Abstract
Fungal N2O production has been progressively recognized, but its controlling factors remain unclear. This study examined the impacts of soil moisture and pH on fungal and bacterial N2O production in two ecosystems, conventional farming and plantation forestry. Four treatments, antibiotic-free soil and soil amended with streptomycin, cycloheximide, or both were used to determine N2O production of fungi versus bacteria. Soil moisture and pH effects were assessed under 65–90 % water-filled pore space (WFPS) and pH 4.0–9.0, respectively. Irrespective of antibiotic treatments, soil N2O fluxes peaked at 85–90 % WFPS and pH 7.0 or 8.0, indicating that both fungi and bacteria preferred more anoxic and neutral or slightly alkaline conditions in producing N2O. However, compared with bacteria, fungi contributed more to N2O production under sub-anoxic and acidic conditions. Real-time polymerase chain reaction of 16S, ITS rDNA, and denitrifying genes for quantifications of bacteria, fungi, and denitrifying bacteria, respectively, showed that fungi were more abundant at acidic pH, whereas total and denitrifying bacteria favored neutral conditions. Such variations in the abundance appeared to be related to the pH effects on the relative fungal and bacterial contribution to N2O production.
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References
IPCC Climate Change TPSB (2007) In: Solomon S et al (eds) Contribution of Working Group I to the fourth assessment report of the intergovernmental panel on climate change. Cambridge University Press, Cambridge
Ravishankara AR, Daniel JS, Portmann RW (2009) Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century. Science 326:123–125
Davidson EA (1991) Microbial production and consumption of greenhouse gases: methane, nitrogen oxide and halomethanes. Am Soc Microbiol, Washington DC
de Boer W, Duyts H, Laanbroek HJ (1988) Autotrophic nitrification in a fertilized acid heath soil. Soil Biol Biochem 20:845–850
Pedersen H, Dunkin K, Firestone M (1999) The relative importance of autotrophic and heterotrophic nitrification in a conifer forest soil as measured by 15N tracer and pool dilution techniques. Biogeochemistry 44:135–150
Pennington PI, Ellis RC (1993) Autotrophic and heterotrophic nitrification in acidic forest and native grassland soils. Soil Biol Biochem 25:1399–1408
Schimel JP, Firestone MK, Killham KS (1984) Identification of heterotrophic nitrification in a sierran forest soil. Appl Environ Microbiol 48:802–806
Kool DM, Dolfing J, Wrage N, Van Groenigen JW (2011) Nitrifier denitrification as a distinct and significant source of nitrous oxide from soil. Soil Biol Biochem 43:174–178
Wrage N, Velthof GL, Laanbroek HJ, Oenema O (2004) Nitrous oxide production in grassland soils: assessing the contribution of nitrifier denitrification. Soil Biol Biochem 36:229–236
Wrage N, Velthof GL, van Beusichem ML, Oenema O (2001) Role of nitrifier denitrification in the production of nitrous oxide. Soil Biol Biochem 33:1723–1732
Carter JP, Hsaio YH, Spiro S, Richardson DJ (1995) Soil and sediment bacteria capable of aerobic nitrate respiration. Appl Environ Microbiol 61:2852–2858
Patureau D, Zumstein E, Delgenes JP, Moletta R (2000) Aerobic denitrifiers isolated from diverse natural and managed ecosystems. Microb Ecol 39:145–152
Takaya N, Catalan-Sakairi MAB, Sakaguchi Y, Kato I, Zhou Z, Shoun H (2003) Aerobic denitrifying bacteria that produce low levels of nitrous oxide. Appl Environ Microbiol 69:3152–3157
Bateman EJ, Baggs EM (2005) Contributions of nitrification and denitrification to N2O emissions from soils at different water-filled pore space. Biol Fertil Soils 41:379–388
Bleakley BH, Tiedje JM (1982) Nitrous oxide production by organisms other than nitrifiers or denitrifiers. Appl Environ Microbiol 44:1342–1348
Bollag JM, Tung G (1972) Nitrous oxide release by soil fungi. Soil Biol Biochem 4:271–276
Kurakov AV, Pakhnenko OV, Kostina NV, Umarov MM (1997) Microscopic fungi producing nitrous oxide in nutrient media and in sterile soil. Eurasian Soil Sci 30:1344–1349
Lavrent’ev R, Zaitsev S, Sudnitsyn I, Kurakov A (2008) Nitrous oxide production by fungi in soils under different moisture levels. Mosc Univ Soil Sci Bull 63:178–183
Mothapo NV, Chen H, Cubeta MA, Shi W (2013) Nitrous oxide producing activity of diverse fungi from distinct agroecosystems. Soil Biol Biochem 66:94–101
Prendergast-Miller MT, Baggs EM, Johnson D (2011) Nitrous oxide production by the ectomycorrhizal fungi Paxillus involutus and Tylospora fibrillosa. FEMS Microbiol Lett 316:31–35
Yanai Y, Toyota K, Morishita T, Takakai F, Hatano R, Limin SH, Darung U, Dohong S (2007) Fungal N2O production in an arable peat soil in Central Kalimantan, Indonesia. Soil Sci Plant Nutr 53:806–811
Jirout J, Šimek M, Elhottová D (2013) Fungal contribution to nitrous oxide emissions from cattle impacted soils. Chemosphere 90:565–572
Kurakov AV, Nosikov AN, Skrynnikova EV, L'Vov NP (2000) Nitrate reductase and nitrous oxide production by Fusarium oxysporum 11dn1 under aerobic and anaerobic conditions. Curr Microbiol 41:114–119
Crenshaw C, Lauber C, Sinsabaugh R, Stavely L (2008) Fungal control of nitrous oxide production in semiarid grassland. Biogeochemistry 87:17–27
Laughlin RJ, Rütting T, Müller C, Watson CJ, Stevens RJ (2009) Effect of acetate on soil respiration, N2O emissions and gross N transformations related to fungi and bacteria in a grassland soil. Appl Soil Ecol 42:25–30
Laughlin RJ, Stevens RJ (2002) Evidence for fungal dominance of denitrification and codenitrification in a grassland soil. Soil Sci Soc Am J 66:1540–1548
Marusenko Y, Huber DP, Hall SJ (2013) Fungi mediate nitrous oxide production but not ammonia oxidation in aridland soils of the southwestern US. Soil Biol Biochem 63:24–36
Hénault C, Grossel A, Mary B, Roussel M, Léonard J (2012) Nitrous oxide emission by agricultural soils: a review of spatial and temporal variability for mitigation. Pedosphere 22:426–433
Shoun H, Tanimoto T (1991) Denitrification by the fungus Fusarium oxysporum and involvement of cytochrome P-450 in the respiratory nitrite reduction. J Biol Chem 266:11078–11082
Shoun H, Kim D-H, Uchiyama H, Sugiyama J (1992) Denitrification by fungi. FEMS Microbiol Lett 94:277–281
Tsuruta S, Takaya N, Zhang L, Shoun H, Kimura K, Hamamoto M, Nakase T (1998) Denitrification by yeasts and occurrence of cytochrome P450nor in Trichosporon cutaneum. FEMS Microbiol Lett 168:105–110
Kobayashi M, Matsuo Y, Takimoto A, Suzuki S, Maruo F, Shoun H (1996) Denitrification, a novel type of respiratory metabolism in fungal mitochondrion. J Biol Chem 271:16263–16267
Tielens AGM, Rotte C, van Hellemond JJ, Martin W (2002) Mitochondria as we don't know them. Trends Biochem Sci 27:564–572
Zhou Z, Takaya N, Sakairi MAC, Shoun H (2001) Oxygen requirement for denitrification by the fungus Fusarium oxysporum. Arch Microbiol 175:19–25
Seo DC, DeLaune RD (2010) Fungal and bacterial mediated denitrification in wetlands: influence of sediment redox condition. Water Res 44:2441–2450
Khalil MI, Baggs EM (2005) CH4 oxidation and N2O emissions at varied soil water-filled pore spaces and headspace CH4 concentrations. Soil Biol Biochem 37:1785–1794
Inubushi K, Naganuma H, Kitahara S (1996) Contribution of denitrification and autotrophic and heterotrophic nitrification to nitrous oxide production in andosols. Biol Fertil Soils 23:292–298
Burth I, Ottow JCG (1983) Influence of pH on the production of N2O and N2 by different denitrifying bacteria and Fusarium solani. Ecol Bull 35:207–215
Herold MB, Baggs EM, Daniell TJ (2012) Fungal and bacterial denitrification are differently affected by long-term pH amendment and cultivation of arable soil. Soil Biol Biochem 54:25–35
Rütting T, Huygens D, Boeckx P, Staelens J, Klemedtsson L (2013) Increased fungal dominance in N2O emission hotspots along a natural pH gradient in organic forest soil. Biol Fertil Soils 49:715–721
Chen H, Mothapo NV, Shi W (2014) The significant contribution of fungi to soil N2O production across diverse ecosystems. Appl Soil Ecol 73:70–77
Blagodatskaya EV, Anderson T-H (1998) Interactive effects of pH and substrate quality on the fungal-to-bacterial ratio and qCO2 of microbial communities in forest soils. Soil Biol Biochem 30:1269–1274
Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4:1340–1451
Rousk J, Brookes PC, Baath E (2009) Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization. Appl Environ Microbiol 75:1589–1596
Frostegård Å, Bååth E, Tunlio A (1993) Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis. Soil Biol Biochem 25:723–730
Arao T (1999) In situ detection of changes in soil bacterial and fungal activities by measuring 13C incorporation into soil phospholipid fatty acids from 13C acetate. Soil Biol Biochem 31:1015–1020
Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 103:626–631
Mueller JP, Barbercheck ME, Bell M, Brownie C, Creamer NG, Hitt A, Hu S, King L, Linker HM, Louws FJ, Marlow S, Marra M, Raczkowski CW, Susko DJ, Wagger MG (2002) Development and implementation of a long-term agricultural systems study: challenges and opportunities. HortTechnology 12:362–368
Sydorovych O, Raczkowski CW, Wossink A, Mueller JP, Creamer NG, Hu S, Bell M, Tu C (2009) A technique for assessing environmental impact risks of agricultural systems. Renew Agric Food Syst 24:234–243
Tian L, Dell E, Shi W (2010) Chemical composition of dissolved organic matter in agroecosystems: correlations with soil enzyme activity and carbon and nitrogen mineralization. Appl Soil Ecol 46:426–435
Tu C, Louws FJ, Creamer NG, Paul Mueller J, Brownie C, Fager K, Bell M, Hu S (2006) Responses of soil microbial biomass and N availability to transition strategies from conventional to organic farming systems. Agric Ecosyst Environ 113:206–215
Petersen SO, Klug MJ (1994) Effects of sieving, storage, and incubation temperature on the phospholipid fatty acid profile of a soil microbial community. Appl Environ Microbiol 60:2421–2430
Bender SF, Plantenga F, Neftel A, Jocher M, Oberholzer H-R, Köhl L, Giles M, Daniell TJ, van der Heijden MG (2013) Symbiotic relationships between soil fungi and plants reduce N2O emissions from soil. ISME J
Weyman-Kaczmarkowa W, Pędziwilk Z (2000) The development of fungi as affected by pH and type of soil, in relation to the occurrence of bacteria and soil fungistatic activity. Microbiol Res 155:107–112
Beare MH, Neely CL, Coleman DC, Hargrove WL (1990) A substrate-induced respiration (SIR) method for measurement of fungal and bacterial biomass on plant residues. Soil Biol Biochem 22:585–594
Fierer N, Jackson JA, Vilgalys R, Jackson RB (2005) Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl Environ Microbiol 71:4117–4120
Kandeler E, Deiglmayr K, Tscherko D, Bru D, Philippot L (2006) Abundance of narG, nirS, nirK, and nosZ genes of denitrifying bacteria during primary successions of a glacier foreland. Appl Environ Microbiol 72:5957–5962
Henry S, Baudoin E, López-Gutiérrez JC, Martin-Laurent F, Brauman A, Philippot L (2004) Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR. J Microbiol Methods 59:327–335
Casciotti KL, Ward BB (2005) Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria. FEMS Microbiol Ecol 52:197–205
Henry S, Bru D, Stres B, Hallet S, Philippot L (2006) Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils. Appl Environ Microbiol 72:5181–5189
Zhang H, Parameswaran P, Badalamenti J, Rittmann BE, Krajmalnik-Brown R (2011) Integrating high-throughput pyrosequencing and quantitative real-time PCR to analyze complex microbial communities. In: Kwon YM, Ricke SC (eds.) High-throughput next generation sequencing, vol. 733. Springer, pp. 107–128
Bouwman AF (1998) Environmental science: nitrogen oxides and tropical agriculture. Nature 392:866–867
Betlach MR, Tiedje JM (1981) Kinetic explanation for accumulation of nitrite, nitric oxide, and nitrous oxide during bacterial denitrification. Appl Environ Microbiol 42:1074–1084
Bonin P, Gilewicz M, Bertrand JC (1989) Effects of oxygen on each step of denitrification on Pseudomonas nautica. Can J Microbiol 35:1061–1064
Cavigelli MA, Robertson GP (2001) Role of denitrifier diversity in rates of nitrous oxide consumption in a terrestrial ecosystem. Soil Biol Biochem 33:297–310
Baggs E, Smales C, Bateman E (2010) Changing pH shifts the microbial sourceas well as the magnitude of N2O emission from soil. Biol Fertil Soils 46:793–805
Barton L, Gleeson DB, Maccarone LD, Zúñiga LP, Murphy DV (2013) Is liming soil a strategy for mitigating nitrous oxide emissions from semi-arid soils? Soil Biol Biochem 62:28–35
Weslien P, Kasimir Klemedtsson Å, Börjesson G, Klemedtsson L (2009) Strong pH influence on N2O and CH4 fluxes from forested organic soils. Eur J Soil Sci 60:311–320
Struwe S, Kjøller A (1994) Potential for N2O production from beech (Fagus silvaticus) forest soils with varying pH. Soil Biol Biochem 26:1003–1009
Yamulki S, Harrison RM, Goulding KWT, Webster CP (1997) N2O, NO and NO2 fluxes from a grassland: effect of soil pH. Soil Biol Biochem 29:1199–1208
Šimek M, Jíšová L, Hopkins DW (2002) What is the so-called optimum pH for denitrification in soil? Soil Biol Biochem 34:1227–1234
Tanimoto T, Hatano K-i, Kim D-h, Uchiyama H, Shoun H (1992) Co-denitrification by the denitrifying system of the fungus Fusarium oxysporum. FEMS Microbiol Lett 93:177–180
Šimek M, Cooper JE (2002) The influence of soil pH on denitrification: progress towards the understanding of this interaction over the last 50 years. Eur J Soil Sci 53:345–354
Bergaust L, Mao Y, Bakken LR, Frostegård Å (2010) Denitrification response patterns during the transition to anoxic respiration and posttranscriptional effects of suboptimal pH on nitrogen oxide reductase in Paracoccus denitrificans. Appl Environ Microbiol 76:6387–6396
Wheeler KA, Hurdman BF, Pitt JI (1991) Influence of pH on the growth of some toxigenic species of Aspergillus, Penicillium and Fusarium. Int J Food Microbiol 12:141–149
Fogel GB, Collins CR, Li J, Brunk CF (1999) Prokaryotic genome size and SSU rDNA copy number: estimation of microbial relative abundance from a mixed population. Microb Ecol 38:93–113
Čuhel J, Šimek M, Laughlin RJ, Bru D, Chèneby D, Watson CJ, Philippot L (2010) Insights into the effect of soil pH on N2O and N2 emissions and denitrifier community size and activity. Appl Environ Microbiol 76:1870–1878
Liu B, Mørkved PT, Frostegård Å, Bakken LR (2010) Denitrification gene pools, transcription and kinetics of NO, N2O and N2 production as affected by soil pH. FEMS Microbiol Ecol 72:407–417
Yu Y, Zhang J, Chen W, Zhong W, Zhu T, Cai Z (2013) Effect of land use on the denitrification, abundance of denitrifiers, and total nitrogen gas production in the subtropical region of China. Biol Fertil Soils 1–9
Philippot L, Čuhel J, Saby NPA, Chèneby D, Chroňáková A, Bru D, Arrouays D, Martin-Laurent F, Šimek M (2009) Mapping field-scale spatial patterns of size and activity of the denitrifier community. Environ Microbiol 11:1518–1526
Throbäck IN, Johansson M, Rosenquist M, Pell M, Hansson M, Hallin S (2007) Silver (Ag+) reduces denitrification and induces enrichment of novel nirK genotypes in soil. FEMS Microbiol Lett 270:189–194
Regna PP, Wasselle LA, Solomons I (1946) The stability of streptomycin. J Biol Chem 165:631–638
Oswald E, Nielsen J (1947) Studies on the stability of streptomycin in solution. Science 105:184–185
MacBean C (2012) The pesticide manual: a world compendium, Sixteenthth edn. British Crop Production Council, Hampshire
Whiffen AJ (1948) The production, assay, and antibiotic activity of actidione, an antiobiotic from Streptomyces griseus. J Bacteriol 56:283
Jefferys E (1952) The stability of antibiotics in soils. J Gen Microbiol 7:295–312
Acknowledgments
This study is funded by the National Institute of Food and Agriculture in United States Department of Agriculture under the project number 2011-67019-30189. We would like to thank Dr. Wayne Robarge and the Environmental and Agricultural Testing Service lab at North Carolina State University for allowing the use of gas chromatograph and other equipment for organic and inorganic C and N analyses. We appreciate staff at the Center for Environmental Farming Systems for helping with soil sampling.
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Chen, H., Mothapo, N.V. & Shi, W. Soil Moisture and pH Control Relative Contributions of Fungi and Bacteria to N2O Production. Microb Ecol 69, 180–191 (2015). https://doi.org/10.1007/s00248-014-0488-0
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DOI: https://doi.org/10.1007/s00248-014-0488-0