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Antibiotics and Microbial Antibiotic Resistance in Soil

  • Ali-Akbar Safari-SineganiEmail author
  • Mehdi Rashtbari
  • Nayereh Younessi
  • Babak Mashkoori
Chapter

Abstract

Induced antibiotic resistance in both clinical and nonclinical strains, caused by selective agents of antibiotic resistance genes, considered as one of the most important challenges of the present century. Evidences support increasing antibiotic resistance in the organic waste- treated soils which might affect soil biological and functional diversity. Manure, toxic compounds like insecticides, herbicides and chemical fertilizers which contain heavy metals are among the most important origins of antibiotic resistance in soil and dissemination of resistance determinants within ecosystem. Heavy metals could confer antibiotic resistance to microorganisms. Most of heavy metal resistance mechanisms are the same as antibiotic resistance. In most soils, heavy metal concentration is also much higher than antibiotic concentration. Therefore, it seems that the first option to control antibiotic resistance is the evaluating of resistance degree in specific habitats like soil, underground waters and manures which could participate in increasing the antibiotic resistance in the environment. Hence, the present paper aims to show the importance of antibiotics in soil and their impact on microbial functions and antibiotic resistance.

Keywords

Antibiotic sorption Enzyme activity Antibiotic function Gene Transfer Heavy metals Multiple antibiotic resistance (MAR) 

References

  1. Alighardashi A, Rashidi A, Neshat AA et al (2014) Environmental risk of selected antibiotics in Iran. IJHSE 1(3):132–137Google Scholar
  2. Amin MM, Hashemi H, Ebrahimi A et al (2012) Effects of oxytetracycline, tylosin, and amoxicillin antibiotics on specific methanogenic activity of anaerobic biomass. Int J Env Health Eng 1(4):1–4Google Scholar
  3. Ansari F (2001) Use of systematic anti-infectives agent in Iran during 1997-1998. Eur J Clin Pharmacol 57(6–7):547–551PubMedCrossRefPubMedCentralGoogle Scholar
  4. Baltz RH (2006) Marcel Faber roundtable: is our antibiotic pipeline unproductive because of starvation, constipation or lack of inspiration? J Ind Microbiol Biotechnol 33:507–513PubMedCrossRefPubMedCentralGoogle Scholar
  5. Baquero F, Alvarez-Ortega C, Martinez J (2009) Ecology and evolution of antibiotic resistance. Environ Microbiol Rep 1:469–476PubMedCrossRefPubMedCentralGoogle Scholar
  6. Berg J, Tom Petersen A, Nybroe O (2005) Copper amendment of agricultural soil selects for bacterial antibiotic resistance in the field. Lett Appl Microbiol 40:146–151CrossRefGoogle Scholar
  7. Bibbal D, Dupouy V, Ferré JP et al (2007) Impact of three ampicillin dosage regimens on selection of ampicillin resistance in Enterobacteriaceae and excretion of blaTEM genes in swine feces. Appl Environ Microbiol 73:4785–4790PubMedPubMedCentralCrossRefGoogle Scholar
  8. Binh CTT, Heuer H, Kaupenjohann M et al (2008) Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids. FEMS Microbiol Ecol 66:25–37PubMedCrossRefPubMedCentralGoogle Scholar
  9. Binh CTT, Heuer H, Gomes NCM et al (2010) Similar bacterial community structure and high abundance of sulfonamide resistance genes in field-scale manures. In Manure: management, uses and environmental impacts. Dellaguardia CS. Hauppauge, NY, New York: Nova Science Publishers, p141–166.Google Scholar
  10. Boxall AB, Blackwell P, Cavallo R et al (2002) The sorption and transport of a sulphonamide antibiotic in soil systems. Toxicol Lett 131:19–28PubMedCrossRefPubMedCentralGoogle Scholar
  11. Bradbury JF (1986) Guide to plant pathogenic bacteria. CAB international, Kew, pp. xviii + 332ppGoogle Scholar
  12. Burkhardt M, Stamm C, Waul C et al (2005) Surface runoff and transport of sulfonamide antibiotics and tracers on manured grassland. J Environ Qual 34:1363–1371PubMedCrossRefPubMedCentralGoogle Scholar
  13. Byrne-Bailey K, Gaze WH, Kay P, Boxall A, Hawkey PM, Wellington EM (2009) Prevalence of sulfonamide resistance genes in bacterial isolates from manured agricultural soils and pig slurry in the United Kingdom. Antimicrob Agents Chemother 53:696–702PubMedCrossRefPubMedCentralGoogle Scholar
  14. Casjens S (1998) The diverse and dynamic structure of bacterial genomes. Ann Rev Genet 32:339–377PubMedCrossRefPubMedCentralGoogle Scholar
  15. Chen W, Liu W, Pan N et al (2013) Oxytetracycline on functions and structure of soil microbial community. J Soil Sci Plant Nutr 13(4):967–975Google Scholar
  16. Chessa L, Pusino G, Pasqualina Mangia N (2016) Soil microbial response to tetracycline in two different soils amended with cow manure. Environ Sci Pollut Res 23:5807–5817CrossRefGoogle Scholar
  17. Clewell DB, Flannagan SE, Jaworski DD (1995) Unconstrained bacterial promiscuity: the Tn916–Tn1545 family of conjugative transposons. Trends Microbiol 3:229–236PubMedCrossRefPubMedCentralGoogle Scholar
  18. Cobine P, Wickramasinghe WA, Harrison MD et al (1999) The Enterococcus hirae copper chaperone CopZ delivers copper (I) to the CopY repressor. FEBS Lett 445:27–30PubMedCrossRefPubMedCentralGoogle Scholar
  19. Dantas G, Sommer MO, Oluwasegun RD, Church GM (2008) Bacteria subsisting on antibiotics. Science 320:100–103PubMedCrossRefPubMedCentralGoogle Scholar
  20. Davies J, Spiegelman GB, Yim G (2006) The world of sub-inhibitory antibiotic concentrations. Curr Opin Microbiol 9:445–453PubMedCrossRefPubMedCentralGoogle Scholar
  21. Ding GC, Radi V, Ter-Hai BS et al (2014) Dynamics of soil bacterial communities in response to repeated application of manure containing sulfadiazine. PLoS One 9(3):1–10Google Scholar
  22. Eager RM, Cunningham CC, Senzer N, Richards DA, Raju RN, Jones B et al (2009) Phase II trial of talabostat and docetaxel in advanced non-small cell lung cancer. Clin Oncol (R Coll Radiol) 21(6):464–472CrossRefGoogle Scholar
  23. Ebadi S, Sohrabi H, Peymani A et al (2018) Identification of antibiotic-producing Streptomyces species in Iran’s soil by phenotypic and genotypic methods. Biotech Health Sci 5(1):e59854Google Scholar
  24. Enne VI, Cassar C, Sprigings K et al (2008) A high prevalence of antimicrobial resistant Escherichia coli isolated from pigs and a low prevalence of antimicrobial resistant E. coli from cattle and sheep in Great Britain at slaughter. FEMS Microbiol Lett 278:193–199PubMedCrossRefPubMedCentralGoogle Scholar
  25. Gao J, Pedersen JA (2005) Adsorption of sulfonamide antimicrobial agents to clay minerals. Environ Sci Technol 39:9509–9516PubMedCrossRefPubMedCentralGoogle Scholar
  26. Ghosh S, LaPara TM (2007) The effects of subtherapeutic antibiotic use in farm animals on the proliferation and persistence of antibiotic resistance among soil bacteria. ISME J 1:191–203PubMedCrossRefPubMedCentralGoogle Scholar
  27. Gotz A, Smalla K (1997) Manure enhances plasmid mobilization and survival of Pseudomonas putida introduced into field soil. Appl Environ Microbiol 63:1980–1986PubMedPubMedCentralGoogle Scholar
  28. Gupta G, Parihar SS, Ahirwar NK et al (2015) Plant growth promoting rhizobacteria (PGPR): current and future prospects for development of sustainable agriculture. J Microb Biochem Technol 7:096–102.  https://doi.org/10.4172/1948-5948.1000188CrossRefGoogle Scholar
  29. Hammesfahr U, Kotzerke A, Lamshöft M, Wilke BM, Kandeler E, Thiele-Bruhn S (2011) Effects of sulfadiazine-contaminated fresh and stored manure on a soil microbial community. Eur J Soil Biol 47:61–68CrossRefGoogle Scholar
  30. Hamscher G, Sczesny S, Höper H et al (2002) Determination of persistent tetracycline residues in soil fertilized with liquid manure by high-performance liquid chromatography with electrospray ionization tandem mass spectrometry. Anal Chem 74:1509–1518PubMedCrossRefPubMedCentralGoogle Scholar
  31. Han I, Congeevaram S, Park J (2009) Improved control of multiple-antibiotic-resistance-related microbial risk in swine manure wastes by autothermal thermophilic aerobic digestion. Water Sci Technol 59(2):267–271PubMedCrossRefPubMedCentralGoogle Scholar
  32. Heise J, Höltge S, Schrader S et al (2006) Chemical and biological characterization of non-extractable sulfonamide residues in soil. Chemosphere 65:2352–2357PubMedCrossRefPubMedCentralGoogle Scholar
  33. Heuer H, Smalla K (2007a) Manure and sulfadiazine synergistically increased bacterial antibiotic resistance in soil over at least two months. Environ Microbiol 9:657–666PubMedCrossRefPubMedCentralGoogle Scholar
  34. Heuer H, Smalla K (2007b) Manure and sulfadiazine synergistically increased bacterial antibiotic resistance in soil over at least two months. Environ Microbiol 9:657–666PubMedCrossRefPubMedCentralGoogle Scholar
  35. Heuer H, Krogerrecklenfort E, Wellington EMH, Egan S, Van Elsas JD, Van Overbeek L et al (2002) Gentamycin resistance genes in environmental bacteria: prevalence and transfer. FEMS Microbiol Ecol 42:289–302PubMedCrossRefPubMedCentralGoogle Scholar
  36. Huddleston AS, Cresswell N, Neves M et al (1997) Molecular detection of streptomycin-producing streptomycetes in Brazilian soils. Appl Environ Microbiol 63:1288–1297PubMedPubMedCentralGoogle Scholar
  37. Jafari N, Behroozi R, Farajzadeh D et al (2014) Antibacterial activity of Pseudonocardia sp. JB05, a rare salty soil actinomycete against Staphylococcus aureus. Biomed Res Int 2014:1–7.  https://doi.org/10.1155/2014/182945CrossRefGoogle Scholar
  38. Jayalakshmi K, Paramasivan M, Sasikala M et al (2017) Review on antibiotic residues in animal products and its impact on environments and human health. J Entomol Zool Stud 5(3):1446–1451Google Scholar
  39. Ji G, Silver S (1995) Bacterial resistance mechanisms for heavy metals of environmental concern. J Ind Microbiol 14:61–75PubMedCrossRefPubMedCentralGoogle Scholar
  40. Jiang SC, Paul JH (1998) Gene transfer by transduction in the marine environment. Appl Environ Microbiol 64:2780–2787PubMedPubMedCentralGoogle Scholar
  41. Kachur AV, Koch CJ, Biaglow JE (1998) Mechanism of copper-catalyzed oxidation of glutathione. Free Radic Res 28:259–269PubMedCrossRefPubMedCentralGoogle Scholar
  42. Klein EY, Van Boeckel TP, Martinez EM et al (2018) Global increase and geographic convergence in antibiotic consumption between 2000 and 2015. Proc Natl Acad Sci USA (PNAS) 115(15):E3463–E3470.  https://doi.org/10.1073/pnas.1717295115CrossRefGoogle Scholar
  43. Kong WD, Zhu YG, Fu BJ et al (2006) The veterinary antibiotic Oxytetracycline and Cu influence functional diversity of the soil microbial community. Environ Pollut 143:129–137PubMedCrossRefPubMedCentralGoogle Scholar
  44. Kong WD, Li CG, Dolhi JM et al (2012) Characteristics of Oxytetracycline sorption and potential bioavailability in soils with various physical-chemical properties. Chemosphere 87:542–548PubMedCrossRefPubMedCentralGoogle Scholar
  45. Kumar K, Gupta SC, Chander Y et al (2005) Antibiotic use in agriculture and its impact on the terrestrial environment. Adv Agron 87:1–54CrossRefGoogle Scholar
  46. Kümmerer K (2009) Antibiotics in the aquatic environment–a review–part I. Chemosphere 75:417–434PubMedCrossRefPubMedCentralGoogle Scholar
  47. Levy SB (2002) The antibiotic paradox: how the misuse of antibiotics destroys their curative powers, 2nd edn. Int Microbiol 5:155–156.  https://doi.org/10.1007/s10123-002-0082-z.CrossRefGoogle Scholar
  48. Levy SB, Marshall B (2004) Antibacterial resistance worldwide: causes, challenges and responses. Nat Med 10:S122–S129PubMedCrossRefPubMedCentralGoogle Scholar
  49. Li Y, Yu Y, Yang Z et al (2016) A comparison of metal distribution in surface dust and soil among super city, town, and rural area. Environ Sci Pollut Res 23:7849–7860CrossRefGoogle Scholar
  50. Lin H, Jin D, Freitag TE et al (2016) A compositional shift in the soil microbiome induced by tetracycline, sulfamonomethoxine and ciprofloxacin entering a plant-soil system. Environ Pollut 212:440–448PubMedCrossRefPubMedCentralGoogle Scholar
  51. Liu B, Li X, Zhang X, Wang J, Gao M (2015) Effects of chlortetracycline on soil microbial communities: comparisons of enzyme activities to the functional diversity via Biolog EcoPlates™. Eur J Soil Biol 68:69–76CrossRefGoogle Scholar
  52. Lorenz MG, Wackernagel W (1994) Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev 58:563–602PubMedPubMedCentralGoogle Scholar
  53. Lunsford RD (1998) Streptococcal transformation: essential features and applications of a natural gene exchange system. Plasmid 39:10–20PubMedCrossRefPubMedCentralGoogle Scholar
  54. Lv G, Pearce CW, Gleason A et al (2013) Influence of montmorilonite on antimicrobial activity of tetracycline (TC) and ciprofloxacin (CIP). J Asian Earth Sci 77:281–286CrossRefGoogle Scholar
  55. Martinez JL (2009) Environmental pollution by antibiotics and by antibiotic resistance determinants. Environ Pollut 157(11):2893–2902PubMedCrossRefPubMedCentralGoogle Scholar
  56. Mashkoori B (2014) The study of number of enteric bacteria and their antibiotic resistance in industrial and traditional dairy cow manures in Hamedan. MSc thesis, Bu-Ali Sina University, Hamedan, Iran (in Persian)Google Scholar
  57. McKinney CW, Loftin KA, Meyer MT et al (2010) tet and sul antibiotic resistance genes in livestock lagoons of various operation type, configuration, and antibiotic occurrence. Environ Sci Technol 44:6102–6109CrossRefGoogle Scholar
  58. Molaei A, Lakzian A, Datta R et al (2017a) Impact of chlortetracycline and sulfapyridine antibiotics on soil enzyme activities. Int Agrophys 31:209–505CrossRefGoogle Scholar
  59. Molaei A, Lakzian A, Gh H et al (2017b) Assessment of some cultural experimental methods to study the effects of antibiotics on microbial activities in a soil: an incubation study. PLoS One 12(7):e0180663PubMedPubMedCentralCrossRefGoogle Scholar
  60. Nielsen KM, van Weerelt MD, Berg TN et al (1997) Natural transformation and availability of transforming DNA to Acinetobacter calcoaceticus in soil microcosms. Appl Environ Microbiol 63:1945–1952PubMedPubMedCentralGoogle Scholar
  61. Nies DH (1999) Microbial heavy-metal resistance. Appl Microbiol Biotechnol 51:730–750PubMedCrossRefPubMedCentralGoogle Scholar
  62. Obst U, Schwartz T, Volkmann H (2006) Antibiotic resistant pathogenic bacteria and their resistance genes in bacterial biofilms. J Artif Organs 29:387–394CrossRefGoogle Scholar
  63. Ohlsen K, Ziebuhr W, Koller KP, Hell W, Wichelhaus T, Hacker J (1998) Effects of subinhibitory concentrations of antibiotics on alpha-toxin (HLA) gene expression of methicillin-sensitive and methicillin-resistant Staphylococcus aureus isolates. Antimicrob Agents Chemother 42:2817–2823PubMedPubMedCentralCrossRefGoogle Scholar
  64. Peak N, Knapp CW, Yang RK et al (2007) Abundance of six tetracycline resistance genes in wastewater lagoons at cattle feedlots with different antibiotic use strategies. Environ Microbiol 9:143–151PubMedCrossRefPubMedCentralGoogle Scholar
  65. Poole RK, Gadd GM (1989) Metal-microbe interactions. Published for the Society for General Microbiology/Published for the Society for General Microbiology by IRL Press. Oxford/New YorkGoogle Scholar
  66. Punitha BC, Hanumantharaju TH, Jayprakash R, Shilpashree VM (2012) Acetamiprid impacton urease and phosphatase activity in selected soils of southern Karnataka. Intl J Basic Appl Chem Sci 2:1–6Google Scholar
  67. Raaijmakers JM, Mazzola M (2012) Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annu Rev Phytopathol 50:403–424PubMedCrossRefPubMedCentralGoogle Scholar
  68. Rashtbari M (2019) Effect of various agricultural antibiotics and biochar and Nano-zeolite amendments on soil microbial population, biodiversity and biological interactions of chickpea (Cicer arietinum L.). PhD thesis in soil biology and biotechnology, Bu Ali Sina University, Hamadan, Iran (unpublished data)Google Scholar
  69. Ruiz N, Montero T, Hernandez-Borrell J et al (2003) The role of Serratia marcescens porins in antibiotic resistance. Microb Drug Resist 9:257–264PubMedCrossRefPubMedCentralGoogle Scholar
  70. Safari Sinegani AA, Younessi N (2017) Antibiotic resistance of bacteria isolated from heavy metal-polluted soils with different land uses. JGAR 10:247–255Google Scholar
  71. Salyers AA, Ama’bile-Cuevas CF (1997) Why are antibiotic resistance genes so resistant to elimination? Antimicrob Agents Chemother 41:2321–2325PubMedPubMedCentralCrossRefGoogle Scholar
  72. Schauss K, Focks A, Heuer H et al (2009) Analysis, fate and effects of antibiotic sulfadiazine in soil ecosystems. Trends Anal Chem 28:612–618CrossRefGoogle Scholar
  73. Schwaiger K, Harms K, Ho¨ lzel CS et al (2009) Tetracycline in liquid manure selects for co-occurrence of the resistance genes tet(M) and tet(L) in Enterococcus faecalis. Vet Microbiol 139:386–392PubMedCrossRefPubMedCentralGoogle Scholar
  74. Silver S, Walderhaug M (1992) Gene regulation of plasmid-and chromosome-determined inorganic ion transport in bacteria. Microbiol Rev 56:195–228PubMedPubMedCentralGoogle Scholar
  75. Srivastava N, Majumder C (2008) Novel biofiltration methods for the treatment of heavy metals from industrial wastewater. J Hazard Mater 151:1–8PubMedCrossRefPubMedCentralGoogle Scholar
  76. Telesinski A, Platkowski M, Cybulska K, Telesinska N, Wrobel J, Pawlowska B (2018) Response of soil enzymes to two antibiotics: polymyxin B and penicillin G. Fresenius Environ Bull 27(5A):3837–3845Google Scholar
  77. Ter Laak TL, Gebbink WA (2006) Estimation of soil sorption coefficients of veterinary pharmaceuticals from soil properties. Environ Toxicol Chem 25:933–941PubMedCrossRefPubMedCentralGoogle Scholar
  78. Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3(9):711–721PubMedCrossRefPubMedCentralGoogle Scholar
  79. Thompson CL, Wang B, Holmes AJ (2008) The immediate environment during postnatal development has long-term impact on gut community structure in pigs. ISME J 2:739–748PubMedCrossRefPubMedCentralGoogle Scholar
  80. Topp E, Chapman R, Devers-Lamrani M et al (2013) Accelerated biodegradation of veterinary antibiotics in agricultural soil following long-term exposure, and isolation of a sulfamethazine-degrading sp. J Environ Qual 42:173–178PubMedCrossRefPubMedCentralGoogle Scholar
  81. van Overbeek LS, Wellington EM, Egan S et al (2002) Prevalence of streptomycin-resistance genes in bacterial populations in European habitats. FEMS Microbiol Ecol 42:277–288PubMedCrossRefPubMedCentralGoogle Scholar
  82. Verlicchi P, Galletti A, Masotti L (2010) Management of hospital wastewaters: the case of the effluent of a large hospital situated in a small town. Water Sci Technol 61:2507–2519PubMedCrossRefPubMedCentralGoogle Scholar
  83. Wegst-Uhrich SR, Navarro DAG, Zimmerman L et al (2014) Assessing antibiotic sorption in soil: a literature review and new case studies on sulfonamides and macrolides. Chem Cent J 8(5):1–12Google Scholar
  84. Wei X, Wu SC, Nie XP, Yediler A, Wong MH (2009) The effects of residual tetracycline on soil enzymatic activities and plant growth. J Environ Science Health B 44:461–471CrossRefGoogle Scholar
  85. Wise R (2002) Antimicrobial resistance: priorities for action. J Antimicrob Chemother 49:585–586PubMedCrossRefPubMedCentralGoogle Scholar
  86. Wright GD (2007) The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol 5:175–186PubMedCrossRefPubMedCentralGoogle Scholar
  87. Younessi N (2017) Evaluation of microbial tolerance to some heavy metals and antibiotics in metal-contaminated soils and water resources in Hamadan province. PhD thesis, Bu-Ali Sina University, Hamedan, Iran (in Persian)Google Scholar
  88. Younessi N, Safari Sinegani AA, Khodakaramian GH (2017) Detection Beta-lactamase gene in the culturable bacteria isolated from agricultural, pasture and mining soils around mines in Hamedan, Iran. Biol J Microorg 6(21):36–48. In Persian with English SummaryGoogle Scholar
  89. Younessi N, Safari Sinegani AA, Khodakaramian G (2019) Detection of antibiotic resistance genes in culturable bacteria isolated from soils around mines in Hamedan. Iran Int J Environ Sci Technol.  https://doi.org/10.1007/s13762-018-02178-2. (online published)CrossRefGoogle Scholar
  90. Zeaiter Z, Mpelli F, Crotti E et al (2018) Methods for the genetic manipulation of marine bacteria. Electron J Biotechn 33:17–28CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Ali-Akbar Safari-Sinegani
    • 1
    Email author
  • Mehdi Rashtbari
    • 1
  • Nayereh Younessi
    • 1
  • Babak Mashkoori
    • 1
  1. 1.Department of Soil Science, College of AgricultureBu-Ali Sina UniversityHamadanIran

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