in

Astragalus-cultivated soil was a suitable bed soil for nurturing Angelica sinensis seedlings from the rhizosphere microbiome perspective

  • An, Z., Guo, F., Chen, Y., Bai, G. & Chen, Z. Rhizosphere bacterial and fungal communities during the growth of Angelica sinensis seedlings cultivated in an Alpine uncultivated meadow soil. PeerJ 8, e8541. https://doi.org/10.7717/peerj.8541 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Munkholm, L. J., Heck, R. J. & Deen, B. Long-term rotation and tillage effects on soil structure and crop yield. Soil Tillage Res. 127, 85–91. https://doi.org/10.1016/j.still.2012.02.007 (2013).

    Article 

    Google Scholar 

  • Jiao, X. L. et al. Effects of maize rotation on the physicochemical properties and microbial communities of American ginseng cultivated soil. Sci. Rep. 9, 8615. https://doi.org/10.1038/s41598-019-44530-7 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wang, X., Chen, Y., Guo, F., Yuan, H. & Guo, Y. Effects of medicinal crop stubbles on physiological and biochemical characteristics of Angelica sinensis seedings. J. Chin. Med. Mater. 40, 2002–2006 (2017).

    Google Scholar 

  • Jin, Y. et al. Effect of various crop residues on growth and disease resisitance of Angelica sinensis seedlings in Min County. Acta Pratacul. Sin. 27, 69–78 (2018).

    MathSciNet 

    Google Scholar 

  • Bai, G., Guo, F., Chen, Y., Yuan, H. & Xiao, W. Differences in physiological resistance traits of Angelica sinensis seedlings from uncultivated and cultivated fields in Min County. Acta Pratacul. Sin. 28, 86–95 (2019).

    Google Scholar 

  • Bai, G. et al. Regulated effects of preceding crop on soil property and cultivating seedlings for Angelica sinensis on cultivated farmland. Chin. J. Eco-Agric. 28, 701–712. https://doi.org/10.13930/j.cnki.cjea.190719 (2020).

    Article 
    CAS 

    Google Scholar 

  • Mendes, R., Garbeva, P. & Raaijmakers, J. M. The rhizosphere microbiome: Significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol. Rev. 37, 634–663 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Tkacz, A., Cheema, J., Chandra, G., Grant, A. & Poole, P. S. Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. Int. Soc. Microb. Ecol. 9, 2349–2359. https://doi.org/10.1038/ismej.2015.41 (2015).

    Article 
    CAS 

    Google Scholar 

  • Berg, G. et al. Microbiome definition re-visited: Old concepts and new challenges. Microbiome 8, 103. https://doi.org/10.1186/s40168-020-00875-0 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chaparro, J. M., Badri, D. V. & Vivanco, J. M. Rhizosphere microbiome assemblage is affected by plant development. ISME J. 8, 790–803. https://doi.org/10.1038/ismej.2013.196 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Uroz, S. et al. Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. Sci. Rep. 6, 27756. https://doi.org/10.1038/srep27756 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chamberlain, L. A. et al. Crop rotation, but not cover crops, influenced soil bacterial community composition in a corn-soybean system in southern Wisconsin. Appl. Soil Ecol. 154, 103603. https://doi.org/10.1016/j.apsoil.2020.103603 (2020).

    Article 

    Google Scholar 

  • Classen, A. T. et al. Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead?. Ecosphere 6, 130. https://doi.org/10.1890/es15-00217.1 (2015).

    Article 

    Google Scholar 

  • Tiemann, L. K. et al. Crop rotational diversity enhances belowground communities and functions in an agroecosystem. Ecol. Lett. 18, 761–771. https://doi.org/10.1111/ele.12453 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Maldonado, S. et al. Enhanced crop productivity and sustainability by using native phosphate solubilizing rhizobacteria in the agriculture of arid zones. Front. Sustain. Food Syst. 4, 607355. https://doi.org/10.3389/fsufs.2020.607355 (2020).

    Article 

    Google Scholar 

  • Gómez Expósito, R., de Bruijn, I., Postma, J. & Raaijmakers, J. M. Current insights into the role of rhizosphere bacteria in disease suppressive soils. Front. Microbiol.y 8, 2529. https://doi.org/10.3389/fmicb.2017.02529 (2017).

    Article 

    Google Scholar 

  • Li, X., Rui, J., Mao, Y., Yannarell, A. & Mackie, R. Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar. Soil Biol. Biochem. 68, 392–401. https://doi.org/10.1016/j.soilbio.2013.10.017 (2014).

    Article 
    CAS 

    Google Scholar 

  • Fierer, N. et al. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. Int. Soc. Microb. Ecol. 6, 1007–1017. https://doi.org/10.1038/ismej.2011.159 (2012).

    Article 
    CAS 

    Google Scholar 

  • Kuffner, M. et al. Culturable bacteria from Zn- and Cd-accumulating Salix caprea with differential effects on plant growth and heavy metal availability. J. Appl. Microbiol. 108, 1471–1484. https://doi.org/10.1111/j.1365-2672.2010.04670.x (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • De Corato, U. Disease-suppressive compost enhances natural soil suppressiveness against soil-borne plant pathogens: A critical review. Rhizosphere 13, 100192. https://doi.org/10.1016/j.rhisph.2020.100192 (2020).

    Article 

    Google Scholar 

  • Brookes, P. C., Landman, A., Pruden, G. & Jenkinson, D. S. Chloroform fumigation chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol. Biochem. 17, 837–842 (1985).

    Article 
    CAS 

    Google Scholar 

  • Arnebrant, K. & Schnürer, J. Changes in atp content during and after chloroform fumigation. Soil Biol. Biochem. 22, 875–877 (1990).

    Article 
    CAS 

    Google Scholar 

  • Toju, H. et al. Community composition of root-associated fungi in a Quercus-dominated temperate forest: “codominance” of mycorrhizal and root-endophytic fungi. Ecol. Evol. 3, 1281–1293. https://doi.org/10.1002/ece3.546 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Magoč, T. & Salzberg, S. L. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bokulich, N. A. et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Methods 10, 57–59. https://doi.org/10.1038/nmeth.2276 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Haas, B. J. et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21, 494–504. https://doi.org/10.1101/gr.112730.110 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Edgar, R. C. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998. https://doi.org/10.1038/nmeth.2604 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267. https://doi.org/10.1128/AEM.00062-07 (2007).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596. https://doi.org/10.1093/nar/gks1219 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Edgar, R. C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272 (2016).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Nguyen, N. H. et al. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248. https://doi.org/10.1016/j.funeco.2015.06.006 (2016).

    Article 

    Google Scholar 

  • Sisk-Hackworth, L., Ortiz-Velez, A., Reed, M. B. & Kelley, S. T. Compositional data analysis of periodontal disease microbial communities. Front. Microbiol. 12, 617949. https://doi.org/10.3389/fmicb.2021.617949 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Khan, M. A. W. et al. Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils. FEMS Microbiol. Ecol. 95, fiy230. https://doi.org/10.1093/femsec/fiy230 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zhang, B., Zhang, J., Liu, Y., Shi, P. & Wei, G. Co-occurrence patterns of soybean rhizosphere microbiome at a continental scale. Soil Biol. Biochem. 118, 178–186. https://doi.org/10.1016/j.soilbio.2017.12.011 (2018).

    Article 
    CAS 

    Google Scholar 

  • Huang, M., Jiang, L., Zou, Y., Xu, S. & Deng, G. Changes in soil microbial properties with no-tillage in Chinese cropping systems. Biol. Fertil. Soils 49, 373–377. https://doi.org/10.1007/s00374-013-0778-6 (2013).

    Article 

    Google Scholar 

  • Unger, P. W. & Cassel, D. K. Tillage implement disturbance effects on soil properties related to soil and water conservation: A literature review. Soil Tillage Res. 19, 363–382 (1991).

    Article 

    Google Scholar 

  • Alvarez, R. & Steinbach, H. S. A review of the effects of tillage systems on some soil physical properties, water content, nitrate availability and crops yield in the Argentine Pampas. Soil Tillage Res. 104, 1–15. https://doi.org/10.1016/j.still.2009.02.005 (2009).

    Article 

    Google Scholar 

  • Essel, E. et al. Bacterial and fungal diversity in rhizosphere and bulk soil under different long-term tillage and cereal/legume rotation. Soil Tillage Res. 194, 104302. https://doi.org/10.1016/j.still.2019.104302 (2019).

    Article 

    Google Scholar 

  • Zhu, Q., Wang, N., Duan, B., Wang, Q. & Wang, Y. Rhizosphere bacterial and fungal communities succession patterns related to growth of poplar fine roots. Sci. Total Environ. 756, 143839. https://doi.org/10.1016/j.scitotenv.2020.143839 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Guseva, K. et al. From diversity to complexity: Microbial networks in soils. Soil Biol. Biochem. 169, 108604. https://doi.org/10.1016/j.soilbio.2022.108604 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jiang, B. et al. Analysis of microbial community structure and diversity in surrounding rock soil of different waste dump sites in fushun western opencast mine. Chemosphere 269, 128777. https://doi.org/10.1016/j.chemosphere.2020.128777 (2020).

    Article 
    ADS 
    MathSciNet 
    CAS 
    PubMed 

    Google Scholar 

  • Liu, J. et al. Pecan plantation age influences the structures, ecological networks, and functions of soil microbial communities. Land Degrad. Dev. 33, 3294–3309. https://doi.org/10.1002/ldr.4389 (2022).

    Article 

    Google Scholar 

  • Lv, X. et al. Strengthening insights in microbial ecological networks from theory to applications. mSystems 4, e00124-19. https://doi.org/10.1128/mSystems.00124-19 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Toju, H., Kishida, O., Katayama, N. & Takagi, K. Networks depicting the fine-scale co-occurrences of fungi in soil Horizons. PLoS ONE 11, e0165987. https://doi.org/10.1371/journal.pone.0165987 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chun, S. J., Cui, Y., Baek, S. H., Ahn, C. Y. & Oh, H. M. Seasonal succession of microbes in different size-fractions and their modular structures determined by both macro- and micro-environmental filtering in dynamic coastal waters. Sci. Total Environ. 784, 147046. https://doi.org/10.1016/j.scitotenv.2021.147046 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Cardinale, M., Grube, M., Erlacher, A., Quehenberger, J. & Berg, G. Bacterial networks and co-occurrence relationships in the lettuce root microbiota. Environ. Microbiol. 17, 239–252. https://doi.org/10.1111/1462-2920.12686 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zhou, Z. et al. Increases in bacterial community network complexity induced by biochar-based fertilizer amendments to karst calcareous soil. Geoderma 337, 691–700. https://doi.org/10.1016/j.geoderma.2018.10.013 (2019).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Olesen, J. M., Bascompte, J., Dupont, Y. L. & Jordano, P. The modularity of pollination networks. Proc. Natl. Acad. Sci. U.S.A. 104, 19891–19896. https://doi.org/10.1073/pnas.0706375104 (2007).

    Article 
    ADS 
    PubMed 
    PubMed Central 
    MATH 

    Google Scholar 

  • Eisenhauer, N. et al. Root biomass and exudates link plant diversity with soil bacterial and fungal biomass. Sci. Rep. 7, 44641. https://doi.org/10.1038/srep44641 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hassan, M. K., McInroy, J. A. & Kloepper, J. W. The interactions of rhizodeposits with plant growth-promoting Rhizobacteria in the rhizosphere: A review. Agriculture 9, 142. https://doi.org/10.3390/agriculture9070142 (2019).

    Article 
    CAS 

    Google Scholar 

  • Sasse, J., Martinoia, E. & Northen, T. Feed your friends: Do plant exudates shape the root microbiome?. Trends Plant Sci. 23, 25–41. https://doi.org/10.1016/j.tplants.2017.09.003 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zhang, F., Xu, X., Wang, G., Wu, B. & Xiao, Y. Medicago sativa and soil microbiome responses to Trichoderma as a biofertilizer in alkaline-saline soils. Appl. Soil Ecol. 153, 103573. https://doi.org/10.1016/j.apsoil.2020.103573 (2020).

    Article 

    Google Scholar 

  • Woźniak, A. Chemical properties and enzyme activity of soil as affected by tillage system and previous crop. Agriculture 9, 262. https://doi.org/10.3390/agriculture9120262 (2019).

    Article 
    CAS 

    Google Scholar 

  • Choudhary, M. et al. Changes in soil biology under conservation agriculture based sustainable intensification of cereal systems in Indo-Gangetic Plains. Geoderma 313, 193–204. https://doi.org/10.1016/j.geoderma.2017.10.041 (2018).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Ai, C. et al. Distinct responses of soil bacterial and fungal communities to changes in fertilization regime and crop rotation. Geoderma 319, 156–166. https://doi.org/10.1016/j.geoderma.2018.01.010 (2018).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Gałązka, A., Gawyjołek, K., Perzyński, A., Gałązka, R. & Jerzy, K. Changes in enzymatic activities and microbial communities in soil under long-term maize monoculture and crop rotation. Pol. J. Environ. Stud. 26, 39–46. https://doi.org/10.15244/pjoes/64745 (2017).

    Article 
    CAS 

    Google Scholar 

  • Tremblay, C., Deslauriers, A., Lafond, J., Lajeunesse, J. & Paré, M. Effects of soil pH and fertilizers on haskap (Lonicera caerulea L) vegetative growth. Agriculture 9, 56. https://doi.org/10.3390/agriculture9030056 (2019).

    Article 
    CAS 

    Google Scholar 

  • Sirisuntornlak, N. et al. Interactive effects of silicon and soil pH on growth, yield and nutrient uptake of maize. SILICON 13, 289–299. https://doi.org/10.1007/s12633-020-00427-z (2021).

    Article 
    CAS 

    Google Scholar 

  • Xu, Y., Ge, Y., Song, J. & Rensing, C. Assembly of root-associated microbial community of typical rice cultivars in different soil types. Biol. Fertil. Soils 56, 249–260. https://doi.org/10.1007/s00374-019-01406-2 (2019).

    Article 
    CAS 

    Google Scholar 

  • Putranta, H., Permatasari, A. K., Sukma, T. A. & Dwandaru, W. S. B. The effect of pH, electrical conductivity, and nitrogen (N) in the soil at yogyakarta special region on tomato plant growth. TEM J.-Technol. Educ. Manag. Inform. 8, 860–865. https://doi.org/10.18421/TEM83-24 (2019).

    Article 

    Google Scholar 

  • Wang, J. et al. Effects of alternate partial root-zone irrigation on soil microorganism and maize growth. Plant Soil 302, 45–52. https://doi.org/10.1007/s11104-007-9453-8 (2007).

    Article 
    CAS 

    Google Scholar 

  • Yang, X., Zhu, K., Loik, M. E. & Sun, W. Differential responses of soil bacteria and fungi to altered precipitation in a meadow steppe. Geoderma 384, 114812. https://doi.org/10.1016/j.geoderma.2020.114812 (2021).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Balota, E. L., Colozzi Filho, A., Andrade, D. S. & Dick, R. P. Long-term tillage and crop rotation effects on microbial biomass and C and N mineralization in a Brazilian Oxisol. Soil Tillage Res. 77, 137–145. https://doi.org/10.1016/j.still.2003.12.003 (2004).

    Article 

    Google Scholar 

  • Franchini, J., Crispino, C., Souza, R., Torres, E. & Hungria, M. Microbiological parameters as indicators of soil quality under various soil management and crop rotation systems in southern Brazil. Soil Tillage Res. 92, 18–29. https://doi.org/10.1016/j.still.2005.12.010 (2007).

    Article 

    Google Scholar 

  • Li, X., Wang, T., Chang, S. X., Jiang, X. & Song, Y. Biochar increases soil microbial biomass but has variable effects on microbial diversity: A meta-analysis. Sci. Total Environ. 749, 141593. https://doi.org/10.1016/j.scitotenv.2020.141593 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Lynch, J. M. & Panting, L. M. Effects of season, cultivation and nitrogen fertiliser on the size of the soil microbial biomass. J. Sci. Food Agric. 33, 249–252 (1982).

    Article 
    CAS 

    Google Scholar 

  • Tan, G. et al. Effects of biochar application with fertilizer on soil microbial biomass and greenhouse gas emissions in a peanut cropping system. Environ. Technol. 42, 9–19. https://doi.org/10.1080/09593330.2019.1620344 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Liu, C. et al. Linkages between nutrient ratio and the microbial community in rhizosphere soil following fertilizer management. Environ. Res. 184, 109261. https://doi.org/10.1016/j.envres.2020.109261 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Li, H. et al. Film mulching, residue retention and N fertilization affect ammonia volatilization through soil labile N and C pools. Agric. Ecosyst. Environ. 308, 107272. https://doi.org/10.1016/j.agee.2020.107272 (2021).

    Article 
    CAS 

    Google Scholar 

  • Jiao, P. et al. Bacteria are more sensitive than fungi to moisture in eroded soil by natural grass vegetation restoration on the Loess Plateau. Sci. Total Environ. 756, 143899. https://doi.org/10.1016/j.scitotenv.2020.143899 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Sommer, J. et al. The tree species matters: Belowground carbon input and utilization in the myco-rhizosphere. Eur. J. Soil Biol. 81, 100–107. https://doi.org/10.1016/j.ejsobi.2017.07.001 (2017).

    Article 
    CAS 

    Google Scholar 

  • Yu, K., Pieterse, C. M. J., Bakker, P. A. H. M. & Berendsen, R. L. Beneficial microbes going underground of root immunity. Plant Cell Environ. 42, 2860–2870. https://doi.org/10.1111/pce.13632 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • de Varennes, A. & Goss, M. J. The tripartite symbiosis between legumes, rhizobia and indigenous mycorrhizal fungi is more efficient in undisturbed soil. Soil Biol. Biochem. 39, 2603–2607. https://doi.org/10.1016/j.soilbio.2007.05.007 (2007).

    Article 
    CAS 

    Google Scholar 

  • Wang, X. et al. Mycorrhizal symbiosis modulates the rhizosphere microbiota to promote rhizobia-legume symbiosis. Mol. Plant 14, 503–516. https://doi.org/10.1016/j.molp.2020.12.002 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zhang, R., Vivanco, J. M. & Shen, Q. The unseen rhizosphere root-soil-microbe interactions for crop production. Curr. Opin. Microbiol. 37, 8–14. https://doi.org/10.1016/j.mib.2017.03.008 (2017).

    Article 
    PubMed 

    Google Scholar 

  • Berendsen, R. L., Pieterse, C. M. & Bakker, P. A. The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478–486. https://doi.org/10.1016/j.tplants.2012.04.001 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar 


  • Source: Ecology - nature.com

    Q&A: Tod Machover on “Overstory Overture,” his new operatic work

    Untitled public forestlands threat Amazon conservation