Academic Appointments

Professional Education

  • PhD, Univ of Tennessee, Knoxville, Ecology & Evolutionary Biology (2003)

Current Research and Scholarly Interests

Ecological and evolutionary community assembly, with emphasis on understanding historical contingency in community structure, ecosystem functioning, biological invasion and ecological restoration, using experimental, theoretical, and comparative methods involving bacteria, protists, fungi, plants, and animals.


  • Nectar microbes in ume orchards, Stanford University (12/7/2017 - Present)

    The goal of this project is to understand how the microorganisms including bacteria and yeasts that colonize the floral nectar of ume, or Japanese apricot (Prunus mume), affect pollination by native honey bees, which is necessary for the production of the apricot. This knowledge will be used to determine how microbial colonization of flowers can be manipulated for more effective pollination. The study site is located in the Minabe/Tanabe region, a GIAHS (Globally Important Agricultural Heritage System) site designated by FAO.


    Minabe and Tanabe, Wakayama, Japan

2018-19 Courses

Stanford Advisees

Graduate and Fellowship Programs

  • Biology (School of Humanities and Sciences) (Phd Program)

All Publications

  • Community-wide consequences of sexual dimorphism: evidence from nectar microbes in dioecious plants ECOLOGY Tsuji, K., Fukami, T. 2018; 99 (11): 2476–84


    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, but the extent of these effects is not well understood. We investigated whether host-associated microbial communities developed differently in the floral nectar of female and male individuals of the dioecious shrubs, Eurya emarginata and E. japonica. We found that nectar-colonizing microbes such as bacteria and fungi were more than twice as prevalent and, overall, more than 10 times as abundant in male flowers as in female flowers. Microbial species composition also differed between flower sexes. To examine potential mechanisms behind these differences, we manipulated the frequency of flower visitation by animals and the order of arrival of microbial species to nectar. Animal visitation frequency affected microbial communities more greatly in male flowers, while arrival order affected them more in female flowers. These sex-specific effects appeared attributable to differences in how animals and microbes altered the chemical characteristics of nectar that limited microbial growth. Taken together, our results provide evidence that sexual dimorphism can have large effects on the structure of host-associated communities.

    View details for DOI 10.1002/ecy.2494

    View details for Web of Science ID 000449937900007

    View details for PubMedID 30216955

  • Vertical foraging shifts in Hawaiian forest birds in response to invasive rat removal PLOS ONE Rankin, E., Knowlton, J. L., Gruner, D. S., Flaspohler, D. J., Giardina, C. P., Leopold, D. R., Buckardt, A., Pitt, W. C., Fukami, T. 2018; 13 (9): e0202869


    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 we isolated and examined the independent and interactive effects of invasive omnivorous Black rats (Rattus rattus) and forest fragment size on the interactions between avian predators and their arthropod prey. Our study examines whether invasive omnivores and ecosystem fragment size impact: 1) the vertical distribution of arthropod species composition and abundance, and 2) the vertical profile of foraging behaviors of five native and two non-native bird species found in our study system. We predicted that the reduced edge effects and greater structural complexity and canopy height of larger fragments would limit the total and proportional habitat space frequented by rats and thus limit their impact on both arthropod biomass and birds' foraging behavior. We experimentally removed invasive omnivorous Black rats across a 100-fold (0.1 to 12 ha) size gradient of forest fragments on Hawai'i Island, and paired foraging observations of forest passerines with arthropod sampling in the 16 rat-removed and 18 control fragments. Rat removal was associated with shifts in the vertical distribution of arthropod biomass, irrespective of fragment size. Bird foraging behavior mirrored this shift, and the impact of rat removal was greater for birds that primarily eat fruit and insects compared with those that consume nectar. Evidence from this model study system indicates that invasive rats indirectly alter the feeding behavior of native birds, and consequently impact multiple trophic levels. This study suggests that native species can modify their foraging behavior in response to invasive species removal and presumably arrival through behavioral plasticity.

    View details for DOI 10.1371/journal.pone.0202869

    View details for Web of Science ID 000445998100007

    View details for PubMedID 30248110

  • Nectar yeasts: a natural microcosm for ecology. Yeast (Chichester, England) Chappell, C. R., Fukami, T. 2018; 35 (6): 417–23


    The species of yeasts that colonize floral nectar can modify the mutualistic relationships between plants and pollinators by changing the chemical properties of nectar. Recent evidence supporting this possibility has led to increased interest among ecologists in studying these fungi as well as the bacteria that interact with them in nectar. Although not fully explored, nectar yeasts also constitute a promising natural microcosm that can be used to facilitate development of general ecological theory. We discuss the methodological and conceptual advantages of using nectar yeasts from this perspective, including simplicity of communities, tractability of dispersal, replicability of community assembly, and the ease with which the mechanisms of species interactions can be studied in complementary experiments conducted in the field and the laboratory. To illustrate the power of nectar yeasts as a study system, we discuss several topics in community ecology, including environmental filtering, priority effects, and metacommunity dynamics. An exciting new direction is to integrate metagenomics and comparative genomics into nectar yeast research to address these fundamental ecological topics.

    View details for DOI 10.1002/yea.3311

    View details for PubMedID 29476620

  • Eco-Evolutionary Buffering: Rapid Evolution Facilitates Regional Species Coexistence despite Local Priority Effects AMERICAN NATURALIST Wittmann, M. J., Fukami, T. 2018; 191 (6): E171–E184


    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 an external species pool, often an unrealistic assumption. Here we develop an eco-evolutionary hypothesis to solve this conundrum. We build a metacommunity model in which local priority effects occur between two species via interspecific interference. Within each species there are two genotypes: one is more resistant to interspecific interference than the other but pays a fitness cost for its resistance. Because of this trade-off, species evolve to become less resistant as they become regionally more common. Rare species can then invade some local patches and consequently recover in regional frequency. This "eco-evolutionary buffering" enables the regional coexistence of species despite local priority effects, even in the absence of immigration from an external species pool. Our model predicts that eco-evolutionary buffering is particularly effective when local communities are small and connected by infrequent dispersal.

    View details for DOI 10.1086/697187

    View details for Web of Science ID 000432225200001

    View details for PubMedID 29750553

  • Genomic diversity of a nectar yeast clusters into metabolically, but not geographically, distinct lineages MOLECULAR ECOLOGY Dhami, M. K., Hartwig, T., Letten, A. D., Banf, M., Fukami, T. 2018; 27 (8): 2067–76


    Both dispersal limitation and environmental sorting can affect genetic variation in populations, but their contribution remains unclear, particularly in microbes. We sought to determine the contribution of geographic distance (as a proxy for dispersal limitation) and phenotypic traits (as a proxy for environmental sorting), including morphology, metabolic ability and interspecific competitiveness, to the genotypic diversity in a nectar yeast species, Metschnikowia reukaufii. To measure genotypic diversity, we sequenced the genomes of 102 strains of M. reukaufii isolated from the floral nectar of hummingbird-pollinated shrub, Mimulus aurantiacus, along a 200-km coastline in California. Intraspecific genetic variation showed no detectable relationship with geographic distance, but could be grouped into three distinct lineages that correlated with metabolic ability and interspecific competitiveness. Despite ample evidence for strong competitive interactions within and among nectar yeasts, a full spectrum of the genotypic and phenotypic diversity observed across the 200-km coastline was represented even at a scale as small as 200 m. Further, more competitive strains were not necessarily more abundant. These results suggest that dispersal limitation and environmental sorting might not fully explain intraspecific diversity in this microbe and highlight the need to also consider other ecological factors such as trade-offs, source-sink dynamics and niche modification.

    View details for DOI 10.1111/mec.14535

    View details for Web of Science ID 000431667800023

    View details for PubMedID 29446179

  • The ecology of insect-yeast relationships and its relevance to human industry PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Madden, A. A., Epps, M., Fukami, T., Irwin, R. E., Sheppard, J., Sorger, D., Dunn, R. R. 2018; 285 (1875)


    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 improve the relationships between humans and yeasts. There is increasing evidence that insects are an essential component of ascomycetous yeast ecology. We propose a 'dispersal-encounter hypothesis' whereby yeasts are dispersed by insects between ephemeral, spatially disparate sugar resources, and insects, in turn, obtain the benefits of an honest signal from yeasts for the sugar resources. We review the relationship between yeasts and insects through three main examples: social wasps, social bees and beetles, with some additional examples from fruit flies. Ultimately, we suggest that over the next decades, consideration of these ecological and evolutionary relationships between insects and yeasts will allow prediction of where new yeast diversity is most likely to be discovered, particularly yeasts with traits of interest to human industry.

    View details for DOI 10.1098/rspb.2017.2733

    View details for Web of Science ID 000428940600007

    View details for PubMedID 29563264

    View details for PubMedCentralID PMC5897634

  • Contrasting effects of yeasts and bacteria on floral nectar traits. Annals of botany Vannette, R. L., Fukami, T. 2018


    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 the effects of dominant species of yeasts and bacteria on the hummingbird-pollinated shrub, Mimulus aurantiacus, in California.Methods: Wildflowers were inoculated with field-relevant titres of either the yeast Metschnikowia reukaufii or the bacterium Neokomagataea sp. (formerly Gluconobacter sp.), both isolated from M. aurantiacus nectar. Newly opened flowers were bagged, inoculated, harvested after 3 d and analysed for microbial abundance, nectar volume, and sugar and amino acid concentration and composition.Key Results: Yeast inoculation reduced amino acid concentration and altered amino acid composition, but had no significant effect on nectar volume or sugar composition. In contrast, bacterial inoculation increased amino acid concentration, enhanced the proportion of nectar sugars comprised by monosaccharides, and reduced nectar volume.Conclusions: The results presented suggest that microbial inhabitants of floral nectar can make nectar characteristics variable among flowers through divergent effects of yeasts and bacteria on nectar chemistry and availability, probably modifying plant-pollinator interactions.

    View details for DOI 10.1093/aob/mcy032

    View details for PubMedID 29562323

  • Priority effects can persist across floral generations in nectar microbial metacommunities OIKOS Toju, H., Vannette, R. L., Gauthier, M. L., Dhami, M. K., Fukami, T. 2018; 127 (3): 345–52

    View details for DOI 10.1111/oik.04243

    View details for Web of Science ID 000426652500002

  • Priority effects are weakened by a short, but not long, history of sympatric evolution. Proceedings. Biological sciences Zee, P. C., Fukami, T. 2018; 285 (1871)


    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 history affected the strength of priority effects. We hypothesized that sympatric evolution of populations belonging to the same guild would lead to niche differentiation, resulting in phenotypic complementarity that weakens priority effects. Consistent with this hypothesis, we found that priority effects tended to be weaker in sympatrically evolved pairs of immigrating populations than in allopatrically evolved pairs. Furthermore, priority effects were weaker under higher phenotypic complementarity. However, these patterns were observed only in populations with a relatively short history of sympatric evolution, and disappeared when populations had evolved together for a long time. Together, our results suggest that the evolutionary history of organismal traits may dictate the strength of priority effects and, consequently, the extent of historical contingency in the assembly of ecological communities.

    View details for DOI 10.1098/rspb.2017.1722

    View details for PubMedID 29386363

  • Species coexistence through simultaneous fluctuation-dependent mechanisms. Proceedings of the National Academy of Sciences of the United States of America Letten, A. D., Dhami, M. K., Ke, P. J., Fukami, T. 2018


    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 have typically focused on just one of two potential mechanisms, the temporal storage effect, to the neglect of the theoretically equally plausible mechanism known as relative nonlinearity of competition. We combined experiments and simulations in a system of nectar yeasts to quantify the relative contribution of the two mechanisms to coexistence. Resource competition models parameterized from single-species assays predicted the outcomes of mixed-culture competition experiments with 83% accuracy. Model simulations revealed that both mechanisms have measurable effects on coexistence and that relative nonlinearity can be equal or greater in magnitude to the temporal storage effect. In addition, we show that their effect on coexistence can be both antagonistic and complementary. These results falsify the common assumption that relative nonlinearity is of negligible importance, and in doing so reveal the importance of testing coexistence mechanisms in combination.

    View details for DOI 10.1073/pnas.1801846115

    View details for PubMedID 29895689

  • Role of priority effects in the early-life assembly of the gut microbiota. Nature reviews. Gastroenterology & hepatology Sprockett, D., Fukami, T., Relman, D. A. 2018; 15 (4): 197–205


    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, particularly if species arrival history varies during the early stage of community development, but their importance to the human gut microbiota and host health remains largely unknown. Here, we explore how priority effects might influence microbial communities in the gastrointestinal tract during early childhood and how the strength of priority effects can be estimated from the composition of the microbial species pool. We also discuss factors that alter microbial transmission, such as delivery mode, diet and parenting behaviours such as breastfeeding, which can influence the likelihood of priority effects. An improved knowledge of priority effects has the potential to inform microorganism-based therapies, such as prebiotics and probiotics, which are aimed at guiding the microbiota towards a healthy state.

    View details for DOI 10.1038/nrgastro.2017.173

    View details for PubMedID 29362469

  • Geographical Variation in Community Divergence: Insights from Tropical Forest Monodominance by Ectomycorrhizal Trees AMERICAN NATURALIST Fukami, T., Nakajima, M., Fortunel, C., Fine, P. A., Baraloto, C., Russo, S. E., Peay, K. G. 2017; 190: S105–S122


    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 characterized by diverse communities of arbuscular mycorrhizal (AM) trees. Such monodominance is a striking potential example of community divergence resulting in alternative stable states. However, it is observed only in some tropical regions. A diverse suite of AM and EM trees locally codominate forest stands elsewhere. We develop a hypothesis to explain this geographical difference using a simulation model of plant community assembly. Simulation results suggest that in a region with a few EM species (e.g., South America), EM trees experience strong selection for convergent traits that match the abiotic conditions of the environment. Consequently, EM species successfully compete against other species to form monodominant stands via positive plant-soil feedbacks. By contrast, in a region with many EM species (e.g., Southeast Asia), species maintain divergent traits because of complex plant-soil feedbacks, with no species having traits that enable monodominance. An analysis of plant trait data from Borneo and Peruvian Amazon was inconclusive. Overall, this work highlights the utility of geographical comparison in understanding the relationship between trait convergence and community convergence.

    View details for DOI 10.1086/692439

    View details for Web of Science ID 000406102900008

    View details for PubMedID 28731828

  • Priority effects are interactively regulated by top-down and bottom-up forces: evidence from wood decomposer communities ECOLOGY LETTERS Leopold, D. R., Wilkie, J., Dickie, I. A., Allen, R. B., Buchanan, P. K., Fukami, T. 2017; 20 (8): 1054–63


    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-decomposing fungi using a factorial manipulation of fungivore (Folsomia candida) presence, nitrogen availability, and fungal assembly history. We found interactive effects of all three factors on fungal species composition and wood decomposition 1 year after the fungi were introduced. The strength of priority effects on community structure was affected primarily by nitrogen availability, whereas the strength of priority effects on decomposition rate was interactively regulated by nitrogen and fungivores. These results demonstrate that top-down and bottom-up forces jointly determine how strongly assembly history affects community structure and function.

    View details for DOI 10.1111/ele.12803

    View details for Web of Science ID 000405917500013

    View details for PubMedID 28677298

  • Movements of four native Hawaiian birds across a naturally fragmented landscape JOURNAL OF AVIAN BIOLOGY Knowlton, J. L., Flaspohler, D. J., Paxton, E. H., Fukami, T., Giardina, C. P., Gruner, D. S., Rankin, E. 2017; 48 (7): 921–31

    View details for DOI 10.1111/jav.00924

    View details for Web of Science ID 000407250900003

  • Dispersal enhances beta diversity in nectar microbes ECOLOGY LETTERS Vannette, R. L., Fukami, T. 2017; 20 (7): 901–10


    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 view that dispersal lowers beta diversity, we found beta diversity was highest when dispersal was least limited. Our analysis suggested that this unexpected pattern might have resulted from stronger priority effects under increased dispersal. Dispersal is highly stochastic, generating variability in species arrival history and consequently the potential for community divergence via priority effects, in these and likely many other microbial, plant, and animal communities. Yet most previous experiments eliminated this possibility. We suggest that the positive effects of dispersal on beta diversity, like the one we report here, may have been greatly underappreciated.

    View details for DOI 10.1111/ele.12787

    View details for Web of Science ID 000403794100011

    View details for PubMedID 28597955

  • Linking modern coexistence theory and contemporary niche theory ECOLOGICAL MONOGRAPHS Letten, A. D., Ke, P., Fukami, T. 2017; 87 (2): 161-177

    View details for DOI 10.1002/ecm.1242

    View details for Web of Science ID 000400406300001

  • Evolutionary priority effects persist in anthropogenically created habitats, but not through nonnative plant invasion. New phytologist Brandt, A. J., Lee, W. G., Tanentzap, A. J., Hayman, E., Fukami, T., Anderson, B. J. 2017


    Evolutionary priority effects, where early-arriving lineages occupy niche space via diversification and preclude dominance of later arrivals, have been observed in alpine and forest communities. However, the potential for evolutionary priority effects to persist in an era of rapid global change remains unclear. Here, we use a natural experiment of historical disturbance in New Zealand to test whether anthropogenic changes in available habitat and nonnative invasion eliminate the role of evolutionary priority effects in community assembly. We also test whether evolutionary priority effects diminish with decreasing resource availability. Older plant clades, as estimated by clade crown age, were relatively more abundant in both primary and secondary grassland. Relative abundance in primary grassland decreased with clade stem age, but only weakly. However, for both clade age estimates, relative abundance decreased with age when nonnative biomass was high and soil moisture was low. Our data show that patterns in community structure consistent with evolutionary priority effects can occur in both primary and secondary grasslands, the latter created by anthropogenic disturbance. However, nonnative invasion may overwhelm the effect of immigration timing on community dominance, possibly as a result of high immigration rates and preadaptation to anthropogenically modified environments.

    View details for DOI 10.1111/nph.14544

    View details for PubMedID 28407248

  • Non-target effects of fungicides on nectar-inhabiting fungi of almond flowers ENVIRONMENTAL MICROBIOLOGY REPORTS Schaeffer, R. N., Vannette, R. L., Brittain, C., Williams, N. M., Fukami, T. 2017; 9 (2): 79-84


    Nectar mediates interactions between plants and pollinators in natural and agricultural systems. Specialized microorganisms are common nectar inhabitants, and potentially important mediators of plant-pollinator interactions. However, their diversity and role in mediating pollination services in agricultural systems are poorly characterized. Moreover, agrochemicals are commonly applied to minimize crop damage, but may present ecological consequences for non-target organisms. Assessment of ecological risk has tended to focus on beneficial macroorganisms such as pollinators, with less attention paid to microorganisms. Here, using culture-independent methods, we assess the impact of two widely-used fungicides on nectar microbial community structure in the mass-flowering crop almond (Prunus dulcis). We predicted that fungicide application would reduce fungal richness and diversity, whereas competing bacterial richness would increase, benefitting from negative effects on fungi. We found that fungicides reduced fungal richness and diversity in exposed flowers, but did not significantly affect bacterial richness, diversity, or community composition. The relative abundance of Metschnikowia OTUs, nectar specialists that can impact pollination, was reduced by both fungicides. Given growing recognition of the importance of nectar microorganisms as mediators of plant-pollinator mutualisms, future research should consider the impact of management practices on plant-associated microorganisms and consequences for pollination services in agricultural landscapes.

    View details for DOI 10.1111/1758-2229.12501

    View details for Web of Science ID 000397493300003

  • Precipitation alters the strength of evolutionary priority effects in forest community assembly of pteridophytes and angiosperms JOURNAL OF ECOLOGY Brandt, A. J., Tanentzap, A. J., Leopold, D. R., Heenan, P. B., Fukami, T., Lee, W. G. 2016; 104 (6): 1673-1681
  • Genetic basis of priority effects: insights from nectar yeast. Proceedings. Biological sciences Dhami, M. K., Hartwig, T., Fukami, T. 2016; 283 (1840): -?


    Priority effects, in which the order of species arrival dictates community assembly, can have a major influence on species diversity, but the genetic basis of priority effects remains unknown. Here, we suggest that nitrogen scavenging genes previously considered responsible for starvation avoidance may drive priority effects by causing rapid resource depletion. Using single-molecule sequencing, we de novo assembled the genome of the nectar-colonizing yeast, Metschnikowia reukaufii, across eight scaffolds and complete mitochondrion, with gap-free coverage over gene spaces. We found a high rate of tandem gene duplication in this genome, enriched for nitrogen metabolism and transport. Both high-capacity amino acid importers, GAP1 and PUT4, present as tandem gene arrays, were highly expressed in synthetic nectar and regulated by the availability and quality of amino acids. In experiments with competitive nectar yeast, Candida rancensis, amino acid addition alleviated suppression of C. rancensis by early arrival of M. reukaufii, corroborating that amino acid scavenging may contribute to priority effects. Because niche pre-emption via rapid resource depletion may underlie priority effects in a broad range of microbial, plant and animal communities, nutrient scavenging genes like the ones we considered here may be broadly relevant to understanding priority effects.

    View details for PubMedID 27708148

    View details for PubMedCentralID PMC5069511

  • Nonlinear, interacting responses to climate limit grassland production under global change PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Zhu, K., Chiariello, N. R., Tobeck, T., Fukami, T., Field, C. B. 2016; 113 (38): 10589-10594


    Global changes in climate, atmospheric composition, and pollutants are altering ecosystems and the goods and services they provide. Among approaches for predicting ecosystem responses, long-term observations and manipulative experiments can be powerful approaches for resolving single-factor and interactive effects of global changes on key metrics such as net primary production (NPP). Here we combine both approaches, developing multidimensional response surfaces for NPP based on the longest-running, best-replicated, most-multifactor global-change experiment at the ecosystem scale-a 17-y study of California grassland exposed to full-factorial warming, added precipitation, elevated CO2, and nitrogen deposition. Single-factor and interactive effects were not time-dependent, enabling us to analyze each year as a separate realization of the experiment and extract NPP as a continuous function of global-change factors. We found a ridge-shaped response surface in which NPP is humped (unimodal) in response to temperature and precipitation when CO2 and nitrogen are ambient, with peak NPP rising under elevated CO2 or nitrogen but also shifting to lower temperatures. Our results suggest that future climate change will push this ecosystem away from conditions that maximize NPP, but with large year-to-year variability.

    View details for DOI 10.1073/pnas.1606734113

    View details for Web of Science ID 000383622600046

    View details for PubMedID 27601643

    View details for PubMedCentralID PMC5035850

  • Forest area and connectivity influence root-associated fungal communities in a fragmented landscape ECOLOGY Vannette, R. L., Leopold, D. R., Fukami, T. 2016; 97 (9): 2374-2383

    View details for DOI 10.1002/ecy.1472

    View details for Web of Science ID 000382527100021

  • Convergence and divergence in a long-term old-field succession: the importance of spatial scale and species abundance ECOLOGY LETTERS Li, S., Cadotte, M. W., Meiners, S. J., Pu, Z., Fukami, T., Jiang, L. 2016; 19 (9): 1101-1109


    Whether plant communities in a given region converge towards a particular stable state during succession has long been debated, but rarely tested at a sufficiently long time scale. By analysing a 50-year continuous study of post-agricultural secondary succession in New Jersey, USA, we show that the extent of community convergence varies with the spatial scale and species abundance classes. At the larger field scale, abundance-based dissimilarities among communities decreased over time, indicating convergence of dominant species, whereas incidence-based dissimilarities showed little temporal tend, indicating no sign of convergence. In contrast, plots within each field diverged in both species composition and abundance. Abundance-based successional rates decreased over time, whereas rare species and herbaceous plants showed little change in temporal turnover rates. Initial abandonment conditions only influenced community structure early in succession. Overall, our findings provide strong evidence for scale and abundance dependence of stochastic and deterministic processes over old-field succession.

    View details for DOI 10.1111/ele.12647

    View details for Web of Science ID 000382542500010

    View details for PubMedID 27373449

  • Hierarchical neighbor effects on mycorrhizal community structure and function. Ecology and evolution Moeller, H. V., Dickie, I. A., Peltzer, D. A., Fukami, T. 2016; 6 (15): 5416-5430


    Theory predicts that neighboring communities can shape one another's composition and function, for example, through the exchange of member species. However, empirical tests of the directionality and strength of these effects are rare. We determined the effects of neighboring communities on one another through experimental manipulation of a plant-fungal model system. We first established distinct ectomycorrhizal fungal communities on Douglas-fir seedlings that were initially grown in three soil environments. We then transplanted seedlings and mycorrhizal communities in a fully factorial experiment designed to quantify the direction and strength of neighbor effects by focusing on changes in fungal community species composition and implications for seedling growth (a proxy for community function). We found that neighbor effects on the composition and function of adjacent communities follow a dominance hierarchy. Specifically, mycorrhizal communities established from soils collected in Douglas-fir plantations were both the least sensitive to neighbor effects, and exerted the strongest influence on their neighbors by driving convergence in neighbor community composition and increasing neighbor seedling vigor. These results demonstrate that asymmetric neighbor effects mediated by ecological history can determine both community composition and function.

    View details for DOI 10.1002/ece3.2299

    View details for PubMedID 27551393

    View details for PubMedCentralID PMC4984514

  • Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators ECOLOGY Vannette, R. L., Fukami, T. 2016; 97 (6): 1410-1419


    Secondary metabolites that are present in floral nectar have been hypothesized to enhance specificity in plant-pollinator mutualism by reducing larceny by non-pollinators, including microorganisms that colonize nectar. However, few studies have tested this hypothesis. Using synthetic nectar, we conducted laboratory and field experiments to examine the effects of five chemical compounds found in nectar on the growth and metabolism of nectar-colonizing yeasts and bacteria, and the interactive effects of these compounds and nectar microbes on the consumption of nectar by pollinators. In most cases, focal compounds inhibited microbial growth, but the extent of these effects depended on compound identity, concentration, and microbial species. Moreover, most compounds did not substantially decrease sugar metabolism by microbes, and microbes reduced the concentration of some compounds in nectar. Using artificial flowers in the field, we also found that the common nectar yeast Metschnikowia reukaufii altered nectar consumption by small floral visitors, but only in nectar containing catalpol. This effect was likely mediated by a mechanism independent of catalpol metabolism. Despite strong compound-specific effects on microbial growth, our results suggest that the secondary metabolites tested here are unlikely to be an effective general defense mechanism for preserving nectar sugars for pollinators. Instead, our results indicate that microbial colonization of nectar could reduce the concentration of secondary compounds in nectar and, in some cases, reduce deterrence to pollinators.

    View details for DOI 10.1890/15-0858.1

    View details for Web of Science ID 000377219900005

    View details for PubMedID 27459772

  • Plant and root endophyte assembly history: interactive effects on native and exotic plants ECOLOGY Sikes, B. A., Hawkes, C. V., Fukami, T. 2016; 97 (2): 484-493

    View details for DOI 10.1890/15-0635.1

    View details for Web of Science ID 000371439800020

  • Florivory and pollinator visitation: a cautionary tale. AoB PLANTS Tsuji, K., Dhami, M. K., Cross, D. J., Rice, C. P., Romano, N. H., Fukami, T. 2016; 8


    Florivory, or damage to flowers by herbivores, can make flowers less attractive to pollinators, potentially resulting in reduced plant fitness. However, not many studies have combined observations with experiments to assess the causal link between florivory and pollination. We conducted field observations at eight sites in northern California, combined with field experiments that involved artificial floral damage, to study the effect of florivory on pollination in the hummingbird-pollinated sticky monkeyflower, Mimulus aurantiacus We used two indicators of pollinator visitation, stigma closure and the presence of microorganisms in floral nectar. The field observations revealed that stigma closure was less frequent in damaged flowers than in intact flowers. In the experiments, however, floral damage did not decrease stigma closure or microbial detection in nectar. Instead, neighbouring flowers were similar for both indicators. These results suggest that the observed negative association between florivory and pollination is not causal and that the location of flowers is more important to pollinator visitation than florivory in these populations of M. aurantiacus.

    View details for DOI 10.1093/aobpla/plw036

    View details for PubMedID 27178063

    View details for PubMedCentralID PMC4940504

  • Mycorrhizal co-invasion and novel interactions depend on neighborhood context ECOLOGY Moeller, H. V., Dickie, I. A., Peltzer, D. A., Fukami, T. 2015; 96 (9): 2336-2347
  • When do plant radiations influence community assembly? The importance of historical contingency in the race for niche space NEW PHYTOLOGIST Tanentzap, A. J., Brandt, A. J., Smissen, R. D., Heenan, P. B., Fukami, T., Lee, W. G. 2015; 207 (2): 468-479


    Plant radiations are widespread but their influence on community assembly has rarely been investigated. Theory and some evidence suggest that radiations can allow lineages to monopolize niche space when founding species arrive early into new bioclimatic regions and exploit ecological opportunities. These early radiations may subsequently reduce niche availability and dampen diversification of later arrivals. We tested this hypothesis of time-dependent lineage diversification and community dominance using the alpine flora of New Zealand. We estimated ages of 16 genera from published phylogenies and determined their relative occurrence across climatic and physical gradients in the alpine zone. We used these data to reconstruct occupancy of environmental space through time, integrating palaeoclimatic and palaeogeological changes. Our analysis suggested that earlier-colonizing lineages encountered a greater availability of environmental space, which promoted greater species diversity and occupancy of niche space. Genera that occupied broader niches were subsequently more dominant in local communities. An earlier time of arrival also contributed to greater diversity independently of its influence in accessing niche space. We suggest that plant radiations influence community assembly when they arise early in the occupancy of environmental space, allowing them to exclude later-arriving colonists from ecological communities by niche preemption.

    View details for DOI 10.1111/nph.13362

    View details for Web of Science ID 000356598800022

    View details for PubMedID 25771829

  • Evolutionary priority effects in New Zealand alpine plants across environmental gradients JOURNAL OF BIOGEOGRAPHY Leopold, D. R., Tanentzap, A. J., Lee, W. G., Heenan, P. B., Fukami, T. 2015; 42 (4): 729-737

    View details for DOI 10.1111/jbi.12441

    View details for Web of Science ID 000350910100012

  • Complex organism-environment feedbacks buffer species diversity against habitat fragmentation ECOGRAPHY Zee, P. C., Fukami, T. 2015; 38 (4): 370-379

    View details for DOI 10.1111/ecog.01027

    View details for Web of Science ID 000352626400005

  • Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 46 Fukami, T. 2015; 46: 1-23
  • Temporal variation in fungal communities associated with tropical hummingbirds and nectarivorous bats FUNGAL ECOLOGY Belisle, M., Mendenhall, C. D., Brenes, F. O., Fukami, T. 2014; 12: 44-51
  • Rapid evolution of adaptive niche construction in experimental microbial populations EVOLUTION Callahan, B. J., Fukami, T., Fisher, D. S. 2014; 68 (11): 3307-3316

    View details for DOI 10.1111/evo.12512

    View details for Web of Science ID 000344379800018

  • Environmental variability counteracts priority effects to facilitate species coexistence: evidence from nectar microbes. Proceedings. Biological sciences / The Royal Society Tucker, C. M., Fukami, T. 2014; 281 (1778): 20132637-?


    The order of species arrival during community assembly can greatly affect species coexistence, but the strength of these effects, known as priority effects, appears highly variable across species and ecosystems. Furthermore, the causes of this variation remain unclear despite their fundamental importance in understanding species coexistence. Here, we show that one potential cause is environmental variability. In laboratory experiments using nectar-inhabiting microorganisms as a model system, we manipulated spatial and temporal variability of temperature, and examined consequences for priority effects. If species arrived sequentially, multiple species coexisted under variable temperature, but not under constant temperature. Temperature variability prevented extinction of late-arriving species that would have been excluded owing to priority effects if temperature had been constant. By contrast, if species arrived simultaneously, species coexisted under both variable and constant temperatures. We propose possible mechanisms underlying these results using a mathematical model that incorporates contrasting effects of microbial species on nectar pH and amino acids. Overall, our findings suggest that understanding consequences of priority effects for species coexistence requires explicit consideration of environmental variability.

    View details for DOI 10.1098/rspb.2013.2637

    View details for PubMedID 24430846

  • Ectomycorrhizal fungal traits reflect environmental conditions along a coastal California edaphic gradient. FEMS microbiology ecology Moeller, H. V., Peay, K. G., Fukami, T. 2014; 87 (3): 797-806


    Multispecies mutualisms, such as the association between trees and ectomycorrhizal fungi, are often shaped by environmental context. Here, we explored the functional mechanisms underlying this environmental filtering. Using a single population of Pinus muricata (Bishop pine) growing along a strong edaphic gradient, we examined how environmental stress affected ectomycorrhizal fungi. The gradient spans c. 400000 years of soil age, and reduced nutrient availability and increased water stress dwarf trees on older sites. Fungal community composition shifted with nutrient and water availability and with the stature of the P. muricata host trees. Not only did pygmy trees host a taxonomically different fungal subset as compared to nonpygmy trees, but associated fungal communities also differed in life history strategies: trees in more stressful conditions hosted fungi with more carbon-intensive foraging strategies. Our results indicate a link between environmental controls of host nutritional status and turnover in the ectomycorrhizal fungal community. The transition to more energy-intensive strategies under nutrient stress may allow for close recycling of recalcitrant nutrient pools within the root zone and facilitate transport of nutrients and water over long distances. These results highlight the value of life history data to understanding the mechanistic underpinnings of species distributions.

    View details for DOI 10.1111/1574-6941.12265

    View details for PubMedID 24289145

  • Honey bees avoid nectar colonized by three bacterial species, but not by a yeast species, isolated from the bee gut. PloS one Good, A. P., Gauthier, M. L., Vannette, R. L., Fukami, T. 2014; 9 (1)

    View details for DOI 10.1371/journal.pone.0086494

    View details for PubMedID 24466119

  • Historical contingency in species interactions: towards niche-based predictions ECOLOGY LETTERS Vannette, R. L., Fukami, T. 2014; 17 (1): 115-124


    The way species affect one another in ecological communities often depends on the order of species arrival. The magnitude of such historical contingency, known as priority effects, varies across species and environments, but this variation has proven difficult to predict, presenting a major challenge in understanding species interactions and consequences for community structure and function. Here, we argue that improved predictions can be achieved by decomposing species' niches into three components: overlap, impact and requirement. Based on classic theories of community assembly, three hypotheses that emphasise related, but distinct influences of the niche components are proposed: priority effects are stronger among species with higher resource use overlap; species that impact the environment to a greater extent exert stronger priority effects; and species whose growth rate is more sensitive to changes in the environment experience stronger priority effects. Using nectar-inhabiting microorganisms as a model system, we present evidence that these hypotheses complement the conventional hypothesis that focuses on the role of environmental harshness, and show that niches can be twice as predictive when separated into components. Taken together, our hypotheses provide a basis for developing a general framework within which the magnitude of historical contingency in species interactions can be predicted.

    View details for DOI 10.1111/ele.12204

    View details for Web of Science ID 000328315900013

    View details for PubMedID 24341984

  • Honey bees avoid nectar colonized by three bacterial species, but not by a yeast species, isolated from the bee gut. PloS one Good, A. P., Gauthier, M. L., Vannette, R. L., Fukami, T. 2014; 9 (1)


    The gut microflora of the honey bee, Apis mellifera, is receiving increasing attention as a potential determinant of the bees' health and their efficacy as pollinators. Studies have focused primarily on the microbial taxa that appear numerically dominant in the bee gut, with the assumption that the dominant status suggests their potential importance to the bees' health. However, numerically minor taxa might also influence the bees' efficacy as pollinators, particularly if they are not only present in the gut, but also capable of growing in floral nectar and altering its chemical properties. Nonetheless, it is not well understood whether honey bees have any feeding preference for or against nectar colonized by specific microbial species. To test whether bees exhibit a preference, we conducted a series of field experiments at an apiary using synthetic nectar inoculated with specific species of bacteria or yeast that had been isolated from the bee gut, but are considered minor components of the gut microflora. These species had also been found in floral nectar. Our results indicated that honey bees avoided nectar colonized by the bacteria Asaia astilbes, Erwinia tasmaniensis, and Lactobacillus kunkeei, whereas the yeast Metschnikowia reukaufii did not affect the feeding preference of the insects. Our results also indicated that avoidance of bacteria-colonized nectar was caused not by the presence of the bacteria per se, but by the chemical changes to nectar made by the bacteria. These findings suggest that gut microbes may not only affect the bees' health as symbionts, but that some of the microbes may possibly affect the efficacy of A. mellifera as pollinators by altering nectar chemistry and influencing their foraging behavior.

    View details for DOI 10.1371/journal.pone.0086494

    View details for PubMedID 24466119

  • Non-Native Plants Disrupt Dual Promotion of Native Alpha and Beta Diversity FOLIA GEOBOTANICA Fukami, T., Bellingham, P. J., Peltzer, D. A., Walker, L. R. 2013; 48 (3): 319-333
  • Patterns and Processes of Microbial Community Assembly MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS Nemergut, D. R., Schmidt, S. K., Fukami, T., O'Neill, S. P., Bilinski, T. M., Stanish, L. F., Knelman, J. E., Darcy, J. L., Lynch, R. C., Wickey, P., Ferrenberg, S. 2013; 77 (3): 342-356


    Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183-206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.

    View details for DOI 10.1128/MMBR.00051-12

    View details for Web of Science ID 000324164400002

    View details for PubMedID 24006468

  • IBI* series winner. Integrating inquiry-based teaching with faculty research. Science Fukami, T. 2013; 339 (6127): 1536-1537

    View details for DOI 10.1126/science.1229850

    View details for PubMedID 23539590

  • Consequences of plant-soil feedbacks in invasion JOURNAL OF ECOLOGY Suding, K. N., Harpole, W. S., Fukami, T., Kulmatiski, A., MacDougall, A. S., Stein, C., van der Putten, W. H. 2013; 101 (2): 298-308
  • Complex plant-soil interactions enhance plant species diversity by delaying community convergence JOURNAL OF ECOLOGY Fukami, T., Nakajima, M. 2013; 101 (2): 316-324
  • Plant-soil feedbacks: the past, the present and future challenges JOURNAL OF ECOLOGY van der Putten, W. H., Bardgett, R. D., Bever, J. D., Bezemer, T. M., Casper, B. B., Fukami, T., Kardol, P., Klironomos, J. N., Kulmatiski, A., Schweitzer, J. A., Suding, K. N., van de Voorde, T. F., Wardle, D. A. 2013; 101 (2): 265-276
  • Animals in a bacterial world, a new imperative for the life sciences PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA McFall-Ngai, M., Hadfield, M. G., Bosch, T. C., Carey, H. V., Domazet-Loso, T., Douglas, A. E., Dubilier, N., Eberl, G., Fukami, T., Gilbert, S. F., Hentschel, U., King, N., Kjelleberg, S., Knoll, A. H., Kremer, N., Mazmanian, S. K., Metcalf, J. L., Nealson, K., Pierce, N. E., Rawls, J. F., Reid, A., Ruby, E. G., Rumpho, M., Sanders, J. G., Tautz, D., Wernegreen, J. J. 2013; 110 (9): 3229-3236


    In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal-bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other's genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal-bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world.

    View details for DOI 10.1073/pnas.1218525110

    View details for Web of Science ID 000315841900016

    View details for PubMedID 23391737

  • Nectar bacteria, but not yeast, weaken a plant-pollinator mutualism. Proceedings. Biological sciences / The Royal Society Vannette, R. L., Gauthier, M. L., Fukami, T. 2013; 280 (1752): 20122601-?


    Mutualistic interactions are often subject to exploitation by species that are not directly involved in the mutualism. Understanding which organisms act as such 'third-party' species and how they do so is a major challenge in the current study of mutualistic interactions. Here, we show that even species that appear ecologically similar can have contrasting effects as third-party species. We experimentally compared the effects of nectar-inhabiting bacteria and yeasts on the strength of a mutualism between a hummingbird-pollinated shrub, Mimulus aurantiacus, and its pollinators. We found that the common bacterium Gluconobacter sp., but not the common yeast Metschnikowia reukaufii, reduced pollination success, seed set and nectar consumption by pollinators, thereby weakening the plant-pollinator mutualism. We also found that the bacteria reduced nectar pH and total sugar concentration more greatly than the yeasts did and that the bacteria decreased glucose concentration and increased fructose concentration whereas the yeasts affected neither. These distinct changes to nectar chemistry may underlie the microbes' contrasting effects on the mutualism. Our results suggest that it is necessary to understand the determinants of microbial species composition in nectar and their differential modification of floral rewards to explain the mutual benefits that plants and pollinators gain from each other.

    View details for DOI 10.1098/rspb.2012.2601

    View details for PubMedID 23222453

  • Nectar bacteria, but not yeast, weaken a plant - pollinator mutualism PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Vannette, R. L., Gauthier, M. L., Fukami, T. 2013; 280 (1752)


    Mutualistic interactions are often subject to exploitation by species that are not directly involved in the mutualism. Understanding which organisms act as such 'third-party' species and how they do so is a major challenge in the current study of mutualistic interactions. Here, we show that even species that appear ecologically similar can have contrasting effects as third-party species. We experimentally compared the effects of nectar-inhabiting bacteria and yeasts on the strength of a mutualism between a hummingbird-pollinated shrub, Mimulus aurantiacus, and its pollinators. We found that the common bacterium Gluconobacter sp., but not the common yeast Metschnikowia reukaufii, reduced pollination success, seed set and nectar consumption by pollinators, thereby weakening the plant-pollinator mutualism. We also found that the bacteria reduced nectar pH and total sugar concentration more greatly than the yeasts did and that the bacteria decreased glucose concentration and increased fructose concentration whereas the yeasts affected neither. These distinct changes to nectar chemistry may underlie the microbes' contrasting effects on the mutualism. Our results suggest that it is necessary to understand the determinants of microbial species composition in nectar and their differential modification of floral rewards to explain the mutual benefits that plants and pollinators gain from each other.

    View details for DOI 10.1098/rspb.2012.2601

    View details for Web of Science ID 000312591600020

    View details for PubMedID 23222453

    View details for PubMedCentralID PMC3574316

  • Rat invasion of islands alters fungal community structure, but not wood decomposition rates OIKOS Peay, K. G., Dickie, I. A., Wardle, D. A., Bellingham, P. J., Fukami, T. 2013; 122 (2): 258-264
  • Context matters: volunteer bias, small sample size, and the value of comparison groups in the assessment of research-based undergraduate introductory biology lab courses. Journal of microbiology & biology education : JMBE Brownell, S. E., Kloser, M. J., Fukami, T., Shavelson, R. J. 2013; 14 (2): 176-182


    The shift from cookbook to authentic research-based lab courses in undergraduate biology necessitates the need for evaluation and assessment of these novel courses. Although the biology education community has made progress in this area, it is important that we interpret the effectiveness of these courses with caution and remain mindful of inherent limitations to our study designs that may impact internal and external validity. The specific context of a research study can have a dramatic impact on the conclusions. We present a case study of our own three-year investigation of the impact of a research-based introductory lab course, highlighting how volunteer students, a lack of a comparison group, and small sample sizes can be limitations of a study design that can affect the interpretation of the effectiveness of a course.

    View details for DOI 10.1128/jmbe.v14i2.609

    View details for PubMedID 24358380

  • Soil-mediated indirect impacts of an invasive predator on plant growth BIOLOGY LETTERS Wardle, D. A., Bellingham, P. J., Fukami, T., Bonner, K. I. 2012; 8 (4): 574-577


    While several studies have shown that invasive plant effects on soil biota influence subsequent plant performance, corresponding studies on how invasive animals affect plants through influencing soil biota are lacking. This is despite the fact that invasive animals often indirectly alter the below-ground subsystem. We studied 18 offshore islands in northern New Zealand, half of which have been invaded by rats that are predators of seabirds and severely reduce their densities, and half of which remain non-invaded; invasion of rats thwarts seabird transfer of resources from ocean to land. We used soil from each island in a glasshouse experiment involving soil sterilization treatments to determine whether rat invasion indirectly influences plant growth through the abiotic pathway (by impairing seabird-driven inputs to soil) or the biotic pathway (by altering the soil community). Rat invasion greatly impaired plant growth but entirely through the abiotic pathway. Plant growth was unaffected by the soil community or its response to invasion, meaning that the responses of plants and soil biota to invasion are decoupled. Our results provide experimental evidence for the powerful indirect effects that predator-instigated cascades can exert on plant and ecosystem productivity, with implications for the restoration of island ecosystems by predator removal.

    View details for DOI 10.1098/rsbl.2012.0201

    View details for Web of Science ID 000306361700027

    View details for PubMedID 22496079

  • Area and the rapid radiation of Hawaiian Bidens (Asteraceae) JOURNAL OF BIOGEOGRAPHY Knope, M. L., Morden, C. W., Funk, V. A., Fukami, T. 2012; 39 (7): 1206-1216
  • Flowers as Islands: Spatial Distribution of Nectar-Inhabiting Microfungi among Plants of Mimulus aurantiacus, a Hummingbird-Pollinated Shrub MICROBIAL ECOLOGY Belisle, M., Peay, K. G., Fukami, T. 2012; 63 (4): 711-718


    Microfungi that inhabit floral nectar offer unique opportunities for the study of microbial distribution and the role that dispersal limitation may play in generating distribution patterns. Flowers are well-replicated habitat islands, among which the microbes disperse via pollinators. This metapopulation system allows for investigation of microbial distribution at multiple spatial scales. We examined the distribution of the yeast, Metschnikowia reukaufii, and other fungal species found in the floral nectar of the sticky monkey flower, Mimulus aurantiacus, a hummingbird-pollinated shrub, at a California site. We found that the frequency of nectar-inhabiting microfungi on a given host plant was not significantly correlated with light availability, nectar volume, or the percent cover of M. aurantiacus around the plant, but was significantly correlated with the location of the host plant and loosely correlated with the density of flowers on the plant. These results suggest that dispersal limitation caused by spatially nonrandom foraging by pollinators may be a primary factor driving the observed distribution pattern.

    View details for DOI 10.1007/s00248-011-9975-8

    View details for Web of Science ID 000306127300001

    View details for PubMedID 22080257

  • Introduced Canopy Tree Species Effect on the Soil Microbial Community in a Montane Tropical Forest PACIFIC SCIENCE Lynch, H. B., Epps, K. Y., Fukami, T., Vitousek, P. M. 2012; 66 (2): 141-150

    View details for DOI 10.2984/66.2.4

    View details for Web of Science ID 000303625400004

  • Phylogenetic relatedness predicts priority effects in nectar yeast communities PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Peay, K. G., Belisle, M., Fukami, T. 2012; 279 (1729): 749-758


    Priority effects, in which the outcome of species interactions depends on the order of their arrival, are a key component of many models of community assembly. Yet, much remains unknown about how priority effects vary in strength among species in a community and what factors explain this variation. We experimented with a model natural community in laboratory microcosms that allowed us to quantify the strength of priority effects for most of the yeast species found in the floral nectar of a hummingbird-pollinated shrub at a biological preserve in northern California. We found that priority effects were widespread, with late-arriving species experiencing strong negative effects from early-arriving species. However, the magnitude of priority effects varied across species pairs. This variation was phylogenetically non-random, with priority effects stronger between closer relatives. Analysis of carbon and amino acid consumption profiles indicated that competition between closer relatives was more intense owing to higher ecological similarity, consistent with Darwin's naturalization hypothesis. These results suggest that phylogenetic relatedness between potential colonists may explain the strength of priority effects and, as a consequence, the degree to which community assembly is historically contingent.

    View details for DOI 10.1098/rspb.2011.1230

    View details for Web of Science ID 000299114100017

    View details for PubMedID 21775330

  • Do assembly history effects attenuate from species to ecosystem properties? A field test with wood-inhabiting fungi ECOLOGY LETTERS Dickie, I. A., Fukami, T., Wilkie, J. P., Allen, R. B., Buchanan, P. K. 2012; 15 (2): 133-141


    Assembly history, or the order of species arrival, can have wide-ranging effects on species, communities and ecosystems. However, it remains unclear whether assembly history primarily affects individual species, with effects attenuating at the level of communities and ecosystems or, alternatively, has consistent effect sizes across increasing levels of ecological organisation. We address this question using a field-based manipulation of assembly history of wood-inhabiting fungi. The largest effect sizes were observed for the frequency of some individual species, and mean effect sizes were lower for community metrics of fungi immigrating from the regional species pool. There was little evidence, however, of attenuation in effect sizes at the ecosystem level (carbon, nitrogen, decomposition) in comparison to the species or community level. These results indicate that assembly history can have strong effects on ecosystem properties even under natural levels of environmental variability.

    View details for DOI 10.1111/j.1461-0248.2011.01722.x

    View details for Web of Science ID 000298848200007

    View details for PubMedID 22188588

  • Evolutionary history, immigration history, and the extent of diversification in community assembly FRONTIERS IN MICROBIOLOGY Knope, M. L., Forde, S. E., Fukami, T. 2012; 3
  • Community assembly: alternative stable states or alternative transient states? ECOLOGY LETTERS Fukami, T., Nakajima, M. 2011; 14 (10): 973-984


    The concept of alternative stable states has long been a dominant framework for studying the influence of historical contingency in community assembly. This concept focuses on stable states, yet many real communities are kept in a transient state by disturbance, and the utility of predictions for stable states in explaining transient states remains unclear. Using a simple model of plant community assembly, we show that the conditions under which historical contingency affects community assembly can differ greatly for stable versus transient states. Differences arise because the contribution of such factors as mortality rate, environmental heterogeneity and plant-soil feedback to historical contingency changes as community assembly proceeds. We also show that transient states can last for a long time relative to immigration rate and generation time. These results argue for a conceptual shift of focus from alternative stable states to alternative transient states for understanding historical contingency in community assembly.

    View details for DOI 10.1111/j.1461-0248.2011.01663.x

    View details for Web of Science ID 000294917700001

    View details for PubMedID 21790934

    View details for PubMedCentralID PMC3187870

  • Linking community and ecosystem dynamics through spatial ecology ECOLOGY LETTERS Massol, F., Gravel, D., Mouquet, N., Cadotte, M. W., Fukami, T., Leibold, M. A. 2011; 14 (3): 313-323


    Classical approaches to food webs focus on patterns and processes occurring at the community level rather than at the broader ecosystem scale, and often ignore spatial aspects of the dynamics. However, recent research suggests that spatial processes influence both food web and ecosystem dynamics, and has led to the idea of 'metaecosystems'. However, these processes have been tackled separately by 'food web metacommunity' ecology, which focuses on the movement of traits, and 'landscape ecosystem' ecology, which focuses on the movement of materials among ecosystems. Here, we argue that this conceptual gap must be bridged to fully understand ecosystem dynamics because many natural cases demonstrate the existence of interactions between the movements of traits and materials. This unification of concepts can be achieved under the metaecosystem framework, and we present two models that highlight how this framework yields novel insights. We then discuss patches, limiting factors and spatial explicitness as key issues to advance metaecosystem theory. We point out future avenues for research on metaecosystem theory and their potential for application to biological conservation.

    View details for DOI 10.1111/j.1461-0248.2011.01588.x

    View details for Web of Science ID 000287528600014

    View details for PubMedID 21272182

  • Evolutionary history, immigration history, and the extent of diversification in community assembly. Frontiers in microbiology Knope, M. L., Forde, S. E., Fukami, T. 2011; 2: 273-?


    During community assembly, species may accumulate not only by immigration, but also by in situ diversification. Diversification has intrigued biologists because its extent varies even among closely related lineages under similar ecological conditions. Recent research has suggested that some of this puzzling variation may be caused by stochastic differences in the history of immigration (relative timing and order of immigration by founding populations), indicating that immigration and diversification may affect community assembly interactively. However, the conditions under which immigration history affects diversification remain unclear. Here we propose the hypothesis that whether or not immigration history influences the extent of diversification depends on the founding populations' prior evolutionary history, using evidence from a bacterial experiment. To create genotypes with different evolutionary histories, replicate populations of Pseudomonas fluorescens were allowed to adapt to a novel environment for a short or long period of time (approximately 10 or 100 bacterial generations) with or without exploiters (viral parasites). Each evolved genotype was then introduced to a new habitat either before or after a standard competitor genotype. Most genotypes diversified to a greater extent when introduced before, rather than after, the competitor. However, introduction order did not affect the extent of diversification when the evolved genotype had previously adapted to the environment for a long period of time without exploiters. Diversification of these populations was low regardless of introduction order. These results suggest that the importance of immigration history in diversification can be predicted by the immigrants' evolutionary past. The hypothesis proposed here may be generally applicable in both micro- and macro-organisms.

    View details for DOI 10.3389/fmicb.2011.00273

    View details for PubMedID 22291685

  • Assembly history dictates ecosystem functioning: evidence from wood decomposer communities ECOLOGY LETTERS Fukami, T., Dickie, I. A., Wilkie, J. P., Paulus, B. C., Park, D., Roberts, A., Buchanan, P. K., Allen, R. B. 2010; 13 (6): 675-684


    Community assembly history is increasingly recognized as a fundamental determinant of community structure. However, little is known as to how assembly history may affect ecosystem functioning via its effect on community structure. Using wood-decaying fungi as a model system, we provide experimental evidence that large differences in ecosystem functioning can be caused by small differences in species immigration history during community assembly. Direct manipulation of early immigration history resulted in three-fold differences in fungal species richness and composition and, as a consequence, differences of the same magnitude in the rate of decomposition and carbon release from wood. These effects - which were attributable to the history-dependent outcome of competitive and facilitative interactions - were significant across a range of nitrogen availabilities observed in natural forests. Our results highlight the importance of considering assembly history in explaining ecosystem functioning.

    View details for DOI 10.1111/j.1461-0248.2010.01465.x

    View details for Web of Science ID 000277867100002

    View details for PubMedID 20412280

  • Assembly history dictates ecosystem functioning: evidence from wood decomposer communities Ecology Letters Fukami T, Dickie IA, Wilkie JP, Paulus BC, Park D, Roberts A, Buchanan PK, Allen RB 2010; 13: 675-684
  • Empirical and theoretical challenges in aboveground-belowground ecology OECOLOGIA van der Putten, W. H., Bardgett, R. D., de Ruiter, P. C., Hol, W. H., Meyer, K. M., Bezemer, T. M., Bradford, M. A., Christensen, S., Eppinga, M. B., Fukami, T., Hemerik, L., Molofsky, J., Schaedler, M., Scherber, C., Strauss, S. Y., Vos, M., Wardle, D. A. 2009; 161 (1): 1-14


    A growing body of evidence shows that aboveground and belowground communities and processes are intrinsically linked, and that feedbacks between these subsystems have important implications for community structure and ecosystem functioning. Almost all studies on this topic have been carried out from an empirical perspective and in specific ecological settings or contexts. Belowground interactions operate at different spatial and temporal scales. Due to the relatively low mobility and high survival of organisms in the soil, plants have longer lasting legacy effects belowground than aboveground. Our current challenge is to understand how aboveground-belowground biotic interactions operate across spatial and temporal scales, and how they depend on, as well as influence, the abiotic environment. Because empirical capacities are too limited to explore all possible combinations of interactions and environmental settings, we explore where and how they can be supported by theoretical approaches to develop testable predictions and to generalise empirical results. We review four key areas where a combined aboveground-belowground approach offers perspectives for enhancing ecological understanding, namely succession, agro-ecosystems, biological invasions and global change impacts on ecosystems. In plant succession, differences in scales between aboveground and belowground biota, as well as between species interactions and ecosystem processes, have important implications for the rate and direction of community change. Aboveground as well as belowground interactions either enhance or reduce rates of plant species replacement. Moreover, the outcomes of the interactions depend on abiotic conditions and plant life history characteristics, which may vary with successional position. We exemplify where translation of the current conceptual succession models into more predictive models can help targeting empirical studies and generalising their results. Then, we discuss how understanding succession may help to enhance managing arable crops, grasslands and invasive plants, as well as provide insights into the effects of global change on community re-organisation and ecosystem processes.

    View details for DOI 10.1007/s00442-009-1351-8

    View details for Web of Science ID 000267345500001

    View details for PubMedID 19412705

    View details for PubMedCentralID PMC2700873

  • Direct and indirect effects of rats: does rat eradication restore ecosystem functioning of New Zealand seabird islands? BIOLOGICAL INVASIONS Mulder, C. P., Grant-Hoffman, M. N., Towns, D. R., Bellingham, P. J., Wardle, D. A., Durrett, M. S., Fukami, T., Bonner, K. I. 2009; 11 (7): 1671-1688
  • Long-Term Effects of Predator Arrival Timing on Prey Community Succession AMERICAN NATURALIST Olito, C., Fukami, T. 2009; 173 (3): 354-362


    The stochastic arrival of competing species and their subsequent interactions have been highlighted as principal forces underlying biotic historical effects in community assembly. However, despite the widely recognized effect of predation on prey communities, the effects that the stochastic arrival of predators may have on assembling communities are poorly understood. We used a microbial microcosm experiment to investigate whether the timing of predator arrival to a prey community undergoing naturalistic succession affected species abundances and community diversity. Predator arrival timing affected the long-term abundance of a prey species that was persistent throughout succession in the absence of predators. Our data indicate that this timing effect occurred indirectly via transient interactions between early-successional prey species and predators. Specifically, we suggest that transient early-successional prey species served as a springboard for early-arriving (but not late-arriving) predators, allowing the exploiting predators to increase their abundances and subsequently alter long-term community dynamics. These results show that the history of predator arrival can have lasting consequences for community structure in ecological succession.

    View details for DOI 10.1086/596538

    View details for Web of Science ID 000263126800011

    View details for PubMedID 19183067

  • Immigration history controls diversification in experimental adaptive radiation NATURE Fukami, T., Beaumont, H. J., Zhang, X., Rainey, P. B. 2007; 446 (7134): 436-439


    Diversity in biological communities is a historical product of immigration, diversification and extinction, but the combined effect of these processes is poorly understood. Here we show that the order and timing of immigration controls the extent of diversification. When an ancestral bacterial genotype was introduced into a spatially structured habitat, it rapidly diversified into multiple niche-specialist types. However, diversification was suppressed when a niche-specialist type was introduced before, or shortly after, introduction of the ancestral genotype. In contrast, little suppression occurred when the same niche specialist was introduced relatively late. The negative impact of early arriving immigrants was attributable to the historically sensitive outcome of interactions involving neutral competition and indirect facilitation. Ultimately, the entire boom-and-bust dynamics of adaptive radiation were altered. These results demonstrate that immigration and diversification are tightly linked processes, with small differences in immigration history greatly affecting the evolutionary emergence of diversity.

    View details for DOI 10.1038/nature05629

    View details for Web of Science ID 000245079500039

    View details for PubMedID 17377582

  • Above- and below-ground impacts of introduced predators in seabird-dominated island ecosystems. Ecology Letters Fukami T, Wardle DA, Bellingham PJ, Mulder CPH, Towns DR, Yeates GW, Bonner KI, Durrett MS, Grant-Hoffman MN, Williamson WM 2006; 9: 1299-1307
  • Species divergence and trait convergence in experimental plant community assembly ECOLOGY LETTERS Fukami, T., Bezemer, T. M., Mortimer, S. R., van der Putten, W. H. 2005; 8 (12): 1283-1290
  • Long-term ecological dynamics: reciprocal insights from natural and anthropogenic gradients PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Fukami, T., Wardle, D. A. 2005; 272 (1577): 2105-2115


    Many ecological dynamics occur over time-scales that are well beyond the duration of conventional experiments or observations. One useful approach to overcome this problem is extrapolation of temporal dynamics from spatial variation. We review two complementary variants of this approach that have been of late increasingly employed: the use of natural gradients to infer anthropogenic effects and the use of anthropogenic gradients to infer natural dynamics. Recent studies have considered a variety of naturally occurring gradients associated with climate, CO2, disturbance and biodiversity gradients, as well as anthropogenic gradients such as those created by biological invasions, habitat fragmentation and land abandonment. These studies show that natural gradients are useful in predicting long-term consequences of human-induced environmental changes, whereas anthropogenic gradients are helpful in inferring the mechanisms behind natural dynamics because covarying factors are often more clearly understood in anthropogenic gradients than in natural gradients. We classify these studies into several categories, each with different strengths and weaknesses, and outline how the limitations can be overcome by combining the gradient-based approach with other approaches. Overall, studies reviewed here demonstrate that the development of basic ecological concepts and the application of these concepts to environmental problems can be more effective when conducted complementarily than when pursued separately.

    View details for DOI 10.1098/rspb.2005.3277

    View details for Web of Science ID 000232634600001

    View details for PubMedID 16191623

  • Dispersal, spatial scale, and species diversity in a hierarchically structured experimental landscape ECOLOGY LETTERS Cadotte, M. W., Fukami, T. 2005; 8 (5): 548-557


    Although there has been growing interest in the effect of dispersal on species diversity, much remains unknown about how dispersal occurring at multiple scales influences diversity. We used an experimental microbial landscape to determine whether dispersal occurring at two different scales - among local communities and among metacommunities - affects diversity differently. At the local scale, dispersal initially had a positive effect and subsequently a neutral effect on diversity, whereas at the metacommunity and landscape scales, dispersal showed a consistently negative effect. The timing in which dispersal affected beta diversity also differed sharply between local communities and metacommunities. These patterns were explained by scale- and time-dependent effects of dispersal in allowing spread of species and in removing spatial refuges from predators. Our results suggest that the relative contribution of opposing mechanisms by which dispersal affects diversity changes considerably over time and space in hierarchical landscapes in which dispersal occurs at multiple scales.

    View details for DOI 10.1111/j.1461-0248.2005.00750.x

    View details for Web of Science ID 000228397000011

    View details for PubMedID 21352459

  • Species divergence and trait convergence in experimental plant community assembly. Ecology Letters Fukami, T., Bezemer, TM, Mortimer, SR, Van der Putten, WH 2005; 8: 1283-1290
  • Constructing nature: Laboratory models as necessary tools for investigating complex ecological communities ADVANCES IN ECOLOGICAL RESEARCH, VOL. 37: POPULATION DYNAMICS AND LABORATORY ECOLOGY Cadotte, M. W., Drake, J. A., Fukami, T. 2005; 37: 333-353
  • Productivity-biodiversity relationships depend on the history of community assembly NATURE Fukami, T., Morin, P. J. 2003; 424 (6947): 423-426


    Identification of the causes of productivity-species diversity relationships remains a central topic of ecological research. Different relations have been attributed to the influence of disturbance, consumers, niche specialization and spatial scale. One unexplored cause is the history of community assembly, the partly stochastic sequential arrival of species from a regional pool of potential community members. The sequence of species arrival can greatly affect community structure. If assembly sequence interacts with productivity to influence diversity, different sequences can contribute to variation in productivity-diversity relationships. Here we report a test of this hypothesis by assembling aquatic microbial communities at five productivity levels using four assembly sequences. About 30 generations after assembly, productivity-diversity relationships took various forms, including a positive, a hump-shaped, a U-shaped and a non-significant pattern, depending on assembly sequence. This variation resulted from idiosyncratic joint effects of assembly sequence, productivity and species identity on species abundances. We suggest that the history of community assembly should be added to the growing list of factors that influence productivity-biodiversity patterns.

    View details for DOI 10.1038/nature01785

    View details for Web of Science ID 000184318400042

    View details for PubMedID 12879069

  • On similarity among local communities in biodiversity experiments OIKOS Fukami, T., Naeem, S., Wardle, D. A. 2001; 95 (2): 340-348