Biology subjects

Obiol, A.

Publications and source records attributed to Obiol, A..

5 recordsLinked to original sources

bioRxiv2026

Fine-scale niche partitioning of prokaryotic communities across the deep chlorophyll maximum coenocline

The Deep Chlorophyll Maximum (DCM) is likely the most important feature organizing the marine epipelagic environment. Within this layer, opposing gradients of light and nutrients create a stratified habitat that supports high phytoplankton biomass and a substantial fraction of oceanic primary production. Despite its ecological importance, most studies treat the DCM as a single depth, overlooking its fine-scale heterogeneity. Here we investigated prokaryotic community organization across the DCM in the northwestern Mediterranean Sea through high-resolution sampling of four profiles collected over two days. Free-living (0.2-3 {micro}m) and particle-associated (3-20 {micro}m) communities were characterized using 16S rRNA gene amplicon sequencing. Prokaryotic communities changed progressively along the vertical gradient, revealing the DCM as a microbial coenocline with continuous community turnover. Fuzzy clustering identified distinct assemblages associated with environmental transitions from warm surface waters to the chlorophyll maximum, the nitrite peak below the DCM, and deeper nitrate-rich layers. In both the free-living and particle-associated fractions, most ASVs remained consistently associated with the same depth-defined clusters across all samplings, indicating stable niche partitioning over short timescales. However, these temporally stable ASVs accounted for a substantially smaller fraction of community sequences in particle-associated communities, suggesting higher dynamism, likely driven by particle-mediated transport. Nevertheless, phylogenetic analyses revealed that closely related ASVs tended to occupy similar depth niches, indicating that habitat preferences are phylogenetically conserved in both size fractions. Our results demonstrate prokaryotic niche partitioning over scales of only a few meters within the DCM, highlighting the importance of fine-scale sampling for understanding microbial community structure and responses to ocean change.

ecology↗

bioRxiv2026

Single-cell sequencing reveals genome streamlining and functional diversity in ecologically dominant marine protists

A large fraction of marine protists, particularly the smallest ones, belong to uncultured lineages that lack genomic data, limiting insights into their ecological roles and evolutionary strategies. Here, we generated 325 single-cell amplified genomes (SAGs) from 2-5 {micro}m planktonic protists, which resulted in 147 genomes from dominant marine species at varying levels of completeness (40 of them >50%). These genomes matched the in situ community, with Prymnesiophyceae, Mamiellophyceae and Chrysophyceae dominating pigmented cells and MAST, Choanoflagellata and Picozoa prevailing among heterotrophic colourless cells. This resource allowed us to describe the genomic architecture of marine protist species, and revealed a pronounced genome streamlining in ecologically successful lineages. Comparative analyses highlighted unique functions enriched in photosynthetic and heterotrophic taxa (including motility, signal transduction, digestion and secondary metabolism), and revealed a broad distribution of gene families with adaptive traits such as polyketide synthases and rhodopsins. This large-scale single-cell genomics dataset provides a mechanistic foundation for investigating functional diversity, ecological strategies and genome evolution in the ocean.

ecology↗

bioRxiv2025

The complex interplay between microalgae and the microbiome in production raceways

Algae-associated microbiomes are underexplored, limiting our understanding of their influence on the productivity of large-scale microalgae reactors. To address this, we monitored microbial dynamics in two microalgae biomass production raceways over two 8-month intervals inoculated with Desmodesmus armatus. One reactor was fed with wastewater, while the other received clean water and fertilizers. Metabarcoding of the 18S and 16S rRNA genes revealed a high microbial diversity across two time series, showing thousands of eukaryotic and prokaryotic species growing alongside the microalgae. Chlorophyta and Fungi were the dominant eukaryotic groups, while Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Bacteroidia dominated the prokaryotic communities. We found contrasting ASVs (Amplicon Sequence Variant) patterns between healthy (D. armatus abundance >70%) and unhealthy (D. armatus abundance <20%) microbiomes, across reactors and time series. Network analysis identified up to 10 potential ecological interactions among D. armatus and its microbiome, predominantly positive. Our results suggest a link between microbiome composition and D. armatus abundance. Specifically, ASVs associated with a healthy microbiome were positively correlated with D. armatus, while ASVs characteristic of an unhealthy microbiome were negatively correlated. Potentially pathogenic bacteria included Mycobacterium and Flavobacterium, whereas potentially beneficial taxa included Geminocystis, Thiocapsa, Ahniella and Bosea. Several fungal ASVs showed context-specific associations, whereas specific P. tribonemae, A. parallelum, A. desmodesmi, Aphelidiomycota sp., Rozellomycota sp. and, Rhizophidium sp. ASVs were identified as potentially harmful. This study reveals the striking diversity and complexity of microalgae-associated microbiomes within raceways, providing valuable insights for optimizing industrial production processes, particularly for wastewater treatment and sustainable green biomass generation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/633910v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@dfa478org.highwire.dtl.DTLVardef@a6ce03org.highwire.dtl.DTLVardef@11f41f6org.highwire.dtl.DTLVardef@12397b2_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO General overview of the metabarcoding methodology. Step 1: Sample collection, 2: DNA extraction of the samples, 3: PCR and DNA sequencing of the 18S and 16S rRNA genes, 4: Processing and quality filtering of the DNA sequencing data, 5: Taxonomic, community, and network analyses and, 6: Interpretation and discussion of the results. C_FIG

microbiology↗

bioRxiv2021

Global patterns and rates of habitat transitions across the eukaryotic tree of life

The successful colonisation of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and terrestrial (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine-terrestrial transitions, but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich environmental phylogenies inferred from a combination of long-read and short-read metabarcoding data spanning the ribosomal DNA operon. Our results show that overall marine and terrestrial microbial communities are phylogenetically distinct, but transitions have occurred in both directions in almost all major eukaryotic lineages, with at least 350 transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has most likely been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-saline habitats, and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that crossing the salt barrier has played an important role in eukaryotic evolution by providing new ecological niches to fill.

evolutionary biology↗

bioRxiv2020

Evolutionary diversification of tiny ocean predators

Unicellular eukaryotic predators have a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionary-diverse organisms have been combined into a single functional group (Heterotrophic flagellates), overlooking their organismal differences. Here we investigate four evolutionary related species belonging to one cosmopolitan family of uncultured marine picoeukaryotic predators: MAST-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A & C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using Single-Cell Genomics. Analyses of 69 single-cells recovered 66-83% of the MAST-4A/B/C/E genomes, which displayed substantial inter-species divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition co-excluded each other (A & C) in the surface global ocean, while species with a different set of GHs appeared to be able to co-exist (species B & C) suggesting further niche diversification associated to prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. Altogether, we show that minute ocean predators from the same family may have different biogeography and genomic content, which need to be accounted to better comprehend marine food webs.

ecology↗