Masayuki Ushio

The Hong Kong University of Science and Technology | UST · Department of Ocean Science

We investigated consequences of plant-soil feedbacks (PSFs) in a tropical montane forest on Mt. Kinabalu in Borneo by measurements of light and soil conditions, ecophysiological analyses of tree seedlings, a long-term adult and seedling census and a simple simulation model. The study plot (2.74 ha) is in a mixed conifer-broadleaf forest with 24% re...

Terrestrial animals must have frequent contact with water to survive, implying that environmental DNA (eDNA) originating from those animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal,...

Ecological theory suggests that large-scale patterns such as community stability can be influenced by changes in interspecific interactions that arise from the behavioural and/or physiological responses of individual species varying over time. Although this theory has experimental support, evidence from natural ecosystems is lacking owing to the ch...

Intra‐annual periodicity of canopy photosynthetic activity and leaf development has been documented in seasonal and weakly seasonal tropical forests in the Amazon and elsewhere. However, vegetative periodicity such as leaf flush and fall in apparently ‘aseasonal’ equatorial tropical forests has not been well documented. Moreover, causal drivers of...

How patterns in community diversity emerge is a long-standing question in ecology. Studies suggested that community diversity and interspecific interactions are interdependent. However, evidence from high-diversity ecological communities is lacking because of practical challenges in characterizing speciose communities and their interactions. Here,...

Comprehensive biodiversity data is crucial for ecosystem protection. The Biome mobile app, launched in Japan, efficiently gathers species observations from the public using species identification algorithms and gamification elements. The app has amassed >6 million observations since 2019. Nonetheless, community-sourced data may exhibit spatial and...

Ecosystem services, which derive in part from biological diversity, are a fundamental support for human society. However, human activities are causing harm to biodiversity, ultimately endangering these critical ecosystem services. Halting nature loss and mitigating these impacts necessitates comprehensive biodiversity distribution data, a requireme...

ELife digest The internet has allowed people to share their experiences through images, videos or audio recordings. This has led to the creation of online communities around a variety of topics, including biodiversity. In 2019, a smartphone app, called Biome, was created to fuel biodiversity engagement by making wildlife surveying an easy and fun a...

Ecosystem services, which derive in part from biological diversity, are a fundamental support for human society. However, human activities are causing harm to biodiversity, ultimately endangering these critical ecosystem services. Halting nature loss and mitigating these impacts necessitates comprehensive biodiversity distribution data, a requireme...

Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small num...

The forest canopy harbors a diverse array of organisms. However, monitoring their biodiversity poses challenges due to limited accessibility and the vast taxonomic diversity. To address these challenges, we present a novel method for capturing arboreal biodiversity by harnessing stemflow as a source of DNA from organisms inhabiting trees. Our metho...

Kunming-Montreal Global Biodiversity Framework increased the demand for biodiversity distribution data. To gather species observation from the public, we introduced a mobile application called 'Biome' in Japan. By employing species identification algorithms and gamification elements, Biome has gathered >5M observations since its launch in 2019. How...

How to achieve sustainable food production while reducing environmental impacts is a major concern in agricultural science, and advanced breeding techniques are promising for achieving such goals. However, rice is usually grown under field conditions and influenced by surrounding ecological community members. How ecological communities influence th...

How to achieve sustainable food production while reducing environmental impacts is a major concern in agricultural science, and advanced breeding techniques are promising for achieving such goals. However, rice is usually grown under field conditions and influenced by surrounding ecological community members. How ecological communities influence th...

The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, tracking and quantifying interactions of marine fish species are practically difficult especially under field conditions, and thus, how temperature influences their interaction strengths u...

The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, tracking and quantifying interactions of marine fish species are practically difficult especially under field conditions, and thus, how temperature influences their interaction strengths u...

The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, tracking and quantifying interactions of marine fish species are practically difficult especially under field conditions, and thus, how temperature influences their interaction strengths u...

The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, tracking and quantifying interactions of marine fish species are practically difficult especially under field conditions, and thus, how temperature influences their interaction strengths u...

The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, tracking and quantifying interactions of marine fish species is practically difficult especially under field conditions, and thus, how temperature influences their interaction strengths un...

Reliable survey of arthropods is a crucial for their conservation, community ecology, and pest control on terrestrial plants. However, efficient and comprehensive surveys are hindered by challenges in collecting arthropods and identifying especially small species. To address this issue, we developed a non-destructive environmental DNA (eDNA) collec...

How to achieve sustainable food production while reducing environmental impacts is a major concern in agricultural science, and advanced breeding techniques are promising for achieving such goals. However, rice is usually grown under field conditions and inevitably influenced by surrounding ecological community members, and whether and how ecologic...

How to achieve sustainable food production while reducing environmental impacts is a major concern in agricultural science, and advanced breeding techniques are promising for achieving such goals. However, rice is usually grown under field conditions and inevitably influenced by surrounding ecological community members, and whether and how ecologic...

The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, tracking and quantifying interactions of marine fish species is practically difficult especially under field conditions, and thus, how temperature influences their interaction strengths un...

The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, tracking and quantifying interactions of marine fish species is practically difficult especially under field conditions, and thus, how temperature influences their interaction strengths un...

Most complex systems in the real world are driven by multiple interactions among components. Identifying these interactions is critical for understanding, forecasting, and controlling system-level phenomena. Transfer entropy (TE) and convergent cross mapping (CCM) are two widely-used approaches for nonparametric causality detection based on time-se...

Ecological dynamics is driven by complex ecological networks. Computational capabilities of artificial networks have been exploited for machine learning purposes, yet whether an ecological network possesses a computational capability and whether/how we can use it remain unclear. Here, we developed two new computational/empirical frameworks based on...

Facilitative interactions between microbial species are ubiquitous in various types of ecosystems on the Earth. Therefore, inferring how entangled webs of interspecific interactions shift through time in microbial ecosystems is an essential step for understanding ecological processes driving microbiome dynamics. By compiling shotgun metagenomic seq...

Background: Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as "dysbiosis" in human microbiomes. Methods: We integrated theore...

How to achieve sustainable food production while reducing environmental impacts is a major concern in agricultural science, and advanced breeding techniques are promising for achieving such goals. However, rice is usually grown under field conditions and inevitably influenced by surrounding ecological community members, and whether and how ecologic...

Understanding potential roles of facilitative interactions between species is one of the major challenges in ecology and microbiology. However, we still have limited knowledge of entangled webs of facilitative interactions in ecosystems. By compiling whole-genome shotgun metagenomic data of an experimental microbial community, we tested the hypothe...

Species utilizing the same resources ultimately do not coexist for long periods of time. Such competitive exclusion mechanisms potentially underly dynamics of microbiomes, causing breakdowns of communities constituted by species with similar genetic backgrounds of resource use. Nonetheless, it remains a major challenge to integrate genomics and eco...

PurposeThe purpose of our study was to investigate soil chemical properties, soil microbial biomass and soil enzyme activities in a gradient of forest degradation in logged over tropical rain forests, Borneo. We hypothesized that the changes of above-ground vegetation could affect soil organic matter, which further influenced soil microbial biomass...

Although lowland tree species in the ever‐wet regions of Southeast Asia are characterized by the supra‐annual cycle of reproduction, the reproductive phenology of montane tree species remains poorly understood. In this study, we investigated the reproductive phenology of montane tree species using litter samples that were collected every 2 weeks fr...

For the conservation and community ecology of arthropods and pest controls on terrestrial plants, survey of arthropods is a crucial step. However, efficient surveys are hindered by challenges in collecting small arthropods, and identifying the species. Environmental DNA (eDNA)-based techniques, such as eDNA metabarcording, help overcome these diffi...

Monitoring of artificial reefs (ARs) has been conducted through such methods as visual censuses, surveys using fishing gear, and echo sounder. These methods have disadvantages: visual census is not possible at ARs in deeper waters, fishing gear surveys are invasive to fish individuals, and echo sounders have difficulty in species identification. A...

Microbiome dynamics are both crucial indicators and drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as dysbiosis in human microbiomes. We here integrate theoretical and empirical bases for an...

Flowers are colonized and inhabited by diverse microbes. Flowers have various mechanisms to suppress microbial growth, such as flower volatiles, reactive oxygen and secondary compounds. Besides, plants rapidly replace flowers that have a short lifespan, and old flowers senesce. They may contribute to avoiding adverse effects of the microbes. In thi...

Abstract Environmental DNA (eDNA) metabarcoding, a method that applies high‐throughput sequencing and universal primer sets to eDNA analysis, has been a promising approach for efficient, comprehensive biodiversity monitoring. However, significant money‐, labor‐, and time‐costs are still required for performing eDNA metabarcoding. In this study, we...

Interspecific interactions influence the dynamics and stability of a marine ecological community, and thus, are key to understanding marine ecosystem dynamics. The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, it currently remains unclear...

Environmental DNA (eDNA) metabarcoding, a method that applies high-throughput sequencing and universal primer sets to eDNA analysis, has been a promising approach for efficient, comprehensive biodiversity monitoring. However, significant money-, labor-, and time-costs are still required for performing eDNA metabarcoding. In the present study, we as...

Among all the different organs of a plant, flowers might have one of the most dynamic microbial communities, since many microbes are transmitted during flowering by insects and pollen. However, little is known about how these microbes affect floral characteristics and plant reproduction. Among the microbes transmitted to flowers, pathogens may have...

Flowers play a central role in plant reproduction by dispersing and receiving pollen grains delivered by animal vectors or air. They are rich in various nutrients, and therefore, provide an ideal habitat for many microbes. Recent studies have revealed that flower microbial communities can be highly variable among species, individuals, or even flora...

Reconstructing large interaction networks from empirical time series data: SI

Reconstructing interactions from observational data is a critical need for investigating natural biological networks, wherein network dimensionality is usually high. However, these pose a challenge to existing methods that can quantify only small interaction networks. Here, we proposed a novel approach to reconstruct high‐dimensional interaction Ja...

Since the early 1970s, many artificial reefs (ARs) have been deployed in Japanese coastal waters to create fisheries grounds. Recently, researchers began to use environmental DNA (eDNA) methods for biodiversity monitoring of aquatic species. A metabarcoding approach using internal standard DNAs [i.e., quantitative MiSeq sequencing (qMiSeq)] makes i...

Ecological dynamics is driven by an ecological network consisting of complex interactions. Information processing capability of artificial networks has been exploited as a computational resource, yet whether an ecological network possesses a computational capability and how we can exploit it remain unclear. Here, we show that ecological dynamics ca...

The deep sea comprises more than 90% of the ocean; therefore, understanding the controlling factors of biodiversity in the deep sea is of great importance for predicting future changes in the functioning of the ocean system. Consensus has recently been increasing on two plausible factors that have often been discussed as the drivers of deep-sea spe...

Given that forest dieback due to emerging pests is increasing under global warming, understanding the relationships between pests, climate, and forest biodiversity is an urgent priority. In Japan, mass attacks of an ambrosia beetle, vectoring a pathogenic fungus, cause oak wilt outbreaks in recent decades. Here, the associations of oak wilt and cli...

Investigation of seasonal variation in fungal communities is essential for understanding biodiversity and ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community composition, makes surveying the seasonality of fungal communities challenging. Recently, water environmental DNA...

Flowers are colonized by and inhabited by diverse microbes. Plants rapidly replace flowers of short lifespan, and old flowers senesce. This may contribute to avoiding adverse effects of the microbes. In this study, we investigate if the flower microbial community on old flowers impedes fruit and seed production in a wild ginger with one-day flowers...

Since the early 1970s, many artificial reefs (ARs) have been deployed in Japanese coastal waters to create fisheries grounds. Recently, researchers began to use environmental DNA (eDNA) methods for biodiversity monitoring of aquatic species. A metabarcoding approach using internal standard DNAs (i.e., quantitative MiSeq sequencing) makes it possibl...

Reconstructing interactions from observational data is a critical need for investigating natural biological networks, wherein network dimensionality (i.e. number of interacting components) is usually high and interactions are time-varying. These pose a challenge to existing methods that can quantify only small interaction networks or assume static...

Resource–consumer interactions are considered a major driving force of population and community dynamics. However, species also interact in many non‐trophic and indirect ways and it is currently not known to what extent the dynamic coupling of species corresponds to the distribution of trophic links. Here, using a 10‐year data set of monthly observ...

The environmental DNA (eDNA) derived from fish in marine sediments is preserved for long periods and could be used as successive proxy data for fish assemblages. However, metabarcoding analysis for fish eDNA has never been applied to marine sediments. In this study, metabarcoding analysis for fish eDNA was applied to the Tohoku Earthquake sediment...

Investigation of the seasonal variation in the fungal community is essential for understanding biodiversity and its ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community compositions, makes surveying the seasonality of fungal communities challenging. Recently, water enviro...

Natural ecosystems are often complex, dynamic and state-dependent (i.e., nonlinear), and it is difficult to forecast their (near) future states if we rely only on linear statistical approaches. In the past few decades, tools of nonlinear time series analysis have been developed to analyze and forecast the state-dependent behavior of nonlinear syste...

Chimarrogale platycephala (Japanese water shrew) is an endangered, semi-aquatic mammal species in Japan, and understanding the C. platycephala habitat is vital for conservation planning. However, the species is difficult to locate using conventional methods, like visual observations and camera/video traps, due to its small size, nocturnal behavior,...

Recent advances in environmental DNA (eDNA) analysis using high‐throughput sequencing (HTS) enable evaluation of intraspecific genetic diversity in a population. As the intraspecific genetic diversity provides invaluable information for wildlife conservation and management, there is an increasing demand to apply eDNA analysis to population genetics...

Interspecific interaction has been a key concept in ecology to understand the structure and dynamics of ecological communities. Important, yet often overlooked, is that an interspecific interaction is a product of multiple biological processes at various temporal and spatial scales, including changes in demographic parameters such as birth and deat...

Natural environments require organisms to possess robust mechanisms allowing responses to seasonal trends. In Arabidopsis halleri, the flowering regulator AhgFLC shows upregulation and downregulation phases along with long-term past temperature, but the underlying machinery remains elusive. Here, we investigate the seasonal dynamics of histone modi...

Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA‐based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivel...

How patterns in community diversity emerge is a long-standing question in ecology. Theories and experimental studies suggested that community diversity and interspecific interactions are interdependent. However, evidence from multitaxonomic, high-diversity ecological communities is lacking because of practical challenges in characterizing speciose...

Isolation and cultivation of microbes from environmental samples have been fundamental and important for species identification and investigating functions and ecology of target microbes. Although cultivation and isolation of microbes are not easy, the natural environment can “culture” any endemic microbes, and thus key information for culturing an...

Picocyanobacteria in lakes generally occur as single cells (single-celled picocyanobacteria; SPcy) or colonies (colonial picocyanobacteria; CPcy), and the latter form has been considered an adaptation to grazing pressure. In addition to direct effects of grazing, grazers may also have important indirect effects on picocyanobacteria, such as those f...

Among terrestrial microorganisms, mushroom-forming fungi have been relatively well investigated, however the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity. Herein, we sought to obtain a comprehensive phylogenetic diversity profile for the early-diverging wood-de...

Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA-based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish ( Plecoglossus altivelis altive...

Abstract Recent advances in environmental DNA (eDNA) analysis using high‐throughput sequencing (HTS) provide a noninvasive way to evaluate the intraspecific genetic diversity of aquatic macroorganisms. However, erroneous sequences present in HTS data can result in false positive haplotypes; therefore, reliable strategies are necessary to eliminate...

Isolation and cultivation of microbes from environmental samples have been fundamental and important for species identification and investigating functions and ecology of target microbes. While cultivation and isolation of microbes are not easy, the natural environment can "culture" any endemic microbes, and thus key information for culturing and i...

Supra‐annually synchronized flowering events occurring in tropical forests in Southeast Asia, known as general flowering (GF), are “spectacular and mysterious” forest events. Recently, studies that combined novel molecular techniques and model‐based theoretical approaches suggested that cool temperature and drought synergistically drove GF. Althoug...

Microbial communities play an important role in driving the dynamics of aquatic ecosystems. As difficulties in DNA sequencing faced by microbial ecologists are continuously being reduced, sample collection methods and DNA extraction protocols are becoming more critical to the outcome of any sequencing study. In the present study, I added a manual,...

Supra-annually synchronized flowering events occurring in tropical forests in Southeast Asia, known as general flowering (GF), are "spectacular and mysterious" forest events. Recently, studies that combined novel molecular techniques and model-based theoretical approaches suggested that cool temperature and drought synergistically drove GF. Althoug...

The spatiotemporal characteristics of litterfall reflect important functional processes in a forest ecosystem, yet seasonal and long‐term patterns in litterfall and relationship between litterfall and climate seasonality have rarely been examined in the aseasonal Southeast Asian tropics. We monitored monthly litterfall and conducted meteorological...

Intra-annual periodicity of canopy photosynthetic activity and leaf development has been documented in seasonal and weakly-seasonal tropical forests in the Amazon and elsewhere. However, vegetative periodicity such as leaf flush and fall in apparently “aseasonal” equatorial tropical forests has not been well documented. Moreover, causal drivers of...

Microbial communities play an important role in driving the dynamics of aquatic ecosystems. As difficulties in DNA sequencing faced by microbial ecologists are continuously being reduced, sample collection methods and the choice of DNA extraction protocols are becoming more critical to the outcome of any sequencing study. In the present study, I ad...

Recent advances in environmental DNA (eDNA) analysis using high-throughput sequencing (HTS) provide a non-invasive way to evaluate the intraspecific genetic diversity of aquatic macroorganisms. However, erroneous sequences present in HTS data can result in false positive haplotypes; therefore, reliable strategies are necessary to eliminate such err...

Owing to a technical error, this Perspective was originally published without its received and accepted dates; the dates "Received: 31 December 2017; Accepted: 23 March 2018" have now been included in all versions.

In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome fu...

Birds play unique functional roles in the maintenance of ecosystems, such as pollination and seed dispersal, and thus monitoring bird species diversity is a first step towards avoiding undesirable consequences of anthropogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have...

Effective ecosystem conservation and resource management require quantitative monitoring of biodiversity, including accurate descriptions of species composition and temporal variations of species abundance. Accordingly, quantitative monitoring of biodiversity has been performed for many ecosystems, but it is often time-and effort-consuming and cost...

Effective ecosystem conservation and resource management require quantitative monitoring of biodiversity, including accurate descriptions of species composition and temporal variations of species abundance. Therefore, quantitative monitoring of biodiversity has been performed for many ecosystems, but it is often time- and effort-consuming and costl...

Birds play unique functional roles in the maintenance of ecosystems, such as pollina-tion and seed dispersal, and thus monitoring bird communities (e.g., monitoring bird species diversity) is a first step towards avoiding undesirable consequences of anthro-pogenic impacts on bird communities. In the present study, we hypothesized that birds, regard...

Natural systems are often complex and dynamic (i.e. nonlinear), making them difficult to understand using linear statistical approaches. Linear approaches are fundamentally based on correlation. Thus, they are ill-posed for dynamical systems, where correlation can occur without causation, and causation may also occur in the absence of correlation....

Environmental DNA (eDNA) is DNA shed by organisms into surrounding environments such as soil and water. The new methods using eDNA as a marker for species detection are being rapidly developed. Here we explore basic knowledge regarding the dependence of the eDNA degradation rate on time and water temperature, and the relationship between eDNA degra...

Lognormal distributions and self-similarity are characteristics associated with a wide range of biological systems. The sequential breakage model has established a link between lognormal distributions and self-similarity and has been used to explain species abundance distributions. To date, however, there has been no similar evidence in studies of...

Supply of non-timber Forest Products (NTFPs) is an important provisioning ecosystem service. It is often argued that forest conservation contributes to poverty alleviation through provisioning of NTFPs to the poor. However, implicit assumptions of the argument that NTFPs are more intensively utilized by poor who lack alternative subsistence options...

Terrestrial animals must have frequent contact with water to maintain their lives, implying that environmental DNA (eDNA) originating from terrestrial animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR...

Diving behavior and its frequency may differ among species of mosquito larvae because of differences in predation pressure. The present study aimed to investigate the relationship between water depth and predation frequency on two mosquito species, Culex tritaeniorhynchus (wetland breeder) and Aedes albopictus (container breeder), by the diving bee...