Biology subjects

Rigonato, J.

Publications and source records attributed to Rigonato, J..

3 recordsLinked to original sources

bioRxiv2025

Ecological processes shaping marine microbial assemblages diverge between equatorial and temperate time-series

Marine microbial communities are structured by a complex interplay of deterministic and stochastic processes, yet how these vary across latitudes remains poorly understood. Most long-term microbial observatories are restricted to temperate regions, limiting our ability to assess latitudinal contrasts in microbial dynamics. Here, we compare coastal microbial communities from two contrasting marine time-series stations using standardized molecular protocols: a new tropical site in the Equatorial Atlantic (EAMO, 6{degrees}S) and a well-studied temperate site in the Mediterranean Sea (BBMO, 41{degrees}N). Monthly 16S and 18S rRNA gene sequencing of two size-fractions (0.22-3 {micro}m and >3 {micro}m) over 41 months (from April 2013 to August 2016) revealed marked differences in taxonomic composition, temporal variability, and ecological assembly processes. Temperate communities exhibited strong seasonal turnover, higher beta-diversity, and tighter coupling with environmental variables such as temperature and daylength. In contrast, tropical communities were compositionally more stable and more governed by biotic factors and stochastic processes such as historical contingency and ecological drift. These patterns were consistent across taxonomic domains and size-fractions, though selection was generally stronger in prokaryotes and the smallest size-fraction. Co-occurrence networks at the temperate site were more densely connected and environmentally responsive compared to tropical networks, where stochastic processes and putative biological interactions gain prominence. This study highlights the importance of integrating observatories from underrepresented latitudes into global microbial monitoring efforts, particularly as climate change alters the amplitude and frequency of environmental drivers across the ocean.

ecology↗

bioRxiv2025

Deviation from Power-Law Distribution when Scaling the Distribution of Marine Plankton Folds from Genomes to Communities

At different scales of living systems, biological entities appear to follow scaling laws, such as power laws, which are often explained from stochastic mechanisms. This is the case for the number of species in a community and the number of genes or protein folds in a genome. Resulting from evolutionary processes combining gene family duplications and expansions with selective pressures, the distribution of protein folds systematically follows a power law in all individually observed genomes. A small number of folds are highly prevalent, while the majority of folds appear only once per genome. However, previous studies on fold occurrence have focused on individual genomes, isolated from their community contexts. In the oceans, plankton communities consist of complex assemblages of species, each exhibiting variable relative abundances. We investigated the consequences of this variability on the composition and distribution of folds by considering the relative abundance of species. By annotating folds to genes of environmental genomes of plankton collected by the Tara Oceans expedition, we show that the relative abundance of folds deviates from the classical power law and instead follows a Type II Pareto distribution. This model, typically observed in other complex organizations such as economics, allows us to classify different categories of folds that exhibit biogeographical differences. Our results show that scaling fold distributions from individual genomes to species communities lead to a deviation from the expected behavior of simple power-law relationship towards a more complex model. This phenomenon could be linked with the variable complexity of marine planktonic ecosystems.

genomics↗

bioRxiv2023

Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: Insights into genetic diversity and major structural variations

1.Population-scale genome sequencing has become essential for exploring genetic diversity and adaptation, particularly in land plants. In contrast, eukaryotic phytoplankton resources remain limited to model reference genomes or community-level metagenomics, leaving a gap in understanding intraspecific variation and evolutionary processes. To address this, we developed a comprehensive biological and genomic resource for the cosmopolitan and ecologically important genus Bathycoccus. Extensive metagenomic data from across the world Ocean are available for this genus, and previous studies have identified four Bathycoccus species and reconstructed 34 metagenome-assembled genomes. Here we report 28 high-quality strain genome sequences using a combination of Oxford Nanopore Technologies long reads and Illumina short reads and associated biological resources. These include 24 Bathycoccus prasinos strains spanning a latitudinal gradient from 40{degrees} to 78{degrees}N, a reference genome for Bathycoccus calidus, and three genomes of the recently identified B3 clade, which we propose as the Bathycoccus catiminus species. Comparative analyses of sequenced genomes with MAGs highlight the complementarity between resources: while MAGs capture environmental diversity and uncover uncultured taxa, the cultured strain genomes provide complete, non-chimeric high-quality assemblies that resolve structural variations and haplotype-level diversity not detected in MAGs. These include the large outlier chromosome (BOC), a putative sexual chromosome revealing a second mating type, and extensive variability in the small outlier chromosome (SOC), associated with viral resistance and genome plasticity. Together, these biological and genomic resources establish Bathycoccus prasinos as a powerful model for studying diversity, adaptation, and evolution of eukaryotic phytoplankton in the ocean, complementing existing global metagenomic datasets. 2. Significance statementEukaryotic phytoplankton are key to ocean ecosystems, yet their intraspecific genomic diversity is poorly understood. We present 28 high-quality genomes and their annotations of the cosmopolitan microalga Bathycoccus, revealing whole genome structural variations, chromosomal haplotype diversity linked to mating and viral resistance, and offering a genomic framework that complements metagenomic data to establish this picoalga as a model for functional and ecological studies.

genomics↗