Biochar improves soil organic carbon stability by shaping the microbial community structures at different soil depths four years after an incorporation in a farmland soil

Ameloot, 2013, Interactions between biochar stability and soil organisms: review and research needs, Eur. J. Soil Sci., 64, 379, 10.1111/ejss.12064 Banerjee, 2018, Keystone taxa as drivers of microbiome structure and functioning, Nat. Rev. Microbiol., 16, 567, 10.1038/s41579-018-0024-1 Bokulich, 2013, Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing, Nat. Methods, 10, 57, 10.1038/nmeth.2276 Bond-Lamberty, 2018, Globally rising soil heterotrophic respiration over recent decades, Nature, 560, 80, 10.1038/s41586-018-0358-x Button, 2022, Deep-C storage: biological, chemical and physical strategies to enhance carbon stocks in agricultural subsoils, Soil Biol. Biochem., 170, 10.1016/j.soilbio.2022.108697 Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335, 10.1038/nmeth.f.303 Celestina, 2019, A single application of fertiliser or manure to a cropping field has limited long-term effects on soil microbial communities, Soil Res., 57, 228, 10.1071/SR18215 Chen, 2018, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics (Oxford, England), 34, i884 Chen, 2018, Biochar amendment changes temperature sensitivity of soil respiration and composition of microbial communities 3 years after incorporation in an organic carbon-poor dry cropland soil, Biol. Fertil. Soils, 54, 175, 10.1007/s00374-017-1253-6 Chen, 2021, Soil carbon persistence governed by plant input and mineral protection at regional and global scales, Ecol. Lett., 24, 1018, 10.1111/ele.13723 Crowther, 2016, Quantifying global soil carbon losses in response to warming, Nature, 540, 104, 10.1038/nature20150 Du, 2021, Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process, Mol. Ecol., 30, 1072, 10.1111/mec.15777 Edgar, 2013, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat. Methods, 10, 996, 10.1038/nmeth.2604 Eilers, 2012, Digging deeper to find unique microbial communities: the strong effect of depth on the structure of bacterial and archaeal communities in soil, Soil Biol. Biochem., 50, 58, 10.1016/j.soilbio.2012.03.011 Fierer, 2007, Toward an ecological classification of soil bacteria, Ecology, 88, 1354, 10.1890/05-1839 Fontaine, 2007, Stability of organic carbon in deep soil layers controlled by fresh carbon supply, Nature, 450, 277, 10.1038/nature06275 Georgiou, 2022, Global stocks and capacity of mineral-associated soil organic carbon, Nat. Commun., 13, 3797, 10.1038/s41467-022-31540-9 Heymann, 2014, Can functional group composition of alkaline isolates from black carbon-rich soils be identified on a sub-100nm scale?, Geoderma, 235–236, 163, 10.1016/j.geoderma.2014.07.011 IPCC, 2021, Summary for policymakers, 3 Jia, 2019, Climate warming alters subsoil but not topsoil carbon dynamics in alpine grassland, Glob. Chang. Biol., 25, 4383, 10.1111/gcb.14823 Jiao, 2018, Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems, Microbiome, 6, 146, 10.1186/s40168-018-0526-0 Jones, 2018, Microbial competition for nitrogen and carbon is as intense in the subsoil as in the topsoil, Soil Biol. Biochem., 117, 72, 10.1016/j.soilbio.2017.10.024 Klindworth, 2013, Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies, Nucleic Acids Res., 41, e1, 10.1093/nar/gks808 Kõljalg, 2013, Towards a unified paradigm for sequence-based identification of fungi, Mol. Ecol., 22, 5271, 10.1111/mec.12481 Laird, 2010, Biochar impact on nutrient leaching from a Midwestern agricultural soil, Geoderma, 158, 436, 10.1016/j.geoderma.2010.05.012 Lehmann, 2011, Biochar effects on soil biota – a review, Soil Biol. Biochem., 43, 1812, 10.1016/j.soilbio.2011.04.022 Lehmann, 2020, Persistence of soil organic carbon caused by functional complexity, Nat. Geosci., 13, 529, 10.1038/s41561-020-0612-3 Li, 2019, Partitioning biochar properties to elucidate their contributions to bacterial and fungal community composition of purple soil, Sci. Total Environ., 648, 1333, 10.1016/j.scitotenv.2018.08.222 Li, 2022, The regulators of soil organic carbon mineralization upon lime and/or phosphate addition vary with depth, Sci. Total Environ., 828, 10.1016/j.scitotenv.2022.154378 Liao, 2022, Nitrogen availability and mineral particles contributed fungal necromass to the newly formed stable carbon pool in the alpine areas of Southwest China, Soil Biol. Biochem., 173, 10.1016/j.soilbio.2022.108788 Liaw, 2007, Classification and regression by randomForest, R News, 2, 18 Liu, 2012, Can biochar amendment be an ecological engineering technology to depress N2O emission in rice paddies?—a cross site field experiment from South China, Ecol. Eng., 42, 168, 10.1016/j.ecoleng.2012.01.016 Liu, 2019, The responses of soil organic carbon mineralization and microbial communities to fresh and aged biochar soil amendments, GCB Bioenergy, 11, 1408, 10.1111/gcbb.12644 Liu, 2021, Quantitative assessment of the effects of biochar amendment on photosynthetic carbon assimilation and dynamics in a rice–soil system, New Phytol., 232, 1250, 10.1111/nph.17651 Liu, 2021, Diurnal dynamics can modify plant–microbial competition for N uptake via C allocation, Biol. Fertil. Soils, 57, 949, 10.1007/s00374-021-01585-x Magoč, 2011, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, 27, 2957, 10.1093/bioinformatics/btr507 Malik, 2020, Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change, ISME J., 14, 1, 10.1038/s41396-019-0510-0 Mayer, 2021, Soil fertility relates to fungal-mediated decomposition and organic matter turnover in a temperate mountain forest, New Phytol., 231, 777, 10.1111/nph.17421 Mendes, 2013, The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms, FEMS Microbiol. Rev., 37, 634, 10.1111/1574-6976.12028 Naisse, 2015, Effect of biochar addition on C mineralisation and soil organic matter priming in two subsoil horizons, J. Soils Sediments, 15, 825, 10.1007/s11368-014-1002-5 Oksanen, 2007 Parks, 2014, STAMP: statistical analysis of taxonomic and functional profiles, Bioinformatics, 30, 3123, 10.1093/bioinformatics/btu494 Quast, 2013, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res., 41, D590, 10.1093/nar/gks1219 R Core Team, 2022 Rethemeyer, 2005, Transformation of organic matter in agricultural soils: radiocarbon concentration versus soil depth, Geoderma, 128, 94, 10.1016/j.geoderma.2004.12.017 Rumpel, 2012, Carbon storage and sequestration in subsoil horizons: knowledge, gaps and potentials, 445 Rumpel, 2018, “4 per 1,000” initiative will boost soil carbon for climate and food security, Nature, 553, 27, 10.1038/d41586-017-09010-w Schweinle, 2015, Assessing the environmental performance of biomass supply chains: methods, results, challenges and limitations. Task 43. TR01, 121 Shao, 2021, Tradeoffs among microbial life history strategies influence the fate of microbial residues in subtropical forest soils, Soil Biol. Biochem., 153, 10.1016/j.soilbio.2020.108112 Shi, 2020, The age distribution of global soil carbon inferred from radiocarbon measurements, Nat. Geosci., 13, 555, 10.1038/s41561-020-0596-z Shi, 2020, Abundance of kinless hubs within soil microbial networks are associated with high functional potential in agricultural ecosystems, Environ. Int., 142, 10.1016/j.envint.2020.105869 Six, 2006, Bacterial and fungal contributions to carbon sequestration in agroecosystems, Soil Sci. Soc. Am. J., 70, 555, 10.2136/sssaj2004.0347 Sohi, 2012, Carbon storage with benefits, Science, 338, 1034, 10.1126/science.1225987 Soil Survey Staff, 1994, 161 Soong, 2021, Five years of whole-soil warming led to loss of subsoil carbon stocks and increased CO2 efflux, Sci. Adv., 7, 10.1126/sciadv.abd1343 Stockmann, 2013, The knowns, known unknowns and unknowns of sequestration of soil organic carbon, Agric. Ecosyst. Environ., 164, 80, 10.1016/j.agee.2012.10.001 Toju, 2012, High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples, PLoS One, 7, 10.1371/journal.pone.0040863 Wang, 2007, Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol., 73, 5261, 10.1128/AEM.00062-07 Wang, 2016, Biochar stability in soil: meta-analysis of decomposition and priming effects, GCB Bioenergy, 8, 512, 10.1111/gcbb.12266 Wang, 2021, The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization, ISME J., 15, 2738, 10.1038/s41396-021-00959-1 Wang, 2022, Global soil profiles indicate depth-dependent soil carbon losses under a warmer climate, Nat. Commun., 13, 5514, 10.1038/s41467-022-33278-w Warnock, 2007, Mycorrhizal responses to biochar in soil – concepts and mechanisms, Plant Soil, 300, 9, 10.1007/s11104-007-9391-5 Woolf, 2010, Sustainable biochar to mitigate global climate change, Nat. Commun., 1, 56, 10.1038/ncomms1053 Wu, 1990, Measurement of soil microbial biomass C by fumigation-extraction—an automated procedure, Soil Biol. Biochem., 22, 1167, 10.1016/0038-0717(90)90046-3 Xing, 2022, Disentangling the effects of nitrogen availability and soil acidification on microbial taxa and soil carbon dynamics in natural grasslands, Soil Biol. Biochem., 164, 10.1016/j.soilbio.2021.108495 Yang, 2022, Fungi determine increased soil organic carbon more than bacteria through their necromass inputs in conservation tillage croplands, Soil Biol. Biochem., 167, 10.1016/j.soilbio.2022.108587 Yuan, 2023, The addition of biochar and nitrogen alters the microbial community and their cooccurrence network by affecting soil properties, Chemosphere, 312, 10.1016/j.chemosphere.2022.137101 Zhao, 2021, Soil microbial community variation with time and soil depth in Eurasian Steppe (Inner Mongolia, China), Ann. Microbiol., 71, 21, 10.1186/s13213-021-01633-9 Zheng, 2016, Biochar decreased microbial metabolic quotient and shifted community composition four years after a single incorporation in a slightly acid rice paddy from Southwest China, Sci. Total Environ., 571, 206, 10.1016/j.scitotenv.2016.07.135 Zheng, 2017, A long-term hybrid poplar plantation on cropland reduces soil organic carbon mineralization and shifts microbial community abundance and composition, Appl. Soil Ecol., 111, 94, 10.1016/j.apsoil.2016.11.017 Zhu, 2017, Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: a review, Environ. Pollut., 227, 98, 10.1016/j.envpol.2017.04.032