The genome, transcriptome and metabolome of Aspergillus welwitschiae Ocstreb1 from wild halophytic rice, Oryza coarctata, indicates its distinctiveness.

Complete genome of Streptomyces anulatus DEF39, an endophytic biocontrol agent against Fusarium graminearum

Phylogenetic and functional genomic analyses were carried out to help explaining the endophytic lifestyle and the biocontrol activity of Streptomyces sp. strain DEF39, able to reduce Fusarium graminearum infection as well as deoxynivalenol production in wheat plants. Specifically, in this work, genes and biosynthetic pathways linked to secondary metabolite production, biocontrol activity, and plant interactions were identified. This approach supports the experimentally validated capability of DEF39 to protect plants from fungal diseases, highlighting the potential of genomics studies. Streptomyces sp. DEF39 was isolated as an endophyte from Secale cereale in Italy and has been shown to colonize wheat ( Triticum spp.) and act as a biocontrol agent of Fusarium head blight. The complete genome (9.12 Mb) (GCA_978019405.1), assembled through a hybrid strategy based on long and short accurate reads combination, is composed of a linear chromosome of 8,887,323 bp with a GC content of 71.59% and a linear plasmid of 233,172 bp with a GC content of 69.27%. Phylogenetic analyses based on the whole genome demonstrated that DEF39 belongs to Streptomyces anulatus species (ANI and dDDH value of 99.13% and 92.8%, respectively with the reference genome GCA_001434355.1). Functional annotation revealed 9,556 genes (CDS). Respectively, antiSMASH and PLaBAse bioinformatic tools predicted 15 putative secondary metabolite biosynthetic gene clusters, as well as 5,203 genes putatively associated with plant growth promotion.

Single-cell genomics, metagenomics, and transcriptomics of Rhizophydium megarrhizum, an obligate fungal parasite of Planktothrix agardhii

Chytrids (phylum Chytridiomycota) are zoosporic fungi that play key roles as parasites of aquatic microorganisms, yet they are understudied and genomic resources for algal-infecting chytrids remain scarce. Here, we present the first comparative genomic analysis of multiple isolates of a single chytrid species (order Rhizophydiales) infecting the cyanobacterium Planktothrix agardhii. Isolates were collected from Sandusky Bay, Lake Erie, across two bloom years (2018 and 2019). Using single cell sequencing and metagenomic assembly, we generated individual genomes averaging 15.36 ± 0.12 Mbp in size with ~ 75% completeness, and a pangenome. Gene ontology analyses highlighted the presence of categories related to cellular structure, biosynthetic regulation, and interspecies interactions. As a preliminary exploration of gene expression during infection, we also performed RNA sequencing on a subset of size-sorted samples. These data suggest that chytrids consistently express high levels of cytoskeletal genes, alongside numerous hypothetical proteins, and that zoospores may upregulate carbohydrate-binding proteins implicated in host recognition. On the host side, P. agardhii showed transcriptional shifts in pathways associated with buoyancy and nutrient acquisition, patterns that could represent defensive adjustments or parasite-driven manipulation. Together, this study generates reference genomes for Planktothrix-infective chytrids, identifies conserved gene content across isolates from different bloom years, and provides preliminary transcriptomic insights into parasite and host responses. These resources lay the foundation for deeper investigations into chytrid genome evolution, infection biology, and their ecological roles in shaping cyanobacterial bloom dynamics.

Decoding the genome of the basidiomycetous yeast Vishniacozyma victoriae D19: a promising fungal model for biotechnology.

A high-quality genome assembly and an in-depth genome analysis of V. victoriae strain D19 are presented, establishing a valuable foundation for future functional studies and providing keys for developing a new chassis for potential industrial applications.

Genomic, spatial, and evolutionary insights into a dominant Mycoplasmatota symbiont colonizing the body wall of deep-sea holothurians

Subcuticular bacteria (SCB) are widespread symbionts of echinoderms and often dominate the body-wall microbiome, suggesting important roles in host physiology. However, their diversity, metabolic properties, and host associations remain poorly characterized. Here, we report a novel dominant SCB lineage associated with deep-sea holothurians, Scotoplanes spp. collected from the Northwest Pacific. We recovered two high-quality genomes, including a 649-kb complete circular genome, and propose a new genus and species, “Candidatus Abyssoplasma scotoplanesicola”, within Mycoplasmatota. The two genomes showed a highly reduced metabolic repertoire, lacking central pathways including glycolysis. In contrast, acidic cell-surface-associated proteins, including large proteins exceeding 5,000 amino acids, accounted for 27.6% of the complete genome and clustered near defense islands. Localized genome plasticity in these regions, revealed by comparison between the two closely related genomes, suggests a possible mechanism for diversification of cell-surface proteins at the host-symbiont interface. “Candidatus Abyssoplasma scotoplanesicola” occupied 76.4–98.9% of the body-wall microbiome of the Scotoplanes specimens. Fluorescence in situ hybridization analysis confirmed that these bacteria formed aggregates on the epidermal side of the body wall. Overall, this study provides genome-and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.

Whole genome sequencing and annotation of a non-pathogenic Fusarium brachygibbosum TZ1MST22 strain isolated from Medicago sativa in Southern Tunisian oases

Bioprospection of Mammaliicoccus sciuri Strain TRQ48 as a Plant-Growth-Promoting Bacteria Associated with Wheat (Triticum turgidum L. subsp. durum) in the Yaqui Valley, Mexico

Bioprospecting of plant growth-promoting bacteria enables the identification of beneficial microbial resources with significant potential for sustainable agricultural applications. In this context, strain TRQ48 was isolated from a commercial field of wheat (Triticum turgidum L. subsp. durum) located in the Yaqui Valley, Mexico, with the aim of exploring its plant growth-promoting potential. The draft genome sequence presented a genomic size of 2,777,016 bp, 32.5% G + C content, 665,763 bp N50, 2 L50, and 19 contigs. Taxonomic affiliation demonstrated that strain TRQ48 belonged to Mammaliicoccus sciuri. Genome annotation identified 2756 coding DNA sequences (CDS) distributed into 259 subsystems, highlighting CDS associated with iron acquisition and metabolism, stress response, and virulence, disease, and defense, among others. Metabolic assays reflect the strain’s capacity to produce siderophores and auxins, relating these positive traits to significantly (p ≤ 0.05) promote growth of wheat shoot length (7.09%) and root and shoot dry weight (75% and 18.43%) compared to uninoculated wheat plants. Biosafety testing indicated that the strain is susceptible to commonly used antibiotics and lacks clinically relevant resistance profiles, matching genomic analysis, which did not reveal any critical virulence factors. Thus, although the presented results show that M. sciuri TRQ48 is a promising beneficial biosafe strain, further studies are still needed to evaluate its performance under agro-ecosystems at commercial levels.