Tadashi Fukami

Tadashi Fukami
Stanford University | SU · Department of Biology

Ph.D.

About

209
Publications
39,542
Reads
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11,956
Citations
Introduction
Tadashi Fukami is Professor in the Department of Biology at Stanford University. He received a Bachelors degree from Waseda University in 1996, a Masters degree from the University of Tokyo in 1998, and a Ph.D. from the University of Tennessee, Knoxville, in 2003. He was a Postdoctoral Fellow at Landcare Research, New Zealand (2003-2005) and an Assistant Professor at the University of Hawaii at Manoa (2006-2008) before joining the Stanford faculty in 2008.
Additional affiliations
September 2015 - present
Stanford University
Position
  • Professor (Associate)
September 2008 - August 2015
Stanford University
Position
  • Professor (Assistant)
January 2006 - August 2008
University of Hawaiʻi at Mānoa
Position
  • Professor (Assistant)
Education
August 1998 - July 2003
University of Tennessee
Field of study
  • Ecology and Evolutionary Biology
April 1996 - March 1998
April 1991 - March 1996
Waseda University
Field of study

Publications

Publications (209)
Article
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Biology 44Y, an IBI prize-winning module, helps students do science by practice, with a focus on plant-pollinator-microbe interactions as a model system.
Article
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The order and timing of species immigration during community assembly can affect species abundances at multiple spatial scales. Known as priority effects, these effects cause historical contingency in the structure and function of communities, resulting in alternative stable states, alternative transient states, or compositional cycles. The mechani...
Article
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Convergence occurs in both species traits and community structure, but how convergence at the two scales influences each other remains unclear. To address this question, we focus on tropical forest monodominance, in which a single, often ectomycorrhizal (EM) tree species occasionally dominates forest stands within a landscape otherwise characterize...
Article
A variety of relationships have been observed between sexual dimorphism and species diversity, from positive to negative and nonsignificant. Although many hypotheses have been proposed to explain these relationships, it has proven difficult to understand why patterns are so variable. Most studies on this topic have used clades as phylogenetically i...
Article
Floral nectar is prone to colonization by nectar-adapted yeasts and bacteria via air-, rain-, and animal-mediated dispersal. Upon colonization, microbes can modify nectar chemical constituents that are plant-provisioned or impart their own through secretion of metabolic by-products or antibiotics into the nectar environment. Such modifications can...
Article
Along with bacteria, fungi can represent a significant component of animal- and plant-associated microbial communities. However, we have only begun to describe these fungi, much less examine their effects on most animals and plants. Bacteria associated with the honey bee, Apis mellifera, have been well characterized across different regions of the...
Article
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A correction to this paper has been published: https://doi.org/10.1007/s00248-021-01755-2
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Ecological selection is a major driver of community assembly. Selection is classified as stabilizing when species with intermediate trait values gain the highest reproductive success, whereas selection is considered directional when fitness is highest for species with extreme trait values. Previous studies have investigated the effects of different...
Data
Supporting Information. DeMalach, N., P.-J. Ke, and T. Fukami. 2021. The effects of ecological selection on species diversity and trait distribution: predictions and an empirical test. Ecology. Appendix S1
Article
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The history of species immigration can dictate how species interact in local communities, thereby causing historical contingency in community assembly. Since immigration history is rarely known, these historical influences, or priority effects, pose a major challenge in predicting community assembly. Here, we provide a graph‐based, non‐parametric,...
Article
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Introduced mammalian predators are responsible for the decline and extinction of many native species, with rats (genus Rattus ) being among the most widespread and damaging invaders worldwide. In a naturally fragmented landscape, we demonstrate the multi-year effectiveness of snap traps in the removal of Rattus rattus and Rattus exulans from lava-s...
Data
Dynamic plant–soil microbe interactions: the neglected effect of soil conditioning time: SI
Article
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Plant–soil feedbacks (PSF) may change in strength over the life of plant individuals as plants continue to modify the soil microbial community. However, the temporal variation in PSF is rarely quantified and its impacts on plant communities remain unknown. Using a chronosequence reconstructed from annual aerial photos of a coastal dune ecosystem, w...
Article
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A detailed evaluation of eight bacterial isolates from floral nectar and animal visitors to flowers shows evidence that they represent three novel species in the genus Acinetobacter . Phylogenomic analysis shows the closest relatives of these new isolates are Acinetobacter apis , Acinetobacter boissieri and Acinetobacter nectaris , previously descr...
Article
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Floral nectar is commonly colonized by yeasts and bacteria, whose growth largely depends on their capacity to assimilate nutrient resources, withstand high osmotic pressures, and cope with unbalanced carbon-to-nitrogen ratios. Although the basis of the ecological success of these microbes in the harsh environment of nectar is still poorly understoo...
Preprint
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Priority effects arise when the history of species arrival influences local species interactions, thereby affecting the composition of ecological communities. The outcome of some priority effects may be more difficult to predict than others, but this possibility remains to be fully investigated. Here, we provide a graph-based, non-parametric, theor...
Article
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Life-history trade-offs among species are major drivers of community assembly. Most studies investigate how trade-offs promote deterministic coexistence of species. It remains unclear how trade-offs may instead promote historically contingent exclusion of species, where species dominance is affected by initial abundances, causing alternative commun...
Article
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Ecological communities typically contain more species when located within geologically older regions. This pattern is traditionally attributed to the long-term accumulation of species in the regional species pool, with local species interactions playing a minor role. We provide evidence suggesting a more important role of local species interactions...
Article
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Ericaceous plants rely on ericoid mycorrhizal fungi for nutrient acquisition. However, the factors that affect the composition and structure of fungal communities associated with the roots of ericaceous plants remain largely unknown. Here, we use a 4.1-myr soil chronosequence in Hawaii to test the hypothesis that changes in nutrient availability wi...
Article
About 90% of all flowering plant species are pollinated by animals. Animals are attracted to flowers because they often provide food in the form of nectar and pollen. While floral nectar is assumed to be initially sterile, it commonly becomes colonized by yeasts after animals have visited the flowers. Although yeast communities in floral nectar app...
Preprint
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Crop tissues harbor microbiomes that can affect host health and yield. However, processes driving microbiome assembly, and resulting effects on ecosystem services, remain poorly understood. This is particularly true of flowering crops that rely on pollinators for yield. We assessed effects of orchard management tactics and landscape context on the...
Preprint
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Microbial communities in the honey bee gut have emerged as a model system to understand the effects of host-associated microbes on animals and plants. The specific distribution patterns of bacterial associates among honey bee gut regions remains a key finding within the field. The mid- and hindgut of foraging bees house a deterministic set of core...
Preprint
Full-text available
Ericaceous plants rely on ericoid mycorrhizal fungi for nutrient acquisition. However, the factors that affect the composition and structure of these fungal communities remain largely unknown. Here, we use a 4.1-myr soil chronosequence in Hawaii to test the hypothesis that changes in nutrient availability with soil age determine the diversity and s...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
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Local ecological communities tend to contain more species when they are located within a geologically older region, a pattern that has traditionally been attributed to the accumulation of species in the regional species pool. In this explanation, local species interactions are assumed to play a minor role in the formation of the regional species po...
Article
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Agricultural practices constitute both the greatest cause of biodiversity loss and the greatest opportunity for conservation1,2, given the shrinking scope of protected areas in many regions. Recent studies have documented the high levels of biodiversity—across many taxa and biomes—that agricultural landscapes can support over the short term1,3,4. H...
Article
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Human modification of the environment, particularly through land-use change, often reduces animal species diversity. However, the effect of land-use change on the gut microbiome of wildlife in human-dominated landscapes is not well understood despite its potential consequences for host health. We sought to quantify the effect of land-use change on...
Preprint
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The species pool hypothesis highlights the effects of historical processes and past adaptation on contemporary patterns of species diversity. This hypothesis has been contentious because it is difficult to test. Here we argue that a trait-based approach enables an effective test of this hypothesis where increasing mismatch between community mean tr...
Article
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Lifelong infection of the gastric mucosa by Helicobacter pylori can lead to peptic ulcers and gastric cancer. However, how the bacteria maintain chronic colonization in the face of constant mucus and epithelial cell turnover in the stomach is unclear. Here, we present a new model of how H. pylori establish and persist in stomach, which involves the...
Data
Gland population islands originate from a small number of founder bacteria. (A) H. pylori experiences a huge bottleneck when establishing initial colonization. Total CFU recovered from a whole stomach at various time points post-infection with Hp GFP (3–5 mice per time point). All mice were infected as adults. “Inoc” represents the 108 CFU inoculum...
Data
Generation of isogenic and equally fit fluorescent H. pylori strains. (A) To generate isogenic fluorescent H. pylori strains in the PMSS1 background (Hp GFP or Hp tdT), the nonessential gene rdxA was replaced via homologous recombination by a construct containing the aphA gene (conferring kanamycin resistance, kanR), the ureA promoter, and either t...
Data
Differences between Hp GFP and Hp tdT genomes. (PDF)
Data
Primers used to generate fluorophore-expression constructs. (PDF)
Data
Organization of H. pylori gland populations as patches occur in multiple co-infected animals. Mapping of location and number of gland-associated bacteria across longitudinal stomach sections from additional animals co-infected with Hp GFP and Hp tdT at 2 weeks post-infection. Each plot represents a single section from one individual mouse. The thre...
Data
Mice infected as neonates maintain a higher density of gland-associated bacteria during chronic infection. (A) Total CFU/g recovered from mice infected as 1-week-old neonates or 6-week-old adults at 1 month post-infection (8–9 animals per group). These are the same 1-month co-infected animals from Fig 3. Gray dotted line, limit of detection; red ba...
Data
High spatial accuracy and resolution analysis of H. pylori gastric colonization with passive CLARITY technique (PACT) and 3D confocal microscopy. (MOV)
Data
Computer simulations that assume adjacent spread and gland resistance recapitulate observations in murine co-infections. Simulation of H. pylori gland colonization and spread, in which 10 randomly selected glands were colonized by Hp GFP and another set of 10 by Hp tdT in a field of 20,000 available glands, and bacteria were allowed to spread over...
Data
Mapping H. pylori biogeography in longitudinal gastric sections. (MOV)
Article
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Modern coexistence theory is increasingly used to explain how differences between competing species lead to coexistence versus competitive exclusion. Although research testing this theory has focused on deterministic cases of competitive exclusion, in which the same species always wins, mounting evidence suggests that competitive exclusion is often...
Article
Beyond its role as a reward for pollinators, floral nectar also provides a habitat for specialized and opportunistic yeasts and bacteria. These microbes modify nectar chemistry, often altering mutualistic relationships between plants and pollinators in ways that we are only beginning to understand. Many studies on this multi-partite system have foc...
Article
Full-text available
Intraspecific trait variation is receiving renewed interest as a factor affecting the structure of multi-species communities within and across trophic levels. One pervasive form of intraspecific trait variation is sexual dimorphism in animals and plants, which might exert large effects particularly on the communities of host-associated organisms, b...
Preprint
Dominance by annual species is commonly viewed as a transient state in plant succession preceding eventual perennial dominance. However, circumstantial evidence suggests that annual-perennial interactions can cause priority effects, allowing persistent annual dominance when annuals are initially more common than perennials. The necessary conditions...
Article
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Worldwide, native species increasingly contend with the interacting stressors of habitat fragmentation and invasive species, yet their combined effects have rarely been examined. Direct negative effects of invasive omnivores are well documented, but the indirect effects of resource competition or those caused by predator avoidance are unknown. Here...
Data
Height of canopy increases with kīpuka size. Canopy heights were averaged over all foraging observations by kīpuka. Data are shown ± SE. Solid black line indicates line of best fit for treated kīpuka and dotted gray for untreated kīpuka. Canopy height increased with kīpuka size and did not differ between treatments. (PDF)
Data
GLMM model averaging results: Proportion of vertical foraging space occupied (canopy utilization by birds). (PDF)
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Post-hoc testing for Species (p-value adjustment method: fdr) of model described in Table D. (PDF)
Data
GLMM model averaging results: Foraging behavior effects on foraging height. (PDF)
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Mean foraging height of birds by rat treatment and horizontal foraging position. Foraging height was unaffected by horizontal foraging position of the bird within the canopy. Different letters indicate significance at p < 0.01. (PDF)
Data
GLMM model averaging results: Kīpuka characteristics and tree height. (PDF)
Data
GLMM model averaging results: Proportion of arthropod biomass per trap. (PDF)
Data
GLMM model averaging results: Foraging heights of Hawaiian forest birds by bird species. (PDF)
Article
Full-text available
Intraspecific trait variation is receiving renewed interest as a factor affecting the structure of multi-species communities within and across trophic levels. One pervasive form of intraspecific trait variation is sexual dimorphism in animals and plants, which might exert large effects particularly on the communities of host-associated organisms, b...
Article
Full-text available
Understanding the origins and maintenance of biodiversity remains one of biology's grand challenges. From theory and observational evidence, we know that variability in environmental conditions through time is likely critical to the coexistence of competing species. Nevertheless, experimental tests of fluctuation-driven coexistence are rare and hav...
Article
Full-text available
Many species of yeast are integral to human society. They produce many of our foods, beverages and industrial chemicals, challenge us as pathogens, and provide models for the study of our own biology. However, few species are regularly studied and much of their ecology remains unclear, hindering the development of knowledge that is needed to improv...
Article
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Inhibitory priority effects, in which early-arriving species exclude competing species from local communities, are thought to enhance regional species diversity via community divergence. Theory suggests, however, that these same priority effects make it difficult for species to coexist in the region unless individuals are continuously supplied from...
Article
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Background and aims: Flowers can be highly variable in nectar volume and chemical composition, even within the same plant, but the causes of this variation are not fully understood. One potential cause is nectar-colonizing bacteria and yeasts, but experimental tests isolating their effects on wildflowers are largely lacking. This study examines th...
Article
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Priority effects, or the effects of species arrival history on local species abundances, have been documented in a range of taxa. However, factors determining the extent to which priority effects affect community assembly remain unclear. Using laboratory populations of the bacterium Pseudomonas fluorescens, we examined whether shared evolutionary h...
Article
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Understanding how microbial communities develop is essential for predicting and directing their future states. Ecological theory suggests that community development is often influenced by priority effects, in which the order and timing of species arrival determine how species affect one another. Priority effects can have long-lasting consequences,...
Article
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This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: [10.1111/oik.4243] The order of species arrival can influence how spe...
Article
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Both top-down (grazing) and bottom-up (resource availability) forces can determine the strength of priority effects, or the effects of species arrival history on the structure and function of ecological communities, but their combined influences remain unresolved. To test for such influences, we assembled experimental communities of wood-decomposin...
Article
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Animals often increase their fitness by moving across space in response to temporal variation in habitat quality and resource availability, and as a result of intra and inter-specific interactions. The long-term persistence of populations and even whole species depends on the collective patterns of individual movements, yet animal movements have be...
Article
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Dispersal is considered a key driver of beta diversity, the variation in species composition among local communities, but empirical tests remain limited. We manipulated dispersal of nectar-inhabiting bacteria and yeasts via flower-visiting animals to examine how dispersal influenced microbial beta diversity among flowers. Contrary to the prevailing...