{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T21:01:44Z","timestamp":1790283704305,"version":"4.1.0"},"reference-count":47,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Reducing synthetic nitrogen (N) fertilizer while maintaining soil fertility and crop productivity is a major challenge for sustainable rice production. Straw return has been widely adopted to enhance soil organic carbon (SOC) sequestration; however, the mechanisms by which reduced N input interacts with straw return to regulate SOC stabilization remain poorly understood. Here we evaluated graded N reduction (0, 20, and 30%) under continuous straw return in a nine-year rice-wheat double-cropping experiment in central China. Soil carbon pools, aggregate stability, organic carbon functional groups, and microbial community structure and function were assessed using carbon fractionation, wet-sieving, FTIR spectroscopy, and metagenomic analyses. We found that 20% N reduction (80%NR) maintained grain yield comparable to conventional N fertilization while significantly increasing readily oxidizable organic carbon (ROOC, +18\u201326%), water-soluble organic carbon (WSOC, +12\u201321%), microbial biomass carbon (MBC, +15\u201324%), and carbon management index (CMI, +42\u201358% relative to NR). Moderate N reduction also enhanced macroaggregate-associated SOC and the relative abundance of aliphatic and aromatic carbon functional groups. Metagenomic analyses revealed that 80%NR enriched Firmicutes (+26%), Actinobacteria (+50%), and Nitrospira, reduced methanogenic archaea, and triggered a metabolic shift from CO oxidation (coxL\/cutL, \u221215 to \u221222%) toward reductive carbon fixation via the Wood\u2013Ljungdahl pathway (hdrA2, +6 to +19%). In contrast, 30% N reduction (70%NR) undermined subsurface aggregate stability and eroded microbial functional diversity, identifying 20% N reduction as an optimal threshold within the tested gradients. These findings provide a mechanistic basis for optimizing nitrogen management in sustainable rice production systems.<\/jats:p>","DOI":"10.3389\/fmicb.2026.1928083","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T05:39:28Z","timestamp":1789364368000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["A 20% nitrogen reduction threshold optimizes soil carbon stability and microbial functional resilience under long-term straw return in a rice\u2013wheat rotation"],"prefix":"10.3389","volume":"17","author":[{"given":"Guohan","family":"Si","sequence":"first","affiliation":[{"name":"Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences; Hongshan Field Scientific Observation and Research Station, Ministry of Agriculture and Rural Affairs","place":["Wuhan, Hubei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huanqi","family":"Jiang","sequence":"additional","affiliation":[{"name":"Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences; Hongshan Field Scientific Observation and Research Station, Ministry of Agriculture and Rural Affairs","place":["Wuhan, Hubei, China"]},{"name":"College of Life Science, Yangtze University","place":["Jingzhou, Hubei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenglin","family":"Peng","sequence":"additional","affiliation":[{"name":"Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences; Hongshan Field Scientific Observation and Research Station, Ministry of Agriculture and Rural Affairs","place":["Wuhan, Hubei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dabing","family":"Xu","sequence":"additional","affiliation":[{"name":"Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences; Hongshan Field Scientific Observation and Research Station, Ministry of Agriculture and Rural Affairs","place":["Wuhan, Hubei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shujun","family":"Zhao","sequence":"additional","affiliation":[{"name":"Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences; Hongshan Field Scientific Observation and Research Station, Ministry of Agriculture and Rural Affairs","place":["Wuhan, Hubei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,14]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1417","DOI":"10.1111\/gcb.13980","article-title":"Nitrogen limitation of decomposition and decay: how can it occur?","volume":"24","author":"Averill","year":"2018","journal-title":"Glob. 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Total Environ."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1071\/ar9951459","article-title":"Soil carbon fractions based on their degree of oxidation, and the development of a carbon management index for agricultural systems","volume":"46","author":"Blair","year":"1995","journal-title":"Aust. J. Agric. Res."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"164347","DOI":"10.1016\/j.scitotenv.2023.164347","article-title":"Nitrogen input on organic amendments alters the pattern of soil-microbe-plant co-dependence","volume":"890","author":"Bossolani","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"5445","DOI":"10.1111\/gcb.16865","article-title":"Formation of soil organic carbon pool is regulated by the structure of dissolved organic matter and microbial carbon pump efficacy: a decadal study comparing different carbon management strategies","volume":"29","author":"Chen","year":"2023","journal-title":"Glob. Chang. Biol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"133","DOI":"10.3390\/agronomy13010133","article-title":"Effects of straw return with nitrogen fertilizer reduction on Rice (Oryza sativa L.) morphology, photosynthetic capacity, yield and water\u2013nitrogen use efficiency traits under different water regimes","volume":"13","author":"Chen","year":"2023","journal-title":"Agronomy"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"e70817","DOI":"10.1111\/gcb.70817","article-title":"Aligning nitrogen form with Rice preference through enhanced-efficiency fertilizers raises yield and cuts emissions","volume":"32","author":"Chen","year":"2026","journal-title":"Glob. Chang. Biol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"1229","DOI":"10.1038\/s41467-022-28715-9","article-title":"Fast-decaying plant litter enhances soil carbon in temperate forests but not through microbial physiological traits","volume":"13","author":"Craig","year":"2022","journal-title":"Nat. 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Manag."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"170497","DOI":"10.1016\/j.scitotenv.2024.170497","article-title":"Microbial mechanisms regulate soil organic carbon mineralization under carbon with varying levels of nitrogen addition in the above-treeline ecosystem","volume":"917","author":"Gaudel","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"124173","DOI":"10.1016\/j.jenvman.2025.124173","article-title":"Responses of soil respiration and its temperature sensitivity to nitrogen and phosphorus depositions in a riparian zone","volume":"374","author":"He","year":"2025","journal-title":"J. Environ. Manag."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"D277","DOI":"10.1093\/nar\/gkh063","article-title":"The KEGG resource for deciphering the genome","volume":"32","author":"Kanehisa","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. 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Manag."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"25296","DOI":"10.1007\/s11356-021-17239-2","article-title":"Differences in responses of ammonia volatilization and greenhouse gas emissions to straw return and paddy-upland rotations","volume":"29","author":"Liu","year":"2022","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref23","first-page":"539","volume-title":"Methods of Soil Analysis Part 2. Chemical and Microbial Properties","author":"Nelson","year":"1982"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"177408","DOI":"10.1016\/j.scitotenv.2024.177408","article-title":"Spatial and temporal evolution and factors influencing soil aggregate stability in the riparian zone during exposure: a case study of the water-level fluctuation zone of the three gorges reservoir, China","volume":"957","author":"Ni","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"ycae038","DOI":"10.1093\/ismeco\/ycae038","article-title":"Galactosamine and mannosamine are integral parts of bacterial and fungal extracellular polymeric substances","volume":"4","author":"Oliva","year":"2024","journal-title":"ISME Commun"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"168397","DOI":"10.1016\/j.scitotenv.2023.168397","article-title":"Assessing the allocations of exogenous N to the soil organic N pool in maize-wheat cropping using (15)N in situ labelling","volume":"908","author":"Ren","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"167463","DOI":"10.1016\/j.scitotenv.2023.167463","article-title":"Reevaluation and novel insights into amino sugar and neutral sugar necromass biomarkers in archaea, bacteria, fungi, and plants","volume":"906","author":"Salas","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"10235","DOI":"10.1038\/s41467-024-53762-9","article-title":"New-to-nature CO(2)-dependent acetyl-CoA assimilation enabled by an engineered B(12)-dependent acyl-CoA mutase","volume":"15","author":"Schulz-Mirbach","year":"2024","journal-title":"Nat. Commun."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"ycaf242","DOI":"10.1093\/ismeco\/ycaf242","article-title":"Vertically stratified carbon fixation and coupling processes in deep-sea sediment","volume":"5","author":"Shi","year":"2025","journal-title":"ISME Commun"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"126950","DOI":"10.1016\/j.jenvman.2025.126950","article-title":"Straw return and nitrogen-phosphorus fertilization coordinates crop yields, soil nutrient function and carbon emissions","volume":"393","author":"Song","year":"2025","journal-title":"J. Environ. Manag."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"114643","DOI":"10.1016\/j.jenvman.2022.114643","article-title":"Fate of Clostridia and other spore-forming Firmicute bacteria during feedstock anaerobic digestion and aerobic composting","volume":"309","author":"Subirats","year":"2022","journal-title":"J. Environ. Manag."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"127112","DOI":"10.1016\/j.jenvman.2025.127112","article-title":"Straw humification coefficient and its relation to soil carbon and nitrogen status","volume":"393","author":"Sun","year":"2025","journal-title":"J. Environ. Manag."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1016\/0038-0717(87)90052-6","article-title":"An extraction method for measuring soil microbial biomass C","volume":"19","author":"Vance","year":"1987","journal-title":"Soil Biol. Biochem."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1097\/00010694-193401000-00003","article-title":"An examination of the Degtjareff method for determining soil organic matter, and a proposed modification of the chromic acid titration method","volume":"37","author":"Walkley","year":"1934","journal-title":"Soil Sci."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"134784","DOI":"10.1016\/j.biortech.2026.134784","article-title":"Differential responses of selectively enriched comammox Nitrospira and ammonia-oxidizing bacteria to ammonia and copper starvation under contrasting dissolved oxygen conditions","volume":"455","author":"Wang","year":"2026","journal-title":"Bioresour. Technol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"162504","DOI":"10.1016\/j.scitotenv.2023.162504","article-title":"Soil extracellular enzyme stoichiometry reflects microbial metabolic limitations in different desert types of northwestern China","volume":"874","author":"Wang","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"25960","DOI":"10.1021\/acs.est.5c07865","article-title":"Synthetic microbial community promotes straw Humification and improves soil organic carbon in cropland","volume":"59","author":"Wang","year":"2025","journal-title":"Environ. Sci. Technol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"123675","DOI":"10.1016\/j.jenvman.2024.123675","article-title":"Soil microbial carbon and nitrogen limitation constraints soil organic carbon stability in arid and semi-arid grasslands","volume":"373","author":"Wu","year":"2025","journal-title":"J. Environ. Manag."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"116225","DOI":"10.1016\/j.envres.2023.116225","article-title":"The effects of continuous straw returning strategies on SOC balance upon fresh straw incorporation","volume":"232","author":"Wu","year":"2023","journal-title":"Environ. Res."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"121051","DOI":"10.1016\/j.jenvman.2024.121051","article-title":"Response of soil organic carbon to straw return in farmland soil in China: a meta-analysis","volume":"359","author":"Xin","year":"2024","journal-title":"J. Environ. Manag."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"e70292","DOI":"10.1111\/gcb.70292","article-title":"Unfolding the potential of soil microbial community diversity for accumulation of Necromass carbon at large scale","volume":"31","author":"Yang","year":"2025","journal-title":"Glob. Chang. Biol."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"111170","DOI":"10.1016\/j.plaphy.2026.111170","article-title":"From major crops to sugarcane: rethinking nitrogen use efficiency for a sustainable future","volume":"232","author":"Yang","year":"2026","journal-title":"Plant Physiol. Biochem."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"106146","DOI":"10.1016\/j.apsoil.2025.106146","article-title":"Metagenomic reconstruction of microbial structure and carbon cycling for annual crop productivity: influence of long-term straw mulching and nitrogen","volume":"211","author":"Yang","year":"2025","journal-title":"Appl. Soil Ecol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.1007\/s11356-022-21883-7","article-title":"Differences in methane and nitrous oxide emissions and soil bacteria communities between straw return methods in Central China","volume":"30","author":"Zhang","year":"2023","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e132","DOI":"10.1093\/nar\/gkq275","article-title":"Ab initio gene identification in metagenomic sequences","volume":"38","author":"Zhu","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"117590","DOI":"10.1016\/j.jenvman.2023.117590","article-title":"Driving factors of soil organic carbon sequestration under straw returning across China's uplands","volume":"335","author":"Zhu","year":"2023","journal-title":"J. Environ. Manag."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1928083\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T20:25:25Z","timestamp":1790281525000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1928083\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,14]]},"references-count":47,"alternative-id":["10.3389\/fmicb.2026.1928083"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1928083","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,14]]},"article-number":"1928083"}}