Biology subjects

Tatsumi, S.

Publications and source records attributed to Tatsumi, S..

10 recordsLinked to original sources

bioRxiv2026

A Passive-Oxygenation Silicone Platform for Biomass Production: Maximizing Labor Productivity and Process Efficiency in Cellular Agriculture Development

The commercial production of cell-based food is currently hindered by existing bioreactor technologies, which require substantial capital investment, specialized operating skills, and complex processing setups. To democratize cell-based food production, we developed the "oxy-thru cultivator"--a simple, autoclavable, closed-bag bioreactor fabricated from polydimethylsiloxane (PDMS). By leveraging the high oxygen-permeability of PDMS, this platform enables passive oxygenation across the entire vessel wall, eliminating the need for external aeration or mechanical sparging. During testing, the cultivator maintained a stable culture environment over 23 days, showing no cytotoxic leachables and retaining both structural integrity and sterility across 10 autoclave cycles. This robustness supported the continuous cultivation of DF-1 cells for 74 days. Using a standardized subculture scheme, we successfully harvested an estimated 2.60 g of cell-based biomass per cultivator over five passages. Notably, the platform achieved a 127% monthly labor productivity compared to conventional bioreactors and was easily operated by researchers without specialized training. Additionally, the system successfully supported the expansion of both mammalian and primary avian cell lines. With a minimal equipment footprint that reduces CapEx, and a reusable silicone vessel that lowers OpEx, the oxy-thru cultivator offers a highly practical, accessible pathway toward scaling up cellular agriculture. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/729703v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@644879org.highwire.dtl.DTLVardef@1d23680org.highwire.dtl.DTLVardef@1f83d9forg.highwire.dtl.DTLVardef@959bf7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Thermophilization, climatic debt, and consequent declines in primary productivity

Species have optimal environmental conditions, and ongoing climate warming is reshaping community composition. In particular, many ecosystems exhibit thermophilization, a shift toward species adapted to warmer conditions. However, this process is often slower in forests, leading to a mismatch between community composition and ambient temperature, referred to as climatic debt. Despite increasing attention, its effects on forest productivity remain unclear. Quantifying tree community responses to warming is therefore essential for predicting future forest dynamics and informing biodiversity conservation. In this study, we analyzed natural forests across Japan using data from the 3rd and 4th National Forest Inventory periods (2009-2018). We first assessed compositional consistency between survey periods using the Bray-Curtis index and excluded plots with high dissimilarity ([≥] 0.8). Species-specific thermal optima were estimated using species distribution models and used to calculate the Community Temperature Index (CTI). Thermophilization was quantified as the temporal change in CTI, while climatic debt was defined as the difference between CTI and mean annual temperature. We then examined the relationship between climatic debt and changes in aboveground biomass, used as a proxy for productivity, using linear mixed-effects models. We found a mean thermophilization rate of 0.005 {degrees}C yr-{superscript 1}. Despite this shift, climatic debt increased at an average rate of -0.022 {degrees}C yr-{superscript 1}, indicating a growing mismatch between climate warming and community thermal composition. Although thermophilization showed no statistically significant association with stand structure, it tended to vary with the proportion of small-diameter trees, suggesting the influence of multiple interacting drivers. Importantly, increasing climatic debt was significantly associated with declines in forest primary productivity, even after accounting for stand structure and regional variation. These results demonstrate that delayed thermal adjustment of tree communities can constrain forest productivity under ongoing climate warming, highlighting the importance of evaluating community-level thermal responses for sustaining forest ecosystem functioning.

ecology↗

bioRxiv2023

Response diversity is key to buffer ecosystem productivity against multiple environmental change drivers

Evidence shows that biodiversity promotes primary productivity. However, it is unclear whether such biodiversity-productivity relationships persist under increasing numbers of environmental changes in the current Anthropocene. Here, we use theoretical and experimental approaches to demonstrate that variation in species responses to changing environments determines the ability of ecological communities to maintain productivity under multiple types of environmental change. Our theory shows that this response diversity determines whether biodiversity-productivity relationships are enhanced or impaired by environmental changes. Communities with high response diversity are expected not only to be productive in a particular environment but to maintain that productivity under multiple conditions. Nevertheless, our theory also predicts that such buffering effects fade with increasing negative environmental impacts on communities. Consistent with this prediction, our biodiversity experiment reveals impaired biodiversity-productivity relationships under multiple environmental change drivers with a negative mean impact. Our results suggest that, in the face of growing multiplicity of environmental changes, policies should encourage conservation of local biota, enabling communities to respond to unprecedented environments that may arise.

ecology↗

bioRxiv2023

Bark traits affect epiphytic bryophyte community assembly in a temperate forest

Bark traits of trees often serve as a key factor determining the community structure of epiphytes. However, the extent to which barks modulate the relative importance of abiotic and biotic assembly processes of epiphytes is poorly understood. Here, using a community phylogenetic approach, we aimed to infer the assembly processes of epiphytic mosses and liverworts on tree species with varying bark traits in a temperate forest of central Japan. We observed a total of 56 moss and 35 liverwort species on 150 trees. Moss communities showed decreasing species richness and a tendency toward phylogenetic overdispersion, that is, higher phylogenetic diversity than expected by chance, in relation to increasing bark roughness, acidity, and wetness. Along the same bark gradients, liverwort communities became phylogenetically clustered. Species richness of both mosses and liverworts increased with the nitrogen content of barks. The results indicate non-random assembly processes such as interspecific competition on resource-rich barks and abiotic filtering associated with environmental harshness and microhabitat variety determined by barks. Our findings imply that bark traits modulate community assembly processes through which epiphyte diversity is maintained.

ecology↗

bioRxiv2022

Jaccard dissimilarity in stochastic community models based on the species-independence assumption

A fundamental problem in ecology is understanding the causes of change in species composition among sites (i.e. beta diversity). At present it is unclear how spatial heterogeneity in species occupancy across sites shapes these patterns. To address this question, we develop probabilistic models that consider two spatial or temporal sites, where presence probabilities vary both among species and between the sites. We derive analytical and approximate formulae for the expectation of pairwise beta-diversity. Using a novel graphical tool, Stochastic Incidence Plots (SIPs), which depict the presence probabilities in two sites across species labels, we develop a means to conceptualize the heterogeneity in presence probabilities: the steepness or unevenness of SIPs reflects species-level heterogeneity, while the degree of overlap between SIPs indicates site-level heterogeneity. Utilizing SIPs and a combinatorial approach in a two-species scenario, we demonstrate that beta-diversity is lower when SIPs are parallel compared to when they are anti-parallel. We also find that this prediction is testable with the well-known checkerboard pattern in incidence matrices. Finally, we applied the method to the species distribution models for five woodpecker species in Switzerland, showing that their spatial distributions will change significantly in the future. Overall, this work improves our understanding of how pairwise beta-diversity responds to occupancy heterogeneity.

ecology↗

bioRxiv2021

ForestScanner: A mobile application for measuring and mapping trees with LiDAR-equipped iPhone and iPad

O_LIGround-based light detection and ranging (LiDAR) is becoming increasingly popular as an alternative means to conventional forest inventory methods. By gauging the distances to multiple points on the surrounding object surfaces, LiDAR acquires 3D point clouds from which tree sizes and spatial distributions can be rapidly estimated. However, the high cost and specialized skills associated with LiDAR technologies have put them out of reach for many potential users. C_LIO_LIWe here introduce ForestScanner, a free, mobile application that allows LiDAR-based forest inventories by means of iPhone or iPad with a built-in LiDAR sensor. ForestScanner does not require any manual analysis of 3D point clouds. As the user scans trees with an iPhone/iPad, ForestScanner estimates the stem diameters and spatial coordinates based on real-time instance segmentation and circle fitting. The users can visualize, check, and share the scanning results in situ. C_LIO_LIBy using ForestScanner, we measured the stem diameters and spatial coordinates of 672 trees within a 1 ha plot in 1 h 39 min with an iPhone and in 1 h 38 min with an iPad (diameter [≥]5 cm; detection rate = 100%). The diameters measured by ForestScanner and a diameter tape were in good agreement; R2=0.963 for iPhone and R2=0.961 for iPad. ForestScanner and a conventional surveying system showed almost identical results for tree mapping (assessed by the spatial distances among trees within 0.04 ha subplots); Mantel R2=0.999 for both iPhone and iPad. ForestScanner reduced the person-hours required for measuring diameters to 25.7%, mapping trees to 9.3%, and doing both to 6.8% of the person-hours taken using a dimeter tape and the conventional surveying system. C_LIO_LIOur results indicate that ForestScanner enables cost-, labor-, and time-efficient forest inventories. The application can increase the accessibility to LiDAR for non-experts (e.g., students, citizen scientists) and enhance resource assessments and biodiversity monitoring in forests worldwide. C_LI

ecology↗

bioRxiv2021

Partitioning the temporal changes in abundance-based beta diversity into loss and gain components

O_LIEcologists have long recognized that the losses and gains in local species abundances can either decrease or increase spatial beta diversity, phenomena often referred to as biotic homogenization and differentiation, respectively. However, quantifying such dynamic impacts of species abundances on beta diversity has remained a methodological challenge. C_LIO_LIHere, we develop a numerical method to additively partition the temporal changes in beta diversity into distinct components that reflect the losses and gains in local species abundances. Our method is based on Ru[z]i[c]ka and Bray-Curtis indices and the normalized abundance-based Whittakers beta diversity. The temporal changes in these measures are partitioned into components that represent biotic homogenization and differentiation driven by abundance losses and gains at both species and community levels. C_LIO_LIApplication of the method to a Swedish fish community dataset revealed decreases in beta diversity between 1990 and 2018. The homogenization of fish communities was explained by gains, but not losses, in species abundances across sites. Species-level partitioning further showed that the homogenization was largely caused by the increased population sizes of a particular species in sites where it was already present. C_LIO_LIThe results highlight that our partitioning method effectively identifies local population and community processes embedded in regional biodiversity patterns. We believe that explicit analyses of the losses and gains in species abundances should bring deeper insights into the dynamics of beta diversity. C_LI

ecology↗

bioRxiv2020

Reassembly of soil fungal communities under reforestation and herbivore exclusion

Soil fungi can help improve ecosystem restoration, yet our understanding of how they reassemble in degraded land is limited. Here, we studied fungal community structure using DNA metabarcoding in reforested sites following agricultural abandonment and overgrazing. Two treatments, namely reforestation using different numbers of tree species and deer exclusion, have been applied for multiple decades in the study sites. We found that local fungal richness (alpha diversity) and total fungal richness (gamma diversity) were 1.9-2.9 and 1.3-1.9 times greater, respectively, in reforested stands than in natural forests. These results were regardless of the number of tree species planted in the reforested stands. Conversely, reforested stands had a spatially homogenized community structure with relatively lower degrees of compositional dissimilarity among sites within each stand (beta diversity). These findings were attributable to lower environmental heterogeneity, stronger dispersal limitation, and a comparatively shorter time since the onset of community assembly in reforested stands. Deer exclosures had no detectable effect on fungal community structure. Overall, the agricultural legacy in fungal community structure appears to have persisted for decades, even under proactive restoration of aboveground vegetation. Direct human intervention belowground may therefore be necessary for the recovery of soil biota once altered.

ecology↗

bioRxiv2020

Partitioning the colonization and extinction components of beta diversity: Spatiotemporal species turnover across disturbance gradients

Changes in species diversity often result from species losses and gains. The dynamic nature of beta diversity (i.e., spatial variation in species composition) that derives from such temporal species turnover, however, has been largely overlooked. Here, we disentangled extinction and colonization components of beta diversity by using the sets of species that went locally extinct and that newly colonized the given sites. We applied this concept of extinction and colonization beta diversity to plant communities that have been repeatedly measured in experimentally disturbed forests. We first found no difference in beta diversity across disturbance gradients when it was analyzed for communities at a single point in time. From this result, we might conclude that disturbance caused no impact on how species assemble across space. However, when we analyzed the extinction and colonization beta diversity, both measures were found to be significantly lower in disturbed sites compared to undisturbed sites. These results indicate that disturbance removed similar subsets of species across space, making communities differentiate, but at the same time induced spatially uniform colonization of new species, causing communities to homogenize. Consequently, the effects of these two processes canceled each other out. The relative importance of extinction and colonization components per se also changed temporally after disturbance. Analyses using extinction and colonization beta diversity allowed us to detect nonrandom dis- and re-assembly dynamics in plant communities. Our results suggest that common practices of analyzing beta diversity at one point in time can mask significant variation driven by disturbance. Acknowledging the extinction-colonization dynamics behind beta diversity is essential for understanding the spatiotemporal organization of biodiversity.

ecology↗

bioRxiv2020

Tree diversity effects on forest productivity increase through time because of spatial partitioning

BackgroundExperimental manipulations of tree diversity have often found overyielding in mixed-species plantations. While most experiments are still in the early stages of stand development, the impacts of tree diversity are expected to accumulate over time. Here, I present findings from a 31-year-old tree diversity experiment (as of 2018) in Japan. ResultsI find that the net diversity effect on stand biomass increased linearly through time. The species mixture achieved 64% greater biomass than the average monoculture biomass 31 years after planting. The complementarity effect was positive and increased exponentially with time. The selection effect was negative and decreased exponentially with time. In the early stages ([≤]3 years), the positive complementarity effect was explained by enhanced growths of early- and mid-successional species in the mixture. Later on ([≥]15 years), it was explained by their increased survival rates owing to vertical spatial partitioning -- i.e., alleviation of self-thinning via canopy stratification. The negative selection effect resulted from suppressed growths of late-successional species in the bottom layer. ConclusionsThe experiment provides pioneering evidence that the positive impacts of diversity-driven spatial partitioning on forest biomass can accumulate over multiple decades. The results indicate that forest biomass production and carbon sequestration can be enhanced by multispecies afforestation strategies.

ecology↗