Tom D Bruns

Tom D Bruns
University of California, Berkeley | UCB · Department of Plant and Microbial Biology

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399
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Publications

Publications (399)
Article
Davison et al. (Reports, 28 August 2015, p. 970) claim that virtual taxa of Glomeromycota show little endemism and that endemism that exists is similar to the levels seen in plant families. We show that this is likely due to the conservative species definition rather than to any ecological pattern.
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After severe wildfires, pine recovery depends on ectomycorrhizal (ECM) fungal spores surviving and serving as partners for regenerating forest trees. We took advantage of a large, severe natural forest fire that burned our long-term study plots to test the response of ECM fungi to fire. We sampled the ECM spore bank using pine seedling bioassays an...
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Settled airborne dust is used as a surrogate for airborne exposure in studies that explore indoor microbes. In order to determine whether detecting differences in dust environments would depend on the sampler type, we compared different passive, settled dust sampling approaches with respect to displaying qualitative and quantitative aspects of the...
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Human occupants are an important source of microbes in indoor environments. In this study, we used DNA sequencing of filter samples to assess the fungal and bacterial composition of air in an environmental chamber under different levels of occupancy, activity, and exposed or covered carpeting. In this office-like, mechanically ventilated environmen...
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Biofuel use is one of many means of addressing global change caused by anthropogenic release of fossil fuel carbon dioxide into Earth's atmosphere. To make a meaningful reduction in fossil fuel use, bioethanol must be produced from the entire plant rather than only its starch or sugars. Enzymes produced by fungi constitute a significant percentage...
Article
Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here we investigate the population structure and environmental adap...
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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...
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Ecologists have long acknowledged the importance of seed banks; yet, despite the fact that many plants rely on mycorrhizal fungi for survival and growth, the structure of ectomycorrhizal (ECM) fungal spore banks remains poorly understood. The primary goal of this study was to assess the geographic structure in pine-associated ECM fungal spore banks...
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There is an error in the first sentence of the Materials and Methods section. The correct sentence is: Experiments were conducted in a controlled environmental chamber (S1 Fig) designed to simulate an office room [15].
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Ectomycorrhizal (EM) fungi form symbiotic associations with plant roots that regulate nutrient exchange between forest plants and soil. Environmental metagenomics approaches that employ next-generation sequencing show great promise for studying EM symbioses, however, metatranscriptomic studies have been constrained by the inherent difficulties asso...
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Fungi play an important role in plant communities and ecosystem function. As a result, variation in fungal community composition can have important consequences for plant fitness. However, there are relatively few empirical data on how dispersal might affect fungal communities and the ecological processes they mediate. We established sampling stati...
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Identifying the ecological processes that structure communities and the consequences for ecosystem function is a central goal of ecology. The recognition that fungi, bacteria, and viruses control key ecosystem functions has made microbial communities a major focus of this field. Because many ecological processes are apparent only at particular spat...
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Genetic analysis of indoor air has uncovered a rich microbial presence, but rarely have both the bacterial and fungal components been examined in the same samples. Here we present a study that examined the bacterial component of passively settled microbes from both indoor and outdoor air over a discrete time period and for which the fungal componen...
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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...
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The predominant hypothesis regarding the composition of microbial assemblages in indoor environments is that fungal assemblages are structured by outdoor air with a moderate contribution by surface growth, whereas indoor bacterial assemblages represent a mixture of bacteria entered from outdoor air, shed by building inhabitants, and grown on surfac...
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Biological communities are often structured by environmental factors even at small spatial scales. Fungi are no exception, though the patterns and mechanisms underlying their community structure are usually unknown. Previous work documented zonation in fungi under tree canopies primarily through their fruiting patterns. Here we investigate the exis...
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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...
Conference Paper
Background/Question/Methods Fungi are a critical component of the diversity and function of terrestrial ecosystems. They regulate decomposition rates, facilitate plant nutrient uptake and have a profound impact on agriculture and economics. Understanding the forces that structure fungal communities thus has important theoretical and practical imp...
Conference Paper
Background/Question/Methods Ecologists have long acknowledged the importance of seed banks, yet despite the fact that many plants rely on mycorrhizal fungal partners for survival and growth, the structure of ectomycorrhizal fungal spore banks is known primarily from the western USA. As secondary successional habitats become more common due to ant...
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Sequence-based surveys of microorganisms in varied environments have found extremely diverse assemblages. A standard practice in current high-throughput sequence (HTS) approaches in microbial ecology is to sequence the composition of many environmental samples at once by pooling amplicon libraries at a common concentration before processing on one...
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Studies of the Monotropoideae (monotropes; Ericaceae), a monophyletic group of non-photosynthetic, mycoheterotrophic, and often rare or endangered plants, have been limited by the inability to propagate them. Monotropes associate with specific fungal hosts, and the only previously known method of seed germination was induction by host fungi or clos...
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Microbial communities play a major role in terrestrial ecosystem functioning, but the determinates of their diversity and functional interactions are not well known. In this study, we explored leaf litter fungal diversity in a diverse Panama lowland tropical forest in which a replicated factorial N, P, K and micronutrient fertilization experiment o...
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This report summarizes a meeting held in Boulder, CO USA (19-20 October 2012) on fungal community analyses using ultra-high-throughput sequencing of the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA (rRNA) genes. The meeting was organized as a two-day workshop, with the primary goal of supporting collaboration among research...
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The indoor microbiome is a complex system that is thought to depend on dispersal from the outdoor biome and the occupants' microbiome combined with selective pressures imposed by the occupants' behaviors and the building itself. We set out to determine the pattern of fungal diversity and composition in indoor air on a local scale and to identify pr...
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Specialization in plant host-symbiont-soil interactions may help mediate plant adaptation to edaphic stress. Our previous field study showed ecological evidence for host-symbiont specificity between serpentine and non-serpentine adapted ecotypes of Collinsia sparsiflora and arbuscular mycorrrhizal fungi (AMF). To test for adapted plant ecotype-AMF...
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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...
Conference Paper
Fungi are vital to terrestrial ecosystems as plant mutualists, pathogens, and decomposers. Similar to other microbes, little is known about beta diversity amongst fungal communities. Additionally, comparisons between culture and high-throughput sequence analyses generally result in different sets of species suggesting culture or amplification biase...
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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...
Conference Paper
Background/Question/Methods Fungal spores and hyphal fragments are common components of the air inside buildings, and they can have adverse impacts on human health. Much of the early work on indoor fungi focused on those that are readily cultured and easily identified by their morphology; such work revealed a relatively small set of common genera....
Article
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...
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Serpentine soil generates distinct plant assemblages, but it is not known how this edaphically extreme environment affects arbuscular mycorrhizal fungal (AMF) assembly or how this may contribute to plant adaptation to serpentine. Our previous studies showed that serpentine and non-serpentine adapted ecotypes of Collinisa sparsiflora associates with...
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The majority of achlorophyllous mycoheterotrophic plant species associate with arbuscular mycorrhizal fungi (AMF). Previous studies have shown that some species are highly specialized towards narrow lineages of AMF and have suggested that only particular lineages of these fungi are targeted by mycoheterotrophic plants. To test this hypothesis, we a...
Conference Paper
Background/Question/Methods Serpentine soil generates distinct plant assemblages, but it is not known if serpentine effects arbuscular mycorrhizal fungal (AMF) assembly or how this may contribute to plant adaptation to serpentine. A previous study showed that serpentine and non-serpentine adapted ecotypes of Collinisa sparsiflora associated with...
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The goals of our project were to document the diversity and distributions of cultivable fungi associated with decaying Miscanthus and sugarcane plants in nature and to further assess biodegradation of host plant cell walls by these fungi in pure cultures. Late in 2008 and early in 2009 we collected decaying Miscanthus and Saccharum from 8 sites in...
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Ectomycorrhizal exploration types have become an increasingly popular functional explanation for observed patterns of fungal community structure. In this study, we examined the relationship between exploration types of ectomycorrhizal fungi and root density. We did so by sampling across a root density gradient formed by the edge-interior transition...
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A gasteroid bolete collected recently in Sarawak on the island of Borneo is described as the new species Spongiforma squarepantsii. A comprehensive description, illustrations, phylogenetic placement and a comparison with a closely allied species are provided.
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In those regions of Europe where they coexist, the F and S intersterility groups (ISGs) of Heterobasidion annosum (Fr.) Bref. are primarily found on Abies spp. and Picea abies (L.) Karst., respectively. Eighty-three isolates of H. annosum were collected from Abies alba Mill. from 19 sites in Italy, including 10 Abies-Picea mixed conifer stands in t...
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Despite more than 100 years of detailed analysis of morphology and macromolecules, the phylogenetic origin of the Monotropoideae remains unclear. In this study partial sequences from the 28S rRNA gene were used to test two alternative hypotheses: (i) that the Monotropoideae share a most recent common ancestor with the Arbutoideae in the Ericaceae o...
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Random amplified polymorphic DNAs were correlated with the intersterility group and the geographic provenance of 36 isolates of Heterobasidion annosum from North America and Europe and of one herbarium collection of basidiocarps from California. This technique is very precise and yields higher resolution than previous studies implementing technique...
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Dispersal limitation plays an important role in a number of equilibrium and nonequilibrium theories about community ecology. In this study we use the framework of island biogeography to look for evidence of dispersal limitation in ectomycorrhizal fungal assemblages on "tree islands," patches of host trees located in a non-host vegetation matrix. Be...
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Pyrosequencing technologies have revolutionized how we describe and compare complex microbial communities. In 454 pyrosequencing data sets, the abundance of reads pertaining to taxa or phylotypes is commonly interpreted as a measure of genic or taxon abundance, useful for quantitative comparisons of community similarity. Potentially systematic bias...
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• In contrast to mycoheterotrophs that associate with ectomycorrhizal and saprotrophic fungi, we know little about the ecophysiology of arbuscular mycorrhizal mycoheterotrophs. Here, we identify the mycorrhizal fungi of two unrelated mycoheterotrophs and one putative partial mycoheterotroph that form arbuscular mycorrhizas, and analyse their carbon...
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Fungi are ubiquitous components of indoor human environments, where most contact between humans and microbes occurs. The majority of these organisms apparently play a neutral role, but some are detrimental to human lifestyles and health. Recent studies that used culture-independent sampling methods demonstrated a high diversity of indoor fungi dist...
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Suillus quiescens sp. nov. is common under Pinus muricata on Santa Cruz and Santa Rosa Islands in the northern Channel Islands of California, and we subsequently found it fruiting at Point Reyes National Seashore on the central coast of California. Sequences from the internal transcribed spacer region show that it is distinct from all 44 species of...