Biology subjects

Ferrera, I.

Publications and source records attributed to Ferrera, I..

10 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

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↗

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

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↗

bioRxiv2023

Vertical distribution and light energy capture by AAP bacteria along contrasted areas of productivity in the Atlantic Ocean

Aerobic anoxygenic phototrophic (AAP) bacteria are a common part of microbial communities in the sunlit ocean. They contain bacteriochlorophyll a-based photosystems that harvest solar energy for their metabolism. Across different oceanic areas and regimes, AAP bacteria seem to be more abundant in eutrophic areas, associated to high chlorophyll concentrations. While most of these studies are based on surface samples, little information is available on their vertical distribution in euphotic zones of the major ocean basins. We hypothesize that AAPs will follow a similar structure to the chlorophyll depth profile across areas with different degrees of stratification. To test this hypothesis, we enumerated AAP cells and determined bacteriochlorophyll a concentrations along the photic zone of a latitudinal transect in the South and Mid Atlantic Ocean. We show that the distribution of AAP bacteria is highly correlated to the chlorophyll a concentration and the abundance of picophytoplankton across vertical and horizontal gradients. Furthermore, we estimate the light energy captured by AAP bacteria across the water column and find that, while they share a common latitudinal pattern of light capture with the picophytoplankton, they display a unique vertical arrangement with highest photoheterotrophic activity is in the surface ocean.

ecology↗

bioRxiv2023

Manipulation in grazing, viral pressure and resource availability leads to success in the isolation of abundant marine bacteria

Isolation of microorganisms is a useful approach to gather knowledge about their genomic properties, physiology, and ecology, in addition to allowing characterization of novel taxa. We performed an extensive isolation effort on samples from seawater manipulation experiments that were carried out during the four astronomical seasons in a coastal site in the NW Mediterranean to evaluate the impact of grazing, viral mortality, resource competition and light on bacterioplankton growth. Isolates were retrieved using two growth media and their full 16S rRNA gene was sequenced to assess their identity and compute their culturability across seasons and experimental conditions. A total of 1643 isolates were obtained, which mainly affiliated to classes Gammaproteobacteria (44%), Alphaproteobacteria (26%) and Bacteroidia (17%). The most commonly isolated genera were Alteromonas and Limimaricola. While isolates varied across culture media, seasons and treatments, those pertaining to class Gammaproteobacteria were the most abundant in all experiments, while Bacteroidia was preferentially enriched in the treatments with reduced grazing. Sixty-one isolates had a similarity below 97% to cultured taxa and are thus putatively novel. Comparison of isolate sequences with 16S rRNA gene amplicon sequences from the same samples showed that the percentage of reads corresponding to isolates was 21.4% within the whole dataset, with dramatical increases in summer virus-reduced (71%) and diluted (47%) treatments. In fact, we were able to isolate the top-10 abundant taxa in several experiments and from the whole dataset. IMPORTANCEThe traditional observation that we can only culture 1% of bacteria for a given environment has recently been questioned on several grounds, among other reasons because it is importantly influenced by environmental conditions. We cultured a high amount of heterotrophic bacterial strains from experiments where seawater environmental conditions had been manipulated and found that decreasing grazing and viral pressure as well as rising nutrient availability are key factors increasing the success in isolating marine bacteria. Our data clearly suggests that the "1% culturability paradigm" needs to be revised and reinforces bacterial cultures as a powerful way to discover new taxa.

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↗

bioRxiv2020

Seasonal niche differentiation between evolutionary closely related marine bacteria

Bacteria are highly dynamic in marine environments, where they play key biogeochemical roles. Here, we tested how similar the niche of closely related marine bacteria is and what are the environmental parameters modulating their ecological responses in a coastal oligotrophic time series. We further explored how conserved the niche is at broader taxonomic levels. We found that, for certain genera, niche similarity decreases as nucleotide divergence increases between closely related amplicon sequence variants, a pattern compatible with selection of similar taxa through habitat filtering. Additionally, we observed evidence of niche partitioning within various genera shown by the distinct seasonal patterns of closely related taxa. At broader levels, we did not observe coherent seasonal trends at the class level, with the order and family ranks conditioned to the patterns that exist at the genus level. This study explores the coexistence of niche overlap and niche partitioning in a coastal marine environment.

microbiology↗

bioRxiv2018

Long-term seasonality of marine photoheterotrophic bacteria reveals low cohesiveness within the different phylogroups

Aerobic anoxygenic phototrophic (AAP) bacteria play a relevant role in the marine microbial food web, but little is known about their long-term seasonal dynamics. Using Illumina amplicon sequencing of the pufM gene coupled with multivariate, time series and co-occurrence analyses we examined their temporal dynamics over a decade at the Blanes Bay Microbial Observatory (NW Mediterranean). Phylogroup K (Gammaproteobacteria) was the most abundant over all seasons, with phylogroups E and G (Alphaproteobacteria) being often abundant in spring. A clear seasonal trend was observed in diversity, with maximum values in winter. Multivariate analyses showed sample clustering by season, with a relevant proportion of the variance (38%) explained by day length, temperature, salinity, phototrophic nanoflagellate abundance and phosphate concentration. Time series analysis showed that only 42% of the Amplicon Sequence Variants (ASVs) analyzed presented marked seasonality but these represented most of the abundance (92%). Interestingly, distinct temporal dynamics were observed within the same phylogroup and even within different ASVs conforming the same Operational Taxonomic Unit (OTU). Likewise, co-occurrence analysis highlighted negative associations between various ASVs within the same phylogroup. Altogether our results picture the AAP assemblage as highly seasonal, containing ecotypes with distinctive niche partitioning rather than being a cohesive functional group.

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↗