Abstract
In this study, changes in plant diversity and aboveground biomass, soil chemical properties, microbial biomass and respiration, microbial composition, and microbial N-cycling potential (represented by the abundance of genes involved in N reaction) were studied after 3 years of urea fertilization (0, 25, 50, and 100 kg N ha−1 year−1) in a semiarid grassland in China. The microbial composition and N-cycling genes were determined using metagenome sequencing. Urea fertilization significantly decreased soil bacterial diversity, possibly through its negative effect on plant diversity, whereas it increased fungal diversity, and microbial biomass and respiration through enhancing aboveground biomass production with increases in the C input into the soil. However, above the threshold N rate of 50 kg N ha−1 year−1, microbial biomass and respiration decreased probably because of a strong N inhibitory effect on aboveground biomass. Further, urea fertilization increased the gene abundances of narH, nrfA, nirB, and napA, which are involved in dissimilatory nitrate reduction, and those of nifH and nifD, involved in N2 fixation, gdh, involved in organic N decomposition, and glnA, involved in glutamine synthesis and ureC. These findings suggested that urea addition has a positive effect on N-turnover potential. Burkholderiales and Rhizobiales play an important role in soil N cycling. Changes in plant community (diversity and biomass) were responsible for the shift in microbial diversity, biomass, and respiration, whereas alterations in inorganic N levels (exchangeable NH4+ and NO3−) potentially affected microbial N cycling. Our results show that N-mediated environmental stresses can play an important role in microbial diversity and functions, which appear to be mediated largely by plant–soil interactions.






References
Alster CJ, German DP, Lu Y, Allison SD (2013) Microbial enzymatic responses to drought and to nitrogen addition in a southern California grassland. Soil Biol Biochem 64:68–79
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 237:41–50
Bardgett RD, Freeman C, Ostle NJ (2008) Microbial contributions to climate change through carbon cycle feedbacks. ISME J 2:805–814
Beck T, Joergensen RG, Kandeler E, Makeschin F, Nuss E, Oberholzer HR, Scheu S (1997) An inter-laboratory comparison of ten different ways of measuring soil microbial biomass C. Soil Biol Biochem 29:1023–1032
Bobbink R, Hicks K, Galloway J, Spranger T, Alkemade R, Ashmore M, Bustamante M, Cinderby S, Davidson E, Dentener F, Emmett B, Erisman JW, Fenn M, Gilliam F, Nordin A, Pardo L, De Vries W (2010) Global assessment of nitrogen deposition effects on terrestrial plant diversity: a synthesis. Ecol Appl 20:30–59
Brooks 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 17:837–842
Bremner JM, Mulvaney CS (1982) Nitrogen-total. In: Page AL, Miller RH, Keeney DR (eds) Methods of soil analysis, part 2, chemical and microbial properties. Agronomy Society of America, Madison, pp 595–624
Chen WQ, Xu R, Wu YT, Chen J, Zhang YJ, Hu TM, Yuan XP, Zhou L, Tan TY, Fan JR (2018) Plant diversity is coupled with beta not alpha diversity of soil fungal communities following N enrichment in a semi-arid grassland. Soil Biol Biochem 116:388–398
DeMalach N (2018) Toward a mechanistic understanding of the effects of nitrogen and phosphorus additions on grassland diversity. Perspect Plant Ecol 32:65–72
DeMalach N, Zaady E, Weiner J, Kadmon R (2016) Size asymmetry of resource competition and the structure of plant communities. J Ecol 104:899–910
Di HJ, Cameron KC, Shen JP, Winefield CS, O'Callaghan M, Bowatte S, He JZ (2009) Nitrification driven by bacteria and not archaea in nitrogen-rich grass-land soils. Nat Geosci 2:621–624
Duan CJ, Fang LC, Yang CL, Chen WB, Cui YX, Li SQ (2018) Reveal the response of enzyme activities to heavy metals through in situ zymography. Ecotoxicol Environ Saf 156:106–115
Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364
Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28:3150–3152
Galloway JN, Townsend AR, Erisman JW, Bekunda M, Cai Z, Freney JR, Martinelli LA, Seitzinger SP, Sutton MA (2008) Transformation of the nitrogen cycle: recent trends, questions, and potential solutions. Science 320:889–892
Harpole WS, Ngai JT, Cleland EE, Seabloom EW, Borer ET, Bracken MES, Elser JJ, Gruner DS, Hillebrand H, Shurin JB, Smith JE (2011) Nutrient co-limitation of primary producer communities. Ecol Lett 14:852–862
Hong JT, Ma XX, Zhang XK, Wang XD (2017) Nitrogen uptake pattern of herbaceous plants: coping strategies in altered neighbor species. Biol Fertil Soils 53:729–735
Jung J, Yeom J, Kim J, Han J, Lim HS, Park H, Hyun S, Park W (2011) Change in gene abundance in the nitrogen biogeochemical cycle with temperature and nitrogen addition in Antarctic soils. Res Microbiol 162:1018–1026
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:D457–D462
Kou YP, Li JB, Wang YS, Li CN, Tu B, Yao MJ, Li XZ (2017) Scale-dependent key drivers controlling methane oxidation potential in Chinese grassland soils. Soil Biol Biochem 111:104–114
Lamb EG, Kembel SW, Cahill JF Jr (2009) Shoot, but not root, competition reduces community diversity in experimental mesocosms. J Ecol 97:155–163
Laverman AM, Speksnijder AGCL, Braster M, Kowal-chuk GA, Verhoef HA, HWv V (2001) Spatiotemporal stability on an ammonia-oxidizing community in a nitrogen-saturated forest soil. Microb Ecol 42:35–45
LeBauer DS, Treseder KK (2008) Nitrogen limitation of net primary productivity in terrestrial ecosystems is globally distributed. Ecology 89:371–379
Leff JW, Jones SE, Prober SM, Barberán A, Borer ET, Firn JL, Harpole WS, Hobbie SE, Hofmockel KS, Knops JMH, McCulley RL, La Pierre K, Risch AC, Seabloom EW, Schütz M, Steenbock C, Stevens CJ, Fierer N (2015) Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc Natl Acad Sci U S A 112:10967–10972
Li H, Durbin R (2009) Fast and accurate short read alignment with burrows–wheeler transform. Bioinformatics 25:1754–1760
Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714
Li Y, Liu YH, Wu SM, Niu L, Tian Y (2015) Microbial properties explain temporal variation in soil respiration in a grassland subjected to nitrogen addition. Sci Rep 5:18496–18506
Liang Y, He X, Liang S, Zhang W, Chen X, Feng S, Su Y (2013) Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China. J Basic Microbiol 54:180–189
Liu L, Greaver TL (2010) A global perspective on belowground carbon dynamics under nitrogen enrichment. Ecol Lett 13:819–828
Lu M, Yang YH, Luo YQ, Fang CM, Zhou XH, Chen JK, Yang X, Li B (2011) Responses of ecosystem nitrogen cycle to nitrogen addition: a meta-analysis. New Phytol 189:1040–1050
Lu X, Mao Q, Gilliam FS, Luo Y, Mo J (2014) Nitrogen deposition contributes to soil acidification in tropical ecosystems. Glob Chang Biol 20:3790–3801
Mergel C, Kloos A, Bothe KH (2001) Seasonal fluctuations in the population of denitrifying and N2-fixing bacteria in an acid soil of a Norway spruce forest. Plant Soil 230:145–160
Nakaji T, Fukami M, Dokiya Y, Lzuta T (2001) Effects of high nitrogen load on growth, photosynthesis and nutrient status of Cryptomeria japonica and Pinus densiflora seedlings. Trees 15:453–461
Nannipieri P, Paul EA (2009) The chemical and functional characterization of soil N and its biotic components. Soil Biol Biochem 41:2357–2369
Nannipieri P, Trasar-Cepeda C, Dick P (2018) Soil enzyme activity: a brief history and biochemistry as a basis for appropriate interpretations and meta-analysis. Biol Fertil Soils 54:11–19
Nelson DW, Sommers LE (1982) Total carbon, organic carbon, and organic matter. In: Page AL, Miller RH, Keeney DR (eds) Methods of soil analysis, part 2, chemical and microbial properties. Agronomy Society of America, Madison, pp 539–552
Nelson MB, Berlemont R, Martiny AC, Martiny JBH (2015) Nitrogen cycling potential of a grassland litter microbial community. Appl Environ Microbiol 81:7012–7022
Ning QS, Gu Q, Shen JP, Lv XT, Yang JJ, Zhang XM, He JZ, Huang JH, Wang H, Xu ZH, Han XG (2015) Effects of nitrogen deposition rates and frequencies on the abundance of soil nitrogen-related functional genes in temperate grassland of northern China. J Soils Sediments 15:694–704
Noguchi H, Park J, Takagi T (2006) MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res 34:5623–5630
Olsen SR, Sommers LE (1982) Phosphorous. In: Page AL, Miller RH, Keeney DR (eds) Methods of soil analysis, part 2, chemical and microbial properties. Agronomy Society of America, Madison, pp 403–430
Pan H, Ying SS, Liu HY, Zeng LZ, Zhang QC, Liu YM, Xu JM, Li Y, Di HJ (2018) Microbial pathways for nitrous oxide emissions from sheep urine and dung in a typical steppe grassland. Biol Fertil Soils 54:717–730
Pratscher J, Dumont MG, Conrad R (2011) Ammonia oxidation coupled to CO2 fixation by archaea and bacteria in an agricultural soil. Proc Natl Acad Sci U S A 108:4170–4175
Ramirez KS, Craine JM, Fierer N (2010) Nitrogen fertilization inhibits soil microbial respiration regardless of the form of nitrogen applied. Soil Biol Biochem 42:2336–2338
Redecker D, Raab P (2006) Phylogeny of the glomeromycota (arbuscular mycorrhizal fungi): recent developments and new gene markers. Mycologia 98:885–895
Rousk J, Bååth 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 4:1340–1351
Sanchez G (2013) PLS path modeling with R. Trowchez Editions, Berkeley
Shen XY, Zhang LM, Shen JP, Li LH, Yuan CL, He JZ (2011) Nitrogen loading levels affect abundance and composition of soil ammonia oxidizing prokaryotes in semiarid temperate grassland. J Soils Sediments 11:1243–1252
Stevens CJ, Dise NB, Mountford JO, Gowing DJ (2004) Impact of nitrogen deposition on the species richness of grasslands. Science 303:1876–1879
Tian XF, Hu HW, Ding Q, Song MH, Xu XL, Zheng Y, Guo LD (2014) Influence of nitrogen fertilization on soil ammonia oxidizer and denitrifier abundance, microbial biomass, and enzyme activities in an alpine meadow. Biol Fertil Soils 50:703–713
Tu QC, He ZL, Wu LY, Xue K, Xie G, Chain P, Reich PB, Hobbie SE, Zhou JZ (2017) Metagenomic reconstruction of nitrogen cycling pathways in a CO2-enriched grassland ecosystem. Soil Biol Biochem 106:99–108
van der Heijden MGA, Bardgett RD, Straalen NMV (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310
Vance ED, Brookes PC, Jenkinson DS (1987) An extraction method for measuring soil microbial biomass C. Soil Biol Biochem 19:703–707
Vestergaard G, Schulz S, Schöler A, Schloter M (2017) Making big data smart—how to use metagenomics to understand soil quality. Biol Fertil Soils 53:479–484
Vitousek PM, Aber JD, Howarth RW, Likens GE, Matson PA, Schindler DW, Schlesinger WH, Tilman DG (1997) Human alteration of the global nitrogen cycle: sources and consequences. Ecol Appl 7:737–750
Wang CH, Butterbach-Bahl K, He NP, Wang QB, Xing X, Han X (2015) Nitrogen addition and mowing affect microbial nitrogen transformations in a C4 grassland in northern China. Eur J Soil Sci 66:485–495
Wang CY, Zhou JW, Liu J, Jiang K, Du DL (2017) Responses of soil N-fixing bacteria communities to Amaranthus retroflexus invasion under different forms of N deposition. Agric Ecosyst Environ 247:329–336
Wang C, Lu XK, Moria T, Mao QG, Zhou KJ, Zhou GY, Nie YX, Mo JM (2018) Responses of soil microbial community to continuous experimental nitrogen additions for 13 years in a nitrogen-rich tropical forest. Soil Biol Biochem 121:103–112
Wei C, Yu Q, Bai E, Lu X, Li Q, Xia J, Kardol P, Liang W, Wang Z, Han X (2013) Nitrogen deposition weakens plant-microbe interactions in grassland ecosystems. Glob Chang Biol 19:3688–3697
Whittaker RJ (2006) Island species-energy theory. J Biogeogr 33:11–12
Xiang XJ, He D, He JS, Myrold DD, Chu HY (2017) Ammonia-oxidizing bacteria rather than archaea respond to short-term urea amendment in an alpine grassland. Soil Biol Biochem 107:218–225
Yang HJ, Li Y, Wu MY, Zhang Z, Li LH, Wan SQ (2011) Plant community responses to nitrogen addition and increased precipitation: the importance of water availability and species traits. Glob Chang Biol 17:2936–2944
Yang T, Adams JM, Shi Y, He JS, Jing X, Chen LT, Tedersoo L, Chu HY (2017) Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity. New Phytol 215:756–765
Zang HD, Blagodatskaya E, Wang JY, Xu XL, Kuzyakov Y (2017) Nitrogen fertilization increases rhizodeposit incorporation into microbial biomass and reduces soil organic matter losses. Biol Fertil Soils 53:419–429
Zehr JP, Kudela RM (2011) Nitrogen cycle of the open ocean: from genes to ecosystems. Annu Rev Mar Sci 3:197–225
Zeng J, Liu XJ, Song L, Lin XJ, Zhang HY, Shen CC, Chu HY (2016) Nitrogen fertilization directly affects soil bacterial diversity and indirectly affects bacterial community composition. Soil Biol Biochem 92:41–49
Zhang CP, Niu DC, Hall SJ, Wen HY, Li XD, Fu H, Wan CG, Elser JJ (2014) Effects of simulated nitrogen deposition on soil respiration components and their temperature sensitivities in a semiarid grassland. Soil Biol Biochem 75:113–123
Zhang C, Liu G, Xue S, Wang G (2016) Soil bacterial community dynamics reflect changes in plant community and soil properties during the secondary succession of abandoned farmland in the Loess Plateau. Soil Biol Biochem 97:40–49
Zhong YQW, Yan WM, Shangguan ZP (2015) Impact of long-term N additions upon coupling between soil microbial community structure and activity, and nutrient-use efficiencies. Soil Biol Biochem 91:151–159
Zhou X, Fornara D, Wasson EA, Wang DM, Ren GD, Christie P, Jia ZJ (2015) Effects of 44 years of chronic nitrogen fertilization on the soil nitrifying community of permanent grassland. Soil Biol Biochem 91:76–83
Zhou J, Jiang X, Zhou B, Zhao B, Ma M, Guan D, Li J, Chen S, Cao F, Shen D, Qin J (2016) Thirty four years of nitrogen fertilization decreases fungal diversity and alters fungal community composition in black soil in northeast China. Soil Biol Biochem 95:135–143
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National Natural Sciences Foundation of China (41771554), National Key Research and Development Program of China (2016YFC0501707), and the Key Technologies R&D Program of China (2015BAC01B03).
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Zhang, C., Song, Z., Zhuang, D. et al. Urea fertilization decreases soil bacterial diversity, but improves microbial biomass, respiration, and N-cycling potential in a semiarid grassland. Biol Fertil Soils 55, 229–242 (2019). https://doi.org/10.1007/s00374-019-01344-z
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DOI: https://doi.org/10.1007/s00374-019-01344-z