Projects
Name
(Antofagasta) Fungal diversity in the Atacama desert of Chile: high potential sources for new species able to produce secondary metabolitest
University
Universidad de Antofagasta
Domain
Microbiology
Departement
Microbiology Unit, Medical Technology Department, Faculty of Health Science, University of Antofagasta, Antofagasta, Chile; Avda. Universidad de Antofagasta #02800
Head
Nicomedes Valenzuela Lopez PhD
Tutor
Nicomedes Valenzuela Lopez PhD
Languages
English, Spanish
Duration
4 weeks
Availability
Cities/Months Jan Feb Mar Apr May Jun Jul Augt Sep Oct Nov Dec
No No No No No No Yes No No No No No
Type of Research Project
- Basic science
What is the background of the project?
The second region of Chile is considered one of the driest areas in the world, which has a large number of diverse ecosystems, with a great diversity of microorganisms that have adapted to extreme living conditions. In last years, many investigations of the Atacama Desert has been focused due to its particular characteristic for extreme environmental conditions. However, the majority of these studies have been performed in bacterial or archaea communities, and few studies on Fungi have been conducted, providing scarce information on their identification and prevalence, as well as, their biotechnological utility. Therefore, the present project aims to contemplate a prospective and systematic study about the diversity of the Fungi kingdom, mainly in the ascomycetous fungi present in the Atacama Desert and its possible biotechnological applications. To comply with the proposal, we will take samples of different substrates (soil, sediment, plant material) and by isolating the fungal specimens by different methods of substrate treatment, these will be subsequently morphologically and by molecular techniques characterized. Secondly, will include the analysis of production of secondary metabolites. As expected results, new fungal species will be obtained for science and the possible biotechnological applications of their secondary metabolites.
What is the aim of the project?
To contemplate a prospective and systematic study about the diversity of the Fungi kingdom, mainly in the ascomycetous fungi present in the Atacama Desert and its possible biotechnological applications
What techniques and methods are used?
To isolate fungal specimens from environmental samples will be collected approximately 10gr of soil in individual plastic bags and will be processed in a maximum period of three days after the collection. Once in the laboratory, each of them will be prepared in serial dilutions according to Stchigel (2000), slightly modified. To identify the isolates by traditional techniques in culture media, using books of Fungi regarding their morphological characteristic, and by molecular methods such as PCR (polymerase chain reaction), amplifying phylogenetic markers as ITS and LSU and sequencing them. The culture media applied for the primary isolation (this means that allow the isolation of different kind of fungi) are as follow: potato dextrose agar (PDA, 20g potato, 20g dextrose, 20g agar, 1L distilled water), carrot potato agar (PCA, 20g of potato, 20g of carrot, 20g of agar, 1 liter of distilled water), both supplemented with chloramphenicol (200 mg / L) to prevent bacterial growth and agar Dichloran Rose Bengal Chlortetracycline (DRBC, 5 g peptone, 10 g glucose, 1 g dihydrogen phosphate potassium [KH2PO4], 0.5 g of magnesium sulfate [MgSO4], 25 mg of rose bengal, 2 mg of dichloran, 200 mg of chloramphenicol, 20 g of agar, 1000 ml of distilled water). The morphological and molecular characterization of the results will be carried out by observing fructification structures using diverse mycological atlases (de Hoog et al. 2001; Guarro et al. 2012) and by amplifying and sequencing the phylogenetic markers of rRNA (LSU and ITS) following the methodology of Valenzuela-López et al. (2017). Once the isolates are grouped at the taxonomic level, they will be derived to the amplification and sequencing of other phylogenetic markers such as: tub2, tef1, rpb2, etc. (Valenzuela-Lopez et al. 2018) To determine the phylogenetic relationships of the species identified by multi-locus sequence analysis, employing different computational softwares. The phylogenetic reconstructions and alignments will be performed using Maximum likelihood (ML) and Bayesian (BI) inference analysis methods, using the MEGA v6.0 program (Tamura et al. 2013) and MrBayes version 3.1.2. (Huelsenbeck & Ronquist 2001), as well as, other platform such as CIPRES Science Gateway (Miller et al. 2012).
What is the role of the student?
- The tasks of the student will be performed on his/her own
- The tasks will be done under supervision
What are the tasks expected to be accomplished by the student?
The student will learn about the preparation of culture media used for fungal isolation as well as their morphological identification. He or She will have to learn how to prepare slides for microscopic observation. In addition, he will learn on molecular biology performing extraction of DNA and amplifying phylogenetic markers by PCR, sequencing the PCR product and verifying it in the computational programs of sequences edition and how to prepare alignments in order to obtain the phylogenetic reconstruction.
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
Theoretical teaching will be held by the tutor explaining basic procedures of microbiology lab, fungi theorics, biosafety procedures, and molecular biology. In addition, the student should prepare a seminar in a meeting.
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
- The student will prepare a poster
- The student will prepare a scientific report
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
Knowledge in Biology, Microbiology. Biosafety, and use of the basic procedure of laboratory
Are there any legal limitations in the student’s involvement
No
Hours
7
Type of students accepted
This project accepts:
- Medical students
- Students in biomedical fields
Articles
- Martin-Gomez;T. ; Valenzuela; N.Knufia epidermidis: a rare finding in a paediatric dermatological sample.European Society of Clinical Microbiology and Infectious Diseases January 2019 Volume 25; Issue 1; Pages 65–66
- Valenzuela; N.; Cano; J. Neocucurbitaria keratinophila: An emerging opportunistic fungus causing superficial mycosis in Spain. Med Mycol. 2018 Nov 29