Contamination by fungal and bacterial species and their metabolites can affect grain quality and health of wheat consumers. In this study, sequence analyses of conserved DNA regions of fungi and bacteria combined with determination of trichothecenes and aflatoxins revealed the microbiome and mycotoxins of wheat from different silo positions (top, middle, and bottom) and storage times (3, 6, 9, and 12 months). The fungal community in wheat on the first day of storage (T₀) included 105 classified species (81 genera) and 41 unclassified species. Four species had over 10% of the relative abundance: Alternaria alternata (12%), Filobasidium floriforme (27%), Fusarium graminearum (12%), and Wallemia sebi (12%). Fungal diversity and relative abundance of Fusarium in wheat from top silo positions were significantly lower than at other silo positions during storage. Nivalenol and deoxynivalenol in wheat were 13–34% higher in all positions at 3 months compared to T₀, and mycotoxins in wheat from middle and bottom positions at 6 to 12 months were 24–57% higher than at T₀. The relative abundance of toxigenic Aspergillus and aflatoxins were low at T₀ and during storage. This study provides information on implementation and design of fungus and mycotoxin management strategies as well as prediction models.

Globally, the trichothecene mycotoxins deoxynivalenol (DON) and nivalenol (NIV) are among the most widely distributed mycotoxins that contaminate small grain cereals. In this study, a bacterial consortium, PGC-3, with de-epoxydation activity was isolated from soil by an in situ soil enrichment method. Screening of 14 soil samples that were sprayed with DON revealed that 4 samples were able to biotransform DON into de-epoxydized DON (dE-DON). Among these, the PGC-3 consortium showed the highest and most stable activity to biotransform DON into dE-DON and NIV into dE-NIV. PGC-3 exhibited de-epoxydation activity at a wide range of pH (5–10) and temperatures (20–37 °C) values under aerobic conditions. Sequential subculturing with a continued exposure to DON substantially reduced the microbial population diversity of this consortium. Analyses of the 16S rDNA sequences indicated that PGC-3 comprised 10 bacterial genera. Among these, one species, Desulfitobacterium, showed a steady increase in relative abundance, from 0.03% to 1.55% (a 52-fold increase), as higher concentrations of DON were used in the subculture media, from 0 to 500 μg/mL. This study establishes the foundation to further develop bioactive agents that can detoxify trichothecene mycotoxins in cereals and enables for the characterization of detoxifying genes and their regulation.

Medicago ruthenica, a wild legume forage widely distributed in the Eurasian steppe, demonstrates high genetic and phenotypic variation. M. ruthenica with a purely yellow flower (YFM), differing from the general phenotype of M. ruthenica with a purple flower (PFM), was recently discovered. The similar characteristics of YFM with Medicago falcata have led to conflicting opinions on its taxonomy using traditional morphological methods. The lack of chemotaxonomy information about M. ruthenica species and the unclear flower coloration mechanisms have hampered their study. Here, we investigated M. ruthenica using targeted metabolomics based on the chemotaxonomy method and elaborated the floral coloration mechanisms using transcriptomics. The identified flavonoids were the same types, but there were different contents in YFM and PFM, especially the contents of cyanidin-3-O-glucoside (C3G), an anthocyanin that causes the purple-reddish color of flowers. The over-accumulation of C3G in PFM was 1,770 times more than YFM. Nineteen anthocyanin-related genes were downregulated in YFM compared with their expression in PFM. Thus, YFM could be defined as a variety of M. ruthenica rather than a different species. The loss of purple flower coloration in YFM was attributed to the downregulation of these genes, resulting in reduced C3G accumulation. The taxonomic characteristics and molecular and physiological characteristics of this species will contribute to further research on other species with similar external morphologies.

Alfalfa (Medicago sativa) is a globally distributed economic legume crop used for forage and ecological restoration. We aimed to explore the mechanisms underlying the cold acclimation observed in this species. Our results for fall plant growth showed that non-dormant alfalfa (SD) maintained a vigorous growth rate compared to that of fall-dormant alfalfa (ZD); however, the winter survival rate of ZD was higher than that of SD. Among the ZD samples, the starch content first accumulated and then decreased; the sucrose content was consumed first along with simultaneous raffinose accumulation, which was followed by sucrose content accumulation, with consistent changes in the corresponding related synthase and hydrolase activity. SD exhibited the opposite trend. The transcriptome data showed that most of the differentially expressed genes were involved in carbon metabolism (ko01200), amino acid biosynthesis (ko01230), and starch and sucrose metabolism (ko00500). Our data clearly show that alfalfa’s cold acclimation mechanism is a complex process, with the establishment of stable carbon homeostasis; sucrose is first converted into starch and raffinose, and then, starch is converted into sucrose, which enables alfalfa’s cold resistance. The process is accompanied by CBF/DREB1A TF regulation. This study provides important insights into the cold acclimation mechanisms of alfalfa.

Background: Medicago ruthenica, a perennial legume forage valuable for ecological restoration and improved breeding, suffers significant harvest losses due to pod shattering. Pod shattering is a trait not only linked to not only pod ventral suture, but also pericarp properties. In this study, we aimed to (1) elucidate the role of pericarp in explosive pod shattering by comparing shattering-susceptible (SPD) and shattering-resistant (RPD) M. ruthenica genotypes, and (2) identify key regulatory genes and pathways underlying this mechanism. Methods: We conducted comparative analyses of pericarp anatomy and physiological traits (pericarp components such as water content, cellulose, hemicellulose, pectin, and lignin; and the activities of enzymes such as cellulose synthase A (CesA), phenylalanine ammonia-lyase (PAL), 4-coumarate: CoA ligase (4CL), cinnamyl alcohol dehydrogenase (CAD), and peroxidase (POD) in SPD and RPD pods). Transcriptome of pod pericarps identified differentially expressed genes (DEGs) for the selection of candidates functional genes. Promoter analysis was performed on candidate functional genes to identify specific regulated factors. The functional role of auxin signaling was validated through exogenous auxin application and the assessment of pod shattering rates and gene expression. Results: SPD pod pericarps exhibited significantly higher lignification of endocarp, lignin, cellulose, hemicellulose and pectin content, but lower water content than RPD. Principal component analysis identified that lignin contributes the highest loading value (0.727) contributor to pod shattering. The activities of five cell wall biosynthesis enzymes were higher in SPD pod pericarps than RPD. Transcriptome analysis identified more than 3419 DEGs in SPD pericarps. KEGG enrichment highlighted “phenylpropanoid biosynthesis” as the most significant pathway. A total of 57 lignin-biosynthesis-related DEGs were upregulated in SPD, including 15 PODs. Promoters of 11 POD genes contained MYB-binding motifs and 8 contained auxin-responsive elements, a total of 76 MYB transcription factors (mostly upregulated) and 9 auxin biosynthesis genes (mostly downregulated) were differentially expressed in SPD. Exogenous auxin application significantly reduced SPD pod shattering to 23.6% and concurrently downregulated PODs expression. Conclusions: This study establishes that enhanced lignification within the pericarp endocarp by the upregulation of lignin biosynthetic genes (particularly PODs), coupled with upregulation by MYB transcription factors and downregulation by auxin, is a core mechanism of explosive pod shattering in M. ruthenica. The identified DEGs, especially MYBs, PODs, and auxin pathway genes, provide gene information for breeding shattering-resistant M. ruthenica varieties through molecular design or marker-assisted selection.