Biodiversity of Aspergillus species in some important agricultural products.

The genus Aspergillus is one of the most important filamentous fungal genera. Aspergillus species are used in the fermentation industry, but they are also responsible of various plant and food secondary rot, with the consequence of possible accumulation of mycotoxins. The aflatoxin producing A. flavus and A. parasiticus, and ochratoxinogenic A. niger, A. ochraceus and A. carbonarius species are frequently encountered in agricultural products. Studies on the biodiversity of toxigenic Aspergillus species is useful to clarify molecular, ecological and biochemical characteristics of the different species in relation to their different adaptation to environmental and geographical conditions, and to their potential toxigenicity. Here we analyzed the biodiversity of ochratoxin producing species occurring on two important crops: grapes and coffee, and the genetic diversity of A. flavus populations occurring in agricultural fields. Altogether nine different black Aspergillus species can be found on grapes which are often difficult to identify with classical methods. The polyphasic approach used in our studies led to the identification of three new species occurring on grapes: A. brasiliensis, A. ibericus, and A. uvarum. Similar studies on the Aspergillus species occurring on coffee beans have evidenced in the last five years that A. carbonarius is an important source of ochratoxin A in coffee. Four new species within the black aspergilli were also identified in coffee beans: A. sclerotioniger, A. lacticoffeatus, A. sclerotiicarbonarius, and A. aculeatinus. The genetic diversity within A. flavus populations has been widely studied in relation to their potential aflatoxigenicity and morphological variants L- and S-strains. Within A. flavus and other Aspergillus species capable of aflatoxin production, considerable diversity is found. We summarise the main recent achievements in the diversity of the aflatoxin gene cluster in A. flavus populations, A. parasiticus and the non-toxigenic A. oryzae. Studies are needed in order to characterise the aflatoxin biosynthetic genes in the new related taxa A. minisclerotigenes and A. arachidicola.

INTRODUCTION

Although they are not considered to be major cause of plant disease, Aspergillus species are responsible for several disorders in various plant and plant products. The most common species are A. niger and A. flavus, followed by A. parasiticus, A. ochraceus, A. carbonarius, and A. alliaceus. They can contaminate agricultural products at different stages including pre-harvest, harvest, processing and handling. Changes due to spoilage by Aspergillus species can be of sensorial, nutritional and qualitative nature like: pigmentation, discoloration, rotting, development of off-odors and off-flavors. However, the most notable consequence of their presence is mycotoxins contamination of foods and feeds. Because they are opportunistic pathogens, most of them are encountered as storage moulds on plant products (Kozakiewicz 1989). Various mycotoxins have been identified in foods and feeds contaminated by Aspergillus species, the most important are the aflatoxins and ochratoxin A (Varga ). Aflatoxins B1, B2, G1, G2 are the most toxic and carcinogenic naturally occurring mycotoxins. Due to their extreme hepatocarcinogenicity, extensive research has been carried out on the natural occurrence, identification, characterisation, biosynthesis, and genetic regulation of aflatoxins (Payne & Brown 1998; Bennett & Klich 2003; Yu ). Aflatoxins pose a risk to human health because of their extensive pre-harvest contamination of corn, cotton, soybean, peanuts and tree nuts, and because residues from contaminated feed may appear in milk. The most important aflatoxin producing species belong to Aspergillus section Flavi, including A. flavus, A. parasiticus and several other species (Bennett & Klich 2003). Extensive research has examined the role of the environment in fostering aflatoxin contamination episodes in corn and cottonseed (Cotty 2006; Cleveland ). However, there is still no firm understanding of why contamination occurs during certain years, but not in others. In this regard, the conflicting involvements of insect damage to the crop, drought, and natural microbiological competition in creating favorable conditions for aflatoxin contamination complicate research efforts.

Ochratoxin A (OTA) is a potent nephrotoxin which may contaminate various food and feed products (grains, legumes, coffee, dried fruits, beer and wine, and meat). It also exhibits carcinogenic, teratogenic and immunotoxic properties in rats and possibly in humans (IARC 1993). The genotoxicity of OTA remains controversial (EFSA 2006). OTA is receiving increasing attention worldwide because of its wide distribution in food and feed and human exposure that most likely comes from low level of OTA contamination of a wide range of different foods (Petzinger & Weidenbach 2002). The economically most important OTA producers belong to Aspergillus sections Circumdati and Nigri (Samson ; Frisvad ).

In this review we briefly analyze the biodiversity and the phylogenetic relationships within two of the most important sections: Flavi and Nigri occurring in some important agricultural products including grapes and derived products, coffee beans and other agricultural products. We find that, while A. flavus is involved in the majority of the agricultural contamination episodes, at least in the United States, the specific role of the S-strain and L-strain A. flavus has not yet been established.

Biodiversity of black aspergilli on grapes from Europe

Black aspergilli, which comprises species belonging to Aspergillus section Nigri, are worldwide distributed and have a significant impact on modern society. Many species cause food spoilage, and several are used in the fermentation industry (Bennett & Klich 1992), or candidate in the biotechnology industries. A. niger has even been granted the GRAS (Generally Regarded As Safe) status in certain industrial production processes by the Food and Drug Administration of the US government. Although the main source of black aspergilli is soil, they are among the most common fungi causing food spoilage and biodeterioration of other material. Various reports evidenced that members of the A. niger species complex, together with A. carbonarius and A. japonicus/aculeatus are frequently responsible for post-harvest decay of fresh fruit (apples, pears, peaches, citrus, grapes, figs, strawberries, tomatoes, melons, etc.) and some vegetables (especially onions, garlic, and yams); furthermore it is also among the commonest fungi isolated from dried fruit, beans, oil seeds and nuts (peanuts, pecans, pistachios, hazelnuts, almonds, walnuts etc.) (JECFA 2001). Recently, the significance of these species has completely changed since some of them, in particular A. carbonarius, is considered as the main source of OTA in grape and wine (Cabanes ; Da Rocha Rosa ; Battilani & Pietri, 2002; Magnoli , Leong ). Over the past five years several surveys and reports were published dealing with the epidemiology, ecology and distribution of black aspergilli occurring in wine grape and dried grape vineyards. Most of the surveys were from Mediterranean and South American countries and Australia. These studies clarified that the biseriate species A. niger “aggregate” and Aspergillus carbonarius, and the uniseriate species A. aculeatus and A. japonicus are the prevalent species occurring on grapes (Da Rocha Rosa ; Battilani ; Serra ; Leong ; Ponsone ). In general species of the A. niger aggregate appear to be the dominant black Aspergillus species in all the countries studied, although some vineyards and years showed higher incidence of A. carbonarius isolates (Cabanes ; Tjamos ). In particular, the occurrence and frequency of ochratoxigenic strains in A. carbonarius and A. niger “aggregate” on grape proved to be similar in the Mediterranean countries and in Australia. On the contrary, A. niger was reported as the main ochratoxigenic species occurring on grapes in South America, while A. carbonarius occurred in Argentina mainly on retailed dried vine fruits with a low capacity to produce OTA (Chulze ).

Ochratoxin A production of black aspergilli occurring on grapes was widely studied in the last years with sometimes ambiguous reports on the toxigenicity and the percentage of toxigenic strains among the species. The OTA producing strains of A. carbonarius ranged between 70 and 100 % when grown in vitro and tested using HPLC, while the range of producing strains was around 2-20 % for A. niger and A. tubingensis (Battilani ; Perrone ). Some reports claimed the production of OTA also by A. japonicus but it has not yet been confirmed (Dalcero ; Battilani ). Recently, Ponsone et al. (2007) studying the occurrence and toxigenicity of Aspergillus species in Argentinean vineyards found that A. niger aggregate was the most frequent species on grapes with 27 % of the isolates producing OTA. The authors also confirmed the production of OTA by A. japonicus and A. aculeatus strains, but this work lacks molecular identification of the strains.

Black aspergilli are one of the more difficult groups concerning classification and identification. The taxonomy of Aspergillus section Nigri has been studied by many taxonomists, leading to various species concepts (Table 1). The difficulties in species recognition within the Aspergillus niger “aggregate” and the fact that most of the studies carried out on black aspergilli occurring on grapes lack molecular characterisation of the strains perplexed the extent of their natural occurrence and species distribution on grapes and food. In this respect, in 2001-2002 a large survey of black aspergilli occurring on grape from 107 vineyards in different European countries was performed within the EU project Wine-Ochra Risk (QLK1-CT-2001-01761) in order to characterise the species diversity and the potential toxigenic strains in the Mediterranean basin. This survey led to the identification of four main populations separated molecularly using AFLP, RFLP and sequence analyses (Bau ; Perrone et al. 2006a, 2006b). These populations included A. carbonarius, A. tubingensis, A. niger, and a group of Aspergillus “uniseriate” isolates morphologically indistinguishable from A. japonicus and A. aculeatus but clearly separated by molecular techniques (Fig. 1). The genetic variability of these four populations observed by AFLP polymorphisms ranged from 15 to 35 % in A. carbonarius, A. tubingensis and the Aspergillus “uniseriate” group and 45-55 % in the A. niger group. The higher genetic diversity encountered in A. niger reflect the complexity of this taxon/group and the difficulties of identification at species level. The main OTA producer was A. carbonarius (95-100 % of strains), while the production of OTA was limited to a smaller proportion of strains in A. niger and A. tubingensis (10-15 % of the strains). No OTA production was observed in strains belonging to Aspergillus “uniseriate” group.

Table 1.

Species concepts of black aspergilli according to different authors.

Raper and Fennell (1965)	Al-Musallam (1980)	Kozakiewicz (1989)	RLFP*analysis	Samson et al. (2004)
A. japonicus	A. japonicus var. japonicus	A. japonicus	A. japonicus	A. japonicus
A. aculeatus	A. japonicus var. aculeatus	A. atroviolaceus	A. aculeatus	A. aculeatus
A. carbonarius	A. carbonarius	A. carbonarius	A. carbonarius	A. carbonarius
		A. fonsecaeus
A. heteromorphus	A. heteromorphus	A. heteromorphus	A. heteromorphus	A. heteromorphus
A. ellipticus	A. ellipticus	A. ellipticus	A. ellipticus	A. ellipticus
	A. helicothrix	A. helicothrix		A. sclerotioniger
				A. homomorphus
A. niger aggregate:
A. niger	A. niger var. niger	A. niger var. niger	A. niger	A. niger
A. tubingensis	A. niger var. niger f. hennebergii	A. niger var. tubingensis	A. tubingensis	A. tubingensis
A. phoenicis	A. niger var. phoenicis	A. niger var. phoenicis	A. foetidus	A. foetidus
A. polverulentus	A. niger var. phoenicis f. pulverulentus	A. niger var. polverulentus	A. brasiliensis	A. brasiliensis (Varga et al. 2007)
A. awamori	A. niger var. awamori	A. niger var. awamori		A. costaricaensis
A. ficuum	A. niger var. nanus			A. lacticoffeatus
A. foetidus	A. niger var. usamii	A. niger var. ficuum		A. piperis
A. foetidus var. pallidus	A. niger var. intermedius	A. citrus var. citrus		A. vadensis
A. foetidus var. acidus	A. foetidus	A. acidus		A. ibericus (Serra et al. 2006)
		A. citrus var. pallidus		A. uvarum (Perrone et al. 2007)

Results of various RLFP analysis by different authors: Kusters-van Someren et al. (1991); Megnegneu et al. (1993); Varga et al. (1993, 1994); Accensi et al. (1999); Parenicova et al. (1997, 2001)

Fig. 1.

AFLP dendrogram evidencing molecular biodiversity of representative black aspergilli isolated from grape in Europe.

This species diversity was also revealed by sequence analyses of partial calmodulin (660 bp) and β-tubulin (1360 bp) genes which confirmed a significant molecular divergence of Aspergillus “uniseriate” group from other Aspergillus species. The description of a new species named A. uvarum isolated only from grape has been recently submitted (Perrone ). Furthermore, during these surveys A. ibericus, a new species closely related to A. carbonarius and unable to produce OTA, was also described (Serra ). Recently, a further characterisation of five atypical A. niger strains (Fig. 1) collected from Portugal grapes evidenced their similarity with other black Aspergillus isolates collected worldwide, which did not fit into any species of Aspergillus section Nigri. This new species called A. brasiliensis has recently been described and characterised by a polyphasic taxonomic approach by Varga et al. (2007) using macro- and micromorphology, secondary metabolite profiles, partial sequences of the β-tubulin, calmodulin and ITS genes, and AFLP analysis.

The morphological and biochemical diversity of black aspergilli occurring on grapes is being summarised in Table 2. They differ both in their micromorphology and in extrolite profiles, but for some species like A. niger, A. tubingensis, A. foetidus and A. brasiliensis molecular data (chemical or DNA based) are needed for their correct identification. The most frequently occurring species, as underlined above, are the “biseriate” A. niger, A. tubingensis and A. carbonarius, together with the “uniseriate” A. japonicus, A. aculeatus and the new species A. uvarum currently found only on European grapes (Perrone ). The other three species A. brasiliensis, A. ibericus and A. foetidus are occasionally found on grapes; in particular A. ibericus and A. brasiliensis were found only in some grape samples from the Iberian Peninsula. A. foetidus was only found on grapes in South American surveys, but its identity has not been confirmed by molecular data (Chulze ; Ponsone ). The molecular diversity of the species within section Nigri is shown in Figs 1 and 2. The AFLP dendrogram (Fig. 1) summarises the data obtained using four different primer combinations for strains isolated from grapes in Europe in comparison with the type-strains of section Nigri. The same grouping was obtained by phylogenetic analysis of partial calmodulin sequence data (Fig. 2) and part of the β-tubulin gene (data not shown). These data indicate the need for molecular characterisation of these populations for a better and comprehensive identification of the complex of species involved in the Aspergillus black rot disease of grapes. In this respect, the molecular diversity of black aspergilli using partial calmodulin gene sequence data was widely exploited in the last three years and led to the development of primer pairs and SSCP tools for the rapid and robust identification of the main species within the section (Perrone ; Susca et al. 2007a, 2007b). In particular the SSCP analysis was successfully used to detect sequence variations contained in an about 180 bp-region of the calmodulin gene in order to identify species of Aspergillus section Nigri. The method developed allows discrimination between 11 Aspergillus species belonging to section Nigri: A. aculeatus, A. japonicus, A. uvarum, A. ellipticus, A. heteromorphus, A. carbonarius, A. ibericus, A. brasiliensis, A. niger, A. foetidus, and A. tubingensis.

Table 2.

Morphological and biochemical diversity of black aspergilli occurring on grapes.

Species	Conidial size (μm)	Color and size of sclerotia (mm)	Source	OTA	Extrolites produced
Biseriates
A. brasiliensis (Varga et al. 2007)	3.5-4.5	Found only in some strain, white, 1-1.5	Soil, grape	−	Naphtho-γ-pyrones (including aurasperone B), pyrophen, tensidol A & B, dihydrocarolic acid, aflavinine
A. carbonarius (Bainier) (Thom 1916)	7-9	Pink to brown, 1	Grape, cocoa, coffee, spices, palm oil, soil, air	+	Pyranonigrin A, naphtho-γ-pyrones
A. foetidus (Thom & Raper 1945)	3.5-4.5	Found only in some strain, white, 1-1.5	Tomato, grape, bottled fruits	−	Antafumicins, asperazine, funalenone, naphtho-γ-pyrones, pyranonigrin A
A. ibericus (Serra et al. 2006)	5-7	−	Grape	−	Naptho-γ-pyrones, pyranonigrin A
A. niger (Tieghem 1867)	3.5-5	−	Grape, cocoa, coffee, cereals, soil, paper, date palm	+/−	Funalenone, kotanins, naphtho-γ-pyrones, pyranonigrin A, pyrophen, tensidol A and B
A. tubingensis ((Schober) Mosseray 1934)	3-5	White to pink, 0.5-0.8	Grape, cocoa, coffee, soil, cereals	+/−	Asperazine, funalenone, naphtho-γ-pyrones, pyranonigrin A, tensidol A & B
Uniseriates
A. aculeatus (lizuka 1953)	4-5	−	Grape, papaya, pistachio, rice, tomato	−	Secalonic acid D & F
A. japonicus (Saito 1906)	4-5	white to cream, 0.5	Grape, green coffee berries, pineapple, sesame seed	−	Secalonic acid D & F
A. uvarum (Perrone et al. submitted)	3-4	dark brown to black	Grape	−	Secalonic acid D, geodin, erdin, asterric acid

Fig. 2.

Phylogenetic tree based on calmodulin sequence data of Aspergillus section Nigri. Numbers above branches are bootstrap values. Only values above 70 % are indicated. * Strains were labelled using accession number of ITEM, Culture Collection of Agri-Food Important Toxigenic Fungi, ISPA-CNR, Bari, Italy.

Furthermore, the distribution and species diversity of black aspergilli has recently been studied in 8 vineyards of Primitivo and Negroamaro varieties in Apulia (a region with high risk of OTA contamination in wine) during three grape growing seasons (2004-2006) within the Work supported by MIUR Project 12818 - SIVINA (D.M. n. 593/2000). Aspergillus niger “aggregate” was predominant from early veraison to ripening representing 80-85 % of contamination. A. carbonarius increased from veraison reaching 15-20 % at ripening stage, while the Aspergillus “uniseriate” were only found from early veraison to ripening decreasing from 15-20 % to 0-5 % of the population. About 600 strains of black aspergilli, representative of the sampling were isolated, identified and characterised for OTA production. Five percent of A. niger aggregate strains (360) resulted produced OTA, while all A. carbonarius strains (200) and none of the Aspergillus “uniseriate” strains (50) were positive to OTA production (Cozzi ). Studies are in progress to characterise the A. niger “aggregate” strains to identify the percentage of A. niger, A. tubingensis and A. brasiliensis strains presence on this south Italian population from grapes. In order to establish a fully correct relationship between species and OTA production, the reported producing isolates and the chemical evidence need to be further confirmed as recommended by Frisvad et al. (2006).

In conclusion, a different species distribution of black aspergilli may occur in Europe in relation with metereological conditions (Battilani ) and geographical areas: A. tubingensis and A. niger proved to be the dominant species in all countries, while A. carbonarius appears to be prevalent in southern Mediterranean areas (south of France, Southern Italy, Portugal and Greece). The distribution of A. ibericus is limited to Spain and Portugal, while A. uvarum occurs more frequently in Italy, France, Greece and Israel.

Biodiversity of black aspergilli on Thai coffee beans

Ochratoxin A contamination of coffee is a worldwide problem. The presence of OTA in green coffee bean has been reported by several authors in wide concentration ranging between 0.2 and 360 μg/kg (Levi ; Taniwaki 2006). Extensive sampling of green coffee beans of both Arabica and Robusta types worldwide indicated that although OTA contamination is more frequent in some areas including mainly African countries, no producing country was found to be free of contamination (Taniwaki 2006). Although previously A. ochraceus was suggested to be sole source of OTA contamination on coffee (Stack ), recent studies indicated that other species, including A. steynii, A. westerdijkiae, A. carbonarius, A. lacticoffeatus, A. sclerotioniger and A. niger are also able to produce OTA on coffee (Téren ; Samson ; Frisvad ). Different types of black aspergilli were reported in coffee bean from different countries. A. niger and A. carbonarius occured most frequently. Extensive studies have been carried out on the mycobiota of Brazilian coffee recently. From the study of arabica coffee beans by Taniwaki et al. (2003), the results showed that A. niger was the species found most commonly (63 % of potential OTA producers), but only 3 % of them produced OTA. A. ochraceus also occurred commonly (31 % of isolates), and 75 % of those studied were capable of OTA production, a much higher percentage than reported elsewhere. A. carbonarius was found (6 % of isolates) only in the hottest region sampled, and only from beans in the drying yard or in storage. However, 77 % of the A.carbonarius isolates were capable of producing OTA. Other studies reported similar species distribution on Brazilian coffee beans. Martins et al. (2003) used a conventional method to identify fungal flora in coffee bean. The predominant fungal genus was Aspergillus, including A. niger (83.3 %), A. ochraceus (53.3 %) and A. flavus (25 %). The incidence of other genera was substantially lower than that of aspergilli. Magnani et al. (2005) isolated and identified Aspergillus spp. that contaminate coffee beans by sequencing the ITS region of the isolates. The incidence of potentially ochratoxigenic species was 82 % with A. niger being found most frequently, followed by A. ochraceus and A. carbonarius. However, the mycobiota of coffee beans in other countries or different type of coffee beans can be significantly different, e.g. in Ilic et al. (2007), Vietnamese Robusta coffee beans were studied, and A. niger was the only ochratoxigenic species recovered. However, in another study carried out by Leong et al. (2007b) A. carbonarius isolates have also been recovered from Vietnamese Robusta and Arabica coffee bean samples.

We examined the mycobiota of coffee beans came from Thailand to clarify which species could be responsible for OTA contamination in this region. Different types of coffee varieties are cultivated in Thailand. Coffea arabica is the one grown in the Northern mountain area with elevation of more than 2 500 feet above sea level and average temperature of 18-25 °C. Coffea canephora var. robusta is grown in the Southern region of Thailand characterised by a totally different geography and climate, with elevation of not more than 500 feet above sea level, much more rain fall and average temperature of 25-35 °C.

Molecular identifications have not been carried out in most studies dealing with the mycobiota of coffee beans, which could lead to mis-identification of some closely-related species. In this study we analyzed the black aspergilli isolated from coffee beans using a polyphasic approach including morphological examinations, analysis of extrolite profiles and sequence analysis.

For Arabica coffee bean samples from the North, two types of samples, parchment coffee bean and green coffee beans were examined. Overall results showed that approximately 75 % of the samples were contaminated by black aspergilli, and similar levels of contamination were observed for isolates belonging to Aspergillus section Circumdati. (Fig. 3) A. niger was the predominant species but there were sometimes more than two species colonising the same beans. The related species A. tubingensis and A. foetidus were also common. Discrimination between A. niger and related species could be easily archeived by partial β-tubulin gene sequencing (Fig. 4). All three species were clustered in separate clade. Compared to the molecular method using sequencing of the ITS regions and with RFLP analysis of rRNA by Magnani et al. (2005), β-tubulin gene sequencing is more applicable and proved to be more efficient for species identification. Surprisingly, A. carbonarius was not detected, possibly as a result of climate selection as A. carbonarius occurs more frequently in hot regions. So species belonging to both sections Circumdati and Nigri could be responsible for OTA contamination in this region.

Fig. 3.

A. Arabica coffee. Ripen cherries on tree. B. depulped cherries. C. dried parchment coffee beans in drying yard. D-F. direct plating of parchment coffee beans on MEA and DG18. G-I. direct plating of green coffee beans on MEA and DG18.

Fig. 4.

Robusta coffee. A. Ripe cherries on tree. B. dried cherries. C. dried coffee beans in drying yard. D-F. direct plating of coffee cherries on MEA and DG18. G-I. direct plating of green coffee beans on MEA and DG18.

Two types of Robusta coffee beans, dried coffee cherries and green coffee beans from the South were also studied. Black aspergilli were the predominant in the mycobiota, with 100 % contamination in coffee cherry samples and approximately 98 % contamination in green coffee bean samples (Fig. 5), much higher than those reported in Brazilian coffee beans (Taniwaki 2003). Both A. carbonarius and A. niger were common and predominant in both types of coffee bean. Aspergillus spp. belonging to section Circumdati (A. westerdijkiae) was detected only in one sample. These results confirm a previous study of Joosten et al. (2001), who found that most of the examined 14 green coffee samples came from Southern Thailand were contaminated by black aspergilli, half of them by A. carbonarius. Based on these data, we presume that black aspergilli, especially A. carbonarius may play an important role in OTA contamination of coffee beans in Southern Thailand.

Fig. 5.

Neighbour-joining tree based on phylogenic analysis of the partial β-tubulin gene sequences of black aspergilli recovered from Thai coffee.

As a result of the survey of ochratoxin-producing aspergilli in Thai coffee beans, we also identified 2 new black Aspergillus species. One of them (A. aculeatinus) is related to A. aculeatus and other uniseriate black aspergilli and could be recovered from both regions, while the other one (A. sclerotiicarbonarius) is related to A. carbonarius and A. ibericus, and was found only in the Southern region of Thailand. Formal description of these species is in progress.

The diversity of black aspergilli recovered from Thai coffee beans is summarised in Table 3. Comparing the occurrence of black aspergilli from different parts of Thailand, remarkable differences were observed. A. carbonarius and A. sclerotiicarbonarius were found only in Southern Thailand while A. foetidus was found only in the Northern region. These differences could be due to differences in the geography, climate and methods used for coffee processing in the two regions. The so-called wet method is used for Arabica coffee processing while the dry method is used for Robusta coffee processing. Principally, the dry method has three basic steps: cleaning, drying and hulling. In Thailand, the whole Robusta cherry is directly dried with sun drying. Suarez-Quiroz et al. (2004) also reported that the dry method seemed to increase the presence of A. niger on the coffee beans. The wet method involves one more processing step: a fermentation step followed by cleaning to separate the beans from the pulp. This may cause changes in the natural substrate leading to changes in the species composition of the fungi colonising the beans. Differences in contact surfaces during processing may also play an important role in fungal contamination.

Table 3.

Distribution and ochratoxin producing abilities of black aspergilli in Thai coffee beans.

Arabica (Northern Thailand)	Robusta (Southern Thailand)	Ochratoxin A production	Ochratoxin B production
A. niger (44 %)	A. niger (28 %)	++	++
A. tubingensis (19 %)	A. tubingensis (17 %)	-	-
A. foetidus (28 %)	-	-	-
A. aculeatinus (9 %)	A. aculeatinus (15 %)	-	-
-	A. carbonarius (35 %)	+++++	-
-	A. sclerotiicarbonarius (5 %)	-	-

In brackets = percent of isolates identified from each type of Thai coffee beans.

Ochratoxin producing abilities of black aspergilli isolated from Thai coffee beans were examined by the agar plug method of Smedsgaard (1997). OTA production was analysed by high performance liquid chromatography. A total of 83 isolates representing 6 species, A. carbonarius, A. niger, A. tubingensis, A. foetidus, A. aculeatinus and A. sclerotiicarbonarius, were analyzed. The results confirmed former studies, only A. carbonarius and A. niger could produce ochratoxins. In this study, 100 % of the A. carbonarius isolates tested could produce large amounts of OTA but none of them produced ochratoxin B (Table 3). This is in agreement with Joosten et al. (2001), who reported that all A. carbonarius strains isolated from Thai coffee produced a significant amount of OTA. Similarly, Pardo et al. (2004) found that all A. carbonarius isolates came from coffee beans from various countries produced OTA, and Leong et al. (2007b) also observed that almost all (110/113) of the examined A. carbonarius isolates came from Vietnamese coffee beans could produce OTA. However, Taniwaki et al. (2003) observed that only 77 % of the A. carbonarius isolates came from Brazilian coffee beans produced OTA. Differences in the ratio of A. carbonarius isolates able to produce OTA could be due to misidentification of the non-OTA producer A. ibericus as A. carbonarius in previous studies. In contrast with previous reports, where 2-3 % of A.niger isolates isolated from coffee beans could produce ochratoxins (Heenan , Taniwaki ), 13 % of the A. niger strains came from Thai coffee could produce both OTA and ochratoxin B but in rather small amounts compared to A. carbonarius (Fig. 6). It is more likely that A. carbonarius is the source of OTA contamination in Thai coffee beans.

Fig. 6.

Comparison of relative average abilities (expressed as Luminescence Unit from Fluorescence detector: LU) to produce ochratoxins of A. carbonarius and A. niger.

In conclusion, diversity of black aspergilli in coffee beans occurring in Thailand depends on a combination of various factors including coffee variety, geographic region, climate and processing method. Significantly, more Robusta than Arabica beans were infected by black aspergilli, in agreement with the findings of Leong et al. (2007b) and Pardo et al. (2004). A. niger and related species are more important as contaminants of Arabica coffee beans in Northern Thailand, while A. carbonarius is responsible for OTA contamination of Robusta coffee beans in Southern parts of Thailand.

Genetic diversity in A. flavus and implications for agriculture

Aspergillus flavus is the most common species associated with aflatoxin contamination of agricultural crops (Cotty , Cotty 1997) (Fig. 7). A. flavus populations are highly diverse and their stability in the soil and on the plant is not well understood. An atoxigenic relative of A. flavus, A. oryzae, is widely used in Asian fermentation processes. It is now increasingly clear that A. oryzae is not a separate species, but actually is only one many examples of atoxigenic variants of A. flavus (Geiser ). As much as 40 % of the soil isolates of A. flavus are incapable of producing aflatoxins (Cotty ). Addition of atoxigenic strains of A. flavus to the soil of susceptible crops to dilute out toxin-producing strains is being used to remediate aflatoxin contamination of cotton and peanuts (Cotty and Bayman 1993, Horn , Horn and Dorner 2002).

Fig. 7.

Causes of A. flavus diversity.

As with other haploid fungal species, genetic isolation in A. flavus may be maintained by a vegetative compatibility system (Leslie 1993). A typical soil population is usually composed of isolates from hundreds of different vegetative compatibility groups (VCGs) (Bayman and Cotty 1991). No genetic exchange was found among A. flavus atoxigenic VCG isolates and toxin-producing isolates collected from six geographically separated regions, suggesting that recombination among VCGs is rare (Ehrlich ).

A. flavus soil populations also contain isolates from two morphologically distinct sclerotial size variants, termed the L-strain for isolates with average sclerotial size greater than 400 μm and the S-strain for isolates with sclerotial size less that 400 μm (Cotty 1997). On typical laboratory growth media S-strain isolates produce higher levels of aflatoxins, more abundant sclerotia, and generally fewer conidia. Atoxigenic S-strain isolates are very rarely found in natural environments. Another consistent difference between S- and L-strain isolates is the size of deletion of portions of the genes, norB and cypA in the aflatoxin cluster. The size of the deletion in the norB-cypA gene was 1.5 kb for S-strain isolates and 0.8 kb for L-strain isolates. The gene cypA encodes a P450 monooxygenase that is necessary for formation of G aflatoxins. The deletion, therefore, is the reason why A. flavus is incapable of producing G aflatoxins. (Ehrlich ). Most interestingly, A. oryzae isolates have an S-strain type deletion even though they morphologically resemble L strain A. flavus and make abundant conidia. When this gap size is included in a phylogenetic dataset that includes polymorphisms in the omtA gene region of the aflatoxin cluster, a clade was distinguished that contained members of both aflatoxin-producing S strain isolates and L strain isolates incapable of AF production. Another clade was distinguished that contained both A. oryzae and L-strain isolates incapable of AF production. From this data we reasoned that the L-strain is the ancestral species and that A. oryzae derived from an atoxigenic L-strain ancestor, whereas S-strain isolates derived from an aflatoxin-producing L-strain ancestor (Chang 2006).

The adaptation of A. flavus to the carbon-rich environment of certain agricultural communities is perhaps conducive to gene loss. Many of the isolates incapable of aflatoxin production have multiple mutations in their aflatoxin cluster genes. A careful study of deletion patterns in different L-strain A. flavus isolates from peanut fields found that, in these isolates, part or most of the aflatoxin biosynthesis gene cluster is missing (Chang ). Isolates of A. oryzae also have large deletions of the aflatoxin gene cluster (Lee ). In some of these isolates the remaining aflatoxin biosynthesis genes Neighboured the telomere. Proximity to the telomere may make the cluster more unstable. In A. parasiticus when normal development is thwarted, by forced repeated mycelial transfer, the resulting isolate permanently loses some of its normal developmental functions (Kale ). It does not form conidia properly or make aflatoxins. The defects in these isolates remain to be determined.

Production of aflatoxin and its precursor metabolites is associated with increased production of conidia (Wilkinson ), but so far, unlike the protective role of melanin, no evidence has been found that the conidia are protected by making the aflatoxin cluster metabolites. It is thought that the red pigmented dothistromin may be a virulence factor for D. septosporum responsible for its pathogenicity to pine (Bradshaw ). Like dothistromin, most of the aflatoxin precursor metabolites are red or orange. Because of their color, the metabolites could have helped to foster dispersal. In addition, since section Flavi isolates are normally saprophytic, polyketide metabolites may increase fungal survival in soil. Such a benefit may be unnecessary in carbon-rich agricultural environments. In such environments, the ability to make aflatoxins could be a vestigial function. To support this conjecture, when section Flavi isolates are collected from non-agricultural soils, almost all of the isolates examined were capable of producing aflatoxins (Ehrlich ). Furthermore, in some soils, A. flavus was not the most prominent species. Understanding the role of aflatoxin production and in general secondary metabolite production may only be possible if attempts are made to duplicate in the laboratory the conditions of the natural environment in which these aspergilli evolved.

CONCLUSIONS

Complexes of pathogenic and opportunistic species of Aspergillus can colonise and induce disease symptoms in various plants and plant products, and produce toxic secondary metabolites (mycotoxins) in the infected tissue. In this chapter we evidenced how environmental conditions, geographical areas and crops can influence both fungal populations associated and production of mycotoxins. In this respect, the studies on economically important Aspergillus species by a polyphasic approach are innovative, strategic and helpful in assessing the biodiversity of the population/species and the potential risk of mycotoxin contamination of the agricultural products. In particular, the phylogenetic analysis of sequences of β-tubulin and calmodulin genes, AFLP polymorphisms and extrolite profiles together with morphological analysis have led to reconsider in the last five years the taxonomy within the Aspergillus section Nigri (about seven new species has been described). Also the reports on the occurrence of black aspergilli in agricultural products and their potential toxigenicity must be reconsidered on the basis of the wide molecular biodiversity found within morphologically undistinguishable strains of this section. Furthermore, there is a need of molecular studies on South-American black Aspergillus populations occurring on grapes and other agricultural products in order to ascertain the species composition and potential toxigenicity. Finally, the presence of an Aspergillus uniseriate population typical of grapes in Europe, named A. uvarum, is an interesting finding that needs further investigation in grapevine areas outside Europe in order to evaluate the distribution of this new species at a global level.

Within A. flavus and other Aspergillus species capable of aflatoxin production, considerable diversity is found. Such diversity makes it more difficult to assign firm taxonomic identity to isolates from such populations. For example, should all A. flavus that are incapable of producing aflatoxins be considered to be A. oryzae? Such isolates are routinely found in agricultural fields, but only some are now classified as A. oryzae. We now know that loss of G-aflatoxin formation in A. flavus is a result of deletions in three genes encoding enzymes required for conv. of O-methylsterigmatocystin to aflatoxin G1 and G2, namely the cytochrome P450, cypA, and the reductases, nadA and norB. The aflatoxin clusters of A. parasiticus and the recently described related taxon, A. minisclerotigenes from Australia, West Africa, and Argentina that produces both B and G aflatoxins contain functional v.s of these genes (Pildain ). Further studies are neded to clarify if the other newly described species, A. arachidicola, which is closely related to A. parasiticus, also carry these genes. The separation between A. parasiticus and A. flavus is estimated to have occurred more than 8 Mya. The conidia of A. minisclerotigenes resemble those of A. flavus while those of A. parasiticus are distinctly different in appearance. Further studies need to be done to sort out what selective factors, both environmental and genetic affect cluster gene stability in these related organisms. In this regard, we need to know if agricultural interactions play a role in causing gene instability? We expect that comparisons of different fungal genomes and developing a better understanding of regulatory relationships may help in answering some of these questions.