An Integrative View of the Phyllosphere Mycobiome of Native Rubber Trees in the Brazilian Amazon

Abstract

The rubber tree, Hevea brasiliensis, is a neotropical Amazonian species. Despite its high economic value and fungi associated with native individuals, in its original area in Brazil, it has been scarcely investigated and only using culture-dependent methods. Herein, we integrated in silico approaches with novel field/experimental approaches and a case study of shotgun metagenomics and small RNA metatranscriptomics of an adult individual. Scientific literature, host fungus, and DNA databases are biased to fungal taxa, and are mainly related to rubber tree diseases and in non-native ecosystems. Metabarcoding retrieved specific phyllospheric core fungal communities of all individuals, adults, plantlets, and leaves of the same plant, unravelling hierarchical structured core mycobiomes. Basidiomycotan yeast-like fungi that display the potential to produce antifungal compounds and a complex of non-invasive ectophytic parasites (Sooty Blotch and Flyspeck fungi) co-occurred in all samples, encompassing the strictest core mycobiome. The case study of the same adult tree (previously studied using culture-dependent approach) analyzed by amplicon, shotgun metagenomics, and small RNA transcriptomics revealed a high relative abundance of insect parasite-pathogens, anaerobic fungi and a high expression of Trichoderma (a fungal genus long reported as dominant in healthy wild rubber trees), respectively. Altogether, our study unravels new and intriguing information/hypotheses of the foliar mycobiome of native H. brasiliensis, which may also occur in other native Amazonian trees.

Effects of synthetic and environmentally friendly fungicides on powdery mildew management and the phyllosphere microbiome of cucumber

“…The genus is well known for the secretion of glycolipids, which can inhibit more than 250 fungal species [60]. It has also been reported to be a member of the core microbiome of the rubber tree (Hevea brasiliensis) phyllosphere and was hypothesized to be involved in inhibiting pathogenic fungi in the phyllosphere [61]. However, the role of Sympodiomycopsis in the cucumber phyllosphere needs to be further investigated.…”

Applying molecular and genetic methods to trees and their fungal communities

“…Newly emerging as other guilds of ecological relevance are distinct spatially distributed communities of fungal epiphytes sitting on aerial surfaces of plant organs, e.g. on the phylloplane of leaves (Bahram et al 2022 ; Ding et al 2022a ; Fonseca et al 2022 ; Gomes et al 2018 ; Howe et al 2016 ; Liber et al 2022 ; Sun et al 2021 ; Vacher et al 2016 ), on surfaces of flowers (anthosphere) and fruits (carposphere; Bill et al 2022 ) or on the bark of stems (caulosphere; Cook et al 2022 ), with potential functions such as of host defense on the tree or advanced inoculation of plant litter for decay directly when fallen (Box 2). Without these various possible microbial confrontations, trees will suffer in different ways.…”

“…Technically more challenging by the need of isolating sensitive RNA for multi-organisms' RNA-seq from difficult environmental probes, by the high abundances (ca. 95%) of disturbing rRNA (potentially solved for eukaryotes by polyA enrichment of mRNA), and among, also, by a gigantic amount of yet unknown genome background data for best functional annotation, first reports are emerging where sequence similarities to established genetic data in databases, motifs in deduced protein products and also parallel meta-genome sequencing of total isolated DNA were made use of (Fonseca et al 2022 ; Hesse et al 2015 ; Liao et al 2014 ; Schneider et al 2021 ). Reconstruction of smaller genomes from environmental metagenomes (metagenome-assembled genomes = MAGs) from individual bacteria has started with suitable bioinformatic tools and pipelines (Zhou et al 2022 ) but for the larger genomes of the many non-model fungi in nature, and for the better transcript annotations of today's possible meta-transcriptomics, this will all still take time.…”

“…Yeast-like basidiomycetes with potential for antifungal-compound production and non-invasive ectophytic fungal pathogens (sooty blotch, flyspeck) were discovered in the barcoding to dominate in the core mycobiome, while the shotgun meta-genomics with the higher sequencing depth and meta-transcriptomic revealed extra abundances of insect pathogens ( Ophiocordycipitaceae ) and anaerobic fungi ( Neocallimastigomycota ), and Trichoderma spp. was detected in meta-transcriptomics as one of the physiologically most active fungal genera besides Fusarium and Hypomyces (Fonseca et al 2022 ). Another recent study demonstrated for meta-genomic ITS and meta-transcriptomic RNA data from matched samples of root- and needle-associated fungal communities of P. abies in comparative bioinformatic workflows the principle power for functional community insights (in the study nutrient-related) but also the current limitations by coverage in available databases, such as of definitions at lower taxonomic levels and available reference genomes (Schneider et al 2021 ).…”

Unraveling potential enzymes and their functional role in fine cocoa beans fermentation using temporal shotgun metagenomics

“…Usually, microbiome studies utilize short-read high-throughput sequencing (HTS) platforms (e.g. : Illumina) that generate very high yields but of short read lengths (150–300 base pairs; Fonseca et al, 2022 ), as the current study. Conversely, long-read HTS platforms (e.g.…”