Soil substrates rather than gene abundance dominate DNRA capacity in the Spartina alterniflora ecotones of estuarine and intertidal wetlands

  • Xiaofei Li
  • Dengzhou Gao
  • Lijun HouEmail author
  • Min LiuEmail author
Regular Article


Background and aims

Dissimilatory nitrate reduction to ammonium (DNRA) plays an important role in keeping nitrate retention as a more bioavailable form (ammonium) in estuarine and intertidal environments. However, the effects of soil abiotic and biotic characteristics on DNRA in Spartina alterniflora ecotones of estuarine and intertidal wetlands remain unclear.


In this study, we used nitrogen isotope tracing and molecular approaches to investigate DNRA activity, and abiotic and biotic factors of both rhizosphere and non-rhizosphere soils in Spartina alterniflora ecotones of the Yangtze estuarine and intertidal wetlands.


DNRA varied significantly throughout the sampling sites, with potential rates of 0.53–3.57 nmol N g−1 h−1. The rates of DNRA were significantly higher in rhizosphere than non-rhizosphere soils at the oligohaline sites. Salinity had more influence on DNRA activity than Spartina alterniflora at the brackish sites. Total organic carbon, nitrate, Fe (II) and sulfide were significantly correlated with DNRA rates and nrfA gene abundance. Soil substrates strongly affected DNRA activity in rhizosphere soil, while nrfA gene abundance was the predominant factor mediating DNRA activity in non-rhizosphere soil. DNRA contributed more to the total nitrate reduction at the brackish than oligohaline sites, suggesting that DNRA plays an important role in nitrate reduction in estuarine and intertidal wetlands.


This study suggests that soil substrates rather than nrfA gene dominate DNRA activity in estuarine and intertidal wetlands after Spartina alterniflora invasion. Our results are helpful to understand the importance of soil characteristics changes induced by the exotic plant invasion to nitrogen cycling in estuarine and intertidal wetlands.


DNRA Spartina alterniflora Biotic variable Environmental implications Estuarine wetlands 



This work was supported by the National Natural Science Foundation of China (Nos. 41725002, 41701548, 41761144062 and 41671463), the Foundation for Excellent Youth Scholar of Fujian Normal University, the Fundamental Research Funds for the Central Universities, Chinese National Key Programs for Fundamental Research and Development (Nos. 2016YFA0600904 and 2016YFE0133700), and Royal Netherlands Academy of Arts and Sciences (No. PSA-SA-E-02). It was also funded by Key Laboratory of Yangtze River Water Environment, Ministry of Education (Tongji University), China (No. YRWEF201804). We thank the two anonymous reviewers for their constructive comments on the early version of this manuscript.

Supplementary material

11104_2018_3914_MOESM1_ESM.docx (230 kb)
ESM 1 (DOCX 229 kb)


  1. An S, Gardner WS (2002) Dissimilatory nitrate reduction to ammonium (DNRA) as a nitrogen link, versus denitrification as a sink in a shallow estuary (Laguna Madre/Baffin Bay, Texas). Mar Ecol Prog Ser 237(4):41–50CrossRefGoogle Scholar
  2. Bernard RJ, Mortazavi B, Kleinhuizen AA (2015) Dissimilatory nitrate reduction to ammonium (DNRA) seasonally dominates NO3 reduction pathways in an anthropogenically impacted sub-tropical coastal lagoon. Biogeochemistry 125(1):47–64CrossRefGoogle Scholar
  3. Bonaglia S, Klawonn I, De Brabandere L, Deutsch B, Thamdrup B, Brüchert V (2016) Denitrification and DNRA at the Baltic Sea oxic–anoxic interface: substrate spectrum and kinetics. Limnol Oceanogr 61(5):1900–1915CrossRefGoogle Scholar
  4. Bonin P, Omnes P, Chalamet A (1998) Simultaneous occurrence of denitrification and nitrate ammonification in sediments of the French Mediterranean coast. Hydrobiologia 389(1–3):169–182CrossRefGoogle Scholar
  5. Brookes PC, Landman A, Pruden G, Jenkinson DS (1985) Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol Biochem 17:837–842CrossRefGoogle Scholar
  6. Canfield DE, Glazer AN, Falkowski PG (2010) The evolution and future of Earth’s nitrogen cycle. Science 330(6001):192–196CrossRefGoogle Scholar
  7. Canion A, Overholt WA, Kostka JE, Huettel M, Lavik G, Kuypers MM (2014) Temperature response of denitrification and anaerobic ammonium oxidation rates and microbial community structure in Arctic fjord sediments. Environ Microbiol 16:3331–3344CrossRefGoogle Scholar
  8. Chen X, Zhong Y (1998) Coastal erosion along the Changjiang deltaic shoreline, China: history and prospective. Estuar Coast Shelf Sci 46:733–742CrossRefGoogle Scholar
  9. Christensen PB, Rysgaard S, Sloth NP, Christensen PB, Rysgaard S, Sloth NP, Dalsgaard T, Schwaerter S (2000) Sediment mineralization, nutrient fluxes, denitrification and dissimilatory nitrate reduction to ammonium in an estuarine fjord with sea cage trout farms. Aquat Microb Ecol 257(21):73–84CrossRefGoogle Scholar
  10. Church JA, White NJ (2006) A 20th century acceleration in global sea-level rise. Geophys Res Lett 33:L01602CrossRefGoogle Scholar
  11. Craft C (2007) Freshwater input structures soil properties, vertical accretion, and nutrient accumulation of Georgia and US tidal marshes. Limnol Oceanogr 52:1220–1230CrossRefGoogle Scholar
  12. Crowe SA, Canfield DE, Mucci A, Sundby B, Maranger R (2012) Anammox, denitrification and fixed-nitrogen removal in sediments from the lower St.. Lawrence Estuary. Biogeosciences 9:4309–4321CrossRefGoogle Scholar
  13. Decleyre H, Heylen K, Van Colen C, Willems A (2015) Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers. Front Microbiol 6:1124CrossRefGoogle Scholar
  14. Deegan LA, Johnson DS, Warren RS, Peterson BJ, Fleeger JW, Fagherazzi S, Wollheim WM (2012) Coastal eutrophication as a driver of salt marsh loss. Nature 490(7420):388–392CrossRefGoogle Scholar
  15. Dell’Anno A, Stefano B, Danovaro R (2002) Quantification, base composition, and fate of extracellular DNA in marine sediments. Limnol Oceanogr 47(3):899–905CrossRefGoogle Scholar
  16. Deng FY, Hou LJ, Liu M, Zheng YL, Yin GY, Li XF, Lin XB, Chen F, Gao J, Jiang XF (2015) Dissimilatory nitrate reduction processes and associated contribution to nitrogen removal in sediments of the Yangtze estuary. J Geophys Res 120:1521–1531CrossRefGoogle Scholar
  17. Domangue RJ, Mortazavi B (2018) Nitrate reduction pathways in the presence of excess nitrogen in a shallow eutrophic estuary. Environ Pollut 238:599–606CrossRefGoogle Scholar
  18. Dong LF, Smith CJ, Papaspyrou S, Stott A, Osborn AM, 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):3171–3179CrossRefGoogle Scholar
  19. Dong LF, Sobey MN, Smith C, Rusmana I, Phillips W, Stott A, Osborn AM, Nedwell DB (2011) Dissimilatory reduction of nitrate to ammonium (DNRA) not denitrification or anammox dominates benthic nitrate reduction in tropical estuaries. Limnol Oceanogr 56:279–291CrossRefGoogle Scholar
  20. Dotaniya ML, Meena VD (2015) Rhizosphere effect on nutrient availability in soil and its uptake by plants: a review. P Natl A Sci India B 85(1):1–12CrossRefGoogle Scholar
  21. Du YH, Guo P, Liu JQ, Wang CY, Yang N, Jiao ZX (2014) Different types of nitrogen deposition show variable effects on the soil carbon cycle process of temperate forests. Glob Chang Biol 20(10):3222–3228CrossRefGoogle Scholar
  22. Dunn RJ, Robertson D, Teasdale PR, Waltham NJ, Welsh DT (2013) Benthic metabolism and nitrogen dynamics in an urbanized tidal creek: domination of DNRA over denitrification as a nitrate reduction pathway. Estuar Coast Shelf Sci 131:271–281CrossRefGoogle Scholar
  23. Fernandes SO, Michotey VD, Guasco S, Bonin PC, Bharathi PAL (2012) Denitrification prevails over anammox in tropical mangrove sediments (Goa, India). Mar Environ Res 74:9–19CrossRefGoogle Scholar
  24. Gao DZ, Li XF, Lin XB, Wu DM, Jin BS, Huang YP, Liu M, Chen X (2017) Soil dissimilatory nitrate reduction processes in the Spartina alterniflora invasion chronosequences of a coastal wetland of southeastern China: Dynamics and environmental implications. Plant Soil 421(1-2):383–399Google Scholar
  25. Gardner WS, McCarthy MJ (2009) Nitrogen dynamics at the sediment-water interface in shallow, sub-tropical Florida bay: why denitrification efficiency may decrease with increased eutrophication. Biogeochemistry 95(2/3):185–198CrossRefGoogle Scholar
  26. Gardner WS, McCarthy MJ, An S, Sobolev D, Sell KS, Brock D (2006) Nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA) support nitrogen dynamics in Texas estuaries. Limnol Oceanogr 51:558–568CrossRefGoogle Scholar
  27. Giblin AE, Weston NB, Banta GT, Tucker J, Hopkinson CS (2010) The effects of salinity on nitrogen losses from an oligohaline estuarine sediment. Estuar Coasts 33:1054–1068CrossRefGoogle Scholar
  28. Giblin AE, Tobias CR, Song BK, Weston N, Banta GT, Rivera-Monroy VH (2013) The importance of dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen cycle of coastal ecosystems. Oceanography 26(3):124–131CrossRefGoogle Scholar
  29. Gilbert F, Souchu P, Bianchi M, Bonin P (1997) Influence of shellfish farming activities on nitrification, nitrate reduction to ammonium and denitrification at the water-sediment interface of the Thau lagoon, France. Mar Ecol Prog Ser 151:143–153CrossRefGoogle Scholar
  30. Goeyens L, De Vries RTP, Bakker JF, Helder W (1987) An experiment on the relative importance of denitrification, nitrate reduction and ammonification in coastal marine sediment. J Sea Res 21(3):171–175CrossRefGoogle Scholar
  31. Greaver TL, Clark CM, Comptonm JE, Vallano D, Talhelm AF, Weaver CP, Band LE, Baron JS, Daavidson EA, Tague CL, Felker-quinn E, Lynch JA, Herrick JD, Liu L, Goddale CL, Novak KJ, Haeuber RA (2016) Key ecological responses to nitrogen are altered by climate change. Nat Clim Chang 6(9):836–843CrossRefGoogle Scholar
  32. Gu ZL, Li Y, Yang YF, Xia SQ, Hermanowicz SW, Alvarez-Cohen L (2018) Inhibition of anammox by sludge thermal hydrolysis and metagenomic insights. Bioresour Technol 270:46–54CrossRefGoogle Scholar
  33. Hardison AK, Algar CK, Giblin AE, Rich JJ (2015) Influence of organic carbon and nitrate loading on partitioning between dissimilatory nitrate reduction to ammonium (DNRA) and N2 production. Geochim Cosmochim Acta 164:146–160CrossRefGoogle Scholar
  34. He Y, Widney S, Ruan M, Herbert E, Li X, Craft C (2016) Accumulation of soil carbon drives denitrification potential and lab incubated gas production along a chronosequence of salt marsh development. Estuar Coast Shelf Sci 172:72–80CrossRefGoogle Scholar
  35. Henry S, Texier S, Hallet S, Bru D, Dambreville C, Chèneby D, Bizouard F, Germon JC, Philippot L (2008) Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates. Environ Microbiol 10(11):3082–3092CrossRefGoogle Scholar
  36. Hietanen S, Kuparinen J (2008) Seasonal and short-term variation in denitrification and anammox at a coastal station on the Gulf of Finland, Baltic Sea. Hydrobiologia 596(1):67–77CrossRefGoogle Scholar
  37. Hinshaw SE, Tatariw C, Flournoy N, Kleinhuizen A, Taylor C, Sobecky PA, Mortazavi B (2017) Vegetation loss decreases salt marsh denitrification capacity: implications for marsh erosion. Environ Sci Technol 51(15):8245–8253CrossRefGoogle Scholar
  38. Hou LJ, Liu M, Carini SA, Gardner WS (2012) Transformation and fate of nitrate near the sediment–water interface of Copano Bay. Cont Shelf Res 35:86–94CrossRefGoogle Scholar
  39. Hou LJ, Zheng YL, Liu M, Gong J, Zhang XL, Yin GY, You L (2013) Anaerobic ammonium oxidation (anammox) bacterial diversity, abundance, and activity in marsh sediments of the Yangtze estuary. J Geophys Res 118:1237–1246CrossRefGoogle Scholar
  40. Jäntti H, Hietanen S (2012) The effects of hypoxia on sediment nitrogen cycling in the Baltic Sea. Ambio 41(2):161–169CrossRefGoogle Scholar
  41. Jian SY, Li JW, Chen J, Wang GS, Mayes MA, Dzantor KE, Dzantor KE, Hui DF, Luo YQ (2016) Soil extracellular enzyme activities, soil carbon and nitrogen storage under nitrogen fertilization: a meta-analysis. Soil Biol Biochem 101:32–43CrossRefGoogle Scholar
  42. Karlson K, Hulth S, Ringdahl K, Rosenberg R (2005) Experimental recolonisation of Baltic Sea reduced sediments: survival of benthic macrofauna and effects on nutrient cycling. Mar Ecol Prog Ser 294:35–49CrossRefGoogle Scholar
  43. Kessler AJ, Roberts KL, Bissett A, Cook PL (2018) Biogeochemical controls on the relative importance of denitrification and dissimilatory nitrate reduction to ammonium in estuaries. Glob Biogeochem Cycles 32:1045–1057Google Scholar
  44. Kirwan ML, Megonigal JP (2013) Tidal wetland stability in the face of human impacts and sea-level rise. Nature 504:53–60CrossRefGoogle Scholar
  45. Koop-Jakobsen K, Giblin AE (2009) Anammox in tidal marsh sediments: the role of salinity, nitrogen loading, and marsh vegetation. Estuar Coasts 32(2):238–245CrossRefGoogle Scholar
  46. Koop-Jakobsen K, Giblin AE (2010) The effect of increased nitrate loading on nitrate reduction via denitrification and DNRA in salt marsh sediments. Limnol Oceanogr 55:789–802CrossRefGoogle Scholar
  47. Liu JE, Han RM, Su HR, Wu YP, Zhang LM, Richardson CJ, Wang GX (2017a) Effects of exotic Spartina alterniflora on vertical soil organic carbon distribution and storage amount in coastal salt marshes in Jiangsu, China. Ecol Eng 106:132–139CrossRefGoogle Scholar
  48. Liu X, Ruecker A, Song B, Xing J, Conner WH, Chow AT (2017b) Effects of salinity and wet–dry treatments on C and N dynamics in coastal-forested wetland soils: implications of sea level rise. Soil Biol Biochem 112:56–67CrossRefGoogle Scholar
  49. Lovley DR, Phillips EJP (1987) Rapid assay for microbially reducible ferric iron in aquatic sediments. Appl Environ Microbiol 53:1536–1540Google Scholar
  50. Mao D, Luo Y, Mathieu J, Wang Q, Feng L, Mu Q, Feng CY, Alvarez PJJ (2013) Persistence of extracellular DNA in river sediment facilitates antibiotic resistance gene propagation. Environ Sci Technol 48(1):71–78CrossRefGoogle Scholar
  51. Mohan SB, Schmid M, Jetten M, Cole J (2004) Detection and widespread distribution of the nrfA gene encoding nitrite reduction to ammonia, a short circuit in the biological nitrogen cycle that competes with denitrification. FEMS Microbiol Ecol 49:433–443CrossRefGoogle Scholar
  52. Morrissey EM, Gillespie JL, Morina JC, Franklin RB (2014) Salinity affects microbial activity and soil organic matter content in tidal wetlands. Glob Chang Biol 20:1351–1362CrossRefGoogle Scholar
  53. Nielsen KM, Johnsen PJ, Bensasson D, Daffonchio D (2007) Release and persistence of extracellular DNA in the environment. Environ Biosaf Res 6(1–2):37–53CrossRefGoogle Scholar
  54. Nishio T, Koike I, Hattori A (1982) Denitrification, nitrate reduction, and oxygen consumption in coastal and estuarine sediments. Appl Environ Microbiol 43(3):648–653Google Scholar
  55. Noe GB, Krauss KW, Lockaby BG, Conner WH, Hupp CR (2013) The effect of increasing salinity and forest mortality on soil nitrogen and phosphorus mineralization in tidal freshwater forested wetlands. Biogeochemistry 114:225–244CrossRefGoogle Scholar
  56. Osborne RI, Bernot MJ, Findlay SE (2015) Changes in nitrogen cycling processes along a salinity gradient in tidal wetlands of the Hudson River, New York, USA. Wetlands 35(2):323–334CrossRefGoogle Scholar
  57. Pietramellara G, Ascher J, Borgogni F, Ceccherini MT, Guerri G, Nannipieri P (2009) Extracellular DNA in soil and sediment: fate and ecological relevance. Biol Fertil Soils 45(3):219–235CrossRefGoogle Scholar
  58. Rasmussen P, Sonnenborg TO, Goncear G, Hinsby K (2013) Assessing impacts of climate change, sea level rise, and drainage canals on saltwater intrusion to coastal aquifer. Hydrol Earth Syst Sci 17:421–443CrossRefGoogle Scholar
  59. Roberts KL, Kessler AJ, Grace MR, Cook PL (2014) Increased rates of dissimilatory nitrate reduction to ammonium (DNRA) under oxic conditions in a periodically hypoxic estuary. Geochim Cosmochim Acta 133:313–324CrossRefGoogle Scholar
  60. Robertson EK, Roberts KL, Burdorf LD, Cook P, Thamdrup B (2016) Dissimilatory nitrate reduction to ammonium coupled to Fe (II) oxidation in sediments of a periodically hypoxic estuary. Limnol Oceanogr 61(1):365–381CrossRefGoogle Scholar
  61. Saeki K, Kunito T, Sakai M (2010) Effects of pH, ionic strength, and solutes on DNA adsorption by andosols. Biol Fertil Soils 46(5):531–535CrossRefGoogle Scholar
  62. Smith CJ, Nedwell DB, Dong LF, Osborn AM (2007) Diversity and abundance of nitrate reductase genes (nar G and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Appl Environ Microbiol 73:3612–3622CrossRefGoogle Scholar
  63. Smith CJ, Dong LF, Wilson J, Stott A, Osborn AM, Nedwell D (2015) Seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia process rates and corresponding key functional genes along an estuarine nitrate gradient. Front Microbiol 6:542Google Scholar
  64. Song GD, Liu SM, Marchant H, Kuypers MMM, Lavik G (2013) Anammox, denitrification and dissimilatory nitrate reduction to ammonium in the East China Sea sediment. Biogeosciences 10(11):6851–6864CrossRefGoogle Scholar
  65. Song BK, Lisa JA, Tobias CR (2014) Linking DNRA community structure and activity in a shallow lagoonal estuarine system. Front Microbiol 5:460CrossRefGoogle Scholar
  66. Tabatabai M (1994) Soil enzymes. In: Weaver R, Angle J, Bottomley P (eds) Methods of soil analysis, part 2: microbiological and biochemical properties. Soil Science Society of America, Madison, pp 775–833Google Scholar
  67. Tang YS, Wang L, Jia JW, Li YL, Zhang WQ, Wang HL, Sun Y (2011) Response of soil microbial respiration of tidal wetlands in the Yangtze River estuary to different artificial disturbances. Ecol Eng 37:1638–1646CrossRefGoogle Scholar
  68. Thamdrup B, Dalsgaard T (2002) Production of N2 through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments. Appl Environ Microbiol 68(3):1312–1318CrossRefGoogle Scholar
  69. Van de Broek M, Vandendriessche C, Poppelmonde D, Merckx R, Temmerman S, Govers G (2018) Long-term organic carbon sequestration in tidal marsh sediments is dominated by old-aged allochthonous inputs in a macrotidal estuary. Glob Chang Biol 24:2498–2512. CrossRefGoogle Scholar
  70. Vance ED, Brookes PC, Jenkinson DS (1987) An extraction method for measuring soil microbial biomass C. Soil Biol Biochem 19:703–707CrossRefGoogle Scholar
  71. Xiao W, Chen X, Jing X, Zhu B (2018) A meta-analysis of soil extracellular enzyme activities in response to global change. Soil Biol Biochem 123:21–32CrossRefGoogle Scholar
  72. Yin GY, Hou LJ, Liu M, Liu ZF, Gardner WS (2014) A novel membrane inlet mass spectrometer method to measure 15NH4 + for isotope-enrichment experiments in aquatic ecosystems. Environ Sci Technol 48(16):9555–9562CrossRefGoogle Scholar
  73. Zhang YH, Ding WS, Luo JF, Donnison A (2010) Changes in soil organic carbon dynamics in an eastern Chinese coastal wetland following invasion by a C4 plant Spartina alterniflora. Soil Biol Biochem 42:1712–1720CrossRefGoogle Scholar
  74. Zhou M, Butterbach-Bahl K, Vereecken H, Brüggemann N (2017) A meta–analysis of soil salinization effects on nitrogen pools, cycles and fluxes in coastal ecosystems. Glob Chang Biol 23(3):1338–1352CrossRefGoogle Scholar
  75. Zuo P, Zhao SH, Liu CA, Wang CH, Liang YB (2012) Distribution of Spartina spp. along China's coast. Ecol Eng 40:160–166CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of EducationFujian Normal UniversityFuzhouChina
  2. 2.School of Geographical SciencesFujian Normal UniversityFuzhouChina
  3. 3.Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic SciencesEast China Normal UniversityShanghaiChina
  4. 4.State Key Laboratory of Estuarine and Coastal ResearchEast China Normal UniversityShanghaiChina

Personalised recommendations