454-Pyrosequencing Reveals Variable Fungal Diversity Across Farming Systems

The Fungal, Nutritional, and Metabolomic Diagnostics of the Oil Palm Elaeis guineensis Affected by Bud Rot Disease in Esmeraldas, Ecuador

The oil palm Elaeis guineensis represents one of the most important crops in Ecuador. Considering that bud rot disease is deadly in Ecuador, more attention has been given to identifying possible causes for palm debility from this disease. We studied the involvement of fungi and nutrients in triggering bud rot disease in E. guineensis. Special emphasis was given to the molecules synthesized by the plant to protect against this devastating disease. Techniques like Diagnosis and Recommendation Integrated System (DRIS) and metagenomic analysis were used to understand the possible implications of biotic and abiotic factors in the development of bud rot disease in oil palm in Ecuador. Liquid chromatography-mass spectrometry (LC-MS) analysis was used to identify the phenolic protection barrier of the palm facing the disease. Our results indicate that fungi from Ascomyceta phylum were found in the tested samples. The species directly involved are different in soil compared with plants. The results indicate a deficiency of chemical elements, such as Ca, Mn, Mg, and Fe, which are responsible for palm debility from bud rot disease. More than 30 compounds with protective roles were identified in the leaves of symptomatic plants from the first stage of the infection.

Characterization and variation of the rhizosphere fungal community structure of cultivated tetraploid cotton

Rhizosphere fungal communities exert important influencing forces on plant growth and health. However, information on the dynamics of the rhizosphere fungal community structure of the worldwide economic crop cotton (Gossypium spp.) is limited. In the present study, next-generation sequencing of nuclear ribosomal internal transcribed spacer-1 (ITS1) was performed to characterize the rhizosphere fungal communities of G. hirsutum cv. TM-1 (upland cotton) and G. barbadense cv. Hai 7124 (island cotton). The plants were grown in field soil (FS) that had been continuously cropped with cotton and nutrient-rich soil (NS) that had not been cropped. The fungal species richness, diversity, and community composition were analyzed and compared among the soil resources, cotton genotypes, and developmental stages. We found that the fungal community structures were different between the rhizosphere and bulk soil and the difference were significantly varied between FS and NS. Our results suggested that cotton rhizosphere fungal community structure variation may have been primarily influenced by the interaction of cotton roots with different soil resources. We also found that the community composition of the cotton rhizosphere fungi varied significantly during different developmental stages. In addition, we observed fungi that was enriched or depleted at certain developmental stages and genotypes in FS and NS, and these insights can lay a foundation for deep research into the dynamics of pathogenic fungi and nutrient absorption of cotton roots. This research illustrates the characteristics of the cotton rhizosphere fungal communities and provides important information for understanding the potential influences of rhizosphere fungal communities on cotton growth and health.

Illumina-MiSeq analysis of fungi in acid lime roots reveals dominance of Fusarium and variation in fungal taxa

A study was conducted to analyze fungal diversity in the roots of acid lime (Citrus aurantifolia) collected from Oman, a semi-arid country located in the South Eastern part of the Arabian Peninsula. MiSeq analysis showed the Ascomycota and Sordariomycetes were the most abundant phylum and class in acid lime roots, respectively. Glomeromycota, Basidiomycota and Microsporidia were the other fungal phyla, while Glomeromycetes and some other classes belonging to Ascomycota and Basidiomycota were detected at lower frequencies. The genus Fusarium was the most abundant in all samples, making up 46 to 95% of the total reads. Some fungal genera of Arbuscular mycorrhizae and nematophagous fungi were detected in some of the acid lime roots. Analysis of the level of fungal diversity showed that no significant differences exist among groups of root samples (from different locations) in their Chao richness and Shannon diversity levels (P < 0.05). Principle component analysis of fungal communities significantly separated samples according to their locations. This is the first study to evaluate fungal diversity in acid lime roots using high throughput sequencing analysis. The study reveals the presence of various fungal taxa in the roots, dominated by Fusarium species and including some mycorrhizae and nematophagous fungi.

Differentiated surface fungal communities at point of harvest on apple fruits from rural and peri-urban orchards

The diverse fungal communities that colonize fruit surfaces are closely associated with fruit development, preservation and quality control. However, the overall fungi adhering to the fruit surface and the inference of environmental factors are still unknown. Here, we characterized the fungal signatures on apple surfaces by sequencing internal transcribed spacer 1 (ITS1) region. We collected the surface fungal communities from apple fruits cultivated in rural and peri-urban orchards. A total of 111 fungal genera belonging to 4 phyla were identified, showing remarkable fungal diversity on the apple surface. Comparative analysis of rural samples harboured higher fungal diversity than those from peri-urban orchards. In addition, fungal composition varied significantly across apple samples. At the genus level, the protective genera Coniothyrium, Paraphaeosphaeria and Periconia were enriched in rural samples. The pathogenic genera Acremonium, Aspergillus, Penicillium and Tilletiposis were enriched in peri-urban samples. Our findings indicate that rural samples maintained more diverse fungal communities on apple surfaces, whereas peri-urban-planted apple carried potential pathogenic risks. This study sheds light on ways to improve fruit cultivation and disease prevention practices.

Fungal Diversity in Tomato Rhizosphere Soil under Conventional and Desert Farming Systems

This study examined fungal diversity and composition in conventional (CM) and desert farming (DE) systems in Oman. Fungal diversity in the rhizosphere of tomato was assessed using 454-pyrosequencing and culture-based techniques. Both techniques produced variable results in terms of fungal diversity, with 25% of the fungal classes shared between the two techniques. In addition, pyrosequencing recovered more taxa compared to direct plating. These findings could be attributed to the ability of pyrosequencing to recover taxa that cannot grow or are slow growing on culture media. Both techniques showed that fungal diversity in the conventional farm was comparable to that in the desert farm. However, the composition of fungal classes and taxa in the two farming systems were different. Pyrosequencing revealed that Microsporidetes and Dothideomycetes are the two most common fungal classes in CM and DE, respectively. However, the culture-based technique revealed that Eurotiomycetes was the most abundant class in both farming systems and some classes, such as Microsporidetes, were not detected by the culture-based technique. Although some plant pathogens (e.g., Pythium or Fusarium) were detected in the rhizosphere of tomato, the majority of fungal species in the rhizosphere of tomato were saprophytes. Our study shows that the cultivation system may have an impact on fungal diversity. The factors which affected fungal diversity in both farms are discussed.

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment

Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping. Bacterial and fungal communities in bulk and rhizosphere soils as well as in the roots and aerial plant parts were analyzed using large-scale metabarcoding. We detected differences in microbial richness and diversity between the cropping regimes. Generally, observed effects were attributed to differences between mixed and row intercropping or mixed intercropping and monoculture. Bacterial and fungal diversity were significantly higher in bulk soil samples of wheat and faba bean grown in mixed compared to row intercropping. Moreover, microbial communities varied between crop species and plant compartments resulting in different responses of these communities toward cropping regimes. Leaf endophytes were not affected by cropping regime but bacterial and fungal community structures in bulk and rhizosphere soil as well as fungal community structures in roots. We further recorded highly complex changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures due to beneficial effects. In addition, we observed plant species-dependent differences indicating that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. To our knowledge, this is the first study investigating microbial communities in different plant compartments with respect to multiple cropping regimes using large-scale metabarcoding. Although a simple design simulating different cropping regimes was used, obtained results contribute to the understanding how cropping regimes affect bacterial and fungal communities and their interactions in different plant compartments. Nonetheless, we need field experiments to properly quantify observed effects in natural ecosystems.

Illumina MiSeq sequencing analysis of fungal diversity in stored dates

Background

Date palm has been a major fruit tree in the Middle East over thousands of years, especially in the Arabian Peninsula. Dates are consumed fresh (Rutab) or after partial drying and storage (Tamar) during off-season. The aim of the study was to provide in-depth analysis of fungal communities associated with the skin (outer part) and mesocarp (inner fleshy part) of stored dates (Tamar) of two cultivars (Khenizi and Burny) through the use of Illumina MiSeq sequencing.

Results

The study revealed the dominance of Ascomycota (94%) in both cultivars, followed by Chytridiomycota (4%) and Zygomycota (2%). Among the classes recovered, Eurotiomycetes, Dothideomycetes, Saccharomycetes and Sordariomycetes were the most dominant. A total of 54 fungal species were detected, with species belonging to Penicillium, Alternaria, Cladosporium and Aspergillus comprising more than 60% of the fungal reads. Some potentially mycotoxin-producing fungi were detected in stored dates, including Aspergillus flavus, A. versicolor and Penicillium citrinum, but their relative abundance was very limited (<0.5%). PerMANOVA analysis revealed the presence of insignificant differences in fungal communities between date parts or date cultivars, indicating that fungal species associated with the skin may also be detected in the mesocarp. It also indicates the possible contamination of dates from different cultivars with similar fungal species, even though if they are obtained from different areas.

Conclusion

The analysis shows the presence of different fungal species in dates. This appears to be the first study to report 25 new fungal species in Oman and 28 new fungal species from date fruits. The study discusses the sources of fungi on dates and the presence of potentially mycotoxin producing fungi on date skin and mesocarp.

Assessing Fungal Population in Soil Planted with Cry1Ac and CPTI Transgenic Cotton and Its Conventional Parental Line Using 18S and ITS rDNA Sequences over Four Seasons

Long-term growth of genetically modified plants (GMPs) has raised concerns regarding their ecological effects. Here, FLX-pyrosequencing of region I (18S) and region II (ITS1, 5.8S, and ITS2) rDNA was used to characterize fungal communities in soil samples after 10-year monoculture of one representative transgenic cotton line (TC-10) and 15-year plantation of various transgenic cotton cultivars (TC-15mix) over four seasons. Soil fungal communities in the rhizosphere of non-transgenic control (CC) were also compared. No notable differences were observed in soil fertility variables among CC, TC-10, and TC-15mix. Within seasons, the different estimations were statistically indistinguishable. There were 411 and 2 067 fungal operational taxonomic units in the two regions, respectively. More than 75% of fungal taxa were stable in both CC and TC except for individual taxa with significantly different abundance between TC and CC. Statistical analysis revealed no significant differences between CC and TC-10, while discrimination of separating TC-15mix from CC and TC-10 with 37.86% explained variance in PCoA and a significant difference of Shannon indexes between TC-10 and TC-15mix were observed in region II. As TC-15mix planted with a mixture of transgenic cottons (Zhongmian-29, 30, and 33B) for over 5 years, different genetic modifications may introduce variations in fungal diversity. Further clarification is necessary by detecting the fungal dynamic changes in sites planted in monoculture of various transgenic cottons. Overall, we conclude that monoculture of one representative transgenic cotton cultivar may have no effect on fungal diversity compared with conventional cotton. Furthermore, the choice of amplified region and methodology has potential to affect the outcome of the comparison between GM-crop and its parental line.