Projects on going 2020

Microbial Ecology – Lake Cadagno

• Microbial populations dynamics in the chemocline of Lake Cadagno - During the last 25 years, the most modern techniques identification have been applied mainly in the fine-scale analysis of the sulfur bacteria living in the Lake Cadagno, and then also applied as a service at the LMA (identification and typing of environmental microorganisms). The dynamics of the bacterial populations, especially the phototrophic ones, is fundamental for the structure and the ecology of the lake, and every year complete physical (CTD), chemical (sulfur compound) and biological (bacterial count by flow cytometry and FISH) profiles are recorded.
• Bioconvection-mediated microbial ecophysiology in aquatic systems: Multi-scale dynamics in the chemocline of meromictic Lake Cadagno (BIOCAD) - In the permanently stratified waters of the Lake Cadagno, in Val Piora, lives a population of bacteria that, thanks to their synchronized movement, can cause the mixing of large volumes of water (up to 1m). This phenomenon is known as bioconvection and has never been studied in a natural environment before. The motile large-celled PSB Chromatium okenii can mix considerable volumes of water, not shaking it directly with their flagella but grouping in search of light in a small area near the front of oxygen diffusion. In this way, the density per volume increases and the water begins to fall, taking the microorganisms with it. The main objective of the BIOCAD project, funded by the Swiss National Research Fund (http://p3.snf.ch/project-179264), is to study the effects of the bioconvection process on the eco-physiology of key microbial species in anaerobic aquatic environments. At the end of this project we can lay the foundations for understanding the consequences of bioconvection on the entire ecosystem of Lake Cadagno and use it as a model for describing similar phenomena in other environments.
• Sequencing of new genomes isolated from the meromictic Lake Cadagno - Genetic knowledge is necessary to better understand its specific role of each microorganism in the ecosystem of Lake Cadagno or more generally in general ecological processes. The project is carried out in collaboration with the Biology Division of the Spiez Laboratory of the Federal Office for Civil Protection, the Zürich University of Applied Science and Mabritec AG (Riehnen).

Resistance to antibiotics in the environment

• Presence of antibiotic resistance genes and bacteria in Lake Lugano and some tributary rivers - From January 2016 a project is underway to assess, through the monitoring of the presence of resistance genes and bacteria resistant to antibiotics, the anthropogenic impact in Lake Ceresio and in some rivers. The genes investigated are the same that are identified in the clinic and that confer resistance to the antibiotics most used in human and veterinary medicine. The isolated bacteria are mainly environmental but they can also play a role in the clinic both as pathogens and as "vectors" of resistance genes. This project fits perfectly into the One-Helath concept of the fight against antibiotic resistance allowing to better understand the role of the environment in the spread of resistance.

  Results could be consulted, as annual report, on the CIPAIS website.

Ecology and biodiversity of aquatic fungi

• Diversity of aquatic ifomycetes in various environments of the Bolle di Magadino - The Bolle di Magadino is a protected area of international importance at the mouth of the river Ticino at Lake Maggiore. The area is covered mainly by forest and comprises various types of aquatic ecosystems. Aquatic hyphomycetes carry out the degradation of dry leaves in these ecosystems, but their activity and diversity depends on differences in abiotic conditions between water bodies, for example their hydrological connectivity. With this project in collaboration with the Fondazione Bolle di Magadino we assess the diversity and activity of aquatic hyphoomycetes in various aquatic ecosystems and cultivate and characterize strains of dominant species. 

Conservation and restoration

• Optimisation of the procedure for the characterisation and fine-tuning of the targeted treatment of biodeteriogens in the field of cultural heritage conservation - This is an activity in close collaboration with the degree course in conservation and restoration. The collaboration between the teachers/researchers active in the degree course and the scientific experts of the Applied Microbiology Laboratory has represented an excellent opportunity for professional growth and synergistic development. In addition, this collaboration represents a great added value for students who have the opportunity to have specialist and multidisciplinary skills at their disposal. Nowadays, even for problems of limited resources, we tend to do a biocide treatment in an empirical way without the support of theoretical and scientific knowledge with chemicals unsafe for the environment and for the professional who has to apply it. Cleaning operations are often carried out mechanically at the expense of the stone. The objective of this activity has been the characterization of the different species of microorganisms present in some case studies (Monumental Cemetery of Lugano, Sacred Mount of Varallo and Sacred Mount of Orta, Church of Santa Maria dal Sasso in Morcote and Convent of Santa Maria dei Fratti Cappuccini in Bigorio), the development of a biocidal treatment (with canonical and innovative products) for each monument in the study, and the monitoring of the effectiveness of the intervention over time.
• Biodeterioration, conservation and restoration of works of art - Biodeteriogenic agents such as bacteria, algae, fungi and moulds are frequently the cause of chromatic alterations, flaps and discolorations of colored surfaces, monuments, sculptures, etc. The conservation of cultural heritage often has to do with the need to characterize these microorganisms to address the treatment in a targeted and if possible environmentally sustainable way. As part of this project, the procedures for characterization and fine-tuning of targeted treatments of different groups of biodetergens are being optimized.
• Characterization and identification of protein binders by mass spectrometry - Based on various historical documents we are aware of the use, since the Middle Ages, of different types of protein binders used on canvases, on boards and on walls. Knowledge of the type of binders used is extremely important for the correct maintenance and restoration of works of art. The characterization and identification of the protein binders used can be acquired through the use of mass spectrometry (MALDI-TOF MS). Preliminary analyses of undegraded pure protein binders have given very promising results that suggest a valid method for the evaluation of protein pictorial binders and be a valuable aid to the conservative restorer. Marta Cicardi has successfully completed her bachelor thesis "Investigation into the phenomena of biodeterioration of the mural paintings of chapel XI at the Sacred Mount of Varallo. Identification, characterization and development factors" and began the master thesis "Monitoring and maintenance in the case of endolytic microorganisms in limestone". 

Environmental microbiology in general

• Occurrence of microplastic pollution on the shores of Lake Lugano – Like other lakes in Switzerland and elsewhere, Lake Lugano receives high quantities of plastic particles. Estimates from surface samples have shown rather high concentrations compared to other Swiss lakes. However, the quantity on the shores remains unknown. In a study in collaboration with CIPAIS and University of Geneva, researchers from LMA quantify and characterize microplastic particles in different segments of the shoreline and correlate these estimates with environmental conditions, such as sediment grain size, distance to important tributaries, wind exposure, etc.
• Catch basins as a possible reservoir of Legionella pneumophila and risk assessment of exposure - In collaboration with the National Reference Centre for Legionella, a project funded by the Lega Pulmonare is underway, which aims to assess whether catch basins can be considered a reservoir of Legionella pneumophila and thus constitute a possible source of contamination and community dissemination. L. pneumophila is the main causative agent of a pulmonary disease commonly called legionnaires' disease that can have a severe course especially in immunocompromised patients. The contamination occurs by inhalation of aerosols so the main sources of contamination can be cooling towers, air conditioning systems, showers, taps, compost, etc. ... Community cases of legionnaires' disease are difficult to trace back to a specific source of contamination, which is also due to the difficulty of isolating virulent strains from the environment. For this reason, this study also plans to test a rapid and specific kit (Legiolert, IDDEX) for the identification of L. pneumophila in drinking water and other water samples.

• INTERREG, EcoAlps Water - The project "Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers (Eco-AlpsWater)", funded under the European programme INTERREG-Alpine Space, focuses in particular on the transnational harmonization of microbiological approaches for the study of water ecosystems. The project involves different European partners (Italy, France, Germany, Slovenia and Austria) and is leading by the Edmund Mach Foundation (S. Michele Alto Adige). Within this project, started in 2019, LMA collaborates with the Institute of Earth Sciences (SUPSI) and as laboratory, we will focus on sample acquisition and processing in view of the analyses that will be established and coordinated among all project partners.

• Metagenomics of the water source rich in heavy metals located in Val Camadra in the Greina region - Following the purchase of a MinION sequencer (Oxford Nanopore) and the development of the related bioinformatics analyses, it was possible to obtain the complete genome of three bacteria in pure culture and a metagenomic analysis of a cyanobacteria biofilm present in a water source loaded with heavy metals located in Val Camadra in the Greina region was carried out. This ecosystem seems to be unique and is extremely interesting as a model for the study of microorganisms resistant to metals. It is well known that cyanobacteria implement defense strategies to seize toxic metals for cells, these mechanisms as well as being interesting from a cognitive point of view can provide biotechnological solutions to the problem of elimination of heavy metals in the environment.
• Experimentation of new technology for pest control - in scientific collaboration with Agroscope, WSL and University of Naples - Dr. Stefano Mazzoleni, and his research group at the University of Naples, have highlighted a self-inhibiting phenomenon due to the DNA of the plant on the germination and root growth of its seeds. The auto-inhibiting effect occurs both in decomposed plant materials in which the DNA of a plant is mixed with microbial DNA produced during the process of decomposition of the same plant material, and using purified DNA following extractions from leaves. The field trials using Cyperus esculentus are conducted by Agroscope and WSL at their new facility in Cadenazzo. The fundamental concept of this experiment is the production of large quantities of plant DNA (C. esculentus) through BAC library (Bacterial Artificial Chromosome) cultivating in the laboratory the microorganism vector Escherichia coli. The BAC library contains the total genome of the plant in fragments of about 110 kbp on average. The same genome is randomly distributed in thousands of separate strains of E. coli, which have been mixed together in a single culture broth (LB medium with chloramphenicol antibiotic 12.5 mg/l) to ensure the greatest possible genetic variability for C. esculentus. The task of LMA-SUPSI is to produce and pre-treat the microorganism containing the BAC library of C. esculentus.
• Enterobactriaceae determination from rhizosphere of desert plants - In 2018, the LMA was contacted by the King Abdullah University of Science and Technology (Dr. Maged Saad, Saudi Arabia). A collaboration has begun for the determination of bacterial strains of the family Enterobacteriaceae. Project title: "MALDI-TOF MS analysis of potential plant growth-promoting bacteria, isolated from different arid regions". The analyses were completed in 2018 and a full report was prepared and sent in early 2019. The results are expected to be published in a scientific article.
• Molds in buildings (indoor molds): study of fungal populations in various inhabited environments and their variations according to the seasons - Molds present in buildings, indicated as indoor molds, are considered one of the main causes of asthma and other respiratory diseases, generating high costs on public health. Their growth is linked to the humidity present in the built environments. In fact, depending on the amount of water available, different groups of molds can develop inside the houses. Other factors that contribute to determining the population of molds in built environments are the materials and technologies used for their construction as well as the climatic conditions to which they are subjected. The contact between human and indoor mold occurs mainly through breathing. The presence of mold leads to the formation of bioaerosols complexes composed of spores, fragments of hyphae and volatile organic compounds that spread in the air.
  The present project aims to carry out a pilot study to determine fungal populations in built and inhabited areas in the southern Alps. It will be conducted on three types of housing: i) one with problems of humidity and visible presence of molds; ii) one without visible problems; iii) a "Minergie" type house, with a controlled ventilation system. Four samples of air / dust will be carried out over the course of a year (one per season), each including: i) two months dust sampling on the ground, taking into account the angles where molds develop easily; iii) sampling by smears on areas with visible mold growth. Temperature and moisture will be monitored during the samplings. For the identification of the different populations at the genus and species levels, the next generation sequencer Illumina iSeq will be used, followed by a bioinformatic analysis for the study of populations.
  The project started in 2019 with several preliminary tests. The four samplings will be performed between October 2019 and and August 2020.
•  Influence of environmental and physiological factors on the micobioma of traditional Ticino cheeses - Traditional Ticino semi-hard cheeses are distinguished by the presence of mold (mainly filamentous fungi) on their surface, which give them a characteristic appearance. The function of these molds during the ripening process is not entirely clear, but it is believed that they can contribute to the development of particular aromas and to modify the consistency of the pasta thanks to the production of lipolytic and proteolytic enzymes. The biodiversity of molds of some soft cheeses such as Brie, Camembert and Roquefort has been studied by various authors, but very little is known about the molds of traditional Ticino cheeses: preliminary work (L. Petrini and O. Petrini , unpublished) have shown the presence of a limited number, about ten, of species of filamentous ascomycetes that are constantly found.
  This project aims to analyze the mycoboma (fungal species) present on the traditional Ticino cheese crust. The pilot study proposes to analyze mountain pastures, with cow's milk and mixed (goat's and cow's milk) semi-hard cheeses, to determine the mycobioma of cheese. For each mountain pasture we propose to analyze 2 forms of cheese.
  The mycobioma will be studied using: i) Classical methods, with direct culture of molds, followed by identification based on morphology; ii) Molecular methods based on the sequencing of specific DNA regions for the identification of molds not recognized by classical and proteomic methods; iii) Proteomic methods based on MALDI-TOF mass spectrometry, which allows the rapid identification of organisms after comparison of their protein profiles with an existing database.; iv) Metabarcoding (next generation sequencing, iSeq Illumina) that allows the determination of all fungal populations present in a single sample.
  The samplings have been performed during summer and late summer 2019. The analysis will continue until 2020.