Oomycete metabarcoding reveals the presence of Lagenidium spp. in phytotelmata

Abstract

The oomycete genus Lagenidium, which includes the mosquito biocontrol agent L. giganteum, is composed of animal pathogens, yet is phylogenetically closely related to the well characterized plant pathogens Phytophthora and Pythium spp. These phylogenetic affinities were further supported by the identification of canonical oomycete effectors in the L. giganteum transcriptome. In this study, culture-independent, metabarcoding analyses aimed at detecting L. giganteum in bromeliad phytotelmata (a proven mosquito breeding ground) microbiomes were performed. Two independent and complementary microbial detection strategies based on the amplification of cox1 DNA barcodes were used and produced globally concordant outcomes revealing that two distinct Lagenidium phylotypes are present in phytotelmata. A total of 23,869 high quality reads were generated from four phytotelmata, with 52%, and 11.5% of these reads taxonomically associated to oomycetes, and Lagenidium spp., respectively. Newly designed Lagenidium-specific cox1 primers combined with cloning/Sanger sequencing produced only Lagenidium spp. sequences, with a majority of variants clustering with L. giganteum. High throughput sequencing based on a Single Molecule Real Time (SMRT) approach combined with broad range cox1 oomycete primers confirmed the presence of L. giganteum in phytotelmata, but indicated that a potentially novel Lagenidium phylotype (closely related to L. humanum) may represent one of the most prevalent oomycetes in these environments (along with Pythium spp.). Phylogenetic analyses demonstrated that all detected Lagenidium phylotype cox1 sequences clustered in a strongly supported, monophyletic clade that included both L. giganteum and L. humanum. Therefore, Lagenidium spp. are present in phytotelmata microbiomes. This observation provides a basis to investigate potential relationships between Lagenidium spp. and phytotelma-forming plants, and reveals phytotelmata as sources for the identification of novel Lagenidium isolates with potential as biocontrol agents against vector mosquitoes.

Decontamination and Annotation of the Draft Genome Sequence of the Oomycete Lagenidium giganteum ARSEF 373

“…An unannotated L. giganteum ARSEF 373 whole-genome assembly (accession number GCA_002286825.1 ) is available in the NCBI Genome database ( 4 ), but we found that both cox1 gene sequences in this assembly differ extensively (~92% identity) from cox1 sequences previously amplified from L. giganteum isolates ( 5 ). Furthermore, one was nearly identical (>99.9%) to a DNA sequence ( SPLM01000079.1 ) in the oomycete Pythium oligandrum , a close relative of Lagenidium ( 6 ), suggesting the presence of contaminating DNA sequences.…”

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

“…Some of the earliest applications of DNA metabarcoding involved the analysis of vertebrate diets [189] and this method remains a powerful tool for understanding herbivory and predation (see [125,[190][191][192]). More recently, metabarcoding has been used to reconstruct plant-pollinator networks [146,147] and identify economically important taxa [155] or those relevant to human health [193,194].…”

Fungi of entomopathogenic potential in Chytridiomycota and Blastocladiomycota, and in fungal allies of the Oomycota and Microsporidia

“…However, other genes coding cuticle-degrading enzymes have been found, such as GH5_27 or GH20; these are characteristic of entomopathogens and are not observed in plant pathogens (Quiroz Velasquez et al 2014;Olivera et al 2016). This dichotomy suggests that fungal and oomycete entomopathogens not only share morphology and pathological strategies, but also evolutionary histories and ecological relationships (Leoro-Garzon et al 2019;Shen et al 2019).…”