Distribution of mycotoxin-producing fungi across major rice production areas of China

Aflatoxins in the rice production chain: A review on prevalence, detection, and decontamination strategies

Rice (Oryza sativa L.) is one of the most consumed cereals that along with several important nutritional constituents typically provide more than 21% of the caloric requirements of human beings. Aflatoxins (AFs) are toxic secondary metabolites of several Aspergillus species that are prevalent in cereals, including rice. This review provides a comprehensive overview on production factors, prevalence, regulations, detection methods, and decontamination strategies for AFs in the rice production chain. The prevalence of AFs in rice is more prominent in African and Asian than in European countries. Developed nations have more stringent regulations for AFs in rice than in the developing world. The contamination level of AFs in the rice varied at different stages of rice production chain and is affected by production practices, environmental conditions comprising temperature, humidity, moisture, and water activity as well as milling operations such as de-husking, parboiling, and polishing. A range of methods including chromatographic techniques, immunochemical methods, and spectrophotometric methods have been developed, and used for monitoring AFs in rice. Chromatographic methods are the most used methods of AFs detection followed by immunochemical techniques. AFs decontamination strategies adopted worldwide involve various physical, chemical, and biological strategies, and even using plant materials. In conclusion, adopting good agricultural practices, implementing efficient AFs detection methods, and developing innovative aflatoxin decontamination strategies are imperative to ensure the safety and quality of rice for consumers.

Mycobiome mediates the interaction between environmental factors and mycotoxin contamination in wheat grains

Environmental factors significantly impact grain mycobiome assembly and mycotoxin contamination. However, there is still a lack of understanding regarding the wheat mycobiome and the role of fungal communities in the interaction between environmental factors and mycotoxins. In this study, we collected wheat grain samples from 12 major wheat-producing provinces in China during both the harvest and storage periods. Our aim was to evaluate the mycobiomes in wheat samples with varying deoxynivalenol (DON) contamination levels and to confirm the correlation between environmental factors, the wheat mycobiome, and mycotoxins. The results revealed significant differences in the wheat mycobiome and co-occurrence network between contaminated and uncontaminated wheat samples. Fusarium was identified as the main differential taxon responsible for inducing DON contamination in wheat. Correlation analysis identified key factors affecting mycotoxin contamination. The results indicate that both environmental factors and the wheat mycobiome play significant roles in the production and accumulation of DON. Environmental factors can affect the wheat mycobiome assembly, and wheat mycobiome mediates the interaction between environmental factors and mycotoxin contamination. Furthermore, a random forest (RF) model was developed using key biological indicators and environmental features to predict DON contamination in wheat with accuracies exceeding 90 %. The findings provide data support for the accurate prediction of mycotoxin contamination and lay the foundation for the research on biological control technologies of mycotoxin through the assembly of synthetic microbial communities.

Determination of aflatoxins in rice from Penang, Malaysia by dispersive liquid-liquid micro-extraction and LC-MS/MS

Rice is one of the crops cultivated in Malaysia, and it is the main diet for most of the population. In this study, dispersive liquid-liquid micro-extraction (DLLME) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to develop, optimise and validate a reliable, easy-to-use and quick approach to detect aflatoxin B1 (AFB1), aflatoxin B2 (AFB2), aflatoxin G1 (AFG1) and aflatoxin G2 (AFG2). The extraction recoveries in DLLME were enhanced by the addition of 5% salt, utilising chloroform as the extraction solvent and acetonitrile as the dispersive solvent. The DLLME parameters - the extraction solvent volume, salt concentration and dispersive solvent volume were optimised with Box-Behnken design (BBD) and response surface methodology (RSM). Under optimised experimental conditions, excellent linearity was obtained with a limit of detection (LOD) ranging from 0.125 to 0.25 ng g-1, a limit of quantitation (LOQ) ranging from 0.25 to 0.3 ng g-1 and a correlation value (R2) of 0.990. The matrix effects were between -11.1% and 19.9%, and recoveries ranged from 87.4% to 117.3%. The optimised and validated method was used effectively to assess aflatoxins contamination in 20 commercial rice samples collected from local supermarkets in Penang, Malaysia. AFB1 was detected at 0.41-0.43 ng g-1 in two rice samples, below the regulatory limit.

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.

Deciphering the Microbiological Mechanisms Underlying the Impact of Different Storage Conditions on Rice Grain Quality

Different storage conditions can influence microbial community structure and metabolic functions, affecting rice grains' quality. However, the microbiological mechanisms by which different storage conditions affect the quality of rice grains are not yet well understood. This study monitored the quality (the content of starch, protein, etc.) and microbial community structure of rice grains stored under different storage conditions with nitrogen gas atmosphere (RA: normal temperature, horizontal ventilation, RB: normal temperature, vertical ventilation, RC: quasi-low temperature, horizontal ventilation). The results revealed that the rice grains stored under condition RB exhibited significantly lower quality compared to condition RA and RC. In addition, under this condition, the highest relative abundance of Aspergillus (16.0%) and Penicillium (0.4%) and the highest levels of aflatoxin A (3.77 ± 0.07 μg/kg) and ochratoxin B1 (3.19 ± 0.05 μg/kg) were detected, which suggested a higher risk of fungal toxin contamination. Finally, co-occurrence network analysis was performed, and the results revealed that butyl 1,2-benzenedicarboxylate was negatively correlated (p < 0.05) with Moesziomyces and Alternaria. These findings will contribute to the knowledge base of rice storage management and guide the development of effective control measures against undesirable microbial activities.

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.

The biodiversity of Aspergillus flavus in stored rice grain leads to a decrease in the overall aflatoxin B1 production in these species

Aspergillus flavus is a significant fungus that poses a threat to food safety by producing mycotoxins in various crops. In this study, A. flavus isolates were obtained from storage rice collected from seven provinces in southern China, and their AFB1 production, biosynthesis genes presence, and diversity were detected. Results showed that 56 out of the 81 A. flavus isolates produced detectable levels of AFB1, and 71 isolates (87.6 %) possessed aflR gene in their AF synthesis gene cluster, while only 41 isolates (50.6 %) had the ver-1 gene present. Genetic diversity analysis using inter-simple sequence repeats (ISSR) markers revealed seven main clusters among the isolates and the genetic similarity coefficients of 81 A. flavus isolates ranged from 0.53 to 1.00. Additionally, coculture assays were conducted using two toxigenic and two atoxigenic isolates from the same grain depot to investigate the effect of intraspecific inhibition on AFB1 production and to assess the AFB1 contamination risk of storage rice. The in situ results demonstrated that the atoxigenic isolates effectively inhibited the AFB1 contamination of toxigenic isolates. These findings provide insight into the genetic diversity of A. flavus isolates populations and highlight the potential food safety hazards of them in stored rice grain in China.

Microbial communities and their correlation with flavor compound formation during the mechanized production of light-flavor Baijiu

Light-flavor Baijiu fermentation is a typical spontaneous solid-state fermentation process fueled by a variety of microorganisms. Mechanized processes have been increasingly employed in Baijiu production to replace traditional manual operation processes, however, the microbiological and physicochemical dynamics in mechanized processes remain largely unknown. Here, we investigated the microbial community succession and flavor compound formation during a whole mechanized fermentation process of light-flavor Baijiu using the conventional dilution plating method, PacBio single-molecule real-time (SMRT) sequencing and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. The results showed that largely different fungal and bacterial communities were involved in the soaking and fermentation processes. A clear succession from Pantoea agglomerans to Bacillus (B.) smithii and B. coagulans in dominant bacterial species and from Cladosporium exasperatum to Saccharomyces cerevisiae and Lichtheimia ramosa in dominant fungal species occurred in the soaking processes. In the fermentation process, the most dominant bacterial species was shifted from Pantoea agglomerans to Lactobacillus (La.) acetotolerans and the most dominant fungal species were shifted from Lichtheimia ramose and Rhizopus arrhizus to Saccharomyces cerevisiae. The bacterial and fungal species positively associated with acidity and the formation of ethanol and different flavor compounds were specified. The microbial species exhibited strong co-occurrence or co-exclusion relationships were also identified. The results are helpful for the improvement of mechanized fermentation process of light-flavor Baijiu production.

Effects of different fertilization conditions and different geographical locations on the diversity and composition of the rhizosphere microbiota of Qingke (Hordeum vulgare L.) plants in different growth stages

Introduction

The excessive use of chemical fertilizer causes increasing environmental and food security crisis. Organic fertilizer improves physical and biological activities of soil. Rhizosphere microbiota, which consist of highly diverse microorganisms, play an important role in soil quality. However, there is limited information about the effects of different fertilization conditions on the growth of Qingke plants and composition of the rhizosphere microbiota of the plants.

Methods

In this study, we characterized the rhizosphere microbiota of Qingke plants grown in three main Qingke-producing areas (Tibet, Qinghai, and Gansu). In each of the three areas, seven different fertilization conditions (m1-m7, m1: Unfertilized; m2: Farmer Practice; m3: 75% Farmer Practice; m4: 75% Farmer Practice +25% Organic manure; m5: 50% Farmer Practice; m6: 50% Farmer Practice +50% Organic manure; m7: 100% Organic manure) were applied. The growth and yields of the Qingke plants were also compared under the seven fertilization conditions.

Results

There were significant differences in alpha diversity indices among the three areas. In each area, differences in fertilization conditions and differences in the growth stages of Qingke plants resulted in differences in the beta diversity of the rhizosphere microbiota. Meanwhile, in each area, fertilization conditions, soil depths, and the growth stages of Qingke plants significantly affected the relative abundance of the top 10 phyla and the top 20 bacterial genera. For most of microbial pairs established through network analysis, the significance of their correlations in each of the microbial co-occurrence networks of the three experimental sites was different. Moreover, in each of the three networks, there were significant differences in relative abundance and genera among most nodes (i.e., the genera Pseudonocardia, Skermanella, Pseudonocardia, Skermanella, Aridibacter, and Illumatobacter). The soil chemical properties (i.e., TN, TP, SOM, AN, AK, CEC, Ca, and K) were positively or negatively correlated with the relative abundance of the top 30 genera derived from the three main Qingke-producing areas (p < 0.05). Fertilization conditions markedly influenced the height of a Qingke plant, the number of spikes in a Qingke plant, the number of kernels in a spike, and the fresh weight of a Qingke plant. Considering the yield, the most effective fertilization conditions for Qingke is combining application 50% chemical fertilizer and 50% organic manure.

Conclusion

The results of the present study can provide theoretical basis for practice of reducing the use of chemical fertilizer in agriculture.

Crop diversity promotes the recovery of fungal communities in saline-alkali areas of the Western Songnen Plain

Introduction

Phytoremediation is an effective strategy for saline land restoration. In the Western Songnen Plain, northeast China, soil fungal community recovery for saline phytoremediation has not been well documented among different cropping patterns. In this study, we tested how rotation, mixture, and monoculture cropping patterns impact fungal communities in saline-alkali soils to assess the variability between cropping patterns.

Methods

The fungal communities of the soils of the different cropping types were determined using Illumina Miseq sequencing.

Results

Mixture and rotation promoted an increase in operational taxonomic unit (OTU) richness, and OTU richness in the mixture system decreased with increasing soil depth. A principal coordinate analysis (PCoA) showed that cropping patterns and soil depths influenced the structure of fungal communities, which may be due to the impact of soil chemistry. This was reflected by soil total nitrogen (TN) and electrical conductivity (EC) being the key factors driving OTU richness, while soil available potassium (AK) and total phosphorus (TP) were significantly correlated with the relative abundance of fungal dominant genus. The relative abundance of Leptosphaerulina, Alternaria, Myrothecium, Gibberella, and Tetracladium varied significantly between cropping patterns, and Leptosphaerulina was significantly associated with soil chemistry. Soil depth caused significant differences in the relative abundance of Fusarium in rotation and mixture soils, with Fusarium more commonly active at 0-15 cm deep soil. Null-model analysis revealed that the fungal community assembly of the mixture soils in 0-15 cm deep soil was dominated by deterministic processes, unlike the other two cropping patterns. Furthermore, fungal symbiotic networks were more complex in rotation and mixture than in monoculture soils, reflected in more nodes, more module hubs, and connectors. The fungal networks in rotation and mixture soils were more stable than in monoculture soils, and mixture networks were obviously more connected than rotations. FUNGuild showed that the relative proportion of saprotroph in rotation and mixture was significantly higher than that in monocultures. The highest proportion of pathotroph and symbiotroph was exhibited in rotation and mixture soils, respectively.

Discussion

Overall, mixture is superior to crop rotation and monocultures in restoring fungal communities of the saline-alkali soils of the Western Songnen Plain, northeast China.

Distribution of Core Root Microbiota of Tibetan Hulless Barley along an Altitudinal and Geographical Gradient in the Tibetan Plateau

The Tibetan Plateau is regarded as the third pole of the earth and is one of the least explored places on the planet. Tibetan hull-less barley (Hordeum vulgare L. var. nudum) is the only cereal crop grown widely in the Tibetan Plateau as a staple food. Extensive and long-term cropping of barley may influence the soil’s chemical and biological properties, including microbial communities. However, microbiota associated with hull-less barley is largely unexplored. This study aimed to reveal the composition and diversity of bacterial and fungal communities associated with the hull-less barley at different elevations in the Tibetan Plateau. The core bacterial and fungal taxa of Tibetan hull-less barley were identified, with Bacillaceae, Blastocatellaceae, Comamonadaceae, Gemmatimonadaceae, Planococcaceae, Pyrinomonadaceae, Sphingomonadaceae, and Nitrospiraceae being the most abundant bacterial taxa and Ceratobasidiaceae, Chaetomiaceae, Cladosporiaceae, Didymellaceae, Entolomataceae, Microascaceae, Mortierellaceae, and Nectriaceae being the most abundant fungal taxa (relative abundance > 1%). Both bacterial and fungal diversities of hull-less barley were affected by altitude and soil properties such as total carbon, total nitrogen, and available phosphorus and potassium. Both bacterial and fungal diversities showed a significant negative correlation with altitude, indicating that the lower elevations provide a conducive environment for the survival and maintenance of hull-less barley-associated microbiota. Our results also suggest that the high altitude-specific microbial taxa may play an important role in the adaptation of the hull-less barley to the earth’s third pole.

Changes to bacterial communities and soil metabolites in an apple orchard as a legacy effect of different intercropping plants and soil management practices

Intercropping is an important soil management practice for increasing orchard productivity and land-use efficiency because it has beneficial effects on soil microbial communities and soil properties. However, there is relatively little information available regarding the effects of different crops/grasses on soil microbial communities and soil metabolic products in apple orchards in arid and semi-arid regions. In this study, we showed the microbial communities of apple, intercropping plants, and sandy waste soil, using the third-generation PacBio SMRT long-read sequencing technology. Our results also revealed that the microbial communities and soil metabolic properties differed significantly between apple and the sandy waste soil and the intercropping plants. Intercropping could significantly enrich diverse microbial species, microbial nitrogen, and microbial carbon of soil. Moreover, intercropping with licorice showed better effects in recruiting beneficial microbes, compared to grass and pepper, significantly enriching species belonging to some well-known taxa with beneficial effects, including Bacillus, Ensifer, Paenibacillus, Rhizobium, and Sphingomonas. Thus, intercropping with licorice may improve apple tree growth and disease resistance. Furthermore, Bradyrhizobium and Rubrobacter were included among the keystone taxa of apple, whereas Bacillus, Chitinophaga, Stenotrophobacter, Rubrobacter, and Luteimonas were the keystone taxa of the intercropping plants. The results of our study suggest that intercropping with licorice is a viable option for increasing apple orchard productivity.

Zinc Nutrition Responses to Agronomic and Yield Traits, Kernel Quality, and Pollen Viability in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is one of the major cereal crops worldwide with wheat and maize. A total of two field experiments were performed to evaluate the response of some rice cultivars to various foliar zinc (Zn) concentrations based on different measurements, such as agronomic, yield, yield compounds, and grain technological parameters. The experimental layout was a split plot in three replicates; the five rice cultivars (Skaha 101, Giza178, Yasmeen, Fourate, and Amber 33) were distributed in the main plots while the four foliar applications of Zn (1,500, 2,000, 2,500 mg/L besides spray water) were occupied the sub-plots. The findings showed significant differences among the five rice cultivars regarding plant height, grain yield, straw yield, biological yield, harvest index, 1,000-grain weight, panicle length, protein percentage, and grain Zn content. There is a significant effect of Zn on all plant attributes. A significant interaction between rice cultivars and foliar application of Zn was observed, whereas fertilizing Giza 178 with foliar application of Zn at the rate of 2,500 mg/L achieved the highest mean values of grain yield and straw yield, biological yield, harvest index, 1,000-grain weight, panicle length, protein %, and Zn content followed by Sakha 101 with Zn application at the rate of 2,000 mg/L, respectively, in both seasons. The rice cultivars significantly differed in hulling (%), broken (%), hardness, grain length, shape, amylose (%), gel consistency, and gelatinization temperature. Unfortunately, the commercial Zn product used was genotoxic to pollen grains with a higher rate of Zn. Aberrations were observed such as stickiness, ultrastructural changes in the exterior and interior walls, partially or fully degenerated grains, and shrunken and unfilled grains. This study concluded that using Zn application at the rate of 2,000 mg/L to protect human and environmental health, the side effects and toxicity of the local commercial Zn product market should be investigated before making recommendations to farmers.

Analysis of the Fungi Community Variation during Rice Storage through High Throughput Sequencing

Rice storage conditions include location, granary depth, storage time, temperature and atmosphere. The fungi community varies during storage, but how these communities change remains unexplored so far. This study collected rice samples from granaries in different horizontal and vertical directions and storage time over two years. High-throughput ITS (Internal Transcribed Spacer) sequencing analysis revealed that Ascomycota (73.81%), Basidiomycota (6.56%) and Mucoromycota (9.42%) were the main Eumycota present during rice storage. The main fungi communities were Aspergillus sp., Fusarium sp., Rhizopus sp., Gibberella sp., Tilletia sp. and Penicillium sp. The contribution of storage time, horizontal orientation and vertical depth effect on fungi community relative abundance were 17.18%, 5.98% and 0.11%, respectively. Aspergillus sp. was the predominant Eubacterium during this process. The horizontal A was mainly occupied by Paraconiothyrium sp. and the location S, had Clavispora sp. Both of these varied dramatically during storage. Furthermore, Aspergillus sp., as a main mycotoxin producer, was the dominant fungi at vertical L1. This study comprehensively analyzed fungi community variation in horizontal and vertical directions to elucidate fungi community variation on rice during storage and to find the detrimental fungi. Therefore, it is important to improve granary ventilation systems and to ensure a uniform atmosphere to control fungi growth.