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

Stanford Advisees

Graduate and Fellowship Programs

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

All Publications

  • 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
  • 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

  • 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

  • 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

  • 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

  • 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
  • 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
  • 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)

    View details for DOI 10.1098/rspb.2012.2601

    View details for Web of Science ID 000312591600020

    View details for PubMedID 23222453

  • 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
  • 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
  • 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

  • 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