Biology subjects

Kawagucci, S.

Publications and source records attributed to Kawagucci, S..

3 recordsLinked to original sources

bioRxiv2023

Millisecond-scale behaviours of plankton quantified in situ and in vitro using the Event-based Vision Sensor (EVS)

The Event-based Vision Sensor (EVS) is a bio-inspired sensor that captures detailed motions of objects, developed with the applicability to become the eyes of machines and especially self-driving cars. Compared to conventional frame-based image sensors as employed in video cameras, EVS has an extremely fast motion capture equivalent to 10,000-fps even with standard optical settings and additionally has high dynamic ranges for brightness and also lower consumption of memory and energy. These features make the EVS an ideal method to tackle questions in biology, such as the fine-scale behavioural ecology. Here, we developed 22 characteristic features for analysing the motions of aquatic particles from the raw data of the EVS, and deployed the EVS system in both natural environments and laboratory aquariums to test its applicability to filming and analysing plankton behaviour. Our EVS monitoring in turbid water at the bottom of Lake Biwa, Japan identified several particles exhibiting distinct cumulative trajectory with periodicities in their motion (up to 16 Hz), suggesting that they were living organisms with rhythmic behaviour. We also carried out EVS monitoring in the deep sea aided by infrared lighting to minimise influence on behaviour, and observed particles with active motion and periodicities over 40 Hz. Furthermore, we used the EVS to observe laboratory cultures of six species of zooplankton and phytoplankton, confirming that they have species-specific motion periodicities of up to 41 Hz. We applied machine learning to automatically classify particles into five categories (four categories of zooplankton plus passive particles), which achieved an accuracy up to 86%. Our attempts to use the EVS for biological observations, especially focusing on its millisecond-scale temporal resolution and wide dynamic range provide a new avenue to investigate rapid and periodical motion and behaviour in small organisms. Given its compact size with low consumption of battery and memory, the EVS will likely be applicable in the near future for the automated monitoring of the behaviour of plankton by edge computing on autonomous floats, as well as quantifying rapid cellular-level activities under microscopy.

animal behavior and cognition↗

bioRxiv2022

Hydrothermal Vent Species Assemblage Networks Identify Regional Connectivity Patterns in the Northwest Pacific

The distribution of species among spatially isolated habitat patches supports regional biodiversity and stability, so understanding the underlying processes and structure is a key target of conservation. Although multivariate statistics can infer the connectivity processes driving species distribution, such as dispersal and habitat suitability, they rarely explore structure. Methods from graph theory, applied to distribution data, give insights into both connectivity pathways and processes by intuitively formatting the data as a network of habitat patches. We apply these methods to empirical data from the hydrothermal vent habitats of the Northwest Pacific. Hydrothermal vents are oases of biological productivity and endemicity on the seafloor that are imminently threatened by anthropogenic disturbances with unknown consequences to biodiversity. Here, we describe the structure of hydrothermal vent species assemblage networks, how local and regional parameters affect their structure, and the implications this has for conservation. Two complementary networks were formed from an extensive species assemblage dataset: a bipartite network of species nodes linked to vent site nodes at which they are present, and a similarity network of vent site nodes linked by weighted edges based on their pairwise assemblage similarity. Using these networks, we assessed the role of individual vent sites in linking their network and identified biogeographic sub-regions. The three sub-regions and two outlying sites are separated by their spatial arrangement and local environmental filters. Both networks detected vent sites that play a disproportionately important role in regional pathways, while the bipartite network also identified key vent sites maintaining the distinct species assemblages of their sub-regions. These regional connectivity pathways provide insights into historical colonisation routes, while sub-regional connectivity pathways are of value when selecting sites for conservation and/or estimating the multi-vent impacts from proposed deep-sea mining.

ecology↗

bioRxiv2021

Diverse DNA modification in marine prokaryotic and viral communities

Chemical modifications of DNA, including methylation, play an important role in prokaryotes and viruses. However, our knowledge of the modification systems in environmental microbial communities, typically dominated by members not yet cultured, is limited. Here, we conducted metaepigenomic analyses by single-molecule real-time sequencing of marine microbial communities. In total, 233 and 163 metagenomic assembly genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTases were not associated with the defense mechanism. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative motifs in the methylation system that are highly conserved in Alphaproteobacteria, illuminating the co-evolutionary history of the methylation system and host genome. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses.

microbiology↗