Abstract
The ability of non-nodulating pioneer plants on newly exposed glacial till to obtain atmospheric N2 was investigated using both acetylene reduction assay (ARA) and 15N2 gas incorporation methods. Plant tissues were also examined for the presence of endophytic diazotrophic bacteria using high-throughput nifH amplification sequencing. Both ARA and 15N2 gas incorporation demonstrated that non-nodulating pioneer plants can obtain atmospheric N2, but the amount was highly variable depending on the plant organ, with clearly higher values in leaves relative to twigs and roots. High-throughput amplification sequencing of nifH genes indicated that a great variety of diazotrophic communities developed in pioneer plant tissues under primary succession. The N2 fixation rate (based on both 15N2 incorporation and ARA) was not directly linked to the abundance of any specific diazotrophs, but was correlated with the Chao1 index and the number of observed species, suggesting that different diazotrophs jointly accounted for N2 fixation activity. Our results highlight that non-nodulating pioneer plants may acquire N through endophytic N2-fixing bacteria as a supplement for other potential N sources in oligotrophic environments in early stages of primary succession following glacier retreat.
Similar content being viewed by others
Data availability
The datasets generated and analyzed during this study are included in the supplementary material.
References
Adams MA, Turnbull TL, Sprent JI, Buchmann N (2016) Legumes are different: leaf nitrogen, photosynthesis, and water use efficiency. Proc Nat Acad Sci USA 113:4098–4103. https://doi.org/10.1073/pnas.1523936113
Bal A, Chanway CP (2012) Evidence of nitrogen fixation in lodgepole pine inoculated with diazotrophic Paenibacillus polymyxa. Botany 90:891–896. https://doi.org/10.1139/B2012-044
Bal A, Anand R, Berge O, Chanway CP (2012) Isolation and identification of diazotrophic bacteria from internal tissues of Pinus contorta and Thuja plicata. Can J for Res 42:807–813. https://doi.org/10.1139/x2012-023
Binkley D, Cromack KJ, Baker DD (1994) Nitrogen fixation by red alder: biology, rates, and controls. In: Hibbs DE, DeBell DS, Tarrant RF (eds) The biology and management of red alder. Oregon State University Press, Corvallis, USA, pp 57–72
Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Caporaso JG (2018) Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6:90. https://doi.org/10.1186/s40168-018-0470-z
Bolyen E, Rideout JR, Dillon MR et al (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852–857. https://doi.org/10.1038/s41587-019-0209-9
Brankatschk R, Töwe S, Kleineidam K, Schloter M, Zeyer J (2011) Abundances and potential activities of nitrogen cycling microbial communities along a chronosequence of a glacier forefield. ISME J 5:1025–1037. https://doi.org/10.1038/ismej.2010.184
Buma B, Bisbing S, Krapek J, Wright G (2017) A foundation of ecology rediscovered: 100 years of succession on the William S. Cooper plots in Glacier Bay. Alaska Ecology 98:1513–1523. https://doi.org/10.1002/ecy.1848
Caccianiga M, Andreis C (2004) Pioneer herbaceous vegetation on glacier forelands in the Italian Alps. Phytocoenologia 34:55–89. https://doi.org/10.1111/j.0105-2896.2005.00266.x
Callahan BJ, Mcmurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP (2016) Dada2: high-resolution sample inference from Illumina amplicon data. Nat Method 13:581–583. https://doi.org/10.1038/nmeth.3869
Carrell AA, Frank AC (2014) Pinus flexilis and Picea engelmannii share a simple and consistent needle endophyte microbiota with a potential role in nitrogen fixation. Front Microbiol 5:333. https://doi.org/10.3389/fmicb.2014.00333
Chapin FS, Walker LR, Fastie CL, Sharman LC (1994) Mechanisms of primary succession following deglaciation at Glacier Bay, Alaska. Ecol Monog 64:149–175. https://doi.org/10.2307/2937039
Chapman WK, Paul L (2012) Evidence that northern pioneering pines with tuberculate mycorrhizae are unaffected by varying soil nitrogen levels. Micro Ecol 64:964–972. https://doi.org/10.1007/s00248-012-0076-0
Cohjo EH, Reis VM, Schenberg AC, Dobereiner J (1993) Interactions of Acetobacter diazotrophicus with an amylolytic yeast in nitrogen-free batch culture. FEMS Microbiol Lett 106:23–31. https://doi.org/10.1111/j.1574-6968.1993.tb05986.x
Dabundo R, Lehmann MF, Treibergs L, Tobias CR, Altabet MA, Moisander PH, Granger J (2014) The contamination of commercial 15N2 gas stocks with 15N-labeled nitrate and ammonium and consequences for nitrogen fixation measurements. PLoS ONE 9:e110335. https://doi.org/10.1371/journal.pone.0110335
Dalton DA, Kramer S, Azios N, Fusaro S, Cahill E, Kennedy C (2004) Endophytic nitrogen fixation in dune grasses (Ammophila arenaria and Elymus mollis) from Oregon. FEMS Microbiol Ecol 49:469–479. https://doi.org/10.1016/j.femsec.2004.04.010
Doty SL, Dosher MR, Singleton GL, Moore AL, van Aken B, Stettler RF, Strand SE, Gordon MP (2005) Identification of an endophytic Rhizobium in stems of Populus. Symbiosis 39:27–35
Doty SL, Oakely B, Xin G, Kang JW, Singleton G, Khan Z, Vajzovic A, Staley JT (2009) Diazotrophic endophytes of native black cottonwood and willow. Symbiosis 47:23–33. https://doi.org/10.1007/BF03179967
Dutta RK, Agrawal M (2002) Effect of tree plantations on the soil characteristics and microbial activity of coal mine spoil land. Trop Ecol 43:315–324
Fulweiler RW, Heiss EM, Rogener MK, Newell SE, LeCleir GR, Kortebein SM, Wilhelm SW (2015) Examining the impact of acetylene on N-fixation and the active sediment microbial community. Front Microbiol 6:48. https://doi.org/10.3389/fmicb.2015.00418
Gaby JC, Buckley DH (2012) A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase. PLoS ONE 7:e42149. https://doi.org/10.1371/journal.pone.0042149
Gehlot HS, Tak N, Kaushik M, Mitra S, Chen W, Poweleit N, Panwar D, Poonar N, Parihar R, Tak A, Sankhla IS, Ojha A, Rao S, Simon M, Junior FBR, Perígolo N, Tripathi A, Sprent J, Young JP, James E, Gyaneshwar P (2013) An invasive Mimosa in India does not adopt the symbionts of its native relatives. Ann Bot 112:179–196. https://doi.org/10.1093/aob/mct112
Germaine K, Keogh E, Garcia-Cabellos G, Borremans B, van der Lelie D, Barac T, Oeyen L, Vangronsveld J, Fiona Moore P, Moore ERB, Campbell CD, Ryan D, Dowling DN (2004) Colonisation of poplar trees by gfp expressing bacterial endophytes. FEMS Microbiol Ecol 48:109–118. https://doi.org/10.1016/j.femsec.2003.12.009
Göransson H, Welc M, Bunemann EK, Christl I, Venterink HO (2016) Nitrogen and phosphorus availability at early stages of soil development in the Damma glacier forefield, Switzerland: implications for establishment of N2-fixing plants. Plant Soil 404:251–261. https://doi.org/10.1007/s11104-016-2821-5
Hardy RWF, Brown RC, Holsten RD (1973) Application of the acetylene-ethylene assay for measurement of nitrogen fixation. Soil Biol Biochem 5:47–81. https://doi.org/10.1016/0038-0717(73)90093-X
Hobbie EA, Macko SA, Shugart HH (1998) Patterns in N dynamics and N isotopes during primary succession in Glacier Bay, Alaska. Chem Geol 152:3–11. https://doi.org/10.1016/S0009-2541(98)00092-8
Hogh-Jensen H, Schjoerring JK (2000) Below-ground nitrogen transfer between different grassland species: direct quantification by N15 leaf feeding compared with indirect dilution of soil N15. Plant Soil 227:171–183. https://doi.org/10.1023/A:1026535401773
Hynes RK, Knowles R (1982) Effect of acetylene on autotrophic and heterotrophic nitrification. Can J Microbiol 28:334–340. https://doi.org/10.1139/m82-049
James EK (2000) Nitrogen fixation in endophytic and associative symbiosis. Field Crop Res 65:197–209. https://doi.org/10.1016/S0378-4290(99)00087-8
Jean M, Mack MC, Johnstone JF (2018) Spatial and temporal variation in moss-associated dinitrogen fixation in coniferous- and deciduous-dominated Alaskan boreal forests. Plant Ecol 219:837–851. https://doi.org/10.1007/s11258-018-0838-y
Kandel SL, Joubert PM, Doty SL (2017) Bacterial endophyte colonization and distribution within plants. Microorganisms 5:77. https://doi.org/10.3390/microorganisms5040077
Katoh K (2002) Mafft: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066. https://doi.org/10.1093/nar/gkf436
Keuter A, Veldkamp E, Corre MD (2014) Asymbiotic biological nitrogen fixation in a temperate grassland as affected by management practices. Soil Biol Biochem 70:38–46. https://doi.org/10.1016/j.soilbio.2013.12.009
Knoth JL, Kim S, Ettl GJ, Doty SL (2014) Biological nitrogen fixation and biomass accumulation within poplar clones as a result of inoculations with diazotrophic endophyte consortia. New Phytol 201:599–609. https://doi.org/10.1111/nph.12536
Koljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM et al (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22:5271–5277. https://doi.org/10.1111/mec.12481
Lammel DR, Cruz LM, Carrer H, Cardoso EJBN (2013) Diversity and symbiotic effectiveness of beta-rhizobia isolated from sub-tropical legumes of a Brazilian Araucaria forest. World J Microbiol Biotech 29:2335–2342. https://doi.org/10.1007/s11274-013-1400-7
Lee YY, Son Y (2005) Diurnal and seasonal patterns of nitrogen fixation in an Alnus hirsuta plantation of central Korea. J Plant Biol 48:332–337. https://doi.org/10.1007/BF03030531
Liu X, Wei S, Wang F, James EK, Guo X, Zagar C, Xia LG, Dong X, Wang YP (2012) Burkholderia and Cupriavidus spp. are the preferred symbionts of Mimosa spp. in southern China. FEMS Microbiol Ecol 80:417–426. https://doi.org/10.1111/j.1574-6941.2012.01310.x
Marrs RH, Roberts RD, Skeffington RA, Bradshaw AD (1983) Nitrogen and the development of ecosystems. In: Lee JA, McNeill S, Rorison IH (eds) Nitrogen as an ecological factor. Blackwell, Oxford, UK, pp 113–136
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet 17:1–10. https://doi.org/10.14806/ej.17.1.200
Morris MR, Standford JA (2011) Floodplain succession and soil nitrogen accumulation on a salmon river in southwestern Kamchatka. Ecol Monogr 81:43–61. https://doi.org/10.1890/08-2296.1
Moyes AB, Kueppers LM, Pett-Ridge J, Carper DL, Vandehey N, O’Neil J, Frank AC (2016) Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer. New Phytol 210:657–668. https://doi.org/10.1111/nph.13850
Myrold DD, Ruess RW, Klug P (1999) Dinitrogen fixation. In: Robertson GP (ed) Standard soil methods for long-term ecological research. Oxford University Press, Oxford, UK, pp 241–256
Nasto MK, Alvarez-Clare S, Lekberg Y, Sullivan BW, Townsend AR, Cleveland CC (2014) Interactions among nitrogen fixation and soil phosphorus acquisition strategies in lowland tropical rain forests. Ecol Lett 17:1282–1289. https://doi.org/10.1111/ele.12335
Padda KP, Puri A, Chanway CP (2016) Plant growth promotion and nitrogen fixation in canola by an endophytic strain of Paenibacillus polymyxa and its GFP-tagged derivative in a long-term study. Botany 94:1209–1217. https://doi.org/10.1139/cjb-2016-0075
Padda KP, Puri A, Chanway CP (2018) Isolation and identification of endophytic diazotrophs from lodgepole pine trees growing at unreclaimed gravel mining pits in central interior British Columbia, Canada. Can J for Res 48:1601–1606. https://doi.org/10.1139/cjfr-2018-0347
Padda KP, Puri A, Chanway C (2019) Endophytic nitrogen fixation – a possible ‘hidden’ source of nitrogen for lodgepole pine trees growing at unreclaimed gravel mining sites. FEMS Microbial Ecol 95:fiz172. https://doi.org/10.1016/0038-0717(83)90071-8
Postgate J (1998) Nitrogen fixation, 3rd edn. Cambridge University Press, Cambridge, UK
Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650. https://doi.org/10.1093/molbev/msp077
Primieri S, Costa MD, Stroschein MRD, Stocco P, Santos JCP, Antunes PM (2016) Variability in symbiotic effectiveness of N2 fixing bacteria in Mimosa scabrella. Appl Soil Ecol 102:19–25. https://doi.org/10.1016/j.apsoil.2016.01.018
Puri A, Padda KP, Chanway CP (2018) Evidence of endophytic diazotrophic bacteria in lodgepole pine and hybrid white spruce trees growing in soils with different nutrient statuses in the West Chilcotin region of British Columbia, Canada. For Ecol Manag 430:558–565. https://doi.org/10.1016/j.foreco.2018.08.049
Puri A, Padda KP, Chanway CP (2020) In vitro and in vivo analyses of plant-growth-promoting potential of bacteria naturally associated with spruce trees growing on nutrient-poor soils. Appl Soil Ecol 149:103538. https://doi.org/10.1016/j.apsoil.2020.103538
Puri A, Padda KP, Chanway CP (2017) Plant growth promotion by endophytic bacteria in nonnative crop hosts. In: Maheshwari D, Annapurna K (eds) Endophytes: crop productivity and protection. Springer, Cham, Switzerland, pp 11–45
Reinhold-Hurek B, Hurek T (2011) Living inside plants: bacterial endophytes. Curr Opin Plant Biol 14:435–443. https://doi.org/10.1016/j.pbi.2011.04.004
Reiter B, Bürgmann H, Burg K, Sessit A (2003) Endophytic nifH gene diversity in African sweet potato. Can J Microbio 49:549–555. https://doi.org/10.1139/W03-070
Rousk K, Sorensen PL, Michelsen A (2016) Nitrogen transfer from four nitrogen fixer associations to plants and soils. Ecosystems 19:1491–1504. https://doi.org/10.1007/s10021-016-0018-7
Saiz E, Sgouridis F, Drijfhout FP, Ullah S (2019) Biological nitrogen fixation in peatlands: comparison between acetylene reduction assay and 15N2 assimilation methods. Soil Biol Biochem 131:157–165. https://doi.org/10.1016/j.soilbio.2019.01.011
Severin I, Stal LJ (2010) NifH expression by five groups of phototrophs compared with nitrogenase activity in coastal microbial mats. FEMS Microbiol Ecol 73:55–67. https://doi.org/10.1111/j.1574-6941.2010.00875.x
Sevilla M, Kennedy C (2000) Genetic analysis of nitrogen fixation and plant-growth stimulating properties of Acetobacter diazotrophicus, an endophyte of sugarcane. In: Triplett EW (ed) Prokaryotic nitrogen fixation: a model system for the analysis of a biological process. Horizon Scientific Press, Wymondham, UK, pp 737–760
Silvester WB, Sollins P, Verhoeven T, Cline SP (1982) Nitrogen fixation and acetylene reduction in decaying conifer boles: effects of incubation time, aeration, and moisture content. Can J for Res 12:646–652. https://doi.org/10.1139/x82-098
Smercina DN, Evans SE, Friesen ML, Tiemann LK (2019) Optimization of the 15N2 incorporation and acetylene reduction methods for free-living nitrogen fixation. Plant Soil 445:595–611. https://doi.org/10.1007/s11104-019-04307-3
Soper FM, Simon C, Jauss V (2021) Measuring nitrogen fixation by the acetylene reduction assay (ARA): is 3 the magic ratio? Biogeochemistry 152:345–351. https://doi.org/10.1007/s10533-021-00761-3
Soper FM, Taylor BN, Winbourne JB, Wong MY, Dynarski KA, Reis CRG, Peoples MB, Cleveland CC, Reed SC, Menge DNL, Perakis SS (2021) A roadmap for sampling and scaling biological nitrogen fixation in terrestrial ecosystems. Methods Ecol Evol 12:1122–1137. https://doi.org/10.1111/2041-210X.13586
Steinaker DF, Wilson SD (2008) Phenology of fine roots and leaves in forest and grassland. J Ecol 96:1222–1229. https://doi.org/10.1111/j.1365-2745.2008.01439.x
Takahashi S, Okada N, Nobuchi T (2013) Relationship between the timing of vessel formation and leaf phenology in ten ring-porous and diffuse-porous deciduous tree species. Ecol Res 28:615–624. https://doi.org/10.1007/s11284-013-1053-x
Uliassi DD, Ruess RW (2002) Limitations to symbiotic nitrogen fixation in primary succession on the Tanana river floodplain. Ecology 83:88–103. https://doi.org/10.1890/0012-9658(2002)083[0088:LTSNFI]2.0.CO;2
Van Berkum P, Bohlool BB (1980) Evaluation of nitrogen fixation by bacteria in association with roots of tropical grasses. Microbiol Rev 44:491–517. https://doi.org/10.1128/mr.44.3.491-517.1980
Vitousek PM, Howarth RW (1991) Nitrogen limitation on land and in the sea: how can it occur? Biogeochemistry 13:87–115. https://doi.org/10.1007/BF00002772
Walker LR, Wardle DA (2014) Plant succession as an integrator of contrasting ecological time scales. Trends Ecol Evol 29:504–510. https://doi.org/10.1016/j.tree.2014.07.002
Walker LR, Clarkson B, Silvester WB, Clarkson BR (2003) Colonization dynamics and facilitative impacts of a nitrogen-fixing shrub in primary succession. J Veg Sci 14:277–290. https://doi.org/10.1111/j.1654-1103.2003.tb02153.x
White AE, Granger J, Selden C, Gradoville MR, Potts L, Bourbonnais A, Fulweiler RW, Knapp AN, Mohr W, Moisander PH, Tobias CR, Caffin M, Wilson ST, Benavides M, Bonnet S, Mulholland MR, Chang BX (2020) A critical review of the 15N2 tracer method to measure diazotrophic production in pelagic ecosystems. Limn Oceanogr Meth 18:129–147. https://doi.org/10.1002/lom3.10353
Zackrisson O, DeLuca TH, Gentili F, Sellstedt A, Jäderlund A (2009) Nitrogen fixation in mixed Hylocomium splendens moss communities. Oecologia 160:309–319. https://doi.org/10.1007/s00442-009-1299-8
Zhang B, Penton CR, Xue C, Wang Q, Zheng T, Tiedje JM (2015) Evaluation of the Ion Torrent Personal Genome Machine for gene-targeted studies using amplicons of the nitrogenase gene nifH. Appl Environ Microbiol 81:4536–4545. https://doi.org/10.1128/aem.00111-15
Zhang J, Luo J, DeLuca TH, Wang G, Sun S, Sun X, Hu Z, Zhang W (2021) Biogeochemical stoichiometry of soil and plant functional groups along a primary successional gradient following glacial retreat on the eastern Tibetan plateau. Global Ecol Conserv 26:e01491. https://doi.org/10.1016/j.gecco.2021.e01491
Zhao LF, Xu YJ, Ma ZQ, Deng ZS, Shan CJ, Wei GH (2013) Colonization and plant growth promoting characterization of endophytic Pseudomonas chlororaphis strain Zong1 isolated from Sophora alopecuroides root nodules. Brazil J Microbiol 44:629–637. https://doi.org/10.1590/S1517-83822013000200043
Zhou J, Bing H, Wu Y, Sun H, Wang J (2018) Weathering of primary mineral phosphate in the early stages of ecosystem development in the Hailuogou Glacier foreland chronosequence. Eur J Soil Sci 69:450–461. https://doi.org/10.1111/ejss.12536
Acknowledgements
The authors appreciate the support of the Alpine Ecosystem Observation and Experiment Station of Mt. Gongga, CAS. This work was financed by the National Natural Science Foundation of China (grant number 41877347) and the Sichuan Science and Technology Program (grant number 2020JDJQ0004).
Author information
Authors and Affiliations
Contributions
S.S., T.H.D., and G.W. planned and designed the research. J.Z., Z.H., X.S., W.W., and W.Z. performed experiments, conducted field work, and analyzed data. S.S. wrote the first draft of the manuscript and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.
Corresponding author
Additional information
Publisher's note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Sun, S., DeLuca, T.H., Zhang, J. et al. Evidence of endophytic nitrogen fixation as a potential mechanism supporting colonization of non-nodulating pioneer plants on a glacial foreland. Biol Fertil Soils 58, 527–539 (2022). https://doi.org/10.1007/s00374-022-01640-1
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00374-022-01640-1