Biology subjects

Walde, M.

Publications and source records attributed to Walde, M..

5 recordsLinked to original sources

bioRxiv2026

Seasonal patterns in Synechococcus pigment diversity at two temperate sites with contrasting oceanic regimes

Competition for light has driven extensive pigment diversification among phytoplankton species, yet how this diversity shapes their spatiotemporal distribution in the field has been little studied so far. The cyanobacterium Synechococcus is an ideal model for addressing this issue, since this group has colonized most light spectral niches in marine environments. Here, we used an approach based on marker read recruitment from metagenomes to analyze the seasonal succession of Synechococcus pigment types (PTs) at two time-series stations off French coasts exhibiting contrasting oceanic regimes. Marked seasonality was observed at both sites. The shallow, permanently mixed English Channel site SOMLIT-Astan was characterized by an alternation between green-light specialists (PT 3a) peaking in spring, and chromatic acclimaters type A (PT 3dA) accounting for most of the Synechococcus community in winter. In contrast, the pigment diversity was much higher at the deep Mediterranean station BOUSSOLE. In the upper layer, the two main PTs were the blue light specialists (PT 3c), which dominated the community in summer and fall, and PT 3dA cells, which were more abundant in spring. The third most abundant PT was chromatic acclimaters type B (PT 3dB), which accounted for up to 15% of the surface community in late fall. Strikingly, PT 3dA was dominant at depth during most of the year. Multivariate analyses between PT abundances, clade abundances and environmental factors, notably water color indexes, suggested new associations between PTs to specific clades and ecological niches. This study provides novel insights for refining distribution models of Synechococcus PTs and phytoplankton groups in general.

microbiology↗

bioRxiv2026

Labyrinthula merlionensis sp. nov.: a novel labyrinthulid infecting marine diatoms

Labyrinthulomycetes are a class of fungus-like heterotrophic protists from the Stramenopiles lineage, recognized for their ecological role as decomposers and contributors to nutrient cycling. They colonize various substrates, from seaweed to terrestrial environments, utilizing ectoplasmic networks for nutrient absorption. This study characterized a novel Labyrinthula strain associated with the marine diatom Biddulphia. Phylogenetic analysis of the full-length 18S rRNA gene positioned this strain as a new species, Labyrinthula merlionensis sp. nov. Scanning electron and light microscopy observations revealed bi-flagellated zoospores and spindle-shaped vegetative cells with ectoplasmic networks. Time-series observations of the interactions between L. merlionensis and Biddulphia were categorised into different phases: establishment, infection, and aggregation. Scanning electron and confocal microscopy observations during the infection phase established the use of ectoplasmic nets to target the marginal ridge regions between diatoms, and the detection of labyrinthulid cells within diatom frustules. These findings enhance the understanding of the diversity, morphology, and ecological roles of Labyrinthulomycetes, particularly their intra- and extra-cellular interactions with diatom hosts.

ecology↗

bioRxiv2025

OligoN-design: A simple and versatile tool to design specific probes and primers from large heterogeneous datasets

High-throughput environmental DNA sequencing has ushered ecological and evolutionary studies into the big data era. With thousands to millions of DNA sequences, designing taxon-specific oligonucleotides is a current bottleneck of molecular studies that rely on primers for Polymerase Chain Reactions (PCRs) or probes for Fluorescence in situ Hybridization (FISH). No software currently exists to design specific oligonucleotides starting from a custom set of sequences. Existing tools rely on specific databases, alignments or phylogenetic trees, or cannot accommodate increasingly large molecular environmental datasets. Here we present oligoN-design, a versatile tool to design oligonucleotides specific to a set of target sequences while minimizing predicted binding to non-target sequences. OligoN-design is simple, reproducible, and adaptable to high-throughput sequencing data analyses. It requires only two fasta files as input, one containing target taxa and the other containing non-target taxa. Using standard bioinformatic formats, it integrates easily with other tools such as BLAST, VSEARCH or MAFFT. OligoN-design allows a range of strategies that we present in detail, from an unsupervised end-to-end usage all the way to a detailed and thorough expert usage. Starting with large, comprehensive ribosomal databases that are widely used by the community (i.e., PR2, SILVA) and the unsupervised function, we were able to replicate known taxa-specific oligonucleotides in under 30 minutes and up to 6 Gb of RAM on a personal laptop. OligoN-design v1, available at github.com/MiguelMSandin/oligoN-design under GNU General Public License version 3.0, is easily installed via bioconda bioconda.github.io/recipes/oligon-design/README.html.

bioinformatics↗

bioRxiv2025

Two Spore Types in a Marine Parasite of Dinoflagellates

Marine alveolates (MALVs) are diverse, primarily parasitic micro-eukaryotes that significantly impact marine ecosystems. The life cycles of most MALVs remain elusive and the role of sexual reproduction in these organisms is a key question that may determine their ecological success. In this study we focus on a widespread dinoflagellate parasite of bloom-forming dinoflagellates, Amoebophrya. After infection, we identified two distinct spores, differing in size, ultrastructure, swimming behavior, lifespan, gene expression, and metabolite composition. The smaller spores serve as infectious propagules, equipped with an apical complex for host invasion. They exhibit a distinct, shorter, and straighter swimming pattern, likely optimized for an extended lifespan while enhancing dispersion and chance for host encounters. Transcriptomic analysis reveals that these smaller spores are primed for efficient protein synthesis upon initiating a new infection. Conversely, the larger spores cannot infect new hosts and are characterized by the expression of meiotic genes, underscoring their sexual nature. They have a shorter lifespan, exhibit more tortuous movement, along display condensed chromosomes, signaling readiness for mating. Interestingly, infected hosts already express meiotic genes, and a single infected host only produces progeny of the same spore type, suggesting that cell fate is determined prior to spore release. Our study provides one of the first formal demonstrations of a sexually specialized cell in MALVs. Isolating compatible strains for cross-breeding and understanding how environmental conditions favor each reproductive route are the next key questions for elucidating the ecological success of MALVs in marine waters. Significance StatementMarine alveolates (MALVs) are ecologically significant parasites that impact carbon cycling, causing major disease outbreaks affecting fisheries and aquaculture, and influencing the dynamics of harmful algal blooms. Despite their diversity and wide host range, much of our knowledge comes from environmental DNA, leaving important aspects of their biology, such as their life cycles, largely unknown. This study provides the first evidence of sexual reproduction in MALVs, linking spore polymorphism to infective or sexual routes. This discovery is crucial as sexual reproduction increases genetic diversity and adaptability, aiding MALVs resilience in changing environments. Understanding MALVs reproductive strategies deepens our insight into their ecological roles and their broader impact on marine ecosystems.

microbiology↗

bioRxiv2022

Viral infection impacts the 3D subcellular structure of the abundant marine diatom Guinardia delicatula

Viruses are key players in marine ecosystems where they infect abundant marine microbes. RNA viruses are emerging as key members of the marine virosphere. They have recently been identified as a potential source of mortality in diatoms, a group of microalgae that accounts for roughly 40% of the primary production in the ocean. Despite their likely importance, their impacts on host populations and ecosystems remain difficult to assess. In this study, we introduce an innovative tool approach that combines automated 3D confocal microscopy with quantitative image analysis and physiological measurements to expand our understanding of viral infection. We followed different stages of infection of the bloom-forming diatom Guinardia delicatula by the RNA virus GdelRNAV-04 until the complete lysis of the host. From 20h after infection, we observed quantifiable changes in subcellular host morphology and biomass. Our microscopy monitoring also showed that viral infection of G. delicatula induced the formation of auxospores as a probable defense strategy against viruses. Our method enables the detection of discriminative morphological features on the subcellular scale and at high throughput for comparing populations, making it a promising approach for the detection quantification of viral infections in the field in the future.

microbiology↗