Abstract
Conservation tillage as an effective alternative to mitigate soil degradation has attracted worldwide attention, but the influences of conservation tillage on soil microbial community and especially function remain unclear. Shotgun metagenomics sequencing was performed to examine the taxonomic and functional community variations of black soils under three tillage regimes, namely no-tillage with residue (maize straw) return (NTS), moldboard plow with residue return (MPS), and moldboard plow without residue return (MPN) in Northeast China. The results revealed: 1) Soil bacterial and archaeal communities differed significantly under different tillage regimes in contrast to soil fungal community. 2) The overlay of less tillage and residues return under NTS led to unique soil microbial community composition and functional composition. Specifically, in contrast to other treatments, NTS increased the relative abundances of some taxa such as Bradyrhizobium, Candidatus Solibacter, and Reyranella, along with the relative abundances of some taxa such as Sphingomonas, Unclassified Chloroflexi and Nitrososphaera decreased; NTS had a unique advantage of increasing the relative abundances of genes involved in ‘ATP-binding cassette (ABC) transporters’ and ‘quorum sensing (QS)’ pathways, while MPN favored the genes involved in ‘flagellar assembly’ pathway and some metabolic pathways such as ‘carbon’ and ‘glyoxylate and dicarboxylate’ and ‘selenocompound’ metabolisms. 3) Significantly different soil bacterial phyla (Acidobacteria, Gemmatimonadetes, and Chloroflexi) and metabolic pathways existed between MPN and another two treatments (NTS and MPS), while did not exist between NTS and MPS. 4) Dissolved organic carbon (DOC) and soil bulk density were significantly affected (P < 0.05) by tillage and accounted for the variance both in microbial (bacterial) community structure and functional composition. These results indicated that a change in tillage regime from conventional to conservation tillage results in a shift of microbial community and functional genes, and we inferred that residue return played a more prominent role than less tillage in functional shifts in the microbial community of black soils.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Antoun H, Beauchamp C J, Goussard N et al., 1998. Potential of Rhizobium and Bradyrhizobium species as plant growth promoting rhizobacteria on non-legumes: effect on radishes (Raphanus sativus L.). Plant and Soil, 204(1): 57–67. doi: https://doi.org/10.1023/A:1004326910584
Babin D, Deubel A, Jacquiod S et al., 2019. Impact of long-term agricultural management practices on soil prokaryotic communities. Soil Biology and Biochemistry, 129: 17–28. doi: https://doi.org/10.1016/j.soilbio.2018.11.002
Bu R Y, Ren T, Lei M J et al., 2020. Tillage and straw-returning practices effect on soil dissolved organic matter, aggregate fraction and bacteria community under rice-rice-rapeseed rotation system. Agriculture, Ecosystems & Environment, 287: 106681. doi: https://doi.org/10.1016/j.agee.2019.106681
Buchfink B, Xie C, Huson D H, 2015. Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1): 59–60. doi: https://doi.org/10.1038/nmeth.3176
Chen X L, Henriksen T M, Svensson K et al., 2020. Long-term effects of agricultural production systems on structure and function of the soil microbial community. Applied Soil Ecology, 147: 103387. doi: https://doi.org/10.1016/j.apsoil.2019.103387
Chevrot R, Rosen R, Haudecoeur E et al., 2006. GABA controls the level of quorum-sensing signal in Agrobacterium tumefaciens. Proceedings of the National Academy of Sciences of the United States of America, 103(19): 7460–7464. doi: https://doi.org/10.1073/pnas.0600313103
Degrune F, Dufrêne M, Colinet G et al., 2015. A novel subphylum method discriminates better the impact of crop management on soil microbial community. Agronomy for Sustainable Development, 35(3): 1157–1166. doi: https://doi.org/10.1007/s13593-015-0291-4
Degrune F, Theodorakopoulos N, Dufrêne M et al., 2016. No favorable effect of reduced tillage on microbial community diversity in a silty loam soil (Belgium). Agriculture, Ecosystems & Environment, 224: 12–21. doi: https://doi.org/10.1016/j.agee.2016.03.017
Dhaliwal S S, Naresh R K, Gupta R K et al., 2020. Effect of tillage and straw return on carbon footprints, soil organic carbon fractions and soil microbial community in different textured soils under rice-wheat rotation: a review. Reviews in Environmental Science and Bio/Technology, 19(1): 103–115. doi: https://doi.org/10.1007/s11157-019-09520-1
Dong W Y, Liu E K, Yan C R et al., 2017. Impact of no tillage vs. conventional tillage on the soil bacterial community structure in a winter wheat cropping succession in northern China. European Journal of Soil Biology, 80: 35–12. doi: https://doi.org/10.1016/j.ejsobi.2017.03.001
Hao J Q, Lin Y, Ren G X et al., 2021. Comprehensive benefit evaluation of conservation tillage based on BP neural network in the Loess Plateau. Soil and Tillage Research, 205: 104784. doi: https://doi.org/10.1016/j.still.2020.104784
Hao M M, Hu H Y, Liu Z et al., 2019. Shifts in microbial community and carbon sequestration in farmland soil under long-term conservation tillage and straw returning. Applied Soil Ecology, 136: 43–54. doi: https://doi.org/10.1016/j.apsoil.2018.12.016
Harper J K, Roth G W, Garalejić B et al., 2018. Programs to promote adoption of conservation tillage: a Serbian case study. Land Use Policy, 78: 295–302. doi: https://doi.org/10.1016/j.landusepol.2018.06.028
Kanokratana P, Uengwetwanit T, Rattanachomsri U et al., 2011. Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis. Microbial Ecology, 61(3): 518–528. doi: https://doi.org/10.1007/s00248-010-9766-7
Kravchenko Y S; Zhang X Y; Liu X B et al., 2011. Mollisols properties and changes in Ukraine and China. Chinese Geographical Science, 21(3): 257–266. doi: https://doi.org/10.1007/s11769-011-0467-z
Lang J, Faure D, 2014. Functions and regulation of quorum-sensing in Agrobacterium tumefaciens. Frontiers in Plant Science, 5: 14. doi: https://doi.org/10.3389/fpls.2014.00014
Legrand F, Picot A, Cobo-Díaz J F et al., 2018. Effect of tillage and static abiotic soil properties on microbial diversity. Applied Soil Ecology, 132: 135–145. doi: https://doi.org/10.1016/j.apsoil.2018.08.016
Li D H, Liu C M, Luo R B et al., 2015. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, 31(10): 1674–1676. doi: https://doi.org/10.1093/bioinformatics/btv033
Li M, He P, Guo X L et al., 2021. Fifteen-year no tillage of a Mollisol with residue retention indirectly affects topsoil bacterial community by altering soil properties. Soil and Tillage Research, 205: 104804. doi: https://doi.org/10.1016/j.still.2020.104804
Li R, Li Y, Kristiansen K et al., 2008. SOAP: short oligonucleotide alignment program. Bioinformatics, 24(5): 713–714. doi: https://doi.org/10.1093/bioinformatics/btn025
Li W, Godzik A, 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22(13): 1658–1659. doi: https://doi.org/10.1093/bioinformatics/btl158
Li Y, Li Z, Cui S et al., 2019. Residue retention and minimum tillage improve physical environment of the soil in croplands: a global meta-analysis. Soil and Tillage Research, 194: 104292. doi: https://doi.org/10.1016/j.still.2019.06.009
Li Y, Zhang Q P, Cai Y J et al., 2020a. Minimum tillage and residue retention increase soil microbial population size and diversity: implications for conservation tillage. Science of the Total Environment, 716: 137164. doi: https://doi.org/10.1016/j.scitotenv.2020.137164
Li Y Z, Song D P, Liang S H et al., 2020b. Effect of no-tillage on soil bacterial and fungal community diversity: a meta-analysis. Soil and Tillage Research, 204: 104721. doi: https://doi.org/10.1016/j.still.2020.104721
Lin B, Lu Y H, 2015. Bacterial and archaeal guilds associated with electrogenesis and methanogenesis in paddy field soil. Geoderma, 259–260: 362–369. doi: https://doi.org/10.1016/j.geoderma.2015.03.001
Liu F T, Kou D, Chen Y L et al., 2021b. Altered microbial structure and function after thermokarst formation. Global Change Biology, 27(4): 823–835. doi: https://doi.org/10.1111/gcb.15438
Liu Y X, Qin Y, Chen T et al., 2021a. A practical guide to amplicon and metagenomic analysis of microbiome data. Protein & Cell, 12(5): 315–330. doi: https://doi.org/10.1007/s13238-020-00724-8
Miura T, Niswati A, Swibawa I G et al., 2016. Shifts in the composition and potential functions of soil microbial communities responding to a no-tillage practice and bagasse mulching on a sugarcane plantation. Biology and Fertility of Soils, 52(3): 307–322. doi: https://doi.org/10.1007/s00374-015-1077-1
Moran M A, 2009. Metatranscriptomics: eavesdropping on complex microbial communities. Microbe, 4(7): 329–335. doi: https://doi.org/10.1128/microbe.4.329.1
Navarro-Noya Y E, Gómez-Acata S, Montoya-Ciriaco N et al., 2013. Relative impacts of tillage, residue management and crop-rotation on soil bacterial communities in a semi-arid agroecosystem. Soil Biology & Biochemistry, 65: 86–95. doi: https://doi.org/10.1016/j.soilbio.2013.05.009
Nelkner J, Henke C, Lin T W et al., 2019. Effect of long-term farming practices on agricultural soil microbiome members represented by metagenomically assembled genomes (MAGs) and their predicted plant-beneficial genes. Genes, 10(6): 424. doi: https://doi.org/10.3390/genes10060424
Noguchi H, Park J, Takagi T, 2006. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Research, 34(19): 5623–5630. doi: https://doi.org/10.1093/nar/gkl723
O’Donnell A G, Seasman M, Macrae A et al., 2001. Plants and fertilisers as drivers of change in microbial community structure and function in soils. Plant and Soil, 232(1–2): 135–145. doi: https://doi.org/10.1023/A:1010394221729
Oksanen, J, Blanchet F G, Kindt R et al., 2013. Vegan: Community Ecology Package. R package version 2.0–10.https://CRAN.R-project.org/package=vegan.
Pankhurst C, Kirkby C, Hawke B et al., 2002. Impact of a change in tillage and crop residue management practice on soil chemical and microbiological properties in a cereal-producing red duplex soil in NSW, Australia. Biology and Fertility of Soils, 35(3): 189–196. doi: https://doi.org/10.1007/s00374-002-0459-3
Parks D H, Beiko R G, 2010. Identifying biologically relevant differences between metagenomic communities. Bioinformatics, 26(6): 715–721. doi: https://doi.org/10.1093/bioinformatics/btq041
Rincon-Florez V A, Carvalhais L C, Dang Y P et al., 2020. Significant effects on soil microbial communities were not detected after strategic tillage following 44 years of conventional or notillage management. Pedobiologia, 80: 150640. doi: https://doi.org/10.1016/j.pedobi.2020.150640
Romero-Salas E A, Navarro-Noya Y E, Luna-Guido M et al., 2021. Changes in the bacterial community structure in soil under conventional and conservation practices throughout a complete maize (Zea mays L.) crop cycle. Applied Soil Ecology, 157: 103733. doi: https://doi.org/10.1016/j.apsoil.2020.103733
Schmidt R, Mitchell J, Scow K, 2019. Cover cropping and no-till increase diversity and symbiotroph: saprotroph ratios of soil fungal communities. Soil Biology & Biochemistry, 129: 99–109. doi: https://doi.org/10.1016/j.soilbio.2018.11.010
Schneijderberg M, Schmitz L, Cheng X et al., 2018. A genetically and functionally diverse group of non-diazotrophic Bradyrhizobium spp. colonizes the root endophytic compartment of Arabidopsis thaliana. BMC Plant Biology, 18: 61. doi: https://doi.org/10.1186/s12870-018-1272-y
Sekaran U, Sagar K L, De Oliveira Denardin L G et al., 2020. Responses of soil biochemical properties and microbial community structure to short and long-term no-till systems. European Journal of Soil Science, 71(6): 1018–1033. doi: https://doi.org/10.1111/ejss.12924
Smith A P, Marín-Spiotta E, Balser T, 2015. Successional and seasonal variations in soil and litter microbial community structure and function during tropical post agricultural forest regeneration: a multiyear study. Global Change Biology, 21(9): 3532–3547. doi: https://doi.org/10.1111/gcb.12947
Somenahally A, Dupont J I, Brady J et al., 2018. Microbial communities in soil profile are more responsive to legacy effects of wheat-cover crop rotations than tillage systems. Soil Biology and Biochemistry, 123: 126–135. doi: https://doi.org/10.1016/j.soilbio.2018.04.025
Souza R C, Cantão M E, Vasconcelos A T R et al., 2013. Soil metagenomics reveals differences under conventional and notillage with crop rotation or succession. Applied Soil Ecology, 72: 49–61. doi: https://doi.org/10.1016/j.apsoil.2013.05.021
Souza R C, Hungria M, Cantão M E et al., 2015. Metagenomic analysis reveals microbial functional redundancies and specificities in a soil under different tillage and crop-management regimes. Applied Soil Ecology, 86: 106–112. doi: https://doi.org/10.1016/j.apsoil.2014.10.010
Sun R B, Li W Y, Dong W X et al., 2018. Tillage changes vertical distribution of soil bacterial and fungal communities. Frontiers in Microbiology, 9: 699. doi: https://doi.org/10.3389/fmicb.2018.00699
Wang H, Wang S L, Wang R et al., 2019. Direct and indirect linkages between soil aggregates and soil bacterial communities under tillage methods. Geoderma, 354: 113879. doi: https://doi.org/10.1016/j.geoderma.2019.113879
Wang H H, Li X, Li X et al., 2020a. Long-term no-tillage and different residue amounts alter soil microbial community composition and increase the risk of maize root rot in northeast China. Soil & Tillage Research, 196: 104452. doi: https://doi.org/10.1016/j.still.2019.104452
Wang H H, Guo Q C, Li X et al., 2020b. Effects of long-term notillage with different straw mulching frequencies on soil microbial community and the abundances of two soil-borne pathogens. Applied Soil Ecology, 148: 103488. doi: https://doi.org/10.1016/j.apsoil.2019.103488
Wang Q, Liang A Z, Chen X W et al., 2021. The impact of cropping system, tillage and season on shaping soil fungal community in a long-term field trial. European Journal of Soil Biology, 102: 103253. doi: https://doi.org/10.1016/j.ejsobi.2020.103253
Wang Y, Li C Y, Tu C et al., 2017. Long-term no-tillage and organic input management enhanced the diversity and stability of soil microbial community. Science of the Total Environment, 609: 341–347. doi: https://doi.org/10.1016/j.scitotenv.2017.07.053
Xing W L, Cheng X R, Xiong J et al., 2020. Variations in soil biological properties in poplar plantations along coastal reclamation stages. Applied Soil Ecology, 154: 103649. doi: https://doi.org/10.1016/j.apsoil.2020.103649
Yan S S, Song J M, Fan J S et al., 2020. Changes in soil organic carbon fractions and microbial community under rice straw return in Northeast China. Global Ecology and Conservation, 22: e00962. doi: https://doi.org/10.1016/j.gecco.2020.e00962
Yang H S, Meng Y, Feng J X et al., 2020. Direct and indirect effects of long-term ditch-buried straw return on soil bacterial community in a rice-wheat rotation system. Land Degradation & Development, 31(7): 851–867. doi: https://doi.org/10.1002/ldr.3481
Yu C, Li Y, Mo R L et al., 2020. Effects of long-term straw retention on soil microorganisms under a rice-wheat cropping system. Archives of Microbiology, 202(7): 1915–1927. doi: https://doi.org/10.1007/s00203-020-01899-8
Zhang, S X, Liu, P, Zhang, S Q et al., 2022. Contribution of rhizodeposit associated microbial groups to SOC varies with maize growth stages. Geoderma, 422: 115947. doi: https://doi.org/10.1016/j.geoderma.2022.115947
Zhang X P, Gao G B, Wu Z Z et al., 2019b. Agroforestry alters the rhizosphere soil bacterial and fungal communities of moso bamboo plantations in subtropical China. Applied Soil Ecology, 143: 192–200. doi: https://doi.org/10.1016/j.apsoil.2019.07.019
Zhang Y, Li X J, Gregorich E G et al., 2019a. Evaluating storage and pool size of soil organic carbon in degraded soils: tillage effects when crop residue is returned. Soil & Tillage Research, 192: 215–221. doi: https://doi.org/10.1016/j.still.2019.05.013
Zhao P Z, Li S, Wang E H et al., 2018. Tillage erosion and its effect on spatial variations of soil organic carbon in the black soil region of China. Soil & Tillage Research, 178: 72–81. doi: https://doi.org/10.1016/j.still.2017.12.022
Author information
Authors and Affiliations
Corresponding author
Additional information
Foundation item: Under the auspices of the Strategic Priority Research Program of the Chinese Academy of Sciences (No. XDA2307050103), National Natural Science Foundation of China (No. 42071064, 41877095), the Project of Changchun Science and Technology Plan (No. 19SS019)
Rights and permissions
About this article
Cite this article
Wang, Q., Jia, S., Liang, A. et al. Residue Return Effects Outweigh Tillage Effects on Soil Microbial Communities and Functional Genes in Black Soil of Northeast China. Chin. Geogr. Sci. 33, 679–692 (2023). https://doi.org/10.1007/s11769-023-1335-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11769-023-1335-3