ORIGINAL RESEARCH published: 23 June 2021 doi: 10.3389/fmicb.2021.658010 Edited by: Saskia Bindschedler, Université de Neuchâtel, Switzerland Reviewed by: Fabio Palmieri, Université de Neuchâtel, Switzerland Martin Tegelaar, Utrecht University, Netherlands *Correspondence: Domenico Pangallo domenico.pangallo@savba.sk Specialty section: This article was submitted to Terrestrial Microbiology, a section of the journal Frontiers in Microbiology Received: 24 January 2021 Accepted: 20 May 2021 Published: 23 June 2021 Citation: Šimonovi ˇ cová A, Vojtková H, Nosalj S, Piecková E, Švehláková H, Kraková L, Drahovská H, Stalmachová B, Ku ˇ cová K and Pangallo D (2021) Aspergillus niger Environmental Isolates and Their Specific Diversity Through Metabolite Profiling. Front. Microbiol. 12:658010. doi: 10.3389/fmicb.2021.658010 Aspergillus niger Environmental Isolates and Their Specific Diversity Through Metabolite Profiling Alexandra Šimonovi ˇ cová 1 , Hana Vojtková 2 , Sanja Nosalj 1 , Elena Piecková 3 , Hana Švehláková 2 , Lucia Kraková 4 , Hana Drahovská 5 , Barbara Stalmachová 2 , Kateˇ rina Ku ˇ cová 2 and Domenico Pangallo 4 * 1 Department of Soil Science, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia, 2 Department of Environmental Engineering, Faculty of Mining and Geology, VSB – Technical University of Ostrava, Ostrava, Czechia, 3 Department of Microbiology, Slovak Medical University in Bratislava, Bratislava, Slovakia, 4 Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia, 5 Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia We present a biological profile of 16 Aspergillus niger environmental isolates from different types of soils and solid substrates across a pH range, from an ultra-acidic (<3.5) to a very strongly alkaline (>9.0) environment. The soils and solid substrates also differ in varying degrees of anthropic pollution, which in most cases is caused by several centuries of mining activity at old mining sites, sludge beds, ore deposits, stream sediments, and coal dust. The values of toxic elements (As, Sb, Zn, Cu, Pb) very often exceed the limit values. The isolates possess different macro- and micromorphological features. All the identifications of Aspergillus niger isolates were confirmed by molecular PCR analysis and their similarity was expressed by RAMP analysis. The biochemical profile of isolates based on FF-MicroPlate tests from the Biolog system showed identical biochemical reactions in 50 tests, while in 46 tests the utilisation reactions differed. The highest similarity of strains isolated from substrates with the same pH, as well as the most suitable biochemical tests for analysis of the phenotypic similarity of isolated strains, were confirmed when evaluating the biochemical profile using multicriterial analysis in the Canoco program. The isolates were screened for mycotoxin production by thin-layer chromatography (TLC), as well. Two of them were able to synthesise ochratoxin A, while none produced fumonisins under experimental conditions. Presence of toxic compounds in contaminated sites may affect environmental microscopic fungi and cause the genome alteration, which may result in changes of their physiology, including the production of different (secondary) metabolites, such as mycotoxins. Keywords: Aspergillus niger environmental isolates, molecular analyses, Biolog FF Microplate TM , multi-criteria data analysis, extrolite profile INTRODUCTION Aspergillus niger is a cosmopolitan representative of microscopic filamentous fungi. Although the main source of this strain is soil, it frequently occurs in various other sources, such as historical and archaeological objects (Abdel-Kareem, 2010; Pangallo et al., 2012; Aldosari et al., 2019; Geweely et al., 2019) or indoor environments (Egbuta et al., 2017; Omar et al., 2018). The ability of Aspergillus Frontiers in Microbiology | www.frontiersin.org 1 June 2021 | Volume 12 | Article 658010