Nitrogen leaching owing to elevated acid deposition remains the main ecosystem threat worldwide. We aimed to contribute to the understanding of the highly variable nitrate losses observed in Europe after acid deposition retreat. Our study proceeded in adjacent beech and spruce forests undergoing acidification recovery and differing in nitrate leaching. We reconstructed soil microbial functional characteristics connected with nitrogen and carbon cycling based on community composition. Our results showed that in the more acidic spruce soil with high carbon content, where Acidobacteria and Actinobacteria were abundant (Proteo:Acido = 1.3), the potential for nitrate reduction and loss via denitrification was high (denitrification: dissimilative nitrogen reduction to ammonium (DNRA) = 3). In the less acidic beech stand with low carbon content, but high nitrogen availability, Proteobacteria were more abundant (Proteo:Acido = 1.6). Proportionally less nitrate could be denitrified there (denitrification:DNRA = 1), possibly increasing its availability. Among 10 potential keystone species, microbes capable of DNRA were identified in the beech soil while instead denitrifiers dominated in the spruce soil. In spite of the former acid deposition impact, distinct microbial functional guilds developed under different vegetational dominance, resulting in different N immobilization potentials, possibly influencing the ecosystem's nitrogen retention ability.

Czech Geological Survey Department of Environmental Geochemistry and Biogeochemistry Prague 118 21 Czech Republic

Department of Ecosystem Biology Faculty of Science University of South Bohemia Branišovská 31 370 05 České Budějovice Czech Republic

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Sci Rep. 2018 Mar 14;8(1):4754. doi: 10.1038/s41598-018-22998-z. PubMed

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Clark CM, et al. Environmental and plant community determinants of species loss following nitrogen enrichment. Ecol Lett. 2007;10:596–607. doi: 10.1111/j.1461-0248.2007.01053.x. PubMed DOI

Cleland EE, Harpole WS. Nitrogen enrichment and plant communities. Year in Ecology and Conservation Biology 2010. 2010;1195:46–61. PubMed

LeBauer DS, Treseder KK. Nitrogen limitation of net primary productivity in terrestrial ecosystems is globally distributed. Ecology. 2008;89:371–379. doi: 10.1890/06-2057.1. PubMed DOI

Kopacek J, et al. Nitrogen, organic carbon and sulphur cycling in terrestrial ecosystems: linking nitrogen saturation to carbon limitation of soil microbial processes. Biogeochemistry. 2013;115:33–51. doi: 10.1007/s10533-013-9892-7. DOI

Treseder KK. Nitrogen additions and microbial biomass: a meta-analysis of ecosystem studies. Ecology Letters. 2008;11:1111–1120. doi: 10.1111/j.1461-0248.2008.01230.x. PubMed DOI

Aber J, et al. Nitrogen saturation in temperate forest ecosystems - Hypotheses revisited. Bioscience. 1998;48:921–934. doi: 10.2307/1313296. DOI

Oulehle F, et al. Major changes in forest carbon and nitrogen cycling caused by declining sulphur deposition. Global Change Biology. 2011;17:3115–3129. doi: 10.1111/j.1365-2486.2011.02468.x. DOI

Evans CD, et al. Recovery from acidification in European surface waters. Hydrol Earth Syst Sc. 2001;5:283–297. doi: 10.5194/hess-5-283-2001. DOI

Tahovska K, et al. Microbial N immobilization is of great importance in acidified mountain spruce forest soils. Soil Biol Biochem. 2013;59:58–71. doi: 10.1016/j.soilbio.2012.12.015. DOI

Evans CD, et al. Evidence that soil carbon pool determines susceptibility of semi-natural ecosystems to elevated nitrogen leaching. Ecosystems. 2006;9:453–462. doi: 10.1007/s10021-006-0051-z. DOI

Taylor PG, Townsend AR. Stoichiometric control of organic carbon-nitrate relationships from soils to the sea. Nature. 2010;464:1178–1181. doi: 10.1038/nature08985. PubMed DOI

Graham, E. B. et al. Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes? Front Microbiol7, doi:10.3389/fmicb.2016.00214 (2016). PubMed PMC

Demoling F, Nilsson LO, Baath E. Bacterial and fungal response to nitrogen fertilization in three coniferous forest soils. Soil Biology & Biochemistry. 2008;40:370–379. doi: 10.1016/j.soilbio.2007.08.019. DOI

Hogberg MN, Baath E, Nordgren A, Arnebrant K, Hogberg P. Contrasting effects of nitrogen availability on plant carbon supply to mycorrhizal fungi and saprotrophs - a hypothesis based on field observations in boreal forest. New Phytologist. 2003;160:225–238. doi: 10.1046/j.1469-8137.2003.00867.x. PubMed DOI

Boot CM, Hall EK, Denef K, Baron JS. Long-term reactive nitrogen loading alters soil carbon and microbial community properties in a subalpine forest ecosystem. Soil Biol Biochem. 2016;92:211–220. doi: 10.1016/j.soilbio.2015.10.002. DOI

Frey SD, Knorr M, Parrent JL, Simpson RT. Chronic nitrogen enrichment affects the structure and function of the soil microbial community in temperate hardwood and pine forests. Forest Ecology and Management. 2004;196:159–171. doi: 10.1016/j.foreco.2004.03.018. DOI

Waldrop MP, Zak DR, Sinsabaugh RL, Gallo M, Lauber C. Nitrogen deposition modifies soil carbon storage through changes in microbial enzymatic activity. Ecological Applications. 2004;14:1172–1177. doi: 10.1890/03-5120. DOI

Knorr M, Frey SD, Curtis PS. Nitrogen additions and litter decomposition: a meta-analysis(vol 86, pg 3252, 2005) Ecology. 2008;89:888–888. doi: 10.1890/0012-9658(2008)89[888b:E]2.0.CO;2. DOI

Janssens IA, et al. Reduction of forest soil respiration in response to nitrogen deposition. Nat Geosci. 2010;3:315–322. doi: 10.1038/ngeo844. DOI

Ramirez KS, Craine JM, Fierer N. Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Global Change Biol. 2012;18:1918–1927. doi: 10.1111/j.1365-2486.2012.02639.x. DOI

Hagedorn F, Spinnler D, Siegwolf R. Increased N deposition retards mineralization of old soil organic matter. Soil Biol Biochem. 2003;35:1683–1692. doi: 10.1016/j.soilbio.2003.08.015. DOI

Boberg JB, Finlay RD, Stenlid J, Lindahl BD. Fungal C translocation restricts N-mineralization in heterogeneous environments. Functional Ecology. 2010;24:454–459. doi: 10.1111/j.1365-2435.2009.01616.x. DOI

Boberg, J. B., Finlay, R. D., Stenlid, J., Ekblad, A. & Lindahl, B. D. Nitrogen and Carbon Reallocation in Fungal Mycelia during Decomposition of Boreal Forest Litter. Plos One9, doi:10.1371/journal.pone.0092897 (2014). PubMed PMC

de Vries FT, Hoffland E, van Eekeren N, Brussaard L, Bloem J. Fungal/bacterial ratios in grasslands with contrasting nitrogen management. Soil Biol Biochem. 2006;38:2092–2103. doi: 10.1016/j.soilbio.2006.01.008. DOI

Schimel JP, Bennett J. Nitrogen mineralization: Challenges of a changing paradigm. Ecology. 2004;85:591–602. doi: 10.1890/03-8002. DOI

Ramirez KS, Lauber CL, Knight R, Bradford MA, Fierer N. Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology. 2010;91:3463–3470. doi: 10.1890/10-0426.1. PubMed DOI

Fierer N, et al. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. Isme J. 2012;6:1007–1017. doi: 10.1038/ismej.2011.159. PubMed DOI PMC

Campbell BJ, Polson SW, Hanson TE, Mack MC, Schuur EAG. The effect of nutrient deposition on bacterial communities in Arctic tundra soil. Environ Microbiol. 2010;12:1842–1854. doi: 10.1111/j.1462-2920.2010.02189.x. PubMed DOI

Davis KER, Sangwan P, Janssen PH. Acidobacteria, Rubrobacteridae and Chloroflexi are abundant among very slow-growing and mini-colony-forming soil bacteria. Environ Microbiol. 2011;13:798–805. doi: 10.1111/j.1462-2920.2010.02384.x. PubMed DOI

Roller BRK, Schmidt TM. The physiology and ecological implications of efficient growth. Isme J. 2015;9:1481–1487. doi: 10.1038/ismej.2014.235. PubMed DOI PMC

Oulehle F, Hofmeister J, Cudlin P, Hruska J. The effect of reduced atmospheric deposition on soil and soil solution chemistry at a site subjected to long-term acidification, Nacetin, Czech Republic. Sci Total Environ. 2006;370:532–544. doi: 10.1016/j.scitotenv.2006.07.031. PubMed DOI

Berge D, Fjeld E, Hindar A, Kaste O. Nitrogen retention in two Norwegian watercourses of different trophic status. Ambio. 1997;26:282–288.

Oulehle, F., Růžek, M., Tahovská, K., Bárta, J. & Myška, O. Carbon and Nitrogen Pools and Fluxes in Adjacent Mature Norway Spruce and European Beech Forests. Forests7 (2016).

Vance ED, Brookes PC, Jenkinson DS. An Extraction Method for Measuring Soil Microbial Biomass-C. Soil Biol Biochem. 1987;19:703–707. doi: 10.1016/0038-0717(87)90052-6. DOI

Brookes PC. Microbial Biomass and Activity Measurements in Soil. J Sci Food Agr. 1985;36:269–270. doi: 10.1002/jsfa.2740360407. DOI

Ste-Marie C, Pare D. Soil, pH and N availability effects on net nitrification in the forest floors of a range of boreal forest stands. Soil Biol Biochem. 1999;31:1579–1589. doi: 10.1016/S0038-0717(99)00086-3. DOI

Santruckova H, Tahovska K, Kopacek J. Nitrogen transformations and pools in N-saturated mountain spruce forest soils. Biology and Fertility of Soils. 2009;45:395–404. doi: 10.1007/s00374-008-0349-4. DOI

Manzoni S, Jackson RB, Trofymow JA, Porporato A. The global stoichiometry of litter nitrogen mineralization. Science. 2008;321:684–686. doi: 10.1126/science.1159792. PubMed DOI

Mooshammer, M., Wanek, W., Zechmeister-Boltenstern, S. & Richter, A. Stoichiometric imbalances between terrestrial decomposer communities and their resources: mechanisms and implications of microbial adaptations to their resources. Front Microbiol5, doi:10.3389/Fmicb.2014.00022 (2014). PubMed PMC

Barta J, Slajsova P, Tahovska K, Picek T, Santruckova H. Different temperature sensitivity and kinetics of soil enzymes indicate seasonal shifts in C, N and P nutrient stoichiometry in acid forest soil. Biogeochemistry. 2014;117:525–537. doi: 10.1007/s10533-013-9898-1. DOI

Leininger S, et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature. 2006;442:806–809. doi: 10.1038/nature04983. PubMed DOI

Muyzer G, Dewaal EC, Uitterlinden AG. Profiling of Complex Microbial-Populations by Denaturing Gradient Gel-Electrophoresis Analysis of Polymerase Chain Reaction-Amplified Genes-Coding for 16s Ribosomal-Rna. Appl Environ Microb. 1993;59:695–700. PubMed PMC

Yu Y, Lee C, Kim J, Hwang S. Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnology and Bioengineering. 2005;89:670–679. doi: 10.1002/bit.20347. PubMed DOI

Borneman J, Hartin RJ. PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microbiol. 2000;66:4356–4360. doi: 10.1128/AEM.66.10.4356-4360.2000. PubMed DOI PMC

Caporaso JG, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. P Natl Acad Sci USA. 2011;108:4516–4522. doi: 10.1073/pnas.1000080107. PubMed DOI PMC

Gardes M, Bruns TD. Its Primers with Enhanced Specificity for Basidiomycetes - Application to the Identification of Mycorrhizae and Rusts. Mol Ecol. 1993;2:113–118. doi: 10.1111/j.1365-294X.1993.tb00005.x. PubMed DOI

Caporaso JG, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–336. doi: 10.1038/nmeth.f.303. PubMed DOI PMC

Bengtsson-Palme J, et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol. 2013;4:914–919.

Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods10, 996-+, doi:10.1038/Nmeth.2604 (2013). PubMed

Quast C, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D596. doi: 10.1093/nar/gks1219. PubMed DOI PMC

Koljalg U, et al. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol. 2013;22:5271–5277. doi: 10.1111/mec.12481. PubMed DOI

Nguyen NH, et al. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 2016;20:241–248. doi: 10.1016/j.funeco.2015.06.006. DOI

Berry, D. & Widder, S. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front Microbiol5, doi:10.3389/fmicb.2014.00219 (2014). PubMed PMC

Weiss S, et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. Isme J. 2016;10:1669–1681. doi: 10.1038/ismej.2015.235. PubMed DOI PMC

Shannon P, et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research. 2003;13:2498–2504. doi: 10.1101/gr.1239303. PubMed DOI PMC

Faust, K. et al. Microbial Co-occurrence Relationships in the Human Microbiome. Plos Comput Biol8, doi:10.1371/journal.pcbi.1002606 (2012). PubMed PMC

Langille, M. G. I. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol31, 814-+, doi:10.1038/nbt.2676 (2013). PubMed PMC

Fish, J. A. et al. FunGene: the functional gene pipeline and repository. Front Microbiol4, doi:10.3389/Fmicb.2013.00291 (2013). PubMed PMC

Braak, C. J. F. t. & Smilauer, P. (2012).

McMurdie, P. J. & Holmes, S. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. Plos One8, doi:10.1371/journal.pone.0061217 (2013). PubMed PMC

Oulehle F, Hruska J. Tree species (Picea abies and Fagus sylvatica) effects on soil water acidification and aluminium chemistry at sites subjected to long-term acidification in the Ore Mts., Czech Republic. J Inorg Biochem. 2005;99:1822–1829. doi: 10.1016/j.jinorgbio.2005.06.008. PubMed DOI

Nacke, H. et al. Pyrosequencing-Based Assessment of Bacterial Community Structure Along Different Management Types in German Forest and Grassland Soils. Plos One6, doi:10.1371/journal.pone.0017000 (2011). PubMed PMC

Prescott CE, Grayston SJ. Tree species influence on microbial communities in litter and soil: Current knowledge and research needs. Forest Ecol Manag. 2013;309:19–27. doi: 10.1016/j.foreco.2013.02.034. DOI

Morrison EW, et al. Chronic nitrogen additions fundamentally restructure the soil fungal community in a temperate forest. Fungal Ecol. 2016;23:48–57. doi: 10.1016/j.funeco.2016.05.011. DOI

Tedersoo, L. et al. Global diversity and geography of soil fungi. Science346, 1078–+, doi:10.1126/science.1256688 (2014). PubMed

Hogberg MN, Hogberg P, Myrold DD. Is microbial community composition in boreal forest soils determined by pH, C-to-N ratio, the trees, or all three? Oecologia. 2007;150:590–601. doi: 10.1007/s00442-006-0562-5. PubMed DOI

Lauber CL, Hamady M, Knight R, Fierer N. Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale. Appl Environ Microb. 2009;75:5111–5120. doi: 10.1128/AEM.00335-09. PubMed DOI PMC

Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology. 2007;88:1354–1364. doi: 10.1890/05-1839. PubMed DOI

Reich PB, et al. Linking litter calcium, earthworms and soil properties: a common garden test with 14 tree species. Ecol Lett. 2005;8:811–818. doi: 10.1111/j.1461-0248.2005.00779.x. DOI

Hobbie, S. E. et al. Tree species effects on decomposition and forest floor dynamics in a common garden. Ecology87, 2288–2297, 10.1890/0012-9658(2006)87[2288:Tseoda]2.0.Co;2 (2006). PubMed

Kielak, A. M., Barreto, C. C., Kowalchuk, G. A., van Veen, J. A. & Kuramae, E. E. The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Front Microbiol7, doi:10.3389/fmicb.2016.00744 (2016). PubMed PMC

Navarrete, A. A. et al. Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon. Frontiers in Microbiology6, doi:10.3389/fmicb.2015.01443 (2015). PubMed PMC

Jones RT, et al. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. Isme Journal. 2009;3:442–453. doi: 10.1038/ismej.2008.127. PubMed DOI PMC

Padden AN, Rainey FA, Kelly DP, Wood AP. Xanthobacter tagetidis sp nov, an organism associated with Tagetes species and able to grow on substituted thiophenes. Int J Syst Bacteriol. 1997;47:394–401. doi: 10.1099/00207713-47-2-394. PubMed DOI

Oyaizumasuchi Y, Komagata K. Isolation of Free-Living Nitrogen-Fixing Bacteria from the Rhizosphere of Rice. J Gen Appl Microbiol. 1988;34:127–164. doi: 10.2323/jgam.34.127. DOI

Daniel H. Buckley, Varisa Huangyutitham, Tyrrell A. Nelson, Angelika Rumberger, and Janice E. Diversity of Planctomycetes in Soil in Relation to Soil History and Environmental Heterogeneity. Thies Appl. Environ. Microbiol.72(7), 4522–4531, doi:10.1128/AEM.00149-06 (2006). PubMed PMC

Elser JJ, Kyle M, Makino W, Yoshida T, Urabe J. Ecological stoichiometry in the microbial food web: a test of the light: nutrient hypothesis. Aquat Microb Ecol. 2003;31:49–65. doi: 10.3354/ame031049. DOI

Dedysh SN, et al. Bryocella elongata gen. nov., sp nov., a member of subdivision 1 of the Acidobacteria isolated from a methanotrophic enrichment culture, and emended description of Edaphobacter aggregans Koch et al. 2008. Int J Syst Evol Micr. 2012;62:654–664. doi: 10.1099/ijs.0.031898-0. PubMed DOI

Naether A, et al. Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils. Appl Environ Microb. 2012;78:7398–7406. doi: 10.1128/AEM.01325-12. PubMed DOI PMC

Cederlund H, et al. Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla. Appl Soil Ecol. 2014;84:62–68. doi: 10.1016/j.apsoil.2014.06.003. DOI

Hartman WH, Richardson CJ, Vilgalys R, Bruland GL. Environmental and anthropogenic controls over bacterial communities in wetland soils. P Natl Acad Sci USA. 2008;105:17842–17847. doi: 10.1073/pnas.0808254105. PubMed DOI PMC

Sun H, et al. Bacterial diversity and community structure along different peat soils in boreal forest. Appl Soil Ecol. 2014;74:37–45. doi: 10.1016/j.apsoil.2013.09.010. DOI

Schimel JP, Weintraub MN. The implications of exoenzyme activity on microbial carbon and nitrogen limitation in soil: a theoretical model. Soil Biology & Biochemistry. 2003;35:549–563. doi: 10.1016/S0038-0717(03)00015-4. DOI

Hansel CM, Fendorf S, Jardine PM, Francis CA. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl Environ Microb. 2008;74:1620–1633. doi: 10.1128/AEM.01787-07. PubMed DOI PMC

Evans CD, Monteith DT, Cooper DM. Long-term increases in surface water dissolved organic carbon: Observations, possible causes and environmental impacts. Environ Pollut. 2005;137:55–71. doi: 10.1016/j.envpol.2004.12.031. PubMed DOI

Goodale CL, Aber JD, Vitousek PM, McDowell WH. Long-term decreases in stream nitrate: Successional causes unlikely; Possible links to DOC? Ecosystems. 2005;8:334–337. doi: 10.1007/s10021-003-0162-8. DOI

Geisseler D, Horwath WR, Joergensen RG, Ludwig B. Pathways of nitrogen utilization by soil microorganisms - A review. Soil Biol Biochem. 2010;42:2058–2067. doi: 10.1016/j.soilbio.2010.08.021. DOI

Barta J, Melichova T, Vanek D, Picek T, Santruckova H. Effect of pH and dissolved organic matter on the abundance of nirK and nirS denitrifiers in spruce forest soil. Biogeochemistry. 2010;101:123–132. doi: 10.1007/s10533-010-9430-9. DOI

Yoon S, Cruz-Garcia C, Sanford R, Ritalahti KM, Loffler FE. Denitrification versus respiratory ammonification: environmental controls of two competing dissimilatory NO3-/NO2- reduction pathways in Shewanella loihica strain PV-4. Isme J. 2015;9:1093–1104. doi: 10.1038/ismej.2014.201. PubMed DOI PMC

Simon, A. et al. Exploiting the fungal highway: development of a novel tool for the in situ isolation of bacteria migrating along fungal mycelium. Fems Microbiol Ecol91, doi:10.1093/femsec/fiv116 (2015). PubMed

Multiple environmental factors, but not nutrient addition, directly affect wet grassland soil microbial community structure: a mesocosm study