23Blastocystis is a common unicellular anaerobic eukaryote that inhabits the large intestine of 24 many animals worldwide, including humans. The finding of Blastocystis in faeces in 25 mammals and birds has led to proposals of zoonotic potential and that these hosts may be the 26 source of many human infections. Blastocystis is, however, a genetically diverse complex of 27 many distinct organisms (termed subtypes; STs), and sampling to date has been limited, both 28 geographically and in the range of hosts studied. In order to expand our understanding of host 29 specificity of Blastocystis STs, 557 samples were examined from various non-primate animal 30 hosts and from a variety of different countries in Africa, Asia and Europe. STs were 31 identified using 'barcoding' of the small subunit rRNA gene using DNA extracted either 32 from culture or directly from faeces. The host and geographic range of several STs has 33 thereby been greatly expanded and the evidence suggests that livestock is not a major 34 contributor to human infection. Two new STs were detected among the barcode sequences 35 obtained; for these, and for three others where the data were incomplete, the corresponding 36 genes were fully sequenced and phylogenetic analysis was undertaken. 37 38

Fungi and plants have engaged in intimate symbioses that are globally widespread and have driven terrestrial biogeochemical processes since plant terrestrialization .500 million years ago. Recently, hitherto unknown nutritional mutualisms involving ancient lineages of fungi and nonvascular plants have been discovered, although their extent and functional significance in vascular plants remain uncertain. Here, we provide evidence of carbon-for-nitrogen exchange between an early-diverging vascular plant (Lycopodiella inundata) and Mucoromycotina (Endogonales) fine root endophyte fungi. Furthermore, we demonstrate that the same fungal symbionts colonize neighboring nonvascular and flowering plants. These findings fundamentally change our understanding of the physiology, interrelationships, and ecology of underground plant-fungal symbioses in modern terrestrial ecosystems by revealing the nutritional role of Mucoromycotina fungal symbionts in vascular plants.

Fungi and plants have engaged in intimate symbioses that are globally widespread and have driven terrestrial biogeochemical processes since plant terrestrialisation >500 Mya. Recently, hitherto unknown nutritional mutualisms involving ancient lineages of fungi and non-vascular plants have been discovered. However, their extent and functional significance in vascular plants remains uncertain. Here, we provide first evidence of abundant carbon-for-nitrogen exchange between an early-diverging vascular plant (Lycopodiaceae) and Mucoromycotina (Endogonales) fine root endophyte regardless of changes in atmospheric CO2 concentration. Furthermore, we provide evidence that the same fungi also colonize neighbouring non-vascular and flowering plants. These findings fundamentally change our understanding of the evolution, physiology, interrelationships and ecology of underground plant-fungal symbioses in terrestrial ecosystems by revealing an unprecedented nutritional role of Mucoromycotina fungal symbionts in vascular plants.

Blastocystis SSU-rDNA sequence data from 317 captive and free-living non-human primates (NHPs) representing 30 genera of apes, Old and New World (OW and NW) monkeys and prosimians were analysed to investigate subtype (ST) and allele distribution among hosts. Excluding 20 mixed ST infections, 27% of the sequences belonged to ST1, 22% to ST2, 34% to ST3, 1% to ST4, 4% to ST5, 11% to ST8, <1% to ST13 and 1% to ST15. The study confirmed cryptic host specificity of ST1 and ST3; conversely, considerable overlap in ST2 alleles exists among humans and NHPs. Subtype distribution in humans and NHPs differs mainly in that ST4 is rarely reported in NHPs while ST5 and ST8 are both unusual in humans. This may be due to host specificity and/or the apparent geographically restricted range of some subtypes. While the distribution of ST1, ST2 and ST3 was independent of NHP group or geographical association, ST5 was seen only in apes and OW monkeys and ST8 primarily in arboreal NHPs and only in species native to Asia or South America.

It has long been postulated that symbiotic fungi facilitated plant migrations onto land through enhancing the scavenging of mineral nutrients and exchanging these for photosynthetically fixed organic carbon. Today, land plant-fungal symbioses are both widespread and diverse. Recent discoveries show that a variety of potential fungal associates were likely available to the earliest land plants, and that these early partnerships were probably affected by changing atmospheric CO concentrations. Here, we evaluate current hypotheses and knowledge gaps regarding early plant-fungal partnerships in the context of newly discovered fungal mutualists of early and more recently evolved land plants and the rapidly changing views on the roles of plant-fungal symbioses in the evolution and ecology of the terrestrial biosphere.

24Removing the requirement for cell culture has led to a substantial increase in the number 25 of lineages of Entamoeba recognized as distinct. Surveying the range of potential host 26 species for this parasite genus has barely been started and it is clear that additional 27 sampling of the same host in different locations often identifies additional diversity. In 28 this study, using small subunit ribosomal RNA gene sequencing, we identify four new 29 lineages of Entamoeba, including the first report of Entamoeba from an elephant, and 30 extend the host range of some previously described lineages. Additionally, examination 31 of microbiome data from a number of host animals suggests that substantial Entamoeba 32 diversity remains to be uncovered. 33 34Keywords: Diversity; next generation sequencing; ribosomal RNA; phylogeny; 35 36 37Over the past 25 years, our understanding of diversity in the genus Entamoeba has 38 increased significantly as a result of complementary developments in DNA amplification, 39 purification and sequencing. Traditionally, naming of species in Entamoeba was based on 40 a mixture of host identity and parasite morphology, the latter being rather limited in these 41 amoeboid organisms and the former being of debatable value due to uncertainty over host 42 ranges of the parasites. DNA sequencing allows quantitative measurement of similarity 43 that is not dependent on such characters and although it is not without its own limitations, 44 it has fundamentally changed our approach to studying diversity in organisms such as 45Entamoeba. 46In this time period, the study of Entamoeba has gone from being dependent on 47 stable laboratory cultures of parasites, preferably in the axenic form, to DNA analysis of 48 organisms directly from stool samples in the absence of even microscopic investigation. 49The latter aspect has been problematic as it is not possible to assign new sequences to 50 previously named species where the original description is dependent on morphology. 51For this reason, many new and distinct Entamoeba sequences have been assigned to 52 'ribosomal lineages' rather than species to reflect the absence of morphological 53 information (Stensvold et al. 2011). 54The new approach is dependent on the reliability of DNA purification from stool 55 samples, which are notorious for the presence of enzyme inhibitors, and the specificity of 56 the primers used for PCR amplification. In addition, investigation of Entamoeba in such 57 samples is largely limited to the ribosomal RNA genes due to the complexity of the 58 DNAs extracted from stool, which often contains DNA from multiple other parasites and 59 may include multiple Entamoeba species. The elimination of culture dependency has led 60 to a dramatic expansion in the number of genetically distinct Entamoeba organisms being 61 recognized but also to a greater understanding of sequence variability within species due 62 to the relative ease with which multiple samples can be studied in parallel.

Endogonales is a lineage of early diverging fungi within Mucoromycota. Many species in this order produce small sporophores (“sporocarps”) containing a large number of zygospores, and many species form symbioses with plants. However, due to limited collections, subtle morphological differentiation, difficulties in growing these organisms in vitro, and idiosyncrasies in their rDNA that make PCR amplification difficult, the systematics and character evolution of these fungi have been challenging to resolve. To overcome these challenges we generated a multigene phylogeny of Endogonales using sporophores collected over the past three decades from four continents. Our results show that Endogonales harbour significant undescribed diversity and form two deeply divergent and well-supported phylogenetic clades, which we delimit as the families Endogonaceae and Densosporaceae fam. nov. The family Densosporaceae consists of the genus Densospora, Sphaerocreas pubescens, and many diverse lineages known only from environmental DNA sequences of plant-endosymbiotic fungi. Within Endogonaceae there are two clades. One corresponds to Endogone and includes the type species, E. pisiformis. Species of Endogone are characterized by above- and below-ground sporophores, a hollow and infolded sporophore form, a loose zygosporangial hyphal mantle, homogeneous gametangia, and an enigmatic trophic mode with no evidence of ectomycorrhizal association for most species. For the other clade we introduce a new generic name, Jimgerdemannia gen. nov. Members of that genus (J. flammicorona and J. lactiflua species complexes, and an undescribed species) are characterized by hypogeous sporophores with a solid gleba, a well-developed zygosporangial hyphal mantle, heterogeneous gametangia, and an ectomycorrhizal trophic mode. Future studies on Densosporaceae and Endogonaceae will be important for understanding fungal innovations including evolution of macroscopic sporophores and symbioses with plants.

Orchid mycorrhizal fungi (OMF) are critical for seed germination and maintaining natural populations of orchids, yet the degree of specificity of most orchids to their mycorrhizal associates remains unknown. Many orchids are at risk of extinction, whether generalists or specialists, but orchid species of narrow fungal specificity are arguably under increased threat due to their requirement for specific fungal symbionts. This study characterises the fungi associated with Aerangis ellisii , a lithophytic orchid from a site in the Central Highlands of Madagascar. Culturable OMF isolated from spontaneous protocorms of this species from the wild were used for seed germination. In vitro germination and seedling development of A. ellisii were achieved with fungi derived from A. ellisii and an isolate from a different Aerangis species 30 km away. The significance of these findings and their importance to conservation strategies for this species and other Aerangis spp. is discussed. These results have important implications for the conservation of A. ellisii populations in Madagascar.