Linking changes in the soil microbial community to C and N dynamics during crop residue decomposition

doi:10.1016/S2095-3119(20)63567-5

摘要/Abstract

摘要：

一方面，中国亚热带红壤区水稻土母质和肥力水平多变；另一方面，细菌多样性和群落组成在土壤生态系统过程和功能中发挥关键作用。但是水稻土的母质和肥力对细菌多样性和群落组成的影响如何仍不清楚，不同母质和肥力水平条件下驱动水稻土细菌多样性、群落组成和特异微生物种群变化的关键因素尚不明确。因此，本研究采集亚热带红壤区具有不同母质（第四纪红黏土或第三纪红砂岩）和不同肥力水平（高肥力或低肥力）的典型样地水稻土样品，通过454高通量测序测定细菌16S rRNA基因的V4−V5区，分析细菌多样性指数和群落组成变化。采用two-way ANOVA和two-way PERMANOVA探明母质和肥力对细菌多样性和群落组成的影响；主坐标分析（PCoA）、冗余分析（RDA）和多元回归树分析（MRT）明确细菌群落的变化，以及驱动该变化的关键土壤因子；共现网络分析阐明属水平特异细菌种群和关键土壤因子的关系；宏基因组差异分析工具（STAMP）确定不同土壤样品间差异物种。结果显示，母质和肥力对水稻土细菌多样性指数变化的贡献相似。但是肥力水平对细菌群落组成的影响要远大于母质。土壤因子，特别是土壤质地与细菌多样性指数密切相关。RDA分析发现土壤有机碳（SOC）是影响细菌群落组成的首要因素，并且25.5 g kg⁻¹有机碳含量是驱动高肥力和低肥力土壤细菌群落组成分异的关键阈值。共现网络分析暗示高肥力水平下，由于土壤环境的改善，细菌趋向于合作关系，并且富营养型细菌占主导地位。STAMP分析发现高肥力水稻土中Massilia和Rhodanobacter等富营养型细菌大量富集；而低肥力土壤中Anaerolinea等贫营养型细菌占主导。研究结果表明，不同母质和肥力水稻土中，土壤质地影响细菌多样性指数变化；而养分水平，特别是有机碳水平决定细菌群落组成的变化。

Abstract:

Crop residues are among the main inputs that allow the organic carbon (C) and nutrients to be maintained in agricultural soil. It is an important management strategy that can improve soil fertility and enhance agricultural productivity. This work aims to evaluate the extent of the changes that may occur in the soil heterotrophic microbial communities involved in organic matter decomposition and C and nitrogen (N) mineralization after the addition of crop residues. Soil microcosm experiments were performed at 28°C for 90 days with the addition of three crop residues with contrasting biochemical qualities: pea (Pisum sativum L.), rapeseed (Brassica napus L.), and wheat (Triticum aestivum L.). Enzyme activities, C and N mineralization, and bacterial and fungal biomasses were monitored, along with the bacterial and fungal community composition, by the high-throughput sequencing of 16S rRNA and ITS genes. The addition of crop residues caused decreases in β-glucosidase and arylamidase activities and simultaneous enhancement of the C mineralization and net N immobilization, which were linked to changes in the soil microbial communities. The addition of crop residues decreased the bacterial and fungal biomasses 90 days after treatment and there were shifts in bacterial and fungal diversity at the phyla, order, and genera levels. Some specific orders and genera were dependent on crop residue type. For example, Chloroflexales, Inquilinus, Rubricoccus, Clitocybe, and Verticillium were identified in soils with pea residues; whereas Thermoanaerobacterales, Thermacetogenum, and Hypoxylon were enriched in soils with rapeseed residues, and Halanaerobiales, Rubrobacter, and Volutella were only present in soils with wheat residues. The findings of this study suggest that soil C and N dynamics in the presence of the crop residues were driven by the selection of specific bacterial and fungal decomposers linked to the biochemical qualities of the crop residues. If crop residue decomposition processes showed specific bacterial and fungal operational taxonomic unit (OTU) signatures, this study also suggests a strong functional redundancy that exists among soil microbial communities.

Key words: crop residue , C and N mineralization , enzyme activities , bacterial and fungal diversity

. [J]. Journal of Integrative Agriculture, 2021, 20(11): 3039-3059.

Cyrine REZGUI, Isabelle TRINSOUTROT-GATTIN, Marie BENOIT, Karine LAVAL, Wassila RIAH-ANGLET. Linking changes in the soil microbial community to C and N dynamics during crop residue decomposition[J]. Journal of Integrative Agriculture, 2021, 20(11): 3039-3059.

参考文献

Abbasi K, Tahir M, Sabir N, Khurshid M. 2014. Impact of the addition of different plant residues on carbon-nitrogen content and nitrogen mineralization-immobilization turnover in a soil incubated under laboratory conditions. Solid Earth Discussions, 6, 197–205.
Abera G, Wolde-meskel E, Bakken L R. 2012. Carbon and nitrogen mineralization dynamics in different soils of the tropics amended with legume residues and contrasting soil moisture contents. Biolology and Fertility of Soils, 48, 51–66.
Abiven S, Recous S, Reyes-Gómez V, Oliver R. 2005. Mineralisation of C and N from root, stem and leaf residue in soil and role of their biochemical quality. Biology and Fertility of Soils, 42, 119–128.
Acosta-Martínez V, Dowd S, Sun Y, Allen V. 2008. Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biology and Biochemistry, 40, 2762–2770.
Adair E C, Parton W J, Grosso S J D, Silver W L, Harmon M E, Hall S A, Burke I C, Hart S C. 2008. Simple three-pool model accurately describes patterns of long-term litter decomposition in diverse climates. Global Change Biology, 14, 2636–2660.
AFNOR (the French Standardisation Association). 2009. Norme XP U 44-163. Characterization of organic matter by potential mineralization of carbon and nitrogen. AFNOR, Official Distributor of Standards according to the decree of 16 June 2009. France. (in French)
Almeida F, Wolf J M, Casadevall A. 2015. Virulence-associated enzymes of cryptococcus neoformans. Eukaryotic Cell, 14, 1173–1185.
Amin B A Z, Chabbert B, Moorhead D, Bertrand I. 2014. Impact of fine litter chemistry on lignocellulolytic enzyme efficiency during decomposition of maize leaf and root in soil. Biogeochemistry, 117, 169–183.
Aneja M K, Sharma S, Fleischmann F, Stich S, Heller W, Bahnweg G, Munch J C, Schloter M. 2006. Microbial colonization of beech and spruce Litter - Influence of decomposition site and plant litter species on the diversity of microbial community. Microbial Ecology, 52, 127–135.
Arcand M M, Helgason B L, Lemke R L. 2016. Microbial crop residue decomposition dynamics in organic and conventionally managed soils. Applied Soil Ecology, 107, 347–359.
Bahri H, Rasse D P, Rumpel C, Dignac M F, Bardoux G, Mariotti A. 2008. Lignin degradation during a laboratory incubation followed by 13C isotope analysis. Soil Biology and Biochemistry, 40, 1916–1922.
Bell C, Carrillo Y, Boot C M, Rocca J D, Pendall E, Wallenstein M D. 2014. Rhizosphere stoichiometry: Are C:N:P ratios of plants, soils, and enzymes conserved at the plant species-level? New Phytologist, 201, 505–517.
Berg B, Kjønaas O J, Johansson M B, Erhagen B, Åkerblom S. 2015. Late stage pine litter decomposition: Relationship to litter N, Mn, and acid unhydrolyzable residue (AUR) concentrations and climatic factors. Forest Ecology and Management, 358, 41–47.
Berg B, McClaugherty C. 2008. Initial litter chemical composition. In: Plant Litter: Decomposition, Humus Formation, Carbon Sequestration. Springer, Berlin, Heidelberg. pp. 53–83.
Bertrand I, Delfosse O, Mary B. 2007. Carbon and nitrogen mineralization in acidic, limed, and calcareous agricultural soils: Apparent and actual effects. Soil Biology and Biochemistry, 39, 276–288.
Bernard L, Mougel C, Maron P A, Nowak V, Lévêque J, Henault C, Haichar F Z, Marol C, Balesdent J, Gibiat F, Lemanceau P, Ranjard L. 2007. Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques. Environmental Microbiology, 9, 752–764.
Blackwood C B, Waldrop M P, Zak D R, Sinsabaugh R L. 2007. Molecular analysis of fungal communities and laccase genes in decomposing litter reveals differences among forest types but no impact of nitrogen deposition. Environmental Microbiology, 9, 1306–1316.
Boer W, Folman L B, Summerbell R C, Boddy L. 2005. Living in a fungal world: Impact of fungi on soil bacterial niche development. FEMS Microbiology Reviews, 29, 795–811.
Borneman J, Hartin R J. 2000. PCR primers that amplify fungal rRNA genes from environmental samples. Applied and Environmental Microbiology, 66, 4356–4360.
Brown S P, Jumpponen A. 2015. Phylogenetic diversity analyses reveal disparity between fungal and bacterial communities during microbial primary succession. Soil Biology and Biochemistry, 89, 52–60.
Caporaso J G, Kuczynski J, Stombaugh J, Bittinger K, Bushman F D, Costello E K, Fierer N, Peña A G, Goodrich J K, Gordon J I, Huttley G A, Kelley S T, Knights D, Koenig J E, Ley R E, Lozupone C A, McDonald D, Muegge B D, Pirrung M, Reeder J, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7, 335–336.
Castellano M J, Mueller K E, Olk D C, Sawyer J E, Six J. 2015. Integrating plant litter quality, soil organic matter stabilization, and the carbon saturation concept. Global Change Biology, 21, 3200–3209.
Cayuela M L, Sinicco T, Mondini C. 2009. Mineralization dynamics and biochemical properties during initial decomposition of plant and animal residue in soil. Applied Soil Ecology, 41, 118–127.
Chen B, Liu E, Tian Q, Yan C, Zhang Y. 2014. Soil nitrogen dynamics and crop residues. A review. Agronomy for Sustainable Development, 34, 429–442.
Chen H, Fan M, Billen N, Stahr K, Kuzyakov Y. 2009. Effect of land use types on decomposition of 14C-labelled maize residue (Zea mays L.). European Journal of Soil Biology, 45, 123–130.
Choudhary M, Sharma P C, Jat H S, McDonald A, Jat M L, Choudhary S, Garg N, Choudhary M, Sharma P C, Jat H S, McDonald A, Jat M L, Choudhary S, Garg N. 2018. Soil biological properties and fungal diversity under conservation agriculture in Indo-Gangetic Plains of India. Journal of Soil Science and Plant Nutrition, 18, 1142–1156.
Claesson M J, Wang Q, O’Sullivan O, Greene-Diniz R, Cole J R, Ross R P, O’Toole P W. 2010. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Research, 38, e200.
Cole J R, Wang Q, Fish J A, Chai B, McGarrell D M, Sun Y, Brown C T, Porras-Alfaro A, Kuske C R, Tiedje J M. 2014. Ribosomal Database Project: Data and tools for high throughput rRNA analysis. Nucleic Acids Research, 42, D633–D642.
Cotrufo M F, Wallenstein M D, Boot C M, Denef K, Paul E. 2013. The microbial efficiency-matrix stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: Do labile plant inputs form stable soil organic matter? Global Change Biology, 19, 988–995
Cusack D F, Torn M S, McDowell W H, Silver W L. 2010. The response of heterotrophic activity and carbon cycling to nitrogen additions and warming in two tropical soils. Global Change Biology, 16, 2555–2572.
Deng Y, Wang Y, Xia Y, Zhang A N, Zhao Y, Zhang T. 2019. Genomic resolution of bacterial populations in saccharin and cyclamate degradation. Science of the Total Environment, 658, 357–366.
Dodor D E, Tabatabai D M A. 2007. Arylamidase activity as an index of nitrogen mineralization in soils. Communications in Soil Science and Plant Analysis, 38, 2197–2207.
Dominati E, Patterson M, Mackay A. 2010. A framework for classifying and quantifying the natural capital and ecosystem services of soils. Ecological Economics, 69, 1858–1868.
Edgar R C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460–2461.
Ekenler M, Tabatabai M A. 2004. β-Glucosaminidase activity as an index of nitrogen mineralization in soils. Communications in Soil Science and Plant Analysis, 35, 1081–1094.
Entwistle E M, Zak D R, Argiroff W A. 2018. Anthropogenic N deposition increases soil C storage by reducing the relative abundance of lignolytic fungi. Ecological Monographs, 88, 225–244.
Fang M, Motavalli P P, Kremer R J, Nelson K A. 2007. Assessing changes in soil microbial communities and carbon mineralization in Bt and non-Bt corn residue-amended soils. Applied Soil Ecology, 37, 150–160.
Fang Y, Nazaries L, Singh B K, Singh B P. 2018. Microbial mechanisms of carbon priming effects revealed during the interaction of crop residues and nutrient inputs in contrasting soils. Global Change Biology, 24, 2775–2790.
Fang Y, Singh B P, Cowie A, Wang W, Arachchi M H, Wang H, Tavakkoli E. 2019. Balancing nutrient stoichiometry facilitates the fate of wheat residue carbon in physically defined soil organic matter fractions. Geoderma, 354, 113–883.
Fernando W G D, Zhang X, Amarasinghe C C. 2016. Detection of Leptosphaeria maculans and Leptosphaeria biglobosa causing blackleg disease in canola from Canadian canola seed lots and dockage. Plants (Basel), 5, 12.
Fierer N, Bradford M A, Jackson R B. 2007. Toward an ecological classification of soil bacteria. Ecology, 88, 1354–1364.
Fontaine S, Mariotti A, Abbadie L. 2003. The priming effect of organic matter: A question of microbial competition? Soil Biology and Biochemistry, 35, 837–843.
Frasier I, Noellemeyer E, Figuerola E, Erijman L, Permingeat H, Quiroga A. 2016. High quality residue from cover crops favor changes in microbial community and enhance C and N sequestration. Global Ecology and Conservation, 6, 242–256.
Gaillard V, Chenu C, Recous S. 2003. Carbon mineralization in soil adjacent to plant residue of contrasting biochemical quality. Soil Biology and Biochemistry, 35, 93–99.
Gangneux C, Akpa-Vinceslas M, Sauvage E, Desaire S, Houot S, Laval K. 2011. Fungal, bacterial and plant dsDNA contributions to soil total DNA extracted from silty soils under different farming practices: Relationships with chloroform-labile carbon. Soil Biology and Biochemistry, 43, 431–437.
Geethanjali P M, Jayashankar P M. 2016. A review on litter decomposition by soil fungal community. IOSR Journal of Pharmacy and Biological Sciences, 11, 01–03.
Geisseler D, Horwath W R, Doane T A. 2009. Significance of organic nitrogen uptake from plant residue by soil microorganisms as affected by carbon and nitrogen availability. Soil Biology and Biochemistry, 41, 1281–1288.
Ghimire B, Ghimire R, VanLeeuwen D, Mesbah A. 2017. Cover crop residues amount and quality effects on soil organic carbon mineralization. Sustainability, 9, 23–16.
Hadas A, Kautsky L, Goek M, Kara E E. 2004. Rates of decomposition of plant residue and available nitrogen in soil, related to residue composition through simulation of carbon and nitrogen turnover. Soil Biology and Biochemistry, 36, 255–266.
Hashem M, Ali E H, Abdel-Basset R. 2013. Recycling rice straw into biofuel. Journal of Agriculture, Science and Technology, 15, 709–721.
Hatakka A, Hammel K E. 2011. Fungal biodegradation of lignocelluloses. In: Hofrichter M, ed., Industrial Applications, the Mycota. Springer, Berlin, Heidelberg. pp. 319–340.
Hermans S M, Buckley H L, Case B S, Curran-Cournane F, Taylor M, Lear G. 2017. Bacteria as emerging indicators of soil condition. Applied Environmental Microbiology, 83, e02826-16.
Hünninghaus M, Koller R, Kramer S, Marhan S, Kandeler E, Bonkowski M. 2017. Changes in bacterial community composition and soil respiration indicate rapid successions of protist grazers during mineralization of maize crop residues. Pedobiologia, 62, 1–8.
Isikhuemhen O S, Mikiashvili N A, Senwo Z N, Ohimain E I. 2014. Biodegradation and sugar release from canola plant biomass by selected white rot fungi. Advances in Biological Chemistry, 04, 395.
Ivancevic B, Karadelev M. 2013. Overview of fungi species in Prespa National Park (Albania). International Journal of Ecosystems and Ecology Science, 3, 679–686.
Jensen E S. 1994. Mineralization-immobilization of nitrogen in soil amended with low C/N ratio plant residue with different particle size. Soil Biology and Biochemistry, 26, 519–521.
Jian S, Li J, Chen J, Wang G, Mayes M A, Dzantor K E, Hui D, Luo Y. 2016. Soil extracellular enzyme activities, soil carbon and nitrogen storage under nitrogen fertilization: A meta-analysis. Soil Biology and Biochemistry, 101, 32–43.
Johansson M B, Berg B, Meentemeyer V. 2011. Litter mass-loss rates in late stages of decomposition in a climatic transect of pine forests. Long-term decomposition in a Scots pine forest. IX. Canadian Journal of Botany, 73, 10.
Johnson J M F, Barbour N W, Weyers S L. 2007. Chemical composition of crop biomass impacts its decomposition. Soil Science Society of America Journal, 71, 155.
Kerdraon L, Balesdent M H, Barret M, Laval V, Suffert F. 2019. Crop residues in wheat–oilseed rape rotation system: a pivotal, shifting platform for microbial meetings. Microbial Ecology, 77, 931–945.
Koceja M E, Bledsoe R B, Goodwillie C, Peralta A L. 2019. Nutrient enrichment increases soil bacterial diversity and decomposition rates of different litter types in a coastal plain wetland. bioRxiv, doi: 10.1101/732883.
Kriau?iūnien? Z, Veli?ka R, Raudonius S. 2012. The influence of crop residues type on their decomposition rate in the soil: A litterbag study. Zemdirbyste (Agriculture), 99, 227–236.
Lashermes G, Gainvors-Claisse A, Recous S, Bertrand I. 2016. Enzymatic strategies and carbon use efficiency of a litter-decomposing fungus grown on maize leaves, stems, and roots. Frontiers in Microbiology, 7, 13–15.
Lee J, Kim J R, Jeong S, Cho J, Kim J Y. 2017. Long-term performance of anaerobic digestion for crop residues containing heavy metals and response of microbial communities. Waste Management, 59, 498–507.
Lee K C, Dunfield P F, Stott M B. 2014. The phylum Armatimonadete. In: Rosenberg E, ed., The Prokaryotes. 4th ed. Other Major Lineages of Bacteria and The Archaea Springer-Verlag, Berlin. pp. 447–458.
Lehtinen T, Schlatter N, Baumgarten A, Bechini L, Krüger J, Grignani C, Zavattaro L, Costamagna C, Spiegel H. 2014. Effect of crop residues incorporation on soil organic carbon and greenhouse gas emissions in European agricultural soils. Soil Use and Management, 30, 524–538.
Li Q, Chai S, Li Y, Huang J, Luo Y, Xiao L, Liu Z. 2018. biochemical components associated with microbial community shift during the pile-fermentation of primary dark tea. Frontiers in Microbiology, 9, 1509.
Lian T, Yu Z, Li Y, Jin J, Wang G, Liu X, Tang C, Franks A, Liu J, Liu J. 2019. The shift of bacterial community composition magnifies over time in response to different sources of soybean residue. Applied Soil Ecology, 136, 163–167.
Linères M, Djackovitch J L. 1993. Caracterisation de la stabilite biologique des apports organiques par l’analyse biochimique. In: Decroux J, Ignazi J C, eds., MatiEres Organiques et Agricultures. QuatriEme JournEes de L’Analyse de Terre et CinquiEme Forum de la Fertilisation RaisonneEe, GEMAS-COMIFER, Paris. pp. 159–168. (in French)
Liu C, Li H, Zhang Y, Si D, Chen Q. 2016. Evolution of microbial community along with increasing solid concentration during high-solids anaerobic digestion of sewage sludge. Bioresource Technology, 216, 87–94.
López A M Q, Silva A L, Dos Santos E C L. 2017. The fungal ability for biobleaching/biopulping/bioremediation of lignin-like compounds of agro-industrial raw material. Química Nova, 40, 916–931.
Luo G, Ling N, Nannipieri P, Chen H, Raza W, Wang M, Guo S, Shen Q. 2017. Long-term fertilisation regimes affect the composition of the alkaline phosphomonoesterase encoding microbial community of a vertisol and its derivative soil fractions. Biology and Fertility of Soils, 53, 375– 388.
Ma A, Zhuang X, Wu J, Cui M, Lv D, Liu C, Zhuang G. 2013. Ascomycota members dominate fungal communities during straw residue decomposition in Arable soil. PLoS ONE, 8, e66146.
Machinet G E, Bertrand I, Barrière Y, Chabbert B, Recous S. 2011. Impact of plant cell wall network on biodegradation in soil: Role of lignin composition and phenolic acids in roots from 16 maize genotypes. Soil Biology and Biochemistry, 43, 1544–1552.
Mago? T, Salzberg S L. 2011. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27, 2957–2963.
De Mandal S, Chatterjee R, Kumar N S. 2017. Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle. BMC Microbiology, 17, 90.
Marchesi J R, Sato T, Weightman A J, Martin T A, Fry J C, Hiom S J, Dymock D, Wade W G. 1998. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Applied and Environmental Microbiology, 64, 795–799.
Masigol H, Khodaparast S A, Woodhouse J N, Rojas-Jimenez K, Fonvielle J, Rezakhani F, Mostowfizadeh-Ghalamfarsa R, Neubauer D, Goldhammer T, Grossart H P. 2019. The contrasting roles of aquatic fungi and oomycetes in the degradation and transformation of polymeric organic matter. Limnology and Oceanography, 64, 2662–2678.
Melillo J M, Aber J D, Linkins A E, Ricca A, Fry B, Nadelhoffer K J. 1989. Carbon and nitrogen dynamics along the decay continuum: plant litter to soil organic matter. Plant and Soil, 115, 189–198.
Moreno-Cornejo J, Zornoza R, Faz A. 2014. Carbon and nitrogen mineralization during decomposition of crop residues in a calcareous soil. Geoderma, 230–231, 58–63.
Moreno-Espíndola I P, Ferrara-Guerrero M J, Luna-Guido M L, Ramírez-Villanueva D A, De León-Lorenzana A S, Gómez-Acata S, González-Terreros E, Ramírez-Barajas B, Navarro-Noya Y E, Sánchez-Rodríguez L M, Fuentes-Ponce M, Macedas-Jímenez J U, Dendooven L. 2018. The bacterial community structure and microbial activity in a traditional organic milpa farming system under different soil moisture conditions. Frontiers in Microbiology, 9, 2737.
Muyzer G, De Waal E C, Uitterlinden A C. 1993. Profiling of complex microbial populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal-RNA. Applied and Environmental Microbiology, 59, 695–700.
Nguyen T T, Marschner P. 2017. Soil respiration, microbial biomass and nutrient availability in soil after addition of residue with adjusted N and P concentrations. Pedosphere, 27, 76–85.
Nicolardot B, Bouziri L, Bastian F, Ranjard L. 2007. A microcosm experiment to evaluate the influence of location and quality of plant residue on residue decomposition and genetic structure of soil microbial communities. Soil Biology and Biochemistry, 39, 1631–1644.
Pascault N, Cécillon L, Mathieu O, Hénault C, Sarr A, Lévêque J, Farcy P, Ranjard L, Maron P A. 2010a. In situ dynamics of microbial communities during decomposition of wheat, rape, and alfalfa residue. Microbial Ecology, 60, 816–828.
Pascault N, Nicolardot B, Bastian F, Thiébeau P, Ranjard L, Maron P A. 2010b. In situ dynamics and spatial heterogeneity of soil bacterial communities under different crop residues management. Microbial Ecology, 60, 291–303.
Pascault N, Ranjard L, Kaisermann A, Bachar D, Christen R, Terrat S, Mathieu O, Lévêque J, Mougel C, Henault C, Lemanceau P, Péan M, Boiry S, Fontaine S, Maron P A. 2013. Stimulation of different functional groups of bacteria by various plant residue as a driver of soil priming effect. Ecosystems, 16, 810–822.
Paterson E, Midwood A J, Millard P. 2009. Through the eye of the needle: A review of isotope approaches to quantify microbial processes mediating soil carbon balance. New Phytologist, 184, 19–33.
Perestelo F, Rodríguez A, Pérez R, Carnicero A, Fuente G D I, Falcón M A. 1996. Short communication: Isolation of a bacterium capable of limited degradation of industrial and labelled, natural and synthetic lignins. World Journal of Microbiology and Biotechnology, 12, 111–112.
Piotrowska A, Wilczewski E. 2012. Effect of catch crop cultivated for green manure and mineral nitrogen fertilization on soil enzymes activities and chemical properties. Geoderma, 189–190, 72–80.
Prescott C E. 2010. Litter decomposition: What controls it and how can we alter it to sequester more carbon in forest soils? Biogeochemistry, 101, 133–149.
Ramirez K S, Craine J M, Fierer N. 2012. Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Global Change Biology, 18, 1918–1927.
Recous S, Lashermes G, Bertrand I. 2017. Couplages et contrôles des cycles du carbone et de l’azote par les communautés microbiennes dans les sols cultivés. In: Quae S, ed., Les Sols et la Vie Souterraine: Des Enjeux Majeurs en AgroEcologie. Quae, Paris. p. 328. (in French)
Recous S, Robin D, Darwis D, Mary B. 1995. Soil inorganic N availability: Effect on maize residue decomposition. Soil Biology and Biochemistry, 27, 1529–1538.
Reddy A P, Simmons C W, D’haeseleer P, Khudyakov J, Burd H, Hadi M, Simmons B A, Singer S W, Thelen M P, Vandergheynst J S. 2013. Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses. PLoS ONE, 8, e77985.
Redin M, Recous S, Aita C, Dietrich G, Skolaude A C, Ludke W H, Schmatz R, Giacomini S J. 2014. How the chemical composition and heterogeneity of crop residues mixtures decomposing at the soil surface affects C and N mineralization. Soil Biology and Biochemistry, 78, 65–75.
Rinkes Z L, Weintraub M N, DeForest J L, Moorhead D L. 2011. Microbial substrate preference and community dynamics during decomposition of Acer saccharum. Fungal Ecology, 4, 396–407.
Rui J, Peng J, Lu Y. 2009. Succession of bacterial populations during plant residue decomposition in rice field soil. Applied and Environmental Microbiology, 75, 4879–4886.
Sacco L P, Castellane T C L, Lopes E M, de Macedo Lemos E G, Alves L M C. 2016. Properties of polyhydroxyalkanoate granules and bioemulsifiers from Pseudomonas sp. and Burkholderia sp. Isolates growing on glucose. Applied Biochemistry and Biotechnology, 178, 990–1001.
Sauvadet M, Chauvat M, Brunet N, Bertrand I. 2017. Can changes in litter quality drive soil fauna structure and functions? Soil Biology and Biochemistry, 107, 94–103.
Sauvadet M, Chauvat M, Fanin N, Coulibaly S, Bertrand I. 2016. Comparing the effects of litter quantity and quality on soil biota structure and functioning: Application to a cultivated soil in Northern France. Applied Soil Ecology, 107, 261–271.
Sauvadet M, Lashermes G, Alavoine G, Recous S, Chauvat M, Maron P A, Bertrand I. 2018. High carbon use efficiency and low priming effect promote soil C stabilization under reduced tillage. Soil Biology and Biochemistry, 123, 64–73.
Schmieder R, Edwards R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27, 863–864.
Shahbaz M, Kuzyakov Y, Sanaullah M, Heitkamp F, Zelenev V, Kumar A, Blagodatskaya E. 2017. Microbial decomposition of soil organic matter is mediated by quality and quantity of crop residues: Mechanisms and thresholds. Biology and Fertility of Soils, 53, 287–301.
Sinsabaugh R L, Follstad Shah J J. 2012. Ecoenzymatic stoichiometry and ecological theory. Annual Review of Ecology, Evolution, and Systematics, 43, 313–343.
Šnajdr J, Cajthaml T, Valášková V, Merhautová V, Petránková M, Spetz P, Leppänen K, Baldrian P. 2011. Transformation of Quercus petraea litter: successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition. FEMS Microbiology Ecology, 75, 291–303.
Van Soest P J. 1963. The use of detergents in the analysis of fibrous feeds. II. A rapid method for the determination of fiber and lignin. Journal of the Association of Official Analytical Chemists, 46, 829–835.
Srour A Y, Ammar H A, Subedi A, Pimentel M, Cook R L, Bond J, Fakhoury A M. 2020. Microbial communities associated with long-term tillage and fertility treatments in a corn–soybean cropping system. Frontiers in Microbiology, 11, 1363.
Stewart C E, Moturi P, Follett R F, Halvorson A D. 2015. Lignin biochemistry and soil N determine crop residue decomposition and soil priming. Biogeochemistry, 124, 335–351.
Suleiman A K A, Lourenço K S, Pitombo L M, Mendes L W, Roesch L F W, Pijl A, Carmo J B, Cantarella H, Kuramae E E. 2018. Recycling organic residue in agriculture impacts soil-borne microbial community structure, function and N2O emissions. Science of the Total Environment, 631–632, 1089–1099.
Tao K, Zhang X, Chen X, Liu X, Hu X, Yuan X. 2019. Response of soil bacterial community to bioaugmentation with a plant residue-immobilized bacterial consortium for crude oil removal. Chemosphere, 222, 831–838.
Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou N S, Wijesundera R, Ruiz L V, Vasco-Palacios A M, Thu P Q, Suija A, Smith M E, Sharp C, Saluveer E, Saitta A, Rosas M, Riit T, Ratkowsky D, Pritsch K, Põldmaa K, Piepenbring M, et al. 2014. Global diversity and geography of soil fungi. Science, 346, 1256688.
Trinsoutrot I, Recous S, Bentz B, Linères M, Cheneby D, Nicolardot B. 2000. Biochemical quality of crop residues and carbon and nitrogen nineralization kinetics under nonlimiting nitrogen conditions. Soil Science Society of America Journal, 64, 918–926.
Trivedi P, Anderson I, Singh B. 2013. Microbial modulators of soil carbon storage: Integrating genomic and metabolic knowledge for global prediction. Trends in Microbiology, 21, 641–651.
Vahdat E, Nourbakhsh F, Basiri M. 2011. Lignin content of range plant residue controls N mineralization in soil. European Journal of Soil Biology, 47, 243–246.
Vargas-García M C, Suárez-Estrella F, López M J, Moreno J. 2007. In vitro studies on lignocellulose degradation by microbial strains isolated from composting processes. International Biodeterioration and Biodegradation, 59, 322–328.
Verzeaux J, Alahmad A, Habbib H, Nivelle E, Roger D, Lacoux J, Decocq G, Hirel B, Catterou M, Spicher F, Dubois F, Duclercq J, Tetu T. 2016. Cover crops prevent the deleterious effect of nitrogen fertilization on bacterial diversity by maintaining the carbon content of ploughed soil. Geoderma, 281, 49–57.
Wang H, Zeng Y, Guo C, Bao Y, Lu G, Reinfelder J R, Dang Z. 2018. Bacterial, archaeal, and fungal community responses to acid mine drainage-laden pollution in a rice paddy soil ecosystem. Science of the Total Environment, 616–617, 107–116.
Wickings K, Grandy A S, Reed S C, Cleveland C C. 2012. The origin of litter chemical complexity during decomposition. Ecology Letters, 15, 1180–1188.
Xiong J, Peng F, Sun H, Xue X, Chu H. 2014. Divergent responses of soil fungi functional groups to short-term warming. Microbial Ecology, 68, 708–715.
Zhang L, Lueders T. 2017. Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey. FEMS Microbiology Ecology, 93, fix103.
Zhang S, Wang Y, Sun L, Qiu C, Ding Y, Gu H, Wang L, Wang Z, Ding Z. 2020. Organic mulching positively regulates the soil microbial communities and ecosystem functions in tea plantation. BMC Microbiology, 20, 103.
Zheng W, Zhao Z, Gong Q, Zhai B, Li Z. 2018. Effects of cover crop in an apple orchard on microbial community composition, networks, and potential genes involved with degradation of crop residues in soil. Biology and Fertility of Soils, 54, 743–759.
Zhou J, Jiang X, Zhou B, Zhao B, Ma M, Guan D, Li J, Chen S, Cao F, Shen D, Qin J. 2016. Thirty-four years of nitrogen fertilization decreases fungal diversity and alters fungal community composition in black soil in Northeast China. Soil Biology and Biochemistry, 95, 135–143.
Ziganshin A M, Liebetrau J, Pröter J, Kleinsteuber S. 2013. Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials. Applied Microbiology and Biotechnology, 97, 5161–5174.