Putting the Mess in Order: Aspergillus welwitschiae (and Not A. niger) Is the Etiological Agent of Sisal Bole Rot Disease in Brazil

Characterization and Fungicide Sensitivity of Phaeosphaeriopsis obtusispora That Causes Marginal Leaf Blight in Agave hybrid H.11648

Sisal is an important tropical cash crop in southern China. Unfortunately, it is threatened by various diseases. In 2022, a new disease tentatively named marginal leaf blight disease (MLBD) was first observed in sisal fields across Guangxi and Guangdong provinces, with an incidence rate ranging from 13% to 30%. In this work, to isolate and identify the pathogens causing MLBD, sisal leaves exhibiting the typical MLBD symptoms were collected, and nine strains were obtained. Pathogenicity tests, morphological observations, and phylogenetic analyses confirmed that two strains, namely 22GX1-3 and 22GD1-4, identified as Phaeosphaeriopsis obtusispora, were the causative pathogens of MLBD. Further investigations into the biological characteristics of P. obtusispora showed that its mycelia exhibited optimal growth on PDA medium, with the most favourable temperature and pH being 25 °C and 7.0, respectively. The mycelia could grow in temperatures ranging from 10 °C to 32 °C but ceased at 35 °C. Lactose and yeast extract powder were also identified as the optimal carbon and nitrogen sources, respectively. Additionally, the effectiveness of various control agents was assessed on a single strain, 22GX1-3. Among the twelve fungicides tested, difenoconazole was proven the most effective, with an EC50 value of 0.5045 µg/mL. To our knowledge, this is the first report for sisal MLBD caused by P. obtusispora. Our results provide crucial pieces of information for the development of effective management strategies to control sisal MLBD caused by P. obtusispora.

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genus Aspergillus. Our evolutionary genomic analyses revealed that nearly 8% of publicly available Aspergillus genomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.

Mutations in the Second Alternative Oxidase Gene: A New Approach to Group Aspergillus niger Strains

Alternative oxidase is a terminal oxidase in the branched mitochondrial electron transport chain of most fungi including Aspergillus niger (subgenus Circumdati, section Nigri). A second, paralogous aox gene (aoxB) is extant in some A. niger isolates but also present in two divergent species of the subgenus Nidulantes-A. calidoustus and A. implicatus-as well as in Penicillium swiecickii. Black aspergilli are cosmopolitan opportunistic fungi that can cause diverse mycoses and acute aspergillosis in immunocompromised individuals. Amongst the approximately 75 genome-sequenced A. niger strains, aoxB features considerable sequence variation. Five mutations were identified that rationally affect transcription or function or terminally modify the gene product. One mutant allele that occurs in CBS 513.88 and A. niger neotype strain CBS 554.65 involves a chromosomal deletion that removes exon 1 and intron 1 from aoxB. Another aoxB allele results from retrotransposon integration. Three other alleles result from point mutations: a missense mutation of the start codon, a frameshift, and a nonsense mutation. A. niger strain ATCC 1015 has a full-length aoxB gene. The A. niger sensu stricto complex can thus be subdivided into six taxa according to extant aoxB allele, which may facilitate rapid and accurate identification of individual species.

Current status of secondary metabolite pathways linked to their related biosynthetic gene clusters in Aspergillus section Nigri

Covering: up to the end of 2021Aspergilli are biosynthetically 'talented' micro-organisms and therefore the natural products community has continually been interested in the wealth of biosynthetic gene clusters (BGCs) encoding numerous secondary metabolites related to these fungi. With the rapid increase in sequenced fungal genomes combined with the continuous development of bioinformatics tools such as antiSMASH, linking new structures to unknown BGCs has become much easier when taking retro-biosynthetic considerations into account. On the other hand, in most cases it is not as straightforward to prove proposed biosynthetic pathways due to the lack of implemented genetic tools in a given fungal species. As a result, very few secondary metabolite biosynthetic pathways have been characterized even amongst some of the most well studied Aspergillus spp., section Nigri (black aspergilli). This review will cover all known biosynthetic compound families and their structural diversity known from black aspergilli. We have logically divided this into sub-sections describing major biosynthetic classes (polyketides, non-ribosomal peptides, terpenoids, meroterpenoids and hybrid biosynthesis). Importantly, we will focus the review on metabolites which have been firmly linked to their corresponding BGCs.

Epidemiological characteristics and financial losses due to avian aspergillosis in households in the Almaty region, Republic of Kazakhstan

Aspergillosis is a severe fungal disease that affects all species and ages of poultry and leads to significant economic losses within the poultry industry. The economic significance of aspergillosis is associated with direct losses due to poultry mortality, a decline in the production of meat and eggs, feed conversion, and poor growth of recovering poultry. Although a decrease in the production of poultry meat and eggs in Kazakhstan due to this fungal disease has been widely reported, studies on the consequent financial losses on affected farms (households) have not been carried out. This study aimed to estimate the financial losses and epidemiological parameters of avian aspergillosis among households affected by the disease in the Almaty region. To achieve the objectives of the research, a survey was conducted involving affected households from February 2018 to July 2019. The affected poultry were diagnosed based on clinical, macroscopical, and microscopical procedures, and once the infection was confirmed, household owners were interviewed. Data were collected from 183 household owners. The median incidence risk and fatality rates were 39 and 26% in chickens, 42 and 22% in turkeys, and 37 and 33% in geese, respectively, with young poultry having a higher incidence risk and fatality rate than adults. Approximately 92.4% of the household owners treated the affected poultry using natural folk methods and 7.6% of household owners used antifungal drugs and antibiotics, spending a median of US $35.20 (min US $0; max US $400) per household throughout the course of the infection. Egg production was reduced by a median of 58.3% when households were affected. The price of poultry fell by a median of 48.6% immediately after recovery due to weight loss. The median of the overall financial losses of households was US $198.50 (min US $11; max US $1,269). The majority of household owners (65%) did not replace their poultry, 9.8% of household owners replaced all their poultry, and the remaining 25.1% replaced only a proportion of the poultry lost at the time of the study. Newly acquired poultry were purchased from neighbors (10.9%), fellow villagers (50%), and state poultry farms (39.1%). This study demonstrates that aspergillosis has an immediate impact on subsistence household owners' livelihoods in the Almaty region of Kazakhstan.

Development of a Specific Nested PCR Assay for the Detection of 16SrI Group Phytoplasmas Associated with Sisal Purple Leafroll Disease in Sisal Plants and Mealybugs

Sisal purple leafroll disease (SPLD) is currently the most destructive disease affecting sisal in China, yet its aetiology remains unclear. In our previous research, it was verified to be associated with phytoplasmas, and nested PCR based on the 16S rRNA gene using universal primers R16mF2/R16mR1 followed by R16F2n/R16R2 was confirmed as the most effective molecular method for the detection of phytoplasmas associated with SPLD (SPLDaP). However, the method has a shortcoming of inaccuracy, for it could produce false positive results. To further manage the disease, accurate detection is needed. In this study, we developed a specific nested PCR assay using universal primers R16F2n/R16R2, followed by a set of primers designed on 16Sr gene sequences amplified from SPLDaP, nontarget bacteria from sisal plants, and other phytoplasma subgroups or groups. This established method is accurate, specific, and effective for detection of 16SrI group phytoplasma in sisal, and its sensitivity is up to 10 fg/μL of total DNA. It also minimized the false positive problem of nested PCR using universal primers R16mF2/R16mR1 followed by R16F2n/R16R2. This method was further used to verify the presence of phytoplasma in Dysmicoccusneobrevipes, and the results showed that D. neobrevipes could be infected by SPLDaP and thus could be a candidate for vector transmission assays.

Proximate composition and spatio-temporal heterogeneity of phytochemicals in Agave sisalana Perrine (sisal) adapted in different agro-ecological zones of Punjab, Pakistan

Exploring extractable phytochemicals from locally adapted sisal plant vegetation vary seasonally at different locations. This study elaborated proximate composition and phytochemical heterogeneity in sisal due to varying environmental conditions analyzed from five districts, i.e., Chakwal, Khushab, Rawalpindi, Faisalabad, and Layyah in Punjab, Pakistan. Extensive surveying and plant sampling across 2 years 2017-2018 and 2018-2019, during mid-spring, summer, autumn, and winter seasons were carried out for understanding the seasonal impact on sisal. The present study was designed in a randomized complete block design (RCBD) and analyzed considering seasonal, yearly, and locational impact. The spatial differences in phytochemicals concentration were strongly associated with environmental conditions prevailing in different seasons. Autumn season reflected saponins, tannins, and flavonoids in higher concentrations during 2018-2019 while steroids and terpenoids were higher during spring 2018-2019. Spatio-temporal variations in the proximate analysis were more apparent in different samples collected from different districts. Data recorded for the Khushab district and autumn season reflected the higher composition of a proximate analysis and phytochemical contents as compared to other seasons. Overall, the spatial differences in phytochemicals concentration were strongly associated with soils and environmental conditions prevailing in different seasons in selected districts.

The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses

Sisal is a common name for different plant varieties in the genus Agave (especially Agave sisalana) used for high-quality natural leaf fiber extraction. Despite the economic value of these plants, we still lack information about the diversity of viruses (virome) in non-tequilana species from the genus Agave. In this work, by associating RNA and DNA deep sequencing we were able to identify 25 putative viral species infecting A. sisalana, A. fourcroydes, and Agave hybrid 11648, including one strain of Cowpea Mild Mottle Virus (CPMMV) and 24 elements likely representing new viruses. Phylogenetic analysis indicated they belong to at least six viral families: Alphaflexiviridae, Betaflexiviridae, Botourmiaviridae, Closteroviridae, Partitiviridae, Virgaviridae, and three distinct unclassified groups. We observed higher viral taxa richness in roots when compared to leaves and stems. Furthermore, leaves and stems are very similar diversity-wise, with a lower number of taxa and dominance of a single viral species. Finally, approximately 50% of the identified viruses were found in all Agave organs investigated, which suggests that they likely produce a systemic infection. This is the first metatranscriptomics study focused on viral identification in species from the genus Agave. Despite having analyzed symptomless individuals, we identified several viruses supposedly infecting Agave species, including organ-specific and systemic species. Surprisingly, some of these putative viruses are probably infecting microorganisms composing the plant microbiota. Altogether, our results reinforce the importance of unbiased strategies for the identification and monitoring of viruses in plant species, including those with asymptomatic phenotypes.

Burkholderia perseverans sp. nov., a bacterium isolated from the Restinga ecosystem, is a producer of volatile and diffusible compounds that inhibit plant pathogens

Gram-negative, aerobic, rod-shaped, non-spore-forming, motile bacteria, designated CBAS 719 ^T, CBAS 732 and CBAS 720 were isolated from leaf litter samples, collected in Espírito Santo State, Brazil, in 2008. Sequences of the 16S rRNA, gyrB, lepA and recA genes showed that these strains grouped with Burkholderia plantarii LMG 9035 ^T, Burkholderia gladioli LMG 2216 ^T and Burkholderia glumae LMG 2196 ^T in a clade of phytopathogenic Burkholderia species. Digital DNA-DNA hybridization experiments and ANI analyses demonstrated that strain CBAS 719 ^T represents a novel species in this lineage that is very closely related with B. plantarii. The genome sequence of the type strain is 7.57 Mbp and its G + C content is 69.01 mol%. The absence of growth on TSA medium supplemented with 3% (w/v) NaCl, citrate assimilation, β-galactosidase (PNPG) activity, and of lipase C14 activity differentiated strain CBAS 719 ^T from B. plantarii LMG 9035 ^T, its nearest phylogenetic neighbor. Its predominant fatty acid components were C_16:0, C_18:1 ω7c, cyclo-C_17:0 and summed feature 3 (C_16:1 ω7c and/or C_15:0 iso 2-OH). Based on these genotypic and phenotypic characteristics, the strains CBAS 719 ^T, CBAS 732 and CBAS 720 are classified in a novel Burkholderia species, for which the name Burkholderia perseverans sp. nov. is proposed. The type strain is CBAS 719 ^T (= LMG 31557 ^T = INN12^T).

Molecular Diversity of Aspergilli in Two Iranian Hospitals

The Aspergillus species are main causative agents of various infections such as invasive aspergillosis (IA) in immunocompromised patients and these infections have high mortality rates. In this study, we provide insight in the species causing aspergillosis in Iran based on morphology and sequence data. Clinical (n = 117) and environmental isolates (n = 54) collected during 2010-2016 from University hospitals in Mashhad and Tehran (Iran) were identified both morphologically and molecularly using partial calmodulin (CaM) gene sequences. Clinical cases were identified based on EORTC/MSG criteria. Aspergillus flavus (n = 96, 55%) was the most prevalent species among the clinical and environmental isolates while A. fumigatus (n = 13, 7.5%) ranked fourth after A. tubingensis (n = 23, 13%) and A. welwitchiae (n = 18, 10%). Species such as A. tubingensis, A. welwitschiae, A. fumigatus, A. sydowii, A. neoniger and A. terreus were present in both clinical and environmental samples indicating the possible environmental source of infections. Interestingly, A. niger was isolated only once. Furthermore, 13 other rare and cryptic Aspergillus species were detected. Pulmonary and respiratory disorders (n = 33), followed by transplantation (n = 23), invasive fungal rhinosinusitis (n = 14), and haematological malignancies (n = 12) were major predisposing factors. According to EORTC/MSG criteria, there were 43 probable cases identified followed by 36 cases for each of proven and possible ones. Correct molecular identification will be useful for further epidemiological studies.

Different repartition of the cryptic species of black aspergilli according to the anatomical sites in human infections, in a French University hospital

Black aspergilli of the section Nigri are rarely differentiated at the species level when originating from human specimens. We wondered whether some cryptic species could be more frequently observed in some clinical entities. We analyzed the 198 black isolates consecutively collected from the external ear canal (EEC; n = 66), respiratory specimens (n = 99), and environment (n = 33). DNA was extracted and species identification was performed upon the partial calmodulin gene. We identified by decreasing frequency: Aspergillus welwitschiae (35.3%), Aspergillus tubingensis (34.3%), Aspergillus niger (17.2%), Aspergillus luchuensis (4%), Aspergillus aff. welwitschiae (3%), Aspergillus neoniger (2%), Aspergillus piperis (1.5%), Aspergillus japonicus (1.0%), Aspergillus vadensis (0.5%), and two Aspergillus tubingensis clade (1%). The distribution of the three main cryptic species was different between EEC and respiratory samples (P < 0.001) but not different between respiratory and environment samples (P = 0.264). Aspergillus welwitschiae was more often associated with EEC (54.5%), whereas A. tubingensis and A. niger were predominant in respiratory samples (39.4 and 26.3%, respectively). Among the 99 respiratory isolates, only 10 were deemed responsible for probable invasive aspergillosis, of which six were mixed with other pathogenic moulds. This study shows the interest to pursue the identification of clinical isolates in the Aspergillus section Nigri to unravel some specific associations with clinical entities. The association of A. welwitschiae with otomycosis suggests a better fitness to infect/colonize the ear canal. Also, members of the Aspergillus section Nigri alone are rarely responsible for invasive aspergillosis.

LAY SUMMARY

We analyzed 198 black aspergilli isolates collected from different samples type to determine their species identification. We observe a different distribution of species between ear canal and respiratory samples (P < 0.001), suggesting a better fitness of A. welwitschiae to infect the ear canal.

Black aspergilli in Brazilian onions: From field to market

The occurrence of black aspergilli in onions has been reported as frequent, and this group of fungi harbors potentially toxigenic species. In addition, Aspergillus niger has been reported as the causative agent of black mold rot, an important postharvest disease that causes damage throughout the world. Brazil stands out as one of the world's largest onion producers. However, few studies have been conducted to investigate the mycobiota in Brazilian onions. For this reason, we investigated the mycobiota of 48 market (n = 25) and field (n = 23) onion bulb samples. Nineteen soil samples were collected from the same fields and evaluated. In field onions and soil samples, Penicillium spp. was the prevalent fungal group, whereas in market samples A. section Nigri was the most frequent group. Due to the taxonomic complexity of this group, species identification was supported by phylogenetic data (CaM gene). A. welwitschiae was the most prevalent species in market samples. Black aspergillus strains were evaluated for fumonisin B₂ (FB₂) and ochratoxin A (OTA) production. Overall, 53% and 2.2% of the strains produced FB₂ and OTA, respectively. The occurrence of FB₂ and OTA was also investigated in onion bulb samples but none showed contamination with these mycotoxins.

Calm Before the Storm: A Glimpse into the Secondary Metabolism of Aspergillus welwitschiae, the Etiologic Agent of the Sisal Bole Rot

Aspergillus welwitschiae is a species of the Nigri section of the genus Aspergillus. In nature, it is usually a saprotroph, decomposing plant material. However, it causes the bole rot disease of Agave sisalana (sisal), a plant species used for the extraction of hard natural fibers, causing great economic loss to this culture. In this study, we isolated and sequenced one genome of A. welwitschiae (isolate CCMB 674 (Collection of Cultures of Microorganisms of Bahia)) from the stem tissues of sisal and performed in silico and wet lab experimental strategies to describe its ability to produce mycotoxins. CCMB 674 possesses 64 secondary metabolite gene clusters (SMGCs) and, under normal conditions, it produces secondary metabolism compounds that could disturb the cellular cycle of sisal or induce abnormalities in plant growth, such as malformin C. This isolate also produces a pigment that might explain the characteristic red color of the affected tissues. Additionally, this isolate is defective for the production of fumonisin B1, and, despite bearing the full cluster for the synthesis of this compound, it did not produce ochratoxin A. Altogether, these results provide new information on possible strategies used by the fungi during the sisal bole rot, helping to better understand this disease and how to control it.