{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T06:09:41Z","timestamp":1789711781809,"version":"4.0.1"},"reference-count":19,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2024YFD1501500"],"award-info":[{"award-number":["2024YFD1501500"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Soil acidification poses a critical threat to global agricultural sustainability, particularly in high-buffering Mollisol (black soil) ecosystems. However, the microbially mediated biochemical mechanisms underlying nitrogen (N) transformation blockages and subsequent phytotoxicity under acid stress remain poorly understood. Here, using a controlled soil acidification gradient (pH 2.0\u20137.0) combined with 16S rRNA gene sequencing, functional profiling (FAPROTAX), quantitative PCR (qPCR), and chemical N speciation, we unravel a key microbially driven mechanism governing acid-induced crop failure. Our findings demonstrate that soil acidification imposes strong deterministic environmental filtering (\u03b2NTI approaching +2) on the rhizosphere microbiome, driving a drastic collapse in microbial phylogenetic diversity (Chao1 index). This structural transition severely alters N-cycling functional guilds, inducing a profound functional bottleneck. In strong acid treatments (pH 2.0\u20134.0), ammonium (NH\n                    <jats:sub>4<\/jats:sub>\n                    <jats:sup>+<\/jats:sup>\n                    ) and nitrate (NO\n                    <jats:sub>3<\/jats:sub>\n                    <jats:sup>\u2013<\/jats:sup>\n                    ) concentrations plummeted to 0.25-fold and 0.20-fold of those in circumneutral soils, respectively. Crucially, nitrite (NO\n                    <jats:sub>2<\/jats:sub>\n                    <jats:sup>\u2013<\/jats:sup>\n                    -N) underwent a 5.85-fold hyper-accumulation, reaching up to 28.52 mg kg\n                    <jats:sup>\u20131<\/jats:sup>\n                    . At the molecular level, this accumulation was driven by a transcriptional and functional decoupling between nitrifying cohorts: while ammonia oxidation genes (\n                    <jats:italic>amoA\/amoB<\/jats:italic>\n                    in\n                    <jats:italic>AOA<\/jats:italic>\n                    and\n                    <jats:italic>AOB<\/jats:italic>\n                    ) were upregulated or sustained under acidity, nitrite oxidoreductase (\n                    <jats:italic>NxrC<\/jats:italic>\n                    ) expression and gaseous denitrification pathways were almost completely suppressed. To decouple nitrite phytotoxicity from direct proton (H\n                    <jats:sup>+<\/jats:sup>\n                    ) stress, exogenous sodium nitrite (NaNO\n                    <jats:sub>2<\/jats:sub>\n                    ) was spiked into neutral soil (pH 7.0) matching the acidification gradient (1.75\u201328.52 mg kg\n                    <jats:sup>\u20131<\/jats:sup>\n                    ; M7\u2013M2). Dose-response validation revealed that NO\n                    <jats:sub>2<\/jats:sub>\n                    <jats:sup>\u2013<\/jats:sup>\n                    -N exceeding 13.21 mg kg\n                    <jats:sup>\u20131<\/jats:sup>\n                    exerted severe phytotoxicity, significantly inhibiting maize germination, leaf area, and height, with total plant mortality occurring at \u226527.78 mg kg\n                    <jats:sup>\u20131<\/jats:sup>\n                    NO\n                    <jats:sub>2<\/jats:sub>\n                    <jats:sup>\u2013<\/jats:sup>\n                    -N. Collectively, this study establishes that acid-induced functional decoupling of the nitrifying community causes a massive NO\n                    <jats:sub>2<\/jats:sub>\n                    <jats:sup>\u2013<\/jats:sup>\n                    -N accumulation, acting as an relatively overlooked, independent phytotoxic driver of crop failure in acidified soils. These insights demonstrate that restoring acidified agroecosystems requires shifting from simple pH neutralization to integrated microbiome management aimed at relieving N-transformation bottlenecks.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1830432","type":"journal-article","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T05:38:14Z","timestamp":1789709894000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Soil acidification drives a massive accumulation of nitrite as a mechanistic bottleneck to inhibit maize growth and productivity"],"prefix":"10.3389","volume":"17","author":[{"given":"Hang","family":"Luo","sequence":"first","affiliation":[{"name":"National Biochar Institute of Shenyang Agricultural University","place":["Shenyang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Di","family":"Xu","sequence":"additional","affiliation":[{"name":"National Biochar Institute of Shenyang Agricultural University","place":["Shenyang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifan","family":"Wang","sequence":"additional","affiliation":[{"name":"National Biochar Institute of Shenyang Agricultural University","place":["Shenyang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianyi","family":"He","sequence":"additional","affiliation":[{"name":"National Biochar Institute of Shenyang Agricultural University","place":["Shenyang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Biochar Institute of Shenyang Agricultural University","place":["Shenyang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Jiang","sequence":"additional","affiliation":[{"name":"National Biochar Institute of Shenyang Agricultural University","place":["Shenyang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"E.","sequence":"additional","affiliation":[{"name":"National Biochar Institute of Shenyang Agricultural University","place":["Shenyang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haijun","family":"Hu","sequence":"additional","affiliation":[{"name":"Zunyi Normal College","place":["Zunyi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenfu","family":"Chen","sequence":"additional","affiliation":[{"name":"National Biochar Institute of Shenyang Agricultural University","place":["Shenyang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,18]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1080\/07388551.2021.1874282","article-title":"Aluminum toxicity and aluminum stress-induced physiological tolerance responses in higher plants.","volume":"41","author":"Chauhan","year":"2021","journal-title":"Crit. 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Total Environ"},{"key":"B4","doi-asserted-by":"publisher","first-page":"108349","DOI":"10.1016\/j.soilbio.2021.108349","article-title":"Long-term excess nitrogen fertilizer increases sensitivity of soil microbial community to seasonal change revealed by ecological network and metagenome analyses.","volume":"160","author":"Li","year":"2021","journal-title":"Soil Biol. Biochem."},{"key":"B5","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1016\/j.pedsph.2024.06.011","article-title":"Soil degradation: A global threat to sustainable use of black soils.","volume":"35","author":"Li","year":"2025","journal-title":"Pedosphere"},{"key":"B6","doi-asserted-by":"publisher","first-page":"3453","DOI":"10.1016\/j.jia.2026.01.016","article-title":"A zoning-based machine learning framework for accurate soil organic matter prediction across mollisol and non-mollisol regions.","volume":"25","author":"Li","year":"2026","journal-title":"J. Integr. 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Chang Biol"},{"key":"B16","doi-asserted-by":"publisher","first-page":"1450","DOI":"10.1016\/j.scib.2026.01.049","article-title":"Impervious surface increase over global border areas regulated by population and topography.","volume":"71","author":"Xiao","year":"2026","journal-title":"Sci. Bull"},{"key":"B17","first-page":"562","article-title":"Research progresses on soil acidification and its effects on soil microorganism-crop systems in agricultural soil.","volume":"55","author":"Xu","year":"2024","journal-title":"Chin. J. Soil Sci."},{"key":"B18","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1038\/nature15743","article-title":"Managing nitrogen for sustainable development.","volume":"528","author":"Zhang","year":"2015","journal-title":"Nature"},{"key":"B19","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1016\/j.baae.2025.12.002","article-title":"Differential responses of soil micro-food web components to global change factors: A meta-analysis.","volume":"90","author":"Zhou","year":"2026","journal-title":"Basic Appl. 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