The diversity of sporocarp-inhabiting fungi (SCIF) was examined using six samples of xylarialean fungi from two different forests in Ibaraki Prefecture, Japan: a moist forest in the Sakuragawa area and an urban dry forest in the Tsukuba area. These fungi were enumerated using direct observation and dilution plate methods. We obtained 44 isolates, and careful morphological and molecular phylogenetic studies of these isolates revealed that approximately 30% of the operating taxonomic units were undescribed or cryptic species related to known fungi. Although typical mycoparasitic fungi, such as helotialean fungi and Trichoderma spp., were not isolated, the genera Acremonium, Acrodontium, and Simplicillium were detected. Comparisons of SCIF communities between the two forests suggested that the number of isolated species in the Sakuragawa area was lower than that in the Tsukuba area. Soil-borne fungi, such as Aspergillus, Beauveria, Penicillium, and Talaromyces, or polypores/corticioid mushrooms, are frequently detected in the Tsukuba area. Factors affecting SCIF communities in the two forests are discussed. Some noteworthy fungi are briefly described with notes on taxonomy, ecology, and molecular phylogeny.

Rhizopus microsporus is a species in the order Mucorales that is known to cause mucormycosis, but it is poorly understood as a host of viruses. Here, we examined 25 clinical strains of R. microsporus for viral infection with a conventional double-stranded RNA (dsRNA) assay using agarose gel electrophoresis (AGE) and the recently established fragmented and primer-ligated dsRNA sequencing (FLDS) protocol. By AGE, five virus-infected strains were detected. Then, full-length genomic sequences of 12 novel RNA viruses were revealed by FLDS, which were related to the families Mitoviridae, Narnaviridae, and Endornaviridae, ill-defined groups of single-stranded RNA (ssRNA) viruses with similarity to the established families Virgaviridae and Phasmaviridae, and the proposed family “Ambiguiviridae.” All the characterized viruses, except a potential phasmavirid with a negative-sense RNA genome, had positive-sense RNA genomes. One virus belonged to a previously established species within the family Mitoviridae , whereas the other 11 viruses represented new species or even new genera. These results show that the fungal pathogen R. microsporus harbors diverse RNA viruses and extend our understanding of the diversity of RNA viruses in the fungal order Mucorales, division Mucoromycota. Identifying RNA viruses from clinical isolates of R. microsporus may expand the repertoire of natural therapeutic agents for mucormycosis in the future. IMPORTANCE: The diversity of mycoviruses in fungal hosts in the division Mucoromycota has been underestimated, mainly within the species Rhizopus microsporus . Only five positive-sense RNA genomes had previously been discovered in this species. Because current sequencing methods poorly complete the termini of genomes, we used fragmented and primer-ligated double-stranded RNA sequencing to acquire the full-length genomes. Eleven novel mycoviruses were detected in this study, including the first negative-sense RNA genome reported in R. microsporus . Our findings extend the understanding of the viral diversity in clinical strains of Mucoromycota, may provide insights into the pathogenesis and ecology of this fungus, and may offer therapeutic options.

A new curvulavirid was isolated from a Japanese strain of the filamentous ascomycete Cryphonectria nitschkei and thoroughly characterized. The virus termed Cryphonectria nitschkei curvulavirus 1 (CnCvV1) has a bi-segmented dsRNA genome. CnCvV1 dsRNA1 encodes an RNA-dependent RNA polymerase (592 amino acids), while dsRNA2 possesses two ORFs, one that encodes a protein associated with the genomic dsRNA and the other that encodes a hypothetical protein of unknown function. CnCvV1 could be experimentally introduced into another virus-free strain of C. nitschkei and two strains of different fungal species within the genus Cryphonectria ( Cryphonectria parasitica and Cryphonectria carpinicola ). Based on phenotypic comparison, the virus caused asymptomatic infection in the three newly established fungal strains. However, there was a reduced colony growth rate and increased CnCvV1 accumulation in an RNA silencing-deficient mutant (Δ dcl2 ), relative to the wt strain EP155 of a model virus host fungus ( C. parasitica ). These findings suggest that CnCvV1 is targeted by RNA silencing in C. parasitica . This study provides a foundation for further exploration of curvulavirids that have been biologically understudied.

Prabaningtyas S, Witjoro A, Laili AN, Devi AS, Sa’diyyah C, Fitria M, Qomaria ZL, Rohman F, Suryanto H, Mawadah I, Saputri DAE, Sa’diyah W. 2025. Exploration of bacteria from Setigi Lake, Gresik District, Indonesia as a candidate for industrial microalgae production. Biodiversitas 26: 1135-1144. The diversity of microorganisms leads to the utilization of biological resources. The aim of this study was to investigate the community structure of microalgae and identify and assess the microbial community and bacterial potential that were collected from Lake Setigi in Gresik District, East Java, Indonesia. The field sampling was done by collecting water from 0, 50, and 100 cm depths. Microalgae were identified according to the guidebook, while the bacterial genome was isolated for metagenomic analysis. The results revealed varying taxa numbers and density of microalgae in Lake Setigi, such as 54 species at a depth of 0-10 cm (35.63 × 108 cells/mL), 42 species at a depth of 50 cm (6.12 × 108cells/mL); and 24 species at a depth of 100 cm (1.56 × 108 cells/mL). Microalgal diversity was categorized as intermediate, well-distributed, or predominant. The three most abundant bacterial phyla were Proteobacteria (56%), Bacteroidetes (16%), and Actinobacteria (13%). The potential functions of the selected bacterial isolates and their species were determined based on the similarity in 16S rRNA gene phylogenetic reconstruction. Isolates IAA17 (Delftia sp.), P15 (Pseudomonas libanensis), S14 (Bacillus subtilis), and SG5 (Lysinibacillus sp.) produced IAA, phosphate solubilization, vitamin B12, and ammonium, respectively, as a result of nitrogen-fixing activity. These abilities of bacteria underline their potential roles in biogeochemical cycling and ecosystem processes.