Soil Microbial Hotspots and Hot Moments: Management vis-a-vis Soil Biodiversity

  • R. K. Yadav
  • M. R. Yadav
  • D. M. Mahala
  • Rakesh Kumar
  • Dinesh Kumar
  • Neelam Yadav
  • S. L. Yadav
  • V. K. Sharma
  • Sunita Yadav


All soils are heterogeneous in nature with differentiation in physical, chemical, and biological properties. Heterogeneity in substrate availability creates microbial hotspots and hot moments in soil. Microbial hotspots are microsites in soil with higher microbial activity and respiration rate compared to bulk soil. Microbial hotspot localization may occur around plant root surface (i.e., rhizosphere), on degrading plant roots (detritusphere), plant root or earthworm burrows (biopores), or surface of soil aggregates. In soil, most prevalent hotspots are found in the rhizosphere and on aggregate surfaces but frequently are of mixed origin. Priming effects are limited in microbial hotspots but are of significance of hot moments (short-term microbial hotspots). Residue decomposition induces significant changes in the microbial community. For concept of soil microbial hotspot and hot moment, we extensively reviewed and examined available literature related to management of soil biodiversity. Long-term cropping sequence had also significantly influenced microbial activity in agricultural soils. Increasing biodiversity through improved crop management practices restores positive aboveground-belowground interactions. In these insights, microbial hotspot management should be considered important in soil sustainability and food security.


Microbial hotspot Hot moment Microbial activity Soil biodiversity 


  1. Anderson TH, Domsch KH (1993) The metabolic quotient for CO2 (qCO2) as a specific activity parameter to assess the effects of environmental conditions, such as pH, on the microbial biomass of forest soils. Soil Biol Biochem 25(3):393–395CrossRefGoogle Scholar
  2. Baldrian P, Merhautová V, Cajthaml T, Petránková M, Šnajdr J (2010) Small-scale distribution of extracellular enzymes, fungal, and bacterial biomass in Quercus petraea forest topsoil. Biol Fertil Soils 46:717–726CrossRefGoogle Scholar
  3. Banfield CC, Dippold MA, Pausch J, Hoang DTT, Kuzyakov Y (2017) Biopore history determines the microbial community composition in subsoil hotspots. Biol Fertil Soils 53:573–588CrossRefGoogle Scholar
  4. Bastian F, Bouziri L, Nicolardot B, Ranjard L (2009) Impact of wheat straw decomposition on successional patterns of soil microbial community structure. Soil Biol Biochem 41:262–275CrossRefGoogle Scholar
  5. Blagodatskaya E, Blagodatsky S, Anderson TH, Kuzyakov Y (2014) Microbial growth and carbon use efficiency in the rhizosphere and root-free soil. PLoS One 9:e93282CrossRefGoogle Scholar
  6. Blagodatskaya E, Dannenmann M, Gasche R, Butterbach-Bahl K (2010) Microclimate and forest management alter fungal to bacterial ratio and N2O emission during rewetting in the forest floor and mineral soil of mountainous beech forests. Biogeochem 97:55–70CrossRefGoogle Scholar
  7. Blagodatskaya EV, Blagodatsky SA, Anderson TH, Kuzyakov Y (2009) Contrasting effects of glucose, living roots and maize straw on microbial growth kinetics and substrate availability in soil. Eur J Soil Sci 60:186–197CrossRefGoogle Scholar
  8. Blagodatsky SA, Yevdokimov IV, Larionova AA, Richter J (1998) Microbial growth in soil and nitrogen turnover: model calibration with laboratory data. Soil Biol Biochem 30:1757–1764CrossRefGoogle Scholar
  9. Denef K, Roobroeck D, Wadu MCM, Lootens P, Boeckx P (2009) Microbial community composition and rhizodeposit-carbon assimilation in differently managed temperate grassland soils. Soil Biol Biochem 41:144–153CrossRefGoogle Scholar
  10. Djukic I, Zehetner F, Mentler A, Gerzabek MH (2010) Microbial community composition and activity in different Alpine vegetation zones. Soil Biol Biochem 42:155–161CrossRefGoogle Scholar
  11. Ehlers K, Bakken LR, Frostegård Å, Frossard E, Bünemann EK (2010) Phosphorus limitation in a Ferralsol: impact on microbial activity and cell internal P pools. Soil Biol Biochem 42:558–566CrossRefGoogle Scholar
  12. Eickhorst T, Tippkotter R (2008) Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH). Soil Biol Biochem 40:1883–1891CrossRefGoogle Scholar
  13. Feng X, Simpson MJ (2009) Temperature and substrate controls on microbial phospholipid fatty acid composition during incubation of grassland soils contrasting in organic matter quality. Soil Biol Biochem 41:804–812CrossRefGoogle Scholar
  14. Goberna M, Insam H, Klammer S, Pascual JA, Sanchez J (2005) Microbial community structure at different depths in disturbed and undisturbed semiarid Mediterranean forest soils. Microb Ecol 50:315–326CrossRefGoogle Scholar
  15. Gray EJ, Smith DL (2005) Intracellular and extracellular PGPR: commonalities and distinctions in the plant-bacterium signaling processes. Soil Biol Biochem 37:395–412CrossRefGoogle Scholar
  16. Grayston SJ, Griffith GS, Mawdsley JL, Campbell CD, Bardgett RD (2001) Accounting for variability in soil microbial communities of temperate upland grassland ecosystems. Soil Biol Biochem 33(4):533–551CrossRefGoogle Scholar
  17. Hamer U, Makeschin F (2009) Rhizosphere soil microbial community structure and microbial activity in set-aside and intensively managed arable land. Plant Soil 316:57–69CrossRefGoogle Scholar
  18. Herron PM, Gage DJ, Pinedo CA, Haider ZK, Cardon ZG (2013) Better to light a candle than curse the darkness: illuminating spatial localization and temporal dynamics of rapid microbial growth in the rhizosphere. Front Plant Sci 4:323CrossRefGoogle Scholar
  19. Hinsinger P, Bengough AG, Vetterlein D, Young IM (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant Soil 321:117–152CrossRefGoogle Scholar
  20. Hoang DT, Pausch J, Razavi BS, Kuzyakova I, Banfield CC, Kuzyakov Y (2016) Hotspots of microbial activity induced by earthworm burrows, old root channels, and their combination in subsoil. Biol Fertil Soils 52(8):1105–1119CrossRefGoogle Scholar
  21. Hoang DT, Bauke SL, Kuzyakov Y, Pausch J (2017) Rolling in the deep: priming effects in earthworm biopores in topsoil and subsoil. Soil Biol Biochem 114:59–71CrossRefGoogle Scholar
  22. Hobbs PR, Sayre K, Gupta R (2008) The role of conservation agriculture in sustainable agriculture. Philos Trans R Soc B 363(1491):543–555CrossRefGoogle Scholar
  23. Jones DL, Nguyen C, Finlay RD (2009) Carbon flow in the rhizosphere: carbon trading at the soil-root interface. Plant Soil 321:5–33CrossRefGoogle Scholar
  24. Kautz T (2014) Research on subsoil biopores and their functions in organically managed soils: a review. Renew Agric Food Syst 30:318–327CrossRefGoogle Scholar
  25. Kibblewhite MG, Ritz K, Swift MJ (2007) Soil health in agricultural systems. Philos Trans R Soc B 363:685–701CrossRefGoogle Scholar
  26. Klumpp K, Fontaine S, Attard E, Le Roux X, Gleixner G, Soussana JF (2009) Grazing triggers soil carbon loss by altering plant roots and their control on soil microbial community. J Ecol 97:876–885CrossRefGoogle Scholar
  27. Kuzyakov Y, Blagodatskaya E (2015) Microbial hotspots and hot moments in soil: concept & review. Soil Biol Biochem 83:184–199CrossRefGoogle Scholar
  28. Kuzyakov Y, Domanski G (2000) Carbon input by plants into the soil. Review. J Plant Nutr Soil Sci 163:421–431CrossRefGoogle Scholar
  29. Kuzyakov Y, Xu XL (2013) Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance. New Phytol 198:656–669CrossRefGoogle Scholar
  30. Lee H, Schuur EAG, Inglett KS, Lavoie M, Chanton JP (2012) The rate of permafrost carbon release under aerobic and anaerobic conditions and its potential effects on climate. Glob Chang Biol 18(2):515–527CrossRefGoogle Scholar
  31. Lee SH, Jang I, Chae N, Choi T, Kang H (2013) Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils. Microbial Ecol 65(2):405–414CrossRefGoogle Scholar
  32. Lei Y, Xiao Y, Li L, Jiang C, Zu C, Li T, Cao H (2017) Impact of tillage practices on soil bacterial diversity and composition under the tobacco-rice rotation in China. J Microbiol 55(5):349–356CrossRefGoogle Scholar
  33. Lu Y, Murase J, Watanabe A, Sugimoto A, Kimura M (2004) Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil. FEMS Microb Ecol 48:179–186CrossRefGoogle Scholar
  34. Marschner P, Marhan S, Kandeler E (2012) Microscale distribution and function of soil microorganisms in the interface between rhizosphere and detritusphere. Soil Biol Biochem 49:174–183CrossRefGoogle Scholar
  35. McIntyre RE, Adams MA, Ford DJ, Grierson PF (2009) Rewetting and litter addition influence mineralisation and microbial communities in soils from a semi-arid intermittent stream. Soil Biol Biochem 41:92–101CrossRefGoogle Scholar
  36. Meena VS, Maurya BR, Verma R, Meena RS, Jatav GK, Meena SK, Meena SK (2013) Soil microbial population and selected enzyme activities as influenced by concentrate manure and inorganic fertilizer in alluvium soil of Varanasi. Bioscan 8(3):931–935Google Scholar
  37. Meena VS, Maurya BR, Verma JP, Aeron A, Kumar A, Kim K, Bajpai VK (2015) Potassium solubilizing rhizobacteria (KSR): isolation, identification, and K-release dynamics from waste mica. Ecol Eng 81:340–347CrossRefGoogle Scholar
  38. Mganga KZ, Razavi BS, Kuzyakov Y (2015) Microbial and enzymes response to nutrient additions in soils of Mt. Kilimanjaro region depending on land use. Eur J Soil Biol 69:33–40CrossRefGoogle Scholar
  39. Miller M, Dick RP (1995) Dynamics of soil C and microbial biomass in whole soil and aggregates in two cropping systems. Appl Soil Ecol 2:253–261CrossRefGoogle Scholar
  40. Nottingham AT, Griffiths H, Chamberlain PM, Stott AW, Tanner EVJ (2009) Soil priming by sugar and leaf-litter substrates: a link to microbial groups. Appl Soil Ecol 42:183–190CrossRefGoogle Scholar
  41. Pietri JA, Brookes PC (2009) Substrate inputs and pH as factors controlling microbial biomass, activity and community structure in an arable soil. Soil Biol Biochem 41:1396–1405CrossRefGoogle Scholar
  42. Ranjard L, Lejon DPH, Mougel C, Schehrer L, Merdinoglu D, Chaussod R (2003) Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environ Microbiol 5(11):1111–1120CrossRefGoogle Scholar
  43. Rasmussen J, Kusliene G, Jacobsen OS, Kuzyakov Y, Eriksen J (2013) Bicarbonate as tracer for assimilated C and homogeneity of 14 C and 15 N distribution in plants by alternative labeling approaches. Plant Soil 371:191–198CrossRefGoogle Scholar
  44. Rousk J, Bååth E (2007) Fungal and bacterial growth in soil with plant materials of different C/N ratios. FEMS Microb Ecol 62:258–267CrossRefGoogle Scholar
  45. Rudolph N, Voss S, Moradi AB, Nagl S, Oswald SE (2013) Spatio-temporal mapping of local soil pH changes induced by roots of lupin and soft-rush. Plant Soil 369:669–680CrossRefGoogle Scholar
  46. Sanaullah M, Blagodatskaya E, Chabbi A, Rumpel C, Kuzyakov Y (2011) Drought effects on microbial biomass and enzyme activities in the rhizosphere of grasses depend on plant community composition. Appl Soil Ecol 48:38–44CrossRefGoogle Scholar
  47. Schimel JP, Weintraub MN (2003) The implications of exoenzyme activity on microbial carbon and nitrogen limitation in soil: a theoretical model. Soil Biol Biochem 35:549–563CrossRefGoogle Scholar
  48. Singh NP, Singh RK, Meena VS, Meena RK (2015) Can we use maize (Zea mays) rhizobacteria as plant growth promoter? Vegetos 28(1):86–99. CrossRefGoogle Scholar
  49. Singh M, Dotaniya ML, Mishra A, Dotaniya CK, Regar KL, Lata M (2016) Role of biofertilizers in conservation agriculture. In: Bisht JK, Meena VS, Mishra PK, Pattanayak A (eds) Conservation agriculture: an approach to combat climate change in Indian Himalaya. Springer, Singapore, pp 113–134. CrossRefGoogle Scholar
  50. Smith AP, Marin-Spiotta E, De Graaf MA, Balser T (2014) Microbial community structure varies across soil organic matter pools during tropical land cover change. Soil Biol Biochem 77:292–303CrossRefGoogle Scholar
  51. Spohn M, Kuzyakov Y (2014) Spatial and temporal dynamics of hotspots of enzyme activity in soil as affected by living and dead roots—a soil zymography analysis. Plant Soil 379:67–77CrossRefGoogle Scholar
  52. Tiemann LK, Grandy AS, Atkinson EE, Marin-Spiotta E, McDaniel MD (2015) Crop rotational diversity enhances belowground communities and functions in an agroecosystem. Ecollet 18(8):761–771Google Scholar
  53. White PM, Rice CW (2009) Tillage effects on microbial and carbon dynamics during plant residue decomposition. Soil Sci Soc Am J 73:138–145CrossRefGoogle Scholar
  54. Yu C, Hu XM, Deng W, Li Y, Xiong C, Ye CH, Li X (2015) Changes in soil microbial community structure and functional diversity in the rhizosphere surrounding mulberry subjected to long-term fertilization. Appl Soil Ecol 86:30–40CrossRefGoogle Scholar
  55. Zak DR, Ringelberg DB, Pregitzer KS, Randlett DS, White DC, Curtis PS (1996) Soil microbial communities beneath Populus grandidentata grown under elevated atmospheric CO2. Ecol Appl 6:257–262CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • R. K. Yadav
    • 1
  • M. R. Yadav
    • 2
  • D. M. Mahala
    • 3
  • Rakesh Kumar
    • 4
  • Dinesh Kumar
    • 4
  • Neelam Yadav
    • 5
  • S. L. Yadav
    • 1
  • V. K. Sharma
    • 6
  • Sunita Yadav
    • 6
  1. 1.Agricultural Research StationAgriculture UniversityKotaIndia
  2. 2.Rajasthan Agricultural Research InstituteJaipurIndia
  3. 3.ICAR-Indian Institute of Maize ResearchLudhianaIndia
  4. 4.ICAR-National Dairy Research InstituteKarnalIndia
  5. 5.Anand Agricultural UniversityAnandIndia
  6. 6.ICAR-Indian Agricultural Research InstituteNew DelhiIndia

Personalised recommendations