Skip to main content

Advertisement

SpringerLink
Log in

Comparative Effect of Fertilization Practices on Soil Microbial Diversity and Activity: An Overview

  • Review Article
  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

Continuously increasing human population demands increased food production, which needs greater fertilizer’s input in agricultural lands to enhance crop yield. In this respect, different fertilization practices gained acceptance among farmers. We reviewed effect of three main fertilization practices (Conventional-, Organic-, and Bio-fertilization) on soil microbial diversity, activity, and community composition. Studies reported that over application of inorganic fertilizers decline soil pH, change soil osmolarity, cause soil degradation, disturb taxonomic diversity and metabolism of soil microbes and cause accumulation of extra nutrients into the soil such as phosphorous (P) accumulation. On the contrary, organic fertilizers increase organic carbon (OC) input in the soil, which strongly encourage growth of heterotrophic microbes. Organic fertilizer vermicompost application provides readily available nutrients to both plants as well as microbes and encourage overall microbial number in the soil. Most recently, role of beneficial bacteria in long-term sustainable agriculture attracted attention of scientists towards their use as biofertilizer in the soil. Studies documented favorable effect of biofertilization on microbial Shannon, Chao and ACE diversity indices in the soil. It is concluded from intensive review of literature that all the three fertilization practices have their own way to benefit the soil with nutrients, but biofertilization provides long-term sustainability to crop lands. When it is used in integration with organic fertilizers, it makes the soil best for microbial growth and activity and increase microbial diversity, providing nutrients to soil for a longer time, thus improving crop productivity.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Data Availability

Not applicable.

Code Availability

Not applicable.

References

  1. De Vries FT, Thébault E, Liiri M et al (2013) Soil food web properties explain ecosystem services across European land use systems. Proc Natl Acad Sci USA 110:14296–14301. https://doi.org/10.1073/pnas.1305198110

    Article  PubMed  PubMed Central  Google Scholar 

  2. Geisseler D, Scow KM (2014) Long-term effects of mineral fertilizers on soil microorganisms—a review. Soil Biol Biochem 75:54–63

    Article  CAS  Google Scholar 

  3. Leff JW, Jones SE, Prober SM et al (2015) Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc Natl Acad Sci USA 112:10967–10972. https://doi.org/10.1073/pnas.1508382112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Zhang Y, Shen H, He X et al (2017) Fertilization shapes bacterial community structure by alteration of soil pH. Front Microbiol. https://doi.org/10.3389/fmicb.2017.01325

    Article  PubMed  PubMed Central  Google Scholar 

  5. Chinnadurai C, Gopalaswamy G, Balachandar D (2014) Long term effects of nutrient management regimes on abundance of bacterial genes and soil biochemical processes for fertility sustainability in a semi-arid tropical Alfisol. Geoderma 232–234:563–572. https://doi.org/10.1016/j.geoderma.2014.06.015

    Article  CAS  Google Scholar 

  6. Dinesh R, Srinivasan V, Hamza S, Manjusha A (2010) Short-term incorporation of organic manures and biofertilizers influences biochemical and microbial characteristics of soils under an annual crop [Turmeric (Curcuma longa L.)]. Bioresour Technol 101:4697–4702. https://doi.org/10.1016/j.biortech.2010.01.108

    Article  CAS  PubMed  Google Scholar 

  7. Francioli D, Schulz E, Lentendu G et al (2016) 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

    Article  PubMed  PubMed Central  Google Scholar 

  8. Hartmann M, Frey B, Mayer J et al (2015) Distinct soil microbial diversity under long-term organic and conventional farming. ISME J 9:1177–1194

    Article  PubMed  Google Scholar 

  9. Bending GD, Turner MK, Rayns F et al (2004) Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes. Soil Biol Biochem 36:1785–1792. https://doi.org/10.1016/j.soilbio.2004.04.035

    Article  CAS  Google Scholar 

  10. Loeppmann S, Blagodatskaya E, Pausch J, Kuzyakov Y (2016) Substrate quality affects kinetics and catalytic efficiency of exo-enzymes in rhizosphere and detritusphere. Soil Biol Biochem 92:111–118. https://doi.org/10.1016/j.soilbio.2015.09.020

    Article  CAS  Google Scholar 

  11. Zhong WH, Cai ZC (2007) Long-term effects of inorganic fertilizers on microbial biomass and community functional diversity in a paddy soil derived from quaternary red clay. Appl Soil Ecol 36:84–91. https://doi.org/10.1016/j.apsoil.2006.12.001

    Article  Google Scholar 

  12. Bhardwaj D, Ansari MW, Sahoo RK, Tuteja N (2014) Biofertilizers function as key player in sustainable agriculture by improving soil fertility, plant tolerance and crop productivity. Microb Cell Fact. https://doi.org/10.1186/1475-2859-13-66

    Article  PubMed  PubMed Central  Google Scholar 

  13. Sheraz-Mahdi S, Hassan GI, Samoon SA et al (2010) Bio-fertilizers in organic agriculture. J Phytol 2(10):42–54

    Google Scholar 

  14. Su JQ, Ding LJ, Xue K et al (2015) Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil. Mol Ecol 24:136–150. https://doi.org/10.1111/mec.13010

    Article  CAS  PubMed  Google Scholar 

  15. Sinsabaugh RL, Lauber CL, Weintraub MN et al (2008) Stoichiometry of soil enzyme activity at global scale. Ecol Lett 11:1252–1264

    Article  PubMed  Google Scholar 

  16. Bender SF, Wagg C, van der Heijden MGA (2016) An underground revolution: biodiversity and soil ecological engineering for agricultural sustainability. Trends Ecol Evol 31:440–452

    Article  PubMed  Google Scholar 

  17. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719–1728

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. McPherson MR, Wang P, Marsh EL et al (2018) Isolation and analysis of microbial communities in soil, rhizosphere, and roots in perennial grass experiments. J Vis Exp. https://doi.org/10.3791/57932

    Article  PubMed  PubMed Central  Google Scholar 

  19. Siles JA, Rachid CTCC, Sampedro I et al (2014) Microbial diversity of a Mediterranean soil and its changes after biotransformed dry olive residue amendment. PLoS ONE. https://doi.org/10.1371/journal.pone.0103035

    Article  PubMed  PubMed Central  Google Scholar 

  20. Bacon CW, Palencia ER, Hinton DM (2015) Abiotic and biotic plant stress-tolerant and beneficial secondary metabolites produced by endophytic Bacillus species. In: Arora NK (ed) Plant microbes symbiosis: applied facets. Springer, Berlin, pp 163–177

    Google Scholar 

  21. Ding LJ, Su JQ, Sun GX et al (2018) Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil. Appl Microbiol Biotechnol 102(4):1969–1982. https://doi.org/10.1007/s00253-017-8704-8

    Article  CAS  PubMed  Google Scholar 

  22. Wagg C, Bender SF, Widmer F, Van Der Heijden MGA (2014) Soil biodiversity and soil community composition determine ecosystem multifunctionality. Proc Natl Acad Sci USA 111:5266–5270. https://doi.org/10.1073/pnas.1320054111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Pal KK, Tilak KVBR, Saxcna AK et al (2001) Suppression of maize root diseases caused by Macrophomina phaseolina, Fusarium moniliforme and Fusarium graminearum by plant growth promoting rhizobacteria. Microbiol Res 156:209–223. https://doi.org/10.1078/0944-5013-00103

    Article  CAS  PubMed  Google Scholar 

  24. Purbey S, Sen N (2005) Response of fenugreek (Trigonella foenum graecum L.) to bioinoculants and plant bioregulators. Indian J Hortic 62:416–418

    Google Scholar 

  25. Pandey A, Tripathi A, Srivastava P et al (2019) Plant growth-promoting microorganisms in sustainable agriculture. Role of plant growth promoting microorganisms in sustainable agriculture and nanotechnology. Elsevier, Amsterdam, pp 1–19

    Google Scholar 

  26. Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37(5):634–663. https://doi.org/10.1111/1574-6976.12028

    Article  CAS  PubMed  Google Scholar 

  27. Hossain MM, Sultana F, Islam S (2017) Plant growth-promoting fungi (PGPF): phytostimulation and induced systemic resistance. In: Singh DP, Singh HB, Prabha R (eds) Plant-microbe interactions in agro-ecological perspectives. Springer, Singapore, pp 135–191

    Google Scholar 

  28. Singh RP, Bijo AJ, Baghel RS et al (2011) Role of bacterial isolates in enhancing the bud induction in the industrially important red alga Gracilaria dura. FEMS Microbiol Ecol 76(2):381–392. https://doi.org/10.1111/j.1574-6941.2011.01057.x

    Article  CAS  PubMed  Google Scholar 

  29. Le Pioufle O, Ganoudi M, Calonne-Salmon M et al (2019) Rhizophagus irregularis MUCL 41833 improves phosphorus uptake and water use efficiency in maize plants during recovery from drought stress. Front Plant Sci 10:897. https://doi.org/10.3389/fpls.2019.00897

    Article  PubMed  PubMed Central  Google Scholar 

  30. Vurukonda SSKP, Vardharajula S, Shrivastava M, SkZ A (2016) Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria. Microbiol Res 184:13–24

    Article  PubMed  Google Scholar 

  31. Waksman SA, Reilly HC, Johnstone DB (1946) Isolation of streptomycin-producing strains of Streptomyces griseus. J Bacteriol 52:393–397

    Article  PubMed  PubMed Central  Google Scholar 

  32. Abou Zeid AZA, Salem HM, El Wahab Eissa IA (1978) Production of gentamicins by Micromonospora purpurea. Zentralblatt fur Bakteriol Parasitenkd Infekt und Hyg Zweite Abteilung 133:261–275. https://doi.org/10.1016/s0323-6056(78)80012-3

    Article  CAS  Google Scholar 

  33. Lindeboom REF, Ilgrande C, Carvajal-Arroyo JM et al (2018) Nitrogen cycle microorganisms can be reactivated after space exposure. Sci Rep 8:1–7. https://doi.org/10.1038/s41598-018-32055-4

    Article  CAS  Google Scholar 

  34. Gougoulias C, Clark JM, Shaw LJ (2014) 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Chotte J-L (2005) Importance of microorganisms for soil aggregation. Microorganisms in soils: roles in genesis and functions. Springer, Berlin, pp 107–119

    Chapter  Google Scholar 

  36. Kuzyakov Y, Xu X (2013) Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance. New Phytol 198:656–669

    Article  CAS  PubMed  Google Scholar 

  37. Van Der Heijden MGA, Bardgett RD, Van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310

    Article  PubMed  Google Scholar 

  38. Rasche F, Musyoki MK, Röhl C et al (2014) Lasting influence of biochemically contrasting organic inputs on abundance and community structure of total and proteolytic bacteria in tropical soils. Soil Biol Biochem 74:204–213. https://doi.org/10.1016/j.soilbio.2014.03.017

    Article  CAS  Google Scholar 

  39. Fraser T, Lynch DH, Entz MH, Dunfield KE (2015) Linking alkaline phosphatase activity with bacterial phoD gene abundance in soil from a long-term management trial. Geoderma 257–258:115–122. https://doi.org/10.1016/j.geoderma.2014.10.016

    Article  CAS  Google Scholar 

  40. Xue K, Wu L, Deng Y et al (2013) Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands. Appl Environ Microbiol 79:1284–1292. https://doi.org/10.1128/AEM.03393-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Bergkemper F, Schöler A, Engel M et al (2016) Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems. Environ Microbiol 18:1988–2000. https://doi.org/10.1111/1462-2920.13188

    Article  CAS  PubMed  Google Scholar 

  42. Bashan Y, De-Bashan LE, Prabhu SR, Hernandez JP (2014) Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998–2013). Plant Soil 378:1–33

    Article  CAS  Google Scholar 

  43. Timm CM, Campbell AG, Utturkar SM et al (2015) Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Front Microbiol. https://doi.org/10.3389/fmicb.2015.01118

    Article  PubMed  PubMed Central  Google Scholar 

  44. Müller DB, Vogel C, Bai Y, Vorholt JA (2016) The plant microbiota: systems-level insights and perspectives. Annu Rev Genet 50:211–234

    Article  PubMed  Google Scholar 

  45. Siebert J, Sünnemann M, Auge H et al (2018) The effects of drought and nutrient addition on soil organisms vary across taxonomic groups, but are constant across seasons. Sci Rep 9(1):639. https://doi.org/10.1038/s41598-018-36777-3

    Article  CAS  Google Scholar 

  46. Ge T, Li B, Zhu Z et al (2017) Rice rhizodeposition and its utilization by microbial groups depends on N fertilization. Biol Fertil Soils 53:37–48. https://doi.org/10.1007/s00374-016-1155-z

    Article  CAS  Google Scholar 

  47. Craven D, Isbell F, Manning P et al (2016) Plant diversity effects on grassland productivity are robust to both nutrient enrichment and drought. Philos Trans R Soc B Biol Sci. https://doi.org/10.1098/rstb.2015.0277

    Article  Google Scholar 

  48. Schmidt JE, Kent AD, Brisson VL, Gaudin ACM (2019) Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling. Microbiome. https://doi.org/10.1186/s40168-019-0756-9

    Article  PubMed  PubMed Central  Google Scholar 

  49. Fan K, Cardona C, Li Y et al (2017) Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields. Soil Biol Biochem 113:275–284. https://doi.org/10.1016/j.soilbio.2017.06.020

    Article  CAS  Google Scholar 

  50. García-Salamanca A, Molina-Henares MA, van Dillewijn P et al (2013) Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil. Microb Biotechnol 6:36–44. https://doi.org/10.1111/j.1751-7915.2012.00358.x

    Article  CAS  PubMed  Google Scholar 

  51. Zhou J, Jiang X, Wei D et al (2017) Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China. Sci Rep. https://doi.org/10.1038/s41598-017-03539-6

    Article  PubMed  PubMed Central  Google Scholar 

  52. Zhao J, Ni T, Li Y et al (2014) Responses of bacterial communities in arable soils in a rice-wheat cropping system to different fertilizer regimes and sampling times. PLoS ONE. https://doi.org/10.1371/journal.pone.0085301

    Article  PubMed  PubMed Central  Google Scholar 

  53. Shim CY, Park IS, Lee CW, Choi JM (2018) Influence of compositions and concentrations of post-planting fertilizers on the growth of ‘nokkwang’ hot pepper plug seedlings. Hortic Sci Technol 36:28–36. https://doi.org/10.12972/kjhst.20180004

    Article  CAS  Google Scholar 

  54. Zhen Z, Liu H, Wang N et al (2014) Effects of manure compost application on soil microbial community diversity and soil microenvironments in a temperate cropland in China. PLoS ONE. https://doi.org/10.1371/journal.pone.0108555

    Article  PubMed  PubMed Central  Google Scholar 

  55. More H (2019) Chemical fertilizers: Examples, advantages and disadvantages. In: Fact Factor. https://thefactfactor.com/facts/pure_science/biology/chemical-fertilizers/2225/. Accessed 23 Jan 2021

  56. Mącik M, Gryta A, Frąc M (2020) Biofertilizers in agriculture: an overview on concepts, strategies and effects on soil microorganisms. Advances in agronomy. Academic Press Inc., Cambridge, pp 31–87

    Google Scholar 

  57. Chen J, Lü S, Zhang Z et al (2018) Environmentally friendly fertilizers: a review of materials used and their effects on the environment. Sci Total Environ 613–614:829–839. https://doi.org/10.1016/j.scitotenv.2017.09.186

    Article  CAS  PubMed  Google Scholar 

  58. Chu H, Lin X, Fujii T et al (2007) Soil microbial biomass, dehydrogenase activity, bacterial community structure in response to long-term fertilizer management. Soil Biol Biochem 39:2971–2976. https://doi.org/10.1016/j.soilbio.2007.05.031

    Article  CAS  Google Scholar 

  59. Lugato E, Berti A, Giardini L (2006) Soil organic carbon (SOC) dynamics with and without residue incorporation in relation to different nitrogen fertilisation rates. Geoderma 135:315–321. https://doi.org/10.1016/j.geoderma.2006.01.012

    Article  CAS  Google Scholar 

  60. Tamilselvi SM, Chinnadurai C, Ilamurugu K et al (2015) Effect of long-term nutrient managements on biological and biochemical properties of semi-arid tropical alfisol during maize crop development stages. Ecol Indic 48:76–87. https://doi.org/10.1016/j.ecolind.2014.08.001

    Article  CAS  Google Scholar 

  61. Aislabie J, Deslippe JR, Dymond JR (2013) Soil microbes and their contribution to soil services. Ecosyst Serv New Zeal Cond trends 143–161

  62. Belay A, Claassens AS, Wehner FC (2002) Effect of direct nitrogen and potassium and residual phosphorus fertilizers on soil chemical properties, microbial components and maize yield under long-term crop rotation. Biol Fertil Soils 35:420–427. https://doi.org/10.1007/s00374-002-0489-x

    Article  CAS  Google Scholar 

  63. Rousk J, Bååth E (2007) Fungal and bacterial growth in soil with plant materials of different C/N ratios. FEMS Microbiol Ecol 62:258–267. https://doi.org/10.1111/j.1574-6941.2007.00398.x

    Article  CAS  PubMed  Google Scholar 

  64. Babin D, Deubel A, Jacquiod S et al (2019) Impact of long-term agricultural management practices on soil prokaryotic communities. Soil Biol Biochem 129:17–28. https://doi.org/10.1016/j.soilbio.2018.11.002

    Article  CAS  Google Scholar 

  65. Le TTH, Fettig J, Meon G (2019) Kinetics and simulation of nitrification at various pH values of a polluted river in the tropics. Ecohydrol Hydrobiol 19:54–65. https://doi.org/10.1016/j.ecohyd.2018.06.006

    Article  Google Scholar 

  66. Deubel A, Hofmann B, Orzessek D (2011) Long-term effects of tillage on stratification and plant availability of phosphate and potassium in a loess chernozem. Soil Tillage Res 117:85–92. https://doi.org/10.1016/j.still.2011.09.001

    Article  Google Scholar 

  67. Long X, Chen C, Xu Z et al (2012) Abundance and community structure of ammonia oxidizing bacteria and archaea in a Sweden boreal forest soil under 19-year fertilization and 12-year warming. J Soils Sediments 12:1124–1133. https://doi.org/10.1007/s11368-012-0532-y

    Article  CAS  Google Scholar 

  68. Hallin S, Jones CM, Schloter M, Philippot L (2009) Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. ISME J 3:597–605

    Article  CAS  PubMed  Google Scholar 

  69. Chen X, Zhang LM, Shen JP et al (2011) Abundance and community structure of ammonia-oxidizing archaea and bacteria in an acid paddy soil. Biol Fertil Soils 47:323–331. https://doi.org/10.1007/s00374-011-0542-8

    Article  CAS  Google Scholar 

  70. Yang D, Xiao X, He N et al (2020) Effects of reducing chemical fertilizer combined with organic amendments on ammonia-oxidizing bacteria and archaea communities in a low-fertility red paddy field. Environ Sci Pollut Res. https://doi.org/10.1007/s11356-020-09120-5

    Article  Google Scholar 

  71. Wang B, Zhao J, Guo Z et al (2015) Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils. ISME J 9:1062–1075. https://doi.org/10.1038/ismej.2014.194

    Article  CAS  PubMed  Google Scholar 

  72. Chang HX, Haudenshield JS, Bowen CR, Hartman GL (2017) Metagenome-wide association study and machine learning prediction of bulk soil microbiome and crop productivity. Front Microbiol. https://doi.org/10.3389/fmicb.2017.00519

    Article  PubMed  PubMed Central  Google Scholar 

  73. Fierer N, Lauber CL, Ramirez KS et al (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017. https://doi.org/10.1038/ismej.2011.159

    Article  CAS  PubMed  Google Scholar 

  74. Nacke H, Thürmer A, Wollherr A et al (2011) Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS ONE. https://doi.org/10.1371/journal.pone.0017000

    Article  PubMed  PubMed Central  Google Scholar 

  75. Chhabra S, Brazil D, Morrissey J et al (2013) Fertilization management affects the alkaline phosphatase bacterial community in barley rhizosphere soil. Biol Fertil Soils 49:31–39. https://doi.org/10.1007/s00374-012-0693-2

    Article  CAS  Google Scholar 

  76. Tan H, Barret M, Mooij MJ et al (2013) Long-term phosphorus fertilisation increased the diversity of the total bacterial community and the phoD phosphorus mineraliser group in pasture soils. Biol Fertil Soils 49:661–672. https://doi.org/10.1007/s00374-012-0755-5

    Article  CAS  Google Scholar 

  77. Chen C, Zhang J, Lu M et al (2016) Microbial communities of an arable soil treated for 8 years with organic and inorganic fertilizers. Biol Fertil Soils 52:455–467. https://doi.org/10.1007/s00374-016-1089-5

    Article  CAS  Google Scholar 

  78. Huang J, Hu B, Qi K et al (2016) Effects of phosphorus addition on soil microbial biomass and community composition in a subalpine spruce plantation. Eur J Soil Biol 72:35–41. https://doi.org/10.1016/j.ejsobi.2015.12.007

    Article  CAS  Google Scholar 

  79. Wakelin SA, Condron LM, Gerard E et al (2017) Long-term P fertilisation of pasture soil did not increase soil organic matter stocks but increased microbial biomass and activity. Biol Fertil Soils 53:511–521. https://doi.org/10.1007/s00374-017-1212-2

    Article  CAS  Google Scholar 

  80. Hamel C, Hanson K, Selles F et al (2006) Seasonal and long-term resource-related variations in soil microbial communities in wheat-based rotations of the Canadian prairie. Soil Biol Biochem 38:2104–2116. https://doi.org/10.1016/j.soilbio.2006.01.011

    Article  CAS  Google Scholar 

  81. Shi Y, Lalande R, Ziadi N et al (2012) An assessment of the soil microbial status after 17 years of tillage and mineral P fertilization management. Appl Soil Ecol 62:14–23. https://doi.org/10.1016/j.apsoil.2012.07.004

    Article  Google Scholar 

  82. Mander C, Wakelin S, Young S et al (2012) Incidence and diversity of phosphate-solubilising bacteria are linked to phosphorus status in grassland soils. Soil Biol Biochem 44:93–101. https://doi.org/10.1016/j.soilbio.2011.09.009

    Article  CAS  Google Scholar 

  83. He D, Xiang X, He JS et al (2016) Composition of the soil fungal community is more sensitive to phosphorus than nitrogen addition in the alpine meadow on the Qinghai-Tibetan Plateau. Biol Fertil Soils 52:1059–1072. https://doi.org/10.1007/s00374-016-1142-4

    Article  CAS  Google Scholar 

  84. Lin X, Feng Y, Zhang H et al (2012) Long-term balanced fertilization decreases arbuscular mycorrhizal fungal diversity in an arable soil in north China revealed by 454 pyrosequencing. Environ Sci Technol 46:5764–5771. https://doi.org/10.1021/es3001695

    Article  CAS  PubMed  Google Scholar 

  85. Liu M, Liu J, Chen X et al (2018) Shifts in bacterial and fungal diversity in a paddy soil faced with phosphorus surplus. Biol Fertil Soils 54:259–267. https://doi.org/10.1007/s00374-017-1258-1

    Article  CAS  Google Scholar 

  86. He JZ, Zheng Y, Chen CR et al (2008) Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches. J Soils Sediments 8:349–358. https://doi.org/10.1007/s11368-008-0025-1

    Article  CAS  Google Scholar 

  87. Li J, Li Z, Wang F et al (2015) Effects of nitrogen and phosphorus addition on soil microbial community in a secondary tropical forest of China. Biol Fertil Soils 51:207–215. https://doi.org/10.1007/s00374-014-0964-1

    Article  CAS  Google Scholar 

  88. Bouwman AF, Beusen AHW, Billen G (2009) Human alteration of the global nitrogen and phosphorus soil balances for the period 1970–2050. Global Biogeochem Cycles. https://doi.org/10.1029/2009GB003576

    Article  Google Scholar 

  89. Bouwman L, Goldewijk KK, Van Der Hoek KW et al (2013) Exploring global changes in nitrogen and phosphorus cycles in agriculture induced by livestock production over the 1900–2050 period. Proc Natl Acad Sci USA 110:20882–20887. https://doi.org/10.1073/pnas.1012878108

    Article  CAS  PubMed  Google Scholar 

  90. Liu L, Zhang T, Gilliam FS et al (2013) Interactive effects of nitrogen and phosphorus on soil microbial communities in a tropical forest. PLoS ONE. https://doi.org/10.1371/journal.pone.0061188

    Article  PubMed  PubMed Central  Google Scholar 

  91. Xu A, Li L, Coulter JA et al (2020) Long-term nitrogen fertilization impacts on soil bacteria, grain yield and nitrogen use efficiency of wheat in semiarid loess plateau, China. Agronomy 10:1175. https://doi.org/10.3390/agronomy10081175

    Article  CAS  Google Scholar 

  92. Ma M, Jiang X, Wang Q et al (2018) Responses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols. Microbiologyopen 7:e00597. https://doi.org/10.1002/mbo3.597

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Li Y, Tremblay J, Bainard LD et al (2020) Long-term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production. Environ Microbiol 22:1066–1088. https://doi.org/10.1111/1462-2920.14824

    Article  CAS  PubMed  Google Scholar 

  94. Dai Z, Liu G, Chen H et al (2020) Long-term nutrient inputs shift soil microbial functional profiles of phosphorus cycling in diverse agroecosystems. ISME J 14:757–770. https://doi.org/10.1038/s41396-019-0567-9

    Article  CAS  PubMed  Google Scholar 

  95. Bhattacharyya R, Kundu S, Prakash V, Gupta HS (2008) Sustainability under combined application of mineral and organic fertilizers in a rainfed soybean-wheat system of the Indian Himalayas. Eur J Agron 28:33–46. https://doi.org/10.1016/j.eja.2007.04.006

    Article  CAS  Google Scholar 

  96. Zhang QC, Shamsi IH, Xu DT et al (2012) Chemical fertilizer and organic manure inputs in soil exhibit a vice versa pattern of microbial community structure. Appl Soil Ecol 57:1–8. https://doi.org/10.1016/j.apsoil.2012.02.012

    Article  Google Scholar 

  97. Aher SB, Lakaria BL, Kaleshananda S et al (2015) Effect of organic farming practices on soil and performance of soybean (Glycine max) under semi-arid tropical conditions in Central India. J Appl Nat Sci 7:67–71. https://doi.org/10.31018/jans.v7i1.564

    Article  CAS  Google Scholar 

  98. Chang KH, Wu RY, Chuang KC et al (2010) Effects of chemical and organic fertilizers on the growth, flower quality and nutrient uptake of Anthurium andreanum, cultivated for cut flower production. Sci Hortic (Amsterdam) 125:434–441. https://doi.org/10.1016/j.scienta.2010.04.011

    Article  CAS  Google Scholar 

  99. Li YC, Li ZW, Lin WW et al (2018) Effects of biochar and sheep manure on rhizospheric soil microbial community in continuous ratooning tea orchards. Chin J Appl Ecol 29:1273–1282. https://doi.org/10.13287/j.1001-9332.201804.036

    Article  Google Scholar 

  100. Xiong W, Li ZW, Liu H et al (2016) Screening for plant growth-promoting rhizobacteria to promote early soybean growth. PLoS ONE 9:2104–2116. https://doi.org/10.1371/journal.pone.0103035

    Article  Google Scholar 

  101. Xiong W, Li Z, Liu H et al (2015) The effect of long-term continuous cropping of black pepper on soil bacterial communities as determined by 454 pyrosequencing. PLoS ONE. https://doi.org/10.1371/journal.pone.0136946

    Article  PubMed  PubMed Central  Google Scholar 

  102. Lupwayi NZ, Larney FJ, Blackshaw RE et al (2017) Pyrosequencing reveals profiles of soil bacterial communities after 12 years of conservation management on irrigated crop rotations. Appl Soil Ecol 121:65–73. https://doi.org/10.1016/j.apsoil.2017.09.031

    Article  Google Scholar 

  103. Zhong W, Gu T, Wang W et al (2010) The effects of mineral fertilizer and organic manure on soil microbial community and diversity. Plant Soil 326:511–522. https://doi.org/10.1007/s11104-009-9988-y

    Article  CAS  Google Scholar 

  104. Kataoka R, Nagasaka K, Tanaka Y et al (2017) Hairy vetch (Vicia villosa), as a green manure, increases fungal biomass, fungal community composition, and phosphatase activity in soil. Appl Soil Ecol 117–118:16–20. https://doi.org/10.1016/j.apsoil.2017.04.015

    Article  Google Scholar 

  105. Sun H, Koal P, Liu D et al (2016) Soil microbial community and microbial residues respond positively to minimum tillage under organic farming in Southern Germany. Appl Soil Ecol 108:16–24. https://doi.org/10.1016/j.apsoil.2016.07.014

    Article  CAS  Google Scholar 

  106. Chaudhry V, Rehman A, Mishra A et al (2012) Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microb Ecol 64:450–460. https://doi.org/10.1007/s00248-012-0025-y

    Article  PubMed  Google Scholar 

  107. Li R, Khafipour E, Krause DO et al (2012) Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities. PLoS ONE. https://doi.org/10.1371/journal.pone.0051897

    Article  PubMed  PubMed Central  Google Scholar 

  108. Tautges NE, Sullivan TS, Reardon CL, Burke IC (2016) Soil microbial diversity and activity linked to crop yield and quality in a dryland organic wheat production system. Appl Soil Ecol 108:258–268. https://doi.org/10.1016/j.apsoil.2016.09.003

    Article  Google Scholar 

  109. Lupatini M, Korthals GW, de Hollander M et al (2017) Soil microbiome is more heterogeneous in organic than in conventional farming system. Front Microbiol. https://doi.org/10.3389/fmicb.2016.02064

    Article  PubMed  PubMed Central  Google Scholar 

  110. Pershina E, Valkonen J, Kurki P et al (2015) Comparative analysis of prokaryotic communities associated with organic and conventional farming systems. PLoS ONE. https://doi.org/10.1371/journal.pone.0145072

    Article  PubMed  PubMed Central  Google Scholar 

  111. Shange RS, Ankumah RO, Ibekwe AM et al (2012) Distinct soil bacterial communities revealed under a diversely managed agroecosystem. PLoS ONE 7:e40338. https://doi.org/10.1371/journal.pone.0040338

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Gajda AM, Czyz EA, Dexter AR (2016) Effects of long-term use of different farming systems on some physical, chemical and microbiological parameters of soil quality. Int Agrophysics 30:165–172. https://doi.org/10.1515/intag-2015-0081

    Article  CAS  Google Scholar 

  113. Granada CE, Passaglia LMP, de Souza EM, Sperotto RA (2018) Is phosphate solubilization the forgotten child of plant growth-promoting rhizobacteria? Front Microbiol. https://doi.org/10.3389/fmicb.2018.02054

    Article  PubMed  PubMed Central  Google Scholar 

  114. Yadav KK, Sarkar S (2019) Biofertilizers, impact on soil fertility and crop productivity under sustainable agriculture. Environ Ecol 37:89–93

    Google Scholar 

  115. Nur Okur (2018) A review-bio-fertilizers-power of beneficial microorganisms in soils. Biomed J Sci Tech Res 4(4):4028–4029. https://doi.org/10.26717/BJSTR.2018.4.001076

    Article  Google Scholar 

  116. Chaparro JM, Badri DV, Vivanco JM (2014) Rhizosphere microbiome assemblage is affected by plant development. ISME J 8:790–803. https://doi.org/10.1038/ismej.2013.196

    Article  CAS  PubMed  Google Scholar 

  117. Gaur V (2010) Biofertilizer-necessity for sustainability. J Adv Dev 1:7–8

    Google Scholar 

  118. Jagtap AD, Jagtap DD, Kadam AS, Patil SB (2009) Effect of different sources of nitrogen on yield and quality of cabbage (Brassica oleracea var. capitata). Ecol Environ Conserv 15:223–227

    Google Scholar 

  119. Kachari M, Korla BN (2009) Effect of biofertilizers on growth and yield of cauliflower cv. PSB K-1. Indian J Hortic 66:496–501

    Google Scholar 

  120. Talwar D, Singh K, Singh J (2017) Effect of biofertilizers on soil microbial count, nutrient availability and uptake under November sown onion. J Appl Nat Sci 9:55–59. https://doi.org/10.31018/jans.v9i1.1149

    Article  CAS  Google Scholar 

  121. Javoreková S, Maková J, Medo J et al (2015) Effect of bio-fertilizers application on microbial diversity and physiological profiling of microorganisms in arable soil. Eurasian J Soil Sci 4:54. https://doi.org/10.18393/ejss.07093

    Article  Google Scholar 

  122. Mandic L, Djukić D, Beatovic I et al (2011) Effect of different fertilizers on the microbial activity and productivity of soil under potato cultivation. African J Biotechnol 10:6954–6960. https://doi.org/10.5897/AJB11.947

    Article  Google Scholar 

  123. Yeshiwas Y, Yikeber Be B, Chekol A, Walle A (2018) Effect of nitrogen fertilizer and farmyard manure on growth and yield of lettuce (Lactuca sativa L.) role of nitrogen fertilizer and farm yard manure on lettuce. Int J Agric Res 13:74–79. https://doi.org/10.3923/ijar.2018.74.79

    Article  Google Scholar 

  124. Chun JH, Kim S, Arasu MV et al (2017) Combined effect of nitrogen, phosphorus and potassium fertilizers on the contents of glucosinolates in rocket salad (Eruca sativa Mill.). Saudi J Biol Sci 24:436–443. https://doi.org/10.1016/j.sjbs.2015.08.012

    Article  CAS  PubMed  Google Scholar 

  125. Panchal B, Patel V, Patel KP, Khimani RA (2018) Effect of biofertilizers, organic manures and chemical fertilizers on microbial population, yield and yield attributes and quality of sweetcorn (Zea mays L., saccharata) cv. Madhuri. Int J Curr Microbiol Appl Sci 7:2423–2431. https://doi.org/10.20546/ijcmas.2018.709.301

    Article  CAS  Google Scholar 

  126. Dong L, Li Y, Xu J et al (2019) Biofertilizers regulate the soil microbial community and enhance Panax ginseng yields. Chin Med (United Kingdom). https://doi.org/10.1186/s13020-019-0241-1

    Article  Google Scholar 

  127. Du JC, Xu J, Niu WH et al (2016) Effects of improving measures on soil micro-ecology and survival rate of ginseng in farmlands. Zhongguo Zhong Yao Za Zhi 41:4334–4339. https://doi.org/10.4268/cjcmm20162307

    Article  PubMed  Google Scholar 

  128. Shen Z, Ruan Y, Chao X et al (2015) Rhizosphere microbial community manipulated by 2 years of consecutive biofertilizer application associated with banana Fusarium wilt disease suppression. Biol Fertil Soils 51:553–562. https://doi.org/10.1007/s00374-015-1002-7

    Article  CAS  Google Scholar 

  129. Yuan S, Wang L, Wu K et al (2014) Evaluation of Bacillus-fortified organic fertilizer for controlling tobacco bacterial wilt in greenhouse and field experiments. Appl Soil Ecol 75:86–94. https://doi.org/10.1016/j.apsoil.2013.11.004

    Article  Google Scholar 

  130. Nandimath AP, Karad DD, Gupta SG, Kharat AS (2017) Consortium inoculum of five thermo-tolerant phosphate solubilizing actinomycetes for multipurpose biofertilizer preparation. Iran J Microbiol 9:295–304

    PubMed  PubMed Central  Google Scholar 

  131. Olanrewaju OS, Babalola OO (2019) Streptomyces: implications and interactions in plant growth promotion. Appl Microbiol Biotechnol 103:1179–1188

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

Authors acknowledge their respective institutions.

Funding

Not applicable.

Author information

Authors and Affiliations

  1. Department of Microbiology, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan

    Muhammad Shehryar Sabir, Farooq Ali, Zeeshan Niaz & Shehzad Ahmed

  2. Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, 25000, Khyber Pakhtunkhwa, Pakistan

    Farah Shahzadi

  3. Department of Microbiology, Abbottabad University of Science and Technology, Abbottabad, 22010, Khyber Pakhtunkhwa, Pakistan

    Qismat Shakeela

Authors
  1. Muhammad Shehryar Sabir
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Farah Shahzadi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Farooq Ali
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Qismat Shakeela
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zeeshan Niaz
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Shehzad Ahmed
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

All authors contributed to conception and design of the study. MSS and FS did literature research, data collection, analysis, and manuscript writing. QS drafted the handover article and reviewed it critically for final approval. SA reanalyzed the article and made possible corrections and additions and approved the final version after agreement of all authors for publication.

Corresponding author

Correspondence to Shehzad Ahmed.

Ethics declarations

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical Approval

Not applicable.

Consent to Participate

Not applicable.

Consent for Publication

Not applicable.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 17 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sabir, M.S., Shahzadi, F., Ali, F. et al. Comparative Effect of Fertilization Practices on Soil Microbial Diversity and Activity: An Overview. Curr Microbiol 78, 3644–3655 (2021). https://doi.org/10.1007/s00284-021-02634-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-021-02634-2

Search

Navigation