Alternaria species associated to wheat black point identified through a multilocus sequence approach

Highlights

• Morphological traits alone are too much variable to be used for Alternaria species identification.

• A multilocus sequence approach is strongly recommend for Alternaria genus re-classification.

• Isolates from black point kernel grouped in Alternaria and Infectoriae sections.

• Number of defined Alternaria species should be reduced.

• We suggest that Section Infectoriae be included in another genus than Alternaria.

Abstract

Black point is one of the most important wheat disease and its incidence is increasing worldwide due to climate change too. Among the fungal genera that can cause black point, Alternaria is one of the predominant genus, often associated with mycotoxin contamination. The correct identification is the baseline for prevention and control of the disease. Taxonomy of the genus Alternaria is not completely clear yet, since its species can be differentiated for few morphological traits and, in some cases, also molecular phylogeny is not very effective in establishing species boundaries. In this study, one-hundred sixty-four strains, isolated from wheat kernels affected by black point sampled worldwide, were analyzed in order to assess their identity. Sequences of elongation factor, β-tubulin, glyceraldehyde-3-phosphate dehydrogenase and allergen alt-a1 genes were used to identify the variability of this population and their phylogenetic relationships. Isolates were grouped in two main clades: the Alternaria section, including A. alternata, A. tenuissima and A. arborescens species, and the Infectoriae section, that includes the two species A. infectoria and A. triticina. Comparison of isolates according with their area of isolation did not show a correlation between phylogeny and geographic origin. Indeed, the isolates grouped on the base of only their phylogenetic relationship. Due to the data arisen by our study, we strongly recommend a multilocus sequence approach to define Alternaria species, based on common genes and procedures to be unanimously shared by scientific community dealing with Alternaria genus. Moreover, we suggest that A. alternata, A. tenuissima, A. turkisafria and A. limoniasperae species would be merged in the defined species A. alternata. Finally we recommend to consider a taxonomic re-evaluation of the Infectoriae section that, for the morphology, sexuality, genetic and mycotoxin profile of the species included, could be defined as different fungal genus from Alternaria.

Introduction

Alternaria species are fungi distributed worldwide as saprophytes, endophytes and plant pathogens in soil, atmosphere, plant materials and food commodities due to their ability to adapt and survive in environmental conditions also far from their optimals (Aust et al., 1980). As plant pathogens, Alternaria spp. have been reported on important crops, including cereals, oil crops, ornamentals, vegetables and fruits (Logrieco et al., 2009). Alternaria spp. are also known for the production of a great number of secondary metabolites such as host specific toxins (HST) required for pathogenicity, a wide number of mycotoxins, and several allergens (Thomma, 2003). The most important mycotoxins produced by Alternaria are alternariol (AOH), alternariol monomethyl ether (AME), altenuene (ALT), tenuazonic acid (TA), altertoxins I, II and III (ATX, Logrieco et al., 2009), AAL-toxin (Wang et al., 1996) and stemphyltoxin III (Davis et al., 1991). Toxicity, mutagenicity and genotoxicity of several of these metabolites have been proved both in vitro and in vivo assays (Lehmann et al., 2006; Ostry, 2008; Schrader et al., 2001; Zhou and Qiang, 2008). In particular, AOH and AME are genotoxic, mutagenic, and could cause double DNA strand breaks and cell cycle arrest (citaz.). Moreover, AOH was reported to have immune-modulating effects (Solhaug et al., 2015). Tenuazoic acid can exert cytotoxic, phytotoxic, antitumoral, antiviral, antibiotic and antibacterial effects (Asam et al., 2013) and causes a human hematologic disorder called “onalay”, reported in central and southern Africa (da Cruz Cabral et al., 2016). Moreover, Yekeler et al. (2001) showed that TA could induce precancerous changes in the esophageal mucosa of mice. The sphinganine-analog AAL-toxin has phytotoxic effects, causing apoptosis of mammalian cells interfering with ceramide biosynthesis (Wang et al., 1996). Altertoxin I was acutely toxic in mice and mutagenic to mammalian cell lines (Schrader et al., 2006), while both ATX-I and ATX-III were reported as potent mutagens and tumor promoters (Ostry, 2008). On the other hand, ATX II and STTX III were proved to be mutagens (Fleck et al., 2016), and, finally, Alternaria mycotoxins have been associated to colon-rectal cancer, occurring significantly in food consummated by humans affected by this pathology (Huybrechts et al., 2018).

The correct identification of fungal taxa is the baseline for further actions to prevent and minimize the diseases and mycotoxin contamination. The taxonomy of the Alternaria genus is a very controversial issue. About 280 species in Alternaria genus were described by Simmons, 1967, Simmons, 1992, Simmons, 1999, Simmons, 2007, based exclusively on morphological traits of colonies growing in particular on sporulation patterns. Indeed, morphological traits have been for a long time the unique tool to classify strains of Alternaria and related genera. This approach is however not always effective, due to the high influence of growth conditions on the morphological features, the high level of similarity among some species and the presence of several strains with intermediate traits (Andrew et al., 2009; Misaghi et al., 1978). Moreover, even species belonging to other fungal genera phylogenetically closed to Alternaria were described with the same morphological criteria (Simmons, 1967, Simmons, 1989, Simmons, 1990a). As a consequence, many studies have been devoted to Alternaria and related genera, often confirming a confused taxonomic back-ground, that has caused a continuous process of taxonomic revision.

Different molecular tools were used to support morphology for the Alternaria taxonomy, including DNA fingerprinting techniques (RAPD, PCR-RFLP, AFLP and ISSR) and sequence analysis of rDNA and protein-coding genes, such as glyceraldehyde-3-phosphate dehydrogenase (gpd), endopolygalacturonase (endoPG), b-tubulin (tub), and allergen alt-a1 (alt-a1). However, although this wide and differentiated range of approaches, the data obtained were not always congruent (Andersen et al., 2009; Andrew et al., 2009; Hong et al., 2005; Hong et al., 2006; Park et al., 2008; Peever et al., 2004; Somma et al., 2011).

More recently, several authors increased the molecular investigations on wide sets of strains belonging to Alternaria and closely related genera, through phylogenetic analyses by using multiple gene approach. Lawrence et al. (2012) investigated the phylogenetic relationships of Embellisia and Nimbya species with species belonging to Alternaria, Ulocladium, Undifilum, Crivellia and Stemphylium genera, by analyzing three genes: internal transcribed spacer (its), gpd and alt a1. This study revealed polyphyly within each genus and incongruence with the morphological classification. Moreover, Alternaria species were resolved in species-groups. When deeper investigations were carried out within the Alternaria genus by using 10 different loci (Lawrence et al., 2013), among which only 5 (alt-a1, gpd, actin, calmodulin - caM - and plasma membrane ATPase), were considered informative for Alternaria phylogeny, the previously defined species-groups in Alternaria were elevated to the taxonomic status of sections. Eight sections in Alternaria genus were defined, Porri, Alternaria, Althernaterae, Sonchi, Gypsophilae, Radicina, Panax and Brassicicola, paraphyletic with the Ulocladium genus, and also other different polyphyletic groups, including A. infectoriae species-group, were described (Lawrence et al., 2013). A further investigation on Alternaria analyzed phylogenetically strains belonging to 25 different species included in A. infectoriae species-group, highly morphologically variable and provided of sexual stage (teleomorphs) (Lawrence et al., 2014). The study grouped all 25 species in a well supported clade, A. infectoriae species-group, that included also strains identified as Pseudoalternaria, Chalatospora, Embellisia and Nimbya. Interestingly, this clade resulted phylogenetically distant from the clade that grouped other species of Alternaria, all lacking the sexual stage. On the other hand, Woudenberg et al., 2013, Woudenberg et al., 2015 defined in Alternaria genus 26 sections, among which the Alternaria section is characterized by the highest number of morpho-species, and A. infectoriae species-group was elevated at Section rank, Infectoriae section. The deeper study focused on Alternaria section (Woudenberg et al., 2015) was performed by using 7 gene regions: alt-a1, gpd, endoPG, ITS, translation elongation factor (tef), RNA polymerase II gene (RPB2) and an anonymous gene region OPA10–2. In previous studies, species belonging to section Alternaria, that were mostly described founded on morphology or host specificity, were not successfully distinguished by sequencing because of their very high level of similarity. Woudenberg et al. (2015) had same difficulties in distinguishing Alternaria morphospecies based on sequences of the used housekeeping genes. Therefore, whole-genome sequencing and transcriptome analyses were also used to integrated phylogenetic study. The data generated allowed the authors to define in Alternaria a single species complex, A. arborescens species complex (AASC), and 11 phylogenetic species, among which A. alternata, that alone synonymised 35 not molecularly distinguished morphospecies.

Contamination of wheat kernels by Alternaria species and related toxins has been reported in different countries worldwide (Logrieco et al., 2009). Alternaria alternata, ubiquitous pathogen on several foodstuffs, and A. triticina, known to be among the causal agents of wheat leaf blight in different geographic areas (Mercado Vergnes et al., 2006), both resulted the predominant species associated with grains, although other species of the Alternaria and Infectoriae sections have been occasionally isolated (Gargouri-Kammoun et al., 2014; Rathod and Chavan, 2010; Vučković et al., 2012). However, all these reports have been more often limited to specific geographical areas or a low number of samples. Moreover, due to the presence of toxigenic species among those belonging to Alternaria section, a correct identification of most occurring species on wheat is not only useful to define their identity, based on the new taxonomic system proposed by Woudenberg et al. (2015), but it is also of key importance to assess the toxicological risk caused by the Alternaria species associated to wheat.

The aims of this work were: a) to study the genetic diversity of the main Alternaria species associated with wheat black point; b) to evaluate the phylogenetic relationships among isolates sampled in Italy and compare them with isolates sampled worldwide; c) to obtain a clearer picture of species borders among the Alternaria species affecting wheat, by using a multilocus sequence approach.