Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-586b7cd67f-2brh9 Total loading time: 0 Render date: 2024-11-26T03:07:51.970Z Has data issue: false hasContentIssue false

Chapter Three - Microbiomes of soils

Published online by Cambridge University Press:  07 March 2020

By
Reuben Margerison ,
OcÉAne Nicolitch  and
Yaqian Zhang
Edited by
Rachael E. Antwis ,
Xavier A. Harrison  and
Michael J. Cox
Rachael E. Antwis
Affiliation:
University of Salford
Xavier A. Harrison
Affiliation:
University of Exeter
Michael J. Cox
Affiliation:
University of Birmingham
Get access

Summary

Soil provides the foundation for life on Earth as well as the food we eat, and is one of the most well-studied of all microbial communities. Here we look in detail at microbiomes of grassland and forest soils, and provide an overview of those associated with more extreme environments, including deserts, peatlands and tundra permafrost. We highlight the key interactions between soil microbiomes and biogeochemical nutrient cycling, particularly in the context of global climate change. We also explore the tight association between plants and the soils in which they grow, and the role of abiotic and biotic factors, such as nutrient availability, litter chemistry, plant exudates and microbial enzyme activity, in regulating those relationships.

Keywords

desertecosystem functioningforestsgrasslandslitterNPKnutrient cyclingpeatlandspermafrosttundra
Type
Chapter
Information
Microbiomes of Soils, Plants and Animals
An Integrated Approach
 , pp. 29 - 54
Publisher: Cambridge University Press
Print publication year: 2020

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Adamo, P, Violante, P. (2000) Weathering of rocks and neogenesis of minerals associated with lichen activity. Applied Clay Science, 16, 229–256.Google Scholar
Aguirre-Garrido, JF, Montiel-Lugo, D, Hernández-Rodríguez, C, et al. (2012) Bacterial community structure in the rhizosphere of three cactus species from semi-arid highlands in central Mexico. Antonie van Leeuwenhoek, 101, 891–904.Google Scholar
Anderson, JM. (1991) The effects of climate change on decomposition processes in grassland and coniferous forests. Ecological Applications, 1, 326–347.CrossRefGoogle ScholarPubMed
Andersen, R, Chapman, S, Artz, RRE. (2013) Microbial communities in natural and disturbed peatlands: A review. Soil Biology and Biochemistry, 57, 979–994.Google Scholar
Anisimov, OA. (2007) Potential feedback of thawing permafrost to the global climate system through methane emission. Environmental Research Letters, 2, 045016.CrossRefGoogle Scholar
Artz, RRE. (2009) Microbial community structure and carbon substrate use in Northern peatlands. In: Baird, AJ, Belya, LR, Comas, X, et al. (Eds.), Carbon Cycling in Northern Peatlands. Geophysical Monograph Series, vol. 184. Washington, DC: American Geophysical Union.Google Scholar
Augé, RM. (2001) Water relations, drought and vesicular–arbuscular mycorrhizal symbiosis. Mycorrhiza, 11, 3–42.Google Scholar
Augusto, L, De Schrijver, A, Vesterdal, L, et al. (2015) Influences of evergreen gymnosperm and deciduous angiosperm tree species on the functioning of temperate and boreal forests. Biological Reviews, 90, 444–466.Google Scholar
Azcón-Aguilar, C, Barea, JM. (1997) Arbuscular mycorrhizas and biological control of soil-borne plant pathogens – an overview of the mechanisms involved. Mycorrhiza, 6, 457–464.CrossRefGoogle Scholar
Bahram, M, Hildebrand, F, Forslund, SK, et al. (2018) Structure and function of the global topsoil microbiome. Nature, 560, 233.Google Scholar
Bakermans, C, Tsapin, AI, Souza‐Egipsy, V, et al. (2003) Reproduction and metabolism at −10°C of bacteria isolated from Siberian permafrost. Environmental Microbiology, 5, 321–326.Google Scholar
Bardgett, RD, Wardle, DA. (2010) Aboveground–Belowground Linkages: Biotic Interactions, Ecosystem Processes, and Global Change. Oxford: Oxford University Press.Google Scholar
Bardgett, RD, van der Putten, WH. (2014) Belowground biodiversity and ecosystem functioning. Nature, 515, 505–511.Google Scholar
Barns, SM, Takala, SL, Kuske, CR. (1999) Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Applied Environmental Microbiology, 65, 1731–1737.Google Scholar
Bates, ST, Berg-Lyons, D, Caporaso, JG, et al. (2011) Examining the global distribution of dominant archaeal populations in soil. The ISME Journal, 5, 908–917.Google Scholar
Bender, SF, Wagg, C, van der Heijden, MGA. (2016) An underground revolution: Biodiversity and soil ecological engineering for agricultural sustainability. Trends in Ecology & Evolution, 31, 440–452.CrossRefGoogle ScholarPubMed
Berg, G, Zachow, C, Müller, H, et al. (2013) Next-generation bio-products sowing the seeds of success for sustainable agriculture. Agronomy, 3, 648–656.CrossRefGoogle Scholar
Bever, JD. (1994) Feedback between plants and their soil communities in an old field community. Ecology, 75, 1965–1977.CrossRefGoogle Scholar
Bever, JD, Westover, KM, Antonovics, J. (1997) Incorporating the soil community into plant population dynamics: The utility of the feedback approach. Journal of Ecology, 85, 561–573.Google Scholar
Bontti, EE, Decant, JP, Munson, SM, et al. (2009) Litter decomposition in grasslands of Central North America (US Great Plains). Global Change Biology, 15, 1356–1363.Google Scholar
Booth, RE, Grime, JP. (2003) Effects of genetic impoverishment on plant community diversity. Journal of Ecology, 91, 721–730.Google Scholar
Boudsocq, S, Niboyet, A, Lata, JC, et al. (2012) Plant preference for ammonium versus nitrate: A neglected determinant of ecosystem functioning? The American Naturalist, 180, 60–69.Google Scholar
Brooker, RW, Maestre, FT, Callaway, RM, et al. (2008) Facilitation in plant communities: The past, the present, and the future. Journal of Ecology, 96, 18–34.Google Scholar
Brown, JH, Gillooly, JF, Allen, AP, et al. (2004) Toward a metabolic theory of ecology. Ecology, 85, 1771–1789.Google Scholar
Brundrett, MC. (2002) Coevolution of roots and mycorrhizas of land plants. New Phytologist, 154, 275–304.CrossRefGoogle ScholarPubMed
Callesen, I, Liski, J, Raulund‐Rasmussen, K, et al. (2003) Soil carbon stores in Nordic well‐drained forest soils – Relationships with climate and texture class. Global Change Biology, 9, 358–370.Google Scholar
Cameron, DD, Neal, AL, van Wees, SCM, et al. (2013) Mycorrhiza-induced resistance: More than the sum of its parts? Trends in Plant Science, 18, 539–545.Google Scholar
Carlsson, G, Huss-Danell, K. (2003) Nitrogen fixation in perennial forage legumes in the field. Plant and Soil, 253, 353–372.Google Scholar
Chapin, FS, Matson, PA, Mooney, HA. (Eds.) (2002) Terrestrial decomposition. In: Principles of Terrestrial Ecosystem Ecology. New York, NY: Springer.CrossRefGoogle Scholar
Cheng, L, Booker, FL, Tu, C, et al. (2012) Arbuscular mycorrhizal fungi increase organic carbon decomposition under elevated CO2. Science, 337, 1084–1087.Google Scholar
Cleveland, CC, Townsend, AR, Schimel, DS, et al. (1999) Global patterns of terrestrial biological nitrogen (N2) fixation in natural ecosystems. Global Biogeochemical Cycles, 13, 623–645.CrossRefGoogle Scholar
Colica, G, Li, H, Rossi, F, et al. (2014) Microbial secreted exopolysaccharides affect the hydrological behavior of induced biological soil crusts in desert sandy soils. Soil Biology and Biochemistry, 68, 62–70.Google Scholar
Colin, Y, Nicolitch, O, Turpault, MP, et al. (2016) Mineral type and tree species determine the functional and taxonomic structure of forest soil bacterial communities. Applied and Environmental Microbiology, 83, 1–23.Google Scholar
Colin, Y, Nicolitch, O, Van Nostrand, JD, et al. (2017) Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence. Scientific Reports, 7, 1–17.Google Scholar
Cowling, DW. (1982) Biological nitrogen fixation and grassland production in the United Kingdom. Philosophical Transactions of the Royal Society Series B: Biological Sciences, 296, 397–404.Google Scholar
Craine, JM, Gelderman, TM. (2011) Soil moisture controls on temperature sensitivity of soil organic carbon decomposition for a mesic grassland. Soil Biology and Biochemistry, 43, 455–457.CrossRefGoogle Scholar
Craven, D, Isbell, F, Manning, P, et al. (2016) Plant diversity effects on grassland productivity are robust to both nutrient enrichment and drought. Philosophical Transactions of the Royal Society B: Biological Sciences, 371, 20150277.Google Scholar
Dass, P, Houlton, BZ, Wang, Y, et al. (2018) Grasslands may be more reliable carbon sinks than forests in California. Environmental Research Letters, 13, 074027.Google Scholar
Dassen, S, Cortois, R, Martens, H, et al. (2017) Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity. Molecular Ecology, 26, 4085–4098.Google Scholar
Davidson, EA, Janssens, IA. (2006) Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature, 440, 165–173.Google Scholar
de Vries, FT, Bardgett, RD. (2012) Plant–microbial linkages and ecosystem nitrogen retention: Lessons for sustainable agriculture. Frontiers in Ecology and the Environment, 10, 425–432.Google Scholar
de Vries, FT, Wallenstein, MD. (2017) Below‐ground connections underlying above‐ground food production: A framework for optimising ecological connections in the rhizosphere. Journal of Ecology. 105, 913–920.CrossRefGoogle Scholar
Delgado-Baquerizo, M, Eldridge, DJ. (2019) Cross-biome drivers of soil bacterial alpha diversity on a worldwide scale. Ecosystems, 22, 1220–1231.Google Scholar
Delgado-Baquerizo, M, Oliverio, AM, Brewer, TE, et al. (2018) A global atlas of the dominant bacteria found in soil. Science, 359, 320–325.Google Scholar
Di, HJ, Cameron, KC, Shen, JP, et al. (2009) Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nature Geoscience, 2, 621–624.Google Scholar
Ehrenfeld, JG, Ravit, B, Elgersma, K. (2005) Feedback in the plant–soil system. Annual Review of Environment and Resources, 30, 75–115.Google Scholar
El-Sayed, WS, Akhkha, A, El-Naggar, MY, et al. (2014) In vitro antagonistic activity, plant growth promoting traits and phylogenetic affiliation of rhizobacteria associated with wild plants grown in arid soil. Frontiers in Microbiology, 5, 651.CrossRefGoogle ScholarPubMed
Falcäo, LL, Silva‐Werneck, JO, Vilarinho, BR, et al. (2014) Antimicrobial and plant growth‐promoting properties of the cacao endophyte Bacillus subtilis ALB 629. Journal of Applied Microbiology, 116, 1584–1592.Google Scholar
Fay, PA, Prober, SM, Harpole, WS, et al. (2015) Grassland productivity limited by multiple nutrients. Nature Plants, 1, 15080.Google Scholar
Ferjani, R, Marasco, R, Rolli, E, et al. (2015) The date palm tree rhizosphere is a niche for plant growth promoting bacteria in the oasis ecosystem. BioMed Research International, 2015, 153851.Google Scholar
Fierer, N. (2017) Embracing the unknown: Disentangling the complexities of the soil microbiome. Nature Reviews Microbiology, 15, 579.Google Scholar
Fierer, N, Jackson, RB. (2006) The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences, 103, 626–631.Google Scholar
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.Google Scholar
Finlay, RD, Ek, H, Odham, G, et al. (1990) Mycelial uptake, translocation and assimilation of 15N-labelled nitrogen by ectomycorrhizal Pinus sylvestris plants. Agriculture, Ecosystems & Environment, 28, 133–137.Google Scholar
Fiore-Donno, AM, Richter-Heitmann, T, Degrune, F, et al. (2019) Functional traits and spatio-temporal structure of a major group of soil protists (Rhizaria: Cercozoa) in a temperate grassland. Frontiers in Microbiology, 10, 1332.Google Scholar
Fisk, MC, Ruether, KF, Yavitt, JB. (2003) Microbial activity and functional composition among northern peatland ecosystems. Soil Biology and Biochemistry, 35, 591–602.Google Scholar
Food and Agriculture Organisation of the United Nations (FAO). (2018) The State of the World’s Forests. Rome: Food and Agriculture Organization of the United Nations.Google Scholar
French, KE, Tkacz, A, Turnbull, LA. (2017) Conversion of grassland to arable decreases microbial diversity and alters community composition. Applied Soil Ecology, 110, 43–52.Google Scholar
Freschet, GT, Cornwell, WK, Wardle, DA, et al. (2013) Linking litter decomposition of above- and below-ground organs to plant–soil feedbacks worldwide. Journal of Ecology, 101, 943–952.Google Scholar
Ganzert, L, Lipsk, A, Hubberten, HW, Wagner, D. (2011) The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica. FEMS Microbiology Ecology, 76, 476–491.Google Scholar
Geisen, S, Mitchell, EA, Adl, S, et al. (2018) Soil protists: A fertile frontier in soil biology research. FEMS Microbiology Reviews, 42, 293–323.Google Scholar
Gibson, DJ. (2008) Grasses and Grassland Ecology. Oxford: Oxford University Press.Google Scholar
Gilichinsky, DA. (2002) Permafrost model of extraterrestrial habitat. In: Horneck, G, Baumstark-Khan, C. (Eds.) Astrobiology. Berlin: Springer.Google Scholar
Golovchenko, AV, Semenova, TA, Polyakova, AV, et al. (2002) The structure of the micromycete complexes of oligotrophic peat deposits in the southern Taiga subzone of west Siberia. Microbiology, 71, 575–581.Google Scholar
Golovchenko, AV, Tikhonova, EY, Zvyaginster, DG. (2007) Abundance, biomass, structure and activity of the microbial complexes of minerotrophic and ombrotrophic peatlands. Microbiology, 76, 630–637.Google Scholar
Gorzelak, MA, Asay, AK, Pickles, BJ, et al. (2015) Inter-plant communication through mycorrhizal networks mediates complex adaptive behaviour in plant communities. Annals of Botany Plants, 7, plv050.Google Scholar
Graham, DE, Wallenstein, MD, Vishnivetskaya, TA, et al. (2012) Microbes in thawing permafrost: The unknown variable in the climate change equation. The ISME Journal, 6, 709.Google Scholar
Grigulis, K, Lavorel, S, Krainer, U, et al. (2013) Relative contributions of plant traits and soil microbial properties to mountain grassland ecosystem services. Journal of Ecology, 101, 47–57.Google Scholar
Grunig, CR, Sieber, TN. (2005) Molecular and phenotypic description of the widespread root symbiont Acephala applanata gen. et sp. nov., formerly known as dark-septate endophyte Type 1. Mycologia, 97, 628–640.Google Scholar
Gubsch, M, Roscher, C, Gleixner, G, et al. (2011) Foliar and soil δ15N values reveal increased nitrogen partitioning among species in diverse grassland communities. Plant, Cell & Environment, 34, 895–908.Google Scholar
Hagerberg, D, Thelin, G, Wallander, H. (2016) The production of ectomycorrhizal mycelium in forests: Relation between forest nutrient status and local mineral sources. Plant and Soil, 252, 279–290.Google Scholar
Hansen, AA, Herbert, RA, Mikkelsen, K, et al. (2007) Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway. Environmental Microbiology, 9, 2870–2884.Google Scholar
Harrison, KA, Bardgett, RD. (2010) Influence of plant species and soil conditions on plant–soil feedback in mixed grassland communities. Journal of Ecology, 98, 384–395.Google Scholar
Hobbie, EA, Högberg, P. (2012). Nitrogen isotopes link mycorrhizal fungi and plants to nitrogen dynamics. New Phytologist, 296, 367–382.Google Scholar
Hobbie, SE. (1996) Temperature and plant species control over litter decomposition in Alaskan tundra. Ecological Monographs, 66, 503–522.Google Scholar
Hobbie, SE, Gough, L. (2004) Litter decomposition in moist acidic and non-acidic tundra with different glacial histories. Oecologia. 140, 113–24.Google Scholar
Hodge, A, Campbell, CD, Fitter, AH. (2001) An arbuscular mycorrhizal fungus accelerates decomposition and acquires nitrogen directly from organic material. Nature, 413, 297–299.Google Scholar
Högberg, MN, Högberg, P. (2002) Extramatrical ectomycorrhizal mycelium contributes one-third of microbial biomass and produces, together with associated roots, half the dissolved organic carbon in a forest soil. New Phytologist, 154, 791–795.Google Scholar
Hooper, DU, Chapin, FS, Ewel, JJ, et al. (2005) Effects of biodiversity on ecosystem functioning: A consensus of current knowledge. Ecological Monographs, 75, 3–35.Google Scholar
Hu, S, Chapin III, FS, Firestone, MK, et al. (2001) Nitrogen limitation of microbial decomposition in a grassland under elevated CO2. Nature, 409, 188–191.Google Scholar
Isbell, F, Craven, D, Connolly, J, et al. (2015) Biodiversity increases the resistance of ecosystem productivity to climate extremes. Nature, 526, 574–577.Google Scholar
Jaatinen, K, Fritze, H, Laine, J, Laiho, R. (2007) Effects of short- and long-term water-level drawdown on the populations and activity of aerobic decomposers in a boreal peatland. Global Change Biology, 13, 491–510.CrossRefGoogle Scholar
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 Biology and Biochemistry, 40, 2843–2853.Google Scholar
Jansson, JK, Hofmockel, KS. (2018) The soil microbiome – From metagenomics to metaphenomics. Current Opinion in Microbiology, 43, 162–168.Google Scholar
Jenkinson, DS. (1990) The turnover of organic carbon and nitrogen in soil. Philosophical Transactions of the Royal Society Series B: Biological Sciences, 329, 361–368.Google Scholar
Johnson, D, Gilbert, L. (2015) Interplant signalling through hyphal networks. New Phytologist, 205, 1448–1453.Google Scholar
Joosten, H, Clarke, D. (2002) Wise Use of Mires and Peatlands: Background and Principles Including a Framework for Decision-making. Greifswald: International Mire Conservation Group.Google Scholar
Jorquera, MA, Shaharoona, B, Nadeem, SM, et al. (2012) Plant growth-promoting rhizobacteria associated with ancient clones of creosote bush (Larrea tridentata). Microbial Ecology, 64, 1008–1017.Google Scholar
Kaiser, C, Koranda, M, Kitzler, B, et al. (2010) Belowground carbon allocation by trees drives seasonal patterns of extracellular enzyme activities by altering microbial community composition in a beech forest soil. New Phytologist, 187, 843–858.Google Scholar
Kaplan, D, Maymon, M, Agapakis, CM, et al. (2013) A survey of the microbial community in the rhizosphere of two dominant shrubs of the Negev Desert highlands, Zygophyllum dumosum (Zygophyllaceae) and Atriplex halimus (Amaranthaceae), using cultivation‐dependent and cultivation‐independent methods. American Journal of Botany, 100, 1713–1725.Google Scholar
Kardol, P, Martijn Bezemer, T, van der Putten, WH. (2006) Temporal variation in plant–soil feedback controls succession. Ecology Letters, 9, 1080–1088.Google Scholar
Keuter, A, Veldkamp, E, Corre, MD. (2014) Asymbiotic biological nitrogen fixation in a temperate grassland as affected by management practices. Soil Biology and Biochemistry, 70, 38–46.Google Scholar
Klironomos, JN. (2002) Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature, 417, 67–70.Google Scholar
Klironomos, JN. (2003) Variation in plant response to native and exotic arbuscular mycorrhizal fungi. Ecology, 84, 2292–2301.CrossRefGoogle Scholar
Kohler, A, Kuo, A, Nagy, LG, et al. (2015) Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nature Genetics, 47, 410–415.Google Scholar
Koziol, L, Bever, JD. (2017) The missing link in grassland restoration: Arbuscular mycorrhizal fungi inoculation increases plant diversity and accelerates succession. Journal of Applied Ecology, 54, 1301–1309.Google Scholar
Kulmatiski, A, Kardol, P. (2008) Getting plant–soil feedbacks out of the greenhouse: Experimental and conceptual approaches. Progress in Botany, 69, 449–472.Google Scholar
Kumar, A, Maurya, BR, Raghuwanshi, R. (2014) Isolation and characterization of PGPR and their effect on growth, yield and nutrient content in wheat (Triticum aestivum L.). Biocatalysis and Agricultural Biotechnology, 3, 121–128.Google Scholar
Lambers, H, Chapin, FS, Pons, TL. (2008a) Plant Physiological Ecology. New York, NY: Springer.Google Scholar
Lambers, H, Raven, JA, Shaver, GR, et al. (2008b) Plant nutrient-acquisition strategies change with soil age. Trends in Ecology & Evolution, 23, 95–103.Google Scholar
Lambers, H, Albornoz, F, Kotula, L, et al. (2018) How belowground interactions contribute to the coexistence of mycorrhizal and non-mycorrhizal species in severely phosphorus-impoverished hyperdiverse ecosystems. Plant and Soil, 424, 11–33.Google Scholar
Landeweert, R, Hoffland, E, Finlay, RD, et al. (2001) Linking plants to rocks: Ectomycorrhizal fungi mobilize nutrients from minerals. Trends in Ecology & Evolution, 16, 248–254.Google Scholar
Lauber, CL, Strickland, MS, Bradford, MA, et al. (2008) The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biology and Biochemistry, 40, 2407–2415.CrossRefGoogle Scholar
Leake, J, Johnson, D, Donnelly, D, et al. (2004) Networks of power and influence: The role of mycorrhizal mycelium in controlling plant communities and agroecosystem functioning. Canadian Journal of Botany, 82, 1016–1045.Google Scholar
LeBauer, DS, Treseder, KK. (2008) Nitrogen limitation of net primary productivity in terrestrial ecosystems is globally distributed. Ecology, 89, 371–379.Google Scholar
Ledeganck, P, Nijs, I, Beyens, L. (2003) Plant functional group diversity promotes soil protist diversity. Protist, 154, 239–249.Google Scholar
Ledgard, SF, Steele, KW. (1992) Biological nitrogen fixation in mixed legume/grass pastures. Plant and Soil, 141, 137–153.Google Scholar
Li, M, Feng, H, Yang, Z, et al. (2011) Diversity of culturable bacteria in the typical frozen soil areas in China. Acta Microbiologica Sinica, 51, 1595–1604.Google Scholar
Li, XR, Jia, RL, Zhang, ZS, et al. (2018) Hydrological response of biological soil crusts to global warming: A ten‐year simulative study. Global Change Biology, 24, 4960–4971.Google Scholar
Lindahl, BD, Ihrmark, K, Boberg, J, et al. (2007) Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. New Phytologist, 173, 611–620.Google Scholar
Lindahl, BD, Tunlid, A. (2015) Ectomycorrhizal fungi – Potential organic matter decomposers, yet not saprotrophs. New Phytologist, 205, 1443–1447.Google Scholar
Lipson, DA, Schmidt, SK, Monson, RK. (2000) Carbon availability and temperature control the post-snowmelt decline in alpine soil microbial biomass. Soil Biology and Biochemistry, 32, 441–448.Google Scholar
Lugtenberg, B. (2015) Introduction to plant–microbe interactions. In: Lugtenberg, B. (Ed.) Principles of Plant–Microbe Interactions. Cham: Springer.Google Scholar
Lüscher, A, Mueller-Harvey, I, Soussana, JF, et al. (2014) Potential of legume-based grassland–livestock systems in Europe: A review. Grass and Forage Science, 69, 206–228.Google Scholar
Lydolph, MC, Jacobsen, J, Arctander, P, et al. (2005) Beringian paleoecology inferred from permafrost-preserved fungal DNA. Applied and Environmental Microbiology, 71, 1012–1017.Google Scholar
Malhi, Y, Baldocchi, DD, Jarvis, PG. (1999) The carbon balance of tropical, temperate and boreal forests. Plant, Cell & Environment, 22, 715–740.Google Scholar
Mangan, SA, Schnitzer, SA, Herre, EA, et al. (2010) Negative plant–soil feedback predicts tree-species relative abundance in a tropical forest. Nature, 466, 752–755.Google Scholar
Mapelli, F, Marasco, R, Balloi, A, et al. (2012) Mineral–microbe interactions: Biotechnological potential of bioweathering. Journal of Biotechnology, 157, 473–481.Google Scholar
Mapelli, F, Marasco, R, Rolli, E, et al. (2013) Potential for plant growth promotion of Rhizobacteria associated with Salicornia growing in Tunisian hypersaline soils. BioMed Research International, 2013, 248078.Google Scholar
Margesin, R. (2012) Psychrophilic microorganisms in alpine soils. In: Lütz, C. (Ed.) Plants in Alpine Regions. Vienna: Springer.Google Scholar
Maron, JL, Marler, M, Klironomos, JN, et al. (2011) Soil fungal pathogens and the relationship between plant diversity and productivity. Ecology Letters, 14, 36–41.Google Scholar
Marques, AC, de Oliveira, LB, Nicoloso, FT, et al. (2017) Biological nitrogen fixation in C4 grasses of different growth strategies of South America natural grasslands. Applied Soil Ecology, 113, 54–62.Google Scholar
Millard, P, Singh, BK. (2010) Does grassland vegetation drive soil microbial diversity? Nutrient Cycling in Agroecosystems, 88, 147–158.Google Scholar
Millet, M, Wortham, H, Sanusi, A, et al. (1997) Low molecular weight organic acids in fogwater in an urban area: Strasbourg (France). Science of the Total Environment, 206, 57–65.Google Scholar
Morales, SE, Mouser, PJ, Ward, N, et al. (2006) Comparison of bacterial communities in New England Sphagnum bogs using terminal restriction fragment length polymorphism (T-RFLP). Microbial Ecology, 52, 34–44.Google Scholar
Nadeem, SM, Ahmad, M, Zahir, ZA, et al. (2014) The role of mycorrhizae and plant growth promoting rhizobacteria (PGPR) in improving crop productivity under stressful environments. Biotechnology Advances, 32, 429–448.Google Scholar
Needelman, BA. (2013) What are soils? Nature Education Knowledge, 4, 2.Google Scholar
Nehls, U, Plassard, C. (2018) Nitrogen and phosphate metabolism in ectomycorrhizas. New Phytologist, 220, 1047–1058.Google Scholar
Newsham, KK, Fitter, AH, Watkinson, AR. (1995) Arbuscular mycorrhiza protect an annual grass from root pathogenic fungi in the field. Journal of Ecology, 83, 991–1000.Google Scholar
Nicolitch, O, Colin, Y, Turpault, MP, et al. (2016) Soil type determines the distribution of nutrient mobilizing bacterial communities in the rhizosphere of beech trees. Soil Biology and Biochemistry, 103, 429–445.Google Scholar
Ochoa-Hueso, R, Delgado-Baquerizo, M, King, PT, et al. (2019) Ecosystem type and resource quality are more important than global change drivers in regulating early stages of litter decomposition. Soil Biology and Biochemistry, 129, 144–152.Google Scholar
Oliver, TH, Heard, MS, Isaac, NJ, et al. (2015) Biodiversity and resilience of ecosystem functions. Trends in Ecology & Evolution, 30, 673–684.Google Scholar
Oquist, MG, Sparrman, T, Klemedtsson, L, et al. (2009) Water availability controls microbial temperature responses in frozen soil CO2 production. Global Change Biology, 15, 2715–2722.Google Scholar
Page, SE, Rieley, JO, Banks, CJ. (2011) Global and regional importance of the tropical peatland carbon pool. Global Change Biology, 17, 798–818.Google Scholar
Pan, Y, Birdsey, RA, Fang, J, et al. (2011) A large and persistent carbon sink in the world’s forests. Science, 333, 988–993.Google Scholar
Pawlowski, J, Audic, S, Adl, S, et al. (2012) CBOL protist working group: Barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biology, 10, e1001419.Google Scholar
Prober, SM, Leff, JW, Bates, ST, et al. (2015) Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide. Ecology Letters, 18, 85–95.Google Scholar
Rasche, F, Knapp, D, Kaiser, C, et al. (2011) Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest. The ISME Journal, 5, 389–402.CrossRefGoogle ScholarPubMed
Reed, SC, Cleveland, CC, Townsend, AR. (2011) Functional ecology of free-living nitrogen fixation: A contemporary perspective. Annual Review of Ecology, Evolution, and Systematics, 42, 489–512.Google Scholar
Reinhart, KO. (2012) The organization of plant communities: Negative plant–soil feedbacks and semiarid grasslands. Ecology, 93, 2377–2385.Google Scholar
Reinsch, S, Koller, E, Sowerby, A, et al. (2017) Shrubland primary production and soil respiration diverge along European climate gradient. Scientific Reports, 7, 43952.Google Scholar
Reynolds, HL, Packer, A, Bever, JD, et al. (2003) Grassroots ecology: Plant–microbe–soil interactions as drivers of plant community structure and dynamics. Ecology, 84, 2281–2291.Google Scholar
Rhoden, SA, Garcia, A, Santos, E, et al. (2015) Phylogenetic analysis of endophytic bacterial isolates from leaves of the medicinal plant Trichilia elegans A. Juss. (Meliaceae). Genetics and Molecular Research, 14, 1515–1525.Google Scholar
Richardson, AE, Simpson, RJ. (2011). Update on microbial phosphorus soil microorganisms mediating phosphorus availability. Plant Physiology, 156, 989–996.Google Scholar
Richardson, AE, Barea, J-M, McNeill, AM, et al. (2009) Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant and Soil, 321, 305–339.Google Scholar
Rivkina, E, Shcherbakova, V, Laurinavichius, K, et al. (2007) Biogeochemistry of methane and methanogenic archaea in permafrost. FEMS Microbiology Ecology, 61, 1–5.Google Scholar
Roesch, LF, Fulthorpe, RR, Riva, A, et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. The ISME Journal, 1, 283–290.Google Scholar
Ruiz-Lozano, JM. (2003) Arbuscular mycorrhizal symbiosis and alleviation of osmotic stress. New perspectives for molecular studies.Mycorrhiza, 13, 309–317.Google Scholar
Sala, OE, Paruelo, JM, Sala, OE, et al. (1997) Ecosystem services in grasslands. In: Daily, GC (Ed.) Nature’s Services: Societal Dependence on Natural Ecosystems. Washington, DC: Island Press.Google Scholar
Schadt, CW, Martin, AP, Lipson, DA, et al. (2003) Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science, 301, 1359–1361.Google Scholar
Scheublin, TR, Logtestijn, RSPV, van der Heijden, MGA. (2007) Presence and identity of arbuscular mycorrhizal fungi influence competitive interactions between plant species. Journal of Ecology, 95, 631–638.Google Scholar
Schimel, JP, Bennett, J. (2004) Nitrogen mineralization: Challenges of a changing paradigm. Ecology, 85, 591–602.Google Scholar
Schimel, J, Schaeffer, SM. (2012) Microbial control over carbon cycling in soil. Frontiers in Microbiology, 26, 348.Google Scholar
Schlesinger, WH, Andrews, JA. (2000) Soil respiration and the global carbon cycle. Biogeochemistry, 48, 7–20.Google Scholar
Semchenko, M, Leff, JW, Lozano, YM, et al. (2018) Fungal diversity regulates plant–soil feedbacks in temperate grassland. Science Advances, 4, eaau4578.Google Scholar
Sharma, S, Szele, Z, Schilling, R, et al. (2006) Influence of freeze–thaw stress on the structure and function of microbial communities and denitrifying populations in soil. Applied and Environmental Microbiology, 72, 2148–2154.Google Scholar
Shelef, O, Helman, Y, Behar, A, et al. (2013) Tri-party underground symbiosis between a weevil, bacteria and a desert plant. PLoS ONE, 8, e76588.Google Scholar
Shukla, KP, Sharma, S, Singh, NK, et al. (2011) Nature and role of root exudates: Efficacy in bioremediation. African Journal of Biotechnology, 10, 9717–9724.Google Scholar
Silvertown, J, Poulton, P, Johnston, E, et al. (2006) The Park Grass Experiment 1856–2006: Its contribution to ecology. Journal of Ecology, 94, 801–814.Google Scholar
Singh, BK, Bardgett, RD, Smith, P, et al. (2010) Microorganisms and climate change: Terrestrial feedbacks and mitigation options. Nature Reviews Microbiology, 8, 779–790.Google Scholar
Smith, SE, Gianinazzi-Pearson, V. (1988) Physiological interactions between symbionts in vesicular–arbuscular mycorrhizal plants. Annual Review of Plant Physiology and Plant Molecular Biology, 39, 221–244.Google Scholar
Smith, SE, Read, DJ. (2008) Mycorrhizal Symbiosis, 3rd edition. New York, NY: Academic Press.Google Scholar
Šnajdr, J, Valášková, V, Merhautová, V, et al. (2008) Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil. Soil Biology and Biochemistry, 40, 2068–2075.Google Scholar
Solly, EF, Schöning, I, Boch, S, et al. (2014) Factors controlling decomposition rates of fine root litter in temperate forests and grasslands. Plant and Soil, 382, 203–218.Google Scholar
Sterngren, AE, Hallin, S, Bengtson, P. (2015) Archaeal ammonia oxidizers dominate in numbers, but bacteria drive gross nitrification in N-amended grassland soil. Frontiers in Microbiology, 6, 1350.Google Scholar
Strullu-Derrien, C, Selosse, MA, Kenrick, P, Martin, FM. (2018) The origin and evolution of mycorrhizal symbioses: From palaeomycology to phylogenomics. New Phytologist, 220, 1012–1030.Google Scholar
Sturm, M, Racine, C, Tape, K. (2001) Climate change: Increasing shrub abundance in the Arctic. Nature, 411, 546–547.Google Scholar
Štursová, M, Baldrian, P. (2011) Effects of soil properties and management on the activity of soil organic matter transforming enzymes and the quantification of soil-bound and free activity. Plant and Soil, 338, 99–110.Google Scholar
Štursová, M, Žifčáková, L, Leigh, MB, et al. (2012) Cellulose utilization in forest litter and soil: Identification of bacterial and fungal decomposers. FEMS Microbiology Ecology, 80, 735–746.Google Scholar
Talbot, JM, Allison, SD, Treseder, KK. (2008) Decomposers in disguise: Mycorrhizal fungi as regulators of soil C dynamics in ecosystems under global change. Functional Ecology, 22, 955–963.Google Scholar
Tedersoo, L, Bahram, M, Toots, M, et al. (2012) Towards global patterns in the diversity and community structure of ectomycorrhizal fungi. Molecular Ecology, 21, 4160–4170.Google Scholar
Tedersoo, L, Bahram, M, Cajthaml, T, et al. (2016) Tree diversity and species identity effects on soil fungi, protists and animals are context dependent. The ISME Journal, 10, 346–362.Google Scholar
Tibbett, M. (2002) Ectomycorrhizal symbiosis can enhance plant nutrition through improved access to discrete organic nutrient patches of high resource quality. Annals of Botany, 89, 783–789.Google Scholar
Tilman, D, Wedin, D. (1991) Dynamics of nitrogen competition between successional grasses. Ecology, 72, 1038–1049.Google Scholar
Tilman, D, Reich, PB, Knops, J, et al. (2001) Diversity and productivity in a long-term grassland experiment. Science, 294, 843–845.Google Scholar
Trap, J, Bonkowski, M, Plassard, C, et al. (2016) Ecological importance of soil bacterivores for ecosystem functions. Plant and Soil, 398, 1–24.Google Scholar
Trinder, CJ, Johnson, D, Artz, RR. (2008) Interactions among fungal community structure, litter decomposition and depth of water table in a cutover peatland. FEMS Microbiology Ecology, 64, 433–448.Google Scholar
Urbanová, M, Šnajdr, J, Baldrian, P. (2015) Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees. Soil Biology and Biochemistry, 84, 53–64.Google Scholar
Uroz, S, Calvaruso, C, Turpault, MP, et al. (2009) Efficient mineral weathering is a distinctive functional trait of the bacterial genus Collimonas. Soil Biology and Biochemistry, 41, 2178–2186.Google Scholar
Uroz, S, Kelly, LC, Turpault, MP, et al. (2015) The mineralosphere concept: Mineralogical control of the distribution and function of mineral-associated bacterial communities. Trends in Microbiology, 23, 751–762.Google Scholar
Uroz, S, Oger, P, Tisserand, E, et al. (2016) Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. Scientific Reports, 6, 27756.Google Scholar
van der Heijden, MGA, Horton, TR. (2009) Socialism in soil? The importance of mycorrhizal fungal networks for facilitation in natural ecosystems. Journal of Ecology, 97, 1139–1150.Google Scholar
van der Heijden, MG, Klironomos, JN, Ursic, M, et al. (1998) Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature, 396, 69–72.Google Scholar
van der Heijden, MGA, Bardgett, RD, van Straalen, NM. (2008) The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology Letters, 11, 296–310.Google Scholar
van der Putten, WH, Bardgett, RD, Bever, JD, et al. (2013) Plant–soil feedbacks: The past, the present and future challenges. Journal of Ecology, 101, 265–276.Google Scholar
van der Putten, WH, Bradford, MA, Pernilla Brinkman, E, et al. (2016) Where, when and how plant–soil feedback matters in a changing world. Functional Ecology, 30, 1109–1121.Google Scholar
van Dommelen, A, Vanderleyden, J. (2007) Associative nitrogen fixation. In: Bothe, H, Ferguson, SJ, Newton, WE. (Eds.) Biology of the Nitrogen Cycle. Amsterdam: Elsevier.Google Scholar
Vance, CP. (2001) Symbiotic nitrogen fixation and phosphorus acquisition: Plant nutrition in a world of declining renewable resources. Plant Physiology, 127, 390–397.Google Scholar
Venter, PC, Nitsche, F, Domonell, A, et al. (2017) The protistan microbiome of grassland soil: Diversity in the mesoscale. Protist, 168, 546–564.Google Scholar
Vicente-Serrano, SM, Gouveia, C, Camarero, JJ, et al. (2013) Response of vegetation to drought time-scales across global land biomes. Proceedings of the National Academy of Sciences, 110, 52–57.Google Scholar
Vishnivetskaya, TA, Petrova, MA, Urbance, J, et al. (2006) Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods. Astrobiology, 6, 400–414.Google Scholar
Vogelsang, KM, Reynolds, HL, Bever, JD. (2006) Mycorrhizal fungal identity and richness determine the diversity and productivity of a tallgrass prairie system. New Phytologist, 172, 554–562.Google Scholar
Wagner, D, Gattinger, A, Embacher, A, et al. (2007) Methanogenic activity and biomass in Holocene permafrost deposits of the Lena Delta, Siberian Arctic and its implication for the global methane budget. Global Change Biology, 13, 1089–1099.Google Scholar
Wallander, H. (2006) External mycorrhizal mycelia – The importance of quantification in natural ecosystems. New Phytologist, 171, 240–242.Google Scholar
Wang, L, Dong, XP, Zhang, W, et al. (2011) Quantitative characters of microorganisms in permafrost at different depths and their relation to soil physicochemical properties. Journal of Glaciology and Geocryology, 2, 436–441.Google Scholar
Wehner, J, Antunes, PM, Powell, JR, et al. (2011) Indigenous arbuscular mycorrhizal fungal assemblages protect grassland host plants from pathogens. PLoS ONE, 6, e27381.Google Scholar
Weigelt, A, Bol, R, Bardgett, RD. (2005) Preferential uptake of soil nitrogen forms by grassland plant species. Oecologia, 142, 627–635.Google Scholar
Weisser, WW, Roscher, C, Meyer, ST, et al. (2017) Biodiversity effects on ecosystem functioning in a 15-year grassland experiment: Patterns, mechanisms, and open questions. Basic and Applied Ecology, 23, 1–73.Google Scholar
White, RP, Murray, S, Rohweder, M. (2000) Pilot Analysis of Global Ecosystems: Grassland Ecosystems. Washington, DC: World Resources Institute.Google Scholar
Whitehead, DC. (1995) Grassland Nitrogen. Wallingford: CAB International.Google Scholar
Whitman, T, Neurath, R, Perera, A, et al. (2018) Microbial community assembly differs across minerals in a rhizosphere microcosm. Environmental Microbiology, 20, 4444–4460.Google Scholar
Williams, RT, Crawford, RL. (1983) Microbial diversity of Minnesota peatlands. Microbial Ecology, 9, 201–214.Google Scholar
Winsborough, C, Basiliko, N. (2010) Fungal and bacterial activity in northern peatlands. Geomicrobiology Journal, 27, 315–320.Google Scholar
Wu, X, Zhang, W, Liu, G, et al. (2012) Bacterial diversity in the foreland of the Tianshan No. 1 glacier, China. Environmental Research Letters, 7, 014038.Google Scholar
Xu, J, Morris, PJ, Liu, J, et al. (2018) PEATMAP: Refining estimates of global peatland distribution based on a meta-analysis. Catena, 160, 134–40.CrossRefGoogle Scholar
Xu, Y, Rossi, F, Colica, G, et al. (2013) Use of cyanobacterial polysaccharides to promote shrub performances in desert soils: A potential approach for the restoration of desertified areas. Biology and Fertility of Soils, 49, 143–152.Google Scholar
Yergeau, E, Kowalchuk, GA. (2008) Responses of Antarctic soil microbial communities and associated functions to temperature and freeze–thaw cycle frequency. Environmental Microbiology, 10, 2223–2235.Google Scholar
Zhang, G, Niu, F, Ma, X, et al. (2007) Phylogenetic diversity of bacteria isolates from the Qinghai–Tibet Plateau permafrost region. Canadian Journal of Microbiology, 53, 1000–1010.Google Scholar
Zhang, N, Wang, D, Liu, Y, et al. (2014) Effects of different plant root exudates and their organic acid components on chemotaxis, biofilm formation and colonization by beneficial rhizosphere-associated bacterial strains. Plant and Soil, 374, 689–700.Google Scholar
Zhou, J, Deng, Y, Shen, L, et al. (2016) Temperature mediates continental-scale diversity of microbes in forest soils. Nature Communications, 7, 12083.Google Scholar

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×