Biology subjects

Tasdemir, D.

Publications and source records attributed to Tasdemir, D..

4 recordsLinked to original sources

bioRxiv2023

Epiphytic and endophytic microbiome of the seagrass Zostera marina: Do they contribute to pathogen reduction in seawater?

Seagrass ecosystems provide crucial ecosystem services for coastal environments and were shown to reduce the abundance of pathogens linked to infections in humans and marine organisms. Among several potential drivers, seagrass phenolics released into seawater have been suggested to play role in pathogen suppression, but the potential involvement of the seagrass microbiome in such effect has not been studied. Here we hypothesized that the microbiome of the eelgrass Zostera marina, especially the leaf epiphytes that are at direct interface between the seagrass host and surrounding seawater, inhibit such pathogenic microorganisms, hence, contribute to their suppression. Using a culture-dependent approach, we isolated 88 bacteria and fungi associated with the surfaces and inner tissues of the eelgrass leaves (healthy and decaying) and the roots, plus 19 strains from surrounding seawater and sediment. We first assessed the broad-spectrum antibiotic activity of microbial extracts against a large panel of common aquatic, human (fecal) and plant pathogens, and finally mined the metabolome of 88 most active extracts. The healthy leaf epibiotic bacteria, particularly Streptomyces sp. strain 131, displayed broad-spectrum and potent antibiotic activity superior to some control drugs. Gram-negative bacteria abundant on healthy leaf surfaces, and few endosphere-associated bacteria and fungi also showed remarkable antimicrobial activity. UPLC-MS/MS-based massive untargeted metabolomics analyses showed the rich specialized metabolite repertoire of strains with low annotation rates, indicating the presence of many undescribed antimicrobials in the extracts. This study contributes to our current understanding on microbial and chemical ecology of seagrasses, implying potential involvement of the seagrass microbiome, especially the leaf epiphytes, in reduction of pathogen load in seawater. Such antibiotic activity is not only beneficial for the health of ocean, human and aquaculture sector, especially in the context of climate change that is expected to exacerbate all infectious diseases, but may also assist seagrass conservation and management strategies.

ecology↗

bioRxiv2023

Metabolomics and Microbiomics Insights into the Differential Surface Fouling of Brown Algae

Marine macroalgae (seaweeds) are key components of marine ecosystems with vital roles in costal habitats. As they release dissolved organic matter and other molecules, seaweeds are under strong settlement pressure by micro- and macro-epibionts. Uncontrolled epibiosis causes surface fouling with detrimental effects on the health and well-being of the organism. Seaweeds control surface epibionts directly by releasing antifouling and antimicrobial metabolites onto their surfaces, and indirectly by recruiting beneficial microorganisms that produce antimicrobial/antifouling metabolites. Three species of the brown algal genus Fucus, F. vesiculosus (FV), F. serratus (FS) and F. distichus subsp. evanescens (FE) form the Fucus belt habitat in the Kiel Fjord, Germany. They often co-occur in the same spot but their blades are fouled differently; we observed FE to be the least fouled, and FV to be the most fouled species. This study was designed to investigate the potential factors underlying different fouling intensities on the surfaces of the three co-occurring Fucus spp. Their surface metabolomes were analysed by comparative untargeted UPLC-MS/MS based metabolomics to identify marker metabolites influencing the surface fouling. The epiphytic microbial communities of the Fucus spp. were also comparatively characterized by high-throughput amplicon sequencing to identify the differences in the surface microbiome of the algae. By employing these omics methods, integrated with multivariate analyses, we identified discriminant metabolites and microbial taxa associated with FE surface, including antimicrobial polar lipids, the fungal genera Mucor, Alternaria, and bacterial genus Yoonia-Loktanella. These taxa have been previously reported to produce antimicrobial and antifouling compounds, suggesting their potential involvement in the fouling resistance (least fouled) observed on the FE surface relative to the co-occurring algae FS and FV. These findings shed light on the surface metabolome and microbiome of Fucus spp. and their influence in different fouling intensities and also have implications for the conservation of coastal habitats.

ecology↗

bioRxiv2022

Reduced glucosinolate content in oilseed rape (Brassica napus L.) by random mutagenesis of BnMYB28 and BnCYP79F1 genes

The presence of anti-nutritive compounds like glucosinolates (GSLs) in the rapeseed meal severely restricts its utilization as animal feed. Therefore, reducing the GSL content to <18 {micro}mol/g dry weight in the seeds is a major breeding target. While candidate genes involved in the biosynthesis of GSLs have been described in rapeseed, comprehensive functional analyses are missing. By knocking out the aliphatic GSL biosynthesis genes BnMYB28 and BnCYP79F1 encoding an R2R3 MYB transcription factor and a cytochrome P450 enzyme, respectively, we aimed to reduce the seed GSL content in rapeseed. After expression analyses on single paralogs, we used an ethyl methanesulfonate (EMS) treated population of the inbred winter rapeseed Express617 to detect functional mutations in the two gene families. Our results provide the first functional analysis by knock-out for the two GSL biosynthesis genes in winter rapeseed. We demonstrate that independent knock-out mutants of the two genes possessed significantly reduced seed aliphatic GSLs, primarily progoitrin. Compared to the wildtype Express617 control plants (36.3 {micro}mol/g DW), progoitrin levels were decreased by 55.3% and 32.4% in functional mutants of BnMYB28 (16.20 {micro}mol/g DW) and BnCYP79F1 (24.5 {micro}mol/g DW), respectively. Our study provides a strong basis for breeding rapeseed with improved meal quality in the future.

plant biology↗

bioRxiv2021

Differential regulation and production of secondary metabolites among isolates of the fungal wheat pathogen Zymoseptoria tritici

The genome of the wheat pathogenic fungus, Zymoseptoria tritici, represents extensive presence-absence variation in gene content. Here, we addressed variation in biosynthetic gene clusters (BGCs) content and biochemical profiles among three isolates. We analysed secondary metabolite properties based on genome, transcriptome and metabolome data. The isolates represent highly distinct genome architecture, but harbor similar repertoire of BGCs. Expression profiles for most BGCs show comparable patterns of regulation among the isolates, suggesting a conserved "biochemical infection program". For all three isolates, we observed a strong up-regulation of an abscisic acid (ABA) gene cluster during biotrophic host colonization, indicating that Z. tritici potentially interfere with host defenses by the biosynthesis of this phytohormone. Further, during in vitro growth the isolates show similar metabolomes congruent with the predicted BGC content. We assessed if secondary metabolite production is regulated by histone methylation using a mutant impaired in formation of facultative heterochromatin (H3K27me3). In contrast to other ascomycete fungi, chromatin modifications play a less prominent role in regulation of secondary metabolites. In summary, we show that Z. tritici has a conserved program of secondary metabolite production contrasting the immense variation in effector expression, some of these metabolites might play a key role during host colonization. Originality-Significance StatementZymoseptoria tritici is one of the most devastating pathogens of wheat. So far the molecular determinants of virulence and their regulation are poorly understood. Previous studies have focused on proteinasous virulence factors and their extensive diversity. In this study, we focus on secondary metabolites produced by Z. tritici. Using a comparative framework, we here characterize core and non-core metabolites produced by Z. tritici by combining genome, transcriptome and metabolome datasets. Our findings indicate highly conserved biochemical profiles contrasting genetic and phenotypic diversity of the field isolates investigated here. This discovery has relevance for future crop protection strategies.

microbiology↗