doi:10.48130/cas-0026-0009

[1]

Chen Y, Ren X, Zhou X, Huang L, Yan L, et al. 2014. Dynamics in the resistant and susceptible peanut (Arachis hypogaea L.) root transcriptome on infection with the Ralstonia solanacearum. BMC Genomics 15(1):1078

doi: 10.1186/1471-2164-15-1078

[2]

Chen K, Wang L, Chen H, Zhang C, Wang S, et al. 2021. Complete genome sequence analysis of the peanut pathogen Ralstonia solanacearum strain Rs-P.362200. BMC Microbiology 21(1):118

doi: 10.1186/s12866-021-02157-7

[3]

Wang Z, Luo W, Cheng S, Zhang H, Zong J, et al. 2023. Ralstonia solanacearum – a soil borne hidden enemy of plants: research development in management strategies, their action mechanism and challenges. Frontiers in Plant Science 14:1141902

doi: 10.3389/fpls.2023.1141902

[4]

An Y, Zhang M. 2024. Advances in understanding the plant-Ralstonia solanacearum interactions: unraveling the dynamics, mechanisms, and implications for crop disease resistance. New Crops 1:100014

doi: 10.1016/j.ncrops.2024.100014

[5]

Luo H, Pandey MK, Zhi Y, Zhang H, Xu S, et al. 2020. Discovery of two novel and adjacent QTLs on chromosome B02 controlling resistance against bacterial wilt in peanut variety Zhonghua 6. Theoretical and Applied Genetics 133(4):1133−1148

doi: 10.1007/s00122-020-03537-9

[6]

Pei X, Xie J, Liang C, Utkina AO. 2026. Next-generation precision breeding in peanut (Arachis hypogaea L.) for disease and pest resistance: from multi-omics to AI-driven innovations. Insects 17(1):63

doi: 10.3390/insects17010063

[7]

Jiang G, Wei Z, Xu J, Chen H, Zhang Y, et al. 2017. Bacterial wilt in China: history, current status, and future perspectives. Frontiers in Plant Science 8:1549

doi: 10.3389/fpls.2017.01549

[8]

Luo H, Pandey MK, Khan AW, Wu B, Guo J, et al. 2019. Next-generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut (Arachis hypogaea L.). Plant Biotechnology Journal 17(12):2356−2369

doi: 10.1111/pbi.13153

[9]

Mundt CC. 2014. Durable resistance: a key to sustainable management of pathogens and pests. Infection, Genetics and Evolution 27:446−455

doi: 10.1016/j.meegid.2014.01.011

[10]

Pathak VM, Verma VK, Rawat BS, Kaur B, Babu N, et al. 2022. Current status of pesticide effects on environment, human health and it's eco-friendly management as bioremediation: a comprehensive review. Frontiers in Microbiology 13:962619

doi: 10.3389/fmicb.2022.962619

[11]

Greenrod STE, Stoycheva M, Elphinstone J, Friman VP. 2022. Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum species complex. BMC Genomics 23(1):689

doi: 10.1186/s12864-022-08909-7

[12]

Steenwyk JL, Knowles S, Bastos RW, Balamurugan C, Rinker D, et al. 2023. Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen. bioRxiv 547508

doi: 10.1101/2023.07.03.547508

[13]

Peressotti E, Wiedemann-Merdinoglu S, Delmotte F, Bellin D, Di Gaspero G, et al. 2010. Breakdown of resistance to grapevine downy mildew upon limited deployment of a resistant variety. BMC Plant Biology 10(1):147

doi: 10.1186/1471-2229-10-147

[14]

Korshunova T, Martynov A. 2024. The phyloperiodic approach removes the 'cryptic species' and puts forward multilevel organismal diversity. Diversity 16(4):220

doi: 10.3390/d16040220

[15]

Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, et al. 2020. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nature Communications 11:2500

doi: 10.1038/s41467-020-16366-7

[16]

Paudel S, Dobhal S, Alvarez AM, Arif M. 2020. Taxonomy and phylogenetic research on Ralstonia solanacearum species complex: a complex pathogen with extraordinary economic consequences. Pathogens 9(11):886

doi: 10.3390/pathogens9110886

[17]

Li L, Kong W, Sun J, Jiang Y, Li T, et al. 2025. MGV-seq: a sensitive and culture-independent method for detecting microbial genetic variation. Frontiers in Microbiology 16:1603255

doi: 10.3389/fmicb.2025.1603255

[18]

Okazaki Y, Fujinaga S, Salcher MM, Callieri C, Tanaka A, et al. 2021. Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing. Microbiome 9(1):24

doi: 10.1186/s40168-020-00974-y

[19]

Attwood SW, Hill SC, Aanensen DM, Connor TR, Pybus OG. 2022. Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic. Nature Reviews Genetics 23(9):547−562

doi: 10.1038/s41576-022-00483-8

[20]

Tan X, Dai X, Chen T, Wu Y, Yang D, et al. 2022. Complete genome sequence analysis of Ralstonia solanacearum strain PeaFJ1 provides insights into its strong virulence in peanut plants. Frontiers in Microbiology 13:830900

doi: 10.3389/fmicb.2022.830900

[21]

Xue QY, Yin YN, Yang W, Heuer H, Prior P, et al. 2011. Genetic diversity of Ralstonia solanacearum strains from China assessed by PCR-based fingerprints to unravel host plant- and site-dependent distribution patterns. FEMS Microbiology Ecology 75(3):507−519

doi: 10.1111/j.1574-6941.2010.01026.x

[22]

Jiang H, Liao B, Ren X, Lei Y, Mace E, et al. 2007. Comparative assessment of genetic diversity of peanut (Arachis hypogaea L.) genotypes with various levels of resistance to bacterial wilt through SSR and AFLP analyses. Journal of Genetics and Genomics 34(6):544−554

doi: 10.1016/S1673-8527(07)60060-5

[23]

Gelaye Y, Luo H. 2024. Optimizing peanut (Arachis hypogaea L.) production: genetic insights, climate adaptation, and efficient management practices: systematic review. Plants 13(21):2988

doi: 10.3390/plants13212988

[24]

Ailloud F, Lowe T, Cellier G, Roche D, Allen C, et al. 2015. Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity. BMC Genomics 16(1):270

doi: 10.1186/s12864-015-1474-8

[25]

Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW, et al. 2009. Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiology Reviews 33(2):376−393

doi: 10.1111/j.1574-6976.2008.00136.x

[26]

Byrne AQ, Vredenburg VT, Martel A, Pasmans F, Bell RC, et al. 2019. Cryptic diversity of a widespread global pathogen reveals expanded threats to amphibian conservation. Proceedings of the National Academy of Sciences of the United States of America 116(41):20382−20387

doi: 10.1073/pnas.1908289116

[27]

Zhang M, Han L, Liao C, Su W, Jiang C. 2025. Comparative genomics reveals key adaptive mechanisms in pathogen host-niche specialization. Frontiers in Microbiology 16:1543610

doi: 10.3389/fmicb.2025.1543610

[28]

Kumar R, Das SP, Choudhury BU, Kumar A, Prakash NR, et al. 2024. Advances in genomic tools for plant breeding: harnessing DNA molecular markers, genomic selection, and genome editing. Biological Research 57(1):80

doi: 10.1186/s40659-024-00562-6

[29]

Carter K, Reyes-Olivares C, Eubanks J, Hanna H, Nielsen SV, et al. 2025. Hidden diversity in the driest desert on Earth: genomics unveils cryptic diversity in an ancient South American gecko lineage (Phyllodactylidae, Garthia). Molecular Phylogenetics and Evolution 213:108448

doi: 10.1016/j.ympev.2025.108448

[30]

Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, et al. 2017. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microbial Genomics 3(6):e000116

doi: 10.1099/mgen.0.000116

[31]

Liang YY, Liu H, Lin QQ, Shi Y, Zhou BF, et al. 2025. Pan-genome analysis reveals local adaptation to climate driven by introgression in oak species. Molecular Biology and Evolution 42(5):msaf088

doi: 10.1093/molbev/msaf088

[32]

Tan X, Tang H, Yang D, Huang J, Wu Y, et al. 2024. Comparative genome analysis of two peanut Ralstonia solanacearum strains with significant difference in pathogenicity reveals 16S rRNA dimethyltransferase RsmA involved in inducing immunity. Chemical and Biological Technologies in Agriculture 11(1):184

doi: 10.1186/s40538-024-00714-6

[33]

Pfeifer E, Rocha EPC. 2024. Phage-plasmids promote recombination and emergence of phages and plasmids. Nature Communications 15:1545

doi: 10.1038/s41467-024-45757-3

[34]

Gyles C, Boerlin P. 2014. Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease. Veterinary Pathology 51(2):328−340

doi: 10.1177/0300985813511131

[35]

Kondrashov FA, Kondrashov AS. 2010. Measurements of spontaneous rates of mutations in the recent past and the near future. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences 365(1544):1169−1176

doi: 10.1098/rstb.2009.0286

[36]

Castillo JA, Greenberg JT. 2007. Evolutionary dynamics of Ralstonia solanacearum. Applied and Environmental Microbiology 73(4):1225−1238

doi: 10.1128/aem.01253-06

[37]

Gelaye Y, Luo H. 2025. Epigenetic mechanisms enhance aflatoxin resistance in peanut crops (Arachis hypogaea L.) through genomic and epigenomic approaches. Crop Science 65(4):e70145

doi: 10.1002/csc2.70145

[38]

Ortiz V, Chang HX, Sang H, Jacobs J, Malvick DK, et al. 2023. Population genomic analysis reveals geographic structure and climatic diversification for Macrophomina phaseolina isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia. Frontiers in Genetics 14:1103969

doi: 10.3389/fgene.2023.1103969

[39]

Zhu D, Zhang Y, Zhu YG. 2023. Human pathogens in the soil ecosystem: occurrence, dispersal, and study method. Current Opinion in Environmental Science & Health 33:100471

doi: 10.1016/j.coesh.2023.100471

[40]

Karpov DS, Kazakova EM, Kovalev MA, Shumkov MS, Kusainova T, et al. 2024. Determinants of antibiotic resistance and virulence factors in the genome of Escherichia coli APEC 36 strain isolated from a broiler chicken with generalized colibacillosis. Antibiotics 13(10):945

doi: 10.3390/antibiotics13100945

[41]

Gopalan-Nair R, Coissac A, Legrand L, Lopez-Roques C, Pécrix Y, et al. 2024. Changes in DNA methylation contribute to rapid adaptation in bacterial plant pathogen evolution. PLoS Biology 22(9):e3002792

doi: 10.1371/journal.pbio.3002792

[42]

Gelaye Y. 2024. Systematic review on Aflatoxin contamination in Ethiopia: current status and implications. Studies in Fungi 9:e013

doi: 10.48130/sif-0024-0013

[43]

Stuwe E, Tóth KF, Aravin AA. 2014. Small but sturdy: small RNAs in cellular memory and epigenetics. Genes & Development 28(5):423−431

doi: 10.1101/gad.236414.113

[44]

Gao Q, Lu S, Wang Y, He L, Wang M, et al. 2023. Bacterial DNA methyltransferase: a key to the epigenetic world with lessons learned from proteobacteria. Frontiers in Microbiology 14:1129437

doi: 10.3389/fmicb.2023.1129437

[45]

Casadesús J, Low D. 2006. Epigenetic gene regulation in the bacterial world. Microbiology and Molecular Biology Reviews 70(3):830−856

doi: 10.1128/mmbr.00016-06

[46]

Takahashi K. 2014. Influence of bacteria on epigenetic gene control. Cellular and Molecular Life Sciences 71(6):1045−1054

doi: 10.1007/s00018-013-1487-x

[47]

Gelaye Y, Luo H. 2025. Application of epigenetics for allergen-free peanut production: a comprehensive review. Epigenetics Insights 18:e006

doi: 10.48130/epi-0025-0006

[48]

Dorman CJ, Deighan P. 2003. Regulation of gene expression by histone-like proteins in bacteria. Current Opinion in Genetics & Development 13(2):179−184

doi: 10.1016/S0959-437X(03)00025-X

[49]

Podkaminski D, Vogel J. 2010. Small RNAs promote mRNA stability to activate the synthesis of virulence factors. Molecular Microbiology 78(6):1327−1331

doi: 10.1111/j.1365-2958.2010.07428.x

[50]

Georg J, Berghoff BA, Schindler D. 2025. Harnessing small RNAs as synthetic post-transcriptional regulators in bacteria. ACS Synthetic Biology 14(7):2405−2417

doi: 10.1021/acssynbio.5c00118

[51]

Gelaye Y. 2026. Integrated breeding, genomics, and epigenetic approaches enhance aflatoxin resistance in peanut (Arachis hypogaea L.) under pathogen and climate stress. Vegetos 39:453−463

doi: 10.1007/s42535-025-01546-x

[52]

Soen Y. 2014. Environmental disruption of host – microbe co-adaptation as a potential driving force in evolution. Frontiers in Genetics 5:168

doi: 10.3389/fgene.2014.00168

[53]

Netea MG, Domínguez-Andrés J, Barreiro LB, Chavakis T, Divangahi M, et al. 2020. Defining trained immunity and its role in health and disease. Nature Reviews Immunology 20(6):375−388

doi: 10.1038/s41577-020-0285-6

[54]

De Marco K, Sanese P, Simone C, Grossi V. 2023. Histone and DNA methylation as epigenetic regulators of DNA damage repair in gastric cancer and emerging therapeutic opportunities. Cancers 15(20):4976

doi: 10.3390/cancers15204976

[55]

Gelaye Y, Li J, Luo H. 2025. Exploring the role of Peanut (Arachis hypogaea L.) root architecture in enhancing adaptation to climate change for sustainable agriculture and resilient crop production: a review. Journal of Genetic Engineering and Biotechnology 23(3):100535

doi: 10.1016/j.jgeb.2025.100535

[56]

Wang HV, Chekanova JA. 2016. Small RNAs: essential regulators of gene expression and defenses against environmental stresses in plants. WIREs RNA 7(3):356−381

doi: 10.1002/wrna.1340

[57]

Lucchini S, Rowley G, Goldberg MD, Hurd D, Harrison M, et al. 2006. H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathogens 2(8):e81

doi: 10.1371/journal.ppat.0020081

[58]

Kan RL, Chen J, Sallam T. 2022. Crosstalk between epitranscriptomic and epigenetic mechanisms in gene regulation. Trends in Genetics 38(2):182−193

doi: 10.1016/j.tig.2021.06.014

[59]

Vignaroli C, Di Sante L, Magi G, Luna GM, Di Cesare A, et al. 2015. Adhesion of marine cryptic Escherichia isolates to human intestinal epithelial cells. The ISME Journal 9(2):508−515

doi: 10.1038/ismej.2014.164

[60]

Cháves-González LE, Morales-Calvo F, Mora J, Solano-Barquero A, Verocai GG, et al. 2022. What lies behind the curtain: cryptic diversity in helminth parasites of human and veterinary importance. Current Research in Parasitology & Vector-Borne Diseases 2:100094

doi: 10.1016/j.crpvbd.2022.100094

[61]

Perry KD, Baker GJ, Powis KJ, Kent JK, Ward CM, et al. 2018. Cryptic Plutella species show deep divergence despite the capacity to hybridize. BMC Evolutionary Biology 18(1):77

doi: 10.1186/s12862-018-1183-4

[62]

Mourkas E, Yahara K, Bayliss SC, Calland JK, Johansson H, et al. 2022. Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter. eLife 11:e73552

doi: 10.7554/elife.73552

[63]

Peltoniemi K, Velmala S, Lloret E, Ollio I, Hyvönen J, et al. 2024. Soil and climatic characteristics and farming system shape fungal communities in European wheat fields. Agriculture, Ecosystems & Environment 370:109035

doi: 10.1016/j.agee.2024.109035

[64]

Ekanayaka AH, Karunarathna SC, Tibpromma S, Dutta AK, Tennakoon DS, et al. 2025. Species evolution: cryptic species and phenotypic noise with a particular focus on fungal systematics. Frontiers in Cellular and Infection Microbiology 15:1497085

doi: 10.3389/fcimb.2025.1497085

[65]

Ling-Hu T, Rios-Guzman E, Lorenzo-Redondo R, Ozer EA, Hultquist JF. 2022. Challenges and opportunities for global genomic surveillance strategies in the COVID-19 era. Viruses 14(11):2532

doi: 10.3390/v14112532

[66]

Soubeyrand S, Estoup A, Cruaud A, Malembic-Maher S, Meynard C, et al. 2024. Building integrated plant health surveillance: a proactive research agenda for anticipating and mitigating disease and pest emergence. CABI Agriculture and Bioscience 5(1):72

doi: 10.1186/s43170-024-00273-8

[67]

Brzozowski L, Mazourek M. 2018. A sustainable agricultural future relies on the transition to organic agroecological pest management. Sustainability 10(6):2023

doi: 10.3390/su10062023

[68]

Vaghefi N, Kikkert JR, Hay FS, Carver GD, Koenick LB, et al. 2018. Cryptic diversity, pathogenicity, and evolutionary species boundaries in Cercospora populations associated with Cercospora leaf spot of Beta vulgaris. Fungal Biology 122(4):264−282

doi: 10.1016/j.funbio.2018.01.008

[69]

Manzoor S, Nabi SU, Rather TR, Gani G, Ahmad Mir Z, et al. 2024. Advancing crop disease resistance through genome editing: a promising approach for enhancing agricultural production. Frontiers in Genome Editing 6:1399051

doi: 10.3389/fgeed.2024.1399051

[70]

Barrett LG, Kniskern JM, Bodenhausen N, Zhang W, Bergelson J. 2009. Continua of specificity and virulence in plant host-pathogen interactions: causes and consequences. New Phytologist 183(3):513−529

doi: 10.1111/j.1469-8137.2009.02927.x

[71]

Deng Y, Ning Y, Yang DL, Zhai K, Wang GL, et al. 2020. Molecular basis of disease resistance and perspectives on breeding strategies for resistance improvement in crops. Molecular Plant 13(10):1402−1419

doi: 10.1016/j.molp.2020.09.018

[72]

Lauber E, González-Fuente M, Escouboué M, Vicédo C, Luneau JS, et al. 2024. Bacterial host adaptation through sequence and structural variations of a single type III effector gene. iScience 27(3):109224

doi: 10.1016/j.isci.2024.109224

[73]

Hamilton CD, Zaricor B, Dye CJ, Dresserl E, Michaels R, et al. 2024. Ralstonia solanacearum pandemic lineage strain UW551 overcomes inhibitory xylem chemistry to break tomato bacterial wilt resistance. Molecular Plant Pathology 25(1):e13395

doi: 10.1111/mpp.13395

[74]

Steenwyk JL, Knowles S, Bastos RW, Balamurugan C, Rinker D, et al. 2024. Evolutionary origin and population diversity of a cryptic hybrid pathogen. Nature Communications 15:8412

doi: 10.1038/s41467-024-52639-1

[75]

Amin A, Zaman W, Park S. 2025. Harnessing multi-omics and predictive modeling for climate-resilient crop breeding: from genomes to fields. Genes 16(7):809

doi: 10.3390/genes16070809

[76]

Paaby AB, Rockman MV. 2014. Cryptic genetic variation: evolution's hidden substrate. Nature Reviews Genetics 15(4):247−258

doi: 10.1038/nrg3688

[77]

Wang J, Xiao S, Zheng L, Pan Y, Zhao D, et al. 2022. Multiomic approaches reveal novel lineage-specific effectors in the potato and tomato early blight pathogen Alternaria solani. Phytopathology Research 4(1):29

doi: 10.1186/s42483-022-00135-z

[78]

Li J, Cornelissen B, Rep M. 2020. Host-specificity factors in plant pathogenic fungi. Fungal Genetics and Biology 144:103447

doi: 10.1016/j.fgb.2020.103447

[79]

Marwaha S, Knowles JW, Ashley EA. 2022. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Medicine 14(1):23

doi: 10.1186/s13073-022-01026-w

[80]

Schreiber KJ, Chau-Ly IJ, Lewis JD. 2021. What the wild things do: mechanisms of plant host manipulation by bacterial type III-secreted effector proteins. Microorganisms 9(5):1029

doi: 10.3390/microorganisms9051029

[81]

Vogt G. 2022. Environmental adaptation of genetically uniform organisms with the help of epigenetic mechanisms − an insightful perspective on ecoepigenetics. Epigenomes 7(1):1

doi: 10.3390/epigenomes7010001

[82]

Hudson O, Resende MFR Jr, Messina C, Holland J, Brawner J. 2024. Prediction of resistance, virulence, and host-by-pathogen interactions using dual-genome prediction models. Theoretical and Applied Genetics 137(8):196

doi: 10.1007/s00122-024-04698-7

[83]

Li Q, Wang B, Yu J, Dou D. 2021. Pathogen-informed breeding for crop disease resistance. Journal of Integrative Plant Biology 63(2):305−311

doi: 10.1111/jipb.13029

[84]

Tharanath AC, Upendra RS, Rajendra K. 2024. Soil symphony: a comprehensive overview of plant–microbe interactions in agricultural systems. Applied Microbiology 4(4):1549−1567

doi: 10.3390/applmicrobiol4040106

[85]

Priyadarshini C, Lal R, Yuan P, Liu W, Adhikari A, et al. 2025. Plant disease suppressiveness enhancement via soil health management. Biology 14(8):924

doi: 10.3390/biology14080924

[86]

Spragge F, Bakkeren E, Jahn MT, Araujo EBN, Pearson CF, et al. 2023. Microbiome diversity protects against pathogens by nutrient blocking. Science 382(6676):eadj3502

doi: 10.1126/science.adj3502

[87]

Gu S, Wei Z, Shao Z, Friman VP, Cao K, et al. 2020. Competition for iron drives phytopathogen control by natural rhizosphere microbiomes. Nature Microbiology 5(8):1002−1010

doi: 10.1038/s41564-020-0719-8

[88]

Geng R, Cheng L, Cao C, Liu Z, Liu D, et al. 2022. Comprehensive analysis reveals the genetic and pathogenic diversity of Ralstonia solanacearum species complex and benefits its taxonomic classification. Frontiers in Microbiology 13:854792

doi: 10.3389/fmicb.2022.854792

[89]

Caballero-Flores G, Pickard JM, Núñez G. 2023. Microbiota-mediated colonization resistance: mechanisms and regulation. Nature Reviews Microbiology 21(6):347−360

doi: 10.1038/s41579-022-00833-7

[90]

Liang J, Wei C, Song X, Wang R, Shi H, et al. 2024. Bacterial wilt affects the structure and assembly of microbial communities along the soil-root continuum. Environmental Microbiome 19(1):6

doi: 10.1186/s40793-024-00548-7

[91]

Bleich RM, Li C, Sun S, Ahn JH, Dogan B, et al. 2023. A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice. Microbiome 11(1):277

doi: 10.1186/s40168-023-01710-y

[92]

Chepsergon J, Moleleki LN. 2023. Rhizosphere bacterial interactions and impact on plant health. Current Opinion in Microbiology 73:102297

doi: 10.1016/j.mib.2023.102297

[93]

Ghaly TM, Gillings MR, Rajabal V, Paulsen IT, Tetu SG. 2024. Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange. Frontiers in Microbiology 15:1338026

doi: 10.3389/fmicb.2024.1338026

[94]

Wu QY, Ma R, Wang X, Ma YN, Wang ZS, et al. 2024. Effects of the invasion of Ralstonia solanacearum on soil microbial community structure in Wuhan, China. mSphere 9(2):e00665−e00623

doi: 10.1128/msphere.00665-23

[95]

Wen T, Zhao M, Liu T, Huang Q, Yuan J, et al. 2020. High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome. BMC Plant Biology 20(1):166

doi: 10.1186/s12870-020-02365-9

[96]

Jang S, Kim D, Seo HW, Ryu CM. 2025. Beyond reductionism: the emerging holistic paradigm in indirect control of pathogen infection. Frontiers in Microbiology 16:1638634

doi: 10.3389/fmicb.2025.1638634

[97]

Elsayed TR, Jacquiod S, Nour EH, Sørensen SJ, Smalla K. 2020. Biocontrol of bacterial wilt disease through complex interaction between tomato plant, antagonists, the indigenous rhizosphere microbiota, and Ralstonia solanacearum. Frontiers in Microbiology 10:2835

doi: 10.3389/fmicb.2019.02835

[98]

Zhou Y, Yang Z, Liu J, Li X, Wang X, et al. 2023. Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease. Nature Communications 14:8126

doi: 10.1038/s41467-023-43926-4

[99]

Zhang W, Zhang BW, Deng JF, Li L, Yi TY, et al. 2021. The resistance of peanut to soil-borne pathogens improved by rhizosphere probiotics under calcium treatment. BMC Microbiology 21(1):299

doi: 10.1186/s12866-021-02355-3

[100]

Priya P, Aneesh B, Harikrishnan K. 2021. Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health. Journal of Microbiological Methods 185:106215

doi: 10.1016/j.mimet.2021.106215

[101]

Du Y, Han X, Tsuda K. 2025. Microbiome-mediated plant disease resistance: recent advances and future directions. Journal of General Plant Pathology 91(1):1−17

doi: 10.1007/s10327-024-01204-1

[102]

Sepúlveda VE, Márquez R, Turissini DA, Goldman WE, Matute DR. 2017. Genome sequences reveal cryptic speciation in the human pathogen Histoplasma capsulatum. mBio 8(6):e01339−e01317

doi: 10.1128/mBio.01339-17

[103]

Stergiopoulos I, Gordon TR. 2014. Cryptic fungal infections: the hidden agenda of plant pathogens. Frontiers in Plant Science 5:506

doi: 10.3389/fpls.2014.00506

[104]

Chen YH, Cohen ZP, Bueno EM, Christensen BM, Schoville SD. 2023. Rapid evolution of insecticide resistance in the Colorado potato beetle, Leptinotarsa decemlineata. Current Opinion in Insect Science 55:101000

doi: 10.1016/j.cois.2022.101000

[105]

Rosso LC, Lax P, Ciancio A, Colagiero M, Pentimone I. 2024. The cryptic microbiota of plant parasitic and entomopathogenic nematodes: diversity, effects on host biology and potential in plant protection. Journal of Pest Science 97(3):1227−1244

doi: 10.1007/s10340-024-01783-0

[106]

Sun T, Liu H, Wang N, Huang M, Banerjee S, et al. 2025. Interactions with native microbial keystone taxa enhance the biocontrol efficiency of Streptomyces. Microbiome 13:126

doi: 10.1186/s40168-025-02120-y

[107]

Mundt CC. 2002. Use of multiline cultivars and cultivar mixtures for disease management. Annual Review of Phytopathology 40:381−410

doi: 10.1146/annurev.phyto.40.011402.113723

[108]

He P, Wang C, Zhang N, Liu B, Yang Y, et al. 2021. Multi-genotype varieties reduce rice diseases through enhanced genetic diversity and show stability and adaptability in the field. Phytopathology Research 3(1):28

doi: 10.1186/s42483-021-00105-x

[109]

Niu B, Wang W, Yuan Z, Sederoff RR, Sederoff H, et al. 2020. Microbial interactions within multiple-strain biological control agents impact soil-borne plant disease. Frontiers in Microbiology 11:585404

doi: 10.3389/fmicb.2020.585404

[110]

Chen J, Xu D, Chao L, Liu H, Bao Y. 2020. Microbial assemblages associated with the rhizosphere and endosphere of an herbage, Leymus chinensis. Microbial Biotechnology 13(5):1390−1402

doi: 10.1111/1751-7915.13558

[111]

Geffersa AG, Burdon JJ, MacFadyen S, Thrall PH, Sprague SJ, et al. 2023. The socio-economic challenges of managing pathogen evolution in agriculture. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences 378(1873):20220012

doi: 10.1098/rstb.2022.0012

[112]

O'Hara NB, Franks SJ, Kane NC, Tittes S, Rest JS. 2021. Evolution of pathogen response genes associated with increased disease susceptibility during adaptation to an extreme drought in a Brassica rapa plant population. BMC Ecology and Evolution 21(1):61

doi: 10.1186/s12862-021-01789-7

[113]

Crone MA, Freemont PS. 2024. Thinking beyond pathogen surveillance: building resilient biotech ecosystems to combat the next pandemic. Frontiers in Science 2:1412291

doi: 10.3389/fsci.2024.1412291

[114]

Ilyaskina D, Altveş S, Dong L, Bouwmeester H, El Aidy S. 2025. Adaptive and metabolic convergence in rhizosphere and gut microbiomes. Microbiome 13:173

doi: 10.1186/s40168-025-02179-7