Pap, B. | Search bioRxiv

bioRxiv2024

Metagenomic peek into a corn mummy

Numerous studies have shown that metagenomics has opened a dimension in reading the contents of archaeological remains as time capsules. Corn mummies are ritual objects from ancient Egypt, created by forming human-shaped figures from cereal grains grown in a mixture of water and earth. The aim of our study was to determine whether ancient DNA could be preserved in the mummy, and if so, which organisms it might have originated from. To find answers, we performed metagenomic analyses on samples taken from a corn mummy dating to the second half of the third century BC. Alongside a number of clearly modern contaminants, we identified organisms that cannot be excluded as being of historical origin. Besides considerable amounts of bacterial sequences belonging to the genus Bacillus, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus and Paenibacillus, we also found traces of plants, animals, and humans. Sequences assigned to the genus Triticum showed the highest similarity to ancient T. turgidum ssp. dicoccum specimens from Egypt and the southern Levant. The fragments identified as of Lepidopteran origin showed the greatest similarity to Sphingidae genomes. Analysis of the human-derived sequences revealed L3 (mtDNA), E, and J (Y chromosome) haplotypes, which are common lineages in Africa today.

bioinformatics↗

bioRxiv2022

Dual RNA-Seq profiling unveils mycoparasitic activities of Trichoderma atroviride against haploid Armillaria ostoyae in antagonistic interaction assays

Armillaria ostoyae, a species among the destructive forest pathogens from the genus Armillaria, causes root rot disease on woody plants worldwide. Efficient control measures to limit the growth and impact of this severe underground pathogen are currently under investigation. In a previous study, a new soilborne fungal isolate, Trichoderma atroviride SZMC 24276, exhibited high antagonistic efficacy, which suggested that it could be utilized as a biocontrol agent. The dual culture assay results indicated that the haploid A. ostoyae derivative SZMC 23085 (C18/9) is highly susceptible to the mycelial invasion of T. atroviride SZMC 24276. In the present study we analyzed the transcriptome of A. ostoyae SZMC 23085 (AO) and that of T. atroviride SZMC 24276 (TA) in in vitro dual culture assays to test the molecular arsenal of Trichoderma antagonism and the defense mechanisms of Armillaria. We conducted time-course analysis, functional annotation, analyzed enriched pathways, and differentially expressed genes (DEGs) including biocontrol-related candidate genes from TA and defense-related candidate genes from AO. The results indicated that TA deployed several biocontrol mechanisms when confronted with AO. In response, AO initiated multiple defense mechanisms to protect against the fungal attack. To our knowledge, the present study offers the first transcriptome analysis of a biocontrol fungus attacking A. ostoyae. Overall, this study provides insights that aid the further exploration of plant pathogen - biocontrol agent interaction mechanisms. IMPORTANCEArmillaria species can survive for decades in the soil on dead woody debris, develop rapidly under favourable conditions, and harmfully infect newly planted forests. Our previous study found Trichoderma atroviride to be highly effective in controlling Armillaria growth; therefore, our current work explored the molecular mechanisms that might play a key role in Trichoderma-Armillaria interactions. Direct confrontation assays combined with time course-based dual transcriptome analysis provided a reliable system for uncovering the interactive molecular dynamics between the fungal plant pathogen and its mycoparasitic partner. Furthermore, using a haploid Armillaria isolate allowed us to survey the deadly prey-invading activities of the mycoparasite and the ultimate defensive strategies of its prey. Our current study provides detailed insights into the essential genes and mechanisms involved in Armillaria defense against Trichoderma and the genes potentially involved in the efficiency of Trichoderma to control Armillaria. In addition, using a sensitive haploid Armillaria strain (C18/9), with its complete genome data already available, also offers the opportunity to test possible variable molecular responses of Armillaria ostoyae towards diverse Trichoderma isolates with varying biocontrol abilities. Initial molecular tests of the dual interactions may soon help to develop a targeted biocontrol intervention with mycoparasites against plant pathogens.

microbiology↗