• Foley, J. A. et al. Global consequences of land use. Science 309, 570–574 (2005).

    Article 

    Google Scholar
     

  • Tscharntke, T. et al. Global food security, biodiversity conservation and the future of agricultural intensification. Biol. Conserv. 151, 53–59 (2012).

    Article 

    Google Scholar
     

  • DeFries, R. S., Foley, J. A. & Asner, G. P. Land-use choices: balancing human needs and ecosystem function. Front. Ecol. Environ. 2, 249–257 (2004).

    Article 

    Google Scholar
     

  • Matson, P. A., Parton, W. J., Power, A. G. & Swift, M. J. Agricultural intensification and ecosystem properties. Science 277, 504–509 (1997).

    Article 

    Google Scholar
     

  • Zabel, F. et al. Global impacts of future cropland expansion and intensification on agricultural markets and biodiversity. Nat. Commun. 10, 2844 (2019).

    Article 

    Google Scholar
     

  • Tsiafouli, M. A. et al. Intensive agriculture reduces soil biodiversity across Europe. Glob. Change Biol. 21, 973–985 (2015).

    Article 

    Google Scholar
     

  • Tilman, D., Balzer, C., Hill, J. & Befort, B. L. Global food demand and the sustainable intensification of agriculture. Proc. Natl Acad. Sci. USA 108, 20260–20264 (2011).

    Article 

    Google Scholar
     

  • Mehrabi, Z., Ellis, E. C. & Ramankutty, N. The challenge of feeding the world while conserving half the planet. Nat. Sustain. 1, 409–412 (2018).

    Article 

    Google Scholar
     

  • Kopittke, P. M., Menzies, N. W., Wang, P., McKenna, B. A. & Lombi, E. Soil and the intensification of agriculture for global food security. Environ. Int. 132, 105078 (2019).

    Article 

    Google Scholar
     

  • Pereira, P., Bogunovic, I., Muñoz-Rojas, M. & Brevik, E. C. Soil ecosystem services, sustainability, valuation and management. Curr. Opin. Environ. Sci. Health 5, 7–13 (2018).

    Article 

    Google Scholar
     

  • Bai, Z. G., Dent, D. L., Olsson, L. & Schaepman, M. E. Proxy global assessment of land degradation. Soil Use Manage. 24, 223–234 (2008).

    Article 

    Google Scholar
     

  • Stockmann, U., Minasny, B. & McBratney, A. B. How fast does soil grow? Geoderma 216, 48–61 (2014).

    Article 

    Google Scholar
     

  • Wall, D. H., Nielsen, U. N. & Six, J. Soil biodiversity and human health. Nature 528, 69–76 (2015).

    Article 

    Google Scholar
     

  • Wilhelm, R. C., van Es, H. M. & Buckley, D. H. Predicting measures of soil health using the microbiome and supervised machine learning. Soil Biol. Biochem. 164, 108472 (2022).

    Article 

    Google Scholar
     

  • König, S., Vogel, H.-J., Harms, H. & Worrich, A. Physical, chemical and biological effects on soil bacterial dynamics in microscale models. Front. Ecol. Evol. https://doi.org/10.3389/fevo.2020.00053 (2020).

  • Six, J., Frey, S. D., Thiet, R. K. & Batten, K. M. Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Sci. Soc. Am. J. 70, 555–569 (2006).

    Article 

    Google Scholar
     

  • Status of the World’s Soil Resources (SWSR) — Main Report, 650 (FAO/Intergovernmental Technical Panel on Soils, 2015).

  • Singh, B. K., Bardgett, R. D., Smith, P. & Reay, D. S. Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat. Rev. Microbiol. 8, 779–790 (2010).

    Article 

    Google Scholar
     

  • Gougoulias, C., Clark, J. M. & Shaw, L. J. 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 (2014).

    Article 

    Google Scholar
     

  • Naylor, D. et al. Soil microbiomes under climate change and implications for carbon cycling. Annu. Rev. Environ. Resour. 45, 29–59 (2020).

    Article 

    Google Scholar
     

  • Berg, I. A. Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl. Environ. Microbiol. 77, 1925–1936 (2011).

    Article 

    Google Scholar
     

  • Yuan, H., Ge, T., Chen, C., O’Donnell, A. G. & Wu, J. Significant role for microbial autotrophy in the sequestration of soil carbon. Appl. Environ. Microbiol. 78, 2328–2336 (2012).

    Article 

    Google Scholar
     

  • Stevenson, F. J. Humus Chemistry: Genesis, Composition, Reactions 2nd edition (Wiley, 1994).

  • Liang, C., Amelung, W., Lehmann, J. & Kästner, M. Quantitative assessment of microbial necromass contribution to soil organic matter. Glob. Change Biol. 25, 3578–3590 (2019).

    Article 

    Google Scholar
     

  • Crowther, T. W. et al. Biotic interactions mediate soil microbial feedbacks to climate change. Proc. Natl Acad. Sci. USA 112, 7033–7038 (2015).

    Article 

    Google Scholar
     

  • Angel, R., Claus, P. & Conrad, R. Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J. 6, 847–862 (2012).

    Article 

    Google Scholar
     

  • Conrad, R. The global methane cycle: recent advances in understanding the microbial processes involved. Environ. Microbiol. Rep. 1, 285–292 (2009).

    Article 

    Google Scholar
     

  • Saunois, M. et al. The global methane budget 2000–2017. Earth Syst. Sci. Data 12, 1561–1623 (2020).

    Article 

    Google Scholar
     

  • Dutta, H. & Dutta, A. The microbial aspect of climate change. Energy Ecol. Environ. 1, 209–232 (2016).

    Article 

    Google Scholar
     

  • Hu, H.-W., Chen, D. & He, J.-Z. Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates. FEMS Microbiol. Rev. 39, 729–749 (2015).

    Article 

    Google Scholar
     

  • Tian, H. et al. A comprehensive quantification of global nitrous oxide sources and sinks. Nature 586, 248–256 (2020).

    Article 

    Google Scholar
     

  • Marschner, P. in Nutrient Cycling in Terrestrial Ecosystems (eds Petra, M. & Zdenko, R.) 159–182 (Springer, 2007).

  • Falkowski, P. G., Fenchel, T. & Delong, E. F. The microbial engines that drive Earth’s biogeochemical cycles. Science 320, 1034–1039 (2008).

    Article 

    Google Scholar
     

  • Saccá, M. L., Barra Caracciolo, A., Di Lenola, M. & Grenni, P. Soil Biological Communities and Ecosystem Resilience (eds Martin, L., Paola, G. & Mauro, G.) 9–24 (Springer, 2017).

  • Jetten, M. S. M. The microbial nitrogen cycle. Environ. Microbiol. 10, 2903–2909 (2008).

    Article 

    Google Scholar
     

  • Kuypers, M. M. M., Marchant, H. K. & Kartal, B. The microbial nitrogen-cycling network. Nat. Rev. Microbiol. 16, 263–276 (2018).

    Article 

    Google Scholar
     

  • Canfield, D. E., Glazer, A. N. & Falkowski, P. G. The evolution and future of Earth’s nitrogen cycle. Science 330, 192–196 (2010).

    Article 

    Google Scholar
     

  • Clark, I. M., Hughes, D. J., Fu, Q., Abadie, M. & Hirsch, P. R. Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils. Sci. Rep. 11, 15905 (2021).

    Article 

    Google Scholar
     

  • Philippot, L., Hallin, S. & Schloter, M. in Advances in Agronomy Vol. 96, 249–305 (Academic, 2007).

  • Hayatsu, M., Tago, K. & Saito, M. Various players in the nitrogen cycle: diversity and functions of the microorganisms involved in nitrification and denitrification. Soil Sci. Plant Nutr. 54, 33–45 (2008).

    Article 

    Google Scholar
     

  • Mackey, K. R. M. & Paytan, A. in Encyclopedia of Microbiology 3rd edition (ed. Moselio, S.) 322–334 (Academic, 2009).

  • Richardson, A. E., Barea, J.-M., McNeill, A. M. & Prigent-Combaret, C. Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant. Soil. 321, 305–339 (2009).

    Article 

    Google Scholar
     

  • Richardson, A. E. & Simpson, R. J. Soil microorganisms mediating phosphorus availability. Plant. Physiol. 156, 989–996 (2011).

    Article 

    Google Scholar
     

  • Li, J.-t. et al. A comprehensive synthesis unveils the mysteries of phosphate-solubilizing microbes. Biol. Rev. 96, 2771–2793 (2021).

    Article 

    Google Scholar
     

  • Kobae, Y. Dynamic phosphate uptake in arbuscular mycorrhizal roots under field conditions. Front. Env. Sci. https://doi.org/10.3389/fenvs.2018.00159 (2019).

  • Oberson, A. & Joner, E. J. in Organic Phosphorus in the Environment (eds Turner, B. L. et al.) 133–164 (CABI, 2005).

  • Compant, S., Samad, A., Faist, H. & Sessitsch, A. A review on the plant microbiome: ecology, functions, and emerging trends in microbial application. J. Adv. Res. 19, 29–37 (2019).

    Article 

    Google Scholar
     

  • Eichmann, R., Richards, L. & Schäfer, P. Hormones as go-betweens in plant microbiome assembly. Plant J. 105, 518–541 (2021).

    Article 

    Google Scholar
     

  • Nascimento, F. X., Hernandez, A. G., Glick, B. R. & Rossi, M. J. The extreme plant-growth-promoting properties of Pantoea phytobeneficialis MSR2 revealed by functional and genomic analysis. Environ. Microbiol. 22, 1341–1355 (2020).

    Article 

    Google Scholar
     

  • Valliere, J. M., Wong, W. S., Nevill, P. G., Zhong, H. & Dixon, K. W. Preparing for the worst: utilizing stress-tolerant soil microbial communities to aid ecological restoration in the Anthropocene. Ecol. Solut. Evid. 1, e12027 (2020).

    Article 

    Google Scholar
     

  • Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T. & Singh, B. K. Plant–microbiome interactions: from community assembly to plant health. Nat. Rev. Microbiol. 18, 607–621 (2020).

    Article 

    Google Scholar
     

  • Rolfe, S. A., Griffiths, J. & Ton, J. Crying out for help with root exudates: adaptive mechanisms by which stressed plants assemble health-promoting soil microbiomes. Curr. Opin. Microbiol. 49, 73–82 (2019).

    Article 

    Google Scholar
     

  • Costa, O. Y. A., Raaijmakers, J. M. & Kuramae, E. E. Microbial extracellular polymeric substances: ecological function and impact on soil aggregation. Front. Microbiol. https://doi.org/10.3389/fmicb.2018.01636 (2018).

  • Sharma, A. et al. Phytohormones regulate accumulation of osmolytes under abiotic stress. Biomolecules 9, 285 (2019).

    Article 

    Google Scholar
     

  • Singh, D. P. et al. Microbial inoculation in rice regulates antioxidative reactions and defense related genes to mitigate drought stress. Sci. Rep. 10, 4818 (2020).

    Article 

    Google Scholar
     

  • Bárzana, G., Aroca, R., Bienert, G. P., Chaumont, F. & Ruiz-Lozano, J. M. New insights into the regulation of aquaporins by the arbuscular mycorrhizal symbiosis in maize plants under drought stress and possible implications for plant performance. Mol. Plant Microbe Interact. 27, 349–363 (2014).

    Article 

    Google Scholar
     

  • Gamalero, E. & Glick, B. R. Bacterial modulation of plant ethylene levels. Plant Physiol. 169, 13–22 (2015).

    Article 

    Google Scholar
     

  • Le Pioufle, O., Ganoudi, M., Calonne-Salmon, M., Ben Dhaou, F. & Declerck, S. Rhizophagus irregularis MUCL 41833 improves phosphorus uptake and water use efficiency in maize plants during recovery from drought stress. Front. Plant Sci. https://doi.org/10.3389/fpls.2019.00897 (2019).

  • Begum, N. et al. Role of arbuscular mycorrhizal fungi in plant growth regulation: implications in abiotic stress tolerance. Front. Plant Sci. https://doi.org/10.3389/fpls.2019.01068 (2019).

  • Köhl, J., Kolnaar, R. & Ravensberg, W. J. Mode of action of microbial biological control agents against plant diseases: relevance beyond efficacy. Front. Plant Sci. https://doi.org/10.3389/fpls.2019.00845 (2019).

  • Hu, L. et al. Root exudate metabolites drive plant–soil feedbacks on growth and defense by shaping the rhizosphere microbiota. Nat. Commun. 9, 2738 (2018).

    Article 

    Google Scholar
     

  • Granato, E. T., Meiller-Legrand, T. A. & Foster, K. R. The evolution and ecology of bacterial warfare. Curr. Biol. 29, R521–R537 (2019).

    Article 

    Google Scholar
     

  • Shah, P. A. & Pell, J. K. Entomopathogenic fungi as biological control agents. Appl. Microbiol. Biotechnol. 61, 413–423 (2003).

    Article 

    Google Scholar
     

  • Soares, F. Ed. F., Sufiate, B. L. & de Queiroz, J. H. Nematophagous fungi: far beyond the endoparasite, predator and ovicidal groups. Agric. Nat. Resour. 52, 1–8 (2018).


    Google Scholar
     

  • Nordbring-Hertz, B., Jansson, H.-B. & Tunlid, A. in eLS (Wiley, 2011); https://doi.org/10.1002/9780470015902.a0000374.pub3.

  • Tian, B., Yang, J. & Zhang, K.-Q. Bacteria used in the biological control of plant-parasitic nematodes: populations, mechanisms of action, and future prospects. FEMS Microbiol. Ecol. 61, 197–213 (2007).

    Article 

    Google Scholar
     

  • Shafi, J., Tian, H. & Ji, M. Bacillus species as versatile weapons for plant pathogens: a review. Biotechnol. Biotechnol. Equip. 31, 446–459 (2017).

    Article 

    Google Scholar
     

  • Bravo, A., Likitvivatanavong, S., Gill, S. S. & Soberón, M. Bacillus thuringiensis: a story of a successful bioinsecticide. Insect Biochem. Mol. Biol. 41, 423–431 (2011).

    Article 

    Google Scholar
     

  • Schnepf, E. et al. Bacillus thuringiensis and its pesticidal crystal proteins. Microbiol. Mol. Biol. Rev. 62, 775–806 (1998).

    Article 

    Google Scholar
     

  • Wei, J.-Z. et al. Bacillus thuringiensis crystal proteins that target nematodes. Proc. Natl Acad. Sci. USA 100, 2760–2765 (2003).

    Article 

    Google Scholar
     

  • Flury, P. et al. Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. ISME J. 10, 2527–2542 (2016).

    Article 

    Google Scholar
     

  • Vurukonda, S. S. K. P., Giovanardi, D. & Stefani, E. Plant growth promoting and biocontrol activity of Streptomyces spp. as endophytes. Int. J. Mol. Sci. 19, 952 (2018).

    Article 

    Google Scholar
     

  • Whipps, J. M. Microbial interactions and biocontrol in the rhizosphere. J. Exp. Bot. 52, 487–511 (2001).

    Article 

    Google Scholar
     

  • MacLeod, M., Arp, H. P. H., Tekman, M. B. & Jahnke, A. The global threat from plastic pollution. Science 373, 61–65 (2021).

    Article 

    Google Scholar
     

  • Sharma, A. et al. Worldwide pesticide usage and its impacts on ecosystem. SN Appl. Sci. 1, 1446 (2019).

    Article 

    Google Scholar
     

  • Gworek, B., Kijeńska, M., Wrzosek, J. & Graniewska, M. Pharmaceuticals in the soil and plant environment: a review. Water Air Soil Pollut. 232, 145 (2021).

    Article 

    Google Scholar
     

  • Tang, F. H. M., Lenzen, M., McBratney, A. & Maggi, F. Risk of pesticide pollution at the global scale. Nat. Geosci. 14, 206–210 (2021).

    Article 

    Google Scholar
     

  • Zumstein, M. T. et al. Biodegradation of synthetic polymers in soils: tracking carbon into CO2 and microbial biomass. Sci. Adv. 4, eaas9024 (2018).

    Article 

    Google Scholar
     

  • Singh, B. & Singh, K. Microbial degradation of herbicides. Crit. Rev. Microbiol. 42, 245–261 (2016).


    Google Scholar
     

  • Teng, Y. & Chen, W. Soil microbiomes — a promising strategy for contaminated soil remediation: a review. Pedosphere 29, 283–297 (2019).

    Article 

    Google Scholar
     

  • Vogt, C. & Richnow, H. H. in Geobiotechnology II: Energy Resources, Subsurface Technologies, Organic Pollutants and Mining Legal Principles (eds Schippers, A. et al.) 123–146 (Springer, 2014).

  • Mishra, S. et al. Recent advanced technologies for the characterization of xenobiotic-degrading microorganisms and microbial communities. Front. Bioeng. Biotechnol. https://doi.org/10.3389/fbioe.2021.632059 (2021).

  • Rolli, E. et al. ‘Cry-for-help’ in contaminated soil: a dialogue among plants and soil microbiome to survive in hostile conditions. Environ. Microbiol. 23, 5690–5703 (2021).

    Article 

    Google Scholar
     

  • Wilpiszeski, R. L. et al. Soil aggregate microbial communities: towards understanding microbiome interactions at biologically relevant scales. Appl. Environ. Microbiol. https://doi.org/10.1128/aem.00324-19 (2019).

  • Blott, S. J. & Pye, K. Particle size scales and classification of sediment types based on particle size distributions: review and recommended procedures. Sedimentology 59, 2071–2096 (2012).

    Article 

    Google Scholar
     

  • Totsche, K. U. et al. Microaggregates in soils. J. Plant Nutr. Soil Sci. 181, 104–136 (2018).

    Article 

    Google Scholar
     

  • Martin, J. P., Martin, W. P., Page, J. B., Raney, W. A. & de Ment, J. D. in Advances in Agronomy Vol. 7 (ed. Norman, A. G.) 1–37 (Academic, 1955).

  • Chotte, J.-L. in Microorganisms in Soils: Roles in Genesis and Functions (eds Varma, A. & Buscot, F.) 107–119 (Springer, 2005).

  • Oades, J. M. Soil organic matter and structural stability: mechanisms and implications for management. Plant. Soil. 76, 319–337 (1984).

    Article 

    Google Scholar
     

  • Six, J., Elliott, E. T. & Paustian, K. Soil macroaggregate turnover and microaggregate formation: a mechanism for C sequestration under no-tillage agriculture. Soil Biol. Biochem. 32, 2099–2103 (2000).

    Article 

    Google Scholar
     

  • Six, J., Bossuyt, H., Degryze, S. & Denef, K. A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics. Soil Tillage Res. 79, 7–31 (2004).

    Article 

    Google Scholar
     

  • Schlüter, S. et al. Microscale carbon distribution around pores and particulate organic matter varies with soil moisture regime. Nat. Commun. 13, 2098 (2022).

    Article 

    Google Scholar
     

  • Acosta, J. A., Martínez-Martínez, S., Faz, A. & Arocena, J. Accumulations of major and trace elements in particle size fractions of soils on eight different parent materials. Geoderma 161, 30–42 (2011).

    Article 

    Google Scholar
     

  • Sessitsch, A., Weilharter, A., Gerzabek, M. H., Kirchmann, H. & Kandeler, E. Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl. Environ. Microbiol. 67, 4215–4224 (2001).

    Article 

    Google Scholar
     

  • Zhang, Q. et al. Fatty-acid profiles and enzyme activities in soil particle-size fractions under long-term fertilization. Soil Sci. Soc. Am. J. 80, 97–111 (2016).

    Article 

    Google Scholar
     

  • Hemkemeyer, M., Christensen, B. T., Martens, R. & Tebbe, C. C. Soil particle size fractions harbour distinct microbial communities and differ in potential for microbial mineralisation of organic pollutants. Soil Biol. Biochem. 90, 255–265 (2015).

    Article 

    Google Scholar
     

  • Briar, S. S. et al. The distribution of nematodes and soil microbial communities across soil aggregate fractions and farm management systems. Soil Biol. Biochem. 43, 905–914 (2011).

    Article 

    Google Scholar
     

  • Hemkemeyer, M., Dohrmann, A. B., Christensen, B. T. & Tebbe, C. C. Bacterial preferences for specific soil particle size fractions revealed by community analyses. Front. Microbiol. https://doi.org/10.3389/fmicb.2018.00149 (2018).

  • Hemkemeyer, M., Christensen, B. T., Tebbe, C. C. & Hartmann, M. Taxon-specific fungal preference for distinct soil particle size fractions. Eur. J. Soil Biol. 94, 103103 (2019).

    Article 

    Google Scholar
     

  • Christensen, B. T. & Olesen, J. E. Nitrogen mineralization potential of organomineral size separates from soils with annual straw incorporation. Eur. J. Soil Sci. 49, 25–36 (1998).

    Article 

    Google Scholar
     

  • Christensen, B. T. Decomposability of organic matter in particle size fractions from field soils with straw incorporation. Soil Biol. Biochem. 19, 429–435 (1987).

    Article 

    Google Scholar
     

  • Luo, G. et al. Long-term fertilisation regimes affect the composition of the alkaline phosphomonoesterase encoding microbial community of a vertisol and its derivative soil fractions. Biol. Fertil. Soils 53, 375–388 (2017).

    Article 

    Google Scholar
     

  • Mummey, D., Holben, W., Six, J. & Stahl, P. Spatial stratification of soil bacterial populations in aggregates of diverse soils. Microb. Ecol. 51, 404–411 (2006).

    Article 

    Google Scholar
     

  • Ranjard, L. et al. Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (RISA). Microb. Ecol. 39, 263–272 (2000).


    Google Scholar
     

  • Raynaud, X. & Nunan, N. Spatial ecology of bacteria at the microscale in soil. PLoS One 9, e87217 (2014).

    Article 

    Google Scholar
     

  • Rillig, M. C., Muller, L. A. H. & Lehmann, A. Soil aggregates as massively concurrent evolutionary incubators. ISME J. 11, 1943–1948 (2017).

    Article 

    Google Scholar
     

  • Trivedi, P. et al. Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content. Environ. Microbiol. 19, 3070–3086 (2017).

    Article 

    Google Scholar
     

  • Borer, B., Tecon, R. & Or, D. Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks. Nat. Commun. 9, 769 (2018).

    Article 

    Google Scholar
     

  • Kong, A. Y. Y., Hristova, K., Scow, K. M. & Six, J. Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments. Soil Biol. Biochem. 42, 1523–1533 (2010).

    Article 

    Google Scholar
     

  • Bhattacharyya, S. S. et al. Soil carbon sequestration, greenhouse gas emissions, and water pollution under different tillage practices. Sci. Total Environ. 826, 154161 (2022).

    Article 

    Google Scholar
     

  • Zhang, W. et al. Differences in the nitrous oxide emission and the nitrifier and denitrifier communities among varying aggregate sizes of an arable soil in China. Geoderma 389, 114970 (2021).

    Article 

    Google Scholar
     

  • Tilman, D. et al. Forecasting agriculturally driven global environmental change. Science 292, 281–284 (2001).

    Article 

    Google Scholar
     

  • Tilman, D., Cassman, K. G., Matson, P. A., Naylor, R. & Polasky, S. Agricultural sustainability and intensive production practices. Nature 418, 671–677 (2002).

    Article 

    Google Scholar
     

  • Hartmann, M., Frey, B., Mayer, J., Mader, P. & Widmer, F. Distinct soil microbial diversity under long-term organic and conventional farming. ISME J. 9, 1177–1194 (2015).

    Article 

    Google Scholar
     

  • Degrune, F. et al. The pedological context modulates the response of soil microbial communities to agroecological management. Front. Ecol. Environ. 7, 261 (2019).

    Article 

    Google Scholar
     

  • Longepierre, M. et al. Limited resilience of the soil microbiome to mechanical compaction within four growing seasons of agricultural management. ISME Commun. 1, 44 (2021).

    Article 

    Google Scholar
     

  • Delitte, M., Caulier, S., Bragard, C. & Desoignies, N. Plant microbiota beyond farming practices: a review. Front. Sustain. Food Syst. https://doi.org/10.3389/fsufs.2021.624203 (2021).

  • Hobbs, P. R., Sayre, K. & Gupta, R. The role of conservation agriculture in sustainable agriculture. Phil. Trans. R. Soc. B 363, 543–555 (2008).

    Article 

    Google Scholar
     

  • Van den Putte, A., Govers, G., Diels, J., Gillijns, K. & Demuzere, M. Assessing the effect of soil tillage on crop growth: a meta-regression analysis on European crop yields under conservation agriculture. Eur. J. Agron. 33, 231–241 (2010).

    Article 

    Google Scholar
     

  • Six, J. et al. Soil organic matter, biota and aggregation in temperate and tropical soils — effects of no-tillage. Agronomie 22, 755–775 (2002).

    Article 

    Google Scholar
     

  • Young, I. M. & Ritz, K. Tillage, habitat space and function of soil microbes. Soil Tillage Res. 53, 201–213 (2000).

    Article 

    Google Scholar
     

  • Degrune, F. et al. Temporal dynamics of soil microbial communities below the seedbed under two contrasting tillage regimes. Front. Microbiol. 8, 1127 (2017).

    Article 

    Google Scholar
     

  • Pittelkow, C. M. et al. Productivity limits and potentials of the principles of conservation agriculture. Nature 517, 365–368 (2015).

    Article 

    Google Scholar
     

  • Babin, D. et al. Impact of long-term agricultural management practices on soil prokaryotic communities. Soil Biol. Biochem. https://doi.org/10.1016/j.soilbio.2018.11.002 (2018).

    Article 

    Google Scholar
     

  • Srour, A. Y. et al. Microbial communities associated with long-term tillage and fertility treatments in a corn–soybean cropping system. Front. Microbiol. https://doi.org/10.3389/fmicb.2020.01363 (2020).

  • Cania, B. et al. Site-specific conditions change the response of bacterial producers of soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides to tillage intensity. Front. Microbiol. https://doi.org/10.3389/fmicb.2020.00568 (2020).

  • Cooper, H. V., Sjögersten, S., Lark, R. M. & Mooney, S. J. To till or not to till in a temperate ecosystem? Implications for climate change mitigation. Environ. Res. Lett. 16, 054022 (2021).

    Article 

    Google Scholar
     

  • Mangalassery, S. et al. To what extent can zero tillage lead to a reduction in greenhouse gas emissions from temperate soils? Sci. Rep. 4, 4586 (2014).

    Article 

    Google Scholar
     

  • Abdalla, M. et al. Conservation tillage systems: a review of its consequences for greenhouse gas emissions. Soil Use Manage. 29, 199–209 (2013).

    Article 

    Google Scholar
     

  • Six, J. et al. The potential to mitigate global warming with no-tillage management is only realized when practised in the long term. Glob. Change Biol. 10, 155–160 (2004).

    Article 

    Google Scholar
     

  • van Kessel, C. et al. Climate, duration, and N placement determine N2O emissions in reduced tillage systems: a meta-analysis. Glob. Change Biol. 19, 33–44 (2013).

    Article 

    Google Scholar
     

  • Hamza, M. A. & Anderson, W. K. Soil compaction in cropping systems: a review of the nature, causes and possible solutions. Soil Tillage Res. 82, 121–145 (2005).

    Article 

    Google Scholar
     

  • Schäffer, B., Stauber, M., Mueller, T. L., Muller, R. & Schulin, R. Soil and macro-pores under uniaxial compression. I. Mechanical stability of repacked soil and deformation of different types of macro-pores. Geoderma 146, 183–191 (2008).

    Article 

    Google Scholar
     

  • Hartmann, M. et al. Resistance and resilience of the forest soil microbiome to logging-associated compaction. ISME J. 8, 226–244 (2014).

    Article 

    Google Scholar
     

  • Sitaula, B. K., Hansen, S., Sitaula, J. I. B. & Bakken, L. R. Methane oxidation potentials and fluxes in agricultural soil: effects of fertilisation and soil compaction. Biogeochemistry 48, 323–339 (2000).

    Article 

    Google Scholar
     

  • Sitaula, B. K., Hansen, S., Sitaula, J. I. B. & Bakken, L. R. Effects of soil compaction on N2O emission in agricultural soil. Chemosphere Glob. Change Sci. 2, 367–371 (2000).

    Article 

    Google Scholar
     

  • Beckett, C. T. S. et al. Compaction conditions greatly affect growth during early plant establishment. Ecol. Eng. 106, 471–481 (2017).

    Article 

    Google Scholar
     

  • Reichert, J. M., Suzuki, L. E. A. S., Reinert, D. J., Horn, R. & Håkansson, I. Reference bulk density and critical degree-of-compactness for no-till crop production in subtropical highly weathered soils. Soil Tillage Res. 102, 242–254 (2009).

    Article 

    Google Scholar
     

  • von Wilpert, K. & Schäffer, J. Ecological effects of soil compaction and initial recovery dynamics: a preliminary study. Eur. J. For. Res. 125, 129–138 (2006).

    Article 

    Google Scholar
     

  • Tim Chamen, W. C., Moxey, A. P., Towers, W., Balana, B. & Hallett, P. D. Mitigating arable soil compaction: a review and analysis of available cost and benefit data. Soil Tillage Res. 146, 10–25 (2015).

    Article 

    Google Scholar
     

  • Beillouin, D., Ben-Ari, T., Malézieux, E., Seufert, V. & Makowski, D. Positive but variable effects of crop diversification on biodiversity and ecosystem services. Glob. Change Biol. 27, 4697–4710 (2021).

    Article 

    Google Scholar
     

  • Smith, R. G., Gross, K. L. & Robertson, G. P. Effects of crop diversity on agroecosystem function: crop yield response. Ecosystems 11, 355–366 (2008).

    Article 

    Google Scholar
     

  • Hooper, D. U. et al. Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecol. Monogr. 75, 3–35 (2005).

    Article 

    Google Scholar
     

  • Galindo-Castañeda, T., Lynch, J. P., Six, J. & Hartmann, M. Improving soil resource uptake by plants through capitalizing on synergies between root architecture and anatomy and root-associated microorganisms. Front. Plant Sci. https://doi.org/10.3389/fpls.2022.827369 (2022).

  • Venter, Z. S., Jacobs, K. & Hawkins, H.-J. The impact of crop rotation on soil microbial diversity: a meta-analysis. Pedobiologia 59, 215–223 (2016).

    Article 

    Google Scholar
     

  • Stefan, L., Hartmann, M., Engbersen, N., Six, J. & Schöb, C. Positive effects of crop diversity on productivity driven by changes in soil microbial composition. Front. Microbiol. 12, 660749 (2021).

    Article 

    Google Scholar
     

  • Peralta, A. L., Sun, Y., McDaniel, M. D. & Lennon, J. T. Crop rotational diversity increases disease suppressive capacity of soil microbiomes. Ecosphere 9, e02235 (2018).

    Article 

    Google Scholar
     

  • Abdalla, M. et al. A critical review of the impacts of cover crops on nitrogen leaching, net greenhouse gas balance and crop productivity. Glob. Change Biol. 25, 2530–2543 (2019).

    Article 

    Google Scholar
     

  • Bacq-Labreuil, A., Crawford, J., Mooney, S. J., Neal, A. L. & Ritz, K. Cover crop species have contrasting influence upon soil structural genesis and microbial community phenotype. Sci. Rep. 9, 7473 (2019).

    Article 

    Google Scholar
     

  • Kong, A. Y. Y. & Six, J. Microbial community assimilation of cover crop rhizodeposition within soil microenvironments in alternative and conventional cropping systems. Plant Soil 356, 315–330 (2012).

    Article 

    Google Scholar
     

  • Kim, N., Zabaloy, M. C., Guan, K. & Villamil, M. B. Do cover crops benefit soil microbiome? A meta-analysis of current research. Soil Biol. Biochem. 142, 107701 (2020).

    Article 

    Google Scholar
     

  • Alahmad, A. et al. Cover crops in arable lands increase functional complementarity and redundancy of bacterial communities. J. Appl. Ecol. 56, 651–664 (2019).

    Article 

    Google Scholar
     

  • Cloutier, M. L. et al. Fungal community shifts in soils with varied cover crop treatments and edaphic properties. Sci. Rep. 10, 6198 (2020).

    Article 

    Google Scholar
     

  • Finney, D. M., Buyer, J. S. & Kaye, J. P. Living cover crops have immediate impacts on soil microbial community structure and function. J. Soil Water Conserv. 72, 361–373 (2017).

    Article 

    Google Scholar
     

  • Vukicevich, E., Lowery, T., Bowen, P., Úrbez-Torres, J. R. & Hart, M. Cover crops to increase soil microbial diversity and mitigate decline in perennial agriculture. A review. Agron. Sustain. Dev. 36, 48 (2016).

    Article 

    Google Scholar
     

  • Sanz-Cobena, A. et al. Do cover crops enhance N2O, CO2 or CH4 emissions from soil in Mediterranean arable systems? Sci. Total Environ. 466-467, 164–174 (2014).

    Article 

    Google Scholar
     

  • Basche, A. D., Miguez, F. E., Kaspar, T. C. & Castellano, M. J. Do cover crops increase or decrease nitrous oxide emissions? A meta-analysis. J. Soil Water Conserv. 69, 471–482 (2014).

    Article 

    Google Scholar
     

  • Tribouillois, H., Constantin, J. & Justes, E. Cover crops mitigate direct greenhouse gases balance but reduce drainage under climate change scenarios in temperate climate with dry summers. Glob. Change Biol. 24, 2513–2529 (2018).

    Article 

    Google Scholar
     

  • Vanlauwe, B. et al. Integrated soil fertility management: operational definition and consequences for implementation and dissemination. Outlook Agric. 39, 17–24 (2010).

    Article 

    Google Scholar
     

  • Barzman, M. et al. Eight principles of integrated pest management. Agron. Sustain. Dev. 35, 1199–1215 (2015).

    Article 

    Google Scholar
     

  • Francioli, D. et al. Mineral vs. organic amendments: microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies. Front. Microbiol. https://doi.org/10.3389/fmicb.2016.01446 (2016).

  • Lentendu, G. et al. Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach. Mol. Ecol. 23, 3341–3355 (2014).

    Article 

    Google Scholar
     

  • Lori, M., Symnaczik, S., Mäder, P., De Deyn, G. & Gattinger, A. Organic farming enhances soil microbial abundance and activity — a meta-analysis and meta-regression. PLoS One 12, e0180442 (2017).

    Article 

    Google Scholar
     

  • Bebber, D. P. & Richards, V. R. A meta-analysis of the effect of organic and mineral fertilizers on soil microbial diversity. Appl. Soil Ecol. 175, 104450 (2022).

    Article 

    Google Scholar
     

  • Rillig, M. C., Tsang, A. & Roy, J. Microbial community coalescence for microbiome engineering. Front. Microbiol. https://doi.org/10.3389/fmicb.2016.01967 (2016).

  • Loaiza Puerta, V., Pujol Pereira, E. I., Wittwer, R., van der Heijden, M. & Six, J. Improvement of soil structure through organic crop management, conservation tillage and grass-clover ley. Soil Tillage Res. 180, 1–9 (2018).

    Article 

    Google Scholar
     

  • Řezáčová, V. et al. Organic fertilization improves soil aggregation through increases in abundance of eubacteria and products of arbuscular mycorrhizal fungi. Sci. Rep. 11, 12548 (2021).

    Article 

    Google Scholar
     

  • Fonte, S. J., Kong, A. Y. Y., van Kessel, C., Hendrix, P. F. & Six, J. Influence of earthworm activity on aggregate-associated carbon and nitrogen dynamics differs with agroecosystem management. Soil Biol. Biochem. 39, 1014–1022 (2007).

    Article 

    Google Scholar
     

  • Fu, B., Chen, L., Huang, H., Qu, P. & Wei, Z. Impacts of crop residues on soil health: a review. Environ. Pollut. Bioavailab. 33, 164–173 (2021).

    Article 

    Google Scholar
     

  • Blanco-Canqui, H. & Lal, R. Crop residue removal impacts on soil productivity and environmental quality. Crit. Rev. Plant Sci. 28, 139–163 (2009).

    Article 

    Google Scholar
     

  • Yang, H. et al. Wheat straw return influences nitrogen-cycling and pathogen associated soil microbiota in a wheat–soybean rotation system. Front. Microbiol. https://doi.org/10.3389/fmicb.2019.01811 (2019).

  • Enebe, M. C. & Babalola, O. O. Soil fertilization affects the abundance and distribution of carbon and nitrogen cycling genes in the maize rhizosphere. AMB Express 11, 24 (2021).

    Article 

    Google Scholar
     

  • Skinner, C. et al. The impact of long-term organic farming on soil-derived greenhouse gas emissions. Sci. Rep. 9, 1702 (2019).

    Article 

    Google Scholar
     

  • Lazcano, C., Zhu-Barker, X. & Decock, C. Effects of organic fertilizers on the soil microorganisms responsible for N2O emissions: a review. Microorganisms https://doi.org/10.3390/microorganisms9050983 (2021).

  • Tilston, E. L., Pitt, D. & Groenhof, A. C. Composted recycled organic matter suppresses soil-borne diseases of field crops. N. Phytol. 154, 731–740 (2002).

    Article 

    Google Scholar
     

  • Bonanomi, G., Antignani, V., Capodilupo, M. & Scala, F. Identifying the characteristics of organic soil amendments that suppress soilborne plant diseases. Soil Biol. Biochem. 42, 136–144 (2010).

    Article 

    Google Scholar
     

  • Briceño, G., Palma, G. & Durán, N. Influence of organic amendment on the biodegradation and movement of pesticides. Crit. Rev. Environ. Sci. Technol. 37, 233–271 (2007).

    Article 

    Google Scholar
     

  • Lehmann, J. & Joseph, S. Biochar for Environmental Management: Science, Technology and Implementation (Routledge, 2015).

  • Wang, D., Fonte, S. J., Parikh, S. J., Six, J. & Scow, K. M. Biochar additions can enhance soil structure and the physical stabilization of C in aggregates. Geoderma 303, 110–117 (2017).

    Article 

    Google Scholar
     

  • Wang, J., Xiong, Z. & Kuzyakov, Y. Biochar stability in soil: meta-analysis of decomposition and priming effects. GCB Bioenergy 8, 512–523 (2016).

    Article 

    Google Scholar
     

  • Lehmann, J. et al. Biochar effects on soil biota — a review. Soil Biol. Biochem. 43, 1812–1836 (2011).

    Article 

    Google Scholar
     

  • Liu, X., Shi, Y., Zhang, Q. & Li, G. Effects of biochar on nitrification and denitrification-mediated N2O emissions and the associated microbial community in an agricultural soil. Environ. Sci. Pollut. Res. 28, 6649–6663 (2021).

    Article 

    Google Scholar
     

  • Zhang, L. et al. Effects of biochar application on soil nitrogen transformation, microbial functional genes, enzyme activity, and plant nitrogen uptake: a meta-analysis of field studies. GCB Bioenergy 13, 1859–1873 (2021).

    Article 

    Google Scholar
     

  • Deb, D., Kloft, M., Lässig, J. & Walsh, S. Variable effects of biochar and P solubilizing microbes on crop productivity in different soil conditions. Agroecol. Sustain. Food Syst. 40, 145–168 (2016).

    Article 

    Google Scholar
     

  • Li, X., Wang, T., Chang, S. X., Jiang, X. & Song, Y. Biochar increases soil microbial biomass but has variable effects on microbial diversity: a meta-analysis. Sci. Total Environ. 749, 141593 (2020).

    Article 

    Google Scholar
     

  • Yoo, G., Lee, Y. O., Won, T. J., Hyun, J. G. & Ding, W. Variable effects of biochar application to soils on nitrification-mediated N2O emissions. Sci. Total Environ. 626, 603–611 (2018).

    Article 

    Google Scholar
     

  • Verhoeven, E. et al. Toward a better assessment of biochar–nitrous oxide mitigation potential at the field scale. J. Environ. Qual. 46, 237–246 (2017).

    Article 

    Google Scholar
     

  • He, Y. et al. Effects of biochar application on soil greenhouse gas fluxes: a meta-analysis. GCB Bioenergy 9, 743–755 (2017).

    Article 

    Google Scholar
     

  • Wang, W. et al. Biochar application alleviated negative plant–soil feedback by modifying soil microbiome. Front. Microbiol. https://doi.org/10.3389/fmicb.2020.00799 (2020).

  • Duan, M. et al. Effects of biochar on reducing the abundance of oxytetracycline, antibiotic resistance genes, and human pathogenic bacteria in soil and lettuce. Environ. Pollut. 224, 787–795 (2017).

    Article 

    Google Scholar
     

  • Liu, Y., Lonappan, L., Brar, S. K. & Yang, S. Impact of biochar amendment in agricultural soils on the sorption, desorption, and degradation of pesticides: a review. Sci. Total Environ. 645, 60–70 (2018).

    Article 

    Google Scholar
     

  • du Jardin, P. Plant biostimulants: definition, concept, main categories and regulation. Sci. Hortic. 196, 3–14 (2015).

    Article 

    Google Scholar
     

  • Le Mire, G. et al. Review: implementing plant biostimulants and biocontrol strategies in the agroecological management of cultivated ecosystems. Biotechnol. Agron. Soc. Environ. 20, 1–15 (2016).


    Google Scholar
     

  • Leggett, M. et al. Soybean response to inoculation with Bradyrhizobium japonicum in the United States and Argentina. Agron. J. 109, 1031–1038 (2017).

    Article 

    Google Scholar
     

  • Coniglio, A., Mora, V., Puente, M. & Cassán, F. in Microbial Probiotics for Agricultural Systems: Advances in Agronomic Use (eds Zúñiga-Dávila, D. et al.) 45–70 (Springer, 2019).

  • Alori, E. T., Dare, M. O. & Babalola, O. O. in Sustainable Agriculture Reviews (ed. Lichtfouse, E.) 281–307 (Springer, 2017).

  • Rillig, M. C. & Mummey, D. L. Mycorrhizas and soil structure. N. Phytol. 171, 41–53 (2006).

    Article 

    Google Scholar
     

  • Mawarda, P. C., Le Roux, X., Dirk van Elsas, J. & Salles, J. F. Deliberate introduction of invisible invaders: a critical appraisal of the impact of microbial inoculants on soil microbial communities. Soil. Biol. Biochem. 148, 107874 (2020).

    Article 

    Google Scholar
     

  • Liu, X., Le Roux, X. & Salles, J. F. The legacy of microbial inoculants in agroecosystems and potential for tackling climate change challenges. iScience 25, 103821 (2022).

    Article 

    Google Scholar
     

  • Cornell, C. et al. Do bioinoculants affect resident microbial communities? A meta-analysis. Front. Agron. https://doi.org/10.3389/fagro.2021.753474 (2021).

  • Bender, S. F., Schlaeppi, K., Held, A. & Van der Heijden, M. G. A. Establishment success and crop growth effects of an arbuscular mycorrhizal fungus inoculated into Swiss corn fields. Agric. Ecosyst. Environ. 273, 13–24 (2019).

    Article 

    Google Scholar
     

  • Schreiter, S. et al. Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce. FEMS Microbiol. Ecol. 90, 718–730 (2014).

    Article 

    Google Scholar
     

  • Mueller, U. G. & Sachs, J. L. Engineering microbiomes to improve plant and animal health. Trends Microbiol. 23, 606–617 (2015).

    Article 

    Google Scholar
     

  • Kennedy, T. L., Suddick, E. C. & Six, J. Reduced nitrous oxide emissions and increased yields in California tomato cropping systems under drip irrigation and fertigation. Agric. Ecosyst. Environ. 170, 16–27 (2013).

    Article 

    Google Scholar
     

  • Fonte, S. J., Barrios, E. & Six, J. Earthworms, soil fertility and aggregate-associated soil organic matter dynamics in the Quesungual agroforestry system. Geoderma 155, 320–328 (2010).

    Article 

    Google Scholar
     

  • Pauli, N., Barrios, E., Conacher, A. J. & Oberthür, T. Soil macrofauna in agricultural landscapes dominated by the Quesungual slash-and-mulch agroforestry system, western Honduras. Appl. Soil. Ecol. 47, 119–132 (2011).

    Article 

    Google Scholar
     

  • Eichorst, S. A. et al. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fiv106 (2015).

  • Musat, N., Musat, F., Weber, P. K. & Pett-Ridge, J. Tracking microbial interactions with NanoSIMS. Curr. Opin. Biotechnol. 41, 114–121 (2016).

    Article 

    Google Scholar
     

  • Bronick, C. J. & Lal, R. Soil structure and management: a review. Geoderma 124, 3–22 (2005).

    Article 

    Google Scholar
     

  • Leave a Reply

    Your email address will not be published. Required fields are marked *