Research Article |
Corresponding author: Chibundu N. Ezekiel ( chaugez@gmail.com ) Academic editor: Cecile Gueidan
© 2020 Chibundu N. Ezekiel, Bart Kraak, Marcelo Sandoval-Denis, Michael Sulyok, Oluwawapelumi A. Oyedele, Kolawole I. Ayeni, Oluwadamilola M. Makinde, Oluwatosin M. Akinyemi, Rudolf Krska, Pedro W. Crous, Jos Houbraken.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Ezekiel CN, Kraak B, Sandoval-Denis M, Sulyok M, Oyedele OA, Ayeni KI, Makinde OM, Akinyemi OM, Krska R, Crous PW, Houbraken J (2020) Diversity and toxigenicity of fungi and description of Fusarium madaense sp. nov. from cereals, legumes and soils in north-central Nigeria. MycoKeys 67: 95-124. https://doi.org/10.3897/mycokeys.67.52716
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Mycological investigation of various foods (mainly cowpea, groundnut, maize, rice, sorghum) and agricultural soils from two states in north-central Nigeria (Nasarawa and Niger), was conducted in order to understand the role of filamentous fungi in food contamination and public health. A total of 839 fungal isolates were recovered from 84% of the 250 food and all 30 soil samples. Preliminary identifications were made, based on macro- and micromorphological characters. Representative strains (n = 121) were studied in detail using morphology and DNA sequencing, involving genera/species-specific markers, while extrolite profiles using LC-MS/MS were obtained for a selection of strains. The representative strains grouped in seven genera (Aspergillus, Fusarium, Macrophomina, Meyerozyma, Neocosmospora, Neotestudina and Phoma). Amongst the 21 species that were isolated during this study was one novel species belonging to the Fusarium fujikuroi species complex, F. madaense sp. nov., obtained from groundnut and sorghum in Nasarawa state. The examined strains produced diverse extrolites, including several uncommon compounds: averantinmethylether in A. aflatoxiformans; aspergillimide in A. flavus; heptelidic acid in A. austwickii; desoxypaxillin, kotanin A and paspalitrems (A and B) in A. aflatoxiformans, A. austwickii and A. cerealis; aurasperon C, dimethylsulochrin, fellutanine A, methylorsellinic acid, nigragillin and pyrophen in A. brunneoviolaceus; cyclosporins (A, B, C and H) in A. niger; methylorsellinic acid, pyrophen and secalonic acid in A. piperis; aspulvinone E, fonsecin, kojic acid, kotanin A, malformin C, pyranonigrin and pyrophen in A. vadensis; and all compounds in F. madaense sp. nov., Meyerozyma, Neocosmospora and Neotestudina. This study provides snapshot data for prediction of food contamination and fungal biodiversity exploitation.
Aflatoxins, chemotaxonomy, food safety, Fusarium, mycology, secondary metabolites
Fungi are ubiquitous and diverse, inhabiting various environments including agricultural soils and the crops grown on them (
Proper characterisation of fungi is fundamental to effectively determine their ecology and roles in the environment. In Nigeria, several studies have focused on fungal contamination of food crops (
Therefore, in view of the need to understand the roles of fungi in food contamination and other processes, we conducted a mycological investigation into agricultural crops (foods) commonly consumed and available in agrarian households and soils on which the crops were grown in two north-central states (Nasarawa and Niger) in Nigeria. The two states were selected for this study, based on previous reports (
Various food (n = 250) and soil (n = 30) samples were collected in two states (Nasarawa and Niger) in north-central Nigeria. Samples were collected in September 2018 (harvest season) and January 2019 (storage season). The distribution of samples by sampling season were: harvest (food, n = 143) and storage (food, n = 107; soil, n = 30). Samples were collected from households within one week of harvest and after three months of storage (storage samples). In each state, food samples (1 kg per sample) were collected from households within three randomly selected communities that are at least 5–20 km apart: Mada station, Tundun Adabu and Yelwa Doma in Nasarawa state and Diko, Nubwa Koro and Sabon Wuse in Niger state. The food samples collected included: cowpea (n = 7); groundnut (n = 53), maize (n = 142), millet (n = 1), rice (n = 23) and sorghum (n = 24). Soil samples were collected from the farmlands belonging to five randomly selected households in each community. Sampled fields were at least 1 km apart. In each field, one composite sample (90–100 g) was collected by traversing the field and taking five subsamples from random points. The depth of soil sampling was 3–4 cm.
Food samples were placed in polyethylene bags whilst soil samples were placed in paper bags. All food samples were fragmented in an electric blender (MX-AC400, Panasonic, India) and stored at 4°C prior to analysis within 48 h. Soil samples were transferred to plastic bags and clods were crushed using a mortar and pestle. Soil samples were then homogenised by hand-mixing prior to immediate fungal analysis.
Fungal isolation
Filamentous fungi, present in the food and soil samples, were isolated and enumerated using the dilution plating technique described by
Characterisation of fungal isolates
Fungal isolates from the food and soil samples were characterised, based on morphological characteristics, DNA sequence data and/or secondary metabolites. The strains were first cultivated on MEA and assessed for macro- and microscopic characters, which were then compared with descriptions in appropriate keys (
To further explore the species diversity and determine the presence of putative novel taxa amongst the fusaria, phylogenetic analyses were carried out, based on BenA, CaM, RPB1, RPB2 and TEF-1a sequences. A first analysis, based on partial RPB2 sequences, was intended to determine the generic distribution of the Nigerian isolates. A second multi-locus analysis, based on the five gene regions above-mentioned, was used to determine the genetic exclusivity of an undescribed phylogenetic clade belonging to the Fusarium fujikuroi species complex (FFSC,
For extrolite profiling, each representative Aspergillus isolate was grown on Czapek yeast autolysate (CYA) agar, MEA and yeast extract sucrose (YES) agar and the selected Fusarium and Neocosmospora strains were grown on OA and PDA prior to extraction (
Extrolites of fungal cultures were determined by a dilute and shoot LC–MS/MS method (
The IBM SPSS v21.0 (SPSS Inc., IL, USA) was applied for data analysis. Data on fungal load were first normalised by a logarithm to base 10 transformation of the original data prior to the calculation of mean values. Means were tested for significance by One-way ANOVA (α = 0.05). Means of the concentrations (µg/kg) of the extrolites, produced by the fungal strains in culture media, were also calculated.
Fungal propagules were recovered from 84% (n = 209) of the 250 food samples and from all of the soil samples (n = 30). The fungal load in the food samples was significantly (p < 0.05) higher at harvest (range: 2.00–6.22; mean: 4.07 ± 0.95 Log10CFU/g) than in storage (range: 2.00–4.60; mean: 3.44 ± 0.69 Log10CFU/g). The load of fungal propagules in the soil samples ranged 2.70–4.20 (mean: 3.45 ± 0.34 Log10CFU/g). Variations observed in fungal load during the two seasons (harvest and storage) may be attributed to the sampling environment and nature of samples. For example, harvest samples were recently collected from the field where crops are in contact with soil and a large diversity of fungal propagules were present (
Based on the fungal isolates recovered from food and soil samples and identified in this study, sample type-specific fungal incidences were estimated as 40.5%, 28%, 14.9%, 9.9%, 4.9% and 1.7% in soil, maize, sorghum, groundnut, cowpea and rice, respectively. Aspergilli were widely distributed in soil and food, although a higher proportion of isolates (35.6%) was recovered from soil compared to the individual foods. Nine Aspergillus species, belonging to two sections, were recovered in this study (Fig.
Four Fusarium species (F. andiyazi, F. madaense sp. nov., F. thapsinum and F. verticillioides), belonging to FFSC, were identified. All the Fusarium spp. were recovered from food samples, except F. verticillioides that was found in both food (maize, rice and sorghum) and soil (Fig.
Macrophomina phaseolina, Meyerozyma caribbica and Phoma species were isolated only from food in Nasarawa state (Fig.
The elucidation of extrolite patterns from fungal strains grown on mycological media, using the highly sensitive LC-MS/MS technique, remains the gold standard chemotaxonomic approach to fungal characterisation (
Extrolites | Aspergillus aflatoxiformans | Aspergillus austwickii | Aspergillus brunneoviolaceus | Aspergillus cerealis | Aspergillus flavus | Aspergillus niger | Aspergillus piperis | Aspergillus vadensis |
---|---|---|---|---|---|---|---|---|
3-Nitropropionic acid | + | + | - | + | + | - | - | - |
Aflatoxicol | + | - | - | - | + | - | - | - |
Aflatoxin B1 | + | + | - | + | + | - | - | - |
Aflatoxin B2 | + | + | - | + | + | - | - | - |
Aflatoxin G1 | + | + | - | + | - | - | - | - |
Aflatoxin G2 | + | + | - | + | - | - | - | - |
Aflatoxin M1 | + | + | - | + | + | - | - | - |
Aflatrem | + | + | - | + | + | - | - | - |
Asparason A | + | + | - | + | + | - | - | - |
Asperfuran | + | + | - | + | + | - | - | - |
Aspergillimide | - | - | + | - | + | - | - | - |
Aspulvinone E | - | - | - | - | - | + | + | + |
Aurasperon B | - | - | - | - | - | - | + | + |
Aurasperon C | - | - | + | - | - | - | + | + |
Aurasperon G | - | - | - | - | - | - | + | + |
Averantin | + | + | - | + | + | - | - | - |
Averantinmethylether | + | - | - | - | - | - | - | - |
Averufin | + | + | - | + | + | - | - | - |
Brevianamid F | + | + | + | + | + | + | + | + |
Citreorosein | - | - | + | - | - | - | - | - |
cyclo(L-Pro-L-Tyr) | + | + | + | + | + | + | + | + |
cyclo(L-Pro-L-Val) | + | + | + | + | + | + | + | + |
Cyclopiazonsäure | + | + | - | + | + | - | - | - |
Cyclosporin A | - | - | - | - | +/- | + | - | - |
Cyclosporin B | - | - | - | - | +/- | + | - | - |
Cyclosporin C | - | - | - | - | +/- | + | - | - |
Cyclosporin H | - | - | - | - | +/- | + | - | - |
Demethylsulochrin | - | - | + | - | - | - | - | - |
Desoxypaxillin | + | + | - | + | + | - | - | - |
Emodin | - | - | + | - | - | + | - | - |
Endocrocin | - | - | + | - | - | + | - | - |
Fellutanine A | - | - | + | - | - | - | - | - |
Fonsecin | - | - | - | - | - | + | + | + |
Heptelidic acid | - | + | - | - | + | - | - | - |
Iso-Rhodoptilometrin | - | - | + | - | - | + | - | - |
Kojic acid | + | + | - | + | + | + | - | + |
Kotanin A | + | + | - | + | + | + | - | + |
Malformin A | - | - | - | - | - | + | - | - |
Malformin C | - | - | - | - | - | + | + | + |
Meleagrin | - | - | + | - | - | - | - | - |
Methylorsellinic acid | - | - | + | - | - | - | + | - |
Nidurufin | + | + | - | + | + | - | - | - |
Nigragillin | - | - | + | - | - | + | + | + |
Norsolorinic acid | + | + | - | + | - | - | - | - |
O-Methylsterigmatocystin | + | + | - | + | + | - | - | - |
Oxaline | - | - | + | - | - | - | - | - |
Paraherquamide E | - | - | + | - | - | - | - | - |
Paspalin | + | + | - | + | + | - | - | - |
Paspalinin | + | + | - | + | + | - | - | - |
Paspalitrem A | + | + | - | + | + | - | - | - |
Paspalitrem B | + | + | - | + | + | - | - | - |
Pyranonigrin | - | - | - | - | - | + | + | + |
Pyrophen | - | - | + | - | - | + | + | + |
Secalonic acid D | - | - | + | - | - | - | + | - |
Sporogen AO1 | - | - | - | - | + | - | - | - |
Sterigmatocystin | + | + | - | + | + | - | - | - |
Tensidol B | - | - | - | - | - | + | - | - |
Versicolorin A | + | + | - | + | + | - | - | - |
Versicolorin C | + | + | - | + | + | - | - | - |
Versiconal acetate | + | + | - | + | - | - | - | - |
Aspergillus metabolites
The extrolite patterns of the Aspergillus species, isolated and identified in this study, except A. tamarii which was not evaluated, are shown in Table
The members of Aspergillus section Nigri (A. brunneoviolaceus, A. niger, A. piperis and A. vadensis) secreted a total of 31 extrolites (Table
Two strains of A. piperis, screened in this study, secreted compounds agreeable to those previously documented in literature (
Extrolites from Fusarium and its related fungal species
A total of 15, 12 and 11 extrolites were found in cultures of Fusarium, Neocosmospora and Neotestudina (Table
Extrolites | Fusarium andiyazi | Fusarium thapsinum | Fusarium verticillioides | Fusarium madaense sp. nov. | Neocosmospora falciformis | Neocosmospora ipomoeae | Neocosmospora suttoniana | Neocosmospora vasinfecta | Neotestudina rosatii |
Beauvericin | - | - | - | + | - | - | - | - | + |
Bikaverin | + | + | + | + | - | - | - | - | + |
Brevianamid F | + | + | + | + | + | + | + | + | + |
cyclo(L-Pro-L-Tyr) | + | + | + | + | + | + | + | + | + |
cyclo(L-Pro-L-Val) | + | + | + | + | - | - | - | + | + |
Cyclosporin A | - | - | - | - | + | - | - | + | - |
Cyclosporin B | - | - | - | - | + | - | - | + | - |
Cyclosporin C | - | - | - | - | + | - | - | + | - |
Cyclosporin D | - | - | - | - | + | - | - | + | - |
Cyclosporin H | - | - | - | - | + | - | - | + | - |
Deoxyfusapyron | + | - | - | + | - | - | - | - | + |
Fumonisin A1 | - | - | + | - | - | - | - | - | - |
Fumonisin B1 | - | - | + | - | - | - | - | - | - |
Fumonisin B2 | - | - | + | - | - | - | - | - | - |
Fumonisin B3 | - | - | + | - | - | - | - | - | - |
Fusapyron | + | - | - | + | - | - | - | - | + |
Fusaric acid | + | + | + | + | - | - | - | + | + |
Fusarin C | - | + | + | + | - | - | - | - | - |
Fusarinolic acid | + | + | + | + | - | - | - | - | - |
Gibepyron D | + | + | + | + | + | + | + | + | + |
Radicicol | - | - | - | - | - | - | - | + | - |
Sulochrin | - | - | - | - | - | - | - | - | + |
Tryptophol | - | - | - | - | + | - | + | - | + |
All the species of Fusarium, except F. andiyazi, produced fusarin C in this study. Beauvericin, bikaverin, deoxyfusapyron and fusapyron were found in cultures of certain species of Fusarium, Neocosmospora and Neotestudina. Specifically, F. madaense sp. nov. and N. rosatii produced all four aforementioned compounds together with the other three species of Fusarium for bikaverin and F. andiyazi for deoxyfusapyron and fusapyron. The immunosuppressant cyclosporins [A (mean: 42.2 mg/kg), B (mean: 27.3 mg/kg), C (mean: 29.9 mg/kg), D (mean: 4.6 mg/kg) and H (mean: 32.9 mg/kg)] were specific to Neocosmospora and were found only in cultures of N. falciformis and N. vasinfecta. Radicicol (323 mg/kg) and sulochrin (1.8 mg/kg) were found in one strain of N. vasinfecta and N. rosatii, respectively. Based on the recorded chemical profiles in this study, the three studied genera are closely related chemotaxonomically. However, F. madaense sp. nov. and N. rosatii seem to be more closely related than the other species. This is the first chemotaxonomic profiling of F. madaense sp. nov., Meyerozyma, Neocosmospora and Neotestudina.
Phylogenetic analyses of Fusarium and Neocosmospora and description of a novel Fusarium species
A first phylogenetic analysis, based on partial RPB2 sequences, was conducted to identify Nigerian isolates morphologically compatible with Fusarium and Neocosmospora spp. (Fig.
The first of 1000 equally parsimonious trees obtained from Maximum-Parsimony (MP) analysis of RPB2 sequences of 76 isolates of Fusarium and Neocosmospora spp. Numbers on the nodes are MP bootstrap values (BS) and Maximum-Likelihood BS values above 70%. Branch lengths are proportional to distance. Ex-type and ex-epitype strains are indicated with T and ET, respectively. The names of 17 species complexes of Fusarium are shown in grey. Nigerian isolates obtained in this study are shown in red together with their geographical origin and source of isolation. The internal square shows MP statistics as follows: TL = tree length, CI = consistency index, RI = retention index and HI = homoplasy index.
To further determine the relationship between the putative novel clade and F. andiyazi, a second analysis was conducted which encompassed 4456 positions of five loci (BenA 525 bp, CaM 545 bp, >RPB1 978 bp, RPB2 1 735 bp and TEF-1a 673 bp), of which 3417 were constant (BenA 406 bp, CaM 421 bp, >RPB1 777 bp, RPB2 1 379 bp and TEF-1a 434 bp), 1018 were variable (BenA 118 bp, CaM 120 bp, RPB1 201 bp, RPB2 356 bp and TEF-1a 223 bp) and 614 were parsimony informative (BenA 64 bp, CaM 63 bp, RPB1 132 bp, RPB2 236 bp and TEF-1a 119 bp). The final alignment included 44 isolates, representing 35 Fusarium spp. from the three biogeographical phylogenetic clades of FFSC (African, American and Asian clades,
The first of 24 equally parsimonious trees obtained from Maximum-Parsimony (MP) analysis of BenA, CaM, RPB1, RPB2 and TEF-1a sequences of 42 isolates of Fusarium spp. Numbers on the nodes are MP bootstrap values (BS) and Maximum-Likelihood BS values above 70%. Branch lengths are proportional to distance. Ex-type strains are indicated with T. Strains corresponding to new species described here are shown in bold. The internal square shows MP statistics as follows: TL = tree length, CI = consistency index, RI = retention index and HI = homoplasy index.
Different from F. thapsinum by the absence of napiform microconidia. Different from F. andiyazi, F. thapsinum and F. verticillioides by its lighter colony pigmentation, growth rates, microconidial septation, presence of true chlamydospores and secondary metabolite patterns.
Nigeria, Nasarawa, Mada Station, from groundnut (Arachis hypogaea), Sep. 2018, C.N. Ezekiel, holotype CBS H-24346, ex-holotype strain CBS 146669 = CPC 38344 = 12B(3)2.
Fusarium madaense sp. nov. (ex-type culture CBS 146669). A–C aspect of colonies on PDA, OA and SNA, respectively, after 14 d at 24°C in the dark D colony reverse on OA (up) and PDA (down) after 14 d at 24 °C in the dark E–G, J aerial conidiophores and phialides H, I sporodochia formed on the surface of carnation leaves K, L sporodochial conidiophores M, N chlamydospores O, P microconidia Q sporodochial conidia. Scale bars: 100 μm (H, I); 20 μm (J); 10 μm (all others).
Colonies grown in the dark at 24°C. On MEA and PDA with an average radial growth rate of 5.9–6.5 mm/d and filling an entire 90 mm Petri dish in 7 d. Surface white to pale rosy buff, flat, velvety to felty with abundant patches of white aerial mycelium; margin regular, filiform. Reverse pale saffron to peach, a pale bay diffusible pigment can be scarcely produced. On OA, occupying an entire 90 mm Petri dish in 7 d. Surface white to pale rosy buff, flat, velvety to felty with abundant patches of white aerial mycelium; margin regular. Reverse pale luteous to saffron. On SNA, reaching 24–25 mm diam. in 7 d. Surface white, velvety, with scarce aerial mycelium, margins filiform. Reverse white.
Conidiophores on aerial mycelium straight, erect, septate, smooth- and thin-walled, commonly simple or reduced to conidiogenous cells, borne laterally on hyphae or laterally branched at various levels, bearing terminal single monophialides; phialides subulate to subcylindrical, smooth- and thin-walled, (17–)25.5–39.5 μm long, (2–)2.5–3.5 μm at widest point, periclinal thickening and collarettes inconspicuous or absent; microconidia hyaline, clavate, smooth- and thin-walled, 0–3-septate, (7–)9–15(–21) × (2–)2.5–4(–5) μm, arranged in long chains at the tip of monophialides. Sporodochia pale to bright orange, formed abundantly on the surface of carnation leaves and on agar surface. Conidiophores in sporodochia, 21–60 μm tall, simple or irregularly and verticillately branched, bearing terminal, single monophialides or groups up 2–3 monophialides; sporodochial phialides doliiform to subcylindrical, (10.5–)13–18(–20.5) × (2.5–)3–4(–4.5) μm, smooth- and thin-walled, with conspicuous periclinal thickening and an often short apical collarette. Sporodochial conidia lunate to falcate, tapering towards apical and basal ends, moderately curved dorsiventrally or with an almost straight ventral part; apical cell more or less equally sized than the adjacent cell, apically slightly elongated to papillate; basal cell distinctly notched, (0–)1–5(–6)-septate, hyaline, thin- and smooth-walled. Aseptate conidia: (38–)38.5–42(–44) × 3.5–4.5 μm; one-septate conidia: (37.5–)40–48(–53) × 3.5–4(–4.5) μm; two-septate conidia: 43 × 3.7 μm; three-septate conidia: (29–)38–48.5(–61.5) × (3–)4–4.5(–5) μm; four-septate conidia: (45–)46.5–54(–59) × (3.5–)4–4.5(–5) μm; five-septate conidia: 47.5–55.5(–60) × 4–4.5 μm; six-septate conidia: 55.5 × 4.5 μm; overall (29–)38.5–50(–61.5) × (3–)4–4.5(–5) μm. Chlamydospores present on MEA, PDA and SNA, globose to subglobose, hyaline, smooth and thick-walled, (6–)6.5–8.5(–10) μm diam., terminal or intercalary in the aerial hyphae, solitary or in chains
Nigeria.
Name refers to Mada Station, a locality in Nasarawa State, Nigeria, where the species was found.
Nigeria, Mada Station, from groundnut (Arachis hypogaea), Sept 2018, C.N. Ezekiel, CBS 146648 = CPC 38321 = 12B(3), CBS 146656 = CPC 38330 = 12B(5); from sorghum, Jan 2019, C.N. Ezekiel, CBS 146651 = CPC 38324 = 7S(6).
Although clearly recognisable based on genetic markers, Fusarium madaense is hardly distinguishable from its closer relatives, based on morphological features only. The novel species is characterised by abundant long, slender and slightly curved macroconidia, a morphology typical of the FFSC. The overall morphology of F. madaense is similar to that of F. andiyazi, F. thapsinum and F. verticillioides; all species are characterised by clavate microconidia formed in long chains from relatively long monophialides. Moreover, the four mentioned species are known to be pathogenic on sorghum (
The proposal of the novel species F. madaense and its differentiation from F. andiyazi, F. thapsinum and F. verticillioides is also supported by secondary metabolite profiling of all the above-mentioned species, as found in this study. Fusarium madaense was the only beauvericin-producing species in our dataset. Nevertheless, it has been reported that F. verticillioides strains can produce trace levels of this toxin (
We have shown the importance of applying robust taxonomic approaches to fungal characterisation in this study. Here, diverse fungal species, including those not previously reported from Nigerian food and soil, as well as a novel Fusarium species, F. madaense sp. nov., were identified and described. Several of these species possess mycotoxigenic, as well as plant, human and animal pathogenic, potential. We further elucidated the secondary metabolite profiles of strains within the identified fungal species. A handful of small molecule compounds were found in the cultures of the strains, including several compounds not previously reported from some strains; a few could serve as species-specific chemotaxonomic markers. Overall, we provide snapshot data on the fungal biodiversity in two north-central Nigerian states. The findings of this study are valuable to guide researchers to predict mycotoxin contamination of crops/food and possible sources of fungal infections in humans and animals, as well as to find, where unavailable and implement where available, strategies towards the control of problematic fungi and the adverse effects they may pose.
The authors are thankful to Oluwaseun T. Ojuri, Oluwabunmi Ogunniran and Dr. Isaac M. Ogara for being helpful during sampling and isolation of fungi. CN Ezekiel deeply appreciates the International Foundation of Sciences (Sweden) for partly supporting this study through an Individual Grant (Number: I-3-E-6046-1).
Tables S1, S2
Data type: COL
Explanation note: Table S1. Strain details and GenBank accession numbers of molecularly identified isolates included in this study. Table S2. Strain data and accession numbers of additional strains included in phylogenetic analyses of Fusarium and related taxa.