VEGETOS: An International Journal of Plant Research & Biotechnology
(Society For Plant Research)

Research Articles

A SOCIETY FOR PLANT RESEARCH PUBLICATION


Volume: 32, Issue: 4, December 2019


Print ISSN : 0970-4078.
Online ISSN : 2229-4473.
Website:www.vegetosindia.org
Pub Email: contact@vegetosindia.org
Page Visits: 77

Doi: 10.1007/s42535-019-00052-1
Doi Link: https://doi.org/10.1007/s42535-019-00052-1
First Page: 620
Last Page: 634
Published: 06 August, 2019

Responses of soil carbon, nitrogen, microbial activity, bacterial community composition and grain yield to farmyard manure amendments in a rainfed agriculture (Paddy) system of Himalaya


Abstract:

The impact of farmyard manure (FYM) amendment (15, 30 and 60 Mg ha−1) on the changes of carbon content, nitrogen content, microbial activity, bacterial community composition and grain yield were investigated in a traditional rainfed agriculture (Oryza sativa L.) system of the Himalaya. Our results showed that carbon (5 to 16%) and nitrogen (37 to 55%) contents were reduced significantly at the end of the paddy cropping season; while the C:N values (46 to 90%) and microbial activity (66 to 122%) were increased significantly at the end of the paddy cropping season as compared to sowing season in the soil amended with FYM. The grain yield of paddy increases significantly with increasing rates of FYM. We found the highest abundance of copiotrophs (Proteobacteria and Firmicutes) in the soil amended with different rates FYM at the end of the paddy cropping season. Differences in soil bacterial communities are associated with different amendment rates of FYM, suggesting that higher FYM amendment rates could change the bacterial community compositions which have an adverse impact on soil carbon and nitrogen contents at the end of the paddy cropping season in the rainfed agriculture system of the Himalaya.

Vegetos

Keywords:


Soil carbon, Soil microbial activity, High throughput sequencing, Copiotrophs and oligotrophs, Himalaya


References:


  1. Abe S, Hashimoto S, Umezane T, Yamaguchi T, Yamamoto S, Yamada S, Endo T, Nakata N (2016) Excessive application of farmyard manure reduces rice yield and enhances environmental pollution risk in paddy fields. Arch Agron Soil Sci 62:1208–1221

  2. Adam G, Duncan H (2001) Development of a sensitive and rapid method for the measurement of total microbial activity using fluorescein diacetate (FDA) in a range of soils. Soil Biol Biochem 33:943–951

  3. Alauzet C, Jumas-Bilak E (2014) The Phylum Deferribacteres and the Genus Caldithrix. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes. Springer, Berlin, Heidelberg

  4. Bergmann G, Bates S, Eilers K, Lauber C, Caporaso J, Walters W, Knight R, Fierer N (2011) The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem 43:1450–1455

  5. Bernard L, Mougel C, Maron P, Nowak V, Lévêque J, Henault C, Haichar F, Berge O, Marol C, Balesdent J, Gibiat F, Lemanceau P, Ranjard L (2007) Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques. Environ Microbiol 9:752–764

  6. Bhadauria T, Ramakrishnan P, Srivastava K (1997) Population dynamics of earthworms during crop rotation under rainfed agriculture in central Himalayas, India. Appl Soil Ecol 6:205–215

  7. Bhattacharyya P, Roy K, Neogi S, Chakravorti S, Behera K, Das K, Bardhan S, Rao K (2012) Effect of long-term application of organic amendment on C storage in relation to global warming potential and biological activities in tropical flooded soil planted to rice. Nutr Cycl Agroecosys 94:273–285

  8. Blagodatskaya E, Blagodatsky S, Anderson T, Kuzyakov Y (2007) Priming effects in Chernozem induced by glucose and N in relation to microbial growth strategies. Appl Soil Ecol 37:95–105

  9. Blanchet G, Gavazov K, Bragazza L, Sinaj S (2016) Responses of soil properties and crop yields to different inorganic and organic amendments in a Swiss conventional farming system. Agr Ecosyst Environ 230:116–126

  10. Breidenbach B, Pump J, Dumont M (2016) microbial community structure in the rhizosphere of rice plants. Front Microbiol 6:1537. https://doi.org/10.3389/fmicb.2015.01537

  11. Buckley DH, Schmidt TM (2001) The structure of microbial communities in soil and the lasting impact of cultivation. Microb Ecol 42:11–21

  12. Chandra A, Saradhi P, Rao KS, Saxena KG, Maikhuri RK (2011a) An investigation into the energy use in relation to yield of traditional crops in central Himalaya, India. Biomass Bioenergy 35:2044–2052

  13. Chandra A, Saradhi P, Maikhuri RK, Saxena KG, Rao KS (2011b) Traditional agrodiversity management: a case study of central himalayan village ecosystem. J Mount Sci 8:62–74

  14. Cheng W, Johnson DW, Fu S (2003) Rhizosphere priming effects on decomposition: controls of fertilization, plant species, and phenology. Soil Sci Soc Am J 67:1418–1427

  15. Choudhary AK, Suri V (2009) Effect of organic manures and inorganic fertilizers on productivity, nutrient uptake and soil fertility in rice (Oryza sativa) wheat (Triticum aestivum) crop sequence in western Himalayas. Curr Adv Agric Sci 1:65–69

  16. Chroňáková A, Schloter-Hai B, Radl V, Endesfelder D, Quince C, Elhottová D, Šimek M, Schloter M (2015) Response of archaeal and bacterial soil communities to changes associated with outdoor cattle overwintering. PLoS ONE 10:e0135627

  17. Constancias F, Prévost-Bouré N, Terrat S, Aussems S, Nowak V, Guillemin J, Bonnotte A, Biju-Duval L, Navel A, Martins J, Maron P, Ranjard L (2014) Microscale evidence for a high decrease of soil bacterial density and diversity by cropping. Agron Sustain Dev 34:831–840

  18. Das S, Jeong S, Das S, Kim P (2017) Composted cattle manure increases microbial activity and soil fertility more than composted swine manure in a submerged rice paddy. Front Microbiol 8:1–8. https://doi.org/10.3389/fmicb.2017.01702

  19. Datta A, Mandal B, Basak N, Badole S, Chaitanya K, Majumder S, Thakur N, Kumar P, Kachroo D (2018) Soil carbon pools under long-term rice-wheat cropping system in Inceptisols of Indian Himalayas. Arch Agron Soil Sci 64:1315–1320

  20. Dennis P, Miller A, Hirsch P (2010) Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol Ecol 72:313–327

  21. Dijkstra F, Cheng W, Johnson D (2006) Plant biomass influences rhizosphere priming effects on soil organic matter decomposition in two differently managed soils. Soil Biol Biochem 38:2519–2526

  22. Dijkstra F, Carrillo Y, Pendall E, Morgan J (2013) Rhizosphere priming: a nutrient perspective. Front Microbiol 4:1–8

  23. Eilers K, Lauber C, Knight R, Fierer N (2010) Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil. Soil Biol Biochem 42:896–903

  24. Fang Y, Nazaries L, Singh B, Singh B (2018) Microbial mechanisms of carbon priming effects revealed during the interaction of crop residue and nutrient inputs in contrasting soils. Glob Chang Biol 24:2775–2790

  25. Ferreras L, Gomez E, Toresani S, Firpo I, Rotondo R (2006) Effect of organic amendments on some physical, chemical and biological properties in a horticultural soil. Bioresour Technol 97:635–640

  26. Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364. https://doi.org/10.1890/05-1839

  27. Fierer N, Lauber C, Ramirez K, Zaneveld J, Bradford M, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017

  28. Fontaine S, Bardoux G, Abbadie L, Mariotti A (2004) Carbon input to soil may decrease soil carbon content. Ecol Lett 7:314–320

  29. Fu SL, Cheng W (2002) Rhizosphere priming effects on the decomposition of soil organic matter in C-4 and C-3 grassland soils. Plant Soil 238:289–294

  30. Garcia-Pausas J, Paterson E (2011) Microbial community abundance and structure are determinants of soil organic matter mineralisation in the presence of labile carbon. Soil Biol Biochem 43:1705–1713

  31. Goldfarb K, Karaoz U, Hanson C, Santee C, Bradford M, Treseder K, Wallenstein M, Brodie E (2011) Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol 2:1–10. https://doi.org/10.3389/fmicb.2011.00094

  32. Green S, Michel F, Hadar Y, Minz D (2004) Similarity of bacterial communities in sawdust- and straw-amended cow manure composts. FEMS Microbiol Lett 233:115–123

  33. Gulde S, Chung H, Amelung W, Chang C, Six J (2008) Soil carbon saturation controls labile and stable carbon pool dynamics. Soil Sci Soc Am J 72:605–612

  34. Han P, Zhang W, Wang G, Sun W, Huang Y (2016) Changes in soil organic carbon in croplands subjected to fertilizer management: a global meta-analysis. Sci Rep 6:27199. https://doi.org/10.1038/srep27199

  35. Hartmann M, Frey B, Mayer J, Mäder P, Widmer F (2015) Distinct soil microbial diversity under long-term organic and conventional farming. ISME J 9:1177–1194

  36. Hernández M, Dumont M, Yuan Q, Conrad R (2015) Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon. Appl Environ Microbiol 81:2244–2253

  37. Hou P, Chien C, Chiang-Hsieh Y, Tseng K, Chow C, Huang H, Chang W (2018) Paddy-upland rotation for sustainable agriculture with regards to diverse soil microbial community. Sci Rep 8:7966. https://doi.org/10.1038/s41598-018-26181-2

  38. Kaur S, and Purohit MK (2013) Rainfall statistics of India-2013. India Meteorological Department, (Ministry of Earth Sciences) Mausam Bhawan, Lodi Road New Delhi—110003

  39. Kaur S, and Purohit MK (2014) Rainfall statistics of India-2014. India Meteorological Department, (Ministry of Earth Sciences) Mausam Bhawan, Lodi Road New Delhi—110003

  40. Kaur S, and Purohit MK (2015) Rainfall statistics of India-2015. India Meteorological Department, (Ministry of Earth Sciences) Mausam Bhawan, Lodi Road New Delhi—110003

  41. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner F (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41:e1. https://doi.org/10.1093/nar/gks808

  42. Koch AL (2001) Oligotrophs versus copiotrophs. Bio Essays 23:657–661

  43. Kukal S, Bawa S (2013) Temporal variations in runoff and soil loss in relation to soil conservation practices in catchments in Shiwaliks of lower Himalayas. Int Soil Wat Conserv Res 1:19–25

  44. Kuramae E, Yergeau E, Wong L, Pijl A, Veen J, Kowalchuk G (2012) Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiol Ecol 79:12–24

  45. Kuzyakov Y, Cheng W (2004) Photosynthesis controls of CO2 efflux from maize rhizosphere. Plant Soil 263:85–99

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

  47. Lal R (2004) Soil carbon sequestration impacts on global climate change and food security. Science 304:1623–1627

  48. Lazcano C, Gómez-Brandón M, Revilla P, Domínguez J (2012) Short-term effects of organic and inorganic fertilizers on soil microbial community structure and function. Biol Fertil Soils 49:723–733

  49. Li JT, Zhang B (2007) Paddy soil stability and mechanical properties as affected by long-term application of chemical fertilizer and animal manure in subtropical China. Pedosphere 17:568–579. https://doi.org/10.1016/S1002-0160(07)60067-8

  50. Li F, Chen L, Zhang J, Yin J, Huang S (2017) Bacterial community structure after long-term organic and inorganic fertilization reveals important associations between soil nutrients and specific taxa involved in nutrient transformations. Front Microbiol 8:187. https://doi.org/10.3389/fmicb.2017.00187

  51. Liu E, Yan C, Mei X, Zhang Y, Fan T (2013) Long-term effect of manure and fertilizer on soil organic carbon pools in dryland farming in northwest China. PLoS ONE 8:e56536

  52. Luo X, Fu X, Yang Y, Cai P, Peng S, Chen W, Huang Q (2016) Microbial communities play important roles in modulating paddy soil fertility. Sci Rep 6:20326. https://doi.org/10.1038/srep20326

  53. Lützow M, Kögel-Knabner I, Ekschmitt K, Flessa H, Guggenberger G, Matzner E, Marschner B (2007) SOM fractionation methods: relevance to functional pools and to stabilization mechanisms. Soil Biol Biochem 39:2183–2207

  54. Mahanta D, Bhattacharyya R, Gopinath K, Tuti M, Mina B, Pandey B, Mishra P, Bisht J, Srivastva A, Bhatt J (2013) Influence of farmyard manure application and mineral fertilization on yield sustainability, carbon sequestration potential and soil property of gardenpea–french bean cropping system in the Indian Himalayas. Sci Hort 164:414–427

  55. Maikhuri RK, Rao KS, Semwal RL (2001a) Changing scenario of Himalayan agro ecosystems: loss of agro biodiversity as an indicator of global environmental change impacts monitoring in central Himalaya, India. Environmentalist 21:23–39

  56. Maikhuri RK, Semwal RL, Rao KS, Saxena KG, Das AK (2001b) Indigenous techniques of agricultural soil fertility maintenance in the central Himalaya. Ecol Environ Conserv 7:15–20

  57. Maikhuri RK, Rawat LS, Semwal RL, Rao KS, Saxena KG (2015) Organic farming in Uttarakhand Himalaya, India. Int J Ecol Environ Sci 41:161–176

  58. Manna M, Swarup A, Wanjari R, Singh Y, Ghosh P, Singh K, Tripathi A, Saha M (2006) Soil organic matter in a west bengal inceptisol after 30 years of multiple cropping and fertilization. Soil Sci Soc Am J 70:121–129

  59. Metsalu T, Vilo J (2015) ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. Nucleic Acids Res 43:W566–W570

  60. Mishra S, Maikhuri RK, and Deepak D (2008) Indigenous soil management to revive below ground biodiversity—case of Garhwal. Leisa India: 13–14

  61. Mohamed N, Saito K, Tal Y, Hill R (2010) Diversity of aerobic and anaerobic ammonia-oxidizing bacteria in marine sponges. ISME J 4:38–48

  62. National bureau of soil survey (NBSS) Staff (1985) Soil map of india (1:7 M). NBSS & LUP, Nagpur

  63. Nayak D, Babu Y, Adhya T (2007) Long-term application of compost influences microbial biomass and enzyme activities in a tropical Aeric Endoaquept planted to rice under flooded condition. Soil Biol Biochem 39:1897–1906

  64. Phillips R, Finzi A, Bernhardt E (2011) Enhanced root exudation induces microbial feedbacks to N cycling in a pine forest under long-term CO2 fumigation. Ecol Lett 14:187–194

  65. Qiao N, Xu X, Hu Y, Blagodatskaya E, Liu Y, Schaefer D, Kuzyakov Y (2016) Carbon and nitrogen additions induce distinct priming effects along an organic-matter decay continuum. Sci Rep 6:19865. https://doi.org/10.1038/srep19865

  66. Ramirez K, Craine J, Fierer N (2012) Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Glob Chang Biol 18:1918–1927

  67. Sasaki H, Nonaka J, Otawa K, Kitazume O, Asano R, Sasaki T, Nakai Y (2009) Analysis of the structure of the bacterial community in the livestock manure-based composting process. Asian Austral J Anim 22:113–118

  68. Singh D, Akhtar Z, Gupta S, Srivastava A, Chakraborty M (2017) Production strategies of organic basmati rice in Tarai region of Uttarakhand, India. Organic Agric 7:21–30

  69. Stewart C, Paustian K, Conant R, Plante A, Six J (2007) Soil carbon saturation: concept, evidence and evaluation. Biogeochemistry 86:19–31

  70. Stewart C, Paustian K, Conant R, Plante A, Six J (2009) Soil carbon saturation: implications for measurable carbon pool dynamics in long-term incubations. Soil Biol Biochemi 41:357–366

  71. Trivedi P, Anderson I, Singh B (2013) Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction. Trends Microbiol 21:641–651

  72. Uz I, Sonmez S, Tavali IE, Citak S, Urasi DS, Citak S (2016) Effect of vermicompost on chemical and biological properties of an alkaline soil with high lime content during celery (Apium graveolens L. var. dulce Mill.) production. Not Bot Horti Agrobo 44:280–290. https://doi.org/10.15835/nbha44110157

  73. van Groenigen K, Qi X, Osenberg C, Luo Y, Hungate B (2014) Faster decomposition under increased atmospheric CO2 limits soil carbon storage. Science 344:508–509

  74. Xuan D, Guong V, Rosling A, Alström A, Chai B, Högberg N (2012) Different crop rotation systems as drivers of change in soil bacterial community structure and yield of rice, Oryza sativa. Biol Fertil Soils 48:217–225

  75. Zhang Y, Chen L, Chen X, Tan M, Duan Z, Wu Z, Li X, Fan X (2015) Response of soil enzyme activity to long-term restoration of desertified land. CATENA 133:64–70

  76. Zhang X, Han X, Yu W, Wang P, Cheng W (2017) Priming effects on labile and stable soil organic carbon decomposition: pulse dynamics over two years. PLoS ONE 12:e0184978

  77. Zhou P, Sheng H, Li Y, Tong C, Ge T, Wu J (2016) Lower C sequestration and N use efficiency by straw incorporation than manure amendment on paddy soils. Agric Ecosyst Environ 219:93–100

  78. Zhu Z, Zeng G, Ge T, Hu Y, Tong C, Shibistova O, He X, Wang J, Guggenberger G, Wu J (2016) Fate of rice shoot and root residues, rhizodeposits, and microbe-assimilated carbon in paddy soil—Part 1: decomposition and priming effect. Biogeosciences 13:4481–4489

  79. Zhu Z, Ge T, Hu Y, Zhou P, Wang T, Shibistova O, Guggenberger G, Su Y, Wu J (2017) Fate of rice shoot and root residues, rhizodeposits, and microbial assimilated carbon in paddy soil—part 2: turnover and microbial utilization. Plant Soil 416:243–257

  80. Zhu Z, Ge T, Liu S, Hu Y, Ye R, Xiao M, Tong C, Kuzyakov Y, Wu J (2018) Rice rhizodeposits affect organic matter priming in paddy soil: the role of N fertilization and plant growth for enzyme activities, CO2 and CH4 emissions. Soil Biol Biochem 116:369–377

  81. Qiao Q, Wang F, Zhang J, Chen Y, Zhang C, Liu G, Zhang G, Ma C, Zhang J (2017) The variation in the rhizosphere microbiome of cotton with soil type, genotype and developmental stage. Sci Rep 7:3940

  82. Paterson E (2003) Importance of rhizodeposition in the coupling of plant and microbial productivity. Eur J Soil Sci 54(4):741–750

  83. Jain SK, Kumar S, Varghese J (2001) Estimation of soil erosion for a Himalayan watershed using GIS technique. Water Resour Manage 15:41–54

  84. Bhadauria T, Kumar P, Maikhuri R, Saxena KG (2014) Effect of application of vermicompost and conventional compost derived from different residues on pea crop production and soil faunal diversity in agricultural system in Garhwal Himalayas India. Nat Sci 6:433–446

  85. Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10(10):996–998

  86. Oliveros JC (2015) Venny. An interactive tool for comparing lists with Venn’s diagrams. https://bioinfogp.cnb.csic.es/tools/venny/index.html

  87. Mishra C, Rawat GS (1998) Livestock grazing and biodiversity conservation: comments on Saberwal. Conserv Biol 12:712–714

  88. Fontaine S, Barot S, Barre P, Bdioui N, Mary B, Rumpel C (2007) Stability of organic carbon in deep soil layers controlled by fresh carbon supply. Nature 450:277–280

  89. Battin TM, Wille A, Sattler B, Psenner R (2001) Phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream. Appl Environ Microbiol 67:799–807

  90. Turner TR, James EK, Poole PS (2013) The plant microbiome. Genome Biol 14:209


  91.  


Acknowledgements :



This work was financially supported by DST (DST-IS-STAC/CO2-SR-148/12(G), SERB (SR/FT/LS-59/2012), UGC-DSK-PDF (BSR/BL/16-17/0146) New Delhi and University of Delhi under strengthened R&D program of Faculty at University of Delhi. Authors are thankful to Dr. R. K. Maikhuri, for his support during the selection of the study site in central Himalaya. Also thankful to Prof. Manu Agarwal, Department of Botany, University of Delhi for his help in Metagenomics studies. Authors are thankful to Dr. Jyotishman Deka for his help in preparing the map of our study area.


Author Information:



J. Dinakaran
Natural Resource Management Laboratory, Department of Botany, University of Delhi (North Campus), Delhi, India
jesudina@gmail.com
Abhishek Chandra
Natural Resource Management Laboratory, Department of Botany, University of Delhi (North Campus), Delhi, India


Krati Vikram
Natural Resource Management Laboratory, Department of Botany, University of Delhi (North Campus), Delhi, India

Kamlapati Chamoli
Department of Botany, A.P.B. Govt. Post Graduate College, Rudraprayag, India

Subodh Tambat
Bionivid, Bengaluru, India

K. S. Rao
Natural Resource Management Laboratory, Department of Botany, University of Delhi (North Campus), Delhi, India




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