Abstract
Fertilizer use has dramatically increased the availability of nitrate (NO3 −) in aquatic systems. Microbe-mediated denitrification is one of the predominant means of NO3 − removal from freshwaters, yet oxygenation (O2)-induced disruptions—e.g., extreme precipitation events—can occur, resulting in a disproportional increase in nitrous oxide (N2O) production and efflux as facultative anaerobic bacterial populations use of O2 as a terminal electron acceptor increases. We examined the effects of 12- and 24-h passive O2 exposure on previously anaerobic bacterial communities focusing on denitrification enzyme activity (DEA), N2O production, and bacterial community 16S rRNA and nitrous oxide reductase gene (nosZ) profiles after 12, 24, and 48 h of anaerobic recovery. Treatments experiencing 24-h O2 exposure had significantly higher DEA 12 h into anaerobic recovery than treatments undergoing 12-h O2 exposure. Initial N2O emissions were significantly lower in the 24-h O2 exposure treatments although by 24 h a dramatic spike (tenfold relative to the 12-h O2 exposure treatments) in N2O concentrations was observed. However, within 6 h (30-h anaerobic recovery) these differences were gone. Community nosZ profiles experiencing 24-h O2 exposure exhibited reduced diversity after 24-h recovery, which corresponded with an increase in N2O emissions. However, after 48 h of anaerobic recovery, nosZ diversity had recovered. These observations highlight the effects of short-term aerobic disruption on denitrification, as well as the effects on the denitrifier community profile. Together, these data suggest that recovery to ambient N cycling is exacerbated by disturbance length due to increased lag time and subsequent loss of denitrifier community diversity.
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References
Alexander RB, Smith RA, Schwarz GE, Boyer EW, Nolan JV, Brakebill JW (2008) Differences in phosphorus and nitrogen delivery to the Gulf of Mexico from the Mississippi River Basin. Environ Sci Technol 42(3):822–830. https://doi.org/10.1021/es0716103
Anderson DM, Glibert PM, Burkholder JM (2002) Harmful algal blooms and eutrophication: nutrient sources, composition, and consequences. Estuaries 25(4):704–726. https://doi.org/10.1007/BF02804901
Arango CP, Tank JL, Schaller JL, Royer TV, Bernot MJ, David MB (2007) Benthic organic carbon influences denitrification in streams with high nitrate concentration. Freshwater Biol 52:1210–1222. https://doi.org/10.1111/j.1365-2427.2007.01758.x
Attard E, Poly F, Commeaux C, Laurent F, Terada A, Smets BF et al (2010) Shifts between Nitrospira- and Nitrobacter-like nitrite oxidizers underlie the response of soil potential nitrite oxidation to changes in tillage practices. Environ Microbiol 12(2):315–326. https://doi.org/10.1111/j.1462-2920.2009.02070.x
Barlett MA, Leff LG (2010) The effects of N:P ratio and nitrogen form on four major freshwater bacterial taxa in biofilms. Can J Microbiol 56(1):32–43. https://doi.org/10.1139/W09-099
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B Met 57(1):289–300. http://www.jstor.org/stable/2346101
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(19):6387–6396. https://doi.org/10.1128/AEM.00608-10
Blackwood CB, Oaks A, Buyer JS (2005) Phylum-and class-specific PCR primers for general microbial community analysis. Appl Environ Microbiol 71(10):6193–6198
Braker G, Dörsch P, Bakken LR (2012) Genetic characterization of denitrifier communities with contrasting intrinsic functional traits. FEMS Microbiol Ecol 79(2):542–554. https://doi.org/10.1111/j.1574-6941.2011.01237.x
Burgin AJ, Hamilton SK (2007) Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways. Front Ecol Environ 5(2):89–96. https://doi.org/10.1890/1540-9295(2007)
Burgin AJ, Groffman PM (2012) Soil O2 controls denitrification rates and N2O yield in a riparian wetland. J Geophys Res Biogeosci. https://doi.org/10.1029/2011JG001799
Camargo JA, Alonso Á (2006) Ecological and toxicological effects of inorganic nitrogen pollution in aquatic ecosystems: a global assessment. Environ Int 32(6):831–849. https://doi.org/10.1016/j.envint.2006.05.002
Cavigelli MA, Robertson GP (2000) The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology 81(5):1402–1414. https://doi.org/10.1890/0012-9658(2000)
Cavigelli MA, Robertson GP (2001) Role of denitrifier diversity in rates of nitrous oxide consumption in a terrestrial ecosystem. Soil Biol Biochem 33(3):297–310. https://doi.org/10.1016/S0038-0717(00)00141-3
Chance B, Sies H, Boveris A (1979) Hydroperoxide metabolism in mammalian organs. Phys Rev 59(3):527. Retrieved from http://physrev.physiology.org/content/59/3/527.abstract
Coates JD, Michaelidou U, Bruce RA, O’Connor SM, Crespi JN, Achenbach, LA (1999) Ubiquity and diversity of dissimilatory (per)chlorate-reducing bacteria. Appl Environ Microbiol 65(12):5234–5241. Retrieved from http://aem.asm.org/content/65/12/5234.abstract
Culman SW, Bukowski R, Gauch HG, Cadillo-Quiroz H, Buckley DH (2009) T-REX: software for the processing and analysis of T-RFLP data. BMC Bioinform 10(1):1–10. https://doi.org/10.1186/1471-2105-10-171
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. https://doi.org/10.1128/AEM.00441-08
DeAngelis KM, Silver WL, Thompson AW, Firestone MK (2010) Microbial communities acclimate to recurring changes in soil redox potential status. Environ Microbiol 12(12):3137–3149. https://doi.org/10.1111/j.1462-2920.2010.02286.x
Diaz RJ, Rosenberg R (2008) Spreading dead zones and consequences for marine ecosystems. Science 321(5891):926–929. http://science.sciencemag.org/content/321/5891/926.abstract
Ding Y, Song X, Wang Y, Yan D (2012) Effects of dissolved oxygen and influent COD/N ratios on nitrogen removal in horizontal subsurface flow constructed wetland. Ecol Eng 46:107–111. https://doi.org/10.1016/j.ecoleng.2012.06.002
Dinno A (2016) Dunn.test: dunn's test of multiple comparisons using rank sums. R package version 1.3.3. https://CRAN.R-project.org/package=dunn.test
Domeignoz-Horta LA, Spor A, Bru D, Breuil M-C, Bizouard F, Léonard J, Philippot L (2015) The diversity of the N2O reducers matters for the N2O:N2 denitrification end-product ratio across an annual and a perennial cropping system. Front Microbiol 6:971. https://doi.org/10.3389/fmicb.2015.00971
Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MMM, et al (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464(7288):543–548. Retrieved from http://dx.doi.org/10.1038/nature08883
Fields S (2004) Global nitrogen: cycling out of control. Environ Health Persp 112(10):A556–A563. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1247398/
Fierer N, Schimel JP (2002) Effects of drying–rewetting frequency on soil carbon and nitrogen transformations. Soil Biol Biochem 34(6):777–787. https://doi.org/10.1016/S0038-0717(02)00007-X
Fowler D, Coyle M, Skiba U, Sutton MA, Cape JN, Reis S, et al (2013) The global nitrogen cycle in the twenty-first century. Philos T R Soc B 368(1621). http://rstb.royalsocietypublishing.org/content/368/1621/20130164.abstract
Fromin N, Pinay G, Montuelle B, Landais D, Ourcival JM, Joffre R, Lensi R (2010) Impact of seasonal sediment desiccation and rewetting on microbial processes involved in greenhouse gas emissions. Ecohydrology 3(3):339–348. https://doi.org/10.1002/eco.115
Gruber N, Galloway JN (2008) An Earth-system perspective of the global nitrogen cycle. Nature 451(7176):293–296. https://doi.org/10.1038/nature06592
Hassan J, Qu Z, Bergaust LL, Bakken LR (2016) Transient accumulation of NO2 − and N2O during denitrification explained by assuming cell diversification by stochastic transcription of denitrification genes. PLoS Comput Biol. https://doi.org/10.1371/journal.pcbi.1004621
Holland HD (2006) The oxygenation of the atmosphere and oceans. Philos Trans R Soc Lond Ser B 361(1470):903–915. Retrieved from http://rstb.royalsocietypublishing.org/content/361/1470/903.abstract
Holtan-Hartwig L, Dörsch P, Bakken LR (2000) Comparison of denitrifying communities in organic soils: kinetics of NO3 − and N2O reduction. Soil Biol Biochem 32(6):833–843. https://doi.org/10.1016/S0038-0717(99)00213-8
Howarth RW, Billen G, Swaney D, Townsend A, Jaworski N, Lajtha K et al (1996) Regional nitrogen budgets and riverine N and P fluxes for the drainages to the North Atlantic Ocean: natural and human influences. Biogeochemistry 35(1):75–139. https://doi.org/10.1007/BF02179825
Imlay JA (2002) How oxygen damages microbes: oxygen tolerance and obligate anaerobiosis. Adv Microb Physiol 46:111–153. https://doi.org/10.1016/S0065-2911(02)46003-1
Jørgensen BB, Revsbech NP (1985) Diffusive boundary layers and the oxygen uptake of sediments and detritus. Limnol Oceanogr 30(1):111–122. https://doi.org/10.4319/lo.1985.30.1.0111
Kartal B, Kuypers MMM, Lavik G, Schalk J, den Camp HJM, Jetten MSM, Strous M (2007) Anammox bacteria disguised as denitrifier: nitrate reduction to dinitrogen gas via nitrite and ammonium. Environ Microbiol 9(3):635–642. https://doi.org/10.1111/j.1462-2920.2006.01183.x
Khanitchaidecha W, Sumino T, Kazama F (2010) Influence of carbon source on biological nitrogen removal by immobilised bacteria. J Water Resour Prot 2(6):527–531. https://doi.org/10.4236/jwarp.2010.26059
Komsta L (2011) Outliers: tests for outliers. http://cran.r-project.org/package=outliers
Körner H, Zumft WG (1989) Expression of denitrification enzymes in response to the dissolved oxygen level and respiratory substrate in continuous culture of Pseudomonas stutzeri. Appl Environ Microb 55(7):1670–1676. http://aem.asm.org/content/55/7/1670.abstract
Köster JR, Well R, Dittert K, Giesemann A, Lewicka-Szczebak D, Mühling K-H et al (2013) Soil denitrification potential and its influence on N2O reduction and N2O isotopomer ratios. Rapid Commun Mass Spectrom 27(21):2363–2373. https://doi.org/10.1002/rcm.6699
Mearns LO, Arritt R, Biner S, Bukovsky MS, McGinnis S, Sain S et al (2012) The North American regional climate change assessment program: overview of phase I results. B Am Meteorol Soc 93(9):1337–1362
Morley N, Baggs EM, Dörsch P, Bakken L (2008) Production of NO, N2O and N2 by extracted soil bacteria, regulation by NO2 − and O2 concentrations. FEMS Microbiol Ecol 65(1):102–112. http://femsec.oxfordjournals.org/content/65/1/102.abstract
Murray RE, Knowles, R (1999) Chloramphenicol inhibition of denitrifying enzyme activity in two agricultural soils. Appl Environ Microbiol 65(8):3487–3492. http://aem.asm.org/content/65/8/3487.abstract
Nahlik AM, Mitsch WJ (2008) The effect of river pulsing on sedimentation and nutrients in created riparian wetlands. J Environ Qual 37(4):1634–1643. https://doi.org/10.2134/jeq2007.0116
Osaka T, Ebie Y, Tsuneda S, Inamori Y (2008) Identification of the bacterial community involved in methane-dependent denitrification in activated sludge using DNA stable-isotope probing. FEMS Microbiol Ecol 64:494–506
Okereke GU (1992) Growth yield of denitrifier using nitrous oxide as a terminal electron acceptor. World J Microbiol Biotechnol 9(1):59–62. https://doi.org/10.1007/BF00656518
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. (2016) Vegan: community ecology package. http://cran.r-project.org/package=vegan
Pachauri RK, Reisinger A (2008) IPCC 2007: climate change 2007: synthesis report. Contribution of working groups I, II and III to the fourth assessment report of the intergovernmental panel on climate change. In: IPCC, p 104
Patureau D, Davison J, Bernet N, Moletta R (1994) Denitrification under various aeration conditions in Comamonas sp., strain SGLY2. FEMS Microbiol Ecol 14(1):71–78. https://doi.org/10.1111/j.1574-6941.1994.tb00092.x
Paulmier A, Kriest I, Oschlies A (2009) Stoichiometries of remineralization and denitrification in global biogeochemical ocean models. Biogeosciences 6(5):923–935
Pett-Ridge J, Firestone MK (2005) Redox fluctuation structures microbial communities in a wet tropical soil. Appl Environ Microbiol 71(11):6998–7007. https://doi.org/10.1128/AEM.71.11.6998-7007.2005
Qu Z, Bakken LR, Molstad L, Frostegård Å, Bergaust LL (2016) Transcriptional and metabolic regulation of denitrification in Paracoccus denitrificans allows low but significant activity of nitrous oxide reductase under oxic conditions. Environ Microbiol. https://doi.org/10.1111/1462-2920.13128
R Core Team (2014) R: a language and environment for statistical computing. Vienna, Austria. http://www.r-project.org/
Ravishankara AR, Daniel JS, Portmann RW (2009) The dominant ozone-depleting substance emitted in the 21st century. Science 326(5949):123–125. http://science.sciencemag.org/content/326/5949/123.abstract
Rich JJ, Heichen RS, Bottomley PJ, Cromack K Jr, Myrold DD (2003) Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils. Appl Environ Microbiol 69(10):5974–5982. https://doi.org/10.1128/AEM.69.10.5974-5982.2003
Ringuet S, Sassano L, Johnson ZI (2011) A suite of microplate reader-based colorimetric methods to quantify ammonium, nitrate, orthophosphate and silicate concentrations for aquatic nutrient monitoring. J Environ Monit 13(2):370–376. https://doi.org/10.1039/C0EM00290A
Royer TV, Tank JL, David MB (2004) Transport and fate of nitrate in headwater agricultural streams in Illinois. J Environ Qual 33:1296–1304. https://doi.org/10.2134/jeq2004.1296
Sanford RA, Wagner DD, Wu Q, Chee-Sanford JC, Thomas SH, Cruz-Garcia C, Rodriguez G, Massol-Deyá KKK, Ritalahti KM, Nissen S, Konstantinidis KT, Löffler FE (2012) Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils. Proc Natl Acad Sci USA 109(48):19708–19714. https://doi.org/10.1073/pnas.1211238109
Scott JT, McCarthy MJ, Gardner WS, Doyle RD (2008) Denitrification, dissimilatory nitrate reduction to ammonium, and nitrogen fixation along a nitrate concentration gradient in a created freshwater wetland. Biogeochemistry 87(1):99–111
Sirivedhin T, Gray KA (2006) Factors affecting denitrification rates in experimental wetlands: field and laboratory studies. Ecol Eng 26(2):167–181. https://doi.org/10.1016/j.ecoleng.2005.09.001
Smith MS, Tiedje JM (1979) Phases of denitrification following oxygen depletion in soil. Soil Biol Biochem 11(3):261–267. https://doi.org/10.1016/0038-0717(79)90071-3
Smith JM, Ogram A (2008) Genetic and functional variation in denitrifier populations along a short-term restoration chronosequence. Appl Environ Microbiol 74(18):5615–5620. https://doi.org/10.1128/AEM.00349-08
Tiedje JM, Sexstone AJ, Myrold DD, Robinson JA (1983) Denitrification: ecological niches, competition and survival. Antonie Van Leeuwenhoek J Microbiol 48(6):569–583. https://doi.org/10.1007/BF00399542
Vitousek PM, Mooney HA, Lubchenco J, Melillo JM (1997) Human domination of earth’s ecosystems. Science 277(5325):494–499. http://science.sciencemag.org/content/277/5325/494.abstract
Ward TE (1985) Characterizing the aerobic and anaerobic microbial activities in surface and subsurface soils. Environ Toxicol Chem 4(6):727–737. https://doi.org/10.1002/etc.5620040603
Weier KL, Doran JW, Power JF, Walters DT (1993) Denitrification and the dinitrogen/nitrous oxide ratio as affected by soil water, available carbon, and nitrate. Soil Sci Soc Am J 57:66–72. https://doi.org/10.2136/sssaj1993.03615995005700010013x
Wickham H (2009) ggplot2: elegant graphics for data analysis. Springer, New York. http://ggplot2.org
Wittorf L, Bonilla-Rosso G, Jones CM, Bäckman O, Hulth S, Hallin S (2016) Habitat partitioning of marine benthic denitrifier communities in response to oxygen availability. Environ Microbiol Rep 8(4):486–492. https://doi.org/10.1111/1758-2229.12393
Yates TT, Si BC, Farrell RE, Pennock DJ (2006) Wavelet spectra of nitrous oxide emission from hummocky terrain during spring snowmelt. Soil Sci Soc Am J 70:1110–1120. https://doi.org/10.2136/sssaj2005.0264
Young IM, Crawford JW (2004) Interactions and self-organization in the soil-microbe complex. Science 304(5677):1634–1637. https://doi.org/10.1126/science.1097394
Zhang Y-G, Nearing MA, Liu BY, Van Pelt RS, Stone JJ, Wei H, Scott RL (2011) Comparative rates of wind versus water erosion from a small semiarid watershed in southern Arizona, USA. Aeolian Res 3(2):197–204. https://doi.org/10.1016/j.aeolia.2011.03.006
Zhu G, Jetten MSM, Kuschk P, Ettwig KF, Yin C (2010) Potential roles of anaerobic ammonium and methane oxidation in the nitrogen cycle of wetland ecosystems. Appl Microbiol Biotechnol 86(4):1043–1055
Zibilske LM, Bradfor JM (2006) Oxygen effects on carbon, polyphenols and nitrogen mineralization potential in soil. Soil Sci Soc Am J 71:133–139. https://doi.org/10.2136/sssaj2006.0167
Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol R 61(4):533–616. http://mmbr.asm.org/content/61/4/533.abstract
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Funding for portions of this project was provided by the NSF IGERT program (award number 0903560) and an internal Kent State University Graduate Student Senate Research Award.
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Van Gray, J.B., Leff, L.G. Impacts of varying durations of passive oxygen exposure on freshwater denitrifier community structure and function. Aquat Ecol 52, 35–49 (2018). https://doi.org/10.1007/s10452-017-9643-2
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DOI: https://doi.org/10.1007/s10452-017-9643-2