Abstract
The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.
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Adnan M, Zheng W, Islam W et al (2018) Carbon catabolite repression in filamentous Fungi. Int J Mol Sci 19:48. https://doi.org/10.3390/ijms19010048
Ahmad F, Husain FM, Ahmad I et al (2011) Rhizosphere and root colonization by bacterial inoculants and their monitoring methods: A critical area in PGPR research. In: Ahmad I, Ahmad F, Pichtel J (ed) Microbes and Microbial Technology: Agricultural and Environmental Applications. Springer Nature, Switzerland, pp 363–391. https://doi.org/10.1007/978-1-4419-7931-5_14
Ali H, Khan E, Sajad MA (2013) Phytoremediation of heavy metals-concepts and applications. Chemosphere 91:869–881
Amundson R (2013) Soil formation. In: Holland HD, Turekian KK (eds) Treatise on geochemistry, 2nd edn. Elsevier Science, USA, pp 1–26. https://doi.org/10.1016/B978-0-08-095975-7.00501-5
Andika IB, Kondo H, Sun L (2016) Interplays between soil-borne plant viruses and RNA silencing-mediated antiviral defense in roots. Front Microbiol 7. https://doi.org/10.3389/fmicb.2016.01458
Angel R, Soares MIM, Ungar ED, Gillor O (2010) Biogeography of soil archaea and bacteria along a steep precipitation gradient. ISME J 4:553–563. https://doi.org/10.1038/ismej.2009.136
Angel R, Claus P, Conrad R (2012) Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J 6:847–862. https://doi.org/10.1038/ismej.2011.141
Angle JC, Morin TH, Solden LM et al (2017) Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions. Nat Commun 8:1567. https://doi.org/10.1038/s41467-017-01753-4
Armada E, Azcón R, López-Castillo OM et al (2015) Autochthonous arbuscular mycorrhizal fungi and Bacillus thuringiensis from a degraded Mediterranean area can be used to improve physiological traits and performance of a plant of agronomic interest under drought conditions. Plant Physiol Biochem 90:64–74. https://doi.org/10.1016/j.plaphy.2015.03.004
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
Avery LM, Lewis Smith RI, West HM (2003) Response of rhizosphere microbial communities associated with Antarctic hairgrass (Deschampsia antarctica) to UV radiation. Polar Biol 26:525–529. https://doi.org/10.1007/s00300-003-0515-y
Bachar A, Al-Ashhab A, Soares MIM et al (2010) Soil microbial abundance and diversity along a low precipitation gradient. Microb Ecol 60:453–461. https://doi.org/10.1007/s00248-010-9727-1
Bahram M, Põlme S, Kõljalg U et al (2012) Regional and local patterns of ectomycorrhizal fungal diversity and community structure along an altitudinal gradient in the Hyrcanian forests of northern Iran. New Phytol 193:465–473. https://doi.org/10.1111/j.1469-8137.2011.03927.x
Bakker PAHM, Berendsen RL, Doornbos RF et al (2013) The rhizosphere revisited: root microbiomics. Front Plant Sci 4:165. https://doi.org/10.3389/fpls.2013.00165
Baldrian P (2003) Interactions of heavy metals with white-rot fungi. Enzym Microb Technol 32:78–91. https://doi.org/10.1016/S0141-0229(02)00245-4
Banerjee S, Helgason B, Wang L et al (2016) Legacy effects of soil moisture on microbial community structure and N2O emissions. Soil Biol Biochem 95:40–50. https://doi.org/10.1016/j.soilbio.2015.12.004
Bar-On YM, Phillips R, Milo R (2018) The biomass distribution on Earth. Proc Natl Acad Sci U S A 115:6506–6511. https://doi.org/10.1073/pnas.1711842115
Barriuso J, Ramos Solano B, Fray RG et al (2008) Transgenic tomato plants alter quorum sensing in plant growth-promoting rhizobacteria. Plant Biotechnol J 6:442–452. https://doi.org/10.1111/j.1467-7652.2008.00331.x
Bass D, Richards TA (2011) Three reasons to re-evaluate fungal diversity “on Earth and in the ocean”. Fungal Biol Rev 25:159–164. https://doi.org/10.1016/j.fbr.2011.10.003
Bastida F, Torres IF, Hernández T, García C (2017) The impacts of organic amendments: do they confer stability against drought on the soil microbial community? Soil Biol Biochem 113:173–183. https://doi.org/10.1016/j.soilbio.2017.06.012
Bates ST, Berg-Lyons D, Caporaso JG et al (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5:908–917. https://doi.org/10.1038/ismej.2010.171
Beauregard MS, Hamel C, Atul-Nayyar S-AM (2010)Long-term phosphorus fertilization impacts soil fungal and bacterial diversity but not AM fungal community in alfalfa. Microb Ecol 59:379–389. https://doi.org/10.1007/s00248-009-9583-z
Bell T, Thomson BC, Bailey M et al (2011) The bacterial biogeography of British soils. Environ Microbiol 13:1642–1654. https://doi.org/10.1111/j.1462-2920.2011.02480.x
Bender SF, Wagg C, van der Heijden MGA (2016) An underground revolution: biodiversity and soil ecological engineering for agricultural sustainability. Trends Ecol Evol 31:440–452. https://doi.org/10.1016/j.tree.2016.02.016
Bengtson P, Sterngren AE, Rousk J (2012) Archaeal abundance across a pH gradient in an arable soil and its relationship to bacterial and fungal growth rates. Appl Environ Microbiol 78:5906–5911. https://doi.org/10.1128/AEM.01476-12
Berendsen RL, Pieterse CMJ, Bakker PAHM (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486. https://doi.org/10.1016/j.tplants.2012.04.001
Berndt R (2012) Species richness, taxonomy and peculiarities of the neotropical rust fungi: are they more diverse in the Neotropics? Biodivers Conserv 21:2299–2322. https://doi.org/10.1007/s10531-011-0220-z
Berruti A, Lumini E, Balestrini R, Bianciotto V (2016) Arbuscular mycorrhizal fungi as natural biofertilizers: let’s benefit from past successes. Front Microbiol 6:1559. https://doi.org/10.3389/fmicb.2015.01559
Bhattacharyya PN, Jha DK (2012) Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28:1327–1350. https://doi.org/10.1007/s11274-011-0979-9
Bhattacharyya A, Majumder NS, Basak P et al (2015) Diversity and distribution of archaea in the mangrove sediment of sundarbans. Archaea 2015:1–14. https://doi.org/10.1155/2015/968582
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
Bonkowski M, Brandt F (2002) Do soil protozoa enhance plant growth by hormonal effects? Soil Biol Biochem 34:1709–1715. https://doi.org/10.1016/S0038-0717(02)00157-8
Brader G, Compant S, Mitter B et al (2014) Metabolic potential of endophytic bacteria. Curr Opin Biotechnol 27:30–37. https://doi.org/10.1016/j.copbio.2013.09.012
Bragard C, Caciagli P, Lemaire O et al (2013) Status and prospects of plant virus control through interference with vector transmission. Annu Rev Phytopathol 51:177–201. https://doi.org/10.1146/annurev-phyto-082712-102346
Bryant JA, Lamanna C, Morlon H et al (2008) Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proc Natl Acad Sci U S A 105:11505–11511. https://doi.org/10.1073/pnas.0801920105
Buil JB, Zoll J, Verweij PE et al (2017) Mycology. In: Pelt-Verkuil EV, van Leeuwen WB, te Witt R (eds) Molecular diagnostics: part 2: clinical, veterinary, agrobotanical and food safety applications. Springer Nature, Singapore, pp 51–74. https://doi.org/10.1007/978-981-10-4511-0_4
Bukin SV, Pavlova ON, Manakov AY et al (2016) The ability of microbial community of Lake Baikal bottom sediments associated with gas discharge to carry out the transformation of organic matter under thermobaric conditions. Front Microbiol 7:690. https://doi.org/10.3389/fmicb.2016.00690
Bulgarelli D, Schlaeppi K, Spaepen S et al (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838. https://doi.org/10.1146/annurev-arplant-050312-120106
Bulgarelli D, Garrido-Oter R, Münch PC et al (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17:392–403. https://doi.org/10.1016/j.chom.2015.01.011
Butterly CR, Phillips LA, Wiltshire JL et al (2016)Long-term effects of elevated CO2 on carbon and nitrogen functional capacity of microbial communities in three contrasting soils. Soil Biol Biochem 97:157–167. https://doi.org/10.1016/j.soilbio.2016.03.010
Capdevila S, Martínez-Granero FM, Sánchez-Contreras M et al (2004) Analysis of Pseudomonas fluorescens F113 genes implicated in flagellar filament synthesis and their role in competitive root colonization. Microbiology 150:3889–3897. https://doi.org/10.1099/mic.0.27362-0
Carson JK, Gonzalez-Quiñones V, Murphy DV et al (2010) Low pore connectivity increases bacterial diversity in soil. Appl Environ Microbiol 76:3936–3942. https://doi.org/10.1128/AEM.03085-09
Cassman NA, Leite MFA, Pan Y et al (2016) Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland. Sci Rep 6:23680. https://doi.org/10.1038/srep23680
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
Cazorla FM, Codina JC, Abad C et al (2008)62-kb plasmids harboring rulAB homologues confer UV-tolerance and epiphytic fitness to Pseudomonas syringae pv. syringae mango isolates. Microb Ecol 56:283–291. https://doi.org/10.1007/s00248-007-9346-7
Cha S, Chae HM, Lee SH, Shim JK (2017) Effect of elevated atmospheric CO2 concentration on growth and leaf litter decomposition of Quercus acutissima and Fraxinus rhynchophylla. PLoS One 12:e0171197. https://doi.org/10.1371/journal.pone.0171197
Chen QH, Xu RL, Tam NFY et al (2008) Use of ciliates (Protozoa: Ciliophora) as bioindicator to assess sediment quality of two constructed mangrove sewage treatment belts in southern China. Mar Pollut Bull 57:689–694. https://doi.org/10.1016/j.marpolbul.2008.03.015
Chodak M, Klimek B, Azarbad H, Jaźwa M (2015) Functional diversity of soil microbial communities under Scots pine, Norway spruce, silver birch and mixed boreal forests. Pedobiologia (Jena) 58:81–88. https://doi.org/10.1016/j.pedobi.2015.04.002
Chu H, Neufeld JD, Walker VK, Grogan P (2011) The influence of vegetation type on the dominant soil bacteria, archaea, and fungi in a low arctic tundra landscape. Soil Sci Soc Am J 75:1756–1765. https://doi.org/10.2136/sssaj2011.0057
Church M, Böttjer D (2013) Diversity, ecology, and biogeochemical influence of N2-fixing microorganisms in the sea. In: Levin SA (ed) Encyclopedia of biodiversity, 2nd edn. Academic, Waltham, pp 608–825. https://doi.org/10.1016/B978-0-12-384719-5.00403-2
Clark CM, Cleland EE, Collins SL et al (2007) Environmental and plant community determinants of species loss following nitrogen enrichment. Ecol Lett 10:596–607. https://doi.org/10.1111/j.1461-0248.2007.01053.x
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
Cortois R, Schröder-Georgi T, Weigelt A et al (2016)Plant–soil feedbacks: role of plant functional group and plant traits. J Ecol 104:1608–1617. https://doi.org/10.1111/1365-2745.12643
Crowther TW, Maynard DS, Leff JW et al (2014) Predicting the responsiveness of soil biodiversity to deforestation: a cross-biome study. Glob Chang Biol 20:2983–2994. https://doi.org/10.1111/gcb.12565
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. Mol Ecol 26:4085–4098. https://doi.org/10.1111/mec.14175
de Araujo ASF, Mendes LW, Lemos LN et al (2018) Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado. Commun Biol 1:135. https://doi.org/10.1038/s42003-018-0129-0
de Campos SB, Youn JW, Farina R et al (2013) Changes in root bacterial communities associated to two different development stages of canola (Brassica napus L. var oleifera) evaluated through next-generation sequencing technology. Microb Ecol 65:593–601. https://doi.org/10.1007/s00248-012-0132-9
Degens BP, Schipper LA, Sparling GP, Vojvodic-Vukovic M (2000) Decreases in organic C reserves in soils can reduce the catabolic diversity of soil microbial communities. Soil Biol Biochem 32:189–196. https://doi.org/10.1016/S0038-0717(99)00141-8
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
Delgado-Baquerizo M, Oliverio AM, Brewer TE et al (2018) A global atlas of the dominant bacteria found in soil. Science 359:320–325. https://doi.org/10.1126/science.aap9516
Delmont TO, Robe P, Cecillon S et al (2011) Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol 77:1315–1324. https://doi.org/10.1128/AEM.01526-10
Deltedesco E, Keiblinger KM, Piepho H-P et al (2020) Soil microbial community structure and function mainly respond to indirect effects in a multifactorial climate manipulation experiment. Soil Biol Biochem 142:107704. https://doi.org/10.1016/j.soilbio.2020.107704
Ding J, Jiang X, Guan D et al (2017) Influence of inorganic fertilizer and organic manure application on fungal communities in a long-term field experiment of Chinese Mollisols. Appl Soil Ecol 111:114–122. https://doi.org/10.1016/j.apsoil.2016.12.003
Donnarumma F, Bazzicalupo M, Blažinkov M et al (2014) Biogeography of Sinorhizobium meliloti nodulating alfalfa in different Croatian regions. Res Microbiol 165:508–516. https://doi.org/10.1016/j.resmic.2014.06.001
Doty SL, Oakley B, Xin G et al (2009) Diazotrophic endophytes of native black cottonwood and willow. Symbiosis 47:23–33. https://doi.org/10.1007/BF03179967
Dressaire E, Yamada L, Song B, Roper M (2016) Mushrooms use convectively created airflows to disperse their spores. Proc Natl Acad Sci U S A 113:2833–2838. https://doi.org/10.1073/pnas.1509612113
Dupuy LX, Silk WK (2016) Mechanisms of early microbial establishment on growing root surfaces. Vadose Zo J 15:vzj2015.06.0094. https://doi.org/10.2136/vzj2015.06.0094
Durand PM, Sym S, Michod RE (2016) Programmed cell death and complexity in microbial systems. Curr Biol 26:R587–R593. https://doi.org/10.1016/j.cub.2016.05.057
Egamberdiyeva D (2007) The effect of plant growth promoting bacteria on growth and nutrient uptake of maize in two different soils. Appl Soil Ecol 36:184–189. https://doi.org/10.1016/j.apsoil.2007.02.005
Egan C, Li DW, Klironomos J (2014) Detection of arbuscular mycorrhizal fungal spores in the air across different biomes and ecoregions. Fungal Ecol 12:26–31. https://doi.org/10.1016/j.funeco.2014.06.004
Engel A, Borchard C, Piontek J et al (2013) CO2 increases 14C primary production in an Arctic plankton community. Biogeosciences 10:1291–1308. https://doi.org/10.5194/bg-10-1291-2013
Eriksson O, Wikström S, Eriksson Å, Lindborg R (2006)Species-rich Scandinavian grasslands are inherently open to invasion. Biol Invasions 8:355–363. https://doi.org/10.1007/s10530-004-4720-6
Ettema CH, Wardle DA (2002) Spatial soil ecology. Trends Ecol Evol 17:177–183. https://doi.org/10.1016/S0169-5347(02)02496-5
Faure D, Vereecke D, Leveau JHJ (2009) Molecular communication in the rhizosphere. Plant Soil 321:279–303. https://doi.org/10.1007/s11104-008-9839-2
Fazi S, Ungaro F, Venturi S et al (2019) Microbiomes in soils exposed to naturally high concentrations of CO2 (Bossoleto Mofette Tuscany, Italy). Front Microbiol 10:2238. https://doi.org/10.3389/fmicb.2019.02238
Fierer N (2017) Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol 15:579–590. https://doi.org/10.1038/nrmicro.2017.87
Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci 103:626–631. https://doi.org/10.1073/pnas.0507535103
Fierer N, Leff JW, Adams BJ et al (2012)Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci U S A 109:21390–21395. https://doi.org/10.1073/pnas.1215210110
Fitzpatrick CR, Copeland J, Wang PW et al (2018) Assembly and ecological function of the root microbiome across angiosperm plant species. Proc Natl Acad Sci U S A 115:E1157–E1165. https://doi.org/10.1073/pnas.1717617115
Foissner W (1999) Soil protozoa as bioindicators: pros and cons, methods, diversity, representative examples. Agric Ecosyst Environ 74:95–112. https://doi.org/10.1016/S0167-8809(99)00032-8
Formánek P, Rejšek K, Vranová V (2014) Effect of elevated CO2, O3 and UV radiation on soils. Sci World J. https://doi.org/10.1155/2014/730149
Gad SC (2014) Ozone. In: Wexler P (ed) Encyclopedia of toxicology, 3rd edn. Academic, USA, pp 747–750. https://doi.org/10.1016/B978-0-12-386454-3.00895-2
Garcia J, Kao-Kniffin J (2018) Microbial group dynamics in plant rhizospheres and their implications on nutrient cycling. Front Microbiol 9:1516. https://doi.org/10.3389/fmicb.2018.01516
Gehring CA, Mueller RC, Haskins KE et al (2014) Convergence in mycorrhizal fungal communities due to drought, plant competition, parasitism, and susceptibility to herbivory: consequences for fungi and host plants. Front Microbiol 5:306. https://doi.org/10.3389/fmicb.2014.00306
Golan JJ, Pringle A (2017)Long-distance dispersal of fungi. Microbiol Spectr 5:309–333. https://doi.org/10.1128/microbiolspec.funk-0047-2016
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
Gourmelon V, Maggia L, Powell JR et al (2016) Environmental and geographical factors structure soil microbial diversity in new caledonian ultramafic substrates: a metagenomic approach. PLoS One 11:e0167405. https://doi.org/10.1371/journal.pone.0167405
Griffin WT, Phelps TJ, Colwell FS, Fredrickson JK (2018) Methods for obtaining deep subsurface microbiological samples by drilling. In: Penny SA (ed) The microbiology of the terrestrial deep subsurface. CRC, Boca Raton, pp 23–44. https://doi.org/10.1201/9781351074568-3
Hamzah TNT, Lee SY, Hidayat A et al (2018) Diversity and characterization of endophytic fungi isolated from the tropical mangrove species, Rhizophora mucronata, and identification of potential antagonists against the soil-borne fungus, Fusarium solani. Front Microbiol 9:1707. https://doi.org/10.3389/fmicb.2018.01707
Hannula SE, Morriën E, De Hollander M et al (2017) Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. ISME J 11:2294–2304. https://doi.org/10.1038/ismej.2017.90
Hartmann A, Schmid M, van Tuinen D, Berg G (2009)Plant-driven selection of microbes. Plant Soil 321:235–257. https://doi.org/10.1007/s11104-008-9814-y
Hassani MA, Durán P, Hacquard S (2018) Microbial interactions within the plant holobiont. Microbiome 6:58. https://doi.org/10.1186/s40168-018-0445-0
Hawksworth DL (2001) The magnitude of fungal diversity: The 1.5 million species estimate revisited. Mycol Res 105:1422–1432. https://doi.org/10.1017/S0953756201004725
Hedrich S, Schippers A (2016) Distribution of acidophilic microorganisms in natural and man-made acidic environments. In: Quatrini R, Johnson DB (eds) Acidophiles: life in extremely acidic environments. Caister Academic Press, Norfolk, pp 153–176. https://doi.org/10.21775/9781910190333.10
Heeb S, Haas D (2001) Regulatory roles of the GacS/GacAtwo-component system in plant-associated and other Gram-negative bacteria. Mol Plant-Microbe Interact 14:1351–1363. https://doi.org/10.1094/MPMI.2001.14.12.1351
Heeb S, Haas D (2007) Regulatory roles of the GacS/GacATwo-component system in plant-associated and other Gram-negative bacteria. Mol Plant-Microbe Interact 14:1351–1363. https://doi.org/10.1094/mpmi.2001.14.12.1351
Hernandez-Garcia A, Kraft DJ, Janssen AFJ et al (2014) Design and self-assembly of simple coat proteins for artificial viruses. Nat Nanotechnol 9:698–702. https://doi.org/10.1038/nnano.2014.169
Horan N (2003) Protozoa. In: Mara D, Horan N (eds) Handbook of water and wastewater microbiology. Academic, San Diego, pp 69–76. https://doi.org/10.1016/B978-012470100-7/50005-4
Hrynkiewicz K, Toljander YK, Baum C et al (2012) Correspondence of ectomycorrhizal diversity and colonisation of willows (Salix spp.) grown in short rotation coppice on arable sites and adjacent natural stands. Mycorrhiza 22:603–613. https://doi.org/10.1007/s00572-012-0437-z
Hrynkiewicz K, Szymańska S, Piernik A, Thiem D (2015) Ectomycorrhizal community structure of Salix and Betula spp. at a saline site in central Poland in relation to the seasons and soil parameters. Water Air Soil Pollut 226:99. https://doi.org/10.1007/s11270-015-2308-7
Huber KJ, Geppert AM, Wanner G et al (2016) The first representative of the globally widespread subdivision 6 Acidobacteria, Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil. Int J Syst Evol Microbiol 66:2971–2979. https://doi.org/10.1099/ijsem.0.001131
Idrees A, Zhang H, Luo M et al (2017) Protein baits, volatile compounds and irradiation influence the expression profiles of odorant-binding protein genes in Bactrocera dorsalis (Diptera: Tephritidae). Appl Ecol Environ Res 15:1883–1899. https://doi.org/10.15666/aeer/1504_18831899
Igalavithana AD, Lee SS, Niazi NK et al (2017) Assessment of soil health in urban agriculture: soil enzymes and microbial properties. Sustain 9:310. https://doi.org/10.3390/su9020310
Intergovernmental Panel on Climate Change (2014) Climate change 2014. Mitigation of Climate Change. https://doi.org/10.1017/cbo9781107415416
Islam W, Qasim M, Noman A et al (2017) Genetic resistance in chickpea against Ascochyta blight: historical efforts and recent accomplishments. J Anim Plant Sci 27:1941–1957
Jacoby R, Peukert M, Succurro A et al (2017) The role of soil microorganisms in plant mineral nutrition—current knowledge and future directions. Front Plant Sci 8:1617. https://doi.org/10.3389/fpls.2017.01617
James EK (2016) Nitrogen Fixation. In: Thomas B, Murray BG, Murphy DJ (eds) Encyclopedia of applied plant sciences (second edition). Academic, San Diego, pp 271–277. https://doi.org/10.1016/B978-0-12-394807-6.00124-6
Jang JH, Woo SY, Kim SH et al (2017) Effects of increased soil fertility and plant growth-promoting rhizobacteria inoculation on biomass yield, energy value, and physiological response of poplar in short-rotation coppices in a reclaimed tideland: a case study in the Saemangeum area of Korea. Biomass Bioenergy 107:29–38. https://doi.org/10.1016/j.biombioe.2017.09.005
Jansson JK, Hofmockel KS (2020) Soil microbiomes and climate change. Nat Rev Microbiol 18:35–46. https://doi.org/10.1038/s41579-019-0265-7
Jha CK, Saraf M (2015) Plant growth promoting Rhizobacteria (PGPR): a review. J Agric Res Dev 5:108–119. https://doi.org/10.13140/RG.2.1.5171.2164
Johnson D, Vandenkoornhuyse PJ, Leake JR et al (2004) Plant communities affect arbuscular mycorrhizal fungal diversity and community composition in grassland microcosms. New Phytol 161:503–515. https://doi.org/10.1046/j.1469-8137.2003.00938.x
Johnston ER, Hatt JK, He Z et al (2019) Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths. Proc Natl Acad Sci U S A 116:15096–15105. https://doi.org/10.1073/pnas.1901307116
Kabil O, Vitvitsky V, Banerjee R (2014) Sulfur as a signaling nutrient through hydrogen sulfide. Annu Rev Nutr 34:171–205. https://doi.org/10.1146/annurev-nutr-071813-105654
Kang JW, Khan Z, Doty SL (2012) Biodegradation of trichloroethylene by an endophyte of hybrid poplar. Appl Environ Microbiol 78:3504–3507. https://doi.org/10.1128/aem.06852-11
Kapulnik Y, Tsror L, Zipori I et al (2010) Effect of AMF application on growth, productivity and susceptibility to Verticillium wilt of olives grown under desert conditions. Symbiosis 52:103–111. https://doi.org/10.1007/s13199-010-0085-z
Karlsson AE, Johansson T, Bengtson P (2012) Archaeal abundance in relation to root and fungal exudation rates. FEMS Microbiol Ecol 80:305–311. https://doi.org/10.1111/j.1574-6941.2012.01298.x
Kembel SW, O’Connor TK, Arnold HK et al (2014) Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest. Proc Natl Acad Sci U S A 111:13715–13720. https://doi.org/10.1073/pnas.1216057111
Knoth JL, Kim SH, Ettl GJ, Doty SL (2014) Biological nitrogen fixation and biomass accumulation within poplar clones as a result of inoculations with diazotrophic endophyte consortia. New Phytol 201:599–609. https://doi.org/10.1111/nph.12536
Koch PL (1998) Isotopic reconstruction of past continental environments. Annu Rev Earth Planet Sci 26:573–613. https://doi.org/10.1146/annurev.earth.26.1.573
Koller R, Scheu S, Bonkowski M, Robin C (2013) Protozoa stimulate N uptake and growth of arbuscular mycorrhizal plants. Soil Biol Biochem 65:204–210. https://doi.org/10.1016/j.soilbio.2013.05.020
Kowalchuk GA, Stephen JR (2001)Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu Rev Microbiol 55:485–529. https://doi.org/10.1146/annurev.micro.55.1.485
Krome K, Rosenberg K, Bonkowski M, Scheu S (2009) Grazing of protozoa on rhizosphere bacteria alters growth and reproduction of Arabidopsis thaliana. Soil Biol Biochem 41:1866–1873. https://doi.org/10.1016/j.soilbio.2009.06.008
Kühdorf K, Münzenberger B, Begerow D et al (2016) Arbutoid mycorrhizas of the genus Cortinarius from Costa Rica. Mycorrhiza 26:497–513. https://doi.org/10.1007/s00572-016-0688-1
Kühne T (2009)Soil-borne viruses affecting cereals-known for long but still a threat. Virus Res 141:174–183. https://doi.org/10.1016/j.virusres.2008.05.019
Laforest-Lapointe I, Messier C, Kembel SW (2016) Host species identity, site and time drive temperate tree phyllosphere bacterial community structure. Microbiome 4:27. https://doi.org/10.1186/s40168-016-0174-1
Lagos ML, Maruyama F, Nannipieri P et al (2015) Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini-review. J Soil Sci Plant Nutr 15:504–523. https://doi.org/10.4067/S0718-95162015005000042
Lakshmanan V, Selvaraj G, Bais HP (2014) Functional soil microbiome: belowground solutions to an aboveground problem. Plant Physiol 166:689–700. https://doi.org/10.1104/pp.114.245811
Lal R (2015) Restoring soil quality to mitigate soil degradation. Sustain 7:5875–5895. https://doi.org/10.3390/su7055875
Lambers H, Clements JC, Nelson MN (2013) How aphosphorus-acquisition strategy based on carboxylate exudation powers the success and agronomic potential of lupines (Lupinus, Fabaceae). Am J Bot 100:263–288. https://doi.org/10.3732/ajb.1200474
Lareen A, Burton F, Schäfer P (2016) Plant root-microbe communication in shaping root microbiomes. Plant Mol Biol 90:575–587. https://doi.org/10.1007/s11103-015-0417-8
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
Lee S, Basu S, Tyler CW, Wei IW (2004) Ciliate populations as bio-indicators at Deer Island Treatment Plant. Adv Environ Res 8:371–378. https://doi.org/10.1016/S1093-0191(02)00118-1
Lee SH, Megonigal PJ, Langley AJ, Kang H (2017) Elevated CO2 and nitrogen addition affect the microbial abundance but not the community structure in salt marsh ecosystem. Appl Soil Ecol 117–118:129–136. https://doi.org/10.1016/j.apsoil.2017.04.004
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 U S A 112:10967–10972. https://doi.org/10.1073/pnas.1508382112
Levy-Booth DJ, Prescott CE, Grayston SJ (2014) Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems. Soil Biol Biochem 75:11–25. https://doi.org/10.1016/j.soilbio.2014.03.021
Lin Y-T, Jia Z, Wang D, Chiu C-Y(2017) Effects of temperature on the composition and diversity of bacterial communities in bamboo soils at different elevations. Biogeosciences 14:4879–4889. https://doi.org/10.5194/bg-14-4879-2017
Lipson DA, Wilson RF, Oechel WC (2005) Effects of elevated atmospheric CO2 on soil microbial biomass, activity, and diversity in a chaparral ecosystem. Appl Environ Microbiol 71:8573–8580. https://doi.org/10.1128/AEM.71.12.8573-8580.2005
Liu J, Sui Y, Yu Z et al (2015) Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of northeast China. Soil Biol Biochem 83:29–39. https://doi.org/10.1016/j.soilbio.2015.01.009
Liu Y, Zhang H, Xiong M et al (2017) Abundance and composition response of wheat field soil bacterial and fungal communities to elevated CO2 and increased air temperature. Biol Fertil Soils 53:3–8. https://doi.org/10.1007/s00374-016-1159-8
Liu X, Pan J, Liu Y et al (2018) Diversity and distribution of Archaea in global estuarine ecosystems. Sci Total Environ 637–638:349–358. https://doi.org/10.1016/j.scitotenv.2018.05.016
Lladó S, López-Mondéjar R, Baldrian P (2017) Forest soil bacteria: diversity, involvement in ecosystem processes, and response to global change. Microbiol Mol Biol Rev 81:e00063–e00016. https://doi.org/10.1128/mmbr.00063-16
Lloyd KG, Schreiber L, Petersen DG et al (2013) Predominant archaea in marine sediments degrade detrital proteins. Nature 496:215–218. https://doi.org/10.1038/nature12033
López-Bucio J, Pelagio-Flores R, Herrera-Estrella A (2015) Trichoderma as biostimulant: exploiting the multilevel properties of a plant beneficial fungus. Sci Hortic (Amsterdam) 196:109–123. https://doi.org/10.1016/j.scienta.2015.08.043
Lucas RW, Casper BB, Jackson JK, Balser TC (2007) Soil microbial communities and extracellular enzyme activity in the New Jersey pinelands. Soil Biol Biochem 39:2508–2519. https://doi.org/10.1016/j.soilbio.2007.05.008
Lugtenberg B, Kamilova F (2009)Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556. https://doi.org/10.1146/annurev.micro.62.081307.162918
Lynch MDJ, Neufeld JD (2015) Ecology and exploration of the rare biosphere. Nat Rev Microbiol 13:217–229. https://doi.org/10.1038/nrmicro3400
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
Martens-Habbena W, Berube PM, Urakawa H et al (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461:976–979. https://doi.org/10.1038/nature08465
Martin LM, Wilsey BJ (2015) Differences in beta diversity between exotic and native grasslands vary with scale along a latitudinal gradient. Ecology 96:1042–1051. https://doi.org/10.1890/14-0772.1
Massalha H, Korenblum E, Malitsky S et al (2017) Live imaging of root-bacteria interactions in a microfluidics setup. Proc Natl Acad Sci U S A 114:4549–4554. https://doi.org/10.1073/pnas.1618584114
Mei C, Flinn B (2009) The use of beneficial microbial endophytes for plant biomass and stress tolerance improvement. Recent Pat Biotechnol 4:81–95. https://doi.org/10.2174/187220810790069523
Mendes R, Kruijt M, De Bruijn I et al (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100. https://doi.org/10.1126/science.1203980
Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663. https://doi.org/10.1111/1574-6976.12028
Midgley GF (2012) Biodiversity and ecosystem function. Science 335:174–175. https://doi.org/10.1126/science.1217245
Miranda ARL, Mendes LW, Rocha SMB et al (2018) Responses of soil bacterial community after seventh yearly applications of composted tannery sludge. Geoderma 318:1–8. https://doi.org/10.1016/j.geoderma.2017.12.026
Mohan JE, Cowden CC, Baas P et al (2014) Mycorrhizal fungi mediation of terrestrial ecosystem responses to global change: mini-review. Fungal Ecol 10:3–19. https://doi.org/10.1016/j.funeco.2014.01.005
Montes MF (2016) Nitrification. In: Charles W (ed) Finkl. Encyclopedia of earth sciences series. Springer Nature, Cham, pp 455–456
Mora C, Tittensor DP, Adl S et al (2011) How many species are there on earth and in the ocean? PLoS Biol 9:e1001127. https://doi.org/10.1371/journal.pbio.1001127
Mosier AC, Li Z, Thomas BC et al (2015) Elevated temperature alters proteomic responses of individual organisms within a biofilm community. ISME J 9:180–194. https://doi.org/10.1038/ismej.2014.113
Müller DB, Vogel C, Bai Y, Vorholt JA (2016) The plant microbiota: systems-level insights and perspectives. Annu Rev Genet 50:211–234. https://doi.org/10.1146/annurev-genet-120215-034952
Myrold DD, Nannipieri P (2014) Classical techniques versus omics approaches. In: Nannipieri P, Pietramellara G, Renella G (eds) Omics in soil Science. Caster Academic Press, Norfolk, pp 179–187
Norby RJ, De Kauwe MG, Walker AP et al (2017) Comment on “Mycorrhizal association as a primary control of the CO2 fertilization effect”. Science 355:358. https://doi.org/10.1126/science.aai7976
Norris LE, Collene AL, Asp ML et al (2009) Comparison of dietary conjugated linoleic acid with safflower oil on body composition in obese postmenopausal women with type 2 diabetes mellitus. Am J Clin Nutr 90:468–476. https://doi.org/10.3945/ajcn.2008.27371
Nottingham AT, Bååth E, Reischke S et al (2019) Adaptation of soil microbial growth to temperature: using a tropical elevation gradient to predict future changes. Glob Chang Biol 25:827–838. https://doi.org/10.1111/gcb.14502
Nouri H, Chavoshi Borujeni S, Nirola R et al (2017) Application of green remediation on soil salinity treatment: a review on halophytoremediation. Process Saf Environ Prot 107:94–107. https://doi.org/10.1016/j.psep.2017.01.021
Nunan N, Daniell TJ, Singh BK et al (2005) Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques. Appl Environ Microbiol 71:6784–6792. https://doi.org/10.1128/AEM.71.11.6784-6792.2005
O’Brien SL, Gibbons SM, Owens SM et al (2016) Spatial scale drives patterns in soil bacterial diversity. Environ Microbiol 18:2039–2051. https://doi.org/10.1111/1462-2920.13231
Ochoa MS, Pedraza RM, Martínez M (2010) Plantas, hongos micorrízicos y bacterias : su compleja red de interacciones. Biológicas 12:65–71
Offre P, Spang A, Schleper C (2013) Archaea in biogeochemical cycles. Annu Rev Microbiol 67:437–457. https://doi.org/10.1146/annurev-micro-092412-155614
Oldroyd GED (2013) Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants. Nat Rev Microbiol 11:252–263. https://doi.org/10.1038/nrmicro2990
Pakostova E, Johnson DB, Bao Z et al (2020) Bacterial and archaeal diversity in sulfide-bearing waste rock at faro mine complex, Yukon Territory, Canada. Geomicrobiol J. https://doi.org/10.1080/01490451.2020.1731020
Pal A, Ghosh S, Paul AK (2006) Biosorption of cobalt by fungi from serpentine soil of Andaman. Bioresour Technol 97:1253–1258. https://doi.org/10.1016/j.biortech.2005.01.043
Panneerselvam P, Kumar U, Senapati A et al (2020) Influence of elevated CO2 on arbuscular mycorrhizal fungal community elucidated using Illumina MiSeq platform in sub-humid tropical paddy soil. Appl Soil Ecol 145:103344. https://doi.org/10.1016/j.apsoil.2019.08.006
Papenfort K, Bassler BL (2016) Quorum sensing signal-response systems in Gram-negative bacteria. Nat Rev Microbiol 14:576–588. https://doi.org/10.1038/nrmicro.2016.89
Paul EA, Coleman DC, Wall DH (2015) Chapter 5 – soil fauna: occurrence, biodiversity, and roles in ecosystem function. In: Paul EA (ed) Soil microbiology, ecology and biochemistry. Academic, San Diego, pp 111–149. https://doi.org/10.1016/B978-0-12-415955-6.00005-0
Pavao-Zuckerman MA (2018) Soil ecology. In: Fath B (ed) Encyclopedia of Ecology, 2nd edn. Elsevier, Amsterdam, pp 600–605. https://doi.org/10.1016/B978-0-444-63768-0.00850-7
Peay KG, Bruns TD (2014) Spore dispersal of basidiomycete fungi at the landscape scale is driven by stochastic and deterministic processes and generates variability in plant-fungal interactions. New Phytol 204:180–191. https://doi.org/10.1111/nph.12906
Peay KG, Schubert MG, Nguyen NH, Bruns TD (2012) Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules. Mol Ecol 21:4122–4136. https://doi.org/10.1111/j.1365-294X.2012.05666.x
Peay KG, Baraloto C, Fine PVA (2013) Strong coupling of plant and fungal community structure across western Amazonian rainforests. ISME J 7:1852–1861. https://doi.org/10.1038/ismej.2013.66
Peck MC, Fisher RF, Long SR (2006) Diverse flavonoids stimulate NodD1 binding to nod gene promoters in Sinorhizobium meliloti. J Bacteriol 188:5417–5427. https://doi.org/10.1128/JB.00376-06
Pepe A, Giovannetti M, Sbrana C (2016) Different levels of hyphal self-incompatibility modulate interconnectedness of mycorrhizal networks in three arbuscular mycorrhizal fungi within the Glomeraceae. Mycorrhiza 26:325–332. https://doi.org/10.1007/s00572-015-0671-2
Pérez-Jaramillo JE, Mendes R, Raaijmakers JM (2016) Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Mol Biol 90:635–644. https://doi.org/10.1007/s11103-015-0337-7
Perotto S, Angelini P, Bianciotto V et al (2013) Interactions of fungi with other organisms. Plant Biosyst 147:208–218. https://doi.org/10.1080/11263504.2012.753136
Perotto S, Daghino S, Martino E (2018) Ericoid mycorrhizal fungi and their genomes: another side to the mycorrhizal symbiosis? New Phytol 220:1141–1147
Peters JW, Boyd ES (2015) Exploring alternative paths for the evolution of biological nitrogen fixation. In: De Bruijn FJ (ed) Biological nitrogen fixation. Wiley, New York, pp 167–176. https://doi.org/10.1002/9781119053095.ch16
Petrokofsky G, Yang K, Reed J (2017) Trees for life: The ecosystem service contribution of trees to food production and livelihoods in the tropics.For Policy Econ 84:62–71. https://doi.org/10.1016/j.forpol.2017.01.012
Phosri C, Põlme S, Taylor AFS et al (2012) Diversity and community composition of ectomycorrhizal fungi in a dry deciduous dipterocarp forest in Thailand. Biodivers Conserv 21:2287–2298. https://doi.org/10.1007/s10531-012-0250-1
Poole P (2017) Shining a light on the dark world of plant root-microbe interactions. Proc Natl Acad Sci U S A 114:4281–4283. https://doi.org/10.1073/pnas.1703800114
Porras-Alfaro A, Herrera J, Natvig DO et al (2011) Diversity and distribution of soil fungal communities in a semiarid grassland. Mycologia 103:10–21. https://doi.org/10.3852/09-297
Prasad PVV, Kakani VG, Reddy KR (2016) Ozone depletion. In: Thomas B, Murray BG, Murphy DJ (ed) Encyclopedia of applied plant sciences. Academic, Sand Diego, pp 318–326.
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
Rädecker N, Pogoreutz C, Voolstra CR et al (2015) Nitrogen cycling in corals: the key to understanding holobiont functioning? Trends Microbiol 23:490–497. https://doi.org/10.1016/j.tim.2015.03.008
Radeva G, Kenarova A, Bachvarova V et al (2014) Phylogenetic diversity of archaea and the archaeal ammonia monooxygenase gene in uranium mining-impacted locations in Bulgaria. Archaea 2014:1–10. https://doi.org/10.1155/2014/196140
Ramirez KS, Leff JW, Barberán A et al (2014) Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally. Proc R Soc B Biol Sci 281:20141988–20141988. https://doi.org/10.1098/rspb.2014.1988
Ravishankara AR, Daniel JS, Portmann RW (2009) Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century. Science 326:123–125. https://doi.org/10.1126/science.1176985
Redeker KR, Cai LL, Dumbrell AJ et al (2018) Noninvasive analysis of the soil microbiome: biomonitoring strategies using the volatilome, community analysis, and environmental data. Adv Ecol Res 59:93–132. https://doi.org/10.1016/bs.aecr.2018.07.001
Reed J, van Vianen J, Foli S et al (2017) Trees for life: the ecosystem service contribution of trees to food production and livelihoods in the tropics. For Policy Econ 84:62–71. https://doi.org/10.1016/j.forpol.2017.01.012
Reef R, Feller IC, Lovelock CE (2010) Nutrition of mangroves. Tree Physiol 30:1148–1160. https://doi.org/10.1093/treephys/tpq048
Rees CED, Green LH, Goldman E, Loessner MJ (2015) Phage identification of bacteria. In: Goldman E, Green LH (eds) Practical handbook of microbiology, 3rd edn. CRC, Boca Raton, pp 99–114
Revell LE, Tummon F, Salawitch RJ et al (2015) The changing ozone depletion potential of N2O in a future climate. Geophys Res Lett 42:10047–10055. https://doi.org/10.1002/2015GL065702
Riedelsberger J, Blatt MR (2017) Editorial: Roots—the hidden provider. Front. Plant Sci 8:1021. https://doi.org/10.3389/fpls.2017.01021
Rillig MC, Mummey DL (2006) Mycorrhizas and soil structure. New Phytol 171:41–53. https://doi.org/10.1111/j.1469-8137.2006.01750.x
Rillig MC, Muller LAH, Lehmann A (2017) Soil aggregates as massively concurrent evolutionary incubators. ISME J 11:1943–1948. https://doi.org/10.1038/ismej.2017.56
Robinson DJ (2001) Plant viruses: soil-borne. Encyclopedia of life sciences. https://doi.org/10.1038/npg.els.0000761
Rochon D, Kakani K, Robbins M, Reade R (2004) Molecular aspects of plant virus transmission by olpidium and plasmodiophorid vectors. Annu Rev Phytopathol 42:211–241. https://doi.org/10.1146/annurev.phyto.42.040803.140317
Rønn R, Vestergård M, Ekelund F (2012) Interactions between bacteria, protozoa and nematodes in soil. Acta Protozool 51:223–235. https://doi.org/10.4467/16890027AP.12.018.0764
Rousk J, Bååth E, Brookes PC et al (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4:1340–1351. https://doi.org/10.1038/ismej.2010.58
Rout ME (2014) The plant microbiome. Adv Bot Res 69:279–309. https://doi.org/10.1016/B978-0-12-417163-3.00011-1
Ruamps LS, Nunan N, Pouteau V et al (2013) Regulation of soil organic C mineralisation at the pore scale. FEMS Microbiol Ecol 86:26–35. https://doi.org/10.1111/1574-6941.12078
Samarakoon M, Hyde K, Promputtha I et al (2016) Evolution of Xylariomycetidae (Ascomycota: Sordariomycetes) Samarakoon. Mycosphere 7:1746–1761. https://doi.org/10.5943/mycosphere
Santoro AE, Buchwald C, McIlvin MR, Casciotti KL (2011) Isotopic signature of N2O produced by marine ammonia-oxidizing archaea. Science 333:1282–1285. https://doi.org/10.1126/science.1208239
Santoyo G, Moreno-Hagelsieb G, del Carmen O-MM, Glick BR (2016) Plant growth-promoting bacterial endophytes. Microbiol Res 183:92–99. https://doi.org/10.1016/j.micres.2015.11.008
Santoyo G, Hernández-Pacheco C, Hernández-Salmerón J, Hernández-León R (2017) The role of abiotic factors modulating the plant-microbe-soil interactions: toward sustainable agriculture. A review. Spanish J Agric Res 15:e03R01. https://doi.org/10.5424/sjar/2017151-9990
Schimel J (2004) Playing scales in the methane cycle: from microbial ecology to the globe. Proc Natl Acad Sci U S A 101:12400–12401. https://doi.org/10.1073/pnas.0405075101
Schimel JP, Schaeffer SM (2012) Microbial control over carbon cycling in soil. Front Microbiol 3. https://doi.org/10.3389/fmicb.2012.00348
Schimel D, Melillo J, Tian H et al (2000) Contribution of increasing CO2 and climate to carbon storage by ecosystems in the United States. Science 287:2004–2006. https://doi.org/10.1126/science.287.5460.2004
Sena HH, Sanches MA, Rocha DFS et al (2018) Production of biosurfactants by soil fungi isolated from the amazon forest. Int J Microbiol 2018:1–8. https://doi.org/10.1155/2018/5684261
Shen C, Liang W, Shi Y et al (2014) Contrasting elevational diversity patterns between eukaryotic soil microbes and plants. Ecology 95:3190–3202. https://doi.org/10.1890/14-0310.1
Siddiqui ZA, Pichtel J (2008) Mycorrhizae: an overview. In: Siddiqui ZA, Akhtar MS, Futai K (eds) Sustainable agriculture and forestry. Springer, Dordrecht, pp 01–35. https://doi.org/10.1007/978-1-4020-8770-7_1
Siles JA, Margesin R (2016) Abundance and diversity of bacterial, archaeal, and fungal communities along an altitudinal gradient in alpine forest soils: what are the driving factors? Microb Ecol 72:207–220. https://doi.org/10.1007/s00248-016-0748-2
Simard SW, Beiler KJ, Bingham MA et al (2012) Mycorrhizal networks: mechanisms, ecology and modelling. Fungal Biol Rev 26:39–60. https://doi.org/10.1016/j.fbr.2012.01.001
Simonin M, Nunan N, Bloor JMG et al (2017)Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms. FEMS Microbiol Lett 364. https://doi.org/10.1093/femsle/fnx077
Singh BK, Munro S, Potts JM, Millard P (2007) Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils. Appl Soil Ecol 36:147–155. https://doi.org/10.1016/j.apsoil.2007.01.004
Singh D, Shi L, Adams JM (2013) Bacterial diversity in the mountains of South-West China: climate dominates over soil parameters. J Microbiol 51:439–447. https://doi.org/10.1007/s12275-013-2446-9
Smith S, Read D (2008) Mycorrhizal symbiosis. https://doi.org/10.1016/B978-0-12-370526-6.X5001-6
Smith SE, Smith FA (2012) Fresh perspectives on the roles of arbuscular mycorrhizal fungi in plant nutrition and growth. Mycologia 104:1–13. https://doi.org/10.3852/11-229
Snoeck D, Lacote R, Kéli J et al (2013) Association of hevea with other tree crops can be more profitable than hevea monocrop during first 12 years. Ind Crop Prod 43:578–586. https://doi.org/10.1016/j.indcrop.2012.07.053
Sorensen PO, Bhatnagar JM, Christenson L et al (2019) Roots mediate the effects of snowpack decline on soil bacteria, fungi, and nitrogen cycling in a northern hardwood forest. Front Microbiol 10:926. https://doi.org/10.3389/fmicb.2019.00926
Sousa RMS, Mendes LW, Antunes JEL et al (2020) Diversity and structure of bacterial community in rhizosphere of lima bean. Appl Soil Ecol 150. https://doi.org/10.1016/j.apsoil.2019.103490
Spang A, Stieglmeier M, Schintlmeister A et al (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci 108:8420–8425. https://doi.org/10.1073/pnas.1013488108
Sun OJ, Tang Z, You Y et al (2014) Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover. Ecol Evol 4:633–647. https://doi.org/10.1002/ece3.969
Sundin GW, Jacobs JL (1999) Ultraviolet radiation (UVR) sensitivity analysis and UVR survival strategies of a bacterial community from the phyllosphere of field-grown peanut (Arachis hypogeae L.). Microb Ecol 38:27–38. https://doi.org/10.1007/s002489900152
Suryantini R, Wulandari RS, Kasiamdari RS (2015) Orchid mycorrhizal fungi: Identification of Rhizoctonia from West Kalimantan. Microbiol Indones 9:157–162. https://doi.org/10.5454/mi.9.4.3
Syller J (2014) Biological and molecular events associated with simultaneous transmission of plant viruses by invertebrate and fungal vectors. Mol Plant Pathol 15:417–426. https://doi.org/10.1111/mpp.12101
Tamada T, Kondo H (2013) Biological and genetic diversity of plasmodiophorid-transmitted viruses and their vectors. J Gen Plant Pathol 79:307–320. https://doi.org/10.1007/s10327-013-0457-3
Tardif S, Yergeau É, Tremblay J et al (2016) The willow microbiome is influenced by soil petroleum-hydrocarbon concentration with plant compartment-specific effects. Front Microbiol 7:1363. https://doi.org/10.3389/fmicb.2016.01363
Taylor DL, Hollingsworth TN, McFarland JW et al (2014) A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning. Ecol Monogr 84:3–20. https://doi.org/10.1890/12-1693.1
Tayyab M, Islam W, Arafat Y et al (2018) Effect of sugarcane straw and goat manure on soil nutrient transformation and bacterial communities. Sustainability 10:2361. https://doi.org/10.3390/su10072361
Tecon R, Or D (2017) Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol Rev 41:599–623. https://doi.org/10.1093/femsre/fux039
Tedersoo L, Bahram M, Dickie IA (2014) Does host plant richness explain diversity of ectomycorrhizal fungi? Re-evaluation of Gao et al. (2013) data sets reveals sampling effects. Mol Ecol 23:992–995. https://doi.org/10.1111/mec.12660
Tedersoo L, Bahram M, Cajthaml T et al (2016) Tree diversity and species identity effects on soil fungi, protists and animals are context dependent. ISME J 10:346–362. https://doi.org/10.1038/ismej.2015.116
Teramoto A, Martins MC, Cunha MG (2011) Avaliação de métodos para preservação de isolados de Corynespora cassiicola (Berk. & M.A. Curtis) C.T. Wei. Pesqui Agropecuária Trop 41: https://doi.org/10.5216/pat.v41i2.12571
Thakur MP, Del Real IM, Cesarz S et al (2019) Soil microbial, nematode, and enzymatic responses to elevated CO2, N fertilization, warming, and reduced precipitation. Soil Biol Biochem 135:184–193. https://doi.org/10.1016/j.soilbio.2019.04.020
Thijs S, Van Dillewijn P, Sillen W et al (2014) Exploring the rhizospheric and endophytic bacterial communities of Acer pseudoplatanus growing on a TNT-contaminated soil: towards the development of a rhizocompetent TNT-detoxifying plant growth promoting consortium. Plant Soil 385:15–36. https://doi.org/10.1007/s11104-014-2260-0
Thomas GW (2018) Soil pH and soil acidity. pp 475–490. https://doi.org/10.2136/sssabookser5.3.c16
Tiemann LK, Grandy AS, Atkinson EE et al (2015) Crop rotational diversity enhances belowground communities and functions in an agroecosystem. Ecol Lett 18:761–771. https://doi.org/10.1111/ele.12453
Totsche KU, Amelung W, Gerzabek MH et al (2018) Microaggregates in soils. J Plant Nutr Soil Sci 181:104–136. https://doi.org/10.1002/jpln.201600451
Tourna M, Stieglmeier M, Spang A et al (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci U S A 108:8420–8425. https://doi.org/10.1073/pnas.1013488108
Trivedi P, Singh BP, Singh BK (2018) Soil carbon: Introduction, importance, status, threat, and mitigation. In: Singh B (ed) Soil carbon storage: modulators, mechanisms and modeling. Academic, London, pp 1–28. https://doi.org/10.1016/B978-0-12-812766-7.00001-9
Uroz S, Ioannidis P, Lengelle J et al (2013) Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation. PLoS One 8:e55929. https://doi.org/10.1371/journal.pone.0055929
Van Aken B, Agathos SN (2001) Biodegradation of nitro-substituted explosives by white-rot fungi: a mechanistic approach. Adv Appl Microbiol 48:1–77. https://doi.org/10.1016/S0065-2164(01)48000-2
van der Heijden MGA, Martin FM, Selosse MA, Sanders IR (2015) Mycorrhizal ecology and evolution: the past, the present, and the future. New Phytol 205:1406–1423. https://doi.org/10.1111/nph.13288
Van Der Linde S, Suz LM, Orme CDL et al (2018) Environment and host as large-scale controls of ectomycorrhizal fungi. Nature 558:243–248. https://doi.org/10.1038/s41586-018-0189-9
Van Groenigen KJ, Osenberg CW, Hungate BA (2011) Increased soil emissions of potent greenhouse gases under increased atmospheric CO2. Nature 475:214–216. https://doi.org/10.1038/nature10176
Van Horn DJ, Barrett JE, Takacs-Vesbach CD et al (2014) Bacterial community composition of divergent soil habitats in a polar desert. FEMS Microbiol Ecol 89:490–494. https://doi.org/10.1111/1574-6941.12306
Van Horn DJ, Van Horn ML, Barrett JE et al (2013) Factors controlling soil microbial biomass and bacterial diversity and community composition in a cold desert ecosystem: role of geographic scale. PLoS One 8:e66103. https://doi.org/10.1371/journal.pone.0066103
Vandenkoornhuyse P, Quaiser A, Duhamel M et al (2015) The importance of the microbiome of the plant holobiont. New Phytol 206:1196–1206. https://doi.org/10.1111/nph.13312
Voriskova J, Baldrian P (2013) Fungal community on decomposing leaf litter undergoes rapid successional changes. ISME J 7:477–486. https://doi.org/10.1038/ismej.2012.116
Vystavna Y, Diadin D, Grynenko V et al (2017) Determination of dominant sources of nitrate contamination in transboundary (Russian Federation/Ukraine) catchment with heterogeneous land use. Environ Monit Assess 189:509. https://doi.org/10.1007/s10661-017-6227-5
Wakelin SA, Macdonald LM, O’Callaghan M et al (2014) Soil functional resistance and stability are linked to different ecosystem properties. Austral Ecol 39:522–531. https://doi.org/10.1111/aec.12112
Walker CB, De La Torre JR, Klotz MG et al (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci U S A 107:8818–8823. https://doi.org/10.1073/pnas.0913533107
Walter K, Don A, Tiemeyer B, Freibauer A (2016) Determining soil bulk density for carbon stock calculations: a systematic method comparison. Soil Sci Soc Am J 80:579–591. https://doi.org/10.2136/sssaj2015.11.0407
Wang J, Soininen J, Zhang Y et al (2011) Contrasting patterns in elevational diversity between microorganisms and macroorganisms. J Biogeogr 38:595–603. https://doi.org/10.1111/j.1365-2699.2010.02423.x
Wang JT, Cao P, Hu HW et al (2014) Altitudinal distribution patterns of soil bacterial and archaeal communities along Mt. Shegyla on the Tibetan plateau. Microb Ecol 69:135–145. https://doi.org/10.1007/s00248-014-0465-7
Wang J, Wang Y, Song X et al (2017) Elevated atmospheric CO2 and drought affect soil microbial community and functional diversity associated with Glycine max. Rev Bras Cienc do Solo 41. https://doi.org/10.1590/18069657rbcs20160460
Waters CM, Bassler BL (2005) Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol 21:319–346. https://doi.org/10.1146/annurev.cellbio.21.012704.131001
Watkinson SC (2015) Molecular ecology. In: Watkinson SC, Boddy L, Money N (eds) The fungi: third edition. Academic, San Diego, pp 189–203
Webster G, Rinna J, Roussel EG et al (2010) Prokaryotic functional diversity in different biogeochemical depth zones in tidal sediments of the Severn Estuary, UK, revealed by stable-isotope probing. FEMS Microbiol Ecol 72:179–197. https://doi.org/10.1111/j.1574-6941.2010.00848.x
Weyens N, Truyens S, Dupae J et al (2010) Potential of the TCE-degrading endophyte Pseudomonas putida W619-TCE to improve plant growth and reduce TCE phytotoxicity and evapotranspiration in poplar cuttings. Environ Pollut 158:2915–2919. https://doi.org/10.1016/j.envpol.2010.06.004
Whipps JM, Hand P, Pink D, Bending GD (2008) Phyllosphere microbiology with special reference to diversity and plant genotype. J Appl Microbiol 105:1744–1755
White DC, Zak DR, Ringelberg DB et al (2010) Compositional and functional shifts in microbial communities due to soil warming. Soil Sci Soc Am J 61:475. https://doi.org/10.2136/sssaj1997.03615995006100020015x
Wihitfield AE, Rotenberg D (2015) Disruption of insect transmission of plant viruses. Curr Opin Insect Sci 88:1–9. https://doi.org/10.1016/j.cois.2015.01.009
Williams A, Pétriacq P, Beerling DJ et al (2018) Impacts of atmospheric CO2 and soil nutritional value on plant responses to rhizosphere colonization by soil bacteria. Front Plant Sci 871:1493. https://doi.org/10.3389/fpls.2018.01493
Winder RS, Shamoun SF (2006) Forest pathogens: friend or foe to biodiversity? Can J Plant Pathol 28:S221–S227. https://doi.org/10.1080/07060660609507378
Winqvist C, Morales MB, Geiger F et al (2010) Persistent negative effects of pesticides on biodiversity and biological control potential on European farmland. Basic Appl Ecol 11:97–105. https://doi.org/10.1016/j.baae.2009.12.001
Workentine ML, Chang L, Ceri H, Turner RJ (2009) The GacS-GacA two-component regulatory system of Pseudomonas fluorescens: a bacterial two-hybrid analysis. FEMS Microbiol Lett 292:50–56. https://doi.org/10.1111/j.1574-6968.2008.01445.x
Wrighton KC (2018) It takes a village: metatranscriptomics resolves a trophic network that sustains methanogenesis in oxic soils. Am Geophys Union, Fall Meet 2018, Abstr #B11C-2157
Xue S, Yang X, Liu G et al (2017) Effects of elevated CO2 and drought on the microbial biomass and enzymatic activities in the rhizospheres of two grass species in Chinese loess soil. Geoderma 286:25–34. https://doi.org/10.1016/j.geoderma.2016.10.025
Yang C, Hamel C, Gan Y, Vujanovic V (2013) Pyrosequencing reveals how pulses influence rhizobacterial communities with feedback on wheat growth in the semiarid prairie. Plant Soil 367:493–505. https://doi.org/10.1007/s11104-012-1485-z
Yang Z, Hautier Y, Borer ET et al (2015) Abundance- and functional-based mechanisms of plant diversity loss with fertilization in the presence and absence of herbivores. Oecologia 179:261–270. https://doi.org/10.1007/s00442-015-3313-7
Ye L, Zhang T (2011) Pathogenic bacteria in sewage treatment plants as revealed by 454 pyrosequencing. Environ Sci Technol 45:7173–7179. https://doi.org/10.1021/es201045e
Young ARJ, Narita M, Narita M (2013) Cell senescence as both a dynamic and a static phenotype. https://doi.org/10.1007/978-1-62703-239-1_1
Yu H, He Z, Wang A et al (2018) Divergent responses of forest soil microbial communities under elevated CO2 in different depths of upper soil layers. Appl Environ Microbiol 84:e01694–e01617. https://doi.org/10.1128/AEM.01694-17
Zak DR, Pregitzer KS, Curtis PS, Holmes WE (2000) Atmospheric CO2 and the composition and function of soil microbial communities. Ecol Appl 10:47–59. https://doi.org/10.2307/2640985
Zhang Y, Cong J, Lu H et al (2014) Community structure and elevational diversity patterns of soil Acidobacteria. J Environ Sci (China) 26:1717–1724. https://doi.org/10.1016/j.jes.2014.06.012
Žifčáková L, Větrovský T, Howe A, Baldrian P (2016) Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter. Environ Microbiol 18:288–301. https://doi.org/10.1111/1462-2920.13026
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This study was funded by the National Science Foundation of China for Distinguished Young Scholars (31625007), the National Natural Science Foundation of China (31971548), and the Natural Sciences and Engineering Research Council of Canada (RGPIN-2014-04181).
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Islam, W., Noman, A., Naveed, H. et al. Role of environmental factors in shaping the soil microbiome. Environ Sci Pollut Res 27, 41225–41247 (2020). https://doi.org/10.1007/s11356-020-10471-2
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DOI: https://doi.org/10.1007/s11356-020-10471-2