Soil Fungi: Methods for Assessing Biodiversity and Functions

TOPICAL COLLECTIONS

Guest Editors

Lidia Nicola

University of Pavia, Environmental Mycology laboratory

Dr. Lidia Nicola is a post-doctoral researcher in the Environmental Mycology laboratory and a contract lecturer in mycology at the University of Pavia, Italy. She obtained her PhD in Biology at Innsbruck University, Austria, in collaboration with the Edmund Mach Agronomical Research Centre, and her project involved discovering the hidden soil microbial diversity under the long-standing problem of Apple Replant Disease, to find eco-friendly solutions for the growers. Her PhD thesis won the Caretta Prize for Environmental and Applied Mycology. Currently, her research is focused on mycology, with two different research lines, the first about the soil fungal biodiversity, the second about the potential of fungi as agents of bioremediation against hydrocarbons and plastics. She has presented her research at several international conferences around the world.

Claudia Maria Oliveira Longa

Fondazione Edmund Mach, Sustainable Ecosystems and Bioresources Department, Plant Pathology and Applied Microbiology Unity

Dr. Claudia Maria Oliveira Longa is a researcher in the Plant Pathology and Applied Microbiology Unity of the Sustainable Ecosystems and Bioresources Department at the Fondazione Edmund Mach, Italy. She obtained her PhD in Ecology with a project on the risk assessment of biological control at the University of Pavia, Italy. Her interests are focused on plant- and soil-associated microbiome and translation of the results into new biotechnological concepts to predict the risk of emerging or invasive pathogens and to discover innovative methods for disease control. She has experience in the setup and execution of metabarcoding analyses of microbial communities. She has long-standing expertise in not only the different aspects of fungal biology including biodiversity and ecology but also in the biological control of plant pathogens. She is a co-inventor of a patented bio fungicide (US8431120B2, Trichoderma atroviride SC1 for biocontrol of fungal diseases in plants).

Collection Overview

Soil hosts an incredible diversity and abundance of fungi. In fact, it is estimated that 1 g of soil contains up to 100,000–1,000,000 fungal cells. From rhizosphere to bulk soil, from tropical to alpine soil, from desert sand to ice-free polar areas, soil fungi represent one of the most diverse assemblages of organisms on Earth. They inhabit a wide range of ecological niches and are responsible for many important ecological functions, such as influencing carbon sequestration through plant life, and carbon, nitrogen, and sulfur mineralization. Indeed, the study of soil fungi is vital for the management of the agroenvironment and the conservation of natural ecosystems. This Methods Collection aims to bring together a wide range of techniques used to study the biodiversity of soil fungi and their functions. The methods can be classified into two broad categories: classical methods and advanced technologies. Examples of the first category are isolation (counting of colony-forming units, moist chamber, selective/semi selective agars), morphological identification of the fungal strains (dyestuffs and special preparation techniques, slide mounting, and microscopy approaches as the electron, light, and fluorescence microscopy), fungal physiology (respiration rates and enzymatic assays). The second includes all nucleic acid sequencing and omics technologies such as metabarcoding, shotgun metagenomics, proteomics, meta-transcriptomics, stable isotope analyses, etc.