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August 2006 - August 2013
Publications
Publications (84)
Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last...
Measurement of spore size and particles can be very tedious and time-consuming. This protocol leverages the particle analysis function in ImageJ to measure spores. It will be able to measure spore length, width, and area.
Microbial fermentation is crucial to the development of flavors in cacao-based products, but how the abiotic environment and pod surface microbiomes can contribute to these different sensory profiles is underdeveloped. To better understand the connections between environment, plant variety, associated pod phyllosphere microbiomes, and the fermentat...
Legumes and their interaction with rhizobia represent one of the most well-characterized symbioses that are widespread across both natural and agricultural environments. However, larger distribution patterns and host associations on isolated Pacific islands with many native and introduced hosts have not been well-documented. Here, we used molecular...
The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in...
This protocol uses a dilution to extinction technique to isolate bacteria from soil but also applicable to other substrates. The isolation takes place in 96-well plates, thus allowed us to replicate the isolation in a high-throughput manner. The second part of the protocol uses high-throughput DNA sequencing to identify the samples. We amplified an...
Legumes and their interaction with rhizobia represent one of the most well-characterized symbioses that are widespread across both natural and agricultural environments. However, larger distribution patterns and host associations on isolated Pacific islands with many native and introduced hosts have not been well-documented. Here, we used molecular...
Studying the signatures of evolution can help to understand genetic processes. Here we demonstrate how the existence of balancing selection can be used to identify the breeding systems of fungi from genomic data. The breeding systems of fungi are controlled by self-incompatibility loci that determine mating types between potential mating partners,...
Mat-forming fungi are common in forest and grassland soils across the world, where their activity contributes to important soil ecological processes. These fungi maintain dominance through aggressive and abundant hyphae that modify their internal physical and chemical environments and through these modifications select for what appears to be a suit...
Plant roots release exudates that fuel microbial activities and can structure rhizosphere microbial communities, but how different plant species use their root exudate to potentially select for different soil microbes in the rhizosphere is not well understood. Here, we investigated how root exudate from plants of three diverging lineages, Lactuca s...
Tropical regions hold one third of the world’s soil organic carbon, but few experiments have warmed tropical soils in situ. The vulnerability of these soils to climate change-induced losses is uncertain with many hypothesizing these soils would be less sensitive to climate change because already-high temperatures in tropical systems might limit mic...
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 microbiom...
Geothermal soils offer unique insight into the way extreme environmental factors shape communities of organisms. However, little is known about the fungi growing in these environments and in particular how localized steep abiotic gradients affect fungal diversity. We used metabarcoding to characterize soil fungi surrounding a hot spring-fed thermal...
A new paedogenetic midge (Diptera: Cecidomyiidae: Winnertziinae: Heteropezini) from O‘ahu Island, Hawai‘i, Neostenoptera hawaiiensis Plakidas, Nguyen, and Ferro, new species, is described and illustrated. A key to all species in the genus is provided. Specimens were emergent from deadwood gathered at Waimea Arboretum and Botanical Garden. Neosteno...
Our current understanding suggests that nutrient management strategies applied to agricultural soils over multiple years are required to cause major and stable shifts in soil microbial communities. However, some studies suggest that agricultural soils can benefit even from sporadic, single additions of organic matter. Here we investigate how single...
Science, technology, engineering, and mathematics (STEM) education is consistently seen as a top priority; however, STEM programs often suffer from low retention. Students who start in STEM degree programs often lose interest or face obstacles that cause them to leave. Here, we describe a non‐traditional approach meant to encourage a range of stude...
Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA comm...
Increasing temperature and decreasing precipitation has led to more frequent and extreme drought events in many regions throughout the world. In the western United States, multi‐year drought events have led to widespread plant mortality and extreme wildfires (Asner et al. 2016, Pickrell and Pennisi 2020). Communities of ectomycorrhizal fungi (EMF)...
Suillus is among the best-known examples of an ectomycorrhizal (ECM) fungal genus that demonstrates a high degree of host specificity. Currently recognized host genera of Suillus include Larix, Pinus, and Pseudotsuga, which all belong to the pinoid clade of the family Pinaceae. Intriguingly, Suillus sporocarps have been sporadically collected in fo...
Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spati...
Geothermal soils offer unique insight into the way extreme environmental factors shape communities of organisms. However, little is known about the fungi growing in these environments and in particular how localized steep abiotic gradients affect fungal diversity. We used metabarcoding to characterize soil fungi surrounding a hot spring-fed thermal...
Anaerobic digestion of organic wastes produces solid residues known as digestates, which have potential as a fertilizer and soil amendment. The majority of research on digestate focuses on their fertilizer value. However, there is a lack of information about additional effects they may have on plant growth, both positive and negative. Understanding...
There were errors in the name of author László G. Nagy and in affiliation no. 31 in the original publication. The original article has been corrected.
Roots are the primary source of organic carbon inputs to most soils. Decomposition is a multi-trophic process involving multiple kingdoms of microbial life, but typically microbial ecology studies focus on one or two major lineages in isolation. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis ("communi...
While there has been significant progress characterizing the ‘symbiotic toolkit’ of ectomycorrhizal (ECM) fungi, how host specificity may be encoded into ECM fungal genomes remains poorly understood.
We conducted a comparative genomic analysis of ECM fungal host specialists and generalists, focusing on the specialist genus Suillus. Global analyses...
The cryptic lifestyle of most fungi necessitates molecular identiication of the guild in environmental studies. Over the past
decades, rapid development and afordability of molecular tools have tremendously improved insights of the fungal diversity
in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about f...
Two common ecological assumptions are that host generalist and rare species are poorer competitors relative to host specialist and more abundant counterparts. While these assumptions have received considerable study in both plant and animals, how they apply to ectomycorrhizal fungi remains largely unknown. To investigate how interspecific competiti...
Human‐altered environments can shape the evolution of organisms. Fungi are no exception, though little is known about how they withstand anthropogenic pollution. Here, we document adaptation in the mycorrhizal fungus Suillus luteus driven by soil heavy metal contamination. Genome scans across individuals from recently polluted and nearby unpolluted...
Two common ecological assumptions are that host generalist and rare species are poorer competitors relative to host specialist and more abundant counterparts. While these assumptions have received considerable study in both plant and animals, how they apply to ectomycorrhizal fungi remains largely unknown. To investigate how interspecific competiti...
Human-altered environments can shape the evolution of organisms. Fungi are no exception, though little is known about how they withstand anthropogenic pollution. Here, we document incipient polygenic local adaptation in the mycorrhizal fungus Suillus luteus driven by recent soil heavy metal contamination. Genome scans across individuals from recent...
Nonnative, invasive feral pigs (Sus scrofa) modify habitats by disturbing soils and vegetation, which can alter biogeochemical processes. Soil microbial communities drive nutrient cycling and therefore also play important roles in shaping ecosystem structure and function, but the responses of soil microbes to nonnative ungulate removal remains poor...
Rhizopogon olivaceotinctus is a rarely collected ectomycorrhizal fungus that has been found primarily in California and southern Oregon. Prior work has shown that it (i) is common in soil spore banks associated with pine forests from these areas; (ii) is rare or absent on trees in undisturbed forests in these same areas; (iii) exhibits an increased...
Appendices supporting Wehr et al (2019) Changes in soil bacterial community diversity following the removal of invasive feral pigs from a Hawaiian tropical montane wet forest
Despite covering vast areas of boreal North America, the ecological factors structuring mycorrhizal fungal communities in peatland forests are relatively poorly understood. To assess how these communities vary by age (younger vs. mature), habitat (fen vs. bog), and host (conifer trees vs. ericaceous shrub), we sampled the roots of two canopy trees...
Despite increasing acknowledgment that microorganisms underpin the healthy functioning of basically all multicellular life, few cross-disciplinary teams address the diversity and function of microbiota across organisms and ecosystems. Our newly formed consortium of junior faculty spanning fields such as ecology and geoscience to mathematics and mol...
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...
Fungi can produce resistant propagules that may last for decades. Basidiospores from ectomycorrhizal fungi had been experimentally shown to last for at least 6 yr, but there are few reports on the longevity of saprotrophic members of mushroom-forming fungi. Here, the author shows evidence of spore longevity of these fungi by collecting, drying, sto...
The genus Suillus represents one of the most recognizable groups of mushrooms in conifer forests throughout the Northern Hemisphere. Although for decades the genus has been relatively well defined morphologically, previous molecular phylogenetic assessments have provided important yet preliminary insights into its evolutionary history. Here we pres...
Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with t...
Rising temperatures associated with climate change have been shown to negatively affect the photosynthetic rates of boreal forest tree saplings at their southern range limits. To quantify the responses of ectomycorrhizal (EM) fungal communities associated with poorly performing hosts, we sampled the roots of Betula papyrifera and Abies balsamea sap...
Twigs are an understudied habitat utilized by many beetle species. Samples of twigs were collected in all six Level III Ecoregions in Louisiana during April and May 2013. The twigs were maintained in emergence chambers from which 942 specimens of adult Coleoptera were obtained, representing 31 families, 111 genera, and 128 species. Beetle richness...
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 temperate and boreal forest ecosystems, nitrogen (N) limitation on tree metabolism is alleviated by ectomycorrhizal (ECM) fungi. As forest soils age, the primary source of N in soil switches from inorganic (NH4 (+), NO3 (-)) to organic (mostly proteins). It has been hypothesized that ECM adapt to the most common N source in their environment, wh...
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...
Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput seq...
A name has been found for a common species in Pholiota subg. Flammuloides fruiting during and soon after snowmelt in the subalpine Abies forests of California: Pholiota olivaceophylla is characterized by rather pale slime-covered basidiocarps, relatively
pale brown ellipsoid to slightly phaseoliform spores, 6.0–8.5 × 3.5–5.0 μm, with an inconspicuo...
Bacteria have been observed to grow with fungi, and those that associate with ectomycorrhizal fungi have often been thought of as symbionts that may either increase or decrease ectomycorrhizal formation rate or provide other unaccounted benefits. To explore this symbiosis from a community ecology perspective, we sampled ectomycorrhizal root tips ov...
A number of recent studies suggest that interspecific competition plays a key role in determining the structure of ectomycorrhizal (ECM) fungal communities. Despite this growing consensus, there has been limited study of ECM fungal community dynamics in abiotically stressful environments, which are often dominated by positive rather than antagonist...
A new species of Russula, subgenus Compactae, is described growing in association with coast live oak (Quercus agrifolia) in California. This species has previously been referred to locally as Russula subnigricans Hongo and Russula eccentrica Peck, but morphological and DNA evidence show that it is a distinct species which we call R. cantharellicol...
A number of recent studies suggest that interspecific competition plays a key role in determining the structure of ectomycorrhizal (ECM) fungal communities. Despite this growing consensus, there has been limited study of ECM fungal community dynamics in abiotically stressful environments, which are often dominated by positive rather than antagonist...
A number of recent studies suggest that interspecific competition plays a key role in determining the structure of ectomycorrhizal (ECM) fungal communities. Despite this growing consensus, there has been limited study of ECM fungal community dynamics in abiotically stressful environments, which are often dominated by positive rather than antagonist...
The taxonomy and phylogeography of Pluteus section Pluteus in the Holarctic region was investigated using morphological and molecular data. Over 300 specimens spanning the major areas of boreal and temperate forests of the Northern Hemisphere were studied and nrITS and tef1 were obtained for phylogenetic analyses. In order to stabilize the taxonomy...
Sixteen dead Ferocactus wislizeni (Engelm.) Britton & Rose (Cactaceae), known variously as fishhook barrel cactus, candy barrel cactus, or compass plant, were discovered in various states of decay near Portal, Arizona during July 2011. A survey of the Coleoptera in the rotting cacti resulted in the collection of 976 specimens representing 11 famili...
The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, relia...
Coarse woody debris is an important biomass pool in forest ecosystems that numerous groups of insects have evolved to take advantage of. These insects are ecologically important and represent useful natural analogs for biomass to biofuel conversion. Using a range of molecular approaches combined with microelectrode measurements of oxygen, we have c...
Based on morphology, fungal species have been considered widespread and as a result, names of species from Europe or eastern North America were applied to species in western North America. However, DNA sequences have shown that many western taxa are different from their European counterparts; one such case is presented here. Comparisons of ITS and...
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...
Identification of three species of Suillus, S. caerulescens, S. ponderosus, and S. imitatus, has always been difficult because of overlapping and non-discrete morphological characters. To solidify the identification of these taxa, we compared the nucleotide sequences from the internal transcribed spacer region (ITS) of the type specimens of S. caer...
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 ex...
This chapter studies the genus Spathaspora. In the determination of the asexual reproduction it is seen that yeast cells are mostly globose and form by multilateral budding. Septate hyphae and pseudohyphae are present. In sexual reproduction it is found that the allantoid asci arise without conjugation and contain a single ascospore. Ascospores are...
In disturbed or pioneer settings, spores and sclerotia of ectomycorrhizal fungi serve as the necessary inoculum for establishment of ectomycorrhizal-dependent trees. Yet, little is known about the persistence of these propagules through time. Here, live field soil was inoculated with known quantities of basidiospores from four pine-associated speci...
Nuclear ribosomal DNA (ITS and ETS) sequences from 39 native Californian (USA) Allium species and congeners were combined with 154 ITS sequences available on GenBank to develop a global Allium phylogeny with the simultaneous goals of investigating the evolutionary history (monophyly) of Allium in the Californian center of diversity and exploring pa...
GenBank, the public repository for nucleotide and protein sequences, is a critical resource for molecular biology, evolutionary biology, and ecology. While some attention has been drawn to sequence errors ([1][1]), common annotation errors also reduce the value of this database. In fact, for
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...
Ascomycete yeasts are found commonly in the guts of basidioma-feeding beetles but little is known about their occurrence in the gut of other insects. In this study we isolated 95 yeasts from the gut of adult insects in five neuropteran families (Neuroptera: Corydalidae, Chrysopidae, Ascalaphidae, Mantispidae and Hemerobiidae) and a roach (Blattodea...
Ascomycete yeasts are found commonly in the guts of basidioma-feeding beetles but little is known about their occurrence in the gut of other insects. In this study we isolated 95 yeasts from the gut of adult insects in five neuropteran families (Neuroptera: Corydalidae, Chrysopidae, Ascalaphidae, Mantispidae and Hemerobiidae) and a roach (Blattodea...
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 informati...
Ascomycete yeasts that both ferment and assimilate xylose were reported previously as associates of insects living in woody substrates. Most notable have been reports of Pichia stipitis-like yeasts that are widely associated with the wood-boring beetle, Odontotaenius disjunctus (Coleoptera: Passalidae), in the eastern United States. Our continuing...
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...
Fourteen yeast isolates belonging to the Metschnikowia clade were isolated from the digestive tracts of lacewings (Neuroptera: Chrysopidae), soldier beetles and leaf beetles (Coleoptera: Cantharidae and Chrysomelidae), and a caddisfly (Trichoptera: Hydropsychidae). The insect hosts were associated with sugary substances of plants, a typical habitat...
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 membranifaci...
Enteroramus dimorphus from the gut of the passalid beetle Odontotaenius disjunctus was described originally as a yeast-like fungus of unknown taxonomic affiliation. The fungus can be observed in situ, attached by a specialized cell to the beetle hindgut wall. In a recent study of yeast endosymbionts from a variety of beetles, we discovered that E....
Enteroramus dimorphus from the gut of the passalid beetle Odontotaenius disjunctus was described originally as a yeast-like fungus of unknown taxonomic affiliation. The fungus can be observed in situ, attached by a specialized cell to the beetle hindgut wall. In a recent study of yeast endosymbionts from a variety of beetles, we discovered that E....
