Biology subjects

Balague, V.

Publications and source records attributed to Balague, V..

12 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

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

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↗

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

Diversity and community structure of aerobic anoxygenic phototrophic bacteria are shaped by the deep chlorophyll maximum

The surface ocean exhibits strong vertical gradients in light, nutrients, and temperature, shaping the phytoplankton distribution which often defines a deep chlorophyll maximum (DCM). Aerobic anoxygenic phototrophic (AAP) bacteria inhabit the euphotic zone, with their abundances following the chlorophyll a variability. While AAP bacterial communities are known to differ across regions with contrasting environmental conditions, their vertical distribution remains poorly understood. We hypothesized that the diversity and community structure of AAP bacteria would vary across the vertical gradient, in relation to changes in environmental variables and following the DCM profile. To test this hypothesis, we studied the composition of AAP communities at different depths along the DCM structure in the South and Central Atlantic Ocean, by means of amplicon sequencing of the pufM gene. The results show significant differences in richness, community structure, and taxonomic composition of samples from different layers of the DCM, highlighting the dependance of AAP bacteria on its structure. Remarkably, the use of primers with broad phylogenetic coverage enabled the recovery of several phylogroups previously detected only through metagenomics. We show that they represent a significant fraction of marine AAP communities, provide clues on their ecological preferences, and confirm their association with the family Candidatus Luxescamonaceae, with genomic potential for carbon fixation.

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↗

bioRxiv2022

Bacterioplankton taxa compete for iron along the early spring-summer transition in the Arctic Ocean

Microbial assemblages under sea ice of Dease Strait, Canadian Arctic, were sequenced for metagenomes and metatranscriptomes of the small size fraction (0.2 to 3 {micro}m). The community from early March was typical for this season, with Alpha- and Gammaproteobacteria as the dominant taxa, followed by Thaumarchaeota and Bacteroidetes. Towards summer, Bacteroidetes and particularly the genus Polaribacter, became increasingly dominant, followed by the Gammaproteobacteria. Analysis of genes responsible for microbial acquisition of iron showed an abundance of ABC transporters for divalent cations and ferrous iron. The most abundant transporters, however, were the outer membrane TonB dependent transporters of iron-siderophore complexes. The abundance of iron acquisition genes suggested this element was essential for the microbial assemblage. Interestingly, Gammaproteobacteria were responsible for most of the siderophore synthesis genes. On the contrary, Bacteroidetes did not synthesize siderophores but accounted for most of the transporters, suggesting a role as cheaters in the competition for siderophores as public goods. Likely, this cheating ability of the Bacteroidetes contributed to their dominance in summer.

ecology↗

bioRxiv2021

Disentangling temporal associations in marine microbial networks

BackgroundMicrobial interactions are fundamental for Earths ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. Omics-based censuses are helpful in predicting microbial interactions through the statistical inference of single (static) association networks. Yet, microbial interactions are dynamic and we have limited knowledge of how they change over time. Here we investigate the dynamics of microbial associations in a 10-year marine time series in the Mediterranean Sea using an approach inferring a time-resolved (temporal) network from a single static network. ResultsA single static network including microbial eukaryotes and bacteria was built using metabarcoding data derived from 120 monthly samples. For the decade, we aimed to identify persistent, seasonal, and temporary microbial associations by determining a temporal network that captures the interactome of each individual sample. We found that the temporal network appears to follow an annual cycle, collapsing and reassembling when transiting between colder and warmer waters. We observed higher association repeatability in colder than in warmer months. Only 16 associations could be validated using observations reported in literature, underlining our knowledge gap in marine microbial ecological interactions. ConclusionsOur results indicate that marine microbial associations follow recurrent temporal dynamics in temperate zones, which need to be accounted for to better understand the functioning of the ocean microbiome. The constructed marine temporal network may serve as a resource for testing season-specific microbial interaction hypotheses. The applied approach can be transferred to microbiome studies in other ecosystems.

microbiology↗

bioRxiv2021

Long-term patterns of an interconnected core marine microbiota

BackgroundOcean microbes constitute [~]70% of the marine biomass, are responsible for [~]50% of the Earths primary production, and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade. ResultsCore microbes were defined as those present in >30% of the monthly samples over 10 years, with the strongest associations. The core microbiota included 259 Operational Taxonomic Units (OTUs) including 182 bacteria, 77 protists, and 1,411 strong and mostly positive ([~]95%) associations. Core bacteria tended to be associated with other bacteria, while core protists tended to be associated with bacteria. The richness and abundance of core OTUs varied annually, decreasing in stratified warmers waters and increasing in colder mixed waters. Most core OTUs had a preference for one season, mostly winter, which featured subnetworks with the highest connectivity. Groups of highly associated taxa tended to include protists and bacteria with predominance in the same season, particularly winter. A group of 13 highly-connected hub-OTUs, with potentially important ecological roles dominated in winter and spring. Similarly, 18 connector OTUs with a low degree but high centrality were mostly associated with summer or autumn and may represent transitions between seasonal communities. ConclusionsWe found a relatively small and dynamic interconnected core microbiota in a model temperate marine-coastal site, with potential interactions being more deterministic in winter than in other seasons. These core microbes would be essential for the functioning of this ecosystem over the year. Other non-core taxa may also carry out important functions but would be redundant and non-essential. Our work contributes to the understanding of the dynamics and potential interactions of core microbes possibly sustaining ocean ecosystem function.

ecology↗

bioRxiv2019

Marked changes in diversity and relative activity of picoeukaryotes with depth in the global ocean

Microbial eukaryotes are key components of the ocean plankton. Yet, our understanding of their community composition and activity in different water layers of the ocean is limited, particularly for picoeukaryotes (0.2-3{micro}m cell size). Here we examined the picoeukaryotic communities inhabiting different vertical zones of the tropical and subtropical global ocean: surface, deep chlorophyll maximum, mesopelagic (including the deep scattering layer and minimum oxygen zone) and bathypelagic. Communities were analysed by high-throughput sequencing of the 18S rRNA gene, as represented by DNA (community structure) and RNA (metabolic expression), followed by delineation of Operational Taxonomic Units (OTUs). We found a clear stratification of the picoeukaryotic communities along the water column, with two differentiated assemblages corresponding to the sunlit and dark ocean. Specific taxonomic groups either increased or decreased their abundances with depth. We used the rRNA:rDNA ratio of each individual OTU as a proxy of its metabolic activity. The highest relative activity was found in the mesopelagic layer for most taxonomic groups, and the lowest in the bathypelagic. Overall, our results characterize the change in community structure and activity of picoeukaryotes in the global-ocean water column, suggesting that the mesopeagic layer is a hot-spot of picoeukaryotic activity.

microbiology↗

bioRxiv2017

Quantifying long-term predictability in microbial plankton dynamics

Determining predictability in community turnover is a key ecological question. In the microbial world, seasonality has been reported for communities inhabiting temperate zones, but not much is known on seasonality for individual species. Specifically, we have a vague understanding on the amount of species displaying predictability during temporal community turnover as well as on their dynamics. Here we developed a Recurrence Index to quantify predictability in microbial species. Applying our index to 18S rDNA metabarcoding data from one of the longest temporal observatories of marine plankton we determined that 13% of the picoeukaryotic and 19% of the nanoeukaryotic species, accounting for about 40% of the community abundance in both fractions, feature predictable dynamics when sampled monthly during 10 years. Thus, most of the species analysed had unpredictable temporal abundance patterns. Altogether, we show that species with both predictable and unpredictable temporal dynamics can occur within the same seasonal microbial community.

ecology↗