Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels. We aimed to determine the composition and putative function of the soil microbiome associated with potato CS. The copy numbers of the scab phytotoxin biosynthetic gene txtAB and the bacterial 16S rRNA gene as well as the diversity and composition of each of the four soil-root system compartments were examined; GS was the only compartment that exhibited significant differences between the H and L groups. Compared to the H group, the L group exhibited a lower txtAB gene copy number, lower bacterial 16S copy number, higher diversity, higher co-occurrence network complexity, and higher community function similarity within the GS microbiome. The community composition and function of the GS samples were further revealed by shotgun metagenomic sequencing. Variovorax, Stenotrophomonas, and Agrobacterium were the most abundant genera that were significantly and positively correlated with the scab severity level, estimated absolute abundance (EAA) of pathogenic Streptomyces, and txtAB gene copy number. In contrast, Geobacillus, Curtobacterium, and unclassified Geodermatophilaceae were significantly negatively correlated with these three parameters. Compared to the function profiles in the L group, several genes involved in “ABC transporters,” the “bacterial secretion system,” “quorum sensing (QS),” “nitrogen metabolism,” and some metabolism by cytochrome P450 were enriched in the H group. In contrast, some antibiotic biosynthesis pathways were enriched in the L group. Based on the differences in community composition and function, a simple model was proposed to explain the putative relationships between the soil microbiome and CS occurrence. The GS microbiome was closely associated with CS severity in the soil-root system, and the occurrence of CS was accompanied by changes in community composition and function. The differential functions provide new clues to elucidate the mechanism underlying the interaction between CS occurrence and the soil microbiome, and varying community compositions provide novel insights into CS occurrence.

Co-contamination of polycyclic aromatic hydrocarbons (PAHs) with heavy metals (HMs) in aquatic environments is a global threat; however, little is understood about PAH biodegradation in these sites. In this study, PAHs’ biodegradation in the presence of HMs in water by a metal-tolerant consortium composed of Bacillus subtilis and fungus Acremonium sp. was investigated. The consortium demonstrated higher tolerance to the tested HMs (Fe²⁺, Al³⁺, Ni²⁺, Cu²⁺, Mn²⁺ and Zn²⁺) than the individual consortium components, and the tolerance to individual metals decreased with increasing metal concentrations. In the absence of HMs in aquatic systems, the consortium efficiently degraded naphthalene, fluorine, phenanthrene, anthracene and fluoranthene individually (50 mmol/L) over 10 days. However, while Ni²⁺ supplementation (5 mmol/L) suppressed phenanthrene and anthracene removal (p ≤ 0.01), enhanced fluoranthene degradation relative to the control was observed. Cu²⁺, Zn²⁺, Fe²⁺ and Al³⁺ supplementation demonstrated significant inhibition against individual phenanthrene, anthracene and fluoranthene removal, and Cu²⁺ showed a more significant effect on the degradation of these PAH compounds compared to other metals. Conversely, Mn²⁺ significantly enhanced the removal of fluorene, phenanthrene and fluoranthene, but inhibited anthracene degradation. HM contamination in aquatic systems did not show any effect on naphthalene bioremediation, possible due to its rapid degradation over a short time. Thus, metals affect PAH aquatic biodegradation by consortia, depending on metal species and PAH compound, underlining the complex nature of co-contaminated systems containing HMs and PAHs. To our knowledge, this is the first study to examine the influence of HMs on PAHs’ bioremediation by such PAH-degrading consortia in water.

Potato common scab, caused by Streptomyces spp., is one of the leading causes of heavy commercial losses in the potato industry and is thus one of the most serious plant diseases worldwide. This study identified and assessed potential biocontrol agents against potato common scab. In total, 110 isolates were obtained through antagonistic tests; among which, Bacillus sp. strain AMCC 101304 was found to be most effective at inhibiting the potato common scab pathogen, Streptomyces scabies. Bacillus sp. strain AMCC 101304 was finally identified as Bacillus altitudinis by morphological observation, physiological and biochemical experimentation, as well as 16S rRNA sequencing and phylogenetic analysis. Pot experiments were conducted twice (in spring and autumn) to verify the biocontrol effect of B. altitudinis AMCC 101304 against potato common scab. In spring, the control efficiency reached 76.34%. In autumn, the disease incidence was reduced from 100% to 34.19% (one treatment with strain AMCC 101304) and 38.42% (two treatments with strain AMCC 101304), and the control efficiency reached 82.50% (one application) and 78.43% (two applications). The present study demonstrated the potential of an isolate, identified as B. altitudinis AMCC 101304, as an effective biocontrol agent for future use in the field.