The aphelids are a small group of intracellular parasitoids of common species of eukaryotic phytoplankton with three known genera Aphelidium, Amoeboaphelidium, and Pseudaphelidium, and ten valid species, which form along with related environmental sequences a very diverged group. The phyla Microsporidia and Cryptomycota, and the class Aphelidea have recently been considered to be а deep branch of Holomycota lineage forming the so called the ARM-clade which is sister to the fungi. In this review we reorganize the taxonomy of ARM-clade, and establish a new superphylum Opisthosporidia with three phyla: Aphelida phyl. nov., Cryptomycota and Microsporidia. We discuss here all aspects of aphelid investigations: history of our knowledge, life cycle peculiarities, the morphology (including the ultrastructure), molecular phylogeny, ecology, and provide a taxonomic revision of the phylum supplied with a list of species. We compare the aphelids with their nearest relatives, the species of Rozella, and improve the diagnosis of the phylum Cryptomycota.

Despite increasingly sophisticated microbiological techniques, and long after the first discovery of microbes, basic knowledge is still lacking to fully appreciate the ecological importance of microbial parasites in fish. This is likely due to the nature of their habitats as many species of fish suffer from living beneath turbid water away from easy recording. However, fishes represent key ecosystem services for millions of people around the world and the absence of a functional ecological understanding of viruses, prokaryotes, and small eukaryotes in the maintenance of fish populations and of their diversity represents an inherent barrier to aquatic conservation and food security. Among recent emerging infectious diseases responsible for severe population declines in plant and animal taxa, fungal and fungal-like microbes have emerged as significant contributors. Here, we review the current knowledge gaps of fungal and fungal-like parasites and pathogens in fish and put them into an ecological perspective with direct implications for the monitoring of fungal fish pathogens in the wild, their phylogeography as well as their associated ecological impact on fish populations. With increasing fish movement around the world for farming, releases into the wild for sport fishing and human-driven habitat changes, it is expected, along with improved environmental monitoring of fungal and fungal-like infections, that the full extent of the impact of these pathogens on wild fish populations will soon emerge as a major threat to freshwater biodiversity.

Sea turtles are presently considered severely endangered species that are historically threatened by many environmental factors. Recently, additional threats to sea turtles from two pathogenic species of fungi in the Fusarium solani species complex (F. falciforme and F. keratoplasticum) have been identified. These species infect marine turtle eggs, causing sea turtle egg fusariosis, and kill their embryos, with recent reports of hatch-failure in seven globally distributed species of endangered sea turtles (Caretta caretta, Chelonia mydas, Dermochelys coriaceae, Eretmochelys imbricata, Lepidochelys olivacea, Lepidochelys kempi and Natator depressus). Mycelia and spores of pathogenic species of Fusarium are produced in disturbed terrestrial soils and are transported to the ocean in coastal run off. We propose that these fungi grow on floating particles of plant tissues (leaves and wood), animal tissues, silt and plastics, which are carried by wind and currents and the turtles themselves to the beaches where the turtles lay their eggs.

The Chytridiomycota phylum contributes to nutrient cycling and the flow of energy between trophic levels in terrestrial and aquatic ecosystems yet remains poorly described or absent from publications discussing fungal communities in these environments. This study contributes to the understanding of three species of soil chytrids in vitro—Gaertneriomyces semiglobifer, Spizellomyces sp. and Rhizophlyctis rosea—in the presence of elevated concentrations of nitrogen and phosphorus and with different sources of nitrogen. Colony growth was measured after 4 weeks as dry weight and total protein. To determine the impacts on zoospore reproduction, motility, lipid content, and attachment to organic substrates, 4- and 8-week incubation times were investigated. Whilst all isolates were able to assimilate ammonium as a sole source of nitrogen, nitrate was less preferred or even unsuitable as a nutrient source for G. semiglobifer and R. rosea, respectively. Increasing phosphate concentrations led to diverse responses between isolates. Zoospore production was also variable between isolates, and the parameters for zoospore motility appeared only to be influenced by the phosphate concentration for Spizellomyces sp. and R. rosea. Attachment rates increased for G. semiglobifer in the absence of an inorganic nitrogen source. These findings highlight variability between the adaptive responses utilised by chytrids to persist in a range of environments and provide new techniques to study soil chytrid biomass and zoospore motility by total protein quantification and fluorescent imaging respectively.

Chytridiomycota (zoosporic true fungi) have a consistent presence in soils and have been frequently identified within many diverse terrestrial environments. However, Chytridiomycota and other early-diverging fungi have low representation in whole-genome sequencing databases compared to Dikarya. New molecular techniques have provided insights into the diversity and abundance of chytrids in soils and the changes in their populations both spatially and temporally. Chytrids complete their life cycle within rapidly changing soil environments where they may be more common within micropores due to protection from predation, desiccation, and extreme temperatures. Reproductive and morphological changes occur in response to environmental changes including pH, fluctuating nutrient concentrations, and metals at levels above toxic thresholds. Rhizoids share some features of hyphae, including the spatial regulation of branching and the ability to attach, adapt to, and proliferate in different substrates, albeit on a microscale. Soil chytrids provide a pool of novel enzymes and proteins which enable a range of lifestyles as saprotrophs or parasites, but also can be utilised as alternative tools with some biotechnological applications. Thus, 3D live-cell imaging and micromodels such as MicroCT may provide insight into zoospore functions and rhizoid plasticity, respectively, in response to various conditions. A combination of classical techniques of soil chytrid baiting with simultaneous molecular and ecological data will provide insights into temporal population changes in response to environmental change. The authors emphasise the need to review and improve DNA-based methodologies for identifying and quantifying chytrids within the soil microbiome to expand our knowledge of their taxonomy, abundance, diversity, and functionality within soil environments.