This is the report from a BSPP Junior Fellowship.
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Before we begin, we should ask ourselves an important question. What is biodiversity and how it can affect human health when it is disturbed? Biodiversity is the variety of life involving the ecosystems, species, populations, and genes. The soil microbiome is the richest component of terrestrial biodiversity and plays a crucial role in carbon and nitrogen cycling as well as soil formation. Soil is also a living dynamic system, and a “healthy soil” promotes a diverse soil microbiota directly contributing to plant growth and animal health. Fungi play essential role in terrestrial ecosystems, organising biodiversity and various ecosystem processes. Arbuscular mycorrhizal fungi (AMF) are the most important class of beneficial microorganisms in agri- and horticultural soils. AMF improve plant growth through the uptake of nutrients as well as protection against plant pathogens.
Human intervention is without doubt affecting the condition of the soil and further the fungi presence, number and resistance which have direct effect on public health through food chain. Mapping/screening fungal communities in soil is considered of utmost importance to understand the eco balances in specific areas and to elucidate how the human interventions could eventually disrupt the microorganism niche equilibrium. Under the umbrella of ONE HEALTH approach, we aim to investigate through this project the variations of fungal communities in different areas across Cyprus. Cyprus climate is ideal for this project and no other studies regarding soil fungal diversity have been conducted. The opportunity given to me by BSPP junior fellowship to work together with researchers at the European University Cyprus (EUC) and start this project came at the perfect timing where hot topics such as climate crisis, recession, food shortage and the increase of population are the main concern these days. The sampling areas were selected based on criteria such as elevation, high and low pollution, agriculture, and non-agriculture (Figure 1). One of the topics that we are most interested in, is the soil ‘’condition’’ in agricultural lands. Most particularly we aim to examine any changes occurred on soil fungal communities upon human intervention. Therefore, on August and December of 2022 we collected samples from agricultural lands that farmers use chemical pesticides and from agricultural lands that use of such chemicals has not occurred (organic agriculture). Furthermore, by the help of EUC faculty members we collected samples from all five districts in non-occupied Cyprus (Figure 1).
Figure 1 (TOP): Sampling locations. Colour coding was assigned based to district and location the samples were collected from
In brief, soil samples were collected from the first 15 – 20 cm belowground and introduced into a sterile plastic bag after removing roots and stones from the samples (Figure 2). Each sample bag was labelled appropriately by indicating the site of collection, time, date, and place (longitude and latitude). Samples were stored in aliquots at -800C prior to processing. One third of the samples will be used to determine the soil characteristics whereas the remaining will be stored and processed accordingly.
Figure 2: Sampling from Troodos Mountain
An important factor in advancing fungal ecology has been the extensive utilisation of culture-independent methods such next generation sequencing (NGS). Utilisation of the internal transcribed spacer (ITS) region from different fungal species significantly increased our understanding of the diversity and functioning of fungi in a range of environments. Furthermore, through NGS we can capture all species that cannot be cultivated in vitro. Currently, we already begun extracting DNA directly from soil samples and we are in the process of checking the quality of the genomic material before shipping it to our collaborators at the Imperial College London. The samples will be sequenced using Illumina MiSeq targeting the universal fungal barcode ITS. Parallel to NGS we are also cultivating the samples in vitro using two methods either by diluting the sample through serial dilutions or by plating a small amount of soil directly on agar (Figure 3).
Figure 3: In vitro cultivation of soil samples
To conclude, fungi are extremely heterogeneous organisms and are widespread in all environments. Research on fungal diversity cannot be considered exhaustive, given the continuous discovery of new species which can also lead to the discovery of new antibiotic agents, which are needed especially now with resistance and lack of options. Likewise, I strongly believe that this project might lead to the discovery of new species and also provide us with more information on how human interaction together with climate crisis threaten the natural diversity of soil fungi. Furthermore, devastating effects following disturbance of fungal communities will directly affect human health not only through food chain but also the quality of life (i.e increased antifungal resistance due to chemical pesticides, vector borne diseases due to climate change). I cannot thank BSPP enough for the support and understanding of certain issues arose during pandemic. Is important to point out that this fellowship was awarded before Covid-19 pandemic. Therefore, this project will not have been made possible if it was not for the initial support of the BSPP Junior fellowship. Thank you very much for making this possible.
Any collaboration is more than welcomed.
Charalampos Filippou
European University Cyprus
