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Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts’ microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.

Plants sense light and temperature changes to regulate flowering time. Here, we show that expression of the Arabidopsis florigen gene, FLOWERING LOCUS T (FT), peaks in the morning during spring, a different pattern than we observe in the laboratory. Providing our laboratory growth conditions with a red/far-red light ratio similar to open-field conditions and daily temperature oscillation is sufficient to mimic the FT expression and flowering time in natural long days. Under the adjusted growth conditions, key light signalling components, such as phytochrome A and EARLY FLOWERING 3, play important roles in morning FT expression. These conditions stabilize CONSTANS protein, a major FT activator, in the morning, which is probably a critical mechanism for photoperiodic flowering in nature. Refining the parameters of our standard growth conditions to more precisely mimic plant responses in nature can provide a powerful method for improving our understanding of seasonal response.

Despite the importance of ectomycorrhizal (ECM) fungi in forest ecosystems, knowledge about the ecological and co-evolutionary mechanisms underlying ECM host associations remains limited. Using a widely distributed group of ECM fungi known to form tight associations with trees in the family Pinaceae, we characterized host specificity among three unique Suillus-host species pairs using a combination of field root tip sampling and experimental bioassays. We demonstrate that the ECM fungus S. subaureus can successfully colonize Quercus hosts in both field and glasshouse settings, making this species unique in an otherwise Pinaceae-specific clade. Importantly, however, we found that the colonization of Quercus by S. subaureus required co-planting with a Pinaceae host. While our experimental results indicate that gymnosperms are required for the establishment of new S. subaureus colonies, Pineaceae hosts are locally absent at both our field sites. Given the historical presence of Pineaceae hosts before human alteration, it appears the current S. subaureus-Quercus associations represent carryover from past host presence. Collectively, our results suggest that patterns of ECM specificity should be viewed not only in light of current forest community composition, but also as a legacy effect of host community change over time.

Exploring the link between above- and belowground biodiversity has been a major theme of recent ecological research, due in large part to the increasingly well-recognized role that soil microorganisms play in driving plant community processes. In this study, we utilized a field-based tree experiment in Minnesota, USA, to assess the effect of changes in plant species richness and phylogenetic diversity on the richness and composition of both ectomycorrhizal and saprotrophic fungal communities. We found that ectomycorrhizal fungal species richness was significantly positively influenced by increasing plant phylogenetic diversity, while saprotrophic fungal species richness was significantly affected by plant leaf nitrogen content, specific root length and standing biomass. The increasing ectomycorrhizal fungal richness associated with increasing plant phylogenetic diversity was driven by the combined presence of ectomycorrhizal fungal specialists in plots with both gymnosperm and angiosperm hosts. Although the species composition of both the ectomycorrhizal and saprotrophic fungal communities changed significantly in response to changes in plant species composition, the effect was much greater for ectomycorrhizal fungi. In addition, ectomycorrhizal but not saprotrophic fungal species composition was significantly influenced by both plant phylum (angiosperm, gymnosperm, both) and origin (Europe, America, both). The phylum effect was caused by differences in ectomycorrhizal fungal community composition, while the origin effect was attributable to differences in community heterogeneity. Taken together, this study emphasizes that plant-associated effects on soil fungal communities are largely guild-specific and provides a mechanistic basis for the positive link between plant phylogenetic diversity and ectomycorrhizal fungal richness.

Fungi typically live in highly diverse communities composed of multiple ecological guilds. Although high-throughput sequencing has greatly increased the ability to quantify the diversity of fungi in environmental samples, researchers currently lack a simple and consistent way to sort large sequence pools into ecologically meaningful categories. We address this issue by introducing FUNGuild, a tool that can be used to taxonomically parse fungal OTUs by ecological guild independent of sequencing platform or analysis pipeline. Using a database and an accompanying bioinformatics script, we demonstrate the application of FUNGuild to three high-throughput sequencing datasets from different habitats: forest soils, grassland soils, and decomposing wood. We found that guilds characteristic of each habitat (i.e., saprotrophic and ectomycorrhizal fungi in forest soils, saprotrophic and arbuscular mycorrhizal fungi in grassland soils, saprotrophic, wood decomposer, and plant pathogenic fungi in decomposing wood) were each well represented. The example datasets demonstrate that while we could quickly and efficiently assign a large portion of the data to guilds, another large portion could not be assigned, reflecting the need to expand and improve the database as well as to gain a better understanding of natural history for many described and undescribed fungal species. As a community resource, FUNGuild is dependent on third-party annotation, so we invite researchers to populate it with new categories and records as well as refine those already in existence.

Spores and sclerotia are the main propagules that allow fungi to persist through unfavorable conditions and disperse into new environments. Despite their importance, very little is known about their longevity and dormancy, especially in ectomycorrhizal fungi. To assess the viability of ectomycorrhizal fungal spores in forest soil, we collected and buried non-sterile forest soil, in pots, in the field distant from an inoculum source. After 6 yr, a subset of this soil was assayed for viable spores by baiting the fungi with Bishop pine (Pinus muricata) seedlings. Our results show that the three most frequent colonizers in year 1 continued to colonize significant percentages of seedlings in year 6: Wilcoxina mikolae (77 %), Rhizopogon vulgaris (13 %) and Suillus brevipes (9 %). While three species that colonized low percentages of seedlings in year 1, Suillus pungens (1 %), Rhizopogon salebrosus (2 %), and Thelephora terrestris (5 %) were not recovered in year 6. Laccaria proxima, a species not seen in year 1, was recovered on a single seedling in year 6. This is the first report of long-term survival of S. brevipes and W. mikolae. Our results reveal a more complete picture of ectomycorrhizal fungal spore longevity in soil spore banks.

Dispersal plays a prominent role in most conceptual models of community assembly. However, direct measurement of dispersal across a whole community is difficult at ecologically relevant spatial scales. For cryptic organisms, such as fungi and bacteria, the scale and importance of dispersal limitation has become a major point of debate. We use an experimental island biogeographic approach to measure the effects of dispersal limitation on the ecological dynamics of an important group of plant symbionts, ectomycorrhizal fungi. We manipulated the isolation of uncolonized host seedlings across a natural landscape and used a range of molecular techniques to measure the dispersal rates of ectomycorrhizal propagules and host colonization. Some species were prolific dispersers, producing annual spore loads on the order of trillions of spores per km 2 . However, fungal propagules reaching host seedlings decreased rapidly with increasing distance from potential spore sources, causing a concomitant reduction in ectomycorrhizal species richness, host colonization and host biomass. There were also strong differences in dispersal ability across species, which correlated well with the predictable composition of ectomycorrhizal communities associated with establishing pine forest. The use of molecular tools to measure whole community dispersal provides a direct confirmation for a key mechanism underlying island biogeography theory and has the potential to make microbial systems a model for understanding the role of dispersal in ecological theory.

Yeasts related to Candida albicans were isolated from the digestive tracts of beetles in eight families and various orders of insects such as earwigs, crickets, and roaches, most of which were caught at light traps or in a few cases directly from plant materials. Based on comparisons of DNA sequences and other taxonomic characteristics, a total of 41 isolates were identified as Candida orthopsilosis, Candida pseudorhagii, Candida maltosa, Candida parapsilosis, Candida tropicalis, Candida neerlandica, Lodderomyces elongisporus, and seven new Candida species. The new species and type strains are designated as Candida gigantensis NRRL Y-27736T, Candida bohiensis NRRL Y-27737T, Candida alai NRRL Y-27739T, Candida buenavistaensis NRRL Y-27734T, Candida frijolesensis NRRL Y-48060T, Candida labiduridarum NRRL Y-27940T, and Candida tetrigidarum NRRL Y-48142T. A phylogeny based on SSU and LSU rRNA gene sequences indicated that most of the new species were closely related to members of the C. albicans/L. elongisporus clade, such as C. albicans, Candida dulbliniensis, C. neerlandica, Candida chauliodes, and Candida corydali. Candida alai was placed near this clade, but no closely related sister taxon was identified. The ecology of the insect-associated yeasts is discussed and compared with the results from other studies.

Microbes that have adopted endosymbiotic life styles not only have evolved to live in specialized habitats within living organisms, but the living habitats also have evolved to accommodate them. The hindgut of the passalid beetle (Odontotaenius disjunctus) is lined with a cuticle that undergoes dramatic topographic changes during the life cycle of the beetle. This manuscript addresses the changes that have been observed in time and space for the cuticular landscape of the hindgut as well as for the microbial communities within the hindgut. Microbial identity is based on morphology, culture, and extrapolation from previously reported passalid gut inhabitants.

14 different yeasts were isolated from the gut of a variety of insects, including beetles, lacewings, fishflies, craneflies, and a cockroach. One of the yeasts was found both in the gut and on the body surface of a beetle larva. Based on ribosomal DNA sequence comparisons and phenotypic characters, the yeasts were identified as Candida membranifaciens, C. tenuis, Pichia nakazawae, and nine undescribed taxa in Saccharomycotina. All the undescribed taxa reproduced only asexually, and they fit within the limits of the polyphyletic genus Candida. The new species and their type strains are Candida blattariae NRRL Y-27703T, C. amphixiae NRRL Y-27704T, C. michaelii NRRL Y-27705T, C. cerambycidarum NRRL Y-27706T, C. gorgasii NRRL Y-27707T, C. endomychidarum NRRL Y-27708T, C. temnochilae NRRL Y-27763T, C. sinolaborantium NRRL Y-27765T, and C. lessepsii NRRL Y-27766T spp. nov. Phylogenetic analysis of combined small and large subunit ribosomal DNA sequences placed C. amphixiae, C. michaelii, C. cerambycidarum, C. gorgasii, C. endomychidarum, and C. lessepsii in a statistically well supported clade with C. blattariae, C. membranifaciens, C. friedrichii, and C. buinensis as sisters to the clade. The other two new taxa, C. temnochilae and C. sinolaborantium, formed an independent clade basal to the major clade containing C. membranifaciens and closely related taxa. C. sinolaborantium occurred in both Panama and the USA, but there were genetic differences between the isolates from the two places.

Dispersal plays a prominent role in most conceptual models of community assembly. However, direct measurement of dispersal across a whole community is difficult at ecologically relevant spatial scales. For cryptic organisms, such as fungi and bacteria, the scale and importance of dispersal limitation has become a major point of debate. We use an experimental island biogeographic approach to measure the effects of dispersal limitation on the ecological dynamics of an important group of plant symbionts, ectomycorrhizal fungi. We manipulated the isolation of uncolonized host seedlings across a natural landscape and used a range of molecular techniques to measure the dispersal rates of ectomycorrhizal propagules and host colonization. Some species were prolific dispersers, producing annual spore loads on the order of trillions of spores per km(2). However, fungal propagules reaching host seedlings decreased rapidly with increasing distance from potential spore sources, causing a concomitant reduction in ectomycorrhizal species richness, host colonization and host biomass. There were also strong differences in dispersal ability across species, which correlated well with the predictable composition of ectomycorrhizal communities associated with establishing pine forest. The use of molecular tools to measure whole community dispersal provides a direct confirmation for a key mechanism underlying island biogeography theory and has the potential to make microbial systems a model for understanding the role of dispersal in ecological theory.

Yeasts similar to Candida kruisii were isolated repeatedly from the digestive tracts of basidioma-feeding beetles, especially nitidulids inhabiting and feeding on a variety of agarics in the southeastern USA and Barro Colorado Island, Panama. Based on the identical sequences of the D1/D2 domains of the LSU rRNA gene (rDNA) and host beetle information, the isolates were grouped into 19 genotypes which varied from C. kruisii by up to 38 nucleotide differences in the D1/D2 region. Phylogenetic analysis of rDNA sequences and phenotypic traits placed the isolates in C. kruisii and in nine undescribed taxa. The new species and type strains are designated as Candida pallodes (NRRL Y-27653(T)), C. tritomae (NRRL Y-27650(T)), C. panamensis (NRRL Y-27657(T)), C. lycoperdinae (NRRL Y-27658(T)), C. atbi (NRRL Y-27651(T)), C. barrocoloradensis (NRRL Y-27934(T)), C. aglyptinia (NRRL Y-27935(T)), C. stri (NRRL Y-48063(T)), and C. gatunensis (NRRL Y-48064(T)). A phylogeny based on analysis of a combined database of sequences of SSU and LSU rDNA and the ITS region showed that the nine new species formed a novel sister clade to C. kruisii that was strongly supported by bootstrap analysis. Candida pallodes, C. tritomae, C. panamensis, and C. lycoperdinae formed one subclade, while C. atbi, C. barrocoloradensis, C. aglyptinia, C. stri, and C. gatunensis formed a second distinct subclade within the larger clade. Candida pallodes and C. atbi showed a strong host specificity to beetle species in the genus Pallodes (Coleoptera: Nitidulidae) collected from a variety of agarics. On the other hand, C. panamensis, C. tritomae, and C. lycoperdinae were associated with several unrelated beetles in Erotylidae, Scarabaeidae, Tenebrionidae, and Curculionidae as well as Lycoperdina ferruginea (Nitidulidae). Candida pallodes, C. tritomae, C. lycoperdinae, and C. atbi have been isolated repeatedly in the USA, while the other five new species have been found only at Barro Colorado Island, Panama.