Understanding Responses of Soil Microbiome to the Nitrogen and Phosphorus Addition in Metasequoia glyptostroboides Plantations of Different Ages.
Nitrogen and phosphorus addition
Soil microbial response
Strain level
Tree ages
Journal
Microbial ecology
ISSN: 1432-184X
Titre abrégé: Microb Ecol
Pays: United States
ID NLM: 7500663
Informations de publication
Date de publication:
Aug 2022
Aug 2022
Historique:
received:
10
05
2021
accepted:
03
09
2021
pubmed:
22
9
2021
medline:
8
9
2022
entrez:
21
9
2021
Statut:
ppublish
Résumé
Nitrogen (N) and phosphorus (P) have significant effects on soil microbial community diversity, composition, and function. Also, trees of different life stages have different fertilization requirements. In this study, we designed three N additions and three P levels (5 years of experimental treatment) at two Metasequoia glyptostroboides plantations of different ages (young, 6 years old; middle mature, 24 years old) to understand how different addition levels of N and P affect the soil microbiome. Here, the N fertilization of M. glyptostroboides plantation land (5 years of experimental treatment) significantly enriched microbes (e.g., Lysobacter, Luteimonas, and Rhodanobacter) involved in nitrification, denitrification, and P-starvation response regulation, which might further lead to the decreasing in alpha diversity (especially in 6YMP soil). The P addition could impact the genes involved in inorganic P-solubilization and organic P-mineralization by increasing soil AP and TP. Moreover, the functional differences in the soil microbiomes were identified between the 6YMP and 24YMP soil. This study provides valuable information that improves our understanding on the effects of N and P input on the belowground soil microbial community and functional characteristics in plantations of different stand ages.
Identifiants
pubmed: 34545413
doi: 10.1007/s00248-021-01863-z
pii: 10.1007/s00248-021-01863-z
doi:
Substances chimiques
Soil
0
Phosphorus
27YLU75U4W
Nitrogen
N762921K75
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
565-579Informations de copyright
© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Allision SD, Lu Y, Weihe C, Goulden ML, Msrtiny AC, Treseder KK, Martiny JBH (2013) Microbial abundance and composition influence litter decomposition response to environmental change. Ecology 94:714–724
doi: 10.1890/12-1243.1
Artursson V, Finlay RD, Jansson JK (2006) Interactions between arbuscular mycorrhizal fungi and bacteria and their potential for stimulating plant growth. Environ Microbiol 8:1–10
pubmed: 16343316
doi: 10.1111/j.1462-2920.2005.00942.x
Beals EW (1984) Bray-Curtis ordination: an effective strategy for analysis of multivariate ecological data. In: Advances in ecological research: Elsevier. 1–55
Bending GD, Turner MK, Rayns F, Marx M-C, Wood M (2004) Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes. Soil Biol Biochem 36:1785–1792
doi: 10.1016/j.soilbio.2004.04.035
Bremner J (1960) Determination of nitrogen in soil by the Kjeldahl method. J Agric Sci 55:11–33
doi: 10.1017/S0021859600021572
Buchfink B, Xie C, Huson DH (2014) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59
pubmed: 25402007
doi: 10.1038/nmeth.3176
Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59–60
pubmed: 25402007
doi: 10.1038/nmeth.3176
Campbell BJ, Polson SW, Hanson TE, Mack MC, Schuur EA (2010) The effect of nutrient deposition on bacterial communities in Arctic tundra soil. Environ Microbiol 12:1842–1854
pubmed: 20236166
doi: 10.1111/j.1462-2920.2010.02189.x
Ceulemans T, Stevens CJ, Duchateau L, Jacquemyn H, Gowing DJ, Merckx R et al (2014) Soil phosphorus constrains biodiversity across European grasslands. Glob Change Biol 20:3814–3822
doi: 10.1111/gcb.12650
Cleveland CC, Reed SC, Townsend AR (2006) Nutrient regulation of organic matter decomposition in a tropical rain forest. Ecology 87:492–503
pubmed: 16637373
doi: 10.1890/05-0525
Colemana DC, Whitmanb WB (2005) Linking species richness, biodiversity and ecosystem function in soil systems. Pedobiologia 49:479–497
doi: 10.1016/j.pedobi.2005.05.006
Dai Z, Liu G, Chen H, Chen C, Wang J, Ai S et al (2020) Long-term nutrient inputs shift soil microbial functional profiles of phosphorus cycling in diverse agroecosystems. ISME J 14:757–770
pubmed: 31827246
doi: 10.1038/s41396-019-0567-9
Dai Z, Su W, Chen H, Barberan A, Zhao H, Yu M et al (2018) Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe. Glob Change Biol 24:3452–3461
doi: 10.1111/gcb.14163
Deng L, Wang G-L, Liu G-B, Shangguan Z-P (2016) Effects of age and land-use changes on soil carbon and nitrogen sequestrations following cropland abandonment on the Loess Plateau China. Ecological Engineering 90:105–112
doi: 10.1016/j.ecoleng.2016.01.086
Ding X, Wei D, Guo W, Wang B, Meng Z, Feng R et al (2019) Biological denitrification in an anoxic sequencing batch biofilm reactor: performance evaluation, nitrous oxide emission and microbial community. Bioresource technology 285:121359
pubmed: 31015181
doi: 10.1016/j.biortech.2019.121359
Dixon PM (2003) VEGAN, a package of R functions for community ecology. J Veg Sci 14:927–930
doi: 10.1111/j.1654-1103.2003.tb02228.x
Dong WY, Zhang XY, Liu XY, Fu XL, Chen FS, Wang HM et al (2015) Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China. Biogeosciences 12:5537–5546
doi: 10.5194/bg-12-5537-2015
Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017
pubmed: 22134642
doi: 10.1038/ismej.2011.159
Freedman Z, Eisenlord SD, Zak DR, Xue K, He Z, Zhou J (2013) Towards a molecular understanding of N cycling in northern hardwood forests under future rates of N deposition. Soil Biol Biochem 66:130–138
doi: 10.1016/j.soilbio.2013.07.010
Grace JB, Anderson TM, Olff H, Scheiner SM (2010) On the specification of structural equation models for ecological systems. Ecol Monogr 80:67–87
doi: 10.1890/09-0464.1
Green SJ, Prakash O, Jasrotia P, Overholt WA, Cardenas E, Hubbard D et al (2012) Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site. Appl Environ Microbiol 78:1039–1047
pubmed: 22179233
pmcid: 3273022
doi: 10.1128/AEM.06435-11
Harpole WS, Tilman D (2007) Grassland species loss resulting from reduced niche dimension. Nature 446:791–793
pubmed: 17384633
doi: 10.1038/nature05684
He D, Xiang X, He J-S, Wang C, Cao G, Adams J, Chu H (2016) Composition of the soil fungal community is more sensitive to phosphorus than nitrogen addition in the alpine meadow on the Qinghai-Tibetan Plateau. Biol Fertil Soils 52:1059–1072
doi: 10.1007/s00374-016-1142-4
Hu A, Wang J, Sun H, Niu B, Si G, Wang J et al (2020) Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments. ISME J 14:931–944
pubmed: 31896789
pmcid: 7082341
doi: 10.1038/s41396-019-0574-x
Huang J, Hu B, Qi K, Chen W, Pang X, Bao W, Tian G (2016) Effects of phosphorus addition on soil microbial biomass and community composition in a subalpine spruce plantation. Eur J Soil Biol 72:35–41
doi: 10.1016/j.ejsobi.2015.12.007
Institute of soil science (1978) Soil physical and chemical analysis. Shanghai Scientific&Technical Publishers, Shanghai
Jansson M (1988) Phosphate uptake and utilization by bacteria and algae. In: Phosphorus in Freshwater Ecosystems: Springer. 177–189
Jia S, Wang Z, Li X, Sun Y, Zhang X, Liang A (2010) N fertilization affects on soil respiration, microbial biomass and root respiration in Larix gmelinii and Fraxinus mandshurica plantations in China. Plant Soil 333:325–336
doi: 10.1007/s11104-010-0348-8
Jing T, Dungait JAJ, Xiankai L, Yunfeng Y, Hartley IP, Wei Z et al (2019) Long-term nitrogen addition modifies microbial composition and functions for slow carbon cycling and increased sequestration in tropical forest soil. Global change biology 25:3276–3281
Johnston ER, Kim M, Hatt JK, Phillips JR, Yao Q, Song Y et al (2019) Phosphate addition increases tropical forest soil respiration primarily by deconstraining microbial population growth. Soil Biol Biochem 130:43–54
doi: 10.1016/j.soilbio.2018.11.026
Józefowska A, Pietrzykowski M, Woś B, Cajthaml T, Frouz J (2017) The effects of tree species and substrate on carbon sequestration and chemical and biological properties in reforested post-mining soils. Geoderma 292:9–16
doi: 10.1016/j.geoderma.2017.01.008
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, Wang Z (2019) MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7:e7359
pubmed: 31388474
pmcid: 6662567
doi: 10.7717/peerj.7359
Kang H, Gao H, Yu W, Yi Y, Wang Y, Ning M (2018) Changes in soil microbial community structure and function after afforestation depend on species and age: case study in a subtropical alluvial island. Sci Total Environ 625:1423–1432
pubmed: 29996439
doi: 10.1016/j.scitotenv.2017.12.180
Kaspari M, Garcia MN, Harms KE, Santana M, Wright SJ, Yavitt JB (2008) Multiple nutrients limit litterfall and decomposition in a tropical forest. Ecol Lett 11:35–43
pubmed: 18021246
LE OSS (1982) Phosphorus 413–414 421–422 Page AL Miller RH Keeney DR, Methods of soil analysis Part 2: Chemical and microbiological properties 2nd ed Agron. Monogr. No. 9, Amer Soc Agron Soil Sci Soc Amer Madison, WI.
LeBauer DS, Treseder KK (2008) Nitrogen limitation of net primary productivity in terrestrial ecosystems is globally distributed. Ecology 89:371–379
pubmed: 18409427
doi: 10.1890/06-2057.1
Leff JW, Jones SE, Prober SM, Barberan A, Borer ET, Firn JL et al (2015) Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. PNAS 112:10967–10972
pubmed: 26283343
pmcid: 4568213
doi: 10.1073/pnas.1508382112
Li D, Liu C-M, Luo R, Sadakane K, Lam T-W (2015) MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674–1676
pubmed: 25609793
doi: 10.1093/bioinformatics/btv033
Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, arXiv preprint arXiv:1303.3997.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079
pubmed: 19505943
pmcid: 2723002
doi: 10.1093/bioinformatics/btp352
Liu C, Jin Y, Hu Y, Tang J, Xiong Q, Xu M et al (2019) Drivers of soil bacterial community structure and diversity in tropical agroforestry systems. Agr Ecosyst Environ 278:24–34
doi: 10.1016/j.agee.2019.03.015
Liu L, Gundersen P, Zhang T, Mo J (2012) Effects of phosphorus addition on soil microbial biomass and community composition in three forest types in tropical China. Soil Biol Biochem 44:31–38
doi: 10.1016/j.soilbio.2011.08.017
Luan J, Xiang C, Liu S, Luo Z, Gong Y, Zhu X (2010) Assessments of the impacts of Chinese fir plantation and natural regenerated forest on soil organic matter quality at Longmen mountain Sichuan, China. Geoderma 156:228–236
doi: 10.1016/j.geoderma.2010.02.021
Mao Q, Lu X, Zhou K, Chen H, Zhu X, Mori T, Mo J (2017) Effects of long-term nitrogen and phosphorus additions on soil acidification in an N-rich tropical forest. Geoderma 285:57–63
doi: 10.1016/j.geoderma.2016.09.017
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal 17:10–12
doi: 10.14806/ej.17.1.200
McHugh TA, Morrissey EM, Mueller RC, Gallegos-Graves V, Kuske CR, Reed SC (2017) Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland. Environ Microbiol 19:1600–1611
pubmed: 28120480
doi: 10.1111/1462-2920.13678
Nelson D, Sommers LE (1983) Total carbon, organic carbon, and organic matter, Methods of soil analysis: Part 2 chemical and microbiological properties 9: 539–579.
Nie Y, Wang M, Zhang W, Ni Z, Hashidoko Y, Shen W (2018) Ammonium nitrogen content is a dominant predictor of bacterial community composition in an acidic forest soil with exogenous nitrogen enrichment. Sci Total Environ 624:407–415
pubmed: 29262382
doi: 10.1016/j.scitotenv.2017.12.142
Pan P, Kang Q, Li X (2003) Determination of total phosphorus in soil by ammonium molybdate spectrophotometry. Chin J Spectrosc Lab 20:697–699
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055
pubmed: 25977477
pmcid: 4484387
doi: 10.1101/gr.186072.114
Patro R, Duggal G, Kingsford C (2015) Salmon: accurate, versatile and ultrafast quantification from RNA-seq data using lightweight-alignment, Biorxiv: 021592
Prakash O, Green SJ, Jasrotia P, Overholt WA, Canion A, Watson DB et al (2012) Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer. Int J Syst Evol Microbiol 62:2457–2462
pubmed: 22140175
doi: 10.1099/ijs.0.035840-0
Pywell RF, Bullock JM, Tallowin JB, Walker KJ, Warman EA, Masters G (2006) Enhancing diversity of species-poor grasslands: an experimental assessment of multiple constraints. J Appl Ecol 44:81–94
doi: 10.1111/j.1365-2664.2006.01260.x
Qu Z, Liu B, Ma Y, Sun H (2020) Differences in bacterial community structure and potential functions among Eucalyptus plantations with different ages and species of trees. Applied Soil Ecology 149:103515
doi: 10.1016/j.apsoil.2020.103515
Rosseel Y (2012) Lavaan: an R package for structural equation modeling and more. Version 0.5–12 (BETA). J Stat Softw 48:1–36
doi: 10.18637/jss.v048.i02
Sarathchandra S, Ghani A, Yeates G, Burch G, Cox N (2001) Effect of nitrogen and phosphate fertilisers on microbial and nematode diversity in pasture soils. Soil Biol Biochem 33:953–964
doi: 10.1016/S0038-0717(00)00245-5
Sarathchandra S, Lee A, Perrott K, Rajan S, Oliver E, Gravett I (1993) Effects of phosphate fertilizer applications on microorganisms in pastoral soil. Soil Research 31:299–309
doi: 10.1071/SR9930299
Schleuss PM, Widdig M, Heintz-Buschart A, Kirkman K, Spohn M (2020) Interactions of nitrogen and phosphorus cycling promote P acquisition and explain synergistic plant growth responses, Ecology: e03003
Segata N, Börnigen D, Morgan XC, Huttenhower C (2013) PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 4:1–11
doi: 10.1038/ncomms3304
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504
pubmed: 14597658
pmcid: 403769
doi: 10.1101/gr.1239303
Shook CL, Ketchen DJ Jr, Hult GTM, Kacmar KM (2004) An assessment of the use of structural equation modeling in strategic management research. Strateg Manag J 25:397–404
doi: 10.1002/smj.385
Steiger JH (2007) Understanding the limitations of global fit assessment in structural equation modeling. Personality Individ Differ 42:893–898
doi: 10.1016/j.paid.2006.09.017
Su JQ, Ding LJ, Xue K, Yao HY, Quensen J, Bai SJ et al (2015) Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil. Mol Ecol 24:136–150
pubmed: 25410123
doi: 10.1111/mec.13010
Sun Y, Men M, Xu B, Meng Q, Bello A, Xu X, Huang X (2019) Assessing key microbial communities determining nitrogen transformation in composting of cow manure using illumina high-throughput sequencing. Waste Manage 92:59–67
doi: 10.1016/j.wasman.2019.05.007
Tomarken AJ, Waller NG (2005) Structural equation modeling: strengths, limitations, and misconceptions. Annu Rev Clin Psychol 1:31–65
pubmed: 17716081
doi: 10.1146/annurev.clinpsy.1.102803.144239
van der Heijden MG, Bardgett RD, van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310
pubmed: 18047587
doi: 10.1111/j.1461-0248.2007.01139.x
Vesterdal L, Clarke N, Sigurdsson BD, Gundersen P (2013) Do tree species influence soil carbon stocks in temperate and boreal forests? For Ecol Manage 309:4–18
doi: 10.1016/j.foreco.2013.01.017
Vitousek PM, Farrington H (1997) Nutrient limitation and soil development: experimental test of a biogeochemical theory. Biogeochemistry 37:63–75
doi: 10.1023/A:1005757218475
Wang C, Xue L, Dong Y, Hou L, Wei Y, Chen J, Jiao R (2019) The development of Chinese fir plantations undergo significant changes in soil microbial metabolic function and enzyme activities. J For Res 24:261–265
doi: 10.1080/13416979.2019.1643441
Wang J, Wang J, Wang L, Zhang H, Guo Z, Geoff Wang G et al (2019) Does stoichiometric homeostasis differ among tree organs and with tree age? Forest Ecology and Management 453:117637
doi: 10.1016/j.foreco.2019.117637
Wang Q, Wang C, Yu W, Turak A, Chen D, Huang Y et al (2018) Effects of nitrogen and phosphorus inputs on soil bacterial abundance, diversity, and community composition in Chinese fir plantations. Frontier in microbiology 9:1543
doi: 10.3389/fmicb.2018.01543
Wang Z, Yang S, Wang R, Xu Z, Feng K, Feng X et al (2020) Compositional and functional responses of soil microbial communities to long-term nitrogen and phosphorus addition in a calcareous grassland. Pedobiologia 78:150612
doi: 10.1016/j.pedobi.2019.150612
Wu T, Yu M, Wang G, Wang Z, Duan X, Dong Y, Cheng X (2012) Effects of stand structure on wind speed reduction in a Metasequoia glyptostroboides shelterbelt. Agrofor Syst 87:251–257
doi: 10.1007/s10457-012-9540-6
Wu X, Xu H, Tuo D, Wang C, Fu B, Lv Y, Liu G (2020) Land use change and stand age regulate soil respiration by influencing soil substrate supply and microbial community. Geoderma 359:113991
doi: 10.1016/j.geoderma.2019.113991
Xiao C, Yang L, Zhang L, Liu C, Han M (2016) Effects of cultivation ages and modes on microbial diversity in the rhizosphere soil of Panax ginseng. J Ginseng Res 40:28–37
pubmed: 26843819
doi: 10.1016/j.jgr.2015.04.004
Xu G, Peng J, Feng C, Fang F, Chen S, Xu Y, Wang X (2015) Evaluation of simultaneous autotrophic and heterotrophic denitrification processes and bacterial community structure analysis. Appl Microbiol Biotechnol 99:6527–6536
pubmed: 25825049
doi: 10.1007/s00253-015-6532-2
Yamaoka K, Nakagawa T, Uno T (1978) Application of Akaike’s information criterion (AIC) in the evaluation of linear pharmacokinetic equations. J Pharmacokinet Biopharm 6:165–175
pubmed: 671222
doi: 10.1007/BF01117450
Yang Q, Lei AP, Li FL, Liu LN, Zan QJ, Shin PK et al (2014) Structure and function of soil microbial community in artificially planted Sonneratia apetala and S. caseolaris forests at different stand ages in Shenzhen Bay China. Marine Pollution Bulletin 85:754–763
pubmed: 24629377
doi: 10.1016/j.marpolbul.2014.02.024
Yao Q, Li Z, Song Y, Wright SJ, Guo X, Tringe SG et al (2018) Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil. Nature Ecology & Evolution 2:499–509
doi: 10.1038/s41559-017-0463-5
Zeng J, Liu X, Song L, Lin X, Zhang H, Shen C, Chu H (2016) Nitrogen fertilization directly affects soil bacterial diversity and indirectly affects bacterial community composition. Soil Biol Biochem 92:41–49
doi: 10.1016/j.soilbio.2015.09.018
Zhang C, Song Z, Zhuang D, Wang J, Xie S, Liu G (2019) 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
doi: 10.1007/s00374-019-01344-z
Zhang H, Wang J, Wang J, Guo Z, Wang GG, Zeng D, Wu T (2018) Tree stoichiometry and nutrient resorption along a chronosequence of Metasequoia glyptostroboides forests in coastal China. For Ecol Manage 430:445–450
doi: 10.1016/j.foreco.2018.08.037
Zhang W, Liu W, Hou R, Zhang L, Schmitz-Esser S, Sun H et al (2018) Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose. ISME J 12:1319–1328
pubmed: 29391488
pmcid: 5931968
doi: 10.1038/s41396-018-0051-y
Zhao Z-B, He J-Z, Quan Z, Wu C-F, Sheng R, Zhang L-M, Geisen S (2020) Fertilization changes soil microbiome functioning, especially phagotrophic protists, Soil Biology and Biochemistry: 107863
Zhong W, Gu T, Wang W, Zhang B, Lin X, Huang Q, Shen W (2009) The effects of mineral fertilizer and organic manure on soil microbial community and diversity. Plant Soil 326:511–522
doi: 10.1007/s11104-009-9988-y
Zhu L, Wu Q, Deng C, Zhang M, Zhang C, Chen H et al (2018) Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes. Environ Microbiol 20:1711–1722
pubmed: 29528548
doi: 10.1111/1462-2920.14096