Zhou, Y. et al. Changes in element accumulation, phenolic metabolism, and antioxidative enzyme activities in the red-skin roots of Panax ginseng. J. Ginseng Res. 41, 307–315 (2016).
Rahman, M. & Punja, Z. K. Biochemistry of ginseng root tissues affected by rusty root symptoms. Plant Physiol. Biochem. 43, 1103–1114 (2005).
Reeleder, R. D., Hoke, S. M. T. & Zhang, Y. Rusted root of ginseng (Panax quinquefolius) is caused by a species of rhexocercosporidium. Phytopathology 96, 1243–1254 (2006).
Lu, X. H. et al. Taxonomy of fungal complex causing red-skin root of Panax ginseng in China. J. Ginseng Res. 44, 506–518 (2020).
Lee, C., Kim, K. Y., Lee, J. E., Kim, S. & An, G. Enzymes hydrolyzing structural components and ferrous ion cause rusty-root symptom on ginseng (Panax ginseng). J. Microbiol. Biotechnol. 21, 192–196 (2011).
Yuan, X., Song, T. J., Yang, J. S., Huang, X. G. & Shi, J. Y. Changes of microbial community in the rhizosphere soil of Atractylodes macrocephala when encountering replant disease. S. Afr. J. Bot. 127, 129–135 (2019).
Mazzola, M. & Manici, L. M. Apple replant disease: role of microbial ecology in cause and control. Annu. Rev. Phytopathol. 50, 45–65 (2012).
Liu, X. et al. Comparison of the characteristics of artificial ginseng bed soils in relation to the incidence of ginseng red skin disease. Exp. Agric. 50, 59–71 (2014).
Wang, Q. X. et al. Analysis of the relationship between rusty root incidences and soil properties in Panax ginseng. 41, 012001 (2016)
Liu, D., Sun, H. & Ma, H. Deciphering microbiome related to rusty roots of Panax ginseng and evaluation of antagonists against pathogenic ilyonectria. Front. Microbiol. 10, 1350 (2019).
Guo, J. H. et al. Significant acidification in major Chinese croplands. Science 327, 1008–1010 (2010).
Wan, W. et al. Responses of the rhizosphere bacterial community in acidic crop soil to pH: changes in diversity, composition, interaction, and function. Sci. Total Environ. 700, 134418 (2020).
Rousk, J. et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340–1351 (2010).
Carrino-Kyker, S. R., Coyle, K. P., Kluber, L. A. & Burke, D. J. Fungal and bacterial communities exhibit consistent responses to reversal of soil acidification and phosphorus limitation over time. Microorganisms 8, 1 (2019).
Sun, L., Chen, S., Chao, L. & Sun, T. Effects of flooding on changes in Eh, pH and speciation of cadmium and lead in contaminated soil. Bull. Environ. Contam. Toxicol. 79, 514–518 (2007).
Dordas, C. Role of nutrients in controlling plant diseases in sustainable agriculture: a review. Agron. Sustain. Dev. 28, 33–46 (2008).
Warren, S. L. J. H. Mineral nutrition of crops: fundamental mechanisms and implications. HortScience 39, 462–462 (2004).
Sun, H., Zhang, Y. Y. & Song, X. X. Study on the soil nutrients and enzyme activity of cultivate ginseng soil in the farmland and wild ginseng soil under forest by canonical correlation analysis. Acta Agriculturae Boreali-Sinica S2 (2010).
Sharma, S., Duveiller, E., Basnet, R., Karki, C. B. & Sharma, R. Effect of potash fertilization on Helminthosporium leaf blight severity in wheat, and associated increases in grain yield and kernel weight. Field Crops Res. 93, 142–150 (2005).
Floch, C., Capowiez, Y. & Biology, S. Enzyme activities in apple orchard agroecosystems: how are they affected by management strategy and soil properties. Soil Biol. Biochem. 41, 61–68 (2009).
Aon, M. A. & Coloneri, A. C. II. Temporal and spatial evolution of enzymatic activities and physico-chemical properties in an agricultural soil. Appl. Soil Ecol. 18, 255–270 (2001).
Cai, Z. et al. Effects of the novel pyrimidynyloxybenzoic herbicide ZJ0273 on enzyme activities, microorganisms and its degradation in Chinese soils. Environ. Sci. Pollut. Res. 22, 4425–4433 (2015).
Antonious, G. F. Impact of soil management and two botanical insecticides on urease and invertase activity. J. Environ. Sci. Health Part B Pestic. Food Contam. Agric. Wastes 38, 479–488 (2003).
Makoi, J. H. J. R. & Ndakidemi, P. A. Selected soil enzymes: examples of their potential roles in the ecosystem. Afr. J. Biotechnol. 7, 181–191 (2008).
Jian, S. et al. Soil extracellular enzyme activities, soil carbon and nitrogen storage under nitrogen fertilization: a meta-analysis. Soil Biol. Biochem. 101, 32–43 (2016).
Schutzendubel, A. & Polle, A. Plant responses to abiotic stresses: heavy metal-induced oxidative stress and protection by mycorrhization. J. Exp. Bot. 53, 1351–1365 (2002).
Chao, A. Non-parametric estimation of the classes in a population. Scand. J. Stat. 11, 265–270 (1984).
Shannon, C. E. J. B. S. T. J. A mathematical theory of communication. Bell Syst. Tech. J. 27, 379–423 (1948).
Simpson, E. H. Measurement of diversity. Nature 163, 688 (1949).
Farh, M. E., Kim, Y. J., Kim, Y. J. & Yang, D. C. Cylindrocarpon destructans/Ilyonectria radicicola-species complex: causative agent of ginseng root-rot disease and rusty symptoms. J. Ginseng Res. 42, 9–15 (2018).
Lombard, L., Der Merwe, N. A. V., Groenewald, J. Z. & Crous, P. W. Generic concepts in Nectriaceae. Stud. Mycol. 80, 189–245 (2015).
Martinezbarrera, O. Y. et al. Does Beauveria bassiana (Hypocreales: Cordycipitaceae) affect the survival and fecundity of the parasitoid Coptera haywardi (Hymenoptera: Diapriidae)?. Environ. Entomol. 48, 156–162 (2019).
Migiro, L. N., Maniania, N. K., Chabi-Olaye, A., Wanjoya, A. & Control, J. V. J. B. Effect of infection by Metarhizium anisopliae (Hypocreales: Clavicipitaceae) on the feeding and oviposition of the pea leafminer Liriomyza huidobrensis (Diptera: Agromyzidae) on different host plants. Biol. Control 56, 179–183 (2011).
Tardy, V. et al. Shifts in microbial diversity through land use intensity as drivers of carbon mineralization in soil. Soil Biol. Biochem. 90, 204–213 (2015).
Yang, L., Lu, X., Li, S. & Wu, B. First report of common bean (Phaseolus vulgaris) root rot caused by Plectosphaerella cucumerina in China. Plant Dis. 102, 1849–1849 (2018).
Baldeweg, F., Warncke, P., Fischer, D. & Gressler, M. J. O. L. Fungal biosurfactants from Mortierella alpina. Org. Lett. 21, 1444–1448 (2019).
Masinova, T., Yurkov, A. & Baldrian, P. J. F. E. Forest soil yeasts: decomposition potential and the utilization of carbon sources. Fungal Ecol. 34, 10–19 (2018).
Hu, H. et al. Fomesafen impacts bacterial communities and enzyme activities in the rhizosphere. Environ. Pollut. 253, 302–311 (2019).
Barriuso, J., Marín, S. & Mellado, R. P. Effect of the herbicide glyphosate on glyphosate-tolerant maize rhizobacterial communities: a comparison with pre-emergency applied herbicide consisting of a combination of acetochlor and terbuthylazine. Environ. Microbiol. 12, 1021–1030 (2010).
Zhao, J. et al. Effects of organic–inorganic compound fertilizer with reduced chemical fertilizer application on crop yields, soil biological activity and bacterial community structure in a rice–wheat cropping system. Appl. Soil Ecol. 99, 1–12 (2016).
Davidova, I. A., Marks, C. R., & Suflita, J. M. Anaerobic hydrocarbon-degrading Deltaproteobacteria. Handbook of Hydrocarbon and Lipid Microbiology 207–243 (2019).
Wang, W. et al. Predatory Myxococcales are widely distributed in and closely correlated with the bacterial community structure of agricultural land. Appl. Soil Ecol. 146, 103365 (2020).
Yadav, S. et al. Cyanobacteria: role in agriculture, environmental sustainability, biotechnological potential and agroecological impact. In Plant-Microbe Interactions in Agro-Ecological Perspectives 257–277 (2017).
Rossi, F., Li, H., Liu, Y. & De Philippis, R. Cyanobacterial inoculation (cyanobacterisation): perspectives for the development of a standardized multifunctional technology for soil fertilization and desertification reversal. Earth Sci. Rev. 171, 28–43 (2017).
Muñoz-Rojas, M. et al. Effects of indigenous soil cyanobacteria on seed germination and seedling growth of arid species used in restoration. Plant Soil 429, 91–100 (2018).
Speirs, L. B. M., Rice, D. T. F., Petrovski, S. & Seviour, R. J. The phylogeny, biodiversity, and ecology of the chloroflexi in activated sludge. Front. Microbiol. 10, 2015 (2019).
Whitman, T. et al. Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter. ISME J. 10, 2918–2930 (2016).
Lladó, S. et al. Functional screening of abundant bacteria from acidic forest soil indicates the metabolic potential of Acidobacteria subdivision 1 for polysaccharide decomposition. Biol. Fertil. Soils 52, 251–260 (2016).
Bousset, L., Ermel, M., Soglonou, B. & Husson, O. Fungal growth is affected by and affects pH and redox potential (Eh) of the growth medium. bioRxiv 401182 (2018).
Mi, C. et al. Unveiling of dominant fungal pathogens associated with rusty root rot of Panax notoginseng based on multiple methods. Plant Dis. 101, 2046–2052 (2017).
Wang, Q. et al. Analysis of rhizosphere bacterial and fungal communities associated with rusty root disease of Panax ginseng. Appl. Soil Ecol. 138, 245–252 (2019).
Li, Z., Guo, S., Tian, S., Liu, Z. & Long, B. Study on the causes for ginseng red skin sickness occurred in albic bed soil. Acta Pedol. Sin. 34, 328–335 (1997).
Shi, J., Yuan, X., Lin, H., Yang, Y. & Li, Z. Y. Differences in soil properties and bacterial communities between the rhizosphere and bulk soil and among different production areas of the medicinal plant Fritillaria thunbergii. Int. J. Int. J. Mol. Sci. 12, 3770–3785 (2011).
Xu, Y. et al. Bacterial communities in soybean rhizosphere in response to soil type, soybean genotype, and their growth stage. Soil Biol. Biochem. 41, 919–925 (2019).
Pei, G., Zhu, Y., Wen, J., Pei, Y. & Li, H. Vinegar residue supported nanoscale zero-valent iron: remediation of hexavalent chromium in soil. Environ. Pollut. 256, 113407 (2019).
Fawcett, J. K. The semi-micro Kjeldahl method for the determination of nitrogen. J. Med. Lab Technol. 12, 1–22 (1954).
Li, Y. et al. Humic acid fertilizer improved soil properties and soil microbial diversity of continuous cropping peanut: a three-year experiment. Sci. Rep. 9, 12014 (2019).
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).
Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).
Price, M. N., Dehal, P. S. & Arkin, A. P. J. P. O. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 90 (2018).
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, 1–18 (2011).
Source: Ecology - nature.com
