Agricultural Soil Management Impacts on Soil Microbial Communities

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Frontier Studies in Soil Science

Part of the book series: Frontier Studies in Soil Science ((FSSS))

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Abstract

Soil microbial communities are significantly affected by agricultural soil management. Inappropriate management can be a cause of land degradation and ecosystem services loss. This chapter aims to assess the impacts of agricultural soil management on soil microbiome. In large amounts, fertilizers and pesticides can affect the soil microbial structure and communities and change ground interactions between different ecological-trophic groups of microorganisms. Soil microbiological activity directly impacts plant biomass production and determines the ecological state of soils. The excessive use of mineral fertilizers affects the mineralization process and reduces microbiological diversity and soil organic matter. Organic fertilizers can positively affect soil properties (e.g., soil structure, fertility) and soil microbiome (diversity, microbial biomass, activity). Nevertheless, before using it, it is essential to identify the presence of antibiotic residues not to increase soil pollution and prevent it from entering the food chain. Control of contamination by antimicrobial substances is crucial for the elimination of spreading antibiotic-resistant bacteria in the environment. This is an additional tool for the prevention formation of soil resistome.

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References

  1. Ashraf MY, Gul A, Ashraf M, Hussain F, Ebert G (2010) Improvement in yield and quality of kinnow (Citrus deliciosa × Citrus nobilis) by potassium fertilisation. J Plant Nutr 33:1625–1637. https://doi.org/10.1080/01904167.2010.496887

    Article  Google Scholar 

  2. Auffret MD, Karhu K, Khachane A, Dungait JAJ, Fraser F, Hopkins DW, Wookey PA, Singh BK, Freitag TE, Hartley IP, Prosser JI (2016) The role of microbial community composition in controlling soil respiration responses to temperature. PLoS One 11(10):e0165448. https://doi.org/10.1371/journal.pone.0165448

    Article  Google Scholar 

  3. Azzi V, Kazpard V, Lartiges B, Kobeissi A, Kanso A, El Samrani AG (2017) Trace metals in phosphate fertilizers Used in Eastern Mediterranean Countries. Clean Soil Air Water 45. https://doi.org/10.1002/clen.201500988

  4. Bai YC, Chang YY, Hussain M, Lu B, Zhang JP, Song XB, Lei XS, Pei D (2020) Soil chemical and microbiological properties are changed by long-term chemical fertilizers that limit ecosystem functioning. Microorganisms 8(5):694. https://doi.org/10.3390/microorganisms8050694

  5. Bakalár T, Pavolová H, Šimková Z, Bednárová L (2022) Phosphorus management in Slovakia—a case study. Sustainability 14(16):10374. https://doi.org/10.3390/su141610374

    Article  Google Scholar 

  6. Bender S, Van der Heijden M (2015) Soil biota enhance agricultural sustainability by improving crop yield, nutrient uptake and reducing nitrogen leaching losses. J Appl Ecol 52:228–239. https://doi.org/10.1111/1365-2664.12351

    Article  Google Scholar 

  7. Bengtsson-Palme J, Kristiansson E, Larsson DGJ (2018) Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiol Rev 2018 Jan 1;42(1):fux053. https://doi.org/10.1093/femsre/fux053

  8. Bulteel AJB, Larson EL, Getahun H (2020) Identifying global research gaps to mitigate antimicrobial resistance: a sco** review. Am J Infect Contr 49:818–824. https://doi.org/10.1016/j.ajic.2020.11.024

    Article  Google Scholar 

  9. Chen W, He ZL, Yang XE, Mishra S, Stoffella PJ (2010) Chlorine nutrition of higher plants: progress and perspectives. J Plant Nutr 33:943–952. https://doi.org/10.1080/01904160903242417

    Article  Google Scholar 

  10. Costa VM, McGrann KM, Hughes DW, Wright GD (2006) Sampling the antibiotic resistome. Science, 20, 311(5759):374–377. https://doi.org/10.1126/science.1120800. PMID: 16424339

  11. Delgado-Baquerizo M et al (2016) Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun 7:10541. https://doi.org/10.1038/ncomms10541

    Article  Google Scholar 

  12. Demyanyuk O, Symochko L, Mostoviak I (2020) Soil microbial diversity and activity in different climatic zones of Ukraine. Regul Mech Biosyst 11(2):338–343 https://doi.org/10.15421/022051

  13. Ding GC, Radl V, Schloter-Hai B, Jechalke S, Heuer H, Smalla K, Schloter M (2014) Dynamics of soil bacterial communities in response to repeated application of manure containing sulfadiazine. PLoS One 26;9(3):e92958. https://doi.org/10.1371/journal.pone.0092958

  14. Garg S, Banerjee B (2021) One world, one health. Indian J Community Med 46(4):581–583. https://doi.org/10.4103/ijcm.ijcm_1230_21

    Article  Google Scholar 

  15. Gaze WH, Zhang L, Abdouslam NA, Hawkey PM, Calvo-Bado L, Royle J, Brown H, Davis S, Kay P, Boxall AB, Wellington EM (2011) Impacts of anthropogenic activity on the ecology of class 1 integrons and integron-associated genes in the environment. ISME J 5(8):1253–61. https://doi.org/10.1038/ismej.2011.15. Epub 2011 Mar 3. PMID: 21368907; PMCID: PMC3146270

  16. Geilfus CM (2018) Review on the significance of chlorine for crop yield and quality. Plant Sci 270:114–122. https://doi.org/10.1016/j.plantsci.2018.02.014

    Article  Google Scholar 

  17. Gheysari M, Mirlatifi SM, Homaee M, Asadi ME, Hoogenboom G (2009) Nitrate leaching in a silage maise field under different irrigation and nitrogen fertilizer rates. Agri Water Manag 96:946–954. https://doi.org/10.1016/j.agwat.2009.01.005

  18. Hachiya T, Sakakibara H (2017) Interactions between nitrate and ammonium in their uptake, allocation, assimilation, and signaling in plants. J Exp Bot. 1;68(10):2501–2512. https://doi.org/10.1093/jxb/erw449

  19. Hammad HM, Chawla MS, Jawad R, Alhuqail A, Bakhat HF, Farhad W, Khan F, Mubeen M, Shah AN, Liu K, Harrison MT, Saud S, Fahad S (2022) Evaluating the impact of nitrogen application on growth and productivity of maize under control conditions. Front Plant Sci 13:885479. https://doi.org/10.3389/fpls.2022.885479

    Article  Google Scholar 

  20. Hao H, Cheng G, Iqbal Z, Ai X, Hussain HI, Huang L, Dai M, Wang Y, Liu Z, Yuan Z (2014) Benefits and risks of antimicrobial use in food-producing animals. Front Microbiol 12(5):288. https://doi.org/10.3389/fmicb.2014.00288

    Article  Google Scholar 

  21. Hartmann M, Frey B, Mayer J, Mader P, Widmer F (2015) Distinct soil microbial diversity under long-term organic and conventional farming. Multidisc J Microbial Ecol 9:1177–1194. https://doi.org/10.1038/ismej.2014.210

    Article  Google Scholar 

  22. Heuer H, Smalla K (2012) Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol Rev 36(6):1083–1104. https://doi.org/10.1111/j.1574-6976.2012.00337.x

    Article  Google Scholar 

  23. Ichihashi Y et al (2020) Multi-omics analysis on an agroecosystem reveals thesignificant role of organic nitrogen to increaseagricultural crop yield. PNAS 117(25):14552–14560. https://doi.org/10.1073/pnas.1917259117

    Article  Google Scholar 

  24. Irfan M, Almotiri A, AlZeyadi ZA (2022) Antibiotics (Basel), 5, 11(10):1362. https://doi.org/10.3390/antibiotics11101362.PMID: 36290020

  25. Kaviani Rad A, Astaykina A, Streletskii R, Afsharyzad Y, Etesami H, Zarei M, Balasundram SK (2022) An overview of antibiotic resistance and abiotic stresses affecting antimicrobial resistance in agricultural soils. Int J Environ Res Pub Health 12;19 (8):4666. https://doi.org/10.3390/ijerph19084666

  26. Kleijn D, Baquero RA, Clough Y, Díaz M, De Esteban J, Fernández F, Gabriel D, Herzog F, Holzschuh A, Jöhl R, Knop E, Kruess A, Marshall EJ, Steffan-Dewenter I, Tscharntke T, Verhulst J, West TM, Yela JL (2006) Mixed biodiversity benefits of agri-environment schemes in five European countries. Ecol Lett Mar; 9(3):243–254; discussion 254–257. https://doi.org/10.1111/j.1461-0248.2005.00869.x

  27. Koch N, Islam NF, Sonowal S, Prasad R, Sarma H (2021) Environmental antibiotics and resistance genes as emerging contaminants: methods of detection and bioremediation. Curr Res Microb Sci 14(2):100027. https://doi.org/10.1016/j.crmicr.2021.100027

    Article  Google Scholar 

  28. Krauss J, Gallenberger I, Steffan-Dewenter I (2011) Decreased functional diversity and biological pest control in conventional compared to organic crop fields. PLoS One 6(5):e19502. https://doi.org/10.1371/journal.pone.0019502

    Article  Google Scholar 

  29. Kubier A, Wilkin RT, Pichler T (2019) Cadmium in soils and groundwater: a review. Appl Geochem 1(108):1–16. https://doi.org/10.1016/j.apgeochem.2019.104388

    Article  Google Scholar 

  30. Larramendy M, Soloneski S (2021) Soil contamination—threats and sustainable solutions. IntechOpen, London. https://doi.org/10.5772/intechopen.87652

    Article  Google Scholar 

  31. Lauber CL, Ramirez KS, Aanderud Z, Lennon J, Fierer N (2013) Temporal variability in soil microbial communities across land-use types. Multidisc J Microbial Ecol 7:1641–1650. https://doi.org/10.1038/ismej.2013.50

    Article  Google Scholar 

  32. Liu X, Liu X, Liu W, Tan Q, Hu C, Li J (2021) Nutritional status of different citrus trees and the recommended dosages of N, P and K for citrus production in China. J Plant Nutr 27:565–574. https://doi.org/10.11674/zwyf.20457

  33. Lupatini M, Korthals GW, de Hollander M, Janssens TK, Kuramae EE (2017) Soil microbiome is more heterogeneous in organic than in conventional farming system. Front Microbiol 4(7):2064. https://doi.org/10.3389/fmicb.2016.02064

    Article  Google Scholar 

  34. Mackenzie JS, McKinnon M, Jeggo M (2014) One health: from concept to practice. Confronting Emerg Zoonoses 19:163–189. https://doi.org/10.1007/978-4-431-55120-1_8

    Article  Google Scholar 

  35. Martin EA, Feit B, Requier F, Friberg H (2019) Assessing the resilience of biodiversity-driven functions in agroecosystems under environmental change. Adv Ecol Res 60:59–123. https://doi.org/10.1016/bs.aecr.2019.02.003

    Article  Google Scholar 

  36. Muratore C, Espen L, Prinsi B (2021) Nitrogen uptake in plants: the plasma membrane root transport systems from a physiological and proteomic perspective. Plants (Basel). Apr 1; 10(4):681. https://doi.org/10.3390/plants10040681

  37. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG (2016) The structure and diversity of human, animal and environmental resistomes. Microbiome, 7, 4(1):54. https://doi.org/10.1186/s40168-016-0199-5.

  38. Patyka VP, Symochko LY (2013) Soil microbiological monitoring of natural and transformed ecosystems in the trans-Carpathian region of Ukraine. Microbiol J 75(2):21–31

    Google Scholar 

  39. Pawuła A (2022) Radioactive elements in phosphorous fertilizer-basalt flour-recommended mineral fertilizer. J Geosci Environ Protect 10:15–32. https://doi.org/10.4236/gep.2022.104002

    Article  Google Scholar 

  40. Pereira P (2020) Ecosystem services in a changing environment. Sci Total Environ 702:135008

    Article  Google Scholar 

  41. Pereira P, Barcelo D, Panagos P (2020) Soil and water threats in a changing environment. Environ Res 186:109501

    Article  Google Scholar 

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

    Article  Google Scholar 

  43. Popp J, Pető K, Nagy J (2013) Pesticide productivity and food security. A review. Agron Sustain Dev 33:243–255. https://doi.org/10.1007/s13593-012-0105-x

    Article  Google Scholar 

  44. Pruden A, Pei R, Storteboom H, Carlson K (2006) Antibiotic resistance genes as emerging contaminants: studies in northern Colorado. Environ Sci Technol 40(23):7445–7450. https://doi.org/10.1021/es060413l

    Article  Google Scholar 

  45. Qian X, Gunturu S, Guo J (2021) Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems. Microbiome 9:108. https://doi.org/10.1186/s40168-021-01047-4

    Article  Google Scholar 

  46. Quaggio JA, Mattos D, Cantarella H, Almeida ELE, Cardoso SAB (2002) Lemon yield and fruit quality affected by NPK fertilisation. Sci Horticult 96:151–162. https://doi.org/10.1016/S0304-4238(02)00121-8

    Article  Google Scholar 

  47. Santos LF, Olivares FL (2021) Plant microbiome structure and benefits for sustainable agriculture. Curr Plant Biol 26:100198. https://doi.org/10.1016/j.cpb.2021.100198

  48. Schmidt R, Gravuer K, Bossange AV, Mitchell J, Scow K (2018) Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil. PLoS One 13:e0192953. https://doi.org/10.1371/journal.pone.0192953

    Article  Google Scholar 

  49. Sengupta S, Chattopadhyay MK, Grossart HP (2013) The multifaceted roles of antibiotics and antibiotic resistance in nature. Front Microbiol 12(4):47. https://doi.org/10.3389/fmicb.2013.00047

    Article  Google Scholar 

  50. Sharma SK, Ramesh A, Sharma MP, Joshi OP, Govaerts B, Steenwerth KL, Karlen DL (2010) Microbial community structure and diversity as indicators for evaluating soil quality. biodiversity, biofuels, agroforestry and conservation agriculture. Sustainable agriculture reviews. Springer, Dordrecht, pp 317–358. https://doi.org/10.1007/978-90-481-9513-8_1

  51. Singh B, Trivedi P (2017) Microbiome and the future for food and nutrient security. Microb Biotechnol 10:50–53. https://doi.org/10.1111/1751-7915.12592

    Article  Google Scholar 

  52. Symochko L (2020) Soil microbiome: diversity, activity, functional and structural successions. Int J Ecosyst Ecol Sci (IJEES) 10(2):277–284. https://doi.org/10.31407/ijees10.206

  53. Symochko L, Bugyna L, Hafiiyak O (2021) Ecological aspects of biosecurity in modern agroecosystems. Int J Ecosyst Ecol Sci (IJEES) 11(1):181–186.https://doi.org/10.31407/ijees11.124

  54. Symochko L, Meleshko T, Symochko V, Boyko N (2018) Microbiological control of soil-borne antibiotic resistance human pathogens in agroecosystems. Int J Ecosyst Ecol Sci (IJEES) 8(3):591–598. https://doi.org/10.31407/ijees8320

  55. Symochko L, Hamuda H, Demyanyuk O, Symochko V, Patyka V (2019) Soil microbial diversity and antibiotic resistance in natural and transformed ecosystems. Int J Ecosyst Ecol Sci (IJEES) 9(3):581–590. https://doi.org/10.31407/ijees

  56. Symochko L.Yu., Kalinichenko A.V. (2018) Soil Microbiome of Primeval Forest Ecosystems in Transcarpathia. Mikrobiolohichnyi Zhurnal, 80 (3), 3–14. doi: https://doi.org/10.15407/microbiolj80.03.003

  57. Trivedi P et al (2021) Enabling sustainable agriculture through understanding and enhancement of microbiomes. New Phytol 230(6), 2129-2147. https://doi.org/10.1111/nph.17319

  58. Wakelin SA (2018) Managing soil microbiology: realising opportunities for the productive land-based sectors. N Z J Agric Res 61:358–376. https://doi.org/10.1080/00288233.2016.1209529

    Article  Google Scholar 

  59. Wang L, Chai B (2022) Fate of antibiotic resistance genes and changes in bacterial community with increasing breeding scale of layer manure. Front Microbiol 9;13:857046. https://doi.org/10.3389/fmicb.2022.857046. eCollection 2022. PMID: 35356511

  60. Wang S, Feng X, Wang Y, Zheng Z, Li T, He S et al (2019) Characteristics of nitrogen loss in slo** farmland with purple soil in southwestern China during maise (Zea mays L.) growth stages. Catena 182:104169. https://doi.org/10.1016/j.catena.2019.104169

  61. Wright GD (2010) The antibiotic resistome. Expert Opin Drug Discov 5(8):779–788. https://doi.org/10.1517/17460441.2010.497535

    Article  Google Scholar 

  62. Xu X, Du X, Wang F, Sha J, Chen Q, Tian G, Zhu Z, Ge S, Jiang Y (2020) Effects of potassium levels on plant growth, accumulation and distribution of carbon, and nitrate metabolism in apple dwarf rootstock seedlings. Front Plant Sci 11. https://doi.org/10.3389/fpls.2020.00904

  63. Yang G, Wagg C, Veresoglou SD, Rillig MC, Hempel S (2018) How soil biota drive ecosystem stability. Trends Plant Sci 23(12):1057–1067. https://doi.org/10.1016/j.tplants.2018.09.007

    Article  Google Scholar 

  64. Yuan HZ, Ge TD, Wu XH, Liu SL, Tong CL, Qin HL et al (2012) Long-term field fertilisation alters the diversity of autotrophic bacteria based on the ribulose 1,5-hiphosphate carboxylase/oxygenase (RubisCO) large subunit genes in paddy soil. Appl Microbiol Biot 95:1061–1071. https://doi.org/10.1007/s00253-011-3760-y

    Article  Google Scholar 

  65. Zhang YG, Li DQ, Wang HM, **ao QM, Liu XD (2006) Molecular diversity of nitrogen-fixing bacteria from the Tibetan Plateau, China. FEMS Microbiol Lett 260:134–142. https://doi.org/10.1111/j.1574-6968.2006.00317.x

    Article  Google Scholar 

  66. Zhao ZB, He JZ, Geisen S et al (2019) Protist communities are more sensitive to nitrogen fertilisation than other microorganisms in diverse agricultural soils. Microbiome 7:33. https://doi.org/10.1186/s40168-019-0647-0

    Article  Google Scholar 

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Symochko, L., Pereira, P. (2024). Agricultural Soil Management Impacts on Soil Microbial Communities. In: Núñez-Delgado, A. (eds) Frontier Studies in Soil Science. Frontier Studies in Soil Science. Springer, Cham. https://doi.org/10.1007/978-3-031-50503-4_6

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