Bổ sung carbon và độ sâu của đất ảnh hưởng đến sự phân bổ và phong phú của các vi khuẩn khử nitơ trong đất nông nghiệp

Springer Science and Business Media LLC - Tập 23 - Trang 7899-7910 - 2016
M. Barrett1, M. I. Khalil2, M. M. R. Jahangir2, C. Lee3, L. M. Cardenas4, G. Collins5,6, K. G. Richards2, V. O’Flaherty1
1Microbial Ecology Laboratory, Microbiology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, Galway, Ireland
2Crops, Environment and Land-Use Department, Teagasc, Johnstown Castle, Co., Wexford, Ireland
3School of Civil & Environmental Engineering, Nanyang Technological University, Singapore, Singapore
4Rothamsted Research, North Wyke, Okehampton, UK
5Microbial EcoEngineering Laboratory, Microbiology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, Galway, Ireland
6Environmental Engineering Laboratory, School of Engineering, University of Glasgow, Glasgow, UK

Tóm tắt

Các gen enzym khử nitrit (nirS và nirK) và gen mã hóa enzym khử oxit nitrous (nosZ) của các quần thể khử nitơ có trong đất đồng cỏ nông nghiệp đã được định lượng bằng phương pháp phản ứng chuỗi polymerase (PCR) theo thời gian thực. Các mẫu được lấy từ ba độ sâu đất khác nhau tại địa điểm đã chọn: tầng A (0–10 cm), tầng B (45–55 cm) và tầng C (120–130 cm). Tác động của việc bổ sung carbon (điều trị 1, đối chứng; điều trị 2, glucose-C; điều trị 3, carbon hữu cơ hòa tan (DOC)) đối với sự phong phú của gen khử nitơ và các lưu lượng N2O và N2 đã được xác định. Nói chung, sự phong phú của vi khuẩn khử nitơ có mối tương quan tốt với các phép đo lưu lượng; nirS có mối tương quan dương với N2O, và nosZ có mối tương quan dương với N2 (P < 0.03). Nồng độ bản sao gen khử nitơ trên mỗi gram đất (GCC) thay đổi tùy thuộc vào loại bổ sung carbon (P < 0.01). GCC của vi khuẩn khử nitơ cao (khoảng 10^7) và tỷ lệ bac:nirK, bac:nirS, bac:nirT và bac:nosZ đều thấp (khoảng 10−1/10) ở tầng A trong cả ba điều trị tương ứng. Việc bổ sung glucose-C đã thúc đẩy quá trình khử nitơ một phần, dẫn đến sự phong phú cao của gen nir và lưu lượng N2O tăng lên so với nhóm đối chứng. Ngược lại, việc bổ sung DOC đã dẫn đến sự phong phú nosZ tương đối cao và phát thải N2, do đó, thúc đẩy quá trình khử nitơ hoàn toàn. Chúng tôi cũng nhận thấy rằng độ sâu của đất ảnh hưởng trực tiếp đến sự phong phú của vi khuẩn, vi sinh vật cổ và vi sinh vật khử nitơ, có thể do sự thay đổi trong sự sẵn có của carbon trong đất theo độ sâu.

Từ khóa

#khử nitơ #nitrit #oxit nitrous #đất nông nghiệp #bổ sung carbon #PCR

Tài liệu tham khảo

Aber JD, Nadelhoffer KJ, Steudler P, Melillo JM (1989) Nitrogen Saturation in Northern Forest Ecosystems. Bioscience 39(6):378–386 Aber JD, McDowell W, Nadelhoffer K, Magill A, Berntson G, Kamakea M, McNulty S, Currie W, Rustad L, Fernandez I (1998) Nitrogen saturation in temperate forest ecosystems. Bioscience 48(11):921–934 Ågren GI, Bosatta E (1988) Nitrogen saturation of terrestrial ecosystems. Environ Pollut 54(3–4):185–197 Bergsma TT, Robertson GP, Ostrom NE (2002) Influence of soil moisture and land use history on denitrification end-products. J Environ Qual 31:711–717 Bouwman AF (2004) Direct emission of nitrous oxide from agricultural soils. Nutr Cycl Agroecosys 46(1):53–70 Boyer EW, Alexander RB, Parton WJ, Li C, Butterbach-Bahl K, Donner SD, Skaggs RW, Del Grosso SJ (2006) Modeling denitrification in terrestrial and aquatic ecosystems at regional scales. Ecol Appl 16:2123–2142 Braker G, Fesefeldt A, Witzel KP (1998) Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 64:3769–3775 Braker G, Zhou J, Wu L, Devol AH, Tiedje JM (2000) Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities. Appl Environ Microbiol 66:2096–2104 Cardenas LM, Hawkins JMB, Chadwick D, Scholefield D (2003) Biogenic gas emissions from soils measured using a new automated laboratory incubation system. Soil Biol Biochem 35:867–870 Carrigg C, Rice O, Kavanagh S, Collins G, O’Flaherty V (2007) DNA extraction method affects microbial community profiles from soils and sediment. Appl Microbiol Biotechnol 77(4):955–964 Casey RE, Taylor MD, Klaine SJ (2001) Mechanisms of nutrient attenuation in a subsurface flow riparian wetland. J Environ Qual 30(5):1732–1737 Cavigelli MA, Robertson GP (2000) The functional significance of denitrifier composition in an terrestrial ecosystem. Ecology 81:1401–1414 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 Chèneby D, Hartmann A, Hénault C, Topp E, Germon JC (1998) Diversity of denitrifying microflora and ability to reduce N2O in two soils. Biol Fert Soils 28:19–26 Clement JC, Pinay G, Marmonier P (2002) Seasonal dynamics of denitrification along topohydrosequences in three different riparian wetlands. J Environ Qual 31:1025–1037 Cofman AI, Levine JS (1986) Relative rates of nitric oxide and nitrous oxide production by nitrifiers, denitrifiers, and nitrate respirers. Appl Environ Microbiol 51(5):938–94 Crutzen PJ (1970) The influence of nitrogen oxide on the atmospheric ozone content. Q J Roy Meteor Soc 96:320–327 Dandie CE, Burton DL, Zebarth BJ, Henderson SL, Trevors JT, Goyer C (2008) Changes in bacterial denitrifier community abundance over time in an agricultural field and their relationship with denitrification activity. Appl Environ Microbiol 74(19):5997–6005 Davidson EA, Seitzinger S (2006) The enigma of progress in denitrification research. Ecol Appl 16:2057–2063 De Vos P (2006) The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. Environ Microbiol 8(11):2012–2021 Deslippe JR, Jamali H, Jha N, Saggar S (2014) Denitrifier community size, structure and activity along a gradient of pasture to riparian soils. Soil Biol Biochem 71:48–60 Devaney D, Godley AR, Hodson ME, Purdy K, Yamulki S (2008) Impact of sewage sludge applications on the biogeochemistry of soils. Water Sci Technol 57(4):513–518 Dhondt K, Boeckx P, Hofman G, Van Cleemput O (2004) Temporal and spatial patterns of denitrification enzyme activity and nitrous oxide fluxes in three adjacent vegetated riparian buffer zones. Biol Fert Soils 40:243–251 Di HJ, Cameron KC, Sherlock RR, Shen J-P, He J-Z, Winefield CS (2010) Nitrous oxide emissions from grazed grassland as affected by a nitrification inhibitor, dicyandiamide, and relationships with ammonia-oxidizing bacteria and archaea. J Soils & Sediments 10(5):943–954 Dong LF, Smith CJ, Papaspyrou S, Stott A, Osborn M, Nedwell DB (2009) Changes in benthic denitrification, nitrate ammonification and anammox process rates and nitrate and nitrite reductase gene abundances along an estuarine nutrient gradient (the Colne Estuary, United Kingdom). Appl Environ Microbiol 75(10):3171–3179 Falk MW, Songa K-G, Matiasekb MG, Wuertz S (2009) Microbial community dynamics in replicate membrane bioreactors—natural reproducible fluctuations. Water Res 43:842–852 Flechard CR, Neftel A, JocherM AC, Fuhrer J (2005) Bi-directionalsoil/atmosphere N2O exchange over two mown grassland systems with contrasting management practices. Global Change Biol 11:2114–2127 Groffman PM, Altabet MA, Böhlke JK, Butterbach-Bahl K, David MB, Firestone MK, Giblin AE, Kana TM, Nielsen LP, Voytek MA (2006) Methods for measuring denitrification: diverse approaches to a difficult problem. Ecol Appl 16:2091–2122 Groffman PM, Butterbach-Bahl K, Fulweiler RW, Gold AJ, Morse JL, Stander EK, Tague C, Tonitto C, Vidon P (2009) Challenges to incorporating spatially and temporally explicit phenomena (hotspots and hot moments) in denitrification models. Biogeochemistry 93(1–2):49–77 Gruntzig V, Nold SC, Zhou J, Tiedje JM (2001) Pseudomonas stutzeri nitrate reductase gene abundance in environmental samples measured by real-time PCR. Appl Environ Microbiol 67:760–768 Hashimoto T, Whang KS, Nagaok K (2006) A quantitative evaluation and phylogenetic characterization of oligotrophic denitrifying bacteria harbored in subsurface upland soil using improved culturability. Biol Fert Soils 42:179–185 Henry S, Baudoin E, Lopez-Gutierrez 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 Henry S, Bru D, Stres B, Hallet S, Philippot L (2006) Quantitative detection of the nosZ gene, encoding nitrous oxiden reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils. Appl Environ Microbiol 72(8):5181–5189 Heylen K, Gevers D, Vanparys B, Wittebolle L, Geets J, Boon N, De Vos P (2006) The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. Environ Microbiol 8:2012–2021 Jahangir MMR, Khalil MI, Johnston PM, Cardenas LM, Butler M, Hatch D, Barrett M, O’Flaherty V, Richards KG (2012) Denitrification potential in subsoils: a mechanism to reduce nitrate leaching to groundwater. Agric Ecosysts Environ 147:13–23 Jarvis SC, Hatch DJ (1994) Potential for denitrification at depth below long-term grass swards. Soil Biol Biochem 26(12):1629–1636 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(9):5957–5962 Khalil MI, Richards KG (2011) Denitrification enzyme activity and potential of subsoils under grazed grasslands assayed by membrane inlet mass spectrometer. Soil Biol Biochem 43(9):1787–1797 Lee C, Kima J, Hwang K, O’Flaherty V, Hwang S (2009) Quantitative analysis of methanogenic community dynamics in three anaerobic batch digesters treating different wastewaters. Water Res 43(1):157–165 Ligi T, Oopkaup K, Truu M, Preem J-K, Nolvak H, Mitsch WJ, Mander Ü, Truu J (2014) Characterization of bacterial communities in soil and sediment of a created riverine wetland complex using high-throughput 16 S rRNA amplicon sequencing. Ecol Eng 72:56–66 Lovely DR, Chapelle FH (1995) Deep subsurface microbial processes. Rev Geophys 33(3):365–381 Martin TL, Kaushik NK, Trevors JT, Whiteley JR (1999) Review: Denitrification in temperate climate riparian zones. Water Air Soil Pollut 111(1–4):171–186 McCarty GW, Bremner JM (1992) Availability of organic carbon for denitrification of nitrate in subsoils. Biol Fert Soils 14(3):219–222 McCarty GW, Bremner JM (1993) Factors affecting the availability of organic carbon for denitrification of nitrate in subsoils. Biol Fert Soils 15(2):132–136 McCune B, Grace JB (2002) Analysis of ecological communities, pg 1–218. Published by MjM Software Design in Gleneden Beach, OR Mei L, Yang L, Wang D, Yin B, Hu J, Yina S (2004) Nitrous oxide production and consumption in serially diluted soil suspensions as related to in situ N2O emission in submerged soils. Soil Biol Biochem 36:1057–1066 Melero S, Pérez-de-Mora A, Murillo J-M, Buegger F, Kleinedamb K, Kublik S, Vanderlinden K, Moreno F, Schloter M (2011) Denitrification in a vertisol under long-term tillage and no-tillage management in dryland agricultural systems: Key genes and potential rates. Appl Soil Ecol 47(3):221–225 Morley NJ, Richardson DJ, Baggs EM (2014) Substrate induced denitrification over or under estimates shifts in soil N2/N2O ratios. PLoS ONE 9(9) Oehler F, Bordenave P, Durand P (2007) Variations of denitrification in a farming catchment area. Agric Ecosyst Environ 120(2–4):313–324 Osaka T, Shirotani K, Yoshie S, Tsuneda S (2008) Effects of carbon source on denitrification efficiency and microbial community structure in a saline wastewater treatment process. Water Res 42:3709–3718 Peralta AL, Matthews JWD, Kent JW (2010) Microbial community structure and denitrification in a wetland mitigation bank. Appl Environ Microbiol 76:4207–4215 Priemé A, Braker G, Tiedje JM (2002) Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl Environ Microbiol 68:1893–1900 Rangeley A, Knowles R (1988) Nitrogen transformations in a Scottish peat soil under laboratory conditions. Soil Biol Biochem 20:385–391 Rasmussen R (2001) Quantification on the LightCycler. In: Meuer S, Wittwer C, Nakagawara K (eds) Rapid cycle real-time PCR: methods and applications. Springer, Berlin Richardson D, Felgate H, Watmough N, Thomson A, Baggs E (2009) Mitigating release of the potent greenhouse gas N2O from the nitrogen cycle—could enzymic regulation hold the key? Trends Biotechnol 27(7):388–397 Robertson GP, Groffman PM (2007) Nitrogen transformation. In: Paul EA (ed) Soil Microbiology, Biochemistry, and Ecology. Springer, New York, pp 341–364 Rypdal K, Winiwarter K (2001) Uncertainties in greenhouse gas inventories—evaluation, comparability and implications. Environ Sci Policy 4:107–116 Scala DJ, Kerkhof LJ (1998) Nitrous oxide reductase (nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments. FEMS Microbiol Lett 162:61–68 Scholefield D, Hawkins JMB, Jackson SM (1997a) A.). Development of a helium atmosphere soil incubation technique for direct measurement of nitrous oxide and dinitrogen fluxes during denitrification. Soil Biol Biochem 29:1345–1352 Scholefield D, Hawkins JMB, Jackson SM (1997b) B.). Use of a flowing helium atmosphere incubation technique to measure the effects of denitrification controls applied to intact soil cores of a clay soil. Soil Biol Biochem 29:1337–1344 Sotomayor D, Rice CW (1996) Denitrification in soil profiles beneath grassland and cultivated soils. Soil Sci Am J 60(6):1822–1828 Stark C, Richards K (2008) The continuing challenge of agricultural nitrogen loss to the environment in the context of global change and advancing research. Dyn Soil, Dyn Plant 2(1):1–12 Tatti E, Goyer C, Burton DL, Wertz S, Zebarth BJ, Chantigny M, Filion M (2015) Tillage management and seasonal effects on denitrifier community abundance, gene expression and structure over winter. Microb Ecol 70(3):795–808 Throbäck IN, Enwall K, Jarvis A, Hallin S (2004) Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol Ecol 49:401–417 Tiedje JM (1988) Ecology of denitrification and dissimilatory nitrate reduction to ammonium. In: Zehnder A (ed) Biology of anaerobic microorganisms. Wiley, New York, N.Y., pp 179–244 Vilain G, Garnier J, Decuq C, Lugnot M (2014) Nitrous oxide production from soil experiments: denitrification prevails over nitrification. Nutr Cycl Agroecosyst 98:169–186 Whelan JA, Russel NB, Whelan MA (2003) A method for the absolute quantification of cDNA using real time PCR. J Immunol Methods 278:261–269 Wrage N, Velthof GL, van Beusichem ML, Oenema O (2001) Role of nitrifier denitrification in the production of nitrous oxide. Soil Biol Biochem 33(12–13):1723–1732 Yu Y, Lee C, Kim J, Hwang S (2005) Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng 89(6):670–679 Zumft WG (1992) The denitrifying prokaryotes, In: Balows A, Truper HG, Dworkin M, Harder W, Schleifer KH, (eds) The Prokaryotes, 2nd edn. Springer-Verlag, New York, pp 554–582 Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61:533–616