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

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Plant Growth Promoting Rhizobacteria for Agricultural Sustainability

Abstract

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.

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References

  • 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):393–395

    Article  Google Scholar 

  • Baldrian P, Merhautová V, Cajthaml T, Petránková M, Å najdr J (2010) Small-scale distribution of extracellular enzymes, fungal, and bacterial biomass in Quercus petraea forest topsoil. Biol Fertil Soils 46:717–726

    Article  CAS  Google Scholar 

  • Banfield CC, Dippold MA, Pausch J, Hoang DTT, Kuzyakov Y (2017) Biopore history determines the microbial community composition in subsoil hotspots. Biol Fertil Soils 53:573–588

    Article  CAS  Google Scholar 

  • 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 41:262–275

    Article  CAS  Google Scholar 

  • 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:e93282

    Article  Google Scholar 

  • 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 97:55–70

    Article  CAS  Google Scholar 

  • 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 60:186–197

    Article  CAS  Google Scholar 

  • Blagodatsky SA, Yevdokimov IV, Larionova AA, Richter J (1998) Microbial growth in soil and nitrogen turnover: model calibration with laboratory data. Soil Biol Biochem 30:1757–1764

    Article  CAS  Google Scholar 

  • 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 41:144–153

    Article  CAS  Google Scholar 

  • Djukic I, Zehetner F, Mentler A, Gerzabek MH (2010) Microbial community composition and activity in different Alpine vegetation zones. Soil Biol Biochem 42:155–161

    Article  CAS  Google Scholar 

  • Ehlers K, Bakken LR, FrostegÃ¥rd Ã…, Frossard E, Bünemann EK (2010) Phosphorus limitation in a Ferralsol: impact on microbial activity and cell internal P pools. Soil Biol Biochem 42:558–566

    Article  CAS  Google Scholar 

  • 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 40:1883–1891

    Article  CAS  Google Scholar 

  • 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 41:804–812

    Article  CAS  Google Scholar 

  • 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 50:315–326

    Article  CAS  Google Scholar 

  • Gray EJ, Smith DL (2005) Intracellular and extracellular PGPR: commonalities and distinctions in the plant-bacterium signaling processes. Soil Biol Biochem 37:395–412

    Article  CAS  Google Scholar 

  • 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):533–551

    Article  CAS  Google Scholar 

  • Hamer U, Makeschin F (2009) Rhizosphere soil microbial community structure and microbial activity in set-aside and intensively managed arable land. Plant Soil 316:57–69

    Article  CAS  Google Scholar 

  • 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 4:323

    Article  Google Scholar 

  • Hinsinger P, Bengough AG, Vetterlein D, Young IM (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant Soil 321:117–152

    Article  CAS  Google Scholar 

  • 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):1105–1119

    Article  CAS  Google Scholar 

  • 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 114:59–71

    Article  CAS  Google Scholar 

  • Hobbs PR, Sayre K, Gupta R (2008) The role of conservation agriculture in sustainable agriculture. Philos Trans R Soc B 363(1491):543–555

    Article  Google Scholar 

  • Jones DL, Nguyen C, Finlay RD (2009) Carbon flow in the rhizosphere: carbon trading at the soil-root interface. Plant Soil 321:5–33

    Article  CAS  Google Scholar 

  • Kautz T (2014) Research on subsoil biopores and their functions in organically managed soils: a review. Renew Agric Food Syst 30:318–327

    Article  Google Scholar 

  • Kibblewhite MG, Ritz K, Swift MJ (2007) Soil health in agricultural systems. Philos Trans R Soc B 363:685–701

    Article  Google Scholar 

  • 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 97:876–885

    Article  CAS  Google Scholar 

  • Kuzyakov Y, Blagodatskaya E (2015) Microbial hotspots and hot moments in soil: concept & review. Soil Biol Biochem 83:184–199

    Article  CAS  Google Scholar 

  • Kuzyakov Y, Domanski G (2000) Carbon input by plants into the soil. Review. J Plant Nutr Soil Sci 163:421–431

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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):515–527

    Article  Google Scholar 

  • 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):405–414

    Article  CAS  Google Scholar 

  • 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):349–356

    Article  CAS  Google Scholar 

  • 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 48:179–186

    Article  CAS  Google Scholar 

  • Marschner P, Marhan S, Kandeler E (2012) Microscale distribution and function of soil microorganisms in the interface between rhizosphere and detritusphere. Soil Biol Biochem 49:174–183

    Article  CAS  Google Scholar 

  • 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 41:92–101

    Article  CAS  Google Scholar 

  • 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):931–935

    CAS  Google Scholar 

  • 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 81:340–347

    Article  Google Scholar 

  • 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 69:33–40

    Article  CAS  Google Scholar 

  • Miller M, Dick RP (1995) Dynamics of soil C and microbial biomass in whole soil and aggregates in two cropping systems. Appl Soil Ecol 2:253–261

    Article  Google Scholar 

  • 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 42:183–190

    Article  Google Scholar 

  • 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 41:1396–1405

    Article  Google Scholar 

  • 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):1111–1120

    Article  CAS  Google Scholar 

  • 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 371:191–198

    Article  CAS  Google Scholar 

  • Rousk J, Bååth E (2007) Fungal and bacterial growth in soil with plant materials of different C/N ratios. FEMS Microb Ecol 62:258–267

    Article  CAS  Google Scholar 

  • 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 369:669–680

    Article  CAS  Google Scholar 

  • 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 48:38–44

    Article  Google Scholar 

  • Schimel JP, Weintraub MN (2003) The implications of exoenzyme activity on microbial carbon and nitrogen limitation in soil: a theoretical model. Soil Biol Biochem 35:549–563

    Article  CAS  Google Scholar 

  • 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. https://doi.org/10.5958/2229-4473.2015.00012.9

    Article  Google Scholar 

  • 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. https://doi.org/10.1007/978-981-10-2558-7_4

    Chapter  Google Scholar 

  • 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 77:292–303

    Article  CAS  Google Scholar 

  • 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 379:67–77

    Article  CAS  Google Scholar 

  • 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):761–771

    CAS  Google Scholar 

  • White PM, Rice CW (2009) Tillage effects on microbial and carbon dynamics during plant residue decomposition. Soil Sci Soc Am J 73:138–145

    Article  CAS  Google Scholar 

  • 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 86:30–40

    Article  Google Scholar 

  • 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 6:257–262

    Article  Google Scholar 

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Yadav, R.K. et al. (2019). Soil Microbial Hotspots and Hot Moments: Management vis-a-vis Soil Biodiversity. In: Kumar, A., Meena, V. (eds) Plant Growth Promoting Rhizobacteria for Agricultural Sustainability . Springer, Singapore. https://doi.org/10.1007/978-981-13-7553-8_9

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