Integrated Phenotypic and Genome‐Informed Characterization of Environmental Aspergillus Isolates With Potential for Citric Acid Production

Aspergillus species are widely used in industrial biotechnology, particularly for citric acid production. This study characterized environmental Aspergillus isolates from Côte d'Ivoire with potential for citric acid production using an integrated phenotypic and genome-informed approach. Isolates recovered from banana rhizosphere soil and decomposing fruits and vegetables were screened for aflatoxin-associated reactions using the ammonia vapor assay and for acidification on bromocresol green-supplemented Czapek-Dox agar. Selected isolates were analyzed by whole-genome sequencing, Kaiju taxonomic profiling, and EggNOG-mapper functional annotation. Citric acid production was quantified under solid-state fermentation using a calibrated colorimetric assay. Among 110 fungal isolates recovered, 24 Aspergillus isolates were grouped into seven morphotypes. Four isolates (E1-E4) showed acidification activity and no detectable aflatoxin-associated reaction under the assay conditions. Morphological and whole-genome taxonomic analyses conservatively affiliated E1-E3 with the Aspergillus niger species complex, whereas E4 remained taxonomically unresolved. E2 showed the highest proportion of reads assigned to A. niger reference sequences (92%) and the greatest representation of predicted functions associated with citrate metabolism and carbohydrate degradation. During solid-state fermentation, E2 exhibited the highest measured citric acid concentration under the tested conditions. Comparative genomic analyses also showed greater similarity among E1-E3 than with E4. Overall, E2 emerged as the most promising candidate for further citric acid production studies, supporting the value of combining quantitative phenotypic assessment with genome-informed characterization of environmental fungal isolates.