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Role of Microorganisms in Regulating Carbon Cycle in Tropical and Subtropical Soils

  • Arjun Singh
  • Murugan Kumar
  • Anil Kumar Saxena
Chapter

Abstract

The tropics and subtropics of the world are the most densely populated regions of the world. A majority of its population thrives on agriculture for sustaining its livelihood and nutritional requirement. With the increase in the global population and many new technological breakthroughs in agriculture, the food production has increased many folds from these regions. These regions are now being called the food bowl of the world. Albeit of these facts, intensive agro-practices have led to increased burden on our natural resources, in particular to our soils. It is now very well established that soil organic carbon content is getting depleted at a faster rate than the rate at which they are being replenished. Naturally, the biogeochemical cycling of the organic matter efficiently and harmoniously is being orchestrated by the soil microbial flora. Studying the responses of soil microbial flora with respect to various cues of the environmental and anthropogenic activities is helping the soil ecologist and microbiologist in monitoring and controlling any disturbances in the soil carbon cycling. Many of the high precision modelling techniques involving amalgamation of high-throughput spectrometric and next-generation genomic tools have helped over time in closely monitoring and generating high-precision modelling of the soil organic carbon cycling of the region.

Keywords

Carbon cycle Methanogenesis Microbial biomass carbon Microorganisms Tropical soil 

References

  1. Allison SD, Vitousek PM (2004) Extracellular enzyme activities and carbon chemistry as drivers of tropical plant litter decomposition. Biotropica 36:285–296Google Scholar
  2. Berg IA (2011) Ecological aspects of distribution of different autotrophic CO2 fixation pathways. Appl Environ Microbiol 77(6):1925–1936CrossRefGoogle Scholar
  3. Bhagat C, Dudhagara P, Tank S (2018) Trends, application and future prospectives of microbial carbonic anhydrase mediated carbonation process for CCUS. J Appl Microbiol 124:316–335CrossRefGoogle Scholar
  4. Bhatnagar JM, Peay KG, Treseder KK (2018) Litter chemistry influences decomposition through activity of specific microbial functional guilds. Ecol Monogr 88:429–444.  https://doi.org/10.1002/ecm.1303 CrossRefGoogle Scholar
  5. Bird JA, Herman DJ, Firestone MK (2011) Rhizosphere priming of soil organic matter by bacterial groups in a grassland soil. Soil Biol Biochem 43:718–725CrossRefGoogle Scholar
  6. Bleidorn C (2016) Third generation sequencing: technology and its potential impact on evolutionary biodiversity research. Syst Biodivers 14:1–8CrossRefGoogle Scholar
  7. Bond-Lamberty B, Bolton H, Fansler S (2016) Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment. PLoS One 11:e0150599CrossRefGoogle Scholar
  8. Boykoff M, Daly M, Fernández Reyes R (2018) World newspaper coverage of climate change or global warming, 2004–2018-June 2018Google Scholar
  9. Brogi SR, Ha SY, Kim K (2018) Optical and molecular characterization of dissolved organic matter (DOM) in the Arctic ice core and the underlying seawater (Cambridge Bay, Canada): implication for increased autochthonous DOM during ice melting. Sci Total Environ 627:802–811CrossRefGoogle Scholar
  10. Buringh P, Buringh P (1979) Introduction to the study of soils in tropical and subtropical regions. Pudoc, WageningenGoogle Scholar
  11. Calderón K, Spor A, Breuil MC (2017) Effectiveness of ecological rescue for altered soil microbial communities and functions. ISME J 11:272CrossRefGoogle Scholar
  12. Cardenas E, Tiedje JM (2008) New tools for discovering and characterizing microbial diversity. Curr Opin Biotechnol 19:544–549.  https://doi.org/10.1016/j.copbio.2008.10.010 CrossRefGoogle Scholar
  13. Cleveland CC, Reed SC, Townsend AR (2006) Nutrient regulation of organic matter decomposition in a tropical rain forest. Ecology 87:492–503CrossRefGoogle Scholar
  14. Conrad R (2007) Microbial ecology of methanogens and methanotrophs. Adv Agron 96:1–63CrossRefGoogle Scholar
  15. Coyne MS, Coyne MS (1999) Soil microbiology: an exploratory approach. Delmar, New YorkGoogle Scholar
  16. Dalal RC, Allen DE, Livesley SJ, Richards G (2008) Magnitude and biophysical regulators of methane emission and consumption in the Australian agricultural, forest, and submerged landscapes: a review. Plant Soil 309:43–76CrossRefGoogle Scholar
  17. Das S, Adhya TK (2012) Dynamics of methanogenesis and methanotrophy in tropical paddy soils as influenced by elevated CO2 and temperature interaction. Soil Biol Biochem 47:36–45CrossRefGoogle Scholar
  18. Datta R, Kelkar A, Baraniya D (2017) Enzymatic degradation of lignin in soil: a review. Sustainability 9:1163CrossRefGoogle Scholar
  19. Derrien M, Lee YK, Park JE (2017) Spectroscopic and molecular characterization of humic substances (HS) from soils and sediments in a watershed: comparative study of HS chemical fractions and the origins. Environ Sci Pollut Res 24:16933–16945CrossRefGoogle Scholar
  20. Derrien M, Kim MS, Ock G (2018) Estimation of different source contributions to sediment organic matter in an agricultural-forested watershed using end member mixing analyses based on stable isotope ratios and fluorescence spectroscopy. Sci Total Environ 618:569–578.  https://doi.org/10.1016/j.scitotenv.2017.11.067 CrossRefGoogle Scholar
  21. Dubbs LL, Whalen SC (2010) Reduced net atmospheric CH4 consumption is a sustained response to elevated CO2 in a temperate forest. Biol Fertil Soils 46:597–606CrossRefGoogle Scholar
  22. Fazli P, Man HC, Shah UKM, Idris A (2013) Characteristics of methanogens and methanotrophs in rice fields: a review. Asia-Pac J Mol Biol Biotechnol 21:3–17Google Scholar
  23. Fierer N (2017) Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol 15:579CrossRefGoogle Scholar
  24. Ge T, Wu X, Chen X (2013) Microbial phototrophic fixation of atmospheric CO2 in China subtropical upland and paddy soils. Geochim Cosmochim Acta 113:70–78CrossRefGoogle Scholar
  25. 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 94:2362–2371CrossRefGoogle Scholar
  26. Gupta S, Allen-Vercoe E, Petrof EO (2016) Fecal microbiota transplantation: in perspective. Ther Adv Gastroenterol 9:229–239CrossRefGoogle Scholar
  27. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685CrossRefGoogle Scholar
  28. Ho A, Kerckhof F, Luke C (2013) Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies. Environ Microbiol Rep 5:335–345CrossRefGoogle Scholar
  29. Howe KJ, Ishida KP, Clark MM (2002) Use of ATR/FTIR spectrometry to study fouling of microfiltration membranes by natural waters. Desalination 147:251–255CrossRefGoogle Scholar
  30. Howe A, Yang F, Williams RJ (2016) Identification of the core set of carbon-associated genes in a bioenergy grassland soil. PLoS One 11:e0166578CrossRefGoogle Scholar
  31. Hu HW, He JZ (2018) Manipulating the soil microbiome for improved nitrogen management. Microbilogy Australia-March 2018, pp 24–27Google Scholar
  32. Hügler M, Gärtner A, Imhoff JF (2010) Functional genes as markers for sulfur cycling and CO2 fixation in microbial communities of hydrothermal vents of the Logatchev field. FEMS Microbiol Ecol 73:526–537Google Scholar
  33. Inbar Y, Chen Y, Hadar Y (1990) Humic substances formed during the composting of organic matter. Soil Sci Soc Am J 54:1316–1323CrossRefGoogle Scholar
  34. Jenkins S, Swenson TL, Lau R (2017) Construction of viable soil defined media using quantitative metabolomics analysis of soil metabolites. Front Microbiol 8:2618CrossRefGoogle Scholar
  35. Ji H, Zhuang S, Zhu Z, Zhong Z (2015) Soil organic carbon pool and its chemical composition in phyllostachy pubescens forests at two altitudes in Jian-ou City, China. PLoS One 10:e0146029CrossRefGoogle Scholar
  36. Johns CW, Lee AB, Springer TI (2017) Using NMR-based metabolomics to monitor the biochemical composition of agricultural soils: a pilot study. Eur J Soil Biol 83:98–105CrossRefGoogle Scholar
  37. Johnston CA, Groffman P, Breshears DD (2004) Carbon cycling in soil. Front Ecol Environ 2:522–528CrossRefGoogle Scholar
  38. Killham K, Prosser JI (2014) The bacteria and archaea. Soil Microbiol Ecol Biochem 4:41–76Google Scholar
  39. Kuzyakov Y (2010) Priming effects: interactions between living and dead organic matter. Soil Biol Biochem 42:1363–1371CrossRefGoogle Scholar
  40. Kuzyakov Y, Domanski G (2000) Carbon input by plants into the soil. Review. J Plant Nutr Soil Sci 163:421–431CrossRefGoogle Scholar
  41. Lacis AA, Schmidt GA, Rind D, Ruedy RA (2010) Atmospheric CO2: principal control knob governing Earth’s temperature. Science (80) 330:356–359CrossRefGoogle Scholar
  42. Li XM, Sun GX, Chen SC (2018) Molecular chemodiversity of dissolved organic matter in paddy soils. Environ Sci Technol 52:963–971.  https://doi.org/10.1021/acs.est.7b00377 CrossRefGoogle Scholar
  43. Liang Y, Van Nostrand JD, Deng Y (2010) Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. ISME J 5:403CrossRefGoogle Scholar
  44. Liang Y, Jiang Y, Wang F (2015) Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover. ISME J 9:2561CrossRefGoogle Scholar
  45. Ling N, Zhu C, Xue C (2016) Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis. Soil Biol Biochem 99:137–149CrossRefGoogle Scholar
  46. Liu Y, Liu X, Cheng K (2016) Responses of methanogenic and methanotrophic communities to elevated atmospheric CO2 and temperature in a paddy field. Front Microbiol 7:1895Google Scholar
  47. Ma K, Lu Y (2011) Regulation of microbial methane production and oxidation by intermittent drainage in rice field soil. FEMS Microbiol Ecol 75:446–456CrossRefGoogle Scholar
  48. Macrae A, Coelho RRR, Peixoto R, Rosado AS (2013) Tropical soil microbial communities. In: The prokaryotes. Springer, Berlin/Heidelberg, pp 85–95CrossRefGoogle Scholar
  49. Michalzik B, Bischoff S, Näthe K (2017) Tree species driving functional properties of mobile organic matter in throughfall and forest floor solutions of beech, spruce and pine forestsGoogle Scholar
  50. Montaño NM, García-Oliva F, Jaramillo VJ (2007) Dissolved organic carbon affects soil microbial activity and nitrogen dynamics in a Mexican tropical deciduous forest. Plant Soil 295:265–277.  https://doi.org/10.1007/s11104-007-9281-x CrossRefGoogle Scholar
  51. Navarrete AA, Venturini AM, Meyer KM (2015) Differential response of Acidobacteria subgroups to forest-to-pasture conversion and their biogeographic patterns in the western Brazilian Amazon. Front Microbiol 6:1443CrossRefGoogle Scholar
  52. Neilson JW, Califf K, Cardona C (2017) Significant impacts of increasing aridity on the arid soil microbiome. MSystems 2:e00195–e00116CrossRefGoogle Scholar
  53. Nicolardi S, Bogdanov B, Deelder AM (2015) Developments in FTICR-MS and its potential for body fluid signatures. Int J Mol Sci 16:27133–27144CrossRefGoogle Scholar
  54. Nottingham AT, Turner BL, Chamberlain PM (2012) Priming and microbial nutrient limitation in lowland tropical forest soils of contrasting fertility. Biogeochemistry 111:219–237CrossRefGoogle Scholar
  55. Paetsch L, Mueller CW, Kögel-Knabner I (2018) Effect of in-situ aged and fresh biochar on soil hydraulic conditions and microbial C use under drought conditions. Sci Rep 8:6852CrossRefGoogle Scholar
  56. Paul EA (2014) Soil microbiology, ecology and biochemistry. Academic, Amsterdam, pp 1–598Google Scholar
  57. Pazinato JM, Paulo EN, Mendes LW (2010) Molecular characterization of the archaeal community in an Amazonian wetland soil and culture-dependent isolation of methanogenic archaea. Diversity 2:1026–1047CrossRefGoogle Scholar
  58. Qiao NA, Schaefer D, Blagodatskaya E (2014) Labile carbon retention compensates for CO2 released by priming in forest soils. Glob Chang Biol 20:1943–1954CrossRefGoogle Scholar
  59. Reddy MS, Joshi S (2018) Carbon dioxide sequestration on biocement-based composites. In: Carbon dioxide sequestration in cementitious construction materials. Elsevier, pp 225–243Google Scholar
  60. Reeburgh WS (1976) Methane consumption in Cariaco Trench waters and sediments. Earth Planet Sci Lett 28:337–344CrossRefGoogle Scholar
  61. Ross SM (1993) Organic matter in tropical soils: current conditions, concerns and prospects for conservation. Prog Phys Geogr 17:265–305CrossRefGoogle Scholar
  62. Saarnio S, Winiwarter W, Leitao J (2009) Methane release from wetlands and watercourses in Europe. Atmos Environ 43:1421–1429CrossRefGoogle Scholar
  63. Schimel J, Schaeffer SM (2012) Microbial control over carbon cycling in soil. Front Microbiol 3:348CrossRefGoogle Scholar
  64. Schmidt MWI, Torn MS, Abiven S (2011) Persistence of soil organic matter as an ecosystem property. Nature 478:49CrossRefGoogle Scholar
  65. Semrau JD, DiSpirito AA, Yoon S (2010) Methanotrophs and copper. FEMS Microbiol Rev 34:496–531CrossRefGoogle Scholar
  66. Serrano-Silva N, Sarria-Guzmán Y, Dendooven L, Luna-Guido M (2014) Methanogenesis and methanotrophy in soil: a review. Pedosphere 24:291–307CrossRefGoogle Scholar
  67. Shively JM, English RS, Baker SH, Cannon GC (2001) Carbon cycling: the prokaryotic contribution. Curr Opin Microbiol 4:301–306CrossRefGoogle Scholar
  68. Swenson TL, Jenkins S, Bowen BP, Northen TR (2015) Untargeted soil metabolomics methods for analysis of extractable organic matter. Soil Biol Biochem 80:189–198CrossRefGoogle Scholar
  69. Swenson TL, Karaoz U, Swenson JM (2018) Linking soil biology and chemistry in biological soil crust using isolate exometabolomics. Nat Commun 9:19CrossRefGoogle Scholar
  70. Thakur IS, Kumar M, Varjani SJ (2018) Sequestration and utilization of carbon dioxide by chemical and biological methods for biofuels and biomaterials by chemoautotrophs: opportunities and challenges. Bioresour Technol 256:478–490CrossRefGoogle Scholar
  71. Tolli J, King GM (2005) Diversity and structure of bacterial chemolithotrophic communities in pine forest and agroecosystem soils. Appl Environ Microbiol 71:8411–8418CrossRefGoogle Scholar
  72. Tripathi BM, Song W, Slik JWF (2016) Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity. Front Microbiol 7:376CrossRefGoogle Scholar
  73. Tu Q, Yu H, He Z (2014) GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Mol Ecol Resour 14:914–928Google Scholar
  74. Vance ED, Brookes PC, Jenkinson DS (1987) An extraction method for measuring soil microbial biomass C. Soil Biol Biochem 19:703–707CrossRefGoogle Scholar
  75. Wendlandt K, Stottmeister U, Helm J (2010) The potential of methane-oxidizing bacteria for applications in environmental biotechnology. Eng Life Sci 10:87–102Google Scholar
  76. Whitaker J, Ostle N, Nottingham AT (2014) Microbial community composition explains soil respiration responses to changing carbon inputs along an A ndes-to-A mazon elevation gradient. J Ecol 102:1058–1071CrossRefGoogle Scholar
  77. Wood SA, Bradford MA (2018) Leveraging a new understanding of how belowground food webs stabilize soil organic matter to promote ecological intensification of agriculture. In: Soil carbon storage. Elsevier, Amsterdam, pp 117–136CrossRefGoogle Scholar
  78. Wu X, Ge T, Yuan H (2014) Changes in bacterial CO 2 fixation with depth in agricultural soils. Appl Microbiol Biotechnol 98:2309–2319CrossRefGoogle Scholar
  79. Yamashita Y, Maie N, Briceño H, Jaffé R (2010) Optical characterization of dissolved organic matter in tropical rivers of the Guayana Shield, VenezuelaGoogle Scholar
  80. Yamashita Y, Panton A, Mahaffey C, Jaffé R (2011) Assessing the spatial and temporal variability of dissolved organic matter in Liverpool Bay using excitation–emission matrix fluorescence and parallel factor analysis. Ocean Dyn 61:569–579.  https://doi.org/10.1007/s10236-010-0365-4 CrossRefGoogle Scholar
  81. Yuan H, Ge T, Chen C (2012) Microbial autotrophy plays a significant role in the sequestration of soil carbon. Appl Environ Microbiol AEM:06881Google Scholar
  82. Zhou WJ, Sha LQ, Schaefer DA (2015) Direct effects of litter decomposition on soil dissolved organic carbon and nitrogen in a tropical rainforest. Soil Biol Biochem 81:255–258.  https://doi.org/10.1016/j.soilbio.2014.11.019 CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2020

Authors and Affiliations

  • Arjun Singh
    • 1
  • Murugan Kumar
    • 1
  • Anil Kumar Saxena
    • 1
  1. 1.ICAR-National Bureau of Agriculturally Important MicroorganismsMauIndia

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