Significance: Rhizobia are soil-dwelling bacteria that form symbioses with legumes and provide biologically useable nitrogen as ammonium for the host plant. High-throughput DNA sequencing has led to a rapid expansion in publication of complete genomes for numerous rhizobia, but analysis of gene function increasingly lags gene discovery. Mariner-based transposon insertion sequencing has allowed us to characterize the fitness contribution of bacterial genes and determine those functionally important in aRhizobium–legume symbiosis at multiple stages of development.

Postharvest soft rot of kiwifruit has resulted in substantial market losses, yet there were few antagonistic yeasts reported to control the disease. This study screened 1113 yeast strains for potential antagonistic yeast to control soft rot of kiwifruit caused by Botryosphaeria dothidea and Diaporthe actinidiae, and strain 37 was selected to evaluate the control efficacy and mechanisms, which was identified as Meyerozyma guilliermondii via molecular biological identification. Our results showed that M. guilliermondii 37 effectively reduced pathogen spore germination rate to 28.52% and decay incidence of inoculated kiwifruit to 42.11% maximumly, whereas cell-free supernatant lacked antifungal activity, implying that M. guilliermondii 37 didn’t produce direct antifungal compounds against the two pathogens. In addition, M. guilliermondii 37 adhered tenaciously to the pathogens’ mycelium and colonized rapidly in kiwifruit flesh. Moreover, yeast strain 37 induced kiwifruit resistance by elevating the defense-related enzyme activity, increasing the antioxidant substances content, and suppressing the cell wall-degrading enzyme activity. Gene expression was consistent with the corresponding enzyme activity. Further postharvest yeast immersion treatment significantly reduced natural decay to 35.69% while maintaining soft-ripe quality. These results indicated that M. guilliermondii 37 might serve as a biocontrol agent against postharvest soft rot in kiwifruit.

Bacterial–fungal interaction (BFI) has significant implications for the health of host plants. While the diffusible antibiotic metabolite-mediated competition in BFI has been extensively characterized, the impact of intercellular contact remains largely elusive. Here, we demonstrate that the intercellular contact is a prevalent mode of interaction between beneficial soil bacteria and pathogenic filamentous fungi. By generating antibiotics-deficient mutants in two common soil bacteria, Lysobacter enzymogenes and Pseudomonas fluorescens , we show that antibiotics-independent BFI effectively inhibits pathogenic fungi. Furthermore, transcriptional and genetic evidence revealed that this antibiotics-independent BFI relies on intercellular contact mediated by the type VI secretion system (T6SS), which may facilitate the translocation of bacterial toxic effectors into fungal cells. Finally, by using a “conidia enrichment” platform, we found that T6SS-mediated fungal inhibition resulting from intercellular contact naturally occurs within the soil microbiome, particularly represented by Pseudomonas fulva . Overall, these results demonstrate that bacteria from the soil microbiome can protect host plants from fungal infection through antibiotics-independent intercellular contacts, thus revealing a naturally occurring and ecologically important mode of BFI in agricultural contexts.

China is the world’s leading kiwifruit producer (Belrose 2016). In September 2016, brown/black spot disease was found on leaves and fruit peel in several kiwifruit orchards in Taishun County, Zhejiang Province and Liupanshui City, Guizhou Province. Diseased leaves and fruit exhibited small irregular brown to black spots (1-2 mm), which exapanded (3-5 mm) and became necrotic with age. Affected leaves became blighted by the fall. Ten orchards in each city were investigated, and approximately 45% of trees were symptomatic in Taishun and Liupanshui (Fig. 1 A-C). Symptomatic tissues of twenty typical infected leaves and fruit were cut into 4-5 mm pieces, surface-sterilized, rinsed three times in sterile distilled water, and cultured on 1.5% potato dextrose agar (PDA) with streptomycin and tetracycline. Petri dishes were incubated at 25°C under a 12-h light / dark cycle. Hyphal-tip from the growing edge of colonies cultured for 3 days at 25°C was transferred to PDA to obtain pure cultures. Fungal colonies were ...

The prevalence of kiwifruit (Actinidia sp.) postharvest rot disease in China was studied from October to December 2014. Approximately 30% of fruits were observed with milky-white, sour-smelling, watery internal tissue (Fig.1a). To identify the causal agent of the disease, 100 fruits (Jinyan’, ‘Hongyang’, ‘Jinkui’, ‘Guichang’ and ‘Qinmei’ cultivars) were arbitrarily collected from Hubei, Sichuan, Henan, Chongqing, Jiangxi, Guizhou and Shaanxi province and stored in controlled-atmosphere rooms (4°C, 2% O2, 5% CO2). After 60 days, 28 fruit were observed to have postharvest rot. Botryosphaeria dothidea (Fig.1b) and Diaporthe nitschke (anamorph: genus Phomopsis), the two most important postharvest fungal pathogens of kiwifruit in China (Li et al. 2015; Zhou et al. 2015), were isolated from most fruits. Most Diaporthe sp. strains were identified morphologically and molecularly as D. ambigua (Fig.1c), previously reported to cause rot in stored kiwifruits in Chile (Auger et al. 2013). Five previously-unidentified...