Fungal diversity in oil palm leaves showing symptoms of Fatal Yellowing disease

<div><p>Oil palm (<i>Elaeis guineensis</i> Jacq.) is an excellent source of vegetable oil for biodiesel production; however, there are still some limitations for its cultivation in Brazil such as Fatal Yellowing (FY) disease. FY has been studied for many years, but its causal agent has never been determined. In Colombia and nearby countries, it was reported that the causal agent of Fatal Yellowing (<i>Pudrición del Cogollo</i>) is the oomycete <i>Phytophthora palmivora</i>, however, several authors claim that Fatal Yellowing and <i>Pudrición del Cogollo</i> (PC) are different diseases. The major aims of this work were to test, using molecular biology tools, Brazilian oil palm trees for the co-occurrence of the oomycete <i>Phytophthora</i> and FY symptoms, and to characterize the fungal diversity in FY diseased and healthy leaves by next generation sequencing. Investigation with specific primers for the genus <i>Phytophthora</i> showed amplification in only one of the samples. Analysis of the fungal ITS region demonstrated that, at the genus level, different groups predominated in all symptomatic samples, while <i>Pyrenochaetopsis</i> and unclassified fungi predominated in all asymptomatic samples. Our results show that fungal communities were not the same between samples at the same stage of the disease or among all the symptomatic samples. This is the first study that describes the evolution of the microbial community in the course of plant disease and also the first work to use high throughput next generation sequencing to evaluate the fungal community associated with leaves of oil palm trees with and without symptoms of FY.</p></div

Identification of fungal OTUs sequences shared by groups of oil palm leaf samples affected by FY in disease stages 2, 5 and 8, but not present in asymptomatic leaves.

<p>Identification of fungal OTUs sequences shared by groups of oil palm leaf samples affected by FY in disease stages 2, 5 and 8, but not present in asymptomatic leaves.</p

Venn diagram.

<p>The number of shared and unique fungal OTUs (at 3% distance) among groups of different stages of FY (stage 2, stage 5 and stage 8) and healthy plants (AP) is shown.</p

Sequence abundance at different taxonomic levels.

<p>Relative abundance of fungal sequences at phyla (A) and class (B) levels in oil palm leaves of plants with (stages 2, 5 and 8) or without Fatal Yellowing based on ITS region sequences. AP—FY <u>A</u>symptomatic <u>P</u>lants; SP—FY <u>S</u>ymptomatic <u>P</u>lants.</p

Identification of fungal OTUs sequences shared by groups of oil palm leaf samples affected by FY in disease stages 2, 5 and 8, but not present in asymptomatic leaves.

<p>Identification of fungal OTUs sequences shared by groups of oil palm leaf samples affected by FY in disease stages 2, 5 and 8, but not present in asymptomatic leaves.</p

Geographical coordinates of sampling sites.

<p>Geographical coordinates of sampling sites.</p

Archaeal community changes associated with cultivation of Amazon Forest soil with oil palm

This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7%) were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1.7 times higher in the native forest soil, according to the Simpson diversity index, and the Chao1 index showed that richness was five times higher in the native forest soil. A phylogenetic tree of unclassified Thaumarchaeota sequences showed that most of the OTUs belong to Miscellaneous Crenarchaeotic Group. Several archaeal genera involved in nutrient cycling (e.g., methanogens and ammonia oxidizers) were identified in both areas, but significant differences were found in the relative abundances of Candidatus Nitrososphaera and unclassified Soil Crenarchaeotic Group (prevalent in the native forest) and Candidatus Nitrosotalea and unclassified Terrestrial Group (prevalent in the oil palm-cultivated area). More studies are needed to culture some of these Archaea in the laboratory so that their metabolism and physiology can be studied