Biology subjects

Montiel, L.

Publications and source records attributed to Montiel, L..

6 recordsLinked to original sources

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↗

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

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↗