Biology subjects

Fukami, T.

Publications and source records attributed to Fukami, T..

16 recordsLinked to original sources

bioRxiv2026

Heatwaves strengthen historical contingency in yeast--bacterium interactions in floral nectar

Heatwaves can affect species abundances by changing how species interact in local communities. However, these effects remain poorly understood, especially when the outcome of species interactions is contingent on their arrival history. We studied how heatwaves affect interactions between the yeast Metschnikowia reukaufii and the bacterium Acinetobacter nectaris, both found in the floral nectar of Diplacus aurantiacus, a hummingbird-pollinated shrub native to California. Microbes were introduced to artificial nectar in different orders of arrival in the presence or absence of simulated two-day heatwaves. Heatwaves made yeast--bacterium interactions more contingent on arrival history, causing large variation in nectar acidity, a factor known to affect hummingbird preference. Specifically, in the absence of heatwaves, Acinetobacter became abundant regardless of arrival history, suppressing Metschnikowia and reducing nectar pH. In contrast, in the presence of heatwaves, Acinetobacter dominance depended on arrival history and heatwave timing. If Acinetobacter arrived after Metschnikowia during a heatwave, it was suppressed by Metschnikowia substantially enough to keep nectar pH at a high level. These results suggest that heatwaves shift species interactions from determinism to historical contingency, with taxonomic and functional consequences.

ecology↗

bioRxiv2026

Sink invaders can increase resident metapopulation size by modifying local conditions and regional connectivity

Populations are regulated by processes operating at both local and regional scales. As a result, species can interact not only within local communities but also through regional-scale processes. However, the feedback between local and regional processes of species interactions in shaping metapopulation dynamics have rarely been tested experimentally. Using nectar microbes as a model system, we examine how a bacterial species dispersing to a sink habitat, sustained by external supply, can interact with a resident yeast species directly by modifying local nectar chemistry and indirectly by altering metapopulation connectivity. We show that the external supply of bacteria increases resident yeast densities, potentially through increased local productivity, and that this benefit is enhanced when the dispersal rate of yeast is reduced in patches supplied with bacteria. Analysis of a metapopulation model indicates that the benefit of dispersal modification on metapopulation size occurs only when local productivity differs across patches, consistent with our interpretation that bacterial supply increases local productivity. Taken together, our results underscore the role of dispersal in shaping how metapopulations experience density-dependence across heterogeneous landscapes, highlight the relevance of material flows across ecosystem boundaries, and suggest a plausible mechanism in which transient species may leave lasting impacts on ecological communities.

ecology↗

bioRxiv2025

Diversity of vector-dispersed microbes peaks at a landscape-defined intermediate rate of dispersal

Dispersal rate has long been considered a primary determinant of species diversity in ecological communities. However, this knowledge is mostly built on studies of organisms that disperse actively by themselves or passively via physical forces. For organisms that disperse passively via other organisms, the landscape matrix that affects their vectors should indirectly shape the diversity of the vectored, but this relationship remains poorly understood. We investigated landscape-dispersal-diversity relationships in nectar-inhabiting bacteria that disperse via flower-visiting insects. Field observation and experiments revealed that bacterial diversity and abundance peaked at an intermediate frequency of insect visits, which was in turn determined by the surrounding landscape characteristics observed at the 200-m radius scale. Based on this finding, we discuss the possibility that species diversity tends to be maximized at an intermediate dispersal rate, especially when habitat patches of vectored organisms constitute consumable resources for their vectors.

ecology↗

bioRxiv2025

Priority effects drive fungal and nematode emergence from insect larvae

Priority effects, in which species arrival history influences community assembly, are increasingly recognized to affect host-parasite systems. However, priority effects across disparate groups of parasitic organisms are poorly understood despite the wide range of taxonomic groups involved. In California oak woodland, we investigated how priority effects between two insect-parasitic fungi (Metarhizium and Beauveria) influenced emergence of nematodes from insect larvae. Field and laboratory results indicated that both fungi were common, but priority effects prevented them from co-emerging from the same larva. Metarhizium- and Beauveria-infected insects did not differ in the species composition of emerging nematodes, but larvae without fungal emergence had distinct nematode communities, with Oscheius almost always emerging without fungi. Experiments indicated that none of the commonly found nematodes (Acrobeloides, Mesorhabditis, Oscheius, and Rhabditis) were entomopathogenic, but that Oscheius could exclude Beauveria if arrived early. This time-dependent exclusion was likely caused by an Ochrobactrum bacterium that Oscheius nematodes carried. Together, these findings suggest that fungi enter insects as primary arrivers, while nematodes come as secondary arrivers to exploit fungus-killed insects, with priority effects influencing both groups. We suggest that this system is a promising natural microcosm for understanding priority effects across disparate groups in host-parasite systems.

ecology↗

bioRxiv2025

Dispersal kernels influence the magnitude of environmental, biotic, and stochastic effects on the maintenance of metacommunity diversity

Dispersal plays a central role in shaping patterns of diversity in metacommunities. However, a primary focus on emigration rates may mischaracterize dispersal effects that actually arise from dispersal kernels. Kernels describe probabilistic movements between donor and recipient patches, but the influence of kernel shape on metacommunity diversity remains unclear. We used simulations to measure how kernels affect diversity across metacommunity scales and ecological contexts. We disentangled causes of these patterns using a novel approach quantifying the effects of environmental filtering, competition, stochasticity, and dispersal on fitness. Although metacommunities with shallow kernels followed expectations where emigration increased alpha-but decreased beta- and gamma-diversity, metacommunities with steeper kernels did not. Steeper kernels maintained regional diversity by reducing interspecific competition and stochastic extinctions, with dispersal conferring weaker benefits but less homogenization. Our work suggests dispersal kernels and emigration rates jointly regulate exposure to environmental variation and the balance of assembly mechanisms in metacommunities.

ecology↗

bioRxiv2025

Regional species coexistence despite local priority effects: the overlooked role of dispersal-community feedback

Many cases of animal-mediated dispersal are non-random, with the animals altering their movement pattern in response to the local species composition of the organisms that the vectoring animals disperse. Yet, this dispersal-community feedback has received little attention in metacommunity ecology. We use a mathematical model to show that dispersal-community feedback can promote regional species coexistence. As a well-characterized system, our model focuses on nectar-inhabiting bacteria and yeast that are dispersed by pollinators and affected by priority effects within flowers once dispersed. Model analysis suggests that bacteria and yeast coexist regionally only when their occurrence in flowers influences the frequency of flower visits by pollinators. This microbe-pollinator feedback creates positive density dependence in each plant, causing competitive exclusion at the plant scale, but spatial partitioning across multiple plants, realizing coexistence at this scale. Our finding highlights dispersal-community feedback as an overlooked potential mechanism of species coexistence.

ecology↗

bioRxiv2024

The development of ecological systems along paths of least resistance

A long-standing question in biology is whether there are common principles that characterize the development of ecological systems (the appearance of a group of taxa), regardless of organismal diversity and environmental context. Classic ecological theory holds that these systems develop following a sequenced orderly process that generally proceeds from fast-growing to slow-growing taxa and depends on life-history trade-offs. However, it is also possible that this developmental order is simply the path with the least environmental resistance for survival of the component species and hence favored by probability alone. Here, we use theory and data to show that the order from fast-to slow-growing taxa is the most likely developmental path for diverse systems when local taxon interactions self-organize to minimize environmental resistance. First, we demonstrate theoretically that a sequenced development is more likely than a simultaneous one, at least until the number of iterations becomes so large as to be ecologically implausible. We then show that greater diversity of taxa and life histories improves the likelihood of a sequenced order from fast-to slow-growing taxa. Using data from bacterial and metazoan systems, we present empirical evidence that the developmental order of ecological systems moves along the paths of least environmental resistance. The capacity of simple principles to explain the trend in the developmental order of diverse ecological systems paves the way to an enhanced understanding of the collective features characterizing the diversity of life.

ecology↗

bioRxiv2024

Bacteria in honeybee crops are decoupled from those in floral nectar and bee mouths

Bacteria in the honeybee gut are a well-recognized factor affecting bee health. However, the primary focus of this research has been the hindgut, while the crop, or honey stomach, is assumed to be dominated by environmentally acquired transient taxa that matter little to the bees. To evaluate this assumption, we examined bacterial taxa in the crop and mouth of Apis mellifera and A. cerana japonica foragers and in the nectar of Prunus mume flowers visited by the bees in the Minabe-Tanabe region of Japan. We found that in bacterial composition, the crop was distinct from both the mouth and the nectar, whereas mouth and nectar samples were indistinguishable. Furthermore, the crop remained similar in bacterial composition and diversity, while the mouth showed a sharp drop in alpha diversity and a large increase in beta diversity, from summer to winter. These results refute the conventional assumption, suggesting instead that the crop contains a conserved bacterial community largely distinct from environmental taxa. We also found that strains of a crop-associated species, Apilactobacillus kunkeei, could be season- and host species-specific. Together, these findings suggest that crop-associated bacterial communities should be studied further to better understand the relationship between honeybees and their gut bacteria.

ecology↗

bioRxiv2023

ncBAF, a chromatin remodeler, enhances PXR-mediated transcriptional activation in the human and mouse liver

Pregnane X receptor (PXR) is one of the key regulators of drug metabolism, gluconeogenesis, and lipid synthesis in the human liver. Activation of PXR by drugs such as rifampicin, simvastatin, and efavirenz causes adverse reactions such as drug{square}drug interaction, hyperglycemia, and dyslipidemia. The inhibition of PXR activation has merit in preventing such adverse events. Here, we demonstrated that bromodomain containing protein 9 (BRD9), a component of non-canonical brahma-related gene 1-associated factor (ncBAF), one of the chromatin remodelers, interacts with PXR. Rifampicin-mediated induction of CYP3A4 expression was attenuated by iBRD9, an inhibitor of BRD9, in human primary hepatocytes and CYP3A/PXR-humanized mice, indicating that BRD9 enhances the transcriptional activation of PXR in vitro and in vivo. Chromatin immunoprecipitation assay reveled that iBRD9 treatment resulted in attenuation of the rifampicin-mediated binding of PXR to the CYP3A4 promoter region, suggesting that ncBAF functions to facilitate the binding of PXR to its response elements. Efavirenz-induced hepatic lipid accumulation was attenuated by iBRD9 in C57BL/6J mice, suggesting that the inhibition of BRD9 would be useful to reduce the risk of efavirenz-induced hepatic steatosis. Collectively, we found that inhibitors of BRD9, a component of ncBAF that plays a role in assisting transactivation by PXR, would be useful to reduce the risk of PXR-mediated adverse reactions.

pharmacology and toxicology↗

bioRxiv2022

pH as an eco-evolutionary driver of priority effects

Priority effects, where arrival order and initial relative abundance modulate local species interactions, can exert taxonomic, functional, and evolutionary influences on ecological communities by driving them to alternative states. It remains unclear if these wide-ranging consequences of priority effects can be explained systematically by a common underlying factor. Here, we identify such a factor in an empirical system. In a series of field and laboratory studies, we focus on how pH affects nectar-colonizing microbes and their interactions with plants and pollinators. In a field survey, we found that nectar microbial communities in a hummingbird-pollinated shrub, Diplacus aurantiacus, exhibited patterns indicative of alternative stable states through domination by either bacteria or yeasts within individual flowers. In laboratory experiments, Acinetobacter nectaris, the bacterium most commonly found in D. aurantiacus nectar, exerted a strongly negative priority effect against Metschnikowia reukaufii, the most common nectar-specialist yeast, by reducing nectar pH. This priority effect likely explains the mutually exclusive pattern of dominance found in the field survey. Furthermore, experimental evolution simulating hummingbird-assisted dispersal between flowers revealed that M. reukaufii could evolve rapidly to improve resistance against the priority effect if constantly exposed to A. nectaris-induced pH reduction. Finally, in a field experiment, we found that low nectar pH could reduce nectar consumption by hummingbirds, suggesting functional consequences of the pH-driven priority effect for plant reproduction. Taken together, these results show that it is possible to identify an overarching factor that governs the eco-evolutionary dynamics of priority effects across multiple levels of biological organization.

ecology↗

bioRxiv2021

Quantifying the scale of genetic diversity extinction in the Anthropocene

More species than ever before are at risk of extinction due to anthropogenic habitat loss and climate change. But even species that are not threatened have seen reductions in their populations and geographic ranges, likely impacting their genetic diversity. Although preserving genetic diversity is key to maintaining adaptability of species, we lack predictive tools and global estimates of genetic diversity loss across ecosystems. By bridging theories of biodiversity and population genetics, we introduce a mathematical framework to understand the loss of naturally occurring DNA mutations within decreasing habitat within a species. Analysing genome-wide variation data of 10,095 geo-referenced individuals from 20 plant and animal species, we show that genome-wide diversity follows a power law with geographic area (the mutations-area relationship), which can predict genetic diversity loss in spatial computer simulations of local population extinctions. Given pre-21st century values of ecosystem transformations, we estimate that over 10% of genetic diversity may already be lost, surpassing the United Nations targets for genetic preservation. These estimated losses could rapidly accelerate with advancing climate change and habitat destruction, highlighting the need for forecasting tools that facilitate implementation of policies to protect genetic resources globally.

ecology↗

bioRxiv2021

Untangling the complexity of priority effects in multi-species communities

The history of species immigration can dictate how species interact in local communities, thereby causing historical contingency in community assembly. Since immigration history is rarely known, these historical influences, or priority effects, pose a major challenge in predicting community assembly. Here, we provide a graph-based, non-parametric, theoretical framework for understanding the predictability of community assembly as affected by priority effects. To develop this frame-work, we first show that the diversity of possible priority effects increases super-exponentially with the number of species. We then point out that, despite this diversity, the consequences of priority effects for multispecies communities can be classified into four basic types, each of which reduces community predictability: alternative stable states, alternative transient paths, compositional cycles, and the lack of escapes from compositional cycles to stable states. Using a neural network, we show that this classification of priority effects enables accurate explanation of community predictability, particularly when each species immigrates repeatedly. We also demonstrate the empirical utility of our theoretical framework by applying it to two experimentally derived assembly graphs of algal and ciliate communities. Based on these analyses, we discuss how the framework proposed here can help guide experimental investigation of the predictability of history-dependent community assembly.

ecology↗

bioRxiv2020

Ecological dynamics of the almond floral microbiome in relation to crop management and pollination

O_LICrop tissues harbor microbiomes that can affect host health and yield. However, processes driving microbiome assembly, and resulting effects on ecosystem services, remain poorly understood. This is particularly true of flowering crops that rely on pollinators for yield. C_LIO_LIWe assessed effects of orchard management tactics and landscape context on the flower microbiome in almond, Prunus dulcis. Fourteen orchards (5 conventional, 4 organic, 5 habitat augmentation) were sampled at two bloom stages to characterize bacterial and fungal communities associated with floral tissues. The surveys were complemented by in vitro experiments to assess effects of arrival order and fungicides on nectar microbial communities, and effects of fungicides and microbes on honey bee foraging. Finally, a field trial was conducted to test effects of fungicides and microbes on pollination. C_LIO_LIAs bloom progressed, bacterial and fungal abundance and diversity increased, across all floral tissue types and management strategies. The magnitude by which microbial abundance and diversity were affected varied, with host proximity to apiaries and orchard management having notable effects on bacteria and fungi, respectively. C_LIO_LIExperiments showed immigration history and fungicides affected the composition of nectar microbial communities, but only fungicides affected pollinator foraging through reduced nectar removal. Neither treatment affected pollination services. C_LIO_LISynthesis and applications. Our results shed light on routes through which management practices can shape microbiota associated with flowers of a pollinator-dependent crop. With growing appreciation for the role of floral-associated microbes in affecting biotic interactions at the floral interface, understanding such drivers can potentially inform microbial-derived ecosystem services in agricultural landscapes, including pollination and biocontrol. C_LI

ecology↗

bioRxiv2020

Higher Variability in Fungi Compared to Bacteria in the Foraging Honey Bee

Microbial communities in the honey bee gut have emerged as a model system to understand the effects of host-associated microbes on animals and plants. The specific distribution patterns of bacterial associates among honey bee gut regions remains a key finding within the field. The mid- and hindgut of foraging bees house a deterministic set of core species that affect host health. In contrast, the crop, or honey stomach, contains a more diverse set of bacteria that is highly variable in composition among individual bees. Whether this contrast between the two gut regions also applies to fungi, another major group of gut-associated microbes, remains unclear despite their potential influence on host health. In honey bees caught foraging at four sites across the San Francisco Peninsula, we found that fungi were much less distinct in species composition between the crop and the mid- and hindgut than bacteria. Unlike bacteria, fungi were highly variable in composition throughout the gut, and much of this variation was attributable to bee collection site. These patterns suggest that the fungi may be passengers rather than functionally significant gut symbionts. However, many of the fungi we found in the bees have been recognized as plant pathogens. Assuming that some fungi remain viable after passage through the gut, the distribution patterns we report here point to the potential importance of honey bees as vectors of fungal pathogens and suggest a more prominent role of honey bees in plant pathogen transmission than generally thought. Importance (Nontechnical explanation of why the work was undertaken)Along with bacteria, fungi make up a significant portion of animal- and plant-associated microbial communities. However, we have only begun to describe these fungi, much less examine their effects on most animals and plants. The honey bee, Apis mellifera, has emerged as a model system for studying host-associated microbes. Honey bees contain well-characterized bacteria specialized to inhabit different regions of the gut. Fungi also exist in the honey bee gut, but their composition and function remain largely undescribed. Here we show that, unlike bacteria, fungi vary substantially in species composition throughout the honey bee gut, contingent on where the bees are sampled. This observation suggests that fungi may be transient passengers and therefore unimportant as gut symbionts. However, our findings also indicate that honey bees could be major vectors of infectious plant diseases as many of the fungi we found in the honey bee gut are recognized as plant pathogens.

ecology↗

bioRxiv2020

Ericoid mycorrhizal diversity increases with soil age and progressive phosphorus limitation across a 4.1 million-year chronosequence

Ericaceous plants rely on ericoid mycorrhizal fungi for nutrient acquisition. However, the factors that affect the composition and structure of these fungal communities remain largely unknown. Here, we use a 4.1-myr soil chronosequence in Hawaii to test the hypothesis that changes in nutrient availability with soil age determine the diversity and species composition of fungi associated with ericoid roots. We sampled roots of a native Hawaiian plant, Vaccinium calycinum, and used DNA metabarcoding to quantify changes in fungal diversity and species composition. We also used a fertilization experiment at the youngest and oldest sites to assess the importance of nutrient limitation. We found an increase in diversity and a clear pattern of species turnover across the chronosequence, driven largely by putative ericoid mycorrhizal fungi. Fertilization with nitrogen at the youngest site and phosphorus at the oldest site reduced total fungal diversity, suggesting a direct role of nutrient limitation. Our results also reveal the presence of novel fungal species associated with Hawaiian Ericaceae and suggest a greater importance of phosphorus availability for communities of ericoid mycorrhizal fungi than is generally assumed.

ecology↗

bioRxiv2020

Greater local diversity under older species pools may arise from enhanced competitive equivalence

Local ecological communities tend to contain more species when they are located within a geologically older region, a pattern that has traditionally been attributed to the accumulation of species in the regional species pool. In this explanation, local species interactions are assumed to play a minor role in the formation of the regional species pool, which is instead thought to be driven by speciation and dispersal occurring across larger areas. Here, we provide evidence suggesting a more important role of local species interactions than generally assumed. In an experiment in which we assembled 320 local communities of root-associated fungi under 80 species pools, we varied the species richness of the experimental species pools and the mean age of the sites from which we collected the fungal species across a 4-myr soil chronosequence in Hawaii. We found that realized local species diversity in the assembled communities increased more extensively with increasing species-pool richness when species were from older sites. We also found that older species pools had lower functional and phylogenetic diversity, indicating that the evolution of greater competitive equivalence among potential colonists enabled higher local diversity under older species pools. Our results suggest that the tendency of older regions to have higher local richness arises not simply because older species pools are more speciose, but also because the constituent species have evolved traits that allow them to co-occur more readily in local communities.

ecology↗