M. Ushio

Boosting biodiversity monitoring using smartphone-driven, rapidly accumulating community-sourced data

The paper evaluates Biome app data quality and shows combining it with traditional surveys improves species distribution model accuracy for conservation.

Unified understanding of nonparametric causality detection in time series

This paper introduces a new nonparametric causality test, UIC, that outperforms existing methods in detecting causality in time series data.

Detecting and validating influential organisms for rice growth: An ecological network approach

The paper identifies influential organisms affecting rice growth using ecological network analysis and field experiments.

Facilitative interaction networks in experimental microbial community dynamics

The paper analyzes facilitative interactions in microbial communities using metagenomic data and metabolic modeling to identify feedback loops and keystone species.

Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics

The paper uses metagenomic analysis to study how genetic resource-use profiles influence community collapse in microbiomes over time.

Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant

The paper develops a non-destructive method to collect and metabarcoding arthropod eDNA from plants, detecting 38 arthropod taxa, including species not observed visually.

Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics

This study shows that abrupt microbiome changes can be predicted using ecological concepts and stability indices in complex microbial communities.

An efficient early-pooling protocol for environmental DNA metabarcoding

This study evaluates an early-pooling protocol for eDNA metabarcoding, showing it reduces costs and time while maintaining accuracy compared to traditional methods.

Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities

This study quantifies how water temperature affects fish-fish interaction strengths in coastal marine communities using eDNA metabarcoding and time-series analysis, showing species-specific temperature responses.

Computational capability of ecological dynamics

This paper demonstrates that ecological networks can function as computational resources, introducing 'Ecological Reservoir Computing' to predict future dynamics and emulate nonlinear systems.

Are microbes growing on flowers evil? Effects of old flower microbes on fruit set in a wild ginger with one-day flowers, Alpinia japonica (Zingiberaceae)

The study investigates whether microbes from old flowers negatively impact fruit set in Alpinia japonica by inoculating new flowers with old flower microbes and analyzing microbial communities.

Quantitative assessment of multiple fish species around artificial reefs using environmental DNA metabarcoding

The paper uses environmental DNA metabarcoding to assess fish species distribution around artificial reefs and finds higher eDNA concentrations at reefs compared to surrounding areas.

Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding

This study uses eDNA metabarcoding to detect seasonal fungal community dynamics in a forest stream over two years, finding regular annual periodicity and variation among functional groups.

Temperature is a dominant driver of distinct annual seasonality of leaf litter production of equatorial tropical rain forests

This study identifies annual temperature-driven leaf litter seasonality in equatorial tropical rain forests using long-term monitoring and statistical analysis.

Interaction capacity underpins community diversity

The paper shows that species interaction capacity, not just network complexity, drives community diversity in ecological systems.

Idea Paper: Predicting culturability of microbes from population dynamics under field conditions

The paper proposes using nonlinear time series analysis to predict microbial culturability from population dynamics in field conditions, finding many taxa exhibit simple or nonlinear dynamics suggesting potential for cultivation with minor condition changes.

Dynamic and synergistic influences of air temperature and rainfall on general flowering in a Bornean lowland tropical forest

The paper analyzes 17 years of phenology data from a Bornean tropical forest to show that general flowering is driven by cumulative cool temperature and drought, with changing relationships over time.

Use of a filter cartridge combined with intra-cartridge bead beating improves detection of microbial DNA from water samples

This study compares DNA extraction methods from water samples, finding that bead-beating inside a filter cartridge increases DNA yield and species richness compared to other methods.

Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing

This study quantifies fish eDNA copy numbers using internal standards and high-throughput sequencing, showing strong correlation with qPCR and enabling efficient biodiversity monitoring.

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

The paper demonstrates that environmental DNA (eDNA) metabarcoding using MiBird primers can detect avian species from water samples, showing potential as a complementary tool for bird monitoring.