in

Soil inoculum identity and rate jointly steer microbiomes and plant communities in the field

  • Hu ZM, Li SG, Guo Q, Niu SL, He NP, Li LH. et al. A synthesis of the effect of grazing exclusion on carbon dynamics in grasslands in China. Global Change Biol. 2016;22:1385–93.

    Article 

    Google Scholar 

  • Lyu X, Li XB, Gong JR, Wang H, Dang DL, Dou HS, et al. Comprehensive grassland degradation monitoring by remote sensing in Xilinhot, Inner Mongolia, China. Sustainability. 2020;12:3682.

    Article 

    Google Scholar 

  • O’Mara FP. The role of grasslands in food security and climate change. Ann Bot-London. 2012;110:1263–70.

    Article 

    Google Scholar 

  • Bryan BA, Gao L, Ye YQ, Sun XF, Connor JD, Crossman ND, et al. China’s response to a national land-system sustainability emergency. Nature. 2018;559:193–204.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Bardgett RD, Bullock JM, Lavorel S, Manning P, Schaffner U, Ostle N. et al. Combatting global grassland degradation. Nat Rev Earth Environ. 2021;2:720–35.

    Article 

    Google Scholar 

  • Chang JF, Ciais P, Gasser T, Smith P, Herrero M, Havlik P, et al. Climate warming from managed grasslands cancels the cooling effect of carbon sinks in sparsely grazed and natural grasslands. Nat Commun. 2021;12:118.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wardle DA, Bardgett RD, Klironomos JN, Setälä H, van der Putten WH, Wall DH. Ecological linkages between aboveground and belowground biota. Science. 2004;304:1629–33.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Feeney DS, Crawford JW, Daniell T, Hallett PD, Nunan N, Ritz K, et al. Three-dimensional microorganization of the soil-root-microbe system. Microb Ecol. 2006;52:151–8.

    PubMed 
    Article 

    Google Scholar 

  • Harris J. Soil microbial communities and restoration ecology: Facilitators or followers? Science. 2009;325:573–4.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Vecrin MP, Muller S. Top-soil translocation as a technique in the re-creation of species-rich meadows. Appl Veg Sci. 2003;6:271–8.

    Article 

    Google Scholar 

  • Middleton EL, Bever JD. Inoculation with a native soil community advances succession in a grassland restoration. Restor Ecol. 2012;20:218–26.

    Article 

    Google Scholar 

  • Wubs ERJ, van der Putten WH, Bosch M, Bezemer TM. Soil inoculation steers restoration of terrestrial ecosystems. Nat Plants. 2016;2:16107.

    PubMed 
    Article 

    Google Scholar 

  • Wubs ERJ, van Heusden T, Melchers PD, Bezemer TM. Soil inoculation steers plant-soil feedback, suppressing ruderal plant species. Front Ecol Evol. 2019;7:451.

    Article 

    Google Scholar 

  • Bever JD. Feedback between plants and their soil communities in an old field community. Ecology. 1994;75:1965–77.

    Article 

    Google Scholar 

  • Bennett JA, Maherali H, Reinhart KO, Lekberg Y, Hart MM, Klironomos J. Plant-soil feedbacks and mycorrhizal type influence temperate forest population dynamics. Science. 2017;355:181–4.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Contos P, Wood JL, Murphy NP, Gibb H. Rewilding with invertebrates and microbes to restore ecosystems: Present trends and future directions. Ecol Evol. 2021;11:7187–200.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Emam T. Local soil, but not commercial AMF inoculum, increases native and non-native grass growth at a mine restoration site. Restor Ecol. 2016;24:35–44.

    Article 

    Google Scholar 

  • Moradi J, Vicentini F, Simackova H, Pizl V, Tajovsky K, Stary J. An investigation into the long-term effect of soil transplant in bare spoil heaps on survival and migration of soil meso and macrofauna. Ecol Eng. 2018;110:158–64.

    Article 

    Google Scholar 

  • Carbajo V, den Braber B, van der Putten WH, De Deyn GB. Enhancement of late successional plants on ex-arable land by soil inoculations. Plos One. 2011;6:e21943.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Ma W, Liang XS, Wang ZW, Luo WT, Yu Q, Han XG. Resistance of steppe communities to extreme drought in northeast China. Plant Soil. 2022;473:181–194.

  • IUSS Working Group WRB. World Reference Base for Soil Resources 2014, update 2015 International soil classification system for naming soils and creating legends for soil maps. World Soil Resources Reports No. 106. FAO, Rome, 2015.

  • Jaunatre R, Buisson E, Dutoit T. Topsoil removal improves various restoration treatments of a Mediterranean steppe (La Crau, southeast France). Appl Veg Sci. 2014;17:236–45.

    Article 

    Google Scholar 

  • Kuo S. Methods of soil analysis. Part 3: chemical methods. Soil Science Society of America: Madison, 1996.

  • Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. P Natl Acad Sci USA. 2008;105:10583–8.

    CAS 
    Article 

    Google Scholar 

  • De Beeck MO, Lievens B, Busschaert P, Declerck S, Vangronsveld J, Colpaert JV. Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies. Plos One. 2014;9:e97629.

    Article 

    Google Scholar 

  • Magoč T, Salzberg SL. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957–63.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Chen SF, Zhou YQ, Chen YR, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Edgar RC. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb. 2007;73:5261–7.

    CAS 
    Article 

    Google Scholar 

  • Quast C, Pruesse E, Gerken J, Peplies J, Yarza P, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41:590–6.

    Article 
    CAS 

    Google Scholar 

  • Kõljalg U, Larsson K-H, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U, et al. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol. 2005;166:1063–8.

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Oostenbrink M. Estimating nematode populations by some selected methods. Nematology, Chapel Hill, 1960.

  • Townshend JL. A modification and evaluation of the apparatus for the Oostenbrink direct cotton wool filter extraction method. Nematologica. 1963;9:106–10.

    Article 

    Google Scholar 

  • Bongers T. De Nematoden van Nederland. In: Vormgeving en technische realisatie. Uitgeverij Pirola, Schoorl, 1994.

  • Ahmad W, Jairjpuri MS. Mononchida: the predaceous nematodes. Nematology Monographs and Perspectives. Brill, Boston, 2010.

  • Li Q, Liang WJ, Zhang XK, Mahamood M. Soil nematodes of grasslands in Northern China. Academic Press: San Diego, 2017.

  • Wu ZY, Raven PH, Hong DY. Flora of China. Science Press: Beijing, 2013.

  • Munson SM, Long AL, Wallace CSA, Webb RH. Cumulative drought and land-use impacts on perennial vegetation across a North American dryland region. Appl Veg Sci. 2016;19:430–41.

    Article 

    Google Scholar 

  • Li YH, Wang W, Liu ZL, Jiang S. Grazing gradient versus restoration succession of leymus chinensis (Trin.) Tzvel. grassland in inner mongolia. Restor Ecol. 2008;16:572–83.

    Article 

    Google Scholar 

  • Liang C, Michalk DL, Millar GD. The ecology and growth patterns of Cleistogenes species in degraded grasslands of eastern Inner Mongolia, China. J Appl Ecol. 2002;39:584–94.

    Article 

    Google Scholar 

  • Liu ZG, Li ZQ. Effects of different grazing regimes on the morphological traits of Carex duriuscula on the Inner Mongolia steppe. China. New Zeal J Agr Res. 2010;53:5–12.

    Article 

    Google Scholar 

  • Liu M, Gong JR, Pan Y, Luo QP, Zhai ZW, Yang LL, et al. Response of dominant grassland species in the temperate steppe of Inner Mongolia to different land uses at leaf and ecosystem levels. Photosynthetica. 2018;56:921–31.

    Article 

    Google Scholar 

  • Bates D, Machler M, Bolker BM, Walker SC. Fitting linear mixed-effects models using lme4. J Stat Softw. 2015;67:1–48.

    Article 
    CAS 

    Google Scholar 

  • Dixon P. Vegan, a package of R functions for community ecology. J Veg Sci. 2003;14:927–30.

    Article 

    Google Scholar 

  • McMurdie PJ, Holmes S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. Plos One. 2013;8:e61217.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • De Cáceres M, Legendre P, Moretti M. Improving indicator species analysis by combining groups of sites. Oikos. 2010;119:1674–84.

    Article 

    Google Scholar 

  • Hartman K, van der Heijden MGA, Wittwer RA, Banerjee S, Walser JC, Schlaeppi K. Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. Microbiome. 2018;6:14.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Aitchison J. A new approach to null correlations of proportions. Mathematical Geology. 1981;13:175–89.

    Article 

    Google Scholar 

  • Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. Plos Comput Biol. 2015;11:e1004226.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Cao YP, Lin W, Li HZ. Two-sample tests of high-dimensional means for compositional data. Biometrika. 2018;105:115–32.

    Article 

    Google Scholar 

  • Csardi G, Nepusz T. The igraph software package for complex network research. InterJ Complex Syst. 2006;1695:1–9.

  • Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol. 2018;16:567–76.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Banerjee S, Schlaeppi K, van der Heijden MGA. Reply to ‘Can we predict microbial keystones?’. Nat Rev Microbiol. 2019;17:194–194.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Zheng HP, Yang TJ, Bao YZ, He PP, Yang KM, Mei XL, et al. Network analysis and subsequent culturing reveal keystone taxa involved in microbial litter decomposition dynamics. Soil Biol Biochem. 2021;157:108230.

    CAS 
    Article 

    Google Scholar 

  • Kardol P, Wardle DA. How understanding aboveground-belowground linkages can assist restoration ecology. Trends Ecol Evol. 2010;25:670–9.

    PubMed 
    Article 

    Google Scholar 

  • Wubs ERJ, van der Putten WH, Mortimer SR, Korthals GW, Duyts H, Wagenaar R, et al. Single introductions of soil biota and plants generate long-term legacies in soil and plant community assembly. Ecol Lett. 2019;22:1145–51.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • St-Denis A, Kneeshaw D, Belanger N, Simard S, Laforest-Lapointe I, Messier C. Species-specific responses to forest soil inoculum in planted trees in an abandoned agricultural field. Appl Soil Ecol. 2017;112:1–10.

    Article 

    Google Scholar 

  • Kitto JAJ, Gray DP, Greig HS, Niyogi DK, Harding JS. Meta-community theory and stream restoration: evidence that spatial position constrains stream invertebrate communities in a mine impacted landscape. Restor Ecol. 2015;23:284–91.

    Article 

    Google Scholar 

  • Ofek M, Hadar Y, Minz D. Ecology of root colonizing Massilia (Oxalobacteraceae). Plos One. 2012;7:e40117.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Lyu D, Backer R, Smith DL. Three plant growth-promoting rhizobacteria alter morphological development, physiology, and flower yield of Cannabis sativa L. Ind Crop Prod. 2022;178:114583.

    CAS 
    Article 

    Google Scholar 

  • Kulmatiski A, Beard KH. Long-term plant growth legacies overwhelm short-term plant growth effects on soil microbial community structure. Soil Biol Biochem. 2011;43:823–30.

    CAS 
    Article 

    Google Scholar 

  • Brewer TE, Handley KM, Carini P, Gilbert JA, Fierer N. Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’. Nat Microbiol. 2017;2:16198.

    Article 
    CAS 

    Google Scholar 

  • Reme J. Development and present state of close-to-nature silviculture. J Landscape Ecol. 2018;11:17–32.

    Article 

    Google Scholar 


  • Source: Ecology - nature.com

    Agro-pastoralists’ perception of climate change and adaptation in the Qilian Mountains of northwest China

    Best practices for instrumenting honey bees