Thirteen novel deoxynivalenol-degrading bacteria are classified within two genera with distinct degradation mechanisms

Shifts in Fusarium Communities and Mycotoxins in Maize Residues, Soils, and Wheat Grains throughout the Wheat Cycle: Implications for Fusarium Head Blight Epidemiology

Fusarium Head Blight (FHB), predominantly caused by Fusarium species, is a devastating cereal disease worldwide. While considerable research has focused on Fusarium communities in grains, less attention has been given to residues and soil, the primary inoculum sources. Knowledge of Fusarium spp. diversity, dynamics, and mycotoxin accumulation in these substrates is crucial for assessing their contribution to wheat head infection and the complex interactions among Fusarium communities throughout the wheat cycle. We monitored six minimum-tillage wheat fields, with maize as the preceding crop, over two years. Soils, maize residues, and wheat grains were sampled at four stages. Fusarium composition was analyzed using a culture-dependent method, species-specific qPCR, and EF1α region metabarcoding sequencing, enabling species-level resolution. The Fusarium communities were primarily influenced by substrate type, accounting for 35.8% of variance, followed by sampling location (8.1%) and sampling stage (3.2%). Among the 32 identified species, F. poae and F. graminearum dominated grains, with mean relative abundances of 47% and 29%, respectively. Conversely, residues were mainly contaminated by F. graminearum, with a low presence of F. poae, as confirmed by species-specific qPCR. Notably, during periods of high FHB pressure, such as in 2021, F. graminearum was the dominant species in grains. However, in the following year, F. poae outcompeted F. graminearum, resulting in reduced disease pressure, consistent with the lower pathogenicity of F. poae. Source Tracker analysis indicated that residues were a more significant source of Fusarium contamination on wheat in 2021 compared to 2022, suggesting that F. graminearum in 2021 primarily originated from residues, whereas F. poae's sources of infection need further investigation. Additionally, multiple mycotoxins were detected and quantified in maize residues during the wheat cycle, raising the question of their ecological role and impact on the soil microbiota.

Deoxynivalenol Detoxification by a Novel Strain of Pichia kudriavzevii via Enzymatic Degradation and Cell Wall Adsorption

Deoxynivalenol (DON) is a mycotoxin that significantly threatens the food and feed industry. Corn steep liquor (CSL) is an acidic byproduct of the corn starch industry, and DON is concentrated in CSL once the material is contaminated. In this work, a Pichia kudriavzevii strain that could remove DON from CSL was isolated and characterized. The strain P. kudriavzevii E4-205 showed detoxifying activity in a pH range of 4.0~7.0 and temperature of 25~42 °C, and 39.4% DON was reduced by incubating this strain in CSL supernatant diluted by 2-fold (5 μg/mL DON) for 48 h at pH 5.0 and 30 °C. Further mechanism studies showed that P. kudriavzevii E4-205 could adsorb DON by the cell wall and degrade DON by intracellular enzymes with NADH as a cofactor. The degradation product was identified as 3,7,8,15-tetrahydroxyscirpene by liquid chromatography-tandem mass spectrometry. DON adsorption by inactivated cells was characterized, and the adsorption followed pseudo first-order kinetics. This study revealed a novel mechanism by which microbes degrade DON and might serve as a guide for the development of DON biological detoxification methods.

The potential of soil microbial communities to transform deoxynivalenol in agricultural soils-a soil microcosm study

Infestation of cereal fields with toxigenic Fusarium species is identified as an environmental source for the mycotoxin deoxynivalenol (DON). During rain events, DON may be washed off from infested plants and enter the soil, where microbial transformation may occur. Although some studies showed DON transformation potential of soil microbial communities in liquid soil extracts, these findings can not be transferred to environmental conditions. Accordingly, microbial transformation of DON in soil has to be investigated under realistic conditions, e.g., microcosms mimicking field situations. In this study, we investigated the potential of soil microbial communities to transform DON in six different agricultural soils at two levels (0.5 and 5 µg g-1). The dissipation and the formation of transformation products were investigated in a period of 35 days and compared to a sterilized control. In addition, we measured soil respiration and applied the phospholipid-derived fatty acid (PLFA) analysis to assess whether soil microbial community characteristics are related to the microbial transformation potential. Dissipation of DON in non-sterilized soils was fast (50% dissipation within 0.6-3.7 days) compared to the sterile control where almost no dissipation was observed. Thus, dissipation was mainly attributed to microbial transformation. We verified that small amounts of DON are transformed to 3-keto-deoxynivalenol (3-keto-DON) and 3-epi-deoxynivalenol (3-epi-DON), which were not detectable after 16-day incubation, indicating further transformation processes. There was a trend towards faster transformation in soils with active and large microbial communities and low fungi-to-bacteria ratio.

Identification and characterization of Achromobacter spanius P-9 and elucidation of its deoxynivalenol-degrading potential

Deoxynivalenol (DON) poses significant challenges due to its frequent contamination of grains and associated products. Microbial strategies for mitigating DON toxicity showed application potential. Eight bacterial isolates with DON degradation activity over 5% were obtained from various samples of organic fertilizer in this study. One of the isolates emerged as a standout, demonstrating a substantial degradation capability, achieving a 99.21% reduction in DON levels. This isolate, underwent thorough morphological, biochemical, and molecular characterization to confirm its identity, and was identified as a new strain of Achromobacter spanius P-9. Subsequent evaluations revealed that the strain P-9 retains its degradation activity after a 24-h incubation, reaching optimal performance at 35 °C with a pH of 8.0. Further studies indicated that Ca2+ ions enhance the degradation process, whereas Zn2+ ions exert an inhibitory effect. This is the pioneering report of DON degradation by Achromobacter spanius, illuminating its prospective utility in addressing DON contamination challenges.

Halophyte Elymus dahuricus colonization regulates microbial community succession by mediating saline-alkaline and biogenic organic matter in bauxite residue

Alkalinity regulation and nutrient accumulation are critical factors in the construction of plant and microbial communities and soil formation in bauxite residue, and are extremely important for sustainable vegetation restoration in bauxite residue disposal areas. However, the establishment and succession of microbial communities driven by plant colonization-mediated improvements in the physicochemical properties of bauxite residues remain poorly understood. Thus, in this study, we determined the saline-alkali properties and dissolved organic matter (DOM) components under plant growth conditions and explored the microbial community diversity and structure using Illumina high-throughput sequencing. The planting of Elymus dahuricus (E. dahuricus) in the bauxite residue resulted in a significant decrease in total alkalinity (TA), exchangeable Na, and electrical conductivity (EC) as well as the release of more tryptophan-like protein compounds and low-molecular-weight humic substances associated with biological activities into the bauxite residue substrate. Taxonomical analysis revealed an initial-stage bacterial and fungal community dominated by alkaline-tolerant Actinobacteriota, Firmicutes, and Ascomycota, and an increase in the relative abundances of the phyla Bacteroidota, Cyanobacteria, Chloroflexi, and Gemmatimonadota. The biological activities of phylum Actinobacteriota, Bacteroidota, and Gemmatimonadota were significantly associated with protein-like and UVA-like humic substances. As eutrophic bacteria, Proteobacteria participate in the transformation of humic substances and can not only utilize small molecules of organic matter and convert them into humic substances but also promote the gradual conversion of humic acids into simple molecular compounds. Our results suggest that plant roots secrete organic matter and microbial metabolites as the main biogenic organic matter that participates in the establishment and succession of the microbial community in bauxite residues. Root length affects bacterial and fungal diversity by mediating the production of protein-like substances.

Four PQQ-Dependent Alcohol Dehydrogenases Responsible for the Oxidative Detoxification of Deoxynivalenol in a Novel Bacterium Ketogulonicigenium vulgare D3_3 Originated from the Feces of Tenebrio molitor Larvae

Deoxynivalenol (DON) is frequently detected in cereals and cereal-based products and has a negative impact on human and animal health. In this study, an unprecedented DON-degrading bacterial isolate D3_3 was isolated from a sample of Tenebrio molitor larva feces. A 16S rRNA-based phylogenetic analysis and genome-based average nucleotide identity comparison clearly revealed that strain D3_3 belonged to the species Ketogulonicigenium vulgare. This isolate D3_3 could efficiently degrade 50 mg/L of DON under a broad range of conditions, such as pHs of 7.0-9.0 and temperatures of 18-30 °C, as well as during aerobic or anaerobic cultivation. 3-keto-DON was identified as the sole and finished DON metabolite using mass spectrometry. In vitro toxicity tests revealed that 3-keto-DON had lower cytotoxicity to human gastric epithelial cells and higher phytotoxicity to Lemna minor than its parent mycotoxin DON. Additionally, four genes encoding pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases in the genome of isolate D3_3 were identified as being responsible for the DON oxidation reaction. Overall, as a highly potent DON-degrading microbe, a member of the genus Ketogulonicigenium is reported for the first time in this study. The discovery of this DON-degrading isolate D3_3 and its four dehydrogenases will allow microbial strains and enzyme resources to become available for the future development of DON-detoxifying agents for food and animal feed.

Post-Harvest Prevention of Fusariotoxin Contamination of Agricultural Products by Irreversible Microbial Biotransformation: Current Status and Prospects

Biological degradation of mycotoxins is a promising environmentally-friendly alternative to chemical and physical detoxification methods. To date, a lot of microorganisms able to degrade them have been described; however, the number of studies determining degradation mechanisms and irreversibility of transformation, identifying resulting metabolites, and evaluating in vivo efficiency and safety of such biodegradation is significantly lower. At the same time, these data are crucial for the evaluation of the potential of the practical application of such microorganisms as mycotoxin-decontaminating agents or sources of mycotoxin-degrading enzymes. To date, there are no published reviews, which would be focused only on mycotoxin-degrading microorganisms with the proved irreversible transformation of these compounds into less toxic compounds. In this review, the existing information about microorganisms able to efficiently transform the three most common fusariotoxins (zearalenone, deoxinyvalenol, and fumonisin B1) is presented with allowance for the data on the corresponding irreversible transformation pathways, produced metabolites, and/or toxicity reduction. The recent data on the enzymes responsible for the irreversible transformation of these fusariotoxins are also presented, and the promising future trends in the studies in this area are discussed.

Two-Step Epimerization of Deoxynivalenol by Quinone-Dependent Dehydrogenase and Candida parapsilosis ACCC 20221

Deoxynivalenol (DON), one of the main mycotoxins with enteric toxicity, genetic toxicity, and immunotoxicity, and is widely found in corn, barley, wheat, and rye. In order to achieve effective detoxification of DON, the least toxic 3-epi-DON (1/357th of the toxicity of DON) was chosen as the target for degradation. Quinone-dependent dehydrogenase (QDDH) reported from Devosia train D6-9 detoxifies DON by converting C3-OH to a ketone group with toxicity of less than 1/10 that of DON. In this study, the recombinant plasmid pPIC9K-QDDH was constructed and successfully expressed in Pichia pastoris GS115. Within 12 h, recombinant QDDH converted 78.46% of the 20 μg/mL DON to 3-keto-DON. Candida parapsilosis ACCC 20221 was screened for its activity in reducing 86.59% of 3-keto-DON within 48 h; its main products were identified as 3-epi-DON and DON. In addition, a two-step method was performed for epimerizing DON: 12 h catalysis by recombinant QDDH and 6 h transformation of the C. parapsilosis ACCC 20221 cell catalyst. The production rates of 3-keto-DON and 3-epi-DON were 51.59% and 32.57%, respectively, after manipulation. Through this study, effective detoxification of 84.16% of DON was achieved, with the products being mainly 3-keto-DON and 3-epi-DON.

Bioorganic fertilizers improve the adaptability and remediation efficiency of Puccinellia distans in multiple heavy metals-contaminated saline soil by regulating the soil microbial community

Soil salinization and heavy metal (HM) pollution are global environmental problems. Bioorganic fertilizers facilitate phytoremediation, but their roles and microbial mechanisms in natural HM-contaminated saline soils have not been explored. Therefore, greenhouse pot trials were conducted with three treatments: control (CK), manure bioorganic fertilizer (MOF), and lignite bioorganic fertilizer (LOF). The results showed that MOF and LOF significantly increased nutrient uptake, biomass, toxic ion accumulation in Puccinellia distans, soil available nutrients, SOC, and macroaggregates. More biomarkers were enriched in MOF and LOF. Network analysis confirmed that MOF and LOF increased the number of bacterial functional groups and fungal community stability and strengthened their positive association with plants; Bacteria have a more significant effect on phytoremediation. Most biomarkers and keystones play important roles in promoting plant growth and stress resistance in the MOF and LOF treatments. In summary, besides enrichment of soil nutrients, MOF and LOF can also improve the adaptability and phytoremediation efficiency of P. distans by regulating the soil microbial community, with LOF having a greater effect.

In-vitro assessment of a novel plant rhizobacterium, Citrobacter freundii, for degrading and biocontrol of food mycotoxin deoxynivalenol

Deoxynivalenol (DON) is one of the most harmful and well-known toxins present in food and animal feed throughout the world. Citrobacter freundii (C. freundii-ON077584), a novel DON-degrading strain, was isolated from rice root-linked soil samples. The degrading properties, including DON concentrations, incubation pH, incubation temperatures, bacterial concentrations, and acid treatment effect on degradation, were evaluated. At pH 7 and an incubation temperature of 37 °C, C. freundii demonstrated the capability to degrade more than 90% of DON. The degraded products of DON were identified as 3-keto-DON and DOM-1, which were confirmed by High Performance Liquid Chromatography (HPLC) and Ultra-Performance Liquid Chromatography hyphenated with Tandem Mass Spectrometry (UPLC-MS/MS) analyses. The mechanism of DON degradation into 3-keto-DON and DOM-1 by this bacterial strain will be further explored to identify and purify novel degrading enzymes that can be cloned to the microorganism and added to the animal feed to degrade the DON in the digestion tract.

Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter

A Gram-stain-negative, halotolerant bacterium designated as PTR5^T was isolated from the roots of rice plants, collected in Ilsan, South Korea. Cells were, aerobic, asporogenous, motile, rod-shaped, white in color, and grew at 5-38 °C (optimum 30 °C), at pH 5.0-0-8.0 (optimum, 7.0) and tolerates up to 10% (w/v) NaCl (optimum, 0% NaCl). According to the EZbioCloud server the most closely related Devosia species to strain PTR5^T based on 16 S rRNA gene sequence comparison are Devosia crocina (97.4%), followed by D. soli (97.2%), D. lucknowensis (96.9%) and D. marina (96.5%). The respiratory quinone was identified as Q-10. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. C_16:0, C_18:1 ω7c 11-methyl and summed feature 8 (comprising C_18:1 ω7c/C_18:1 ω6c) constituted the main cellular fatty acids. The draft genome sequence of strain PTR5^T was 3,689,283 bp in size. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and amino acid identity (AAI) values between strain PTR5^T and its close relative were 72.8-76.8%, 19-20.7% and 70.3-75%, respectively. The G + C content was 63.7%. Strain PTR5^T was able to produce siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Genes for siderophore production, auxin responsive and tryptophan biosynthesis were present in the genome of novel strain. Also, gene clusters involved in detoxification of various metal pollutants and antibiotics were also revealed in the genome of novel strain PTR5^T, this suggest that novel strain can facilitate bioremediation of heavy metals and antibiotics in contaminated areas. This study aimed to determine the detailed taxonomic position of the strain PTR5^T using the modern polyphasic approach. On the basis of evidence presented in this study, strain PTR5^T is considered to represent a novel species of the genus Devosia, for which the name Devosia oryzisoli sp. nov. (type strain PTR5^T (KCTC 82691^T = TBRC 15163^T) is proposed.

Year-Long Microbial Succession on Microplastics in Wastewater: Chaotic Dynamics Outweigh Preferential Growth

Microplastics are a globally-ubiquitous aquatic pollutant and have been heavily studied over the last decade. Of particular interest are the interactions between microplastics and microorganisms, especially the pursuit to discover a plastic-specific biome, the so-called plastisphere. To follow this up, a year-long microcosm experimental setup was deployed to expose five different microplastic types (and silica beads control) to activated aerobic wastewater in controlled conditions, with microbial communities being measured four times over the course of the year using 16S rDNA (bacterial) and ITS (fungal) amplicon sequencing. The biofilm community shows no evidence of a specific plastisphere, even after a year of incubation. Indeed, the microbial communities (particularly bacterial) show a clear trend of increasing dissimilarity between plastic types as time increases. Despite little evidence for a plastic-specific community, there was a slight grouping observed for polyolefins (PE and PP) in 6–12-month biofilms. Additionally, an OTU assigned to the genus Devosia was identified on many plastics, increasing over time while showing no growth on silicate (natural particle) controls, suggesting this could be either a slow-growing plastic-specific taxon or a symbiont to such. Both substrate-associated findings were only possible to observe in samples incubated for 6–12 months, which highlights the importance of studying long-term microbial community dynamics on plastic surfaces.

Deoxynivalenol Degradation by Various Microbial Communities and Its Impacts on Different Bacterial Flora

Deoxynivalenol, a mycotoxin that may present in almost all cereal products, can cause huge economic losses in the agriculture industry and seriously endanger food safety and human health. Microbial detoxifications using microbial consortia may provide a safe and effective strategy for DON mitigation. In order to study the interactions involving DON degradation and change in microbial flora, four samples from different natural niches, including a chicken stable (expJ), a sheep stable (expY), a wheat field (expT) and a horse stable (expM) were collected and reacted with purified DON. After being co-incubated at 30 °C with 130 rpm shaking for 96 h, DON was reduced by 74.5%, 43.0%, 46.7%, and 86.0% by expJ, expY, expT, and expM, respectively. After DON (0.8 mL of 100 μg/mL) was co-cultivated with 0.2 mL of the supernatant of each sample (i.e., suspensions of microbial communities) at 30 °C for 96 h, DON was reduced by 98.9%, 99.8%, 79.5%, and 78.9% in expJ, expY, expT, and expM, respectively, and was completely degraded after 8 days by all samples except of expM. DON was confirmed being transformed into de-epoxy DON (DOM-1) by the microbial community of expM. The bacterial flora of the samples was compared through 16S rDNA flux sequencing pre- and post the addition of DON. The results indicated that the diversities of bacterial flora were affected by DON. After DON treatment, the most abundant bacteria belong to Galbibacter (16.1%) and Pedobacter (8.2%) in expJ; Flavobacterium (5.9%) and Pedobacter (5.5%) in expY; f_Microscillaceae (13.5%), B1-7BS (13.4%), and RB41 (10.5%) in expT; and Acinetobacter (24.1%), Massilia (8.8%), and Arthrobacter (7.6%) in expM. This first study on the interactions between DON and natural microbial flora provides useful information and a methodology for further development of microbial consortia for mycotoxin detoxifications.

Plant Beneficial Bacteria as Bioprotectants against Wheat and Barley Diseases

Wheat and barley are the main cereal crops cultivated worldwide and serve as staple food for a third of the world's population. However, due to enormous biotic stresses, the annual production has significantly reduced by 30-70%. Recently, the accelerated use of beneficial bacteria in the control of wheat and barley pathogens has gained prominence. In this review, we synthesized information about beneficial bacteria with demonstrated protection capacity against major barley and wheat pathogens including Fusarium graminearum, Zymoseptoria tritici and Pyrenophora teres. By summarizing the general insights into molecular factors involved in plant-pathogen interactions, we show to an extent, the means by which beneficial bacteria are implicated in plant defense against wheat and barley diseases. On wheat, many Bacillus strains predominantly reduced the disease incidence of F. graminearum and Z. tritici. In contrast, on barley, the efficacy of a few Pseudomonas, Bacillus and Paraburkholderia spp. has been established against P. teres. Although several modes of action were described for these strains, we have highlighted the role of Bacillus and Pseudomonas secondary metabolites in mediating direct antagonism and induced resistance against these pathogens. Furthermore, we advance a need to ascertain the mode of action of beneficial bacteria/molecules to enhance a solution-based crop protection strategy. Moreover, an apparent disjoint exists between numerous experiments that have demonstrated disease-suppressive effects and the translation of these successes to commercial products and applications. Clearly, the field of cereal disease protection leaves a lot to be explored and uncovered.

Structure-Function Analysis of a Quinone-Dependent Dehydrogenase Capable of Deoxynivalenol Detoxification

The pyrroloquinoline quinone (PQQ)-dependent dehydrogenase DepA detoxifies deoxynivalenol (DON) by converting the C3-OH into a keto group. Herein, two crystal structures of DepA and its complex with PQQ were determined, together with biochemical evidence confirming the interactions of DepA with PQQ and DON and revealing a unique tyrosine residue important for substrate selection. Furthermore, four loops over the active site essential for DepA activity were identified, of which three loops were stabilized by PQQ, and the fourth loop invisible in both structures was considered important for binding DON, together constituting a lid for the active site. Preliminary engineering of the loop showed its potential for enzyme improvement. This study provides structural insights into how a PQQ-dependent dehydrogenase is equipped with the function of DON conversion and for the first time shows the necessity of a lid structure for PQQ-dependent dehydrogenase activity, laying foundation for structure-based design to enhance catalysis efficiency.

Biocontrol Methods in Avoidance and Downsizing of Mycotoxin Contamination of Food Crops

By increasing the resistance of seeds against abiotic and biotic stress, the possibility of cereal mold contamination and hence the occurrence of secondary mold metabolites mycotoxins decreases. The use of biological methods of seed treatment represents a complementary strategy, which can be implemented as an environmental-friendlier approach to increase the agricultural sustainability. Whereas the use of resistant cultivars helps to reduce mold growth and mycotoxin contamination at the very beginning of the production chain, biological detoxification of cereals provides additional weapons against fungal pathogens in the later stage. Most efficient techniques can be selected and combined on an industrial scale to reduce losses and boost crop yields and agriculture sustainability, increasing at the same time food and feed safety. This paper strives to emphasize the possibility of implementation of biocontrol methods in the production of resistant seeds and the prevention and reduction in cereal mycotoxin contamination.

Deoxynivalenol: Toxicology, Degradation by Bacteria, and Phylogenetic Analysis

Deoxynivalenol (DON) is a toxic secondary metabolite produced by fungi that contaminates many crops, mainly wheat, maize, and barley. It affects animal health, causing intestinal barrier impairment and immunostimulatory effect in low doses and emesis, reduction in feed conversion rate, and immunosuppression in high doses. As it is very hard to completely avoid DON’s production in the field, mitigatory methods have been developed. Biodegradation has become a promising method as new microorganisms are studied and new enzymatic routes are described. Understanding the common root of bacteria with DON degradation capability and the relationship with their place of isolation may bring insights for more effective ways to find DON-degrading microorganisms. The purpose of this review is to bring an overview of the occurrence, regulation, metabolism, and toxicology of DON as addressed in recent publications focusing on animal production, as well as to explore the enzymatic routes described for DON’s degradation by microorganisms and the phylogenetic relationship among them.

Biological Detoxification of Mycotoxins: Current Status and Future Advances

Mycotoxins are highly toxic metabolites produced by fungi that pose a huge threat to human and animal health. Contamination of food and feed with mycotoxins is a worldwide issue, which leads to huge financial losses, annually. Decades of research have developed various approaches to degrade mycotoxins, among which the biological methods have been proved to have great potential and advantages. This review provides an overview on the important advances in the biological removal of mycotoxins over the last decade. Here, we provided further insight into the chemical structures and the toxicity of the main mycotoxins. The innovative strategies including mycotoxin degradation by novel probiotics are summarized in an in-depth discussion on potentialities and limitations. We prospected the promising future for the development of multifunctional approaches using recombinant enzymes and microbial consortia for the simultaneous removal of multiple mycotoxins.

Enhanced biodegradation of chlortetracycline via a microalgae-bacteria consortium

Microbial removal of Chlortetracycline (CTC) at low CTC concentrations (in the order of 10-20 mg/L) has been reported. In this study, a novel microalgae-bacteria consortium was developed for effective CTC biodegradation at higher concentrations (up to 80 mg/L). The microalgae-bacteria consortium is resistant to up to 80 mg/L CTC, while the pure microalgal culture could only tolerate 60 mg/L CTC. CTC removal in the initial 12 h was primarily via biosorption by the microalgae-bacteria consortium and the adsorption capacity increased from 61.71 to 102.53 mg/g biomass in 12 h. Further, CTC biodegradation by the microalgae-bacteria consortium was catalyzed by extracellular enzymes secreted under antibiotic stress. The symbiotic bacterial diversity was analyzed by high throughput sequencing. The aerobic bacteria Porphyrobacter and Devosia were the dominant genera in the consortium. In the presence of CTC, a microbial community shift occurred with Chloroptast, Spingopyxis, and Brevundimonas being the dominant genera.

Current and emerging tools of computational biology to improve the detoxification of mycotoxins

Biological organisms carry a rich potential for removing toxins from our environment, but identifying suitable candidates and improving them remain challenging. We explore the use of computational tools to discover strains and enzymes that detoxify harmful compounds. In particular, we will focus on mycotoxins-fungi-produced toxins that contaminate food and feed-and biological enzymes that are capable of rendering them less harmful. We discuss the use of established and novel computational tools to complement existing empirical data in three directions: discovering the prospect of detoxification among underexplored organisms, finding important cellular processes that contribute to detoxification, and improving the performance of detoxifying enzymes. We hope to create a synergistic conversation between researchers in computational biology and those in the bioremediation field. We showcase open bioremediation questions where computational researchers can contribute and highlight relevant existing and emerging computational tools that could benefit bioremediation researchers.

Destruction of the soil microbial ecological environment caused by the over-utilization of the rice-crayfish co-cropping pattern

The rice-crayfish co-cropping pattern is a traditional method for the intensive utilization of rice fields. In recent years, this pattern has been over-developed in many countries and regions, especially in China, because of its simple agronomic technology and high economic benefits. However, little is known about the potential ecological problems regarding soil microorganisms caused by the over-utilization of this pattern. The results show that rice-crayfish co-cropping, when over-utilized for a long time, reduced soil microbial richness and diversity compared with rice monocropping. A decrease in bacterial abundance in the nitrogen cycle and an increase in bacterial abundance in the carbon cycle led to a decrease in the nitrogen cycle function and an increase in the carbon cycle function. In an analysis of bacteria that are sensitive to cropping patterns, it was found that in the rice-crayfish co-cropping, the relative abundances of sensitive OTUs from Firmicutes (Bacillus and Clostridium) and Chloroflexi (Anaerolineaceae) were significantly higher during the entire growth period than those observed in the rice monocropping pattern, while the relative abundances of sensitive OTUs from Nitrospirae (Nitrospira), Gemmatimonadetes (Gemmatimonas), and Actinobacteria (Nocardioides) were significantly lower than those observed in the rice monocropping pattern. A network analysis shows that growth-period-sensitive OTUs drive the co-occurrence network modules, although the OTUs also have positive and negative correlations among modules but a positive synergistic effect on the regulation of soil nutrients. In addition, OTUs that were sensitive at the booting stage and filling stage were the key microbial groups in the rice-crayfish co-cropping and rice monocropping networks, respectively. Understanding the classifications and functions of sensitive microbes present during the rice growth period is the basis for formulating a microbial flora management strategy for the rice-crayfish co-cropping pattern, which is of great significance for adjusting agricultural management measures and controlling current soil microbial ecological problems.

Bacterial Enrichment Cultures Biotransform the Mycotoxin Deoxynivalenol into a Novel Metabolite Toxic to Plant and Porcine Cells

The mycotoxin deoxynivalenol (DON), produced in wheat, barley and maize by Fusarium graminearum and Fusarium culmorum, is threatening the health of humans and animals. With its worldwide high incidence in food and feed, mitigation strategies are needed to detoxify DON, maintaining the nutritional value and palatability of decontaminated commodities. A promising technique is biological degradation, where microorganisms are used to biotransform mycotoxins into less toxic metabolites. In this study, bacterial enrichment cultures were screened for their DON detoxification potential, where DON and its potential derivatives were monitored. The residual phytotoxicity was determined through a bioassay using the aquatic plant Lemna minor L. Two bacterial enrichment cultures were found to biotransform DON into a still highly toxic metabolite for plants. Furthermore, a cytotoxic effect was observed on the cellular viability of intestinal porcine epithelial cells. Through liquid chromatography high-resolution mass spectrometry analysis, an unknown compound was detected, and tentatively characterized with a molecular weight of 30.0 Da (i.e., CH₂O) higher than DON. Metabarcoding of the subsequently enriched bacterial communities revealed a shift towards the genera Sphingopyxis, Pseudoxanthomonas, Ochrobactrum and Pseudarthrobacter. This work describes the discovery of a novel bacterial DON-derived metabolite, toxic to plant and porcine cells.

Biodegradation of Deoxynivalenol by Nocardioides sp. ZHH-013: 3-keto-Deoxynivalenol and 3-epi-Deoxynivalenol as Intermediate Products

Deoxynivalenol (DON) is one of the most devastating and notorious contaminants in food and animal feed worldwide. A novel DON-degrading strain, Nocardioides sp. ZHH-013, which exhibited complete mineralization of DON, was isolated from soil samples. The intermediate products of DON generated by this strain were identified by high-performance liquid chromatography and ultra-performance liquid chromatography tandem mass spectrometry analyses. It was shown that, on an experimental level, 3-keto-DON was a necessary intermediate product during the conversion from DON to 3-epi-DON. Furthermore, the ZHH-013 strain could also utilize 3-epi-DON. This DON degradation pathway is a safety concern for food and feed. The mechanism of DON and 3-epi-DON elimination will be further studied, so that new enzymes for DON degradation can be identified.

Effects of temperature and soil fauna on the reduction and leaching of deoxynivalenol and zearalenone from Fusarium graminearum-infected maize stubbles

A microcosm study was conducted at two different temperatures under laboratory conditions to investigate the regulatory capacity and the interactive performance of two soil fauna species (Aporrectodea caliginosa, earthworms, and Proisotoma minuta, collembolans) on the reduction of Fusarium toxins in contaminated maize stubbles. Single and mixed species treatments were exposed to artificially infected maize stubbles highly contaminated with the mycotoxins deoxynivalenol (DON) (10,462 µg kg⁻¹) and zearalenone (ZEN) (2,780 µg kg⁻¹) at 17 °C and 25 °C for time periods of 3 and 6 weeks. Immediately after the respective end of incubation, the microcosms were heavily watered to determine the leaching potential of DON and ZEN from contaminated maize stubbles. Maize residues, soil, and eluted water (percolate) samples were analysed for mycotoxin content using liquid chromatography coupled to mass spectrometry. The biomass of introduced earthworms and number of collembolans were monitored to get information about their adaptability to the experimental conditions. While the decline of ZEN was temperature-dependent, but not influenced by faunal activities, a reduction of DON due to faunal impact was observed by trend. In the leaching experiment, 67–82% of the DON content in the residual maize stubbles leached from the plant material by irrigation and was detected in the soil (1.9–3.4 µg kg⁻¹) and in the percolate (12–295 µg L⁻¹). In the case of ZEN, 27–50% of the mycotoxin leached from the residual maize stubbles due to watering but was only occasionally detected in traces in the soil and not found in the percolate. The results clearly reveal a leaching potential of both DON and ZEN, respectively, but a mobilisation with water was only observed for DON. Temperature confirmed to be a key factor, affecting the fate of the mycotoxins in the soil by driving the interaction between different soil fauna members as well as functional and trophic levels within the soil food web.

Streptomyces strains modulate dynamics of soil bacterial communities and their efficacy in disease suppression caused by Phytophthora capsici

The responses of rhizosphere bacterial communities of Streptomyces (SS14 and IT20 stains) treated-pepper plants following inoculation by Phytophthora capsici (PC) was investigated using Illumina MiSeq sequencing. Distinct modulation of the bacteriome composition was found for PC samples with the highest relative abundance (RA) of Chitinophaga (22 ± 0.03%). The RA of several bacterial operational taxonomic units (OTUs) was affected and caused changes in alpha and beta-diversity measures. In IT20, the RA of Cyanobacteria was enriched compared to SS14 (72%) and control samples (47%). Phylotypes belonging to Devosia, Promicromonospora, Kribbella, Microbacterium, Amylocolatopsis, and Pseudomonas genera in the rhizosphere were positively responding against the pathogen. Our findings show that the phosphate solubilizing strain IT20 has higher microbial community responders than the melanin-producing strain SS14. Also, positive interactions were identified by comparing bacterial community profiles between treatments that might allow designing synthetic bio-inoculants to solve agronomic problems in an eco-friendly way.

Microbial detoxification of mycotoxins in food and feed

Mycotoxins are metabolites produced by fungi growing in food or feed, which can produce toxic effects and seriously threaten the health of humans and animals. Mycotoxins are commonly found in food and feed, and are of significant concern due to their hepatotoxicity, nephrotoxicity, carcinogenicity, mutagenicity, and ability to damage the immune and reproductive systems. Traditional physical and chemical detoxification methods to treat mycotoxins in food and feed products have limitations, such as loss of nutrients, reagent residues, and secondary pollution to the environment. Thus, there is an urgent need for new detoxification methods to effectively control mycotoxins and treat mycotoxin pollution. In recent years, microbial detoxification technology has been widely used for the degradation of mycotoxins in food and feed because this approach offers the potential for treatment with high efficiency, low toxicity, and strong specificity, without damage to nutrients. This article reviews the application of microbial detoxification technology for removal of common mycotoxins such as Aflatoxin, Ochratoxin, Zearalenone, Deoxynivalenol, and Fumonisins, and discusses the development trend of this important technology.

Defining the wheat microbiome: Towards microbiome-facilitated crop production

Wheat is one of the world's most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production.

A mycotoxin transporter (4D) from a library of deoxynivalenol-tolerant microorganisms

New strategies are needed to mitigate the mycotoxin deoxynivalenol (DON) in feed and food products. Microbial DNA fragments were generated from a library of DON-tolerant microorganisms. These fragments were screened in DON-sensitive yeast strains for their ability to modify or transport DON. Fragments were cloned into a PCR8/TOPO vector, and recombined into the yeast vector, pYES-DEST52. Resulting yeast transformants were screened in the presence of 100 ppm DON. Transformants that were able to grow in the presence of DON were plated on a selective medium, and the cloned microbial DNA fragments were sequenced. BLAST queries of one microbial DNA fragment (4D) showed a high degree of similarity to an ABC transporter. A series of screening and inhibition assays were conducted with a transport inhibitor (propanol), to test the hypothesis that 4D is a mycotoxin transporter. DON concentrations did not change for yeast transformants expressing 4D. The ability of yeast transformants expressing 4D to transport DON was inhibited by the addition of propanol. Moreover, yeast transformants expressing a known efflux pump (PDR5) showed similar trends in propanol transport inhibition compared to 4D. Future work should consider mycotoxin transporters such as 4D to the development of transgenic plants to limit DON accumulation in seeds.

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Microbial DNA fragments were generated from a library of DON-tolerant microorganisms.

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Fragments were screened in DON-sensitive yeast strains for their ability to modify or transport DON.

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BLAST queries of one microbial fragment (4D) showed a high degree of similarity to an ABC transporter.

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Transformants expressing a known efflux pump (PDR5) showed similar trends in propanol transport inhibition compared to 4D.

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Future work should consider mycotoxin transporters such as 4D to the development of transgenic plants.

Microbiological Detoxification of Mycotoxins: Focus on Mechanisms and Advances

Some fungal species of the genera Aspergillus, Penicillium, and Fusarium secretes toxic metabolites known as mycotoxins, have become a global concern that is toxic to different species of animals and humans. Biological mycotoxins detoxification has been studied by researchers around the world as a new strategy for mycotoxin removal. Bacteria, fungi, yeast, molds, and protozoa are the main living organisms appropriate for the mycotoxin detoxification. Enzymatic and degradation sorptions are the main mechanisms involved in microbiological detoxification of mycotoxins. Regardless of the method used, proper management tools that consist of before-harvest prevention and after-harvest detoxification are required. Here, in this review, we focus on the microbiological detoxification and mechanisms involved in the decontamination of mycotoxins.

In Vitro Assessment of Biocontrol Effects on Fusarium Head Blight and Deoxynivalenol (DON) Accumulation by DON-Degrading Bacteria

Fusarium head blight (FHB) of cereals is a severe disease caused by the Fusarium graminearum species complex. It leads to the accumulation of the mycotoxin deoxynivalenol (DON) in grains and other plant tissues and causes substantial economic losses throughout the world. DON is one of the most troublesome mycotoxins because it is a virulence factor to host plants, including wheat, and exhibits toxicity to plants and animals. To control both FHB and DON accumulation, a biological control approach using DON-degrading bacteria (DDBs) is promising. Here, we performed a disease control assay using an in vitro petri dish test composed of germinated wheat seeds inoculated with F. graminearum (Fg) and DDBs. Determination of both grown leaf lengths and hyphal lesion lengths as a measure of disease severity showed that the inoculation of seeds with the DDBs Devosia sp. strain NKJ1 and Nocardioides spp. strains SS3 or SS4 were protective against the leaf growth inhibition caused by Fg. Furthermore, it was as effective against DON accumulation. The inoculation with strains SS3 or SS4 also reduced the inhibitory effect on leaves treated with 10 µg mL^-1 DON solution (without Fg). These results indicate that the DDBs partially suppress the disease by degrading DON.

Review on the Biological Detoxification of Mycotoxins Using Lactic Acid Bacteria to Enhance the Sustainability of Foods Supply

The challenges to fulfill the demand for a safe food supply are dramatically increasing. Mycotoxins produced by certain fungi cause great economic loss and negative impact on the sustainability of food supplies. Moreover, the occurrence of mycotoxins at high levels in foods poses a high health threat for the consumers. Biological detoxification has exhibited a high potential to detoxify foodstuffs on a cost-effective and large scale. Lactic acid bacteria showed a good potential as an alternative strategy for the elimination of mycotoxins. The current review describes the health and economic impacts associated with mycotoxin contamination in foodstuffs. Moreover, this review highlights the biological detoxification of common food mycotoxins by lactic acid bacteria.

A quinone-dependent dehydrogenase and two NADPH-dependent aldo/keto reductases detoxify deoxynivalenol in wheat via epimerization in a Devosia strain

The Fusarium mycotoxin deoxynivalenol (DON) is typically controlled by fungicides. Here, we report DON detoxification using enzymes from the highly active Devosia strain D6-9 which degraded DON at 2.5 μg/min/10⁸ cells. Strain D6-9 catabolized DON to 3-keto-DON and 3-epi-DON, completely removing DON in wheat. Genome analysis of three Devosia strains (D6-9, D17, and D13584), with strain D6-9 transcriptomes, identified three genes responsible for DON epimerization. One gene encodes a quinone-dependent DON dehydrogenase QDDH which oxidized DON into 3-keto-DON. Two genes encode the NADPH-dependent aldo/keto reductases AKR13B2 and AKR6D1 that convert 3-keto-DON into 3-epi-DON. Recombinant proteins expressed in Escherichia coli efficiently degraded DON in wheat grains. Molecular docking and site-directed mutagenesis revealed that residues S497, E499, and E535 function in QDDH's DON-oxidizing activity. These results advance potential microbial and enzymatic elimination of DON in agricultural samples and lend insight into the underlying mechanisms and molecular evolution of DON detoxification.

Biocontrol of Bacterial Wilt Disease Through Complex Interaction Between Tomato Plant, Antagonists, the Indigenous Rhizosphere Microbiota, and Ralstonia solanacearum

Ralstonia solanacearum (biovar2, race3) is the causal agent of bacterial wilt and this quarantine phytopathogen is responsible for massive losses in several commercially important crops. Biological control of this pathogen might become a suitable plant protection measure in areas where R. solanacearum is endemic. Two bacterial strains, Bacillus velezensis (B63) and Pseudomonas fluorescens (P142) with in vitro antagonistic activity toward R. solanacearum (B3B) were tested for rhizosphere competence, efficient biological control of wilt symptoms on greenhouse-grown tomato, and effects on the indigenous rhizosphere prokaryotic communities. The population densities of B3B and the antagonists were estimated in rhizosphere community DNA by selective plating, real-time quantitative PCR, and R. solanacearum-specific fliC PCR-Southern blot hybridization. Moreover, we investigated how the pathogen and/or the antagonists altered the composition of the tomato rhizosphere prokaryotic community by 16S rRNA gene amplicon sequencing. B. velezensis (B63) and P. fluorescens (P142)-inoculated plants showed drastically reduced wilt disease symptoms, accompanied by significantly lower abundance of the B3B population compared to the non-inoculated pathogen control. Pronounced shifts in prokaryotic community compositions were observed in response to the inoculation of B63 or P142 in the presence or absence of the pathogen B3B and numerous dynamic taxa were identified. Confocal laser scanning microscopy (CLSM) visualization of the gfp-tagged antagonist P142 revealed heterogeneous colonization patterns and P142 was detected in lateral roots, root hairs, epidermal cells, and within xylem vessels. Although competitive niche exclusion cannot be excluded, it is more likely that the inoculation of P142 or B63 and the corresponding microbiome shifts primed the plant defense against the pathogen B3B. Both inoculants are promising biological agents for efficient control of R. solanacearum under field conditions.

Biodegradation of Deoxynivalenol by a Novel Microbial Consortium

Deoxynivalenol (DON), a common mycotoxin of type B trichothecene, is produced mainly by several Fusarium species. DON causes great losses in farming and poses severe safety risks to human and animal health. Thus, DON contamination in cereals and DON toxicity are of worldwide concern. In this study, we screened the bacterial consortium C20, which efficiently degraded almost 70 μg ml⁻¹ DON within 5 days. The bacterial consortium also had the ability to degrade 15-acetyl-DON, 3-acetyl-DON, and T-2 toxin. The bacterial consortium C20 was able to degrade DON under a wide range of pH and temperature conditions. The optimal temperature and pH for DON degradation were 30°C and pH 8.0, respectively. The bacterial consortium C20 comprised of different bacterial genera, and several strains were found to significantly increase when cultured in Mineral Medium with 100 μg ml⁻¹ DON based on the analysis of the sequences of the hypervariable V3-V4 region of the 16S rRNA gene. 3-keto-DON was confirmed as a degradation product of DON by liquid chromatography/time-of-flight/mass spectrometry (LC-TOF-MS) and nuclear magnetic resonance (NMR) analyses. The results indicated that the bacterial consortium C20 is a potential candidate for the biodegradation of DON in a safe and environmentally friendly manner.

Understanding the Bacterial Response to Mycotoxins: The Transcriptomic Analysis of Deoxynivalenol-Induced Changes in Devosia mutans 17-2-E-8

Deoxynivalenol (DON) is a major fusarium toxin widely detected in cereal grains. The inadvertent exposure to this fungal secondary-metabolite gives rise to a myriad of adverse health effects including appetite loss, emesis, and suppression of the immune system. While most of the attention this mycotoxin has gained in the past four decades was related to its eukaryotic toxicity (monogastric animals and plants more precisely), recent studies have begun to reveal its negative influence on prokaryotes. Recently presented evidence indicates that DON can negatively affect many bacterial species, raising the possibility of DON-induced imbalances within the microbiota of the human and animal gut, in addition to other environmental niches. This in turn has led to a greater interest in understanding bacterial responses toward DON, and the involved mechanism(s) and metabolic pathways, in order to build a more comprehensive picture of DON-induced changes in both prokaryotes and eukaryotes alike. This study reveals the transcriptomic profiling of Devosia mutans strain 17-2-E-8 after the inclusion of DON within its growth medium. The results highlight three adaptive mechanisms involved in the response of D. mutans 17-2-E-8 to this mycotoxin, which include: (a) activation of adenosine 5’-triphosphate-binding cassette transporters; (b) engagement of a toxin-specific pyrroloquinoline quinone-dependent detoxification pathway; and finally (c) the upregulation of auxiliary coping proteins such as porins, glutathione S-transferases, and phosphotransferases. Some of the identified mechanisms are universal in nature and are shared with other bacterial genera and species.

Efficacy of a Yeast Cell Wall Extract to Mitigate the Effect of Naturally Co-Occurring Mycotoxins Contaminating Feed Ingredients Fed to Young Pigs: Impact on Gut Health, Microbiome, and Growth

Mycotoxins are produced by fungi and are potentially toxic to pigs. Yeast cell wall extract (YCWE) is known to adsorb mycotoxins and improve gut health in pigs. One hundred and twenty growing (56 kg; experiment 1) and 48 nursery piglets (6 kg; experiment 2) were assigned to four dietary treatments in a 2 × 2 factorial design for 35 and 48 days, respectively. Factors were mycotoxins (no addition versus experiment 1: 180 μg/kg aflatoxins and 14 mg/kg fumonisins; or experiment 2: 180 μg/kg aflatoxins and 9 mg/kg fumonisins, and 1 mg/kg deoxynivalenol) and YCWE (0% versus 0.2%). Growth performance, blood, gut health and microbiome, and apparent ileal digestibility (AID) data were evaluated. In experiment 1, mycotoxins reduced ADG and G:F, and duodenal IgG, whereas in jejunum, YCWE increased IgG and reduced villus width. In experiment 2, mycotoxins reduced BW, ADG, and ADFI. Mycotoxins reduced ADG, which was recovered by YCWE. Mycotoxins reduced the AID of nutrients evaluated and increased protein carbonyl, whereas mycotoxins and YCWE increased the AID of the nutrients and reduced protein carbonyl. Mycotoxins reduced villus height, proportion of Ki-67-positive cells, and increased IgA and the proportion of bacteria with mycotoxin-degrading ability, whereas YCWE tended to increase villus height and reduced IgA and the proportion of pathogenic bacteria in jejunum. The YCWE effects were more evident in promoting gut health and growth in nursery pigs, which showed higher susceptibility to mycotoxin effects.

Detoxification of Deoxynivalenol by a Mixed Culture of Soil Bacteria With 3-epi-Deoxynivalenol as the Main Intermediate

Deoxynivalenol (DON) is a widely distributed mycotoxin that frequently occurs in various agricultural raw materials and feeds. DON acts as a virulence factor that accelerates the spread of plant diseases; moreover, its accumulation in grains causes yield loss and serious health problems to humans and livestock. Biodegradation of DON into less- or non-toxic substances using naturally existing microorganisms is considered the best approach for DON detoxification. Although various single isolates and mixed cultures capable of detoxifying DON have been reported, details of the metabolic pathways and the degrading enzymes/coding genes involved are scarce. In this study, we aimed to isolate DON-degrading bacteria from soil samples and explore the mechanisms. Toward this end, 85 soil samples collected from different provinces in China were enriched under aerobic conditions with mineral media containing 50 μg/ml of DON as the sole carbon source. The bacterial consortium LZ-N1 exhibited highly efficient and steady DON-transforming activity. High-throughput sequencing was used to characterize the composition of the involved microflora, and analysis of 16S rRNA sequences indicated that LZ-N1 was composed of at least 11 bacterial genera, with Pseudomonas accounting for nearly half the relative abundance. Coincubation of a mixed culture of two novel strains from the LZ-N1 consortium, namely Pseudomonas sp. Y1 and Lysobacter sp. S1, showed sustained transformation of DON into the metabolite 3-epi-deoxynivalenol, with no degradation products detected after 72 h. The cell-free supernatant, lysate, and cell debris of the mixed culture possessed DON-degrading ability, with the supernatant reaching a DON degradation rate of 100% within 48 h with 50 μg/ml of DON. This is the first report of two-step enzymatic epimerization of DON by a mixed culture, which may provide a new insight into this pathway for future applications in detoxification of DON-contaminated cereals and feed.

Altered intestinal microbiota associated with colorectal cancer

The gut microbiota plays an important role in the development and progression of colorectal cancer (CRC). To learn more about the dysbiosis of carcinogenesis, we assessed alterations in gut microbiota in patients with CRC. A total of 23 subjects were enrolled in this study: 9 had CRC (CRC group) and 14 had normal colons (normal group). The microbiome of the mucosal-luminal interface of each subject was sampled and analyzed using 16S rRNA gene amplicon sequencing. We also used Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to predict microbial functional profiles. The microbial composition of the mucosal lumen differed between the groups, and the presence of specific bacteria may serve as a potential biomarker for colorectal carcinogenesis. We identified a significant reduction in Eubacterium, which is a butyrate-producing genera of bacteria, and a significant increase in Devosia in the gut microbiota of CRC patients. Different levels of gut microflora in healthy and CRC samples were identified. The observed abundance of bacterial species belonging to Eubacterium and Devosia may serve as a promising biomarker for the early detection of CRC.

Draft Genome Sequence of Deoxynivalenol-Degrading Actinomycete Nocardioides sp. Strain LS1, Isolated from Wheat Leaves in Japan

Actinomycete Nocardioides sp. strain LS1, isolated from wheat leaf, is a bacterium that degrades and assimilates the mycotoxin deoxynivalenol (DON) as the carbon source.

Actinomycete Nocardioides sp. strain LS1, isolated from wheat leaf, is a bacterium that degrades and assimilates the mycotoxin deoxynivalenol (DON) as the carbon source. This is the first study of the genome sequence of the DON-degrading genus Nocardioides, and it facilitates the study of genes encoding the DON-degrading pathway.

Conversion of DON to 3-epi-DON in vitro and toxicity reduction of DON in vivo by Lactobacillus rhamnosus

Lactobacillus rhamnosus can convert DON to 3-epi-DON in vitro and reduce DON toxicity in vivo.

Addressing the mycotoxin deoxynivalenol contamination with soil-derived bacterial and enzymatic transformations targeting the C3 carbon

The search for feasible biological means of detoxifying mycotoxins has attained successful accomplishments in the past twenty years due to the involvement of many teams coming from diverse backgrounds and research expertise. The recently witnessed breakthroughs in the field of bacterial genomics (including next-generation sequencing), proteomics, and computational biology helped all in shaping the current understanding of how microorganisms/mycotoxins/environmental factors intertwined and interact together, hence paving the road for some substantial discoveries. This perspective review summarises the advances that were observed in the past two decades within the deoxynivalenol (DON) bio-detoxification field. It highlights the research efforts and progresses that were made in the arena of the aerobic oxidation and epimerization of this mycotoxin at the C3 carbon carried out by multiple Devosia species. Moreover, it sets practical examples and discusses how the recent standing-knowledge of bacterial detoxifications of this mycotoxin has evolved into a fascinating potential of empirical bacterial and enzymatic solutions aiming at addressing DON contamination. The obtained results argue for determining the involved enzyme’s co-factors and defining the chemistry behind the established catalytic activity at an early stage of investigation to maximise the chances of isolating the responsible enzymes.

Microbial Inhibition of Fusarium Pathogens and Biological Modification of Trichothecenes in Cereal Grains

Fungi of the genus Fusarium infect cereal crops during the growing season and cause head blight and other diseases. Their toxic secondary metabolites (mycotoxins) contaminate grains. Several dozen toxic compounds produced by fungal pathogens have been identified to date. Type B trichothecenes—deoxynivalenol, its acetyl derivatives and nivalenol (produced mainly by F. graminearum and F. culmorum)—are most commonly detected in cereal grains. “T-2 toxin” (produced by, among others, F. sporotrichioides) belongs to type-A trichothecenes which are more toxic than other trichothecenes. Antagonistic bacteria and fungi can affect pathogens of the genus Fusarium via different modes of action: direct (mycoparasitism or hyperparasitism), mixed-path (antibiotic secretion, production of lytic enzymes) and indirect (induction of host defense responses). Microbial modification of trichothecenes involves acetylation, deacetylation, oxidation, de-epoxidation, and epimerization, and it lowers the pathogenic potential of fungi of the genus Fusarium. Other modifing mechanisms described in the paper involve the physical adsorption of mycotoxins in bacterial cells and the conjugation of mycotoxins to glucose and other compounds in plant and fungal cells. The development of several patents supports the commercialization and wider application of microorganisms biodegrading mycotoxins in grains and, consequently, in feed additives.