Fungal pathogens and antagonists in root-soil zone in organic and integrated systems of potato production

For tuberizing crops like potato (Solanum tuberosum), the geocaulosphere, or the thin zone of soil in contact with and influenced by the tuber, is a distinct habitat that exists between the potato and the soil environment. Geocaulosphere soil that remains associated with the tuber after harvest is called tare soil. However, beyond potato pathogens, the microbes present in tare soil are understudied. We used ITS and 16S metabarcoding to characterize the microbial communities present in 130 tare soils of commercially produced seed potatoes used for potato production in Oregon. In 2018 and 2019, tare soils were opportunistically sampled from seed potatoes that were collected from farmers in the Columbia Basin of OR. This sampling effort included seed tubers of 23 cultivars that had originated from 40 commercial seed farms in 11 states. We identified a core microbiome consisting of 61 bacterial and 26 fungal taxa, some of which are not common to the potato microbiome, and others which have been reported to either possess biocontrol activities, promote plant growth, or cause disease in potato. Seed grower farm accounted for the greatest amount of compositional variation among tare soil microbiome samples, with more similar communities found on seed tubers grown on farms near to each other. Learning which factors shape tare soil microbial community composition and if those communities influence plant health are essential steps towards potato microbiome management.

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Genome Sequencing and Comparative Genomic Analysis of Attenuated Strain Gibellulopsis nigrescens GnVn.1 Causing Mild Wilt in Sunflower

Dong,

Liu,

Zhao

et al. 2024

JoF

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Gibellulopsis nigrescens, previously classified in the Verticillium genus until 2007, is an attenuated pathogen known to provide cross-protection against Verticillium wilt in various crops. To investigate the potential mechanisms underlying its reduced virulence, we conducted genome sequencing, annotation, and a comparative genome analysis of G. nigrescens GnVn.1 (GnVn.1), an attenuated strain isolated from sunflower. The genome sequencing and annotation results revealed that the GnVn.1 genome consists of 22 contigs, with a total size of 31.79 Mb. We predicted 10,876 genes, resulting in a gene density of 342 genes per Mb. The pathogenicity gene prediction results indicated 1733 high-confidence pathogenicity factors (HCPFs), 895 carbohydrate-active enzymes (CAZys), and 359 effectors. Moreover, we predicted 40 secondary metabolite clusters (SMCs). The comparative genome analysis indicated that GnVn.1 contains more CAZys, SMCs, predicted effectors, and HCPF genes than Verticillium dahliae (VdLs.17) and Verticillium alfalfae (VaMas.102). The core–pan analysis results showed that GnVn.1 had more specific HCPFs, effectors, CAZys, and secreted protein (SP) genes, and lost many critical pathogenic genes compared to VdLs.17 and VaMs.102. Our results indicate that the GnVn.1 genome harbors more pathogenicity-related genes than the VdLs.17 and VaMs.102 genomes. These abundant genes may play critical roles in regulating virulence. The loss of critical pathogenic genes causes weak virulence and confers biocontrol strategies to GnVn.1.

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Fungal pathogens and antagonists in root-soil zone in organic and integrated systems of potato production

Cited by 3 publications

References 51 publications

Preservation of winter garlic depending on the elements of postharvest treatment

Preservation of winter garlic depending on the elements of postharvest treatment

Characterizing Variation in the Bacterial and Fungal Tare Soil Microbiome of Seed Potato

Genome Sequencing and Comparative Genomic Analysis of Attenuated Strain Gibellulopsis nigrescens GnVn.1 Causing Mild Wilt in Sunflower

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