Contrasting response of rice rhizosphere microbiomes to in situ cadmium-contaminated soil remediation

Highlights

● Changes in soil properties and microbial communities regulated rhizosphere protistan assemblages.

● Bacterial community was more sensitive to soil amendments than protists and fungi.

● Soil amendments trigger the role of specific protistan taxa Cercozoa on microbial interactions.

Abstract

Understanding the responses of different rhizosphere microbial lineages to soil amendments during in situ remediation of Cd-contaminated soil is of great importance in the assessment of the restoration and crop health. Here, we evaluated the effects of lime (LM), biochar (BC), pig manure (PM), and a commercial Mg-Ca-Si conditioner (CMC) on the rice rhizosphere soil physicochemical properties and community assembly of bacteria, fungi, and protists in a six-year consecutive application of soil amendments field trial. Our results indicated that among the four amendments, the BC and CMC had the best efficiency in increasing soil pH, which were 5.2% and 16.2%, respectively. Despite the differences in soil Cd concentrations is not noticeable, all the soil amendment treatments significantly decreased the proportion of available Cd in total Cd compared to the control. Soil amendments significantly altered the diversity of bacterial community, while they had no effect on fungal and protistan communities. Linear discriminant analysis effect size (LEfSe) showed that the bacteria was more sensitive to soil amendment-induced changes. For protists, treatments with LM and BC changed the groups of protistan consumers, while treatments with PM and CMC significantly increased the relative abundances of protistan phototrophs. Co-occurrence network analysis revealed that soil amendments increased microbial network complexity and triggered the role of protists, especially for the predatory protists Cercozoa, on microbial trophic interactions. Further variation partitioning analysis revealed that edaphic properties, bacterial and fungal communities compositions together explained the 77% of the total variation in protistan community, and the stronger correlations between diversity of bacterial and protistan communities suggested that the bacteria community was a more important biotic driver of the protistan community. Overall, our findings demonstrate the distinct responses of rice rhizosphere microbial communities to soil amendment applications, highlighting the interactive associations between microbiomes, which is vital for enhancing our ability to develop effective strategies for sustainable soil management. This study enhances our understanding of the ecological roles of protists under soil amendment applications and highlights their potential contributions in bioremediation and environmental applications for Cd-contaminated soil.

Graphical abstract

Keywords

cadmium / soil amendments / soil protist community / microbial interactions

References

[1] Asiloglu, R., 2022. Biochar–microbe interaction: more protist research is needed. Biochar4, 72.

[2] Bastian, M., Heymann, S., Jacomy, M., 2009. Gephi: An open source software for exploring and manipulating networks. ICWSM3, 361–362.

[3] Benjamini, Y., Hochberg, Y., 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B Methodological57, 289–300.

[4] Chen, B., Xiong, W., Qi, J., Pan, H., Chen, S., Peng, Z., Gao, H., Zhang, L., Jiang, Y., Wei, G., Jiao, S., 2021. Trophic interrelationships drive the biogeography of protistan community in agricultural ecosystems. Soil Biology & Biochemistry163, 108445.

[5] Chen, H., Teng, Y., Lu, S., Wang, Y., Wang, J. 2015. Contamination features and health risk of soil heavy metals in China. Science of the Total Environment512–513, 143–153.

[6] Chen, J., Li, Y., Wen, S., Rosanoff, A., Yang, G., Sun, X., 2017. Magnesium fertilizer-induced increase of symbiotic microorganisms improves forage growth and quality. Journal of Agricultural and Food Chemistry65, 3253–3258.

[7] Cheng, Z., Shi, J., He, Y., Chen, Y., Wang, Y., Yang, X., Wang, T., Wu, L., Xu, J., 2023a. Enhanced soil function and health by soybean root microbial communities during in situ remediation of Cd-contaminated soil with the application of soil amendments. mSystems0, e01049–e22.

[8] Cheng, Z., Shi, J., He, Y., Wu, L., Xu, J., 2022. Assembly of root-associated bacterial community in cadmium contaminated soil following five-year consecutive application of soil amendments: Evidences for improved soil health. Journal of Hazardous Materials426, 128095.

[9] Cheng, Z., Zheng, Q., Shi, J., He, Y., Yang, X., Huang, X., Wu, L., Xu, J., 2023b. Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars. ISME COMMUN.3, 1–13.

[10] Degrune, F., Dumack, K., Fiore-Donno, A.M., Bonkowski, M., Sosa-Hernández, M.A., Schloter, M., Kautz, T., Fischer, D., Rillig, M.C., 2019. Distinct communities of Cercozoa at different soil depths in a temperate agricultural field. FEMS Microbiology Ecology95, fiz041.

[11] Delgado-Baquerizo, M., Reich, P.B., Trivedi, C., Eldridge, D.J., Abades, S., Alfaro, F.D., Bastida, F., Berhe, A.A., Cutler, N.A., Gallardo, A., García-Velázquez, L., Hart, S.C., Hayes, P.E., He, J.Z., Hseu, Z.Y., Hu, H.W., Kirchmair, M., Neuhauser, S., Pérez, C.A., Reed, S.C., Santos, F., Sullivan, B.W., Trivedi, P., Wang, J.T., Weber-Grullon, L., Williams, M.A., Singh, B.K., 2020. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nature Ecology & Evolution4, 210–220.

[12] Edgar, R.C., 2016. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv 081257

[13] Erlacher, A., Cernava, T., Cardinale, M., Soh, J., Sensen, C.W., Grube, M., Berg, G., 2015. Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L. Frontiers in Microbiology 6, 53

[14] Fan, K., Delgado-Baquerizo, M., Guo, X., Wang, D., Zhu, Y., Chu, H., 2021. Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment. ISME Journal15, 550–561.

[15] Fierer, N., 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. Nature Reviews Microbiology15, 579–590.

[16] Fiore-Donno, A.M., Richter-Heitmann, T., Degrune, F., Dumack, K., Regan, K.M., Marhan, S., Boeddinghaus, R.S., Rillig, M.C., Friedrich, M.W., Kandeler, E., Bonkowski, M., 2019. Functional traits and spatio-temporal structure of a major group of soil protists (Rhizaria: Cercozoa) in a temperate grassland. Frontiers in Microbiology10, 1332.

[17] Flues, S., Bass, D., Bonkowski, M., 2017. Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function. Environmental Microbiology19, 3297–3309.

[18] Geisen, S., Mitchell, E.A.D., Adl, S., Bonkowski, M., Dunthorn, M., Ekelund, F., Fernández, L.D., Jousset, A., Krashevska, V., Singer, D., Spiegel, F.W., Walochnik, J., Lara, E., 2018. Soil protists: a fertile frontier in soil biology research. FEMS Microbiology Reviews42, 293–323.

[19] Geisen, S., Mitchell, E.A.D., Wilkinson, D.M., Adl, S., Bonkowski, M., Brown, M.W., Fiore-Donno, A.M., Heger, T.J., Jassey, V.E.J., Krashevska, V., Lahr, D.J.G., Marcisz, K., Mulot, M., Payne, R., Singer, D., Anderson, O.R., Charman, D.J., Ekelund, F., Griffiths, B.S., Rønn, R., Smirnov, A., Bass, D., Belbahri, L., Berney, C., Blandenier, Q., Chatzinotas, A., Clarholm, M., Dunthorn, M., Feest, A., Fernández, L.D., Foissner, W., Fournier, B., Gentekaki, E., Hájek, M., Helder, J., Jousset, A., Koller, R., Kumar, S., La Terza, A., Lamentowicz, M., Mazei, Y., Santos, S.S., Seppey, C.V.W., Spiegel, F.W., Walochnik, J., Winding, A., Lara, E., 2017. Soil protistology rebooted: 30 fundamental questions to start with. Soil Biology & Biochemistry111, 94–103.

[20] Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C., Burgaud, G., de Vargas, C., Decelle, J., del Campo, J., Dolan, J.R., Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W.H.C.F., Lara, E., Le Bescot, N., Logares, R., Mahé, F., Massana, R., Montresor, M., Morard, R., Not, F., Pawlowski, J., Probert, I., Sauvadet, A.L., Siano, R., Stoeck, T., Vaulot, D., Zimmermann, P., Christen, R., 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Research41, D597–D604.

[21] Guo, S., Tao, C., Jousset, A., Xiong, W., Wang, Z., Shen, Z., Wang, B., Xu, Z., Gao, Z., Liu, S., Li, R., Ruan, Y., Shen, Q., Kowalchuk, G.A., Geisen, S., 2022. Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health. ISME Journal16, 1–12.

[22] Guo, S., Xiong, W., Hang, X., Gao, Z., Jiao, Z., Liu, H., Mo, Y., Zhang, N., Kowalchuk, G.A., Li, R., Shen, Q., Geisen, S., 2021. Protists as main indicators and determinants of plant performance. Microbiome9, 64.

[23] Hamid, Y., Tang, L., Sohail, M.I., Cao, X., Hussain, B., Aziz, M.Z., Usman, M., He, Z., Yang, X., 2019. An explanation of soil amendments to reduce cadmium phytoavailability and transfer to food chain. Science of the Total Environment660, 80–96.

[24] Harder, C.B., Rønn, R., Brejnrod, A., Bass, D., Al-Soud, W.A., Ekelund, F., 2016. Local diversity of heathland Cercozoa explored by in-depth sequencing. ISME Journal10, 2488–2497.

[25] He, L., Zhong, H., Liu, G., Dai, Z., Brookes, P.C., Xu, J., 2019. Remediation of heavy metal contaminated soils by biochar: Mechanisms, potential risks and applications in China. Environmental Pollution252, 846–855.

[26] Hou, D., O’Connor, D., Igalavithana, A.D., Alessi, D.S., Luo, J., Tsang, D.C.W., Sparks, D.L., Yamauchi, Y., Rinklebe, J., Ok, Y.S., 2020. Metal contamination and bioremediation of agricultural soils for food safety and sustainability. Nature Reviews Earth & Environment1, 366–381.

[27] Hou, D., Wang, R., Gao, X., Wang, K., Lin, Z., Ge, J., Liu, T., Wei, S., Chen, W., Xie, R., Yang, X., Lu, L., Tian, S., 2018. Cultivar-specific response of bacterial community to cadmium contamination in the rhizosphere of rice (Oryza sativa L. ). Environmental Pollution241, 63–73.

[28] Hussain, B., Ashraf, M.N., Shafeeq-ur-Rahman, Abbas, A., Li, J., Farooq, M., 2021. Cadmium stress in paddy fields: Effects of soil conditions and remediation strategies. Science of the Total Environment754, 142188.

[29] Johansen, J.L., Rønn, R., Ekelund, F., 2018. Toxicity of cadmium and zinc to small soil protists. Environmental Pollution242, 1510–1517.

[30] Kõljalg, U., Larsson, K.H., Abarenkov, K., Nilsson, R.H., Alexander, I.J., Eberhardt, U., Erland, S., Høiland, K., Kjøller, R., Larsson, E., Pennanen, T., Sen, R., Taylor, A.F.S., Tedersoo, L., Vrålstad, T. 2005. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytologist166, 1063–1068.

[31] Li, F., Sun, A., Jiao, X., Bi, L., Zheng, Y., He, J.Z., Hu, H.W., 2021. Specific protistan consumers and parasites are responsive to inorganic fertilization in rhizosphere and bulk soils. Journal of Soils and Sediments21, 3801–3812.

[32] Li, H.Z., Zhu, D., Sun, A.Q., Qin, Y.F., Lindhardt, J.H., Cui, L., 2022. Effects of soil protists on the antibiotic resistome under long term fertilization. Environmental Pollution307, 119516.

[33] Montgomery, D.R., 2007. Soil erosion and agricultural sustainability. Proceedings of the National Academy of Sciences of the United States of America104, 13268–13272.

[34] Nguyen, B.A.T., Chen, Q.L., He, J.Z., Hu, H.W., 2020. Oxytetracycline and ciprofloxacin exposure altered the composition of protistan consumers in an agricultural soil. Environmental Science & Technology54, 9556–9563.

[35] Oksanen, J., Kindt, R., Legendre, P., Hara, B., Simpson, G., Solymos, P., Henry, M., Stevens, H., Maintainer, H., 2009. The vegan Package

[36] Oliverio, A.M., Geisen, S., Delgado-Baquerizo, M., Maestre, F.T., Turner, B.L., Fierer, N., 2020. The global-scale distributions of soil protists and their contributions to belowground systems. Science Advances6, eaax8787.

[37] Philippot, L., Raaijmakers, J.M., Lemanceau, P., van der Putten, W.H., 2013. Going back to the roots: the microbial ecology of the rhizosphere. Nature Reviews Microbiology11, 789–799.

[38] Pietrzykowski, M., Socha, J., van Doorn, N.S., 2014. Linking heavy metal bioavailability (Cd, Cu, Zn and Pb) in Scots pine needles to soil properties in reclaimed mine areas. Science of the Total Environment 470–471, 501–510

[39] Qi, Q., Hu, C., Lin, J., Wang, X., Tang, C., Dai, Z., Xu, J., 2022. Contamination with multiple heavy metals decreases microbial diversity and favors generalists as the keystones in microbial occurrence networks. Environmental Pollution306, 119406.

[40] Qian, F., Su, X., Zhang, Y., Bao, Y., 2023. Variance of soil bacterial community and metabolic profile in the rhizosphere vs. non-rhizosphere of native plant Rumex acetosa L. from a Sb/As co-contaminated area in China. Journal of Hazardous Materials456, 131681.

[41] Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., Glöckner, F.O., 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research41, D590–D596.

[42] Rosenberg, K., Bertaux, J., Krome, K., Hartmann, A., Scheu, S., Bonkowski, M., 2009. Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana. ISME Journal3, 675–684.

[43] Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W.S., Huttenhower, C., 2011. Metagenomic biomarker discovery and explanation. Genome Biology12, R60.

[44] Shi, L., Guo, Z., Peng, C., Xiao, X., Feng, W., Huang, B., Ran, H., 2019. Immobilization of cadmium and improvement of bacterial community in contaminated soil following a continuous amendment with lime mixed with fertilizers: A four-season field experiment. Ecotoxicology and Environmental Safety171, 425–434.

[45] Shi, X., Zhang, C., Wang, H., Zhang, F., 2005. Effect of Si on the distribution of Cd in rice seedlings. Plant and Soil272, 53–60.

[46] Stoeck, T., Bass, D., Nebel, M., Christen, R., Jones, M.D.M., Breiner, H.W., Richards, T.A., 2010. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology19, 21–31.

[47] Sun, A., Jiao, X., Chen, Q., Trivedi, P., Li, Z., Li, F., Zheng, Y., Lin, Y., Hu, H., He, J., 2021. Fertilization alters protistan consumers and parasites in crop-associated microbiomes. Environmental Microbiology23, 2169–2183.

[48] Tu, C., Wei, J., Guan, F., Liu, Y., Sun, Y., Luo, Y., 2020. Biochar and bacteria inoculated biochar enhanced Cd and Cu immobilization and enzymatic activity in a polluted soil. Environment International137, 105576.

[49] Van Der Heijden, M.G.A., Hartmann, M., 2016. Networking in the plant microbiome. PLoS Biology14, e1002378.

[50] Wang, X., Dai, Z., Zhao, H., Hu, L., Dahlgren, R.A., Xu, J., 2023. Heavy metal effects on multitrophic level microbial communities and insights for ecological restoration of an abandoned electroplating factory site. Environmental Pollution327, 121548.

[51] Wang, X., Fang, L., Beiyuan, J., Cui, Y., Peng, Q., Zhu, S., Wang, M., Zhang, X., 2021. Improvement of alfalfa resistance against Cd stress through rhizobia and arbuscular mycorrhiza fungi co-inoculation in Cd-contaminated soil. Environmental Pollution277, 116758.

[52] Wang, X., Lu, X., Li, Z., Cheng, Q., Zhou, Y., Lei, M., 2021. Liming alters microbial community composition and its co-occurrence patterns in Cd- and Pb-contaminated agricultural soil. Applied Soil Ecology166, 104064.

[53] White, T.J., Bruns, T., Lee, S., Taylor, J., others, 1990. Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics. In: Innis, M.A., Gelfand, D.H., Sninsky, J.J., White, T.J., eds. PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego

[54] Wu, C., Chao, Y., Shu, L., Qiu, R., 2022. Interactions between soil protists and pollutants: An unsolved puzzle. Journal of Hazardous Materials429, 128297.

[55] Xiong, W., Song, Y., Yang, K., Gu, Y., Wei, Z., Kowalchuk, G.A., Xu, Y., Jousset, A., Shen, Q., Geisen, S., 2020. Rhizosphere protists are key determinants of plant health. Microbiome8, 27.

[56] Xu, M., Hao, X., Xiong, Z., Liao, H., Wang, L., Zhang, T., Luo, X., Chen, W., Huang, Q., 2021a. Soil amendments change bacterial functional genes more than taxonomic structure in a cadmium-contaminated soil. Soil Biology & Biochemistry154, 108126.

[57] Xu, M., Huang, Q., Xiong, Z., Liao, H., Lv, Z., Chen, W., Luo, X., Hao, X., 2021b. Distinct responses of rare and abundant microbial taxa to in situ chemical stabilization of cadmium-contaminated soil. mSystems6, e01040–e21.

[58] Yang, R., Sun, W., Guo, L., Li, B., Wang, Q., Huang, D., Gao, W., Xu, R., Li, Y., 2022. Response of soil protists to antimony and arsenic contamination. Environmental Pollution315, 120387.

[59] Zhang, L., Ma, B., Tang, C., Yu, H., Lv, X., Mazza Rodrigues, J.L., Dahlgren, R.A., Xu, J., 2021. Habitat heterogeneity induced by pyrogenic organic matter in wildfire-perturbed soils mediates bacterial community assembly processes. ISME Journal15, 1943–1955.

[60] Zhao, Z.B., He, J.Z., Geisen, S., Han, L.L., Wang, J.T., Shen, J.P., Wei, W.X., Fang, Y.T., Li, P.P., Zhang, L.M., 2019. Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils. Microbiome7, 33.

Ethics declarations

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Funding

This work was jointly supported by the National Natural Science Foundation of China (42177007), China Agriculture Research System of MOF and MARA (CARS-04), the Natural Science Foundation of Zhejiang Province (LGN22D010004), and Ningbo Natural Science Foundation (No. 2022S111).

Data availability

Sequences from this study were deposited at Genome Sequence Archive in the BIG Data Center, Chinese Academy of Sciences, under the accession numbers CRA007388 for bacteria, CRA007389 for fungi, and CRA007390 for protist.

Electronic supplementary material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s42832-023-0203-5 and is accessible for authorized users.

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