Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review.

The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome.

Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding.

Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen-one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estimating their relative abundance based on mock communities and (ii) the degree of taxonomic resolution using phylogenetic trees. Furthermore, our pipelines were also applied to DNA sequences from symptomatic walnut husks and twigs. Overall, our results showed that the ITS2 region was a better barcode than ITS1 and ITS, resulting in significantly higher sensitivity and/or similarity of composition values. The ITS3/ITS4_KYO1 primer set allowed to cover a wider range of fungal diversity, compared to the other primer sets also targeting the ITS2 region, namely, GTAA and GTAAm. Adding an extraction step to the ITS2 sequence influenced both positively and negatively the taxonomic resolution at the genus and species level, depending on the primer pair considered. Taken together, these results suggested that Kyo set without ITS2 extraction was the best pipeline to assess the broadest fungal diversity, with a more accurate taxonomic assignment, in walnut organs with dieback symptoms.

Influence of Maize Residues in Shaping Soil Microbiota and Fusarium spp. Communities.

Fusarium head blight (FHB) is a devastating fungal disease of small grain cereals including wheat. Causal fungal agents colonize various components of the field during their life cycle including previous crop residues, soil, and grains. Although soil and residues constitute the main inoculum source, these components have received much less attention than grains. This study aimed at disentangling the role of previous crop residues in shaping soil microbiota, including Fusarium spp. communities, in fields under wheat-maize rotation. Such knowledge may contribute to better understand the complex interactions between Fusarium spp. and soil microbiota. Dynamics of bacterial and fungal communities, with a special focus on Fusarium spp., were monitored in soils at 3 time points: during wheat cultivation (April 2015 and 2017) and after maize harvest (November 2016) and in maize residues taken from fields after harvest. Shifts in microbiota were also evaluated under mesocosm experiments using soils amended with maize residues. Fusarium graminearum and F. avenaceum were predominant on maize residues but did not remain in soils during wheat cultivation. Differences in soil bacterial diversity and compositions among years were much lower than variation between fields, suggesting that bacterial communities are field-specific and more conserved over time. In contrast, soil fungal diversity and compositions were more influenced by sampling time. Maize residues, left after harvest, led to a soil enrichment with several fungal genera, including Epicoccum, Fusarium, Vishniacozyma, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus, and Bullera, but not with bacterial genera. Likewise, under mesocosm conditions, the addition of maize residues had a stronger influence on fungal communities than on bacterial communities. In particular, addition of maize significantly increased soil fungal richness, while bacteria were much less prone to changes. Based on co-occurrence networks, OTUs negatively correlated to Fusarium spp. were identified, such as those assigned to Epicoccum and Vishniacozyma. Altogether, our results allowed to gain a deeper insight into the complex microbiota interactions in soils, with bacteria and fungi responding differently to environmental disturbances.

Complete Genome Sequence of the Plant-Pathogenic Fungus Colletotrichum lupini.

Colletotrichum is a fungal genus (Ascomycota, Sordariomycetes, Glomerellaceae) that includes many economically important plant pathogens that cause devastating diseases of a wide range of plants. In this work, using a combination of long- and short-read sequencing technologies, we sequenced the genome of Colletotrichum lupini RB221, isolated from white lupin (Lupinus albus) in France during a survey in 2014. The genome was assembled into 11 nuclear chromosomes and a mitochondrial genome with a total assembly size of 63.41 Mb and 36.55 kb, respectively. In total, 18,324 protein-encoding genes have been predicted, of which only 39 are specific to C. lupini. This resource will provide insight into pathogenicity factors and will help provide a better understanding of the evolution and genome structure of this important plant pathogen.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis.

The fungal phytopathogen Colletotrichum lupini is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate C. lupini gene expression and protein synthesis during lupin infection, using, respectively, an RNAseq-based transcriptomic approach and a mass spectrometry-based proteomic approach. Patterns of differentially-expressed genes in planta were evaluated from 24 to 84 hours post-inoculation, and compared to in vitro cultures. A total of 897 differentially-expressed genes were identified from C. lupini during interaction with white lupin, of which 520 genes were predicted to have a putative function, including carbohydrate active enzyme, effector, protease or transporter-encoding genes, commonly described as pathogenicity factors for other Colletotrichum species during plant infection, and 377 hypothetical proteins. Simultaneously, a total of 304 proteins produced during the interaction were identified and quantified by mass spectrometry. Taken together, the results highlight that the dynamics of symptoms, gene expression and protein synthesis shared similarities to those of hemibiotrophic pathogens. In addition, a few genes with unknown or poorly-described functions were found to be specifically associated with the early or late stages of infection, suggesting that they may be of importance for pathogenicity. This study, conducted for the first time on a species belonging to the Colletotrichum acutatum species complex, presents an opportunity to deepen functional analyses of the genes involved in the pathogenicity of Colletotrichum spp. during the onset of plant infection.

Water Microbiota in Greenhouses With Soilless Cultures of Tomato by Metabarcoding and Culture-Dependent Approaches.

Water supply, in hydroponic greenhouses, can originate from groundwater, surface water or rainwater stored in open tanks. To limit contamination of water supply, several methods have been used including active and passive methods such as slow filtration techniques which consist in passing the nutrient solutions slowly through filters. The purpose of this study was to describe the microbiota associated with water sampled before entering greenhouses and in recirculating nutrient solutions, either before or after running through a biofiltration system. Metabarcoding analysis revealed that water ecosystems were unique niches for diverse bacterial and fungal communities. Microbial composition varied greatly across storage conditions (groundwater vs. rainwater) and among greenhouses, suggesting that water microbiota is site- and storage-condition-specific. Nonetheless, we found that microbiota structure in open-stored water (either coming from ground or rain) shared a higher degree of similarity than with water directly pumped out of the ground. Open-stored waters were characterized by predominant taxa, notably those involved in aerobic chemoheterotrophy, such as the Sphingomonadaceae and Hyphomicrobiaceae families. Water directly collected from the ground showed the lowest levels of fungal and bacterial richness while also characterized by a significantly higher level of bacterial equitability and an enrichment in taxa involved in N-cycling. Slow filtration allowed reducing cultivable bacterial loads as well Pythium spp. and Fusarium oxysporum propagules, based on culture-dependent results, without compromising microbiota richness and diversity. Although compositional structure was similar following biofiltration, significant differences in bacterial (but not fungal) taxa abundance were reported, with primarily an enrichment of Chelativorans, Mycobacterium, and Gemmata as well as a depletion of Rhodobacter, Aminobacter, and Ellin329. The exact mechanisms by which such taxa would be favored at the expense of other remained unknown. Besides the accurate description of microbiota found in water at both taxonomical and predicted functional levels, our study allowed comparing the water microbiota between various storage system and following biofiltration. Although preliminary, our results provide a first insight into the potential microbial diversity, which can increase ecosystem functionality.

Phylogenetic Diversity and Effect of Temperature on Pathogenicity of Colletotrichum lupini.

Although lupin anthracnose caused by Colletotrichum lupini is a significant threat for spring and winter lupin crops, it has been poorly studied so far. This study aimed at characterizing the (i) phylogenetic, (ii) morphological, and (iii) physiological diversity of collected isolates from anthracnose-affected lupins. The genetic identification of representative isolates (n = 71) revealed that they were all C. lupini species, further confirming that lupin anthracnose is caused by this species. However, multilocus sequencing on these isolates and 16 additional reference strains of C. lupini revealed a separation into two distinct genetic groups, both of them characterized by a very low genetic diversity. The diversity of morphological characteristics of a selected subset of C. lupini isolates was further evaluated. To the best of our knowledge, microsclerotia production observed for some isolates has never been reported so far within the Colletotrichum acutatum species complex. Finally, the modeling of growth responses of a subset of C. lupini strains revealed the capacity of some strains to grow in vitro at 5°C. This ability was also evidenced in planta, because C. lupini DNA was detectable in plants from 14 days postinoculation at 5°C onward, whereas symptoms began to appear a week later, although at a very low level. Since lupin crops are planted during winter or early spring, growth studies in vitro and in planta demonstrated the capability of the species to grow at temperatures ranging from 5 to 30°C, with an optimum close to 25°C. In this study, C. lupini-specific primers were also designed for real-time quantitative PCR on fungal DNA and allowed the detection of C. lupini in asymptomatic field samples. These results open perspectives to detect earlier and limit the development of this pathogen in lupin crops.

Microbiota Associated with Dromedary Camel Milk from Algerian Sahara.

Despite the fact that camel milk represents a valuable food source, the fungal diversity of raw camel milk has been poorly studied so far. Here, we investigated the fungal and bacterial communities found in dromedary camel milk from Ghardaia, a representative region of Algerian Sahara. The application of both culture-dependent and independent molecular techniques, based on dHPLC analysis and metabarcoding of ITS region, provided a complementary biodiversity assessment of camel milk fungi which was composed of 15 different taxa. Yeast species belonged to Filobasidium, Naganishia, Malassezia, Mrakia, Rhodotorula, and Yarrowia genera; and mold species belonged to Fusarium, Cladosporium, and Penicillium genera. All three techniques revealed that the fungal community was dominated by species belonging to the former genus Cryptococcus (Filobasidium and Naganishia) although none of them was able to encompass the entire fungal diversity alone. In addition, massive parallel 16S rRNA tag sequencing was applied to gain an insight into the diversity of bacterial communities which were dominated by Pseudomonas spp. Our results provide an initial insight about fungal and bacterial population found in dromedary camel milk from Algerian Sahara.

A novel metabarcoding approach to investigate Fusarium species composition in soil and plant samples.

The genus Fusarium contains more than 300 species, most of which are plant pathogens. Appropriate molecular tools for accurately and rapidly describing temporal and spatial shifts in Fusarium communities would be useful for the development of control strategies. Here, we present a new Fusarium-specific primer pair targeting the translation elongation factor 1-α (EF1α) gene with amplicons of ~430 bp, suitable for MiSeq metabarcoding sequencing. Mock Fusarium communities were used to evaluate its resolution and to optimize read filtering and downstream analyses. The use of the DADA2 pipeline coupled with operational taxonomic unit (OTU) picking at 98% similarity cut-off significantly increased the accuracy of read filtering. Building a phylogenetic tree using a manually curated database as a reference allowed taxonomic assignment at the species or species-complex level. This methodology was tested on soil and maize residue samples collected from crop fields. Up to 18 Fusarium OTUs, belonging to 17 species and 8 species complexes, were obtained, with F. oxysporum being the most abundant species in soil samples, while F. graminearum and F. avenaceum were the most abundant in maize residues. We demonstrated the high performance of this workflow which could be further used for profiling Fusarium species composition and dynamics during the cultivation cycle.

Co-occurrence analysis reveal that biotic and abiotic factors influence soil fungistasis against Fusarium graminearum.

The current study determined the levels of soil fungistasis against a soil-borne pathogen inoculum, Fusarium graminearum (Fg, a major causal agent of Fusarium Head Blight (FHB)), in 31 wheat fields by quantifying Fg growth after a 15-day incubation period using qPCR in autoclaved versus non-autoclaved soils. The results were used to define the six most Fg-resistant and the six most Fg-conducive soils. By using a metabarcoding approach, the diversity of the bacterial communities was significantly higher in Fg-resistant soils than in Fg-conducive soils. Microbial taxa potentially contributing to Fg-fungistasis of soil were selected if they were significantly more prevalent and/or abundant in Fg-resistant soils than in Fg-conducive soils. Some of these candidate indicators, e.g. Pseudomonas spp. and Bacillus spp., have been reported previously as effective biocontrol agents against plant pathogens. Correlation-based network analysis further showed that the members of the bacterial communities in Fg-resistant soils were more connected than in Fg-conducive soils. Moreover, network modules was found significantly correlated with certain edaphic abiotics factors (such as the soil manganese and nitrogen content) and Fg-fungistasis. Such observations may suggest and emphasize, although conceptual, the importance of synergistic rather than individual effects of network members, and the nutrient use efficiency in contributing to Fg-resistance of soils in wheat fields in France.

Combined Metabarcoding and Co-occurrence Network Analysis to Profile the Bacterial, Fungal and Fusarium Communities and Their Interactions in Maize Stalks.

Fusarium Head Blight (FHB) is one of the most devastating diseases of cereals worldwide, threatening both crop production by affecting cereal grain development, and human and animal health by contaminating grains with mycotoxins. Despite that maize residues constitute the primary source of inoculum for Fusarium pathogenic species, the structure and diversity of Fusarium spp. and microbial communities in maize residues have received much less attention than in grains. In this study, a metabarcoding approach was used to study the bacterial, fungal and Fusarium communities encountered in maize stalks collected from 8 fields in Brittany, France, after maize harvest during fall 2015. Some predominant genera found in maize residues were cereal or maize pathogens, such as the fungal Fusarium, Acremonium, and Phoma genera, and the bacterial Pseudomonas and Erwinia genera. Furthermore, a high predominance of genera with previously reported biocontrol activity was found, including the bacterial Sphingomonas, Pedobacter, Flavobacterium, Pseudomonas, and Janthinobacterium genera; and the fungal Epicoccum, Articulospora, Exophiala, and Sarocladium genera. Among Fusarium spp., F. graminearum and F. avenaceum were dominant. We also found that the maize cultivar and previous crop could influence the structure of microbial communities. Using SparCC co-occurrence network analysis, significant negative correlations were obtained between Fusarium spp. responsible for FHB (including F. graminearum and F. avenaceum) and bacterial OTUs classified as Sphingomonas and fungal OTUs classified as Sarocladium and Epicoccum. Considering that isolates belonging to these taxa have already been associated with antagonist effect against different Fusarium spp. and/or other pathogenic microorganisms and due to their predominance and negative associations with Fusarium spp., they may be good candidates as biocontrol agents. Combining the use of Fusarium-specific primers with universal primers for bacteria and fungi allowed us to study the microbial communities, but also to track correlations between Fusarium spp. and other bacterial and fungal genera, using co-occurrence network analysis. Such approach could be a useful tool as part of a screening strategy for novel antagonist candidates against toxigenic Fusarium spp., allowing the selection of taxa of interest.

Atoxigenic Aspergillus flavus Isolates Endemic to Almond, Fig, and Pistachio Orchards in California with Potential to Reduce Aflatoxin Contamination in these Crops.

In California, aflatoxin contamination of almond, fig, and pistachio has become a serious problem in recent years due to long periods of drought and probably other climatic changes. The atoxigenic biocontrol product Aspergillus flavus AF36 has been registered for use to limit aflatoxin contamination of pistachio since 2012 and for use in almond and fig since 2017. New biocontrol technologies employ multiple atoxigenic genotypes because those provide greater benefits than using a single genotype. Almond, fig, and pistachio industries would benefit from a multi-strain biocontrol technology for use in these three crops. Several A. flavus vegetative compatibility groups (VCGs) associated with almond, fig, and pistachio composed exclusively of atoxigenic isolates, including the VCG to which AF36 belongs to, YV36, were previously characterized in California. Here, we report additional VCGs associated with either two or all three crops. Representative isolates of 12 atoxigenic VCGs significantly (P < 0.001) reduced (>80%) aflatoxin accumulation in almond and pistachio when challenged with highly toxigenic isolates of A. flavus and A. parasiticus under laboratory conditions. Isolates of the evaluated VCGs, including AF36, constitute valuable endemic, well-adapted, and efficient germplasm to design a multi-crop, multi-strain biocontrol strategy for use in tree crops in California. Availability of such a strategy would favor long-term atoxigenic A. flavus communities across the affected areas of California, and this would result in securing domestic and export markets for the nut crop and fig farmer industries and, most importantly, health benefits to consumers.

Distribution and incidence of atoxigenic Aspergillus flavus VCG in tree crop orchards in California: A strategy for identifying potential antagonists, the example of almonds.

To identify predominant isolates for potential use as biocontrol agents, Aspergillus flavus isolates collected from soils of almond, pistachio and fig orchard in the Central Valley of California were tested for their membership to 16 atoxigenic vegetative compatibility groups (VCGs), including YV36, the VCG to which AF36, an atoxigenic isolate commercialized in the United States as biopesticide, belongs. A surprisingly large proportion of isolates belonged to YV36 (13.3%, 7.2% and 6.6% of the total almond, pistachio and fig populations, respectively), while the percentage of isolates belonging to the other 15 VCGs ranged from 0% to 2.3%. In order to gain a better insight into the structure and diversity of atoxigenic A. flavus populations and to further identify predominant isolates, seventeen SSR markers were then used to genetically characterize AF36, the 15 type-isolates of the VCGs and 342 atoxigenic isolates of the almond population. There was considerable genetic diversity among isolates with a lack of differentiation among micro-geographical regions or years. Since isolates sharing identical SSR profiles from distinct orchards were rare, we separated them into groups of at least 3 closely-related isolates from distinct orchards that shared identical alleles for at least 15 out of the 17 loci. This led to the identification of 15 groups comprising up to 24 closely-related isolates. The group which contained the largest number of isolates were members of YV36 while five groups were also found to be members of our studied atoxigenic VCGs. These results suggest that these 15 groups, and AF36 in particular, are well adapted to various environmental conditions in California and to tree crops and, as such, are good candidates for use as biocontrol agents.

Community Structure of Aspergillus flavus and A. parasiticus in Major Almond-Producing Areas of California, United States.

Several nut crops, including almond, pistachio, and walnut, can become contaminated with mycotoxins. Of greatest economic significance are aflatoxins, which are mainly produced by members of Aspergillus section Flavi. The distribution of the two sclerotial-size morphotypes of Aspergillus flavus (i.e., S and L strains) and A. parasiticus, the main species responsible for aflatoxin production among section Flavi, was monitored in the soil of almond orchards in California over a 5-year period from 2007 to 2011, excluding 2009. In total, 4,349 Aspergillus isolates were collected from 28 almond orchards located in the northern, central, and southern Central Valley in California. Overall, A. flavus L strain was the most frequent, followed by A. parasiticus and A. flavus S strain. However, variations in the spatial distribution of these three taxa were found between the three regions. Over the 5-year period, higher frequencies of L strain were more often observed in the southern region (79.9 to 95.1%, depending on year) compared with the northern region (21.4 to 47.1%). In the north, A. parasiticus was the most common strain, with frequencies of 28.5 to 61% for the various years. In addition, the frequency of aflatoxin-producing isolates among L strains fluctuated from year to year. A significant increase (P = 0.0001) was observed from 2008 (75% of the isolates produced aflatoxins) to 2007 (59%), and a decrease was observed from 2010 (61%) to 2011 (53%). Aflatoxin-producing L strain isolates were significantly more prevalent than atoxigenic isolates in each region during the 5-year survey, except in 2011 in the north, where more isolates were atoxigenic (56%) than aflatoxin-producing (44%). Our results indicate that the structure of A. flavus and A. parasiticus communities in the soil and the proportion of toxigenic isolates vary across regions and years. Such knowledge may help devise appropriate aflatoxin control strategies, including the use of atoxigenic isolates as biological control agents adapted to the soil environments in each region.

Maize kernel antioxidants and their potential involvement in Fusarium ear rot resistance.

The potential involvement of antioxidants (α-tocopherol, lutein, zeaxanthin, ß-carotene, and ferulic acid) in the resistance of maize varieties to Fusarium ear rot was the focus of this study. These antioxidants were present in all maize kernel stages, indicating that the fumonisin-producing fungi (mainly Fusarium verticillioides and Fusarium proliferatum ) are likely to face them during ear colonization. The effect of these compounds on fumonisin biosynthesis was studied in F. verticillioides liquid cultures. In carotenoid-treated cultures, no inhibitory effect of fumonisin accumulation was observed while a potent inhibitory activity was obtained for sublethal doses of α-tocopherol (0.1 mM) and ferulic acid (1 mM). Using a set of genotypes with moderate to high susceptibility to Fusarium ear rot, ferulic acid was significantly lower in immature kernels of the very susceptible group. Such a relation was nonexistent for tocopherols and carotenoids. Also, ferulic acid in immature kernels ranged from 3 to 8.5 mg/g, i.e., at levels consistent with the in vitro inhibitory concentration. Overall, our data support the fact that ferulic acid may contribute to resistance to Fusarium ear rot and/or fumonisin accumulation.

Chlorogenic acid and maize ear rot resistance: a dynamic study investigating Fusarium graminearum development, deoxynivalenol production, and phenolic acid accumulation.

Fusarium graminearum is the causal agent of Gibberella ear rot and produces trichothecene mycotoxins. Basic questions remain unanswered regarding the kernel stages associated with trichothecene biosynthesis and the kernel metabolites potentially involved in the regulation of trichothecene production in planta. In a two-year field study, F. graminearum growth, trichothecene accumulation, and phenolic acid composition were monitored in developing maize kernels of a susceptible and a moderately resistant variety using quantitative polymerase chain reaction and liquid chromatography coupled with photodiode array or mass spectrometry detection. Infection started as early as the blister stage and proceeded slowly until the dough stage. Then, a peak of trichothecene accumulation occurred and infection progressed exponentially until the final harvest time. Both F. graminearum growth and trichothecene production were drastically reduced in the moderately resistant variety. We found that chlorogenic acid is more abundant in the moderately resistant variety, with levels spiking in the earliest kernel stages induced by Fusarium infection. This is the first report that precisely describes the kernel stage associated with the initiation of trichothecene production and provides in planta evidence that chlorogenic acid may play a role in maize resistance to Gibberella ear rot and trichothecene accumulation.

The dent stage of maize kernels is the most conducive for fumonisin biosynthesis under field conditions.

The fungal pathogen Fusarium verticillioides infects maize ears and produces fumonisins, known for their adverse effects on human and animal health. Basic questions remain unanswered regarding the kernel stage(s) associated with fumonisin biosynthesis and the kernel components involved in fumonisin regulation during F. verticillioides-maize interaction under field conditions. In this 2-year field study, the time course of F. verticillioides growth and fumonisin accumulation in developing maize kernels, along with the variations in kernel pH and amylopectin content, were monitored using relevant and accurate analytical tools. In all experiments, the most significant increase in fumonisin accumulation or in fumonisin productivity (i.e., fumonisin production per unit of fungus) was shown to occur within a very short period of time, between 22/32 and 42 days after inoculation and corresponding to the dent stage. This stage was also characterized by acidification in the kernel pH and a maximum level of amylopectin content. Our data clearly support published results based on in vitro experiments suggesting that the physiological stages of the maize kernel play a major role in regulating fumonisin production. Here we have validated this result for in planta and field conditions, and we demonstrate that under such conditions the dent stage is the most conducive for fumonisin accumulation.

Factors of the Fusarium verticillioides-maize environment modulating fumonisin production.

Fumonisins are mycotoxins mainly produced by two Fusarium species: F. verticillioides and F. proliferatum. These toxins are of great concern due to their widespread contamination in maize and their adverse effects on animal and human health. In the past decade, progress was made in identifying the genes required for fumonisin biosynthesis. Additionally, molecular mechanisms involved in the regulation of fumonisin production have been very recently elucidated. By covering the latest advances concerning the factors modulating fumonisin production, this review aims at presenting an integrated approach of the overall mechanisms involved in the regulation of fumonisin biosynthesis during maize kernel colonization.