Mulches assist degraded soil recovery via stimulating biogeochemical cycling: metagenomic analysis.

Item request has been placed! ×
Item request cannot be made. ×
loading   Processing Request
  • Additional Information
    • Source:
      Publisher: Springer International Country of Publication: Germany NLM ID: 8406612 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1432-0614 (Electronic) Linking ISSN: 01757598 NLM ISO Abbreviation: Appl Microbiol Biotechnol Subsets: MEDLINE
    • Publication Information:
      Original Publication: Berlin ; New York : Springer International, c1984-
    • Subject Terms:
    • Abstract:
      Soil degradation of urban greening has caused soil fertility loss and soil organic carbon depletion. Organic mulches are made from natural origin materials, and represent a cost-effective and environment-friendly remediation method for urban greening. To reveal the effects of organic mulch on soil physicochemical characteristics and fertility, we selected a site that was covered with organic mulch for 6 years and a nearby lawn-covered site. The results showed that soil organic matter, total nitrogen, and available phosphorus levels were improved, especially at a depth of 0-20 cm. The activities of cellulase, invertase, and dehydrogenase in soil covered with organic mulch were 17.46%, 78.98%, and 283.19% higher than those under lawn, respectively. The marker genes of fermentation, aerobic respiration, methanogenesis, and methane oxidation were also enriched in the soil under organic mulch. Nitrogen cycling was generally repressed by the organic mulch, but the assimilatory nitrate and nitrite reduction processes were enhanced. The activity of alkaline phosphatase was 12.63% higher in the mulch-covered soil, and functional genes involved in phosphorus cycling were also enriched. This study presents a comprehensive investigation of the influence of organic mulch on soil microbes and provides a deeper insight into the recovery strategy for soil degradation following urban greening. KEY POINTS: • Long-term cover with organic mulches assists soil recovery from degradation • Soil physical and chemical properties were changed by organic mulches • Organic mulches enhanced genes involved in microbially mediated C and P cycling • Soil organic matter was derived from decomposition of organic mulch and carbon fixation • N cycling was repressed by mulches, except for assimilatory NO 2 - and NO 3 - reductions.
      (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
    • References:
      Beeckman F, Motte H, Beeckman T (2018) Nitrification in agricultural soils: impact, actors and mitigation. Curr Opin Biotechnol 50:166. https://doi.org/10.1016/j.copbio.2018.01.014. (PMID: 10.1016/j.copbio.2018.01.01429414056)
      Byrne LB, Bruns MA, Kim KC (2008) Ecosystem properties of urban land covers at the aboveground-belowground interface. Ecosystems 11(7):1065–1077. https://doi.org/10.1007/s10021-008-9179-3. (PMID: 10.1007/s10021-008-9179-3)
      Chang EH, Chung RS, Tsai YH (2010) Effect of different application rates of organic fertilizer on soil enzyme activity and microbial population. Soil Sci Plant Nutr 53(2):132–140. https://doi.org/10.1111/j.1747-0765.2007.00122.x. (PMID: 10.1111/j.1747-0765.2007.00122.x)
      Chen S, Gao R, Xiang X, Yang H, Ma H, Zheng T, Xiao Y, Zhang X, Li H, Fan G, Yu Y (2021) Straw mulching and nitrogen application altered ammonia oxidizers communities and improved soil quality in the alkaline purple soil of southwest China. AMB Express 11(1):52. https://doi.org/10.1186/s13568-021-01211-x. (PMID: 10.1186/s13568-021-01211-x338259888026789)
      Dai Z, Hu J, Fan J, Fu W, Wang H, Hao M (2021) No-tillage with mulching improves maize yield in dryland farming through regulating soil temperature, water and nitrate-N. Agr Ecosyst Environ 309:107288. https://doi.org/10.1016/j.agee.2020.107288. (PMID: 10.1016/j.agee.2020.107288)
      Faci JM, Araguees R, Zribi W, Medina E (2015) Efficiency of inorganic and organic mulching materials for soil evaporation control. Soil Tillage Res 148:40–45. https://doi.org/10.1016/j.jarmap.2020.100287. (PMID: 10.1016/j.jarmap.2020.100287)
      Flessa H, Potthoff M, Loftfield N (2002) Greenhouse estimates of CO2 and N2O emissions following surface application of grass mulch: importance of indigenous microflora of mulch. Soil Biol Biochem 34(6):875–879. https://doi.org/10.1016/S0038-0717(02)00028-7. (PMID: 10.1016/S0038-0717(02)00028-7)
      Galand PE, Pereira O, Hochart C, Auguet JC, Debroas D (2018) A strong link between marine microbial community composition and function challenges the idea of functional redundancy. ISME J 12(10):2470–2478. https://doi.org/10.1038/s41396-018-0158-1. (PMID: 10.1038/s41396-018-0158-1299258806155072)
      Gs S, Lal R (2004) Mulching effects on phosphorus and sulfur concentrations in a Miamian soil in central Ohio, USA. Land Degrad Dev 15:351–365. https://doi.org/10.1002/ldr.599. (PMID: 10.1002/ldr.599)
      Hosseini Bai S, Blumfield TJ, Reverchon F (2014) The impact of mulch type on soil organic carbon and nitrogen pools in a sloping site. Biol Fertil Soils 50(1):37–44. https://doi.org/10.1007/s00374-013-0829-z. (PMID: 10.1007/s00374-013-0829-z)
      Huang Z, Xu Z, Chen C (2008) Effect of mulching on labile soil organic matter pools, microbial community functional diversity and nitrogen transformations in two hardwood plantations of subtropical Australia. Appl Soil Ecol 40(2):229–239. https://doi.org/10.1016/j.apsoil.2008.04.009. (PMID: 10.1016/j.apsoil.2008.04.009)
      Jian J, Du X, Reiter M, Stewart R (2020) A meta-analysis of global cropland soil carbon changes due to cover cropping. Soil Biol Biochem 143:107735. https://doi.org/10.1016/j.soilbio.2020.107735. (PMID: 10.1016/j.soilbio.2020.107735)
      Jiang D, Jiang N, Jiang H, Chen L (2023) Urease inhibitors increased soil ureC gene abundance and intracellular urease activity when extracellular urease activity was inhibited. Geoderma 430:116295. https://doi.org/10.1016/j.geoderma.2022.116295. (PMID: 10.1016/j.geoderma.2022.116295)
      Jin X, Guijun Y, Xu X, Yang H, Feng H, Li Z, Shen J, Zhao C, Lan Y (2015) Combined multi-temporal optical and radar parameters for estimating LAI and biomass in winter wheat using HJ and RADARSAR-2 data. Remote Sens 7 https://doi.org/10.3390/rs71013251.
      Jordon MW, Smith P, Long PR, Bürkner P-C, Petrokofsky G, Willis KJ (2022) Can regenerative agriculture increase national soil carbon stocks? Simulated country-scale adoption of reduced tillage, cover cropping, and ley-arable integration using RothC. Sci Total Environ 825:153955. https://doi.org/10.1016/j.scitotenv.2022.153955. (PMID: 10.1016/j.scitotenv.2022.15395535189215)
      Kader MA, Senge M, Mojid MA, Ito K (2017) Recent advances in mulching materials and methods for modifying soil environment. Soil Tillage Res 168:155–166. https://doi.org/10.1016/j.still.2017.01.001. (PMID: 10.1016/j.still.2017.01.001)
      Kuypers MMM, Marchant HK, Kartal B (2018) The microbial nitrogen-cycling network. Nat Rev Microbiol 16(5):263–276. https://doi.org/10.1038/nrmicro.2018.9. (PMID: 10.1038/nrmicro.2018.929398704)
      Leadbeater DR, Oates NC, Bennett JP, Li Y, Dowle AA, Taylor JD, Alponti JS, Setchfield AT, Alessi AM, Helgason T, McQueen-Mason SJ, Bruce NC (2021) Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh. Microbiome 9(1):48. https://doi.org/10.1186/s40168-020-00964-0. (PMID: 10.1186/s40168-020-00964-0335970337890819)
      Lee DK, Nguyen VT, Littlefield S (1996) Comparison of methods for determination of nitrogen levels in soil, plant and body tissues, and water. Commun Soil Sci Plant Anal 27:783–793. https://doi.org/10.1080/00103629609369595. (PMID: 10.1080/00103629609369595)
      Li Y, Dong S, Liu S, Zhou H, Gao Q, Cao G, Wang X, Su X, Zhang Y, Tang L, Zhao H, Wu X (2015a) Seasonal changes of CO2, CH4 and N2O fluxes in different types of alpine grassland in the Qinghai-Tibetan Plateau of China. Soil Biol Biochem 80:306–314. https://doi.org/10.1016/j.soilbio.2014.10.026. (PMID: 10.1016/j.soilbio.2014.10.026)
      Li ZP, Wu FZ, Yang WQ, Xu ZF, Huang L (2015b) Soil invertase and urease activities at different periods in subalpine forest gap in western Sichuan. Acta Ecol Sin 35(12):3919–3925. https://doi.org/10.5846/STXB201308302177. (PMID: 10.5846/STXB201308302177)
      Li D, Luo R, Liu CM, Leung CM, Ting HF, Sadakane K, Yamashita H, Lam TW (2016) MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods (san Diego, Calif) 102:3–11. https://doi.org/10.1016/j.ymeth.2016.02.020. (PMID: 10.1016/j.ymeth.2016.02.02027012178)
      Li X, Xie J, Zhang Q, Lyu M, Xiong X, Liu X, Lin T, Yang Y (2020) Substrate availability and soil microbes drive temperature sensitivity of soil organic carbon mineralization to warming along an elevation gradient in subtropical Asia. Geoderma 364:114198. https://doi.org/10.1016/j.geoderma.2020.114198. (PMID: 10.1016/j.geoderma.2020.114198)
      Liu F, Zhang Y, Liang H, Gao D (2021) Resilience of methane cycle and microbial functional genes to drought and flood in an alkaline wetland: a metagenomic analysis. Chemosphere 265:129034. https://doi.org/10.1016/j.chemosphere.2020.129034.
      Liu F, Yupeng Z, Liang H, Gao D (2019a) Long-term harvesting of reeds affects greenhouse gas emissions and microbial functional genes in alkaline wetlands. Water Res 164:114936. https://doi.org/10.1016/j.watres.2019.114936. (PMID: 10.1016/j.watres.2019.11493631382148)
      Liu F, Zhang Y, Liang H, Gao D (2019b) Specific quorum sensing molecules of ammonia oxidizers and their role during ammonium metabolism in Zhalong wetland, China. Sci Total Environ 666:1106–1113. https://doi.org/10.1016/j.scitotenv.2019.02.261. (PMID: 10.1016/j.scitotenv.2019.02.26130970476)
      Martir-Torres MC, Bruns MA (2013) Comparative diversity and abundance of ammonia monooxygenase genes in mulched and vegetated soils. Soil Biol Biochem 57:758–768. https://doi.org/10.1016/j.soilbio.2012.10.016. (PMID: 10.1016/j.soilbio.2012.10.016)
      McIntyre BD, Gold CS, Ssali H, Riha SJ (2003) Effects of mulch location on banana weevil, soil and plant nutrients, soil water and biomass in banana fields. Biol Fertil Soils 39(2):74–79. https://doi.org/10.1007/s00374-003-0681-7. (PMID: 10.1007/s00374-003-0681-7)
      Murata T, Kanao-Koshikawa M, Takamatsu T (2005) Effects of Pb, Cu, Sb, In and Ag contamination on the proliferation of soil bacterial colonies, soil dehydrogenase activity, and phospholipid fatty acid profiles of soil microbial communities. Water Air Soil Pollut 164(1–4):103–118. https://doi.org/10.1007/s11270-005-2254-x. (PMID: 10.1007/s11270-005-2254-x)
      Ni X, Song W, Zhang H, Yang X, Wang L (2016) Effects of mulching on soil properties and growth of tea olive (Osmanthus fragrans). PLoS One 11(8):e0158228. https://doi.org/10.1371/journal.pone.0158228.
      Qian X, Gu J, Pan H-j, Zhang K-y, Sun W, Wang X-j, Gao H (2015) Effects of living mulches on the soil nutrient contents, enzyme activities, and bacterial community diversities of apple orchard soils. Eur J Soil Biol 70:23–30. https://doi.org/10.1016/j.ejsobi.2015.06.005. (PMID: 10.1016/j.ejsobi.2015.06.005)
      Raymond NS, Gómez-Muñoz B, van der Bom FJT, Nybroe O, Jensen LS, Müller-Stöver DS, Oberson A, Richardson AE (2021) Phosphate-solubilising microorganisms for improved crop productivity: a critical assessment. New Phytol 229(3):1268–1277. https://doi.org/10.1111/nph.16924. (PMID: 10.1111/nph.1692432929739)
      Renuka N, Guldhe A, Prasanna R, Singh P, Bux F (2018) Microalgae as multi-functional options in modern agriculture: current trends, prospects and challenges. Biotechnol Adv 36(4):1255–1273. https://doi.org/10.1016/j.biotechadv.2018.04.004. (PMID: 10.1016/j.biotechadv.2018.04.00429673972)
      Sainju UM, Schomberg HH, Singh BP, Whitehead WF, Tillman PG, Lachnicht-Weyers SL (2007) Cover crop effect on soil carbon fractions under conservation tillage cotton. Soil Tillage Res 96(1–2):205–218. https://doi.org/10.1016/j.biotechadv.2018.04.004. (PMID: 10.1016/j.biotechadv.2018.04.004)
      Santos-Júnior CD, Sarmento H, de Miranda FP, Henrique-Silva F, Logares R (2020) Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter. Microbiome 8(1):151. https://doi.org/10.1186/s40168-020-00930-w. (PMID: 10.1186/s40168-020-00930-w331269257597016)
      Scharenbroch BC, Lloyd JE, Johnson-Maynard JL (2005) Distinguishing urban soils with physical, chemical, and biological properties. Pedobiologia - Int J Soil Biol 49(4):283–296. https://doi.org/10.1016/j.pedobi.2004.12.002. (PMID: 10.1016/j.pedobi.2004.12.002)
      Sharma RR, Sharma VP (2003) Mulch type influences plant growth, albinism disorder and fruit quality in strawberry (Fragaria×ananassaDusch.). Fruits 58(4):221–227. https://doi.org/10.1051/fruits:2003010. (PMID: 10.1051/fruits:2003010)
      Souza RC, Hungria M, Cantão ME, Vasconcelos ATR, Nogueira MA, Vicente VA (2015) Metagenomic analysis reveals microbial functional redundancies and specificities in a soil under different tillage and crop-management regimes. Appl Soil Ecol 86:106–112. https://doi.org/10.1016/j.apsoil.2014.10.010. (PMID: 10.1016/j.apsoil.2014.10.010)
      Sui L, Tang C, Cheng K, Yang F (2022) Biochar addition regulates soil phosphorus fractions and improves release of available phosphorus under freezing-thawing cycles. Sci Total Environ 848:157748. https://doi.org/10.1016/j.scitotenv.2022.157748. (PMID: 10.1016/j.scitotenv.2022.15774835926613)
      Sun X, Wang G, Ye Y, Ma Q, Guan Q, Jones DL (2021a) Response of nitrogen fractions in the rhizosphere and bulk soil to organic mulching in an urban forest plantation. J For Res 32(6):2577–2588. https://doi.org/10.1007/s11676-021-01310-2. (PMID: 10.1007/s11676-021-01310-2)
      Sun X, Ye Y, Guan Q, Jones DL (2021b) Organic mulching masks rhizosphere effects on carbon and nitrogen fractions and enzyme activities in urban greening space. J Soils Sediments 21(4):1621–1632. https://doi.org/10.1007/s11368-021-02900-7. (PMID: 10.1007/s11368-021-02900-7)
      Sun X, Ye Y, Liao J, Tang Y, Guan Q (2021c) Organic mulching alters the composition, but not the diversity, of rhizosphere bacterial and fungal communities. Appl Soil Ecol 168:104167. https://doi.org/10.1016/j.apsoil.2021.104167. (PMID: 10.1016/j.apsoil.2021.104167)
      Sun X, Ye Y, Ma Q, Guan Q, Jones D (2021d) Variation in enzyme activities involved in carbon and nitrogen cycling in rhizosphere and bulk soil after organic mulching. Rhizosphere 19:100376. https://doi.org/10.1016/j.rhisph.2021.100376. (PMID: 10.1016/j.rhisph.2021.100376)
      Wang H, Cheng M, Dsouza M, Weisenhorn P, Zheng T, Gilbert JA (2018a) Soil bacterial diversity is associated with human population density in urban greenspaces. Environ Sci Technol 52(9):5115–5124. https://doi.org/10.1021/acs.est.7b06417. (PMID: 10.1021/acs.est.7b0641729624051)
      Wang G, Chen L, Zhang D, Qin S, Peng Y, Yang G, Wang J, Yu J, Wei B, Liu Y, Li Q, Kang L, Wang Y, Yang Y (2022a) Divergent trajectory of soil autotrophic and heterotrophic respiration upon permafrost thaw. Environ Sci Technol 56(14):10483–10493. https://doi.org/10.1021/acs.est.1c07575. (PMID: 10.1021/acs.est.1c0757535748652)
      Wang G, Gao Q, Yang Y, Hobbie SE, Reich PB, Zhou J (2022b) Soil enzymes as indicators of soil function: a step toward greater realism in microbial ecological modeling. Glob Change Biol 28(5):1935–1950. https://doi.org/10.1111/gcb.16036. (PMID: 10.1111/gcb.16036)
      Wang J, Niu W, Guo L, Liu L, Li Y, Dyck M (2018b) Drip irrigation with film mulch improves soil alkaline phosphatase and phosphorus uptake. Agri Water Manag 258–267 https://doi.org/10.1016/j.agwat.2017.12.022.
      Wang G, Jin Z, Wang X, George TS, Feng G, Zhang L (2022c) Simulated root exudates stimulate the abundance of Saccharimonadales to improve the alkaline phosphatase activity in maize rhizosphere. Applied Soil Ecology(170-):170 https://doi.org/10.1016/j.apsoil.2021.104274.
      Whalen ED, Grandy AS, Sokol NW, Keiluweit M, Ernakovich J, Smith RG, Frey SD (2022) Clarifying the evidence for microbial- and plant-derived soil organic matter, and the path toward a more quantitative understanding. Glob Change Biol 28(24):7167–7185. https://doi.org/10.1111/gcb.16413. (PMID: 10.1111/gcb.16413)
      Wu L-s, Feng S, Nie Y-y, Zhou J-h, Yang Z-r, Zhang J (2015) Soil cellulase activity and fungal community responses to wetland degradation in the Zoige Plateau, China. J Mt Sci 12(2):471–482. https://doi.org/10.1007/s11629-014-3183-1. (PMID: 10.1007/s11629-014-3183-1)
      Xiao R, Tian Y, Xu G (2020) Spatial gradient of urban green field influenced by soil sealing. Sci Total Environ 735:139490. https://doi.org/10.1016/j.scitotenv.2020.139490. (PMID: 10.1016/j.scitotenv.2020.13949032470673)
      Xie W, Wang Z, Cao Y, Zhang X, He W (2015) Relationship between arsenic and soil alkaline phosphatase activity based on changes of soil moisture. Acta Sci Circum 35(10):3261–3268. https://doi.org/10.13671/j.hjkxxb.2014.1072. (PMID: 10.13671/j.hjkxxb.2014.1072)
      Xu YC, Shen QR, Li ML, Dittert K, Sattelmacher B (2004) Effect of soil water status and mulching on N2O and CH4 emission from lowland rice field in China. Biol Fertil Soils 39(3):215–217. https://doi.org/10.1007/s00374-003-0692-4. (PMID: 10.1007/s00374-003-0692-4)
      Xu D, Ling J, Qiao F, Xi P, Zeng Y, Zhang J, Lan C, Jiang Z, Peng A, Li P (2022) Organic mulch can suppress litchi downy blight through modification of soil microbial community structure and functional potentials. BMC Microbiol 22(1):1–12. https://doi.org/10.1186/s12866-022-02492-3. (PMID: 10.1186/s12866-022-02492-3)
      Yadav GS, Das A, Lal R, Babu S, Datta M, Meena RS, Patil SB, Singh R (2019) Impact of no-till and mulching on soil carbon sequestration under rice (Oryza sativa L.)-rapeseed (Brassica campestris L. var. rapeseed) cropping system in hilly agro-ecosystem of the Eastern Himalayas, India. Agr Ecosyst Environ 275:81–92. https://doi.org/10.1016/j.agee.2019.02.001. (PMID: 10.1016/j.agee.2019.02.001)
      Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y (2017) ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 8(1):28–36. https://doi.org/10.1111/2041-210X.12628. (PMID: 10.1111/2041-210X.12628)
      Yuan L, Chen X, Jia J, Chen H, Shi Y, Ma J, Liang C, Liu Y, Xie H, He H, Zhang X, Peng X, Lu C (2021) Stover mulching and inhibitor application maintain crop yield and decrease fertilizer N input and losses in no-till cropping systems in Northeast China. Agr Ecosyst Environ 312:107360. https://doi.org/10.1016/j.agee.2021.107360. (PMID: 10.1016/j.agee.2021.107360)
      Zhang Z, Kaye JP, Bradley BA, Amsili JP, Suseela V (2022) Cover crop functional types differentially alter the content and composition of soil organic carbon in particulate and mineral-associated fractions. Glob Change Biol 28(19):5831–5848. https://doi.org/10.1111/gcb.16296. (PMID: 10.1111/gcb.16296)
      Zhang Q, Chen M, Leng Y, Wang X, Fu Y, Wang D, Zhao X, Gao W, Li N, Chen X, Fan C, Li Q (2023) Organic substitution stimulates ammonia oxidation-driven N2O emissions by distinctively enriching keystone species of ammonia-oxidizing archaea and bacteria in tropical arable soils. Sci Total Environ 872:162183. https://doi.org/10.1016/j.scitotenv.2023.162183. (PMID: 10.1016/j.scitotenv.2023.16218336804975)
    • Contributed Indexing:
      Keywords: Biogeochemical cycling; Metagenomic; Organic mulches; Soil degradation; Soil enzyme
    • Accession Number:
      0 (Soil)
      7440-44-0 (Carbon)
      N762921K75 (Nitrogen)
      27YLU75U4W (Phosphorus)
    • Publication Date:
      Date Created: 20231230 Date Completed: 20240103 Latest Revision: 20240117
    • Publication Date:
      20240117
    • Accession Number:
      10.1007/s00253-023-12824-6
    • Accession Number:
      38159114