Phylogeny of cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales) from Hawaii and New York reveals novel species within the Cercospora beticola complex

Integrating the Soil Microbiota and Metabolome Reveals the Mechanism through Which Controlled Release Fertilizer Affects Sugarcane Growth

Root-soil underground interactions mediated by soil microorganisms and metabolites are crucial for fertilizer utilization efficiency and crop growth regulation. This study employed a combined approach of soil microbial community profiling and non-targeted metabolomics to investigate the patterns of root-associated microbial aggregation and the mechanisms associated with metabolites under varying controlled-release fertilizer (CRF) application rates. The experimental treatments included five field application rates of CRF (D1: 675 kg/ha; D15: 1012.5 kg/ha; D2: 1350 kg/ha; D25: 1687.5 kg/ha; and D3: 2025 kg/ha) along with traditional fertilizer as a control (CK: 1687.5 kg/ha). The results indicated that the growth of sugarcane in the field was significantly influenced by the CRF application rate (p < 0.05). Compared with CK, the optimal field application of CRF was observed at D25, resulting in a 16.3% to 53.6% increase in sugarcane yield. Under the condition of reducing fertilizer application by 20%, D2 showed a 13.3% increase in stem yield and a 6.7% increase in sugar production. The bacterial ACE index exhibited significant differences between D25 and D1, while the Chao1 index showed significance among the D25, D1, and CK treatments. The dominant bacterial phyla in sugarcane rhizosphere aggregation included Proteobacteria, Actinobacteriota, and Acidobacteriota. Fungal phyla comprised Rozellomycota, Basidiomycota, and Ascomycota. The annotated metabolic pathways encompassed biosynthesis of secondary metabolites, carbohydrate metabolism, and lipid metabolism. Differential analysis and random forest selection identified distinctive biomarkers including Leotiomycetes, Cercospora, Anaeromyxobacter, isoleucyl-proline, and methylmalonic acid. Redundancy analysis unveiled soil pH, soil organic carbon, and available nitrogen as the primary drivers of microbial communities, while the metabolic profiles were notably influenced by the available potassium and phosphorus. The correlation heatmaps illustrated potential microbial-metabolite regulatory mechanisms under CRF application conditions. These findings underscore the significant potential of CRF in sugarcane field production, laying a theoretical foundation for sustainable development in the sugarcane industry.

Development of a Novel Diagnostic Tool for Cercospora Species Based on BOX-PCR System

The genus Cercospora contains many devastating plant pathogens linked to leaf spot diseases afflicting various plants. Identification of Cercospora species based on morphology or host plant association has proven unreliable due to simple morphology and wide host range in many cases; hence, multi-gene DNA sequence data are essential for accurate species identification. Considering the complexity and cost involved in application of multi-locus DNA phylogenetic approaches for species delineation in Cercospora; rapid and cost-effective methods are urgently needed for species recognition. In this study, we applied rep-PCR (repetitive-sequence based polymerase chain reaction) fingerprinting methods referred to as BOX-PCR to differentiate species of Cercospora. Cluster analysis of the banding patterns of 52 Cercospora strains indicated the ability of BOX-PCR technique using BOXA1R primer to generate species-specific DNA fingerprints from all the tested strains. Since this technique was able to discriminate between all the 20 examined Cercospora species during this study, which corresponded well to the species identified based on multi-gene DNA sequence data, our findings revealed the efficiency of BOX-PCR system as a suitable complementary method for molecular identification of the genus Cercospora at species level.

Publicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case in Colletotrichum

Publicly available and validated DNA reference sequences useful for phylogeny estimation and identification of fungal pathogens are an increasingly important resource in the efforts of plant protection organizations to facilitate safe international trade of agricultural commodities. Colletotrichum species are among the most frequently encountered and regulated plant pathogens at U.S. ports-of-entry. The RefSeq Targeted Loci (RTL) project at NCBI (BioProject no. PRJNA177353) contains a database of curated fungal internal transcribed spacer (ITS) sequences that interact extensively with NCBI Taxonomy, resulting in verified name-strain-sequence type associations for >12,000 species. We present a publicly available dataset of verified and curated name-type strain-sequence associations for all available Colletotrichum species. This includes an updated GenBank Taxonomy for 238 species associated with up to 11 protein coding loci and an updated RTL ITS dataset for 226 species. We demonstrate that several marker loci are well suited for phylogenetic inference and identification. We improve understanding of phylogenetic relationships among verified species, verify or improve phylogenetic circumscriptions of 14 species complexes, and reveal that determining relationships among these major clades will require additional data. We present detailed comparisons between phylogenetic and similarity-based approaches to species identification, revealing complex patterns among single marker loci that often lead to misidentification when based on single-locus similarity approaches. We also demonstrate that species-level identification is elusive for a subset of samples regardless of analytical approach, which may be explained by novel species diversity in our dataset and incomplete lineage sorting and lack of accumulated synapomorphies at these loci.

Unravelling unexplored diversity of cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales, Ascomycota) in tropical Africa

Cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales, Ascomycota) are one of the largest and most diverse groups of hyphomycetes causing a wide range of diseases of economically important plants as well as of plants in the wild. Although more than 6000 species are known for this group, the documentation of this fungal group is far from complete. Especially in the tropics, the diversity of cercosporoid fungi is poorly known. The present study aims to identify and characterise cercosporoid fungi collected on host plants belonging to Fabaceae in Benin, West Africa. Information on their morphology, host species and DNA sequence data (18S rDNA, 28S rDNA, ITS and tef1) is provided. DNA sequence data were obtained by a simple and non-culture-based method for DNA isolation which has been applied for cercosporoid fungi for the first time in the context of the present study. Among the loci used for the phylogenetic analysis, tef1 provided the best resolution together with the multigene dataset. Species delimitation in many cases, however, was only possible by combining molecular sequence data with morphological characteristics. Based on forty specimens recently collected in Benin, 18 species are presented with morphological descriptions, illustrations and sequence data. Among these, six species in the genus Cercospora and two species in Pseudocercospora are proposed as species new to science. The newly described species are Cercospora (C.) beninensis on Crotalariamacrocalyx, C.parakouensis on Desmodiumtortuosum, C.rhynchophora on Vignaunguiculata, C.vignae-subterraneae on Vignasubterranea, C.tentaculifera on Vignaunguiculata, C.zorniicola on Zorniaglochidiata, Pseudocercosporasennicola on Sennaoccidentalis and Pseudocercosporatabei on Vignaunguiculata. Eight species of cercosporoid fungi are reported for Benin for the first time, three of them, namely C.cf.canscorina, C.cf.fagopyri and C.phaseoli-lunati are new for West Africa. The presence of two species of cercosporoid fungi on Fabaceae previously reported from Benin, namely Nothopassalorapersonata and Passaloraarachidicola, is confirmed.