Biology subjects

Logares, R.

Publications and source records attributed to Logares, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Seasonal population structure and adaptive signatures across long-term marine microbial time series

Long-term microbial population dynamics can reveal how ocean microbiomes respond to environmental variation, but resolving within-species change requires suitable genomic references. We integrated 30 PacBio HiFi long-read metagenome-assembled genomes (MAGs) from the northwestern Mediterranean Sea with monthly Illumina metagenomes from neighboring time series spanning 12 and 7 years. Population differentiation varied widely among genomes and often differed in magnitude between sites, while a subset showed increasing differentiation with temporal distance. Genetic diversity and population structure were frequently seasonal, with populations associated with warm or cold waters and others spanning both thermal regimes. Candidate adaptive genes accounted for 1.6-3.0% of coding sequences, and many were detected in both time series. Their pN/pS trajectories included regular seasonal fluctuations consistent with changing strain or ecotype contributions, alongside irregular temporal patterns. These results show that combining long-read MAG references with dense short-read time series can resolve seasonal population structure, site-specific differentiation, and candidate adaptive variation within marine microbial species, providing a framework for tracking contemporary population-genomic change in the ocean.

ecology↗

bioRxiv2026

Temperature-driven dynamics of Chlorella sorokiniana and its microbiome

Temperature is a critical factor in microalgal production, yet its impact on microalgae and their microbiome remains poorly understood. Here, we investigated the responses of Chlorella sorokiniana and its microbial community to temperature increases in four wastewater-based cultures over two months. Two Test cultures were subjected to a thermal gradient from 20 {degrees}C to 34 {degrees}C, and two were Controls at 20 {degrees}C. Eukaryotic and bacterial communities were analyzed using 18S and 16S rRNA gene sequencing, and the microalga genome was reconstructed using PacBio HiFi sequencing and functionally annotated. Control cultures remained stable, whereas Test cultures showed a decline in C. sorokiniana relative abundance and biomass from approximately 24 {degrees}C. In contrast, photosynthetic efficiency remained stable until temperatures exceeded 33 {degrees}C. Above 22-24 {degrees}C, the bacterial community, dominated by Fontibacter, Flavobacterium, and Luteolibacter, was replaced by taxa whose relative abundance increased with rising temperature and microalgal decline, pointing to bacteria better adapted to the stress conditions. Candidate predator-prey dynamics with the protist Cercozoa also intensified as temperature increased. Microalgal genome annotation identified 28 candidate genes corresponding to seven of eight literature-informed high-temperature/heat-stress targets, primarily associated with protein homeostasis, Reactive oxygen species protection, membrane lipid remodeling, and protein degradation. Collectively, these genes likely support the microalga's response and adaptation to environmental stress. Overall, culture destabilization resulted from interacting thermal, microbial, and grazing-related processes rather than temperature alone. Early microbiome changes may therefore provide useful warning signals of culture instability and help improve the management of large-scale microalgal production systems.

microbiology↗

bioRxiv2026

Decadal signatures of seasonal and ENSO-driven selection in microbial populations in distant oceans

Despite the crucial role of the ocean microbiome for global ecosystem processes, its response to global change remains poorly understood. Global change will exert selection on microbial species through changes in the genetic composition of their populations, favouring strains that are better adapted to new conditions. Analyzing long-term genomic variation in microbial populations inhabiting climatically comparable but oceanographically distinct regions may provide insights into their responses to future environmental conditions. We analyzed coastal marine microbiomes from two distant long-term observatories with Mediterranean-type climates but contrasting oceanographic regimes: the Blanes Bay Microbial Observatory (BBMO; Northwestern Mediterranean Sea) and the Microbes in the Coastal Region of Orange County (MiCRO; California coast, Pacific Ocean). Sampling conducted at least monthly during 15 and 10 years, respectively, yielded 1,535 Metagenome-Assembled Genomes (MAGs) in BBMO and 1,068 MAGs plus 187 Single-Amplified Genomes (SAGs) in MiCRO. Among these, we found 250 genomes with intraspecific (>95% genome similarity) representatives occurring at both sites. In contrast, at the strain-level threshold ([≥]99% genome similarity), only 13 BBMO genomes matched 15 closely related representatives in MiCRO. As genome similarity increased, we observed a shift from cosmopolitan to more coastal distributions and a slight increase in genome size, pointing to niche adaptation. Across both time series, we observed widespread seasonal population structure, with most genomes (~70%) showing significant seasonal structuring of variant composition. Moreover, in MiCRO, ~76% of the tested genomes also showed El Nino Southern Oscillation (ENSO)-associated structure in variant composition beyond seasonal effects. Focusing on a Prochlorococcus genome with intraspecific representatives at both locations (>96% genome similarity) we further found recurrent seasonal mutations and non-synonymous to synonymous mutation ratios (pN/pS) from multiple genes, together with signatures of positive selection (higher pN/pS) coinciding with El Nino events in MiCRO. This suggests an imprint of ENSO in marine microbial populations. Thus, beyond seasonality, long-term climatic oscillations may shape microbial populations. This has implications for understanding how the ocean microbiome will respond to long-term environmental change and prolonged disturbances through population-level genomic variation.

microbiology↗

bioRxiv2026

A global genomic survey of prokaryotic carbon fixation reveals an oxygen-tolerant rTCA cycle in the surface ocean

Autotrophic carbon fixation, the conversion of inorganic carbon into biomass, underpins life on Earth. Prokaryotes can carry out this process via at least seven biochemically distinct pathways, yet the phylogenetic and environmental distribution of most remains poorly resolved. Screening approximately 40 billion genes from reference genomes, metagenome-assembled genomes (MAGs) and unbinned metagenomic contigs, we provide a global assessment of the phylogeny and ecophysiology of prokaryotic autotrophs. Most pathway marker genes occurred in unbinned contigs and low-quality MAGs, representing phylogenetically distinct lineages absent from isolate genomes and quality filtered MAGs. Established autotrophs accounted for the large majority of pathway detections in quality filtered MAGs, largely recapitulating known biology from cultivated model organisms. Against this backdrop, the reductive TriCarboxylic Acid (rTCA) cycle, long considered restricted to anoxic environments, was detected in three phylogenetically distinct Campylobacterota lineages from oxygenated surface seawater, suggesting a previously unrecognized and unexpected niche for this pathway. We show that all three MAGs share an enzyme variant, previously described in other oxygen-tolerant lineages, that likely underlies their presence in the oxygenated surface ocean. Read mapping across global ocean metagenomes indicates that the organisms carrying it could be far more widespread than the scarcity of recovered MAGs alone would suggest. Together, these findings illustrate that the current view of global autotrophic carbon fixation is largely shaped by what genome-resolved methods can readily recover, while the true phylogenetic and ecological distribution of autotrophic carbon fixation appears to be much broader.

microbiology↗

bioRxiv2026

The natural history of bacterial bloomers in a decade-long time series

Bacterial bloomers--populations that experience rapid and significant increases in abundance in response to environmental triggers--briefly dominate marine microbial communities, potentially impacting the ecosystem by channeling large amounts of nutrients and affecting carbon fluxes. Due to their ephemeral nature, bacterial bloomers are challenging to capture, and it remains unknown whether they are restricted to specific taxonomic groups or whether they exhibit recurrent patterns. We analyzed a decade-long time series from the Blanes Bay Microbial Observatory (BBMO, NW Mediterranean Sea) to investigate bacterial bloomers in two size fractions (free-living (0.2-3 {micro}m) and particle-attached (3-20 {micro}m) communities. We identified 57 Amplicon Sequence Variants (ASVs), less than 1% of the total bacterial richness, exhibiting recurrent or chaotic blooming-like behavior. Bloomers spanned diverse phyla, though some taxonomic coherence appeared within families containing multiple blooming taxa. Monthly sampling detected bloom events on average 4.6 {+/-} 1.9 times per year across both size fractions. Once seasonality was accounted for, blooms showed weak associations with biological and physicochemical variables, likely a consequence of monthly sampling resolution. Nonetheless, a marked shift in the blooming community within the particle-attached size fraction coincided with ecosystem disturbances from the nearby harbour restoration, suggesting that bloomers may act as disturbance sentinels. Metagenomic data showed that blooms led to marked shifts in the community functional potential. Overall, our findings underscore the importance of investigating bloom dynamics to understand microbial contributions to biogeochemical cycles and stress the need for higher-frequency sampling to accurately capture these transient but ecologically relevant events.

microbiology↗

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

Global geography outweighs long-term dynamics in shaping marine microbial population structure

Marine microbial populations play essential roles in ocean ecosystems, yet the processes shaping their genomic structure across space and time remain poorly understood. Here, we examined the population-scale patterns of 1,505 prokaryotic metagenome-assembled genomes (MAGs) retrieved from the Northwestern Mediterranean Sea in two long-term coastal time series, along 15 and 7 years in these sites, as well as in the global ocean. We found that populations were generally more genomically differentiated across large spatial scales than across long temporal scales. Among a subset of 389 MAGs well represented in all datasets, 68.4% showed weak population divergence over time but strong global-scale differentiation. This was evident in the abundant and widespread cyanobacteria Prochlorococcus and Synechococcus. In contrast, only 6.4% of the MAGs exhibited weak divergence over time and space, with SAR11 MAGs being a clear example, likely reflecting their high dispersal and recombination rates. Other groups, such as SAR86 and Flavobacteriales, showed strong divergence at temporal and spatial scales, suggesting seasonal and/or regional adaptation. Positive selection was more readily detectable in the long-term coastal observatories than in the global ocean, despite the more significant population divergence observed across broad geographic scales. Temperature consistently showed a significant association with the population structure of many MAGs. Overall, our results highlight the dominant influence of large geographic scales in shaping microbial population structure alongside taxon-specific responses to temporal variation, particularly seasonality. Altogether, our work advances the understanding of microbial population structure across broad spatial and temporal scales, a critical step toward predicting microbial dynamics in a changing ocean.

ecology↗

bioRxiv2025

Microbiome composition and function vary with depth in the Mediterranean gorgonian Eunicella singularis

BackgroundThe Gorgonian coral, Eunicella singularis, is one of the main components of Mediterranean marine animal forests, whose canopies play a key role in Mediterranean sublittoral ecosystems due to their capacity to provide shelter, food, and nursery ground to several species. Like other gorgonian species, E. singularis faces environmental threats with potential repercussions on the associated biodiversity. This photophilic octocoral, spanning the Western Mediterranean, Adriatic, and Aegean Seas at depths of 10-70m, engages in symbiosis with Symbiodiniaceae dinoflagellates, thereby influencing their resilience in nutrient-poor habitats. However, mesophotic populations ([~]60m depth) are characterized by very low Symbiodiniaceae density, prompting questions regarding metabolic adaptations. The associations of corals with specific bacteria that differ from those in the surrounding seawater suggest a role in host health and physiology. In particular, in mesophotic colonies, bacteria may perform activities that Symbiodinium typically carries out in shallow colonies. Here, we applied metagenomics techniques to analyze the changes in the microbiome of Eunicella singularis with depth, analyzing DNA samples from shallow (12m) and mesophotic (57m) colonies in the Northwestern Mediterranean Sea. ResultsHigh-coverage metagenomes (ca. 80 Gb per sample) were generated from E. singularis colony samples. We observed significant changes in the relative abundance of prokaryotic and microbial eukaryotic symbionts with depth. Mesophotic samples exhibited higher levels of symbiotic prokaryotes, dominated by Endozoicomonas and Bermanella, whereas shallow samples were enriched with the symbiotic dinoflagellate Symbiodiniaceae. The metabolic potential of the microbiome also varied with depth. The shallow microbiome showed a prevalence of photosynthesis and carbon fixation pathways. In turn, the mesophotic microbiome exhibited a higher abundance of metabolic functions related to vitamin biosynthesis, energy metabolism, especially carbon metabolism, as well as pathways associated with carbohydrates, amino acids, and cofactors. ConclusionsOur results indicate that the structure and metabolic function of the microbiome of Eunicella singularis change with depth. In the absence of symbiotic dinoflagellates, associated bacteria seem to use different sources of carbon, in addition to cycling nutrients and vitamins, which could influence coral health. These findings gain significance in the context of global change, as shifts in oceanic conditions may affect the coral microbiome.

ecology↗

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

Functional redundancy enables emergent metabolic dynamics in marine microbiomes

Understanding how marine microbiomes will respond to ongoing global change is crucial. Functional redundancy, the capacity of different microbes to perform the same function, is considered a key mechanism underpinning the stability and resilience of the ocean microbiome. Although the extent of functional redundancy remains debated, investigating its manifestation in environmentally similar and interconnected microbial communities may provide critical insights into its role in shaping microbial community dynamics. We hypothesized that examining the long-term synchrony and rhythmicity of temperate microbial communities in such locations could provide insight into the role of functional redundancy. High functional redundancy at the community level would manifest as rhythmic and synchronous metabolic functions across sites, even in the absence of synchrony or rhythmicity at finer organizational levels, such as individual genes or taxa, thereby contributing to community resilience. Conversely, low functional redundancy would imply that synchrony and rhythmicity extend to both the contributing genes and taxa, suggesting a greater vulnerability of the community to environmental variability. To test this framework, we analyzed the long-term synchrony and rhythmicity of two marine-coastal microbiomes in the Mediterranean Sea, separated by approximately 150 km and connected by a dominant southwest current. Monthly collected metagenomes from a seven-year period were examined at the levels of metabolic functions (e.g., KEGG pathways), predicted genes (open reading frames), and taxa. We found functions, genes, and taxa exhibiting high, low, or anti-synchrony, as well as displaying rhythmic or non-rhythmic patterns. Although rhythmic behavior was observed on average across all organizational levels, consistent with the seasonal dynamics expected in temperate Mediterranean waters, average synchrony across microbiomes remained low. Focusing specifically on 45 markers of key biogeochemical functions, we revealed that several functions exhibited high synchrony and rhythmicity, in sharp contrast to the low synchrony and rhythmicity among the most abundant genes and taxa contributing to those functions. This suggests that functional redundancy and complementary dynamics at lower organizational levels, with distinct taxa contributing to key metabolic functions at different times, lead to rhythmic and synchronous dynamics at higher levels through emergent self-organization. Together, our results highlight functional redundancy and emergent self-organized dynamics as key mechanisms supporting the stability and resilience of marine microbiomes under environmental change.

ecology↗

bioRxiv2025

Metagenomic-based network analysis reveals the importance of vitamin cross-feeding in marine microbial assemblages

Vitamins play a fundamental role in microbial metabolism and interactions, yet their scarcity in marine environments and the limited ability for de novo synthesis of some vitamins often leads to metabolic dependencies and cross-feeding among microbial taxa. Using a decade-long time-series metagenomics dataset from the Blanes Bay Microbial Observatory (BBMO), we investigated the role of vitamin biosynthesis in structuring the seasonal marine microbial interactions among prokaryotes and eukaryotes. Gene co-occurrence analysis revealed that vitamin-related metabolism had the highest number of associations among all metabolic pathways, underscoring the potential role of vitamins in microbial interactions. Metagenome-assembled genome (MAG) co-occurrence analysis further identified the prokaryotic biosynthesis of cobalamin (B12) and thiamine (B1) as key mediators of these associations. Rather than between complete vitamin synthesizers and auxotrophs, the main associations were found between partial synthesizers, suggesting that vitamer cross-feeding may represent an essential microbial interaction in sustaining vitamin biosynthesis throughout the year. While complete cobalamin synthesizers dominate in summer, partial synthesizers and lower-ligand activators are more prevalent in winter, driving cross-feeding interactions. In contrast, thiamine biosynthesis is more widespread, with complete synthesizers peaking in winter. The association strength, however, was maximum between prokaryotic vitamin producers and eukaryotes, highlighting the dependence of eukaryotes on bacterial vitamin production. These results provide novel insights into seasonal metabolic interdependencies, emphasizing the ecological significance of vitamin biosynthesis in marine ecosystems.

microbiology↗

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↗

bioRxiv2024

Global population structure of a unicellular marine predator

Unicellular predators, especially marine heterotrophic flagellates (HFs), are fundamental to marine food webs, facilitating the flow of nutrients from bacteria and the smallest primary producers to upper trophic levels. Comprehending their distributions and diversity is essential for understanding the functioning of marine ecosystems. The uncultured MArine STramenopiles clade 4 (MAST-4) constitutes a crucial HF member of the ocean microbiome with a predatory (bacterivorous) lifestyle. Temperature gradients have influenced the evolution and biogeography of MAST-4 species. Yet, similarly to most uncultured microbes, there is limited information on the population diversity and structure within MAST-4 species. This information is key for better comprehending the ecological roles and adaptations of different MAST-4 species to specific ocean niches. Here, we investigate the population diversity and structure on the global scale of the MAST-4 species A, B, C, and E by combining metagenomics and single-cell genomics data from the Tara Oceans expedition. We found substantial population divergence in the abundant MAST-4A and C species, while lower levels of divergence were observed in species B and E. Temperature and salinity were the main drivers structuring the populations within the four MAST-4 species. The analysis of positively selected gene clusters within each MAST-4 species revealed genomic areas likely the basis of population adaptation to different niches. Overall, our results contribute to a better comprehension of the population diversity and structure of four species belonging to an important group of unicellular predators, offering insights into their ecological roles and adaptations in the global ocean. The results also contribute to understanding microbial populations, a dimension of diversity that remains poorly known for most wild species and is pivotal in global change.

ecology↗

bioRxiv2024

A fungi hotspot deep down the ocean: explaining the presence of Gjaerumia minor in Equatorial Pacific bathypelagic waters

A plant parasite associated with the white haze disease in apples, the Basidiomycota Gjaerumia minor, has been found in most samples of the global bathypelagic ocean. An analysis of environmental 18S rDNA sequences on 12 vertical profiles of the Malaspina 2010 expedition shows that the relative abundance of this cultured species actually increases with depth while its distribution is remarkably different between the deep waters of the Pacific and Atlantic oceans, being present in higher concentrations in the former. This is evident from sequence analysis and a microscopic survey with a species-specific newly designed TSA-FISH probe. Several hints point to the hypothesis that G. minor is transported to the deep ocean attached to particles, and the absence of G. minor in bathypelagic Atlantic waters could then be explained by the absence of this organism in surface waters of the equatorial Atlantic. The good correlation of G. minor biomass with recalcitrant carbon and free-living prokaryotic biomass in South Pacific waters, together with the identification of the observed cells as yeast and not as a resting spore (teliospore), point to the possibility that once arrived at deep layer this species keeps on growing and thriving.

ecology↗

bioRxiv2023

Unifying microorganisms and macrograzers in rocky shore ecological networks

Over the past decades, our understanding of the vital role microbes play in ecosystem processes has greatly expanded. However, we still have limited knowledge about how microbial communities interact with larger organisms. Many existing representations of microbial interactions are based on co-occurrence patterns, which do not provide clear insights into trophic or non-trophic relationships. In this study, we untangled trophic and non-trophic interactions between macroscopic and microscopic organisms on a marine rocky shore. Five abundant mollusk grazers were selected, and their consumptive (grazing) and non-consumptive (grazer pedal mucus) interactions with bacteria in biofilms were measured using 16S rRNA amplicon sequencing. While no significant effects on a commonly used measure of biofilm grazing (Chlorophyll-a concentration) were observed, detailed image analysis revealed that all grazers had a detrimental impact on biofilm cover. Moreover, different grazers exhibited distinct effects on various bacterial groups. Some groups, such as Rhodobacteraceae, Saprospiraceae, Flavobacteriaceae, and Halieaceae, experienced positive effects from specific grazers, while others, like Rhizobiaceae, Rhodobacteraceae, and Flavobacteriaceae were negatively affected by certain grazers. This study presents the first attempt to construct an interaction network between macroorganisms and bacteria. It demonstrates that the strength of trophic and non-trophic interactions varies significantly depending on the mollusk grazer or bacterial group involved. Notably, certain bacterial groups exhibited a generalized response, while others showed specialized responses to specific macroorganisms in trophic or non-trophic interactions. Overall, this work highlights the potential for integrating microbes into ecological networks, providing valuable insights and methodologies for quantifying interactions across Domains. This research complements the previous ecological network, showing that mollusk grazers interact not only trophically but also non-trophically with epilithic biofilms. It identifies three drivers affecting microbial community assembly, crucial for understanding macro-microorganism dynamics in intertidal systems.

ecology↗

bioRxiv2023

Marine picoplankton metagenomes from eleven vertical profiles obtained by the Malaspina Expedition in the tropical and subtropical oceans

The Ocean microbiome has a crucial role on Earths biogeochemical cycles, but also represents a tremendous potential for biological applications as part of the bluebiotechnology. During the last decade, global cruises such as Tara Oceans or the Malaspina Expedition have expanded our knowledge on the diversity and genetic repertoire of marine microbes. Nevertheless, there is still a gap of knowledge on broad scale patterns between photic and bathypelagic dark ocean microbes derived from the lack of detailed vertical profiles covering contrasting oceans depth regions. Here we present a dataset of 76 microbial metagenomes of the picoplankton size fraction (0.2-3.0 m) collected in 11 stations along the Malaspina Expedition circumnavigation that cover vertical profiles sampling at 7 depths, from the surface to the 4000 m deep (or the sea floor in shallower waters). This Malaspina Microbial Vertical Profiles metagenomes (MProfile) dataset produced 1.66 Tbp of raw DNA sequences that assembled into a total 25.3 Gbp. After gene prediction and annotation, we built a 46.3 million non-redundant gene compendium with their corresponding annotations (M-GeneDB-VP), clustered at 95% sequence similarity. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic tropical and subtropical ocean at a global scale, while increasing our general knowledge on the Ocean microbiome.

microbiology↗

bioRxiv2023

Global biogeography of the smallest plankton across ocean depths

Tiny ocean plankton (picoplankton) are fundamental for the functioning of the biosphere, but the ecological mechanisms shaping their biogeography are partially understood. Comprehending whether these microorganisms are structured by niche vs. neutral processes is highly relevant in the context of global change. The ecological drivers structuring picoplankton communities differ between prokaryotes and minute eukaryotes (picoeukaryotes) in the global surface ocean: while prokaryotic communities are shaped by a balanced combination of dispersal, selection, and drift, picoeukaryotic communities are mainly shaped by dispersal limitation. Yet, whether or not the relative importance of these processes in structuring picoplankton varies as we dive into the deep ocean was unknown. Here we investigate the mechanisms structuring picoplanktonic communities inhabiting different ocean depths. We analyzed 451 samples from the tropical and subtropical global ocean and the Mediterranean Sea covering the epi- (0-200m), meso- (200- 1,000m), and bathypelagic (1,000-4,000m) depth zones. We found that selection decreased with depth possibly due to lower habitat heterogeneity. In turn, dispersal limitation increased with depth, possibly due to dispersal barriers such as water masses and bottom topography. Picoplankton {beta}-diversity positively correlated with environmental heterogeneity and water mass variability in both the open-ocean and the Mediterranean Sea. However, this relationship tended to be weaker for picoeukaryotes than for prokaryotes. Community patterns were generally more pronounced in the Mediterranean Sea, probably because of its substantial cross-basin environmental heterogeneity and deep-water isolation. Altogether, we found that different combinations of ecological mechanisms shape the biogeography of the smallest members of the ocean microbiome across ocean depths.

ecology↗

bioRxiv2021

Linking extreme seasonality and gene expression in arctic marine protists

At high latitudes, strong seasonal differences in light availability affect marine organisms and restrict the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45-10 m protist assemblages sampled over 13 months in a time series station in an arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in arctic samples from Tara Oceans, suggesting that arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.

microbiology↗