Temporal and spatial variation of microbial communities in stored rice grains from two major depots in China

Analysis of wheat fungal community succession in traditional storage structures using Illumina MiSeq sequencing technology

The diversity of fungi in wheat with different deoxynivalenol (DON) content at various periods post-harvest and in the environment of storage were investigated. The changes in DON content were measured with ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), and an amplicon sequence analysis of fungi was performed in traditional storage structures using high-throughput sequencing. The changes in temperature, humidity, and CO2 concentration were collected by sensors. In addition, we analyzed principal component analysis, species composition, species differences, and community differences of fungi. There was an obvious separation of the fungal communities under different storage conditions and times. Many fungal genera were gradually decreasing during storage and were eventually undetectable, and many fungal genera that were undetectable at first gradually increased during storage and even became dominant fungal genera. The competition between fungi was fierce. The competition between fungi were affected by the presence of DON. As the initial DON content increased, the contribution of inter-group differences became more obvious. The temperature, humidity, and CO2 concentration of wheat in the silo's environment changed with extended storage time. The content of DON decreased with extended storage time. We had investigated the changes in DON content and their correlation with the changes in fungal communities and environmental factors, which showed a high degree of correlation. This study offers theoretical justification for optimizing safe wheat grain in traditional storage conditions.

Characterization of core microbiota of barley seeds from different continents for origin tracing and quarantine pathogen assessment

Seeds are important microbial vectors, and seed-associated pathogens can be introduced into a country through trade, resulting in yield and quality losses in agriculture. The aim of this study was to characterize the microbial communities associated with barley seeds, and based on which, to develop technical approaches to trace their geographical origins, and to inspect and identify quarantine pathogens. Our analysis defined the core microbiota of barley seed and revealed significant differences in the barley seed-associated microbial communities among different continents, suggesting a strong geographic specificity of the barley seed microbiota. By implementing a machine learning model, we achieved over 95% accuracy in tracing the origin of barley seeds. Furthermore, the analysis of co-occurrence and exclusion patterns provided important insights into the identification of candidate biocontrol agents or microbial inoculants that could be useful in improving barley yield and quality. A core pathogen database was developed, and a procedure for inspecting potential quarantine species associated with barley seed was established. These approaches proved effective in detecting four fungal and three bacterial quarantine species for the first time in the port of China. This study not only characterized the core microbiota of barley seeds but also provided practical approaches for tracing the regional origin of barley and identifying potential quarantine pathogens.

Airborne microorganisms and key environmental factors shaping their community patterns in the core production area of the Maotai-flavor Baijiu

Airborne microorganisms are important parts of the Moutai-flavor Baijiu brewing microbial community, which directly affects the quality of Baijiu. However, environmental factors usually shape airborne microbiomes in different distilleries, even in the different production areas of the same distillery. Unfortunately, current understanding of environmental factors shaping airborne microbiomes in distilleries is very limited. To bridge this gap, we compared airborne microbiomes in the Moutai-flavor Baijiu core production areas of different distilleries in the Chishui River Basin and systematically investigated the key environmental factors that shape the airborne microbiomes. The top abundant bacterial communities are mainly affiliated to the phyla Actinobacteriota, Firmicutes, and Proteobacteri, whereas Ascomycota and Basidiomycota are the predominant fungal communities. The Random Forest analysis indicated that the biomarkers in three distilleries are Saccharomonospora and Bacillus, Thermoactinomyces, Oceanobacillus, and Methylobacterium, which are the core functional flora contributing to the production of Daqu. The correlation and network analyses showed that the distillery age and environmental temperature have a strong regulatory effect on airborne microbiomes, suggesting that the fermentation environment has a domesticating effect on air microbiomes. Our findings will greatly help us understand the relationship between airborne microbiomes and environmental factors in distilleries and support the production of the high-quality Moutai-flavor Baijiu.

Isolation and Characterization of Paenibacillus polymyxa B7 and Inhibition of Aspergillus tubingensis A1 by Its Antifungal Substances

Screening of Bacillus with antagonistic effects on paddy mold pathogens to provide strain resources for biological control of mold in Oryza sativa L. screening of Bacillus isolates antagonistic towards Aspergillus tubingensis from rhizosphere soil of healthy paddy; classification and identification of antagonistic strains by biological characteristics and 16S rDNA sequence analysis; transcriptome sequencing after RNA extraction from Bacillus-treated Aspergillus tubingensis; and extraction of inhibitory crude proteins of Bacillus by ammonium sulfate precipitation; inhibitory crude protein and Bacillus spp. were treated separately for A. tubingensis and observed by scanning electron microscopy (SEM). An antagonistic strain of Bacillus, named B7, was identified as Paenibacillus polymyxa by 16S rDNA identification and phylogenetic evolutionary tree comparison analysis. Analysis of the transcriptome results showed that genes related to secondary metabolite biosynthesis such as antifungal protein were significantly downregulated. SEM results showed that the mycelium of A. tubingensis underwent severe rupture after treatment with P. polymyxa and antifungal proteins, respectively. In addition, the sporocarp changed less after treatment with P. polymyxa, and the sporangium stalks had obvious folds. P. polymyxa B7 has a good antagonistic effect against A. tubingensis and has potential for biocontrol applications of paddy mold pathogens.

Effects of zinc oxide nanocomposites on microorganism growth and protection of physicochemical quality during maize storage

Maize moldy and spoilage due to microbial growth is a significant challenge in grain storage. This study aimed to evaluate the effectiveness of a zinc oxide nanocomposite, ZnO@mSiO2, prepared in our previous research, in inhibiting mold growth and preserving maize cell quality. The results demonstrated that ZnO@mSiO2 could effectively inhibit the growth of dominant microorganism, Aspergillus flavus, Talaromyces variabilis, Penicillium citrinum and Fusarium graminearum, in maize storage. Aspergillus flavus was selected as the model fungus, ZnO@mSiO2 effectively disrupted fungal hyphae structure, leading to reduced hyphal mass and inhibited spore germination. The inhibitory effect of ZnO@mSiO2 on mold growth was concentration-dependent. However, the ZnO@mSiO2 at an appropriate concentration (not exceeding 3.0 g/kg) preserved the integrity of maize cell membranes and enhancing the antioxidant activity within maize cells. The findings highlight the potential of ZnO@mSiO2 as an effective protectant to inhibit mold growth and preserve maize quality during storage.

Interactions among the composition changes in fungal communities and the main mycotoxins in simulated stored wheat grains

BACKGROUND

There are significant food safety risks associated with wheat spoilage due to fungal growth and mycotoxin contamination. Nevertheless, a few studies have examined how stored wheat grain microbial communities and mycotoxins vary in different storage conditions. In this study, changes in deoxynivalenol (DON) and deoxynivalenol-3-glucoside (D3G) content were measured with ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), and an amplicon sequence analysis of fungi was performed on stored wheat grains from different storage conditions using high-throughput sequencing. The detailed interactions among the composition changes in the fungal community and the DON content of simulated stored wheat grains were also analyzed.

RESULTS

Alternaria, Fusarium, Mrakia, and Aspergillus were the core fungal taxa, and the fungal communities of samples stored under different conditions were observed to be different. Aspergillus relative abundances increased, whereas Fusarium decreased. This led to an increase in the content of DON. The content of DON increased about 67% with 12% moisture and at 25 °C after 2 months of storage, which was influenced by the stress response of Fusarium. Correlations in fungal and mycotoxins changes were observed. There may be potential value in these findings for developing control strategies to prevent mildew infestations and mycotoxins contamination during grain storage.

CONCLUSION

In storage, the more the fungal community composition and the relative abundance of Fusarium change, the more mycotoxins will be produced. We should therefore reduce competition between fungal communities through pre-storage treatment and through measures during storage. © 2023 Society of Chemical Industry.

Germination of pecan seeds changes the microbial community

Endophytes are core of the plant-associated microbiome, and seed endophytes are closely related to the plant growth and development. Seed germination is an important part of pecan's life activities, but the composition and changes of microbes during different germination processes have not yet been revealed in pecan seeds. In order to deeply explore the characteristics of endophytes during the germination process of pecan, high-throughput sequencing was performed on seeds at four different germination stages. Findings of present study was found that the diversity and composition of microorganisms were different in different germination stages, and the microbial richness and diversity were highest in the seed endocarp break stage. It was speculated that the change of endophytes in pecan seeds was related to the germination stage. By evaluating the relationship between microbial communities, the core microbiota Cyanobacteria, Proteobacteria and Actinobacteria (bacterial) and Anthophyta and Ascomycota (fungal) core microbiota were identified in germinating pecan seeds. Finally, biomarkers in different germination processes of pecan seeds were identified by LEfSe analysis, among which Proteobacteria, Gamma proteobacteria and, Cyanobacteria and Ascomycota and Sordariomycetes were most abundant. Thus, this study will help to explore the interaction mechanism between pecan seeds and endophytes in different germination processes, and provide materials for the research and development of pecan seed endophytes.

Temporal and Habitat Dynamics of Soil Fungal Diversity in Gravel-Sand Mulching Watermelon Fields in the Semi-Arid Loess Plateau of China

Mulching is an important agricultural management tool for increasing watermelon productivity and land-use efficiency because it helps improve water use efficiency and reduce soil erosion. However, there is relatively little available information regarding the effects of long-term continuous monoculture farming on soil fungal communities and related fungal pathogens in arid and semiarid regions. In this study, we characterized the fungal communities of four treatment groups, including gravel-sand-mulched farmland, gravel-sand-mulched grassland, fallow gravel-sand-mulched grassland, and native grassland, using amplicon sequencing. Our results revealed that the soil fungal communities differed significantly between mulched farmland and mulched grassland as well as the fallow mulched grassland. Gravel-sand mulch significantly impaired the diversity and composition of soil fungal communities. Soil fungal communities were more sensitive to gravel-sand mulch in grassland than in other habitats. Long-term continuous monoculture (more than 10 years) led to decreased abundance of Fusarium species, which contains include agronomically important plant pathogens. In the gravel-mulched cropland, some Penicillium and Mortierella fungi were significantly enriched with increasing mulch duration, suggesting potential beneficial properties of those fungi that could be applied to disease control. We also found that long-term gravel mulching in continuous monoculture farming could potentially form disease-suppressive soils and alter soil microbial biodiversity and fertility. Our study provides insights into the exploration of novel agricultural management strategies along with continuous monoculture practice to control watermelon wilt disease by maintaining a more sustainable and healthier soil environment. IMPORTANCE Gravel-sand mulching is a traditional agricultural practice in arid and semiarid regions, providing a surface barrier for soil and water conservation. However, application of such practice in monocropping systems may lead to outbreaks of several devastating plant diseases, such as watermelon Fusarium wilt. Our results with amplicon sequencing suggest that soil fungal communities differ significantly between mulched farmland and mulched grassland and are more sensitive to gravel-sand mulch in grassland. Under continuous monoculture regimens, long-term gravel mulch is not necessarily detrimental and may result in decreased Fusarium abundance. However, some known beneficial soil fungi may be enriched in the gravel-mulch cropland as mulch duration increases. A possible explanation for the reduction in Fusarium abundance may be the formation of disease-suppressive soils. This study provides insight into the need to explore alternative strategies using beneficial microbes for sustainable watermelon wilt control in continuous monocropping system.