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Management of Soil Microbial Communities: Opportunities and Prospects (a Review)

  • SOIL BIOLOGY
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Abstract

The possibilities of regulating soil microbial communities via various agricultural practices and the application of microbial preparations are considered. The total biomass, diversity and activity of microorganisms, as well as the intensity of certain processes, such as nitrogen transformation, can be regulated by agricultural practices. The complicated non-selective effect of these techniques on the microbial community, as well as the high variability of their effects, remains as the challenge. The effectiveness of microbial preparations is determined by the survival rate of introduced microorganisms in the soil, the variety of soil and climatic conditions, and the competition with native soil microorganisms. More rigorous testing of the effectiveness of microbial preparations and biofertilizers by analogy with medical preparations is needed. Integration of agrobiotechnologies with modern concepts of microbial ecology based on molecular-biological methods for studying soil microbial communities is required to develop effective microbial preparations.

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REFERENCES

  1. A. A. Alferov, Associative Nitrogen, Crops, and Agroecosystem Sustainability (Russian Academy of Sciences, Moscow, 2020) [in Russian].

    Google Scholar 

  2. E. V. Blagodatskaya, M. Semenov, and A. V. Yakushev, Activity and Biomass of Soil Microorganisms under Conditions of Changing Environment (KMK, Moscow, 2016) [in Russian].

    Google Scholar 

  3. T. G. Dobrovol’skaya, D. G. Zvyagintsev, I. Yu. Chernov, A. V. Golovchenko, G. M. Zenova, L. V. Lysak, N. A. Manucharova, O. E. Marfenina, L. M. Polyanskaya, A. L. Stepanov, and M. M. Umarov, “The role of microorganisms in the ecological functions of soils,” Eurasian Soil Sci. 48, 959–967 (2015). https://doi.org/10.1134/S1064229315090033

    Article  Google Scholar 

  4. D. G. Zvyagintsev, I. P. Bab’eva, and G. M. Zenova, Biology of Soils (Moscow State Univ., Moscow, 2005) [in Russian].

    Google Scholar 

  5. V. M. Semenov, “Functions of carbon in mineralization-immobilization cycle of nitrogen in soil,” Agrokhimiya, No. 6, 78–96 (2020).

    Google Scholar 

  6. M. V. Semenov, “Metabarcoding and metagenomics in soil ecology research: achievements, challenges, and prospects,” Biol. Bull. Rev. 11, 40–53 (2021).

    Google Scholar 

  7. M. V. Semenov, D. A. Nikitin, A. L. Stepanov, and V. M. Semenov, “The structure of bacterial and fungal communities in the rhizosphere and root-free loci of gray forest soil,” Eurasian Soil Sci. 52, 319–332 (2019). https://doi.org/10.1134/S1064229319010137

    Article  Google Scholar 

  8. M. S. Sokolov, A. I. Marchenko, S. S. Sanin, E. Yu. Toropova, V. A. Chulkina, and A. F. Zakharov, “Healthy soils of agrocenoses as an indicator of its quality and resistance to biotic and abiotic stresses,” Izv. Timiryazevsk. S-kh. Akad., No. 1, 13–22 (2009).

  9. I. A. Tikhonovich and A. A. Zavalin, “Prospective use of nitrogen-fixing and phytostimulating microorganisms to increase the efficiency of the agro-industrial complex and improve the agro-ecological situation in Russian Federation,” Plodorodie, No. 5, 28–31 (2016).

    Google Scholar 

  10. M. M. Umarov, “Nitrogen fixation in associations of organisms,” Probl. Agrokhim. Ekol., No. 2, 22–26 (2009).

  11. M. M. Umarov, A. V. Kurakov, and A. L. Stepanov, Microbiological Transformation of Nitrogen in Soil (GEOS, Moscow, 2007) [in Russian].

    Google Scholar 

  12. T. I. Chernov and A. D. Zhelezova, “The dynamics of soil microbial communities on different timescales: a review,” Eurasian Soil Sci. 53, 643–652 (2020). https://doi.org/10.1134/S106422932005004X

    Article  Google Scholar 

  13. T. I. Chernov, A. K. Tkhakakhova, E. A. Ivanova, O. V. Kutovaya, and V. I. Turusov, “Seasonal dynamics of the microbiome of chernozems of the long-term agrochemical experiment in Kamennaya Steppe,” Eurasian Soil Sci. 48, 1349–1353 (2015). https://doi.org/10.1134/S1064229315120054

    Article  Google Scholar 

  14. E. Aguilera, L. Lassaletta, A. Sanz-Cobena, J. Garnier, and A. Vallejo, “The potential of organic fertilizers and water management to reduce N2O emissions in Mediterranean climate cropping systems. A review,” Agric. Ecosyst. Environ. 164, 32–52 (2013). https://doi.org/10.1016/j.agee.2012.09.006

    Article  Google Scholar 

  15. A. Argaw and A. Mnalku, “Effectiveness of native Rhizobium on nodulation and yield of faba bean (Vicia faba L.) in Eastern Ethiopia,” Arch. Agron. Soil Sci. 63 (10), 1390–1403 (2017).

    Google Scholar 

  16. M. S. Aulakh, J. W. Doran, and A. R. Mosier, Soil Denitrification—Significance, Measurement, and Effects of Management (Springer-Verlag, New York, 1992). https://doi.org/10.1007/978-1-4612-2844-8_1

  17. R. A. Bahulikar, I. Torres-Jerez, E. Worley, K. Craven, and M. K. Udvardi, “Diversity of nitrogen-fixing bacteria associated with switchgrass in the native tallgrass prairie of northern Oklahoma,” Appl. Environ. Microbiol. 80 (18), 5636–5643 (2014).

    Google Scholar 

  18. Y. Bashan, J. W. Kloepper, L. E. de-Bashan, and P. Nannipieri, “A need for disclosure of the identity of microorganisms, constituents, and application methods when reporting tests with microbe-based or pesticide-based products,” Biol. Fertil. Soils 52, 283–284 (2016).

    Google Scholar 

  19. Y. Bashan, L. E. de-Bashan, S. R. Prabhu, and J.‑P. Hernandez, “Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998–2013),” Plant Soil 378 (1), 1–33 (2014).

    Google Scholar 

  20. Y. Bashan, S. R. Prabhu, L. E. de-Bashan, and J. W. Kloepper, “Disclosure of exact protocols of fermentation, identity of microorganisms within consortia, formation of advanced consortia with microbe-based products,” Biol. Fertil. Soils. 56, 443–445 (2020).

    Google Scholar 

  21. A. Basu, P. Prasad, S. N. Das, S. Kalam, R. Z. Sayyed, M. S. Reddy, and H. El Enshasy, “Plant growth promoting rhizobacteria (PGPR) as green bioinoculants: recent developments, constraints, and prospects,” Sustainability 13 (3), 1140 (2021).

    Google Scholar 

  22. D. P. Bebber and V. R. Richards, “A meta-analysis of the effect of organic and mineral fertilizers on soil microbial diversity, bioRxiv, 2020. https://doi.org/10.1101/2020.10.04.325373

  23. S. Berg, P. G. Dennis, C. Paungfoo-Lonhienne, J. Anderson, N. Robinson, R. Brackin, A. Royle, L. DiBella, and S. Schmidt, “Effects of commercial microbial biostimulants on soil and root microbial communities and sugarcane yield,” Biol. Fertil. Soils 56, 565–580 (2019).

    Google Scholar 

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

    Google Scholar 

  25. D. Bottrill, S. M. Ogbourne, N. Citerne, T. Smith, M. B. Farrar, H.-W. Hu, N. Omidvar, J. Wang, J. Burton, W. Kämper, and S. H. Bai, “Short-term application of mulch, roundup and organic herbicides did not affect soil microbial biomass or bacterial and fungal diversity,” Chemosphere 244, 125436 (2020). https://doi.org/10.1016/j.chemosphere.2019.125436

    Article  Google Scholar 

  26. A. Bravo, M. Brands, V. Wewer, P. Dörmann, and M. J. Harrison, “Arbuscular mycorrhiza-specific enzymes FatM and RAM 2 fine-tune lipid biosynthesis to promote development of arbuscular mycorrhiza,” New Phytol. 214 (4), 1631–1645 (2017).

    Google Scholar 

  27. M. C. Brundrett and L. Tedersoo, “Evolutionary history of mycorrhizal symbioses and global host plant diversity,” New Phytol. 220 (4), 1108–1115 (2018).

    Google Scholar 

  28. E. K. Bünemann, G. D. Schwenke, and L. van Zwieten, “Impact of agricultural inputs on soil organisms—a review,” Soil Res. 44 (4), 379–406 (2006). https://doi.org/10.1071/SR05125

    Article  Google Scholar 

  29. P. Calvo, L. Nelson, and J. W. Kloepper, “Agricultural uses of plant biostimulants,” Plant Soil 383 (1), 3–41 (2014).

    Google Scholar 

  30. L. Canfora, C. Costa, F. Pallottino, and S. Mocali, “Trends in soil microbial Inoculants research: a science mapping approach to unravel strengths and weaknesses of their application,” Agriculture 11 (2), 158 (2021).

    Google Scholar 

  31. Y. Chen, J.-B. Fan, L. Du, H. Xu, Q.-H. Zhang, and Y.-Q. He, “The application of phosphate solubilizing endophyte Pantoea dispersa triggers the microbial community in red acidic soil,” Appl. Soil Ecol. 84, 235–244 (2014).

    Google Scholar 

  32. P. Beschoren da Costa, C. E. Granada, A. Ambrosini, F. Moreira, R. de Souza, J. F. M. dos Passos, L. Arruda, and L. M. P. Passaglia, “A model to explain plant growth promotion traits: a multivariate analysis of 2.211 bacterial isolates,” PLoS One 9 (12), e116020 (2014).

    Google Scholar 

  33. J. L. De Bruin, P. Pedersen, S. P. Conley, J. M. Gaska, S. L. Naeve, J. E. Kurle, R. W. Elmore, L. J. Giesler, and L. J. Abendroth, “Probability of yield response to inoculants in fields with a history of soybean,” Crop Sci. 50, 265–272 (2010).

    Google Scholar 

  34. R. Dixon and D. Kahn, “Genetic regulation of biological nitrogen fixation,” Nat. Rev. Microbiol. 2, 621–631 (2004).

    Google Scholar 

  35. F. P. do Amaral, V. C. S. Pankievicz, A. C. M Arisi, E. M. de Souza, F. Pedrosa, and G. Stacey, “Differential growth responses of Brachypodium distachyon genotypes to inoculation with plant growth promoting rhizobacteria,” Plant Mol. Biol. 90, 689–697 (2016).

    Google Scholar 

  36. M. Dubois, L. van den Broeck, and D. Inzé, “The pivotal role of ethylene in plant growth,” Trends Plant Sci. 23 (4), 311–323 (2018).

    Google Scholar 

  37. D. Egamberdieva, S. J. Wirth, A. A. Alqarawi, E. F. Abd-Allah, and A. Hashem, “Phytohormones and beneficial microbes: essential components for plants to balance stress and fitness,” Front. Microbiol. 8, 2104 (2017).

    Google Scholar 

  38. G. C. Ferri, A. L. Braccini, F. B. G. Anghinoni, and L. Caiubi Pereira, “Effects of associated co-inoculation of Bradyrhizobium japonicum with Azospirillum brasilense on soybean yield and growth,” Afr. J. Agric. Res. 12 (1), 6–11 (2017).

    Google Scholar 

  39. K. J. Field and S. Pressel, “Unity in diversity: structural and functional insights into the ancient partnerships between plants and fungi,” New Phytol. 220 (4), 996–1011 (2018).

    Google Scholar 

  40. P. Garbeva and L. Weisskopf, “Airborne medicine: bacterial volatiles and their influence on plant health,” New Phytol. 226 (1), 32–43 (2020).

    Google Scholar 

  41. S. Geisen, E. A. D. Mitchell, S. Adl, M. Bonkowski, M. Dunthorn, F. Ekelund, L. D. Fernández, A. Jousset, V. Krashevska, D. Singer, F. W. Spiegel, J. Walochnik, and E. Lara, “Soil protists: a fertile frontier in soil biology research,” FEMS Microbiol. Rev. 42 (3), 293–323 (2018).

    Google Scholar 

  42. D. Geisseler and K. M. Scow, “Long-term effects of mineral fertilizers on soil microorganisms—a review,” Soil Biol. Biochem. 75, 54–63 (2014). https://doi.org/10.1016/j.soilbio.2014.03.023

    Article  Google Scholar 

  43. B. R. Glick, “Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase,” FEMS Microbiol. Lett. 251, 1–7 (2005).

    Google Scholar 

  44. D. J. Hatch, G. Goodlass, A. Joynes, and M. A. Shepherd, “The effect of cutting, mulching and applications of farmyard manure on nitrogen fixation in a red clover/grass sward,” Bioresour. Technol. 98, 3243–3248 (2007). https://doi.org/10.1016/j.biortech.2006.07.017

    Article  Google Scholar 

  45. R. J. Haynes, “Size and activity of the soil microbial biomass under grass and arable management,” Biol. Fertil. Soils 30, 210–216 (1999). https://doi.org/10.1007/s003740050610

    Article  Google Scholar 

  46. Y. He, H. A. Pantigoso, Z. Wu, and J. M. Vivanco, “Co-inoculation of Bacillus sp. and Pseudomonas putida at different development stages acts as a biostimulant to promote growth, yield and nutrient uptake of tomato,” J. Appl. Microbiol. 127 (1), 196–207 (2019).

    Google Scholar 

  47. J. Holátko, M. Brtnický, J. Kučerík, M. Kotianová, J. Elbl, A. Kintl, J. Kynický, O. Benada, R. Datta, and J. Jansa, “Glomalin—Truths, myths, and the future of this elusive soil glycoprotein,” Soil Biol. Biochem. 153, 108116 (2021). https://doi.org/10.1016/j.soilbio.2020.108116

    Article  Google Scholar 

  48. I. Hussain, G. Aleti, R. Naidu, M. Puschenreiter, Q. Mahmood, M. M. Rahman, F. Wang, S. Shaheen, J. H. Syed, and T. G. Reichenauer, “Microbe and plant assisted-remediation of organic xenobiotics and its enhancement by genetically modified organisms and recombinant technology: a review,” Sci. Total Environ. 628, 1582–1599 (2018).

    Google Scholar 

  49. L. E. Jackson, F. J. Calderon, K. L. Steenwerth, K. M. Scow, and D. E. Rolston, “Responses of soil microbial processes and community structure to tillage events and implications for soil quality,” Geoderma 114, 305–317 (2003). https://doi.org/10.1016/S0016-7061(03)00046-6

    Article  Google Scholar 

  50. K. Johnsen, C. S. Jacobsen, V. Torsvik, and J. Sørensen, “Pesticide effects on bacterial diversity in agricultural soils—a review,” Biol. Fertil. Soils 33 (6), 443–453 (2001). https://doi.org/10.1007/s003740100351

    Article  Google Scholar 

  51. A. Kalia and S. K. Gosal, “Effect of pesticide application on soil microorganisms,” Arch. Agron. Soil Sci. 57 (6), 569–596 (2011). https://doi.org/10.1080/03650341003787582

    Article  Google Scholar 

  52. C. Kallenbach and A. S. Grandy, “Controls over soil microbial biomass responses to carbon amendments in agricultural systems: a meta-analysis,” Agric. Ecosyst. Environ. 144, 241–252 (2011). https://doi.org/10.1016/j.agee.2011.08.020

    Article  Google Scholar 

  53. L. M. Kaminsky, R. V. Trexler, R. J. Malik, K. L. Hockett, and T. H. Bell, “The inherent conflicts in developing soil microbial inoculants,” Trends Biotechnol. 37 (2), 140–151 (2019).

    Google Scholar 

  54. R. Karamanos, N. Flore, and J. Harapiak, “Re-visiting use of Penicillium bilaii with phosphorus fertilization of hard red spring wheat,” Can. J. Plant Sci. 90, 265–277 (2010).

    Google Scholar 

  55. Z. Khatoon, S. Huang, M. Rafique, A. Fakhar, M. A. Kamran, and G. Santoyo, “Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems,” J. Environ. Manage. 273, 111118 (2020).

    Google Scholar 

  56. J. Köhl, R. Kolnaar, and W. J. Ravensberg, “Mode of action of microbial biological control agents against plant diseases: relevance beyond efficacy,” Front. Plant Sci. 10, 845 (2019).

    Google Scholar 

  57. H. D. Krewulak and H. J. Vogel, “Structural biology of bacterial iron uptake,” Biochim. Biophys. Acta, Biomembr. 1778, 1781–804 (2008).

    Google Scholar 

  58. C. Lazcano, M. Gómez-Brandón, P. Revilla, and J. Domínguez, “Short-term effects of organic and inorganic fertilizers on soil microbial community structure and function: a field study with sweet corn,” Biol. Fertil. Soils. 49, 723–733 (2013). https://doi.org/10.1007/s00374-012-0761-7

    Article  Google Scholar 

  59. S. Li, X. Jiang, X. Wang, and A. L. Wright, “Tillage effects on soil nitrification and the dynamic changes in nitrifying microorganisms in a subtropical rice-based ecosystem: a long-term field study,” Soil Tillage Res. 150, 132–138 (2015). https://doi.org/10.1016/j.still.2015.02.005

    Article  Google Scholar 

  60. H. Liu, X. Tan, J. Guo, X. Liang, Q. Xie, and S. Chen, “Bioremediation of oil-contaminated soil by combination of soil conditioner and microorganism,” J. Soils Sediments 20 (4), 2121–2129 (2020).

    Google Scholar 

  61. S. Liu, Y. Zhang, Y. Zong, Z. Hu, S. Wu, J. Zhou, Y. Jin, and J. Zou, “Response of soil carbon dioxide fluxes, soil organic carbon and microbial biomass carbon to biochar amendment: a meta-analysis,” GCB Bioenergy 8, 392–406 (2016). https://doi.org/10.1111/gcbb.12265

    Article  Google Scholar 

  62. I. Loaces, L. Ferrando, and A. F. Scavino, “Dynamics, diversity and function of endophytic siderophore-producing bacteria in rice,” Microb. Ecol. 61 (3), 606–618 (2011).

    Google Scholar 

  63. M. Lori, S. Symnaczik, P. Mäder, G. De Deyn, and A. Gattinger, “Organic farming enhances soil microbial abundance and activity—a meta-analysis and meta-regression,” PLoS One 12, e0180442 (2017). https://doi.org/10.1371/journal.pone.0180442

    Article  Google Scholar 

  64. S. Louca, M. F. Polz, F. Mazel, M. B. N. Albright, J. A. Huber, M. I. O’Connor, M. Ackermann, A. S. Hahn, D. S. Srivastava, S. A. Crowe, M. Doebeli, and L. Wegener Parfrey, “Function and functional redundancy in microbial systems,” Nat. Ecol. Evol. 2 (6), 936–943 (2018).

    Google Scholar 

  65. M. Lu, Y. Yang, Y. Luo, C. Fang, X. Zhou, J. Chen, X. Yang, and B. Li, “Responses of ecosystem nitrogen cycle to nitrogen addition: a meta-analysis,” New Phytol. 189, 1040–1050 (2011). https://doi.org/10.1111/j.1469-8137.2010.03563.x

    Article  Google Scholar 

  66. L. B. Martínez-García, G. Korthals, L. Brussaard, H. Bracht Jørgensen, and G. B. De Deyn, “Organic management and cover crop species steer soil microbial community structure and functionality along with soil organic matter properties,” Agric. Ecosyst. Environ. 263, 7–17 (2018). https://doi.org/10.1016/j.agee.2018.04.018

    Article  Google Scholar 

  67. H. Massalha, E. Korenblum, S. Malitsky, O. H. Shapiro, and A. Aharoni, “Live imaging of root–bacteria interactions in a microfluidics setup,” Proc. Natl. Acad. Sci. U.S.A. 114, 4549–4554 (2017).

    Google Scholar 

  68. P. C. Mawarda, X. Le Roux, J. D. van Elsas, and J. Falcao Salles, “Deliberate introduction of invisible invaders: a critical appraisal of the impact of microbial inoculants on soil microbial communities,” Soil Biol. Biochem. 148, 107874 (2020).

    Google Scholar 

  69. M. D. McDaniel, L. K. Tiemann, and A. S. Grandy, “Does agricultural crop diversity enhance soil microbial biomass and organic matter dynamics? A meta-analysis,” Ecol. Appl. 24, 560–570 (2014). https://doi.org/10.1890/13-0616.1

    Article  Google Scholar 

  70. P. Mehta, R. Sharma, C. Putatunda, and A. Walia, “Endophytic fungi: role in phosphate solubilization,” in Advances in Endophytic Fungal Research (Springer-Verlag, Cham, 2019), pp. 183–209.

    Google Scholar 

  71. M. Naveed, B. Mitter, S. Yousaf, M. Pastar, M. Afzal, and A. Sessitsch, “The endophyte Enterobacter sp. FD17: a maize growth enhancer selected based on rigorous testing of plant beneficial traits and colonization characteristics,” Biol. Fertil. Soils 50, 249–262 (2014).

    Google Scholar 

  72. F. Nobbe and L. Hiltner, US Patent No. 570 813 (1896).

  73. A. Nuzzo, A. Satpute, U. Albrecht, and S. L. Strauss, “Impact of soil microbial amendments on tomato rhizosphere microbiome and plant growth in field soil,” Microb. Ecol. 80 (2), 398–409 (2020).

    Google Scholar 

  74. M. del Carmen Orozco-Mosqueda, C. Velázquez-Becerra, L. I. Macías-Rodríguez, G. Santoyo, I. Flores-Cortez, R. Alfaro-Cuevas, and E. Valencia-Cantero, “Arthrobacter agilis UMCV2 induces iron acquisition in Medicago truncatula (strategy I plant) in vitro via dimethylhexadecylamine emission,” Plant Soil 362 (1), 51–66 (2013).

    Google Scholar 

  75. Y.-S. Park, S. Dutta, M. Ann, J. M. Raaijmakers, and K. Park, “Promotion of plant growth by Pseudomonas fluorescens strain SS101 via novel volatile organic compounds,” Biochem. Biophy. Res. Commun. 461 (2), 361–365 (2015).

    Google Scholar 

  76. J. J. Parnell, R. Berka, H. A. Young, J. M. Sturino, Y. Kang, D. M. Barnhart, and M. V. DiLeo, “From the lab to the farm: an industrial perspective of plant beneficial microorganisms,” Front. Plant Sci. 7, 1110 (2016).

    Google Scholar 

  77. M. Parniske, “Arbuscular mycorrhiza: the mother of plant root endosymbiosis,” Nat. Rev. Microbiol. 6 (10), 763–775 (2008).

    Google Scholar 

  78. M. B. Peoples, D. F. Herridge, and J. K. Ladha, “Biological nitrogen fixation: an efficient source of nitrogen for sustainable agricultural production?” Plant Soil 174, 3–28 (1995).

    Google Scholar 

  79. D. Pflugfelder, R. Metzner, D. van Dusschoten, R. Reichel, S. Jahnke, and R. Koller, “Non-invasive imaging of plant roots in different soils using magnetic resonance imaging (MRI),” Plant Methods 13, 102 (2017).

    Google Scholar 

  80. D. S. Powlson, P. C. Prookes, and B. T. Christensen, “Measurement of soil microbial biomass provides an early indication of changes in total soil organic matter due to straw incorporation,” Soil Biol. Biochem. 19, 159–164 (1987). https://doi.org/10.1016/0038-0717(87)90076-9

    Article  Google Scholar 

  81. J. R. Reeve, C. W. Schadt, L. Carpenter-Boggs, S. Kang, J. Zhou, and J. P. Reganold, “Effects of soil type and farm management on soil ecological functional genes and microbial activities,” ISME J. 4, 1099–1107 (2010). https://doi.org/10.1038/ismej.2010.42

    Article  Google Scholar 

  82. F. Ren, N. Sun, M. Xu, X. Zhang, L. Wu, and M. Xu, “Changes in soil microbial biomass with manure application in cropping systems: a meta-analysis,” Soil Tillage Res. 194, 104291 (2019). https://doi.org/10.1016/j.still.2019.06.008

    Article  Google Scholar 

  83. W. Riah, K. Laval, E. Laroche-Ajzenberg, C. Mougin, X. Latour, and I. Trinsoutrot-Gattin, “Effects of pesticides on soil enzymes: a review,” Environ. Chem. Lett. 12 (2), 257–273 (2014). https://doi.org/10.1007/s10311-014-0458-2

    Article  Google Scholar 

  84. T. Rijavec and A. Lapanje, “Hydrogen cyanide in the rhizosphere: not suppressing plant pathogens, but rather regulating availability of phosphate,” Front. Microbiol. 7, 1785 (2016).

    Google Scholar 

  85. M. C. Rillig, P. W. Ramsey, S. Morris, and E. A. Paul, “Glomalin, an arbuscular-mycorrhizal fungal soil protein, responds to land-use change,” Plant Soil 253 (2), 293–299 (2003).

    Google Scholar 

  86. M. C. Rillig, “Arbuscular mycorrhizae, glomalin, and soil aggregation,” Can. J. Soil Sci. 84, 355–363 (2004). https://doi.org/10.4141/S04-003

    Article  Google Scholar 

  87. M. C. Rillig, N. F. Mardatin, E. F. Leifheit, and P. M. Antunes, “Mycelium of arbuscular mycorrhizal fungi increases soil water repellency and is sufficient to maintain water-stable soil aggregates,” Soil Biol. Biochem. 42, 1189–1191 (2010).

    Google Scholar 

  88. J. I. Rilling, J. J. Acuña, P. Nannipieri, F. Cassan, F. Maruyama, and M. A. Jorquera, “Current opinion and perspectives on the methods for tracking and monitoring plant growth promoting bacteria,” Soil Biol. Biochem. 130, 205–219 (2019).

    Google Scholar 

  89. D. Rojas-Solís, E. Zetter-Salmón, M. Contreras-Pérez, M. del Carmen Rocha-Granados, L. Macías-Rodríguez, and G. Santoyo, “Pseudomonas stutzeri E25 and Stenotrophomonas maltophilia CR71 endophytes produce antifungal volatile organic compounds and exhibit additive plant growth-promoting effects,” Biocatal. Agric. Biotechnol. 13, 46–52 (2018).

    Google Scholar 

  90. R. Ruser and R. Schulz, “The effect of nitrification inhibitors on the nitrous oxide (N2O) release from agricultural soils—a review,” J. Plant Nutr. Soil Sci. 178, 171–188 (2015). https://doi.org/10.1002/jpln.201400251

    Article  Google Scholar 

  91. M. S. Santos, M. A. Nogueira, and M. Hungria, “Microbial inoculants: reviewing the past, discussing the present and previewing an outstanding future for the use of beneficial bacteria in agriculture,” AMB Express 9 (1), 205 (2019).

    Google Scholar 

  92. L. Schütz, A. Gattinger, M. Meier, A. Müller, T. Boller, P. Mäder, and N. Mathimaran, “Improving crop yield and nutrient use efficiency via biofertilization—a global meta-analysis,” Front. Plant Sci. 8, 2204 (2018).

    Google Scholar 

  93. M. V. Semenov, G. S. Krasnov, V. M. Semenov, and A. H. C. van Bruggen, “Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems,” Appl. Soil Ecol. 154, 103641 (2020).

    Google Scholar 

  94. A. Shakoor, S. M. Shahzad, N. Chatterjee, M. S. Arif, T. H. Farooq, M. M. Altaf, M. A. Tufail, A. A. Dar, and T. Mehmood, “Nitrous oxide emission from agricultural soils: application of animal manure or biochar? A global meta-analysis,” J. Environ. Manage. 285, 112170 (2021). https://doi.org/10.1016/j.jenvman.2021.112170

    Article  Google Scholar 

  95. A. Shamseldin, A. Abdelkhalek, and M. J. Sadowsky, “Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review,” Symbiosis 71 (2), 91–109 (2017).

    Google Scholar 

  96. D. N. Smercina, S. E. Evans, M. L. Friesen, and L. K. Tiemann, “To fix or not to fix: controls on free-living nitrogen fixation in the rhizosphere,” Appl. Environ. Microbiol. 85 (6), e02546-18 (2019).

    Google Scholar 

  97. R. D. Souza, A. Ambrosini, and L. M. Passaglia, “Plant growth-promoting bacteria as inoculants in agricultural soils,” Genet. Mol. Biol. 38 (4), 401–419 (2015).

    Google Scholar 

  98. X. S. Tai, W. L. Mao, G. X. Liu, T. Chen, W. Zhang, X. K. Wu, H. Z. Long, B. G. Zhang, and Y. Zhang, “High diversity of nitrogen-fixing bacteria in the upper reaches of the Heihe River, northwestern China,” Biogeosciences 10, 5589–5600 (2013).

    Google Scholar 

  99. C. Thomsen, L. Loverock, V. Kokkoris, T. Holland, P. A. Bowen, and M. Hart, “Commercial arbuscular mycorrhizal fungal inoculant failed to establish in a vineyard despite priority advantage,” Peer J 9, e11119 (2021).

    Google Scholar 

  100. S. Torabian, S. Farhangi-Abriz, and M. D. Denton, “Do tillage systems influence nitrogen fixation in legumes? A review,” Soil Tillage Res. 185, 113–121 (2019). https://doi.org/10.1016/j.still.2018.09.006

    Article  Google Scholar 

  101. D. Trabelsi and R. Mhamdi, “Microbial inoculants and their impact on soil microbial communities: a review,” BioMed Res. Int. 2013, 863240 (2013).

    Google Scholar 

  102. K. K. Treseder, “Nitrogen additions and microbial biomass: a meta-analysis of ecosystem studies,” Ecol. Lett. 11, 1111–1120 (2008). https://doi.org/10.1111/j.1461-0248.2008.01230.x

    Article  Google Scholar 

  103. C. Tu, J. B. Ristaino, and S. Hu, “Soil microbial biomass and activity in organic tomato farming systems: effects of organic inputs and straw mulching,” Soil Biol. Biochem. 38, 247–255 (2006). https://doi.org/10.1016/j.soilbio.2005.05.002

    Article  Google Scholar 

  104. O. Tyc, C. Song, J. S. Dickschat, M. Vos, and P. Garbeva, “The ecological role of volatile and soluble secondary metabolites produced by soil bacteria,” Trends Microbiol. 25 (4), 280–292 (2017).

    Google Scholar 

  105. A. H. C. van Bruggen and M. R. Finckh, “Plant diseases and management approaches in organic farming systems,” Annu. Rev. Phytopathol. 54, 25–54 (2016).

    Google Scholar 

  106. A. H. C. van Bruggen, M. He, V. V. Zelenev, V. M. Semenov, A. M. Semenov, E. V. Semenova, T. V. Kuznetsova, A. K. Khodzaeva, A. M. Kuznetsov, and M. V. Semenov, “Relationships between greenhouse gas emissions and cultivable bacterial populations in conventional, organic and long-term grass plots as affected by environmental variables and disturbances,” Soil Biol. Biochem. 114, 145–159 (2017).

    Google Scholar 

  107. D. van Dusschoten, R. Metzner, J. Kochs, J. A. Postma, D. Pflugfelder, J. Bühler, U. Schurr, and S. Jahnke, “Quantitative 3D analysis of plant roots growing in soil using magnetic resonance imaging,” Plant Physiol. 170 (3), 1176–1188 (2016).

    Google Scholar 

  108. Z. S. Venter, K. Jacobs, and H. J. Hawkins, “The impact of crop rotation on soil microbial diversity: a meta-analysis,” Pedobiologia 59 (4), 215–223 (2016). https://doi.org/10.1016/j.pedobi.2016.04.001

    Article  Google Scholar 

  109. J. Wang, D. R. Chadwick, Y. Cheng, and X. Yan, “Global analysis of agricultural soil denitrification in response to fertilizer nitrogen,” Sci. Total Environ. 616, 908–917 (2018). https://doi.org/10.1016/j.scitotenv.2017.10.229

    Article  Google Scholar 

  110. J. Wang and J. Zou, “No-till increases soil denitrification via its positive effects on the activity and abundance of the denitrifying community,” Soil Biol. Biochem. 142, 107706 (2020). https://doi.org/10.1016/j.soilbio.2020.107706

    Article  Google Scholar 

  111. X. Wei, T. Ge, C. Wu, S. Wang, K. Mason-Jones, Y. Li, Z. Zhu, Y. Hu, C. Liang, J. Shen, J. Wu, and Y. Kuzyakov, “T4-like phages reveal the potential role of viruses in soil organic matter mineralization,” Environ. Sci. Technol. 55 (9), 6440–6448 (2021). https://doi.org/10.1021/acs.est.0c06014

    Article  Google Scholar 

  112. A. Wolińska, A. Kuźniar, U. Zielenkiewicz, A. Banach, D. Izak, Z. Stępniewska, and M. Błaszczyk, “Metagenomic analysis of some potential nitrogen-fixing bacteria in arable soils at different formation processes,” Microb. Ecol. 73 (1), 162–176 (2017).

    Google Scholar 

  113. M. E. Xenia and R. V. Refugio, “Microorganisms metabolism during bioremediation of oil contaminated soils,” J. Bioremed. Biodegrad. 7 (2), 1000340 (2016).

    Google Scholar 

  114. S. H. Youseif, F. H. Abd El-Megeed, and S. A. Saleh, “Improvement of faba bean yield using Rhizobium/Agrobacterium inoculant in low-fertility sandy soil,” Agronomy 7 (1), 2 (2017). https://doi.org/10.3390/agronomy7010002

    Article  Google Scholar 

  115. M. Zhou, B. Zhu, S. Wang, X. Zhu, H. Vereecken, and N. Brüggemann, “Stimulation of N2O emission by manure application to agricultural soils may largely offset carbon benefits: a global meta-analysis,” Global Change Biol. 23, 4068–4083 (2017). https://doi.org/10.1111/gcb.13648

    Article  Google Scholar 

  116. Z. Zhou, C. Wang, and Y. Luo, “Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality,” Nat. Commun. 11, 3072 (2020). https://doi.org/10.1038/s41467-020-16881-7

    Article  Google Scholar 

  117. S. M. Zuber and M. B. Villamil, “Meta-analysis approach to assess effect of tillage on microbial biomass and enzyme activities,” Soil Biol. Biochem. 97, 176–187 (2016). https://doi.org/10.1016/j.soilbio.2016.03.011

    Article  Google Scholar 

  118. Plant for performance and grow with confidence with biotrinsic. https://www.indigoag.com/biologicals/for-farmers.

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Funding

This study was supported by the Russian Foundation for Basic Research, project no. 20-116-50004.

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  1. Dokuchaev Soil Science Institute, per. Pyzhevskii 7, 119017, Moscow, Russia

    T. I. Chernov & M. V. Semenov

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  1. T. I. Chernov
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Translated by D. Konyushkov

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Chernov, T.I., Semenov, M.V. Management of Soil Microbial Communities: Opportunities and Prospects (a Review). Eurasian Soil Sc. 54, 1888–1902 (2021). https://doi.org/10.1134/S1064229321120024

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