João Trovão

Saxispiralis lemnorum MUM 23.14 is an extremotolerant microcolonial black fungus, originally isolated from a biodeteriorated limestone artwork in Portugal. This recently introduced species belongs to the Aeminiaceae family, representing the second member of this monophyletic clade. This fungus exhibits a unique set of characteristics, including xerophily, cold tolerance, high UV radiation tolerance, and an exceptional ability to thrive in NaCl concentrations of up to 30% while also enduring pH levels ranging from 5 to 11. To gain insights into its genomic traits associated with stress resistance mechanisms, specialization, and their potential implications in stone biodeterioration, we conducted a comprehensive genome sequencing and analysis. This draft genome not only marks the first for the Saxispiralis genus but also the second for the Aeminiaceae family. Furthermore, we performed two comparative genomic analyses: one focusing on the closest relative within the Aeminiaceae family, Aeminium ludgeri, and another encompassing the genome of different extremotolerant black fungi. In this study, we successfully achieved high genome completeness for S. lemnorum and confirmed its close phylogenetic relationship to A. ludgeri. Our findings revealed traits contributing to its extremophilic nature and provided insights into potential mechanisms contributing to stone biodeterioration. Many traits are common to both Aeminiaceae species and are shared with other black fungi, while numerous unique traits may be attributed to species-specific characteristics.

Microbial communities are known to contribute deeply to geochemical cycles, including weathering, protection from erosion and mineral precipitation. Studies aiming to understand mining areas’ microbiomes are of high relevance since they can help pinpoint the occurrence of environmental shifts, key bioremediation species, environmental metals recovery strategies, and microorganisms with relevant industrial properties. Nonetheless, so far, the study of Portuguese gold-rich areas’ microbiomes has been largely neglected. The main goal of this study was to apply high-throughput sequencing methods to study the microbiome (Bacteria and Fungi) and predict their functional/metabolic profiles in an abandoned Portuguese gold mining area (considering zones without a history of mining, the tailings and the flooded mine interior). The results obtained revealed high bacterial and fungal diversities at these sites while also pinpointing the presence of relative homogenous bacterial and heterogenous fungal communities. Areas without mining history were mainly dominated by WD2101 soil groups, Sphingomonas, Candidatus Solibacter, Helotiales, unclassified Fungi and Arxotrichum. The tailings were mainly colonized by Bryobacter, WD2101 soil groups, WPS-2 genera, Starmerella, Helotiales and Mollisia. On the other hand, the mine area displayed a dominance of Crossiella, Gemmataceae, Acidobacteriaceae (Subgroup 1), Acidiphilium, Mortierella, unclassified Fungi and Chaetothyriales. Furthermore, we verified that contrary to bacteria, the fungal structural diversity is somewhat more restricted to each site. In addition, metabolic, functional and ecological profiles revealed a strong distinction for both bacterial and fungal communities while also revealing the presence of well-adapted communities to each of the particular microenvironments considered.

In Portugal, the Cova da Beira region is well-known for the production of Prunus spp. and is considered the main peach production area in the country. In the spring of 2021 and 2022, field surveys in peach and nectarine orchards showed symptoms of decline such as cankers, gummosis, dry branches, abortion of flowers, mummified fruits and the partial or total death of some plants. Brown rot is caused by three species of the genus Monilinia, M. fructigena, M. laxa and M. fructicola, the last is an OEPP/EPPO A2 quarantine organism on peach trees. Brown rot disease had previously been described in the Cova da Beira region, however, the recent high mortality and severity of symptoms raised doubts as to the species involved. Symptomatic plant material was collected from thirteen orchards and used for fungal isolation and molecular detection according to the OEPP/EPPO standard. M. fructicola was confirmed morphologically and molecularly in two orchards, and molecularly (duplex real-time PCR) detected in two others. Whole genome sequencing using Oxford Nanopore MinION was also carried out to confirm the identification. Pathogenicity tests were performed on peach, nectarine and sweet cherry fruit according to Koch’s postulates. Based on all the results obtained, we report the first detection of M. fructicola in P. persica in Portugal.