Pietro Buzzini

Microorganisms, microbiomes, and their products (e.g., enzymes, metabolites, antibiotics, etc.) are key players in the functioning of both natural and anthropized Earth ecosystems; they can be exploited for both research purposes and biotechnological applications, including fighting the big challenges of our era, such as climate change. Culture collections (CCs) and microbial Biological Resource Centres (mBRCs) are repositories of microorganisms that investigate and safeguard biodiversity and facilitate the scientific and industrial communities’ access to microbial strains and related know-how by providing external users with skills and services. Considering this, CCs and mBRCs are pivotal institutions for the valorisation of microorganisms, the safeguarding of life, and the fostering of excellent bioscience. The aim of this review is to present the state-of-the-art of Italian CCs and mBRCs, highlighting strengths, weaknesses, threats, and opportunities. Italy is, indeed, a hotspot of microbial biodiversity with a high rate of endemism and incredible potential, not only for the food and beverage sector (i.e., “Made in Italy” products), where microorganisms can have a beneficial or a spoiling function, but also to guarantee environmental sustainability and foster the bioeconomy through the design of new bioprocesses and products. However, weaknesses, such as the lack of management rules in accordance with international quality standards, are also analysed and ways of overcoming them are discussed. In this context, an overview is given of the Joint Research Unit MIRRI-IT and the European-funded SUS-MIRRI.IT project, which aims to improve the management and sustainability of Italian microbial collections, and serves as a starting point for an innovative revolution in the context of CCs and mBRCs worldwide.

Here, we explore the possible ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria). While ancient DNA (aDNA) has been extensively used to study human, animal, and plant evolution, this research focuses on ancient microbial diversity, specifically fungi. Fungal DNA is often underestimated in metagenomic samples, however here we hypothesise the possibility of retrieving ancient fungal sequences from Ötzi’s gut. A robust bioinformatic pipeline has been developed to detect and authenticate fungal aDNA from stomach, small intestine, and large intestine samples. We revealed the presence of Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, that were particularly abundant in the stomach and small intestine. We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they thrived in his gut after his death due to their adaptability to harsh and cold environments. This research provides insight into the coexistence of ancient humans with specific fungal species and proposes and validates a conservative bioinformatic approach for detecting fungal aDNA in historical metagenomic samples. Significance statement: Despite their essential interactions with all kingdoms of life, limited molecular studies have focused on ancient fungi. Here, we developed a thorough bioinformatic pipeline that allowed us to detect the presence of ancient DNA likely belonging to Pseudogymnoascus destructans and P. verrucosus in the gut of Ötzi, a human naturally mummified over 3,000 years ago in the Tyrolean Alps. Both species can survive harsh environmental conditions, and P. destructans is known for its pathogenicity, suggesting that Ötzi may have accidentally ingested them and providing valuable insights into how ancient humans coexisted with specific fungal species. We propose a highly reliable methodology for detecting ancient fungal DNA in metagenomic studies of historical samples that can have broader applications to understand ancient ecosystems and their interactions.

The concept of fastidious microorganisms currently found in scientific literature is mainly related to the difficulty of isolating/culturing/preserving bacteria. Eukaryotes are investigated much less in this respect, although they represent a fundamental part of the microbial world. Furthermore, not only isolation, but also identification and culturing (in the perspective of long-term preservation) should be considered key aspects often impacting on the study of fastidious microorganisms, especially in terms of preservation in culture collections and biotechnological exploitation. The present review aimed to investigate the current state of the art on fastidious eukaryotes, with special emphasis on the efforts to improve their isolation, identification, culturing and long-term preservation in culture collections practices. A few case studies focused on some fastidious eukaryotic microorganisms (including possible customized solutions to overcome specific issues) are also presented: isolation and preservation of slow-growing fungi, culturing of Haematococcus lacustris, isolation of unialgal strains of Cyanidiophytina (Rhodophyta), identification of Metschnikowia pulcherrima clade yeasts, isolation and preservation of Pyricularia species, preservation of Halophytophtora spp.