454-Pyrosequencing Reveals Variable Fungal Diversity Across Farming Systems

Abstract

Oasis farming system is common in some parts of the world, especially in the Arabian Peninsula and several African countries. In Oman, the farming system in the majority of farms follows a semi-oasis farming (SOF) system, which is characterized by growing multiple crops mainly for home consumption, but also for local market. This study was conducted to investigate fungal diversity using pyrosequencing approach in soils from a farm utilizing a SOF system which is cultivated with date palms, acid limes and cucumbers. Fungal diversity from this farm was compared to that from an organic farm (OR) growing cucumbers and tomatoes. Fungal diversity was found to be variable among different crops in the same farm. The observed OTUs, Chao1 richness estimates and Shannon diversity values indicated that soils from date palms and acid limes have higher fungal diversity compared to soil from cucumbers (SOF). In addition, they also indicated that the level of fungal diversity is higher in the rhizosphere of cucumbers grown in OR compared to SOF. Ascomycota was the most dominant phylum in most of the samples from the OR and SOF farms. Other dominant phyla are Microsporidia, Chytridiomycota, and Basidiomycota. The differential level of fungal diversity within the SOF could be related to the variation in the cultural practices employed for each crop.

High Fungal Diversity and Dominance by Ascomycota in Dam Reservoir Soils of Arid Climates

“…The results of physicochemical analysis indicated that KH and MA soils are loamy sand, whereas WT soil is sandy loam. Loamy sand soils are commonly used for growing several crops, including tomatoes and cucumbers (Kazeeroni and Al-Sadi, 2016). Soil pH is an important consideration for farmers.…”

“…Determination of electrical conductivity (EC) and pH were as explained by Zhang et al (2005). Total nitrogen was analyzed using Kjeltec Analyser (FOSS TECATOR, Sweden) (Kazeeroni and Al-Sadi, 2016). Potassium (K), sodium (Na) and calcium (Ca) contents were analyzed with flame photometric method (Sheerwood 450 flame photometer).…”

“…Different techniques have been used for characterizing fungal diversity in soil samples, including the use of culture-based techniques and molecular approaches (Johnsen et al, 2001;Nannipieri et al, 2003;Langarica-Fuentes et al, 2014;Al-Mazroui and Al-Sadi, 2015;Kazeeroni and Al-Sadi, 2016). Among several culture-based techniques, serial dilution and direct plating proved to be efficient in analyzing fungal diversity from different soils and substrates Al-Sadi, 2015, 2016;Al-Sadi et al, 2015b).…”

Illumina MiSeq sequencing analysis of fungal diversity in stored dates

“…Dates palm ( Phoenix dactylifera L.) is one of the oldest and most important fruit trees in the Middle East [1, 2]. The total worldwide production of dates is around 7.2 million tons, with approximately 5.1 million tons produced by countries in the Middle East [3].…”

“…However, with the development in molecular techniques, several DNA-based approaches were developed which enabled the detection of several fungal species that are either difficult to grow on synthetic media, or those which are slow growing and usually outgrown by fast growing species. These include the use of pyrosequencing or MiSeq sequencing which made the detection and identification of fungal and bacterial species easy, not only from plant and food material but also from environmental samples such as water and soil [1, 11–15]. …”