Harrison PA, Berry PM, Simpson G, Haslett JR, Blicharska M, Bucur M, Dunford R, Egoh B, Garcia-Llorente M, Geamănă N, et al. Linkages between biodiversity attributes and ecosystem services: a systematic review. Ecosyst Serv. 2014;9:191–203.
Article
Google Scholar
Yachi S, Loreau M. Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proc Natl Acad Sci. 1999;96:1463.
Article
CAS
Google Scholar
Naeem S, Li S. Biodiversity enhances ecosystem reliability. Nature. 1997;390:507–9.
Article
CAS
Google Scholar
Walker BH. Biodiversity and ecological redundancy. Conserv Biol. 1992;6:18–23.
Article
Google Scholar
Brook BW, Sodhi NS, Bradshaw CJA. Synergies among extinction drivers under global change. Trends Ecol Evol. 2008;23:453–60.
Article
Google Scholar
Bellard C, Leclerc C, Courchamp F. Combined impacts of global changes on biodiversity across the USA. Sci Rep. 2015;5:11828.
Article
CAS
Google Scholar
Jordan WR, Peters RL, Allen EB. Ecological restoration as a strategy for conserving biological diversity. Environ Manag. 1988;12:55–72.
Article
Google Scholar
Fox JE, Gulledge J, Engelhaupt E, Burow ME, McLachlan JA. Pesticides reduce symbiotic efficiency of nitrogen-fixing rhizobia and host plants. Proc Natl Acad Sci. 2007;104:10282.
Article
CAS
Google Scholar
Ramirez KS, Craine JM, Fierer N. Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Glob Change Biol. 2012;18:1918–27.
Article
Google Scholar
Leff JW, Jones SE, Prober SM, Barberán A, Borer ET, Firn JL, Harpole WS, Hobbie SE, Hofmockel KS, Knops JMH, et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc Natl Acad Sci. 2015;112:10967.
Article
CAS
Google Scholar
Chambers CA, Smith SE, Smith FA. Effects of ammonium and nitrate ions on mycorrhizal infection, nodulation and growth of Trifolium subterraneum. New Phytol. 1980;85:47–62.
Article
CAS
Google Scholar
van Diepen LTA, Lilleskov EA, Pregitzer KS, Miller RM. Simulated nitrogen deposition causes a decline of intra- and extraradical abundance of arbuscular mycorrhizal fungi and changes in microbial community structure in northern hardwood forests. Ecosystems. 2010;13:683–95.
Article
Google Scholar
Young IM, Ritz K. Tillage, habitat space and function of soil microbes. Soil Tillage Res. 2000;53:201–13.
Article
Google Scholar
Kabir Z. Tillage or no-tillage: Impact on mycorrhizae. Can J Plant Sci. 2005;85:23–9.
Article
Google Scholar
Riedo J, Wettstein FE, Rösch A, Herzog C, Banerjee S, Büchi L, Charles R, Wächter D, Martin-Laurent F, Bucheli TD, et al. Widespread occurrence of pesticides in organically managed agricultural soils—the ghost of a conventional agricultural past? Environ Sci Technol. 2021;55:2919–28.
Article
CAS
Google Scholar
Stein LY, Klotz MG. The nitrogen cycle. Curr Biol. 2016;26:R94–8.
Article
CAS
Google Scholar
Hachiya T, Sakakibara H. Interactions between nitrate and ammonium in their uptake, allocation, assimilation, and signaling in plants. J Exp Bot. 2017;68:2501–12.
CAS
Google Scholar
Zhu Y, Qi B, Hao Y, Liu H, Sun G, Chen R, Song S. Appropriate NH4+/NO3− ratio triggers plant growth and nutrient uptake of flowering Chinese cabbage by optimizing the pH value of nutrient solution. Front Plant Sci. 2021;12:656144.
Article
Google Scholar
Beeckman F, Motte H, Beeckman T. Nitrification in agricultural soils: impact, actors and mitigation. Curr Opin Biotechnol. 2018;50:166–73.
Article
CAS
Google Scholar
Galloway JN, Aber JD, Erisman JW, Seitzinger SP, Howarth RW, Cowling EB, Cosby BJ. The nitrogen cascade. Bioscience. 2003;53:341–56.
Article
Google Scholar
Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, et al. Complete nitrification by Nitrospira bacteria. Nature. 2015;528:504–9.
Article
CAS
Google Scholar
van Kessel MAHJ, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJM, Kartal B, Jetten MSM, Lücker S. Complete nitrification by a single microorganism. Nature. 2015;528:555–9.
Article
Google Scholar
Laudick J. Microbial biostimulants in organic farming systems: patterns of current use and an investigation of their efficacy in different soil environments. The Ohio State University. 2017.
Isbell S, Fleishman S, Cloutier M, Kaminsky L, Borrelli K, Bell T: Management of soil microbes on organic farms. eOrganic. 2021;34646. http://eorganic.org/node/34646.
Kaminsky LM, Trexler RV, Malik RJ, Hockett KL, Bell TH. The inherent conflicts in developing soil microbial inoculants. Trends Biotechnol. 2019;37:140–51.
Article
CAS
Google Scholar
King WL, Bell TH. Can dispersal be leveraged to improve microbial inoculant success? Trends Biotechnol. 2022;40:12–21.
Article
CAS
Google Scholar
Hijri M. Analysis of a large dataset of mycorrhiza inoculation field trials on potato shows highly significant increases in yield. Mycorrhiza. 2016;26:209–14.
Article
Google Scholar
King WL, Kaminsky LM, Richards SC, Bradley BA, Kaye JP, Bell TH. Farm-scale differentiation of active microbial colonizers. ISME Commun. 2022;2:39.
Article
Google Scholar
Fuentes S, van Nood E, Tims S, Heikamp-de Jong I, ter Braak CJF, Keller JJ, Zoetendal EG, de Vos WM. Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection. ISME J. 2014;8:1621–33.
Article
Google Scholar
Wubs ERJ, van der Putten WH, Bosch M, Bezemer TM. Soil inoculation steers restoration of terrestrial ecosystems. Nat Plants. 2016;2:16107.
Article
Google Scholar
Calderón K, Spor A, Breuil M-C, Bru D, Bizouard F, Violle C, Barnard RL, Philippot L. Effectiveness of ecological rescue for altered soil microbial communities and functions. ISME J. 2017;11:272–83.
Article
Google Scholar
Garland JL, Lehman RM. Dilution/extinction of community phenotypic characters to estimate relative structural diversity in mixed communities. FEMS Microbiol Ecol. 1999;30:333–43.
Article
CAS
Google Scholar
King WL, Kaminsky LM, Gannett M, Thompson GL, Kao-Kniffin J, Bell TH. Soil salinization accelerates microbiome stabilization in iterative selections for plant performance. New Phytol. 2022;234:2101–10.
Article
CAS
Google Scholar
Trivedi C, Delgado-Baquerizo M, Hamonts K, Lai K, Reich PB, Singh BK. Losses in microbial functional diversity reduce the rate of key soil processes. Soil Biol Biochem. 2019;135:267–74.
Article
CAS
Google Scholar
Kaye J, Finney D, White C, Bradley B, Schipanski M, Alonso-Ayuso M, Hunter M, Burgess M, Mejia C. Managing nitrogen through cover crop species selection in the U.S. mid-Atlantic. PLoS ONE. 2019;14:e0215448.
Article
CAS
Google Scholar
Sims GK, Ellsworth TR, Mulvaney RL. Microscale determination of inorganic nitrogen in water and soil extracts. Commun Soil Sci Plant Anal. 1995;26:303–16.
Article
CAS
Google Scholar
Doane TA, Horwáth WR. Spectrophotometric determination of nitrate with a single reagent. Anal Lett. 2003;36:2713–22.
Article
CAS
Google Scholar
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.
Article
CAS
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
Article
CAS
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Article
CAS
Google Scholar
Kõljalg U, Larsson K-H, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, et al. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol. 2005;166:1063–8.
Article
Google Scholar
R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria; 2012.
Fox J, Weisberg S. An R companion to applied regression. 3rd ed. Thousand Oaks: Sage; 2019.
Google Scholar
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.
Article
CAS
Google Scholar
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin P, O'Hara B, Simpson G, Solymos P, Stevens H, Wagner H. Vegan: community ecology package. R Package Version 22-1 2015, 2:1-2.
Aphalo PJ. Learn R …as you learnt your mother tongue. Helsinki: Leanpub; 2016.
Google Scholar
Pereira-Marques J, Hout A, Ferreira RM, Weber M, Pinto-Ribeiro I, van Doorn L-J, Knetsch CW, Figueiredo C. Impact of host DNA and sequencing depth on the taxonomic resolution of whole metagenome sequencing for microbiome analysis. Front Microbiol. 2019;10:1277.
Article
Google Scholar
Andrews S: FastQC. A quality control tool for high throughput sequence data [Online]. vol. 2015. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32:3047–8.
Article
CAS
Google Scholar
Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.
Article
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Article
CAS
Google Scholar
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, et al. KBase: the United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol. 2018;36:566–9.
Article
CAS
Google Scholar
Freitas TAK, Li P-E, Scholz MB, Chain PSG. Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic Acids Res. 2015;43:e69–e69.
Article
Google Scholar
Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.
Article
CAS
Google Scholar
Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, Solden LM, Liu P, Narrowe AB, Rodríguez-Ramos J, Bolduc B, et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 2020;48:8883–900.
Article
CAS
Google Scholar
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics (Oxford, England). 2013;29:1072–5.
Article
CAS
Google Scholar
Fiegna F, Moreno-Letelier A, Bell T, Barraclough TG. Evolution of species interactions determines microbial community productivity in new environments. ISME J. 2015;9:1235–45.
Article
Google Scholar
Philippot L, Spor A, Hénault C, Bru D, Bizouard F, Jones CM, Sarr A, Maron P-A. Loss in microbial diversity affects nitrogen cycling in soil. ISME J. 2013;7:1609–19.
Article
CAS
Google Scholar
Griffiths BS, Ritz K, Wheatley R, Kuan HL, Boag B, Christensen S, Ekelund F, Sørensen SJ, Muller S, Bloem J. An examination of the biodiversity–ecosystem function relationship in arable soil microbial communities. Soil Biol Biochem. 2001;33:1713–22.
Article
CAS
Google Scholar
Klemedtsson L, Berg P, Clarholm M, Schnürer J, Rosswall T. Microbial nitrogen transformations in the root environment of barley. Soil Biol Biochem. 1987;19:551–8.
Article
CAS
Google Scholar
Downing AL. Relative effects of species composition and richness on ecosystem properties in ponds. Ecology. 2005;86:701–15.
Article
Google Scholar
Peter H, Beier S, Bertilsson S, Lindström ES, Langenheder S, Tranvik LJ. Function-specific response to depletion of microbial diversity. ISME J. 2011;5:351–61.
Article
CAS
Google Scholar
Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 2010;4:1340–51.
Article
Google Scholar
Barberan A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N. Continental-scale distributions of dust-associated bacteria and fungi. Proc Natl Acad Sci. 2015;112:5756–61.
Article
CAS
Google Scholar
Griffiths BS, Ritz K, Bardgett RD, Cook R, Christensen S, Ekelund F, Sørensen SJ, Bååth E, Bloem J, De Ruiter PC, et al. Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity–ecosystem function relationship. Oikos. 2000;90:279–94.
Article
Google Scholar
Singh BK, Quince C, Macdonald CA, Khachane A, Thomas N, Al-Soud WA, Sørensen SJ, He Z, White D, Sinclair A, et al. Loss of microbial diversity in soils is coincident with reductions in some specialized functions. Environ Microbiol. 2014;16:2408–20.
Article
Google Scholar
Wagg C, Bender SF, Widmer F, van der Heijden MGA. Soil biodiversity and soil community composition determine ecosystem multifunctionality. Proc Natl Acad Sci. 2014;111:5266–70.
Article
CAS
Google Scholar
Jiao S, Zhang B, Zhang G, Chen W, Wei G. Stochastic community assembly decreases soil fungal richness in arid ecosystems. Mol Ecol. 2021;30:4338–48.
Article
Google Scholar
Liu N, Hu H, Ma W, Deng Y, Wang Q, Luo A, Meng J, Feng X, Wang Z. Relative importance of deterministic and stochastic processes on soil microbial community assembly in temperate grasslands. Microorganisms. 1929;2021:9.
Google Scholar
Dini-Andreote F, Stegen JC, van Elsas JD, Salles JF. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc Natl Acad Sci. 2015;112:E1326.
Article
CAS
Google Scholar
Shi Y, Li Y, Xiang X, Sun R, Yang T, He D, Zhang K, Ni Y, Zhu Y-G, Adams JM, Chu H. Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain. Microbiome. 2018;6:27.
Article
Google Scholar
Aguilar P, Sommaruga R. The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time. Mol Ecol. 2020;29:3117–30.
Article
Google Scholar
Tripathi BM, Stegen JC, Kim M, Dong K, Adams JM, Lee YK. Soil pH mediates the balance between stochastic and deterministic assembly of bacteria. ISME J. 2018;12:1072–83.
Article
CAS
Google Scholar
Kaminsky LM, Esker PD, Bell TH. Abiotic conditions outweigh microbial origin during bacterial assembly in soils. Environ Microbiol. 2021;23:358–71.
Article
CAS
Google Scholar
Carbonetto B, Rascovan N, Álvarez R, Mentaberry A, Vázquez MP. Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas. PLoS ONE. 2014;9:e99949.
Article
Google Scholar
Berns AE, Philipp H, Narres HD, Burauel P, Vereecken H, Tappe W. Effect of gamma-sterilization and autoclaving on soil organic matter structure as studied by solid state NMR, UV and fluorescence spectroscopy. Eur J Soil Sci. 2008;59:540–50.
Article
CAS
Google Scholar
Swenson W, Wilson DS, Elias R. Artificial ecosystem selection. Proc Natl Acad Sci. 2000;97:9110.
Article
CAS
Google Scholar
Panke-Buisse K, Poole AC, Goodrich JK, Ley RE, Kao-Kniffin J. Selection on soil microbiomes reveals reproducible impacts on plant function. ISME J. 2015;9:980–9.
Article
CAS
Google Scholar