foundation for restoration practices that can
return resilience to the soil-plant ecosystem.
REFERENCESANDNOTES
- J. Clardy, M. A. Fischbach, C. R. Currie, The natural history of
antibiotics.Curr. Biol. 19 , R437–R441 (2009). doi:10.1016/
j.cub.2009.04.001; pmid: 19515346 - G. Schwilchet al., Operationalizing ecosystem services for
the mitigation of soil threats: A proposed framework.
Ecol. Indic. 67 , 586–597 (2016). doi:10.1016/
j.ecolind.2016.03.016 - M. Cherlet, C. Hutchinson, J. Reynolds, J. Hill, S. Sommer,
G. von Maltitz, Eds.,World Atlas of Desertification(Publication
Office of the European Union, Luxembourg, 2018). - United Nations Convention to Combat Desertification,
The Global Land Outlook(ed. 1, 2017);www.unccd.int/
actions/global-land-outlook-glo. - J. K. Greenet al., Large influence of soil moisture on long-
term terrestrial carbon uptake.Nature 565 , 476–479 (2019).
doi:10.1038/s41586-018-0848-x; pmid: 30675043 - S. I. Seneviratneet al., Investigating soil moisture-climate
interactions in a changing climate: A review.Earth Sci. Rev.
99 , 125–161 (2010). doi:10.1016/j.earscirev.2010.02.004 - D. A. Robinsonet al., Experimental evidence for drought
induced alternative stable states of soil moisture.Sci. Rep. 6 ,
20018 (2016). doi:10.1038/srep20018; pmid: 26804897 - D. A. Robinsonet al., Global environmental changes impact
soil hydraulic functions through biophysical feedbacks.
Global Change Biol. 25 , 1895–1904 (2019). doi:10.1111/
gcb.14626; pmid: 30900360 - R. M. B. Harriset al., Biological responses to the press and
pulse of climate trends and extreme events.Nat. Clim. Change
8 , 579–587 (2018). doi:10.1038/s41558-018-0187-9 - M. J. van der Ploeg, J. E. M. Baartman, D. A. Robinson,
Biophysical landscape interactions: Bridging disciplines and
scale with connectivity.Land Degrad. Dev. 29 , 1167– 1175
(2018). doi:10.1002/ldr.2820 - J. H. Dane, R. J. Lenhard, inEncyclopedia of Soils in the
Environment, D. Hillel, Ed. (Academic Press, 2005),
pp. 231–237. - N. G. McDowellet al., Predicting Chronic Climate-Driven
Disturbances and Their Mitigation.Trends Ecol. Evol. 33 , 15– 27
(2018). doi:10.1016/j.tree.2017.10.002; pmid: 29146414 - M. Reichsteinet al., Climate extremes and the carbon cycle.
Nature 500 , 287–295 (2013). doi:10.1038/nature12350;
pmid: 23955228 - C. S. Holling, Resilience and Stability of Ecological Systems.
Annu. Rev. Ecol. Syst. 4 ,1–23 (1973). doi:10.1146/annurev.
es.04.110173.000245 - J. M. Porr, J. Masoliver, K. Lindenberg, Bistability driven by
dichotomous noise.Phys. Rev. A 44 , 4866–4875 (1991).
doi:10.1103/PhysRevA.44.4866; pmid: 9906538 - M. Schefferet al., Anticipating critical transitions.Science
338 , 344–348 (2012). doi:10.1126/science.1225244;
pmid: 23087241 - R. D. Bardgett, T. Caruso, Soil microbial community
responses to climate extremes: Resistance, resilience and
transitions to alternative states.Philos. Trans. R. Soc. London
Ser. B 375 , 20190112 (2020). doi:10.1098/rstb.2019.0112;
pmid: 31983338 - E. K. Bünemannet al., Soil quality–A critical review.
Soil Biol. Biochem. 120 , 105–125 (2018). doi:10.1016/
j.soilbio.2018.01.030 - N. Fierer, S. A. Wood, C. P. Bueno de Mesquita, How
microbes can, and cannot, be used to assess soil health.
Soil Biol. Biochem. 153 , 108111 (2021). doi:10.1016/
j.soilbio.2020.108111 - J. P. Schimel, Life in Dry Soils: Effects of Drought on Soil
Microbial Communities and Processes.Annu. Rev. Ecol.
Evol. Syst. 49 , 409–432 (2018). doi:10.1146/annurev-
ecolsys-110617-062614 - J. Harris, Soil microbial communities and restoration ecology:
Facilitators or followers?Science 325 , 573–574 (2009).
doi:10.1126/science.1172975; pmid: 19644111 - E. K. Hallet al., Understanding how microbiomes influence
the systems they inhabit.Nat. Microbiol. 3 , 977–982 (2018).
doi:10.1038/s41564-018-0201-z; pmid: 30143799 - P. Trivedi, P. M. Schenk, M. D. Wallenstein, B. K. Singh, Tiny
Microbes, Big Yields: Enhancing food crop production with
biological solutions.Microb. Biotechnol. 10 , 999–1003 (2017).
doi:10.1111/1751-7915.12804; pmid: 28840959 - I. Saha, S. Datta, D. Biswas, Exploring the Role of Bacterial
Extracellular Polymeric Substances for Sustainable Development
in Agriculture.Curr. Microbiol. 77 , 3224–3239 (2020).
doi:10.1007/s00284-020-02169-y; pmid: 32876713- F. T. Maestre, R. Solé, B. K. Singh, Microbial biotechnology
as a tool to restore degraded drylands.Microb. Biotechnol.
10 , 1250–1253 (2017). doi:10.1111/1751-7915.12832;
pmid: 28834240 - E. R. J. Wubs, W. H. van der Putten, M. Bosch, T. M. Bezemer,
Soil inoculation steers restoration of terrestrial ecosystems.
Nat. Plants 2 , 16107 (2016). doi:10.1038/nplants.2016.107;
pmid: 27398907 - J. A. Lau, J. T. Lennon, Evolutionary ecology of plant-microbe
interactions: Soil microbial structure alters selection on
plant traits.New Phytol. 192 , 215–224 (2011). doi:10.1111/
j.1469-8137.2011.03790.x; pmid: 21658184 - W. H. van der Puttenet al., Plant-soil feedbacks: The past, the
present and future challenges.J. Ecol. 101 , 265–276 (2013).
doi:10.1111/1365-2745.12054 - X. Peng, M. A. Bruns, Development of a nitrogen-fixing
cyanobacterial consortium for surface stabilization of
agricultural soils.J. Appl. Phycol. 31 , 1047–1056 (2019).
doi:10.1007/s10811-018-1597-9 - J. S. Singh, V. C. Pandey, D. P. Singh, Efficient soil
microorganisms: A new dimension for sustainable agriculture
and environmental development.Agric. Ecosyst. Environ. 140 ,
339 – 353 (2011). doi:10.1016/j.agee.2011.01.017 - L. Quiza, M. St-Arnaud, E. Yergeau, Harnessing phytomicrobiome
signaling for rhizosphere microbiome engineering.Front.
Plant Sci. 6 , 507 (2015). doi:10.3389/fpls.2015.00507;
pmid: 26236319 - R. Backeret al., Plant growth-promoting rhizobacteria: Context,
mechanisms of action, and roadmap to commercialization
of biostimulants for sustainable agriculture.Front. Plant Sci. 9 ,
1473 (2018). doi:10.3389/fpls.2018.01473; pmid: 30405652 - V. C. S. Pankievicz, T. B. Irving, L. G. S. Maia, J. M. Ané,
Are we there yet? The long walk towards the development of
efficient symbiotic associations between nitrogen-fixing
bacteria and non-leguminous crops.BMC Biol. 17 , 99 (2019).
doi:10.1186/s12915-019-0710-0; pmid: 31796086 - F. Stagnari, A. Maggio, A. Galieni, M. Pisante, Multiple
benefits of legumes for agriculture sustainability:
An overview.Chem. Biol. Technol. Agric. 4 ,1–13 (2017).
doi:10.1186/s40538-016-0085-1 - C. Franche, K. Lindström, C. Elmerich, Nitrogen-fixing
bacteria associated with leguminous and non-leguminous
plants.Plant Soil 321 , 35–59 (2009). doi:10.1007/
s11104-008-9833-8 - M. Charpentier, G. Oldroyd, How close are we to nitrogen-
fixing cereals?Curr. Opin. Plant Biol. 13 , 556–564 (2010).
doi:10.1016/j.pbi.2010.08.003; pmid: 20817544 - G. E. D. Oldroyd, O. Leyser, A plant’s diet, surviving in a
variable nutrient environment.Science 368 , eaba0196
(2020). doi:10.1126/science.aba0196; pmid: 32241923 - M. Bueno Batista, R. Dixon, Manipulating nitrogen regulation
in diazotrophic bacteria for agronomic benefit.Biochem. Soc.
Trans. 47 , 603–614 (2019). doi:10.1042/BST20180342;
pmid: 30936245 - I. Prietoet al., Species-specific roles of ectomycorrhizal fungi
in facilitating interplant transfer of hydraulically redistributed
water between Pinus halepensis saplings and seedlings.
Plant Soil 406 , 15–27 (2016). doi:10.1007/s11104-016-2860-y - A. Schüßler, D. Schwarzott, C. Walker, A new fungal phylum,
the Glomeromycota: Phylogeny and evolution.Mycol. Res.
105 , 1413–1421 (2001). doi:10.1017/S0953756201005196 - S. E. Smith, F. A. Smith, I. Jakobsen, Mycorrhizal fungi
can dominate phosphate supply to plants irrespective of
growth responses.Plant Physiol. 133 , 16–20 (2003).
doi:10.1104/pp.103.024380; pmid: 12970469 - P. Bonfante, I.-A. Anca, Plants, mycorrhizal fungi, and
bacteria: A network of interactions.Annu. Rev. Microbiol. 63 ,
363 – 383 (2009). doi:10.1146/annurev.micro.091208.
073504 ; pmid: 19514845 - J. M. Barea, R. Azcón, C. Azcón-Aguilar, inMicroorganisms in
Soils: Roles in Genesis and Functions, A. Varma, F. Buscot,
Eds. (Springer, 2005), pp. 195–212. - M. A. Hassani, P. Durán, S. Hacquard, Microbial interactions
within the plant holobiont.Microbiome 6 , 58 (2018).
doi:10.1186/s40168-018-0445-0; pmid: 29587885 - J. Zhouet al., Different Arbuscular Mycorrhizal Fungi
Cocolonizing on a Single Plant Root System Recruit Distinct
Microbiomes.mSystems 5 , e00929-20 (2020). doi:10.1128/
mSystems.00929-20; pmid: 33323417 - E. T. Kierset al., Reciprocal rewards stabilize cooperation in
the mycorrhizal symbiosis.Science 333 , 880–882 (2011).
doi:10.1126/science.1208473; pmid: 21836016
47. M. Buée, W. de Boer, F. Martin, L. van Overbeek, E. Jurkevitch,
The rhizosphere zoo: An overview of plant-associated
communities of microorganisms, including phages, bacteria,
archaea, and fungi, and of some of their structuring
factors.Plant Soil 321 , 189–212 (2009). doi:10.1007/
s11104-009-9991-3
48. J. J. Parnellet al., From the lab to the farm: An industrial
perspective of plant beneficial microorganisms.Front. Plant Sci.
7 , 1110 (2016). doi:10.3389/fpls.2016.01110; pmid: 27540383
49. J. Köhl, R. Kolnaar, W. J. Ravensberg, Mode of Action of
Microbial Biological Control Agents Against Plant Diseases:
Relevance Beyond Efficacy.Front. Plant Sci. 10 , 845 (2019).
doi:10.3389/fpls.2019.00845; pmid: 31379891
50. M. R. Griffin, inAdvances in Endophytic Research, V. C. Verma,
A. C. Gange, Eds. (Springer, 2014), pp. 257–282.
51. J. A. Vorholt, Microbial life in the phyllosphere.Nat. Rev.
Microbiol. 10 , 828–840 (2012). doi:10.1038/nrmicro2910;
pmid: 23154261
52. J. Imam, P. K. Singh, P. Shukla, Plant microbe interactions in
post genomic era: Perspectives and applications.Front.
Microbiol. 7 , 1488 (2016). doi:10.3389/fmicb.2016.01488;
pmid: 27725809
53. C. Knief, Analysis of plant microbe interactions in the era of next
generation sequencing technologies.Front. Plant Sci. 5 , 216
(2014). doi:10.3389/fpls.2014.00216; pmid: 24904612
54. R. P. Jacoby, S. Kopriva, Metabolic niches in the rhizosphere
microbiome: New tools and approaches to analyse
metabolic mechanisms of plant-microbe nutrient exchange.
J. Exp. Bot. 70 , 1087–1094 (2019). doi:10.1093/jxb/ery438;
pmid: 30576534
55. Y. Baiet al., Functional overlap of the Arabidopsis leaf and
root microbiota.Nature 528 , 364–369 (2015). doi:10.1038/
nature16192; pmid: 26633631
56. S. Pfeilmeieret al., The plant NADPH oxidase RBOHD is
required for microbiota homeostasis in leaves.Nat. Microbiol.
6 , 852–864 (2021). doi:10.1038/s41564-021-00929-5;
pmid: 34194036
57. A. C. Huanget al., A specialized metabolic network selectively
modulatesArabidopsisroot microbiota.Science 364 , eaau6389
(2019). doi:10.1126/science.aau6389; pmid: 31073042
58. K. Zhalninaet al., Dynamic root exudate chemistry and
microbial substrate preferences drive patterns in rhizosphere
microbial community assembly.Nat. Microbiol. 3 , 470– 480
(2018). doi:10.1038/s41564-018-0129-3; pmid: 29556109
59. T. H. Mauchlineet al., An analysis of Pseudomonas genomic
diversity in take-all infected wheat fields reveals the lasting
impact of wheat cultivars on the soil microbiota.Environ.
Microbiol. 17 , 4764–4778 (2015). doi:10.1111/1462-
2920.13038; pmid: 26337499
60. H. Matsumotoet al., Bacterial seed endophyte shapes
disease resistance in rice.Nat. Plants 7 , 60–72 (2021).
doi:10.1038/s41477-020-00826-5; pmid: 33398157
61. Z. Weiet al., Initial soil microbiome composition and functioning
predetermine future plant health.Sci. Adv. 5 , eaaw0759
(2019). doi:10.1126/sciadv.aaw0759; pmid: 31579818
62. F. T. Maestreet al., Increasing aridity reduces soil microbial
diversity and abundance in global drylands.Proc. Natl. Acad.
Sci. U.S.A. 112 , 15684–15689 (2015). doi:10.1073/
pnas.1516684112; pmid: 26647180
63. R. L. Barnard, C. A. Osborne, M. K. Firestone, Responses of
soil bacterial and fungal communities to extreme desiccation
and rewetting.ISME J. 7 , 2229–2241 (2013). doi:10.1038/
ismej.2013.104; pmid: 23823489
64. S. R. Ragusa, D. S. de Zoysa, P. Rengasamy, The effect of
microorganisms, salinity and turbidity on hydraulic
conductivity of irrigation channel soil.Irrig. Sci. 15 , 159– 166
(1994). doi:10.1007/BF00193683
65. L. Lichneret al., Algae influence the hydrophysical
parameters of a sandy soil.Catena 108 , 58–68 (2013).
doi:10.1016/j.catena.2012.02.016
66. F. T. de Vrieset al., Land use alters the resistance and
resilience of soil food webs to drought.Nat. Clim. Change 2 ,
276 – 280 (2012). doi:10.1038/nclimate1368
67. R. F. Harris, inWater Potential Relations in Soil Microbiology,
J. Parr, W. Gardner, L. Elliot, Eds. (Soil Science Society of
America, Madison, WI, 1981), pp. 23–95.
68. E. Uhlírová, D. Elhottová, J. Tríska, H. Santrůcková,
Physiology and microbial community structure in soil at
extreme water content.Folia Microbiol. 50 , 161–166 (2005).
doi:10.1007/BF02931466; pmid: 16110922
69. N. Fiereret al., Cross-biome metagenomic analyses of soil
microbial communities and their functional attributes.
Proc. Natl. Acad. Sci. U.S.A. 109 , 21390–21395 (2012).
doi:10.1073/pnas.1215210110; pmid: 23236140
Cobanet al.,Science 375 , eabe0725 (2022) 4 March 2022 8 of 10
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