A comparative assessment of factors which influence microbial biomass carbon and nitrogen levels in soil. Biol Rev 67:321–358
Wardle DA (2002) Communities and ecosystems: linking the aboveground and belowground components. Princeton University Press, Princeton
Wardle DA, Yeates GW, Watson RN, Nicholson KS (1995) The detritus food-web and the diversity of soil fauna as indicators of disturbance regimes in agro-ecosystems. In: Collins HP, Robertson GP, Klug MJ (eds) The significance and regulation of soil biodiversity. Springer, Netherlands, pp 35–43
Wardle DA, Bardgett RD, Klironomos JN et al (2004) Ecological linkages between aboveground and belowground biota. Science 304:1629–1633
Warnock DD, Lehmann J, Kuyper TW, Rillig MC (2007) Mycorrhizal responses to biochar in soil—concepts and mechanisms. Plant Soil 300:9–20. https://doi.org/10.1007/s11104-007-9391-5
Washbourne C-L, Renforth P, Manning DAC (2012) Investigating carbonate formation in urban soils as a method for capture and storage of atmospheric carbon. Sci Total Environ 431:166–175. https://doi.org/10.1016/j.scitotenv.2012.05.037
Watt M, Hugenholtz P, White R, Vinall K (2006) Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Environ Microbiol 8:871–884. https://doi.org/10.1111/j.1462-2920.2005.00973.x
Wei B, Yang L (2010) A review of heavy metal contaminations in urban soils, urban road dusts and agricultural soils from China. Microchem J 94:99–107. https://doi.org/10.1016/j.microc.2009.09.014
West AW, Sparling GP (1986) Modifications to the substrate-induced respiration method to permit measurement of microbial biomass in soils of differing water contents. J Microbiol Methods 5:177–189. https://doi.org/10.1016/0167-7012(86)90012-6
West PC, Gerber JS, Engstrom PM et al (2014) Leverage points for improving global food security and the environment. Science 345:325–328. https://doi.org/10.1126/science.1246067
Whisenant S (1999) Repairing damaged wildlands: a process-orientated, landscape-scale approach. Cambridge University Press, Cambridge
White MA, Nemani RR, Thornton PE, Running SW (2002) Satellite evidence of phenological differences between urbanized and rural areas of the Eastern United States deciduous broadleaf forest. Ecosystems 5:260–273. https://doi.org/10.1007/s10021-001-0070-8
Wieder WR, Bonan GB, Allison SD (2013) Global soil carbon projections are improved by modelling microbial processes. Nat Clim Chang 3:909–912. https://doi.org/10.1038/nclimate1951
Williamson JC, Johnson DB (1991) Microbiology of soils at opencast coal sites. II. Population transformations occurring following land restoration and the influence of ryegrass/fertilizer amendments. J Soil Sci 42:9–15. https://doi.org/10.1111/j.1365-2389.1991.tb00086.x
Wilson SD, Gerry AK (1995) Strategies for mixed-grass prairie restoration: herbicide, tilling, and nitrogen manipulation. Restor Ecol 3:290–298. https://doi.org/10.1111/j.1526-100X.1995.tb00096.x
Winterberg H (1898) Zur Methodik der Bakterienzahlung. Zeitschr F Hyg 29:75–93
Wittebolle L, Marzorati M, Clement L et al (2009) Initial community evenness favours functionality under selective stress. Nature 458:623–626. https://doi.org/10.1038/nature07840
Wolfaardt GM, Hendry MJ, Korber DR (2008) Microbial distribution and diversity in saturated, high pH, uranium mine tailings, Saskatchewan, Canada. Can J Microbiol 54:932–940
Woltemade CJ (2010) Impact of residential soil disturbance on infiltration rate and stormwater runoff. JAWRA 46:700–711. https://doi.org/10.1111/j.1752-1688.2010.00442.x
Wood SA, Almaraz M, Bradford MA et al (2015a) Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture. Front Microbiol 6:90. https://doi.org/10.3389/fmicb.2015.00090
Wood SA, Bradford MA, Gilbert JA et al (2015b) Agricultural intensification and the functional capacity of soil microbes on smallholder African farms. J Appl Ecol 52:744–752
Wooley JC, Godzik A, Friedberg I (2010) A primer on metagenomics. PLoS Comput Biol 6:e1000667. https://doi.org/10.1371/journal.pcbi.1000667
Wortley L, Hero J-M, Howes M (2013) Evaluating ecological restoration success: a review of the literature. Restor Ecol 21:537–543. https://doi.org/10.1111/rec.12028
Wortmann CS, Quincke JA, Drijber RA et al (2008) Soil microbial community change and recovery after one-time tillage of continuous no-till. Agron J 100:1681. https://doi.org/10.2134/agronj2007.0317
Wu T, Chellemi DO, Graham JH et al (2008) Comparison of soil bacterial communities under diverse agricultural land management and crop production practices. Microb Ecol 55:293–310
Wu D, Hugenholtz P, Mavromatis K et al (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:1056–1060. https://doi.org/10.1038/nature08656
Wynendaele E, Bronselaer A, Nielandt J et al (2013) Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides. Nucleic Acids Res 41:D655–D659. https://doi.org/10.1093/nar/gks1137
Xu X, Thornton PE, Post WM (2013) A global analysis of soil microbial biomass carbon, nitrogen and phosphorus in terrestrial ecosystems. Glob Ecol Biogeogr 22:737–749. https://doi.org/10.1111/geb.12029
Xu Z, Hansen MA, Hansen LH et al (2014) Bioinformatic approaches reveal metagenomic characterization of soil microbial community. PLoS One 9:e93445. https://doi.org/10.1371/journal.pone.0093445
Xu W, Ge Z, Poudel DR (2015) Application and optimization of biolog ecoplates in functional diversity studies of soil microbial communities. MATEC Web Conf 22:04015. https://doi.org/10.1051/matecconf/20152204015
Yamamoto K, Ohdachi SD, Kasahara Y (2010) Detection of effects of a high trophic level predator, Sorex unguiculatus (Soricidae, Mammalia), on a soil microbial community in a cool temperate forest in Hokkaido, using the Arisa method. Microbes Environ 25:197–203. https://doi.org/10.1264/jsme2.ME10111
Yang G, Liu N, Lu W et al (2014) The interaction between arbuscular mycorrhizal fungi and soil phosphorus availability influences plant community productivity and ecosystem stability. J Ecol 102:1072–1082. https://doi.org/10.1111/1365-2745.12249
Yousaf S, Khan S, Aslam MT (2013) Effect of pesticides on the soil microbial activity. Pak J Zool 5(4):1063–1067
Zelles L, Bai QY, Beck T, Beese F (1992) Signature fatty acids in phospholipids and lipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils. Soil Biol Biochem 24:317–323. https://doi.org/10.1016/0038-0717(92)90191-Y
Zhang W, Youjin L, Zifang W et al (2011) 2010 international conference on energy, environment and development—ICEED2010Effects of conservation tillage on organic carbon, nitrogen and enzyme activities in a hydragric anthrosol of Chongqing, China. Energy Procedia 5:30–36. https://doi.org/10.1016/j.egypro.2011.03.006
Zhang C, Tian H, Chen G et al (2012) Impacts of urbanization on carbon balance in terrestrial ecosystems of the Southern United States. Environ Pollut 164:89–101. https://doi.org/10.1016/j.envpol.2012.01.020
Zhang Q, Dijkstra FA, Liu X et al (2014) Effects of biochar on soil microbial biomass after four years of consecutive application in the North China Plain. PLoS One 9. https://doi.org/10.1371/journal.pone.0102062
Zhang T, Li S, Sun X et al (2015) The earthworm Eisenia fetida can help desalinate a coastal saline soil in Tianjin, North China. PLoS One 10:e0144709. https://doi.org/10.1371/journal.pone.0144709
Zhou D, Zhao SQ, Liu S, Oeding J (2013) A meta-analysis on the impacts of partial cutting on forest structure and carbon storage. Biogeosciences 10:3691–3703. https://doi.org/10.5194/bg-10-3691-2013
Zhuang X, Gao J, Ma A et al (2013) Bioactive molecules in soil ecosystems: masters of the underground. Int J Mol Sci 14:8841–8868. https://doi.org/10.3390/ijms14058841
Ziadi N, Angers DA, Gagnon B et al (2014) Long-term tillage and synthetic fertilization affect soil functioning and crop yields in a corn–soybean rotation in eastern Canada. Can J Soil Sci 94:365–376. https://doi.org/10.4141/cjss2013-067
Zimmerman AR, Gao B, Ahn M-Y (2011) Positive and negative carbon mineralization priming effects among a variety of biochar-amended soils. Soil Biol Biochem 43:1169–1179. https://doi.org/10.1016/j.soilbio.2011.02.005
Zuber SM, Villamil MB (2016) Meta-analysis approach to assess effect of tillage on microbial biomass and enzyme activities. Soil Biol Biochem 97:176–187. https://doi.org/10.1016/j.soilbio.2016.03.011
Acknowledgments
The author thanks Hermano Zenaide Neto for research assistance.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Ethics declarations
Conflict of Interest
Vicky L. McKinley declares that she has no conflict of interest.
Ethical Approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
McKinley, V.L. (2019). Effects of Land Use and Restoration on Soil Microbial Communities. In: Hurst, C. (eds) Understanding Terrestrial Microbial Communities. Advances in Environmental Microbiology, vol 6. Springer, Cham. https://doi.org/10.1007/978-3-030-10777-2_7
Download citation
DOI: https://doi.org/10.1007/978-3-030-10777-2_7
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-10775-8
Online ISBN: 978-3-030-10777-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)