Limnology and Oceanography

The picocyanobacterium Prochlorococcus is a fundamental contributor to ocean primary productivity. While its free-living population has been extensively studied, primarily using flow cytometric analyses, the size and distribution of its particle-associated population is not well understood. Using filter fractionated samples from cruises in the Pacific Ocean, Atlantic Ocean, and Mediterranean Sea, we generated metagenomic data using internal standards, yielding absolute genome equivalent counts of Prochlorococcus cells in different size fractions. We used these data to model a relationship between relative and absolute genome equivalent counts, yielding a correction factor that we validated using published datasets. We then applied the correction factor to size-fractionated global metagenomic data from the TARA Oceans Project, which has widespread Prochlorococcus cells in size fractions >1.6 m throughout the transects, to calculate the fraction of the total Prochlorococcus population in large size fractions. The ''particle-associated'' population fraction increased with net primary productivity. Dissolved inorganic carbon was also directly correlated with increased particle association, which, combined with other evidence, could indicate an association with upwelling. We also examined the relationship between particle-associated population and carbon export at 150 m by incorporating published estimates of carbon flux based on TARA optical scattering data. This study highlights the potential importance of particle-associated Prochlorococcus to carbon flux in marine ecosystems and offers a way to convert relative to absolute genome equivalents of microorganisms in archival metagenomic datasets.

Marine diatoms contribute to about 20% of global primary production. We present the first basin-scale, multiyear assessment of diatom communities in the North Pacific, combining taxonomically high-resolution RuBisCO large subunit gene (rbcL) metabarcoding with concurrent environmental measurements. Using a nine-year time series of daily samples resolved at the species level via ~500 bp rbcL fragments, we performed multivariate analyses across biogeographic provinces, identifying significant correlations between community structure and environmental drivers such as temperature and macronutrient availability. We report the prevalence of a previously overlooked centric diatom species in the North Pacific, Eunotogramma lunatum, which appears to be near-dominant even in subarctic high-nitrate, low-chlorophyll waters where pennate diatoms are typically favored. These results demonstrate the power of rbcL for large-scale ocean monitoring and provide a critical baseline for future studies of diatom population dynamics, climate change impacts, and ecosystem resilience in a key marine region.

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.

Intertidal mudflats are low hydrodynamic energy environments hosting microphytobenthic communities that experience strong spatiotemporal variability in light regimes, including changes in spectral quality and light intensity that can lead to cellular photooxidative stress. To cope with these fluctuations, autotrophs exhibit diverse and highly plastic adaptations that are often species-dependent and shaped by their ecological niches. This study investigates photophysiological responses and metabolic remodeling in a diatom assemblage originating from a natural winter microphytobenthic biofilm under contrasting red and blue light intensities. To this end, photosynthetic parameters were monitored alongside changes in lipophilic metabolites, including untargeted lipids and lipophilic pigments. While few metabolites showed temporal remodeling, rapid and contrasting changes were observed within 30 minutes in response to both spectral quality and light intensity. Red light treatments induced broader remodeling of lipophilic metabolites than blue light, whereas blue light appeared to have a greater impact on photosynthetic parameters. Moreover, red light induced xanthophyll-cycle responses comparable to those observed under blue light at equivalent incident intensity. We discuss these metabolic responses in relation to diatom photoadaptive strategies, placing these findings within the intertidal environmental framework. This work further underlines the importance of understanding rapid metabolic plasticity in coping with light fluctuations, providing new insights into the photoregulatory strategies of natural microphytobenthic communities.

Aerobiological studies have largely focused on near-surface sampling and horizontal biogeographic patterns, while vertical structuring of airborne microbial communities within the atmospheric boundary layer (ABL) remains poorly understood. Here, we investigated microbial communities across the lower and upper ABL in a low-orography coastal site on the Antarctic Peninsula, representative of the Southern Ocean marine ABL and with low direct human influence. Airborne microorganisms were sampled simultaneously using ground-based and aerial platforms on five occasions. Community composition, abundance, and cell morphometry were assessed using metabarcoding and epifluorescence microscopy and interpreted alongside atmospheric observations. Airborne bacterial and eukaryotic communities showed consistent vertical stratification, although partial taxonomic overlap indicates vertical connectivity between atmospheric layers. Lower ABL communities were more diverse than upper ABL counterpart, compositionally homogeneous, and dominated by marine-associated taxa, reflecting strong influence from local sources and turbulent mixing. In contrast, upper ABL communities were less diverse but more heterogeneous among sampling events, enriched in stress-tolerant, terrestrial and plant-associated taxa, consistent with atmospheric filtering, selective upward transport, and long-range atmospheric inputs. Upper-layer samples also exhibited higher microbial abundance and greater prevalence of elongated cell morphologies, suggesting particle accumulation aloft and aerodynamic selection permanence. Together, these findings identify the Southern Ocean ABL as a vertically structured microbial habitat organized into two partially decoupled sublayers, in which atmospheric dynamics regulate microbial dispersal, ecosystem connectivity, and biogeographic patterns.

Offshore wind farms are rapidly expanding to meet growing demands for renewable energy, with development expected to extend further offshore into deeper waters. This expansion requires a robust understanding of the long-term ecological consequences of offshore wind farms (OWFs) and how these may interact with ongoing climate change. We used the coupled hydrodynamic-ecosystem-biogeochemical water-column model (GOTM-ERSEM-BFM) to investigate ecosystem-wide responses to environmental changes associated with OWFs and climate warming. Specifically, we examined OWF-related scenarios of reduced benthic suspension-feeding activity, representing potential effects of contaminant emissions from OWFs, and reduced wind forcing, together with increased sea surface temperature. The scenarios were simulated individually and in combination to explore potential interactive effects. These scenarios were simulated at two contrasting locations in the North Sea, representing a well-mixed coastal site and a seasonally stratified offshore site. The coastal site exhibited comparatively modest ecosystem responses across the scenarios, whereas responses were generally stronger at the deeper offshore site. At the offshore site, changes in stratification altered vertical nutrient dynamics and contributed to pronounced differences in ecosystem responses between the surface and bottom layers. Our results demonstrate that ecosystem responses to OWF-related and climate-driven environmental changes are strongly dependent on local environmental conditions, suggesting that ecological consequences may differ substantially as wind farm development expands into deeper offshore environments.

Newly established freshwater aquaria rely on development of biofilter nitrifying populations to prevent ammonia and nitrite accumulation that can negatively impact fish health. Although initial fish loads impact water chemistry of new aquaria, little is known about the corresponding impact on microbial community succession within freshwater aquarium biofilters. To address this gap, fourteen home aquarium systems were established, stocked with a range of fish loads, and maintained for eight months. Aquaria were sampled regularly to monitor nitrogen species, microbial community composition (16S rRNA gene sequencing), and the abundance of nitrifiers (qPCR). Aquaria with higher fish loads developed microbial communities that were compositionally distinct from those with lower fish loads, and were dominated by Pseudomonas, Rhodobacter, and Planctomycetes. These patterns are consistent with increased nutrient availability supporting biofilm development, whereas lower fish loads may delay biofilm maturation. Increasing the number of fish in an aquarium significantly increased maximum ammonia and nitrite concentrations, although both were ultimately depleted within similar timeframes across treatments. Comammox Nitrospira were among the most abundant biofilter nitrifiers and were present in all biofilter samples regardless of fish load. Ammonia-oxidizing bacteria were detected at relatively low abundance but showed increases in relative abundance within high fish load aquarium filters. Ammonia-oxidizing archaea were below sequencing detection limits and detected only at low levels by qPCR, suggesting that their establishment in aquarium biofilters may require higher initial inoculation or longer timeframes. Overall, these results demonstrate that fish load shapes microbial community development in newly established aquarium biofilters, and that comammox Nitrospira dominate among nitrifiers during early biofilter establishment.

Giant clams are some of the largest bivalve molluscs. They form a vital partnership with Symbiodiniaceae dinoflagellates that supply most of their energetic requirements. However, the factors that shape giant clam-associated photosymbiont communities remain unknown. Here, we profiled Symbiodiniaceae communities using ITS2 metabarcoding in eight giant clam species (Hippopus hippopus, H. porcellanus, Tridacna crocea, T. derasa, T. gigas, T. maxima, T. noae and T. squamosa) from 11 sites across the Philippine archipelago. Symbiodiniaceae community structure was shaped by an interplay between giant clam host and environment. Most giant clams were dominated by members of a single symbiont genus, with Cladocopium as the most prevalent, followed by Durusdinium and Symbiodinium. However, giant clam hosts also exhibited flexibility in their symbiotic partners that was evident across sites. Differences in giant clam-associated symbiont communities may contribute to differences in holobiont function and adaptability to variable environments. These findings deepen our understanding of giant clam-Symbiodiniaceae associations, offering a framework for predicting how giant clams may be affected by increasingly stressful reef conditions and, more importantly, informing strategies to improve mariculture and conservation practices.

Antarctica represents a significant, unresolved, and unstable source of methane to the atmosphere. To advance our understanding of the biological filter of methane in Antarctica, here we identify the taxa and functional genes present during methane oxidation in an Antarctic Methane Seep. Methane oxidation was present in all sediments, including in a non seep control site. Using 16S rRNA analysis alongside metagenomics, we found that ANaerobic MEthane oxidizing (ANME) archaea coupled to Sulfate-Reducing Bacteria (SRB), documented as the most important marine methane sink in other locations, were not present. Instead, we observed the presence of denitrification-dependent methane oxidizers, including the anaerobic genus Candidatus Methylomirabilis, alongside the nitrate reducing archaea Candidatus Methanoperedens through short-read metagenomic classification. In addition, we note the presence of multiple aerobic methanotrophs, with a particularly high abundance of the Methylobacter, Methylomonas, and Methyloprofundus genera. Our results support denitrification-mediated methane oxidation and aerobic methanotrophy as the primary potential methane sinks in the Ross Sea. The widespread methane oxidation, including in control sediment, combined with the possibility of anaerobic methane oxidation linked to denitrification rather than sulfate reduction highlights the ubiquity and uniqueness of the Antarctic methane cycle.

Diatoms are major contributors to marine primary production, yet current approaches for monitoring their abundance and function rely on coarse satellite chlorophyll estimates or sparse cell count and carbon fixation measurements. Molecular markers are a promising approach for high-resolution measurement of both abundance and metabolic activity through analysis of environmental DNA (eDNA) and RNA (eRNA). We present an isothermal quantitative recombinase polymerase amplification (qRPA) assay targeting rbcL gene copies and transcripts of marine diatoms, operating at low temperature and producing results in less than 15 min. We demonstrate specificity and calibration across diverse diatom taxa, then apply the assay to eDNA and eRNA samples from the Mare Chiara Long-Term Ecological Research site in the Bay of Naples, Italy, alongside microscopy, chlorophyll, physicochemical, and carbon-fixation data. Diatom rbcL DNA tracked abundance across five orders of magnitude despite seasonal shifts in community composition. Combining molecular and optical data revealed increased cellular rbcL copies and chlorophyll in low-light winter populations, suggesting enhanced photosynthetic capacity despite lower abundance. Furthermore, rbcL RNA reflected total carbon fixation rates and identified populations with differing carbon fixation activity. These results support rapid, RPA-based rbcL quantification as a robust approach for biomolecular ocean observing.

Snow algae are major biological drivers of snow darkening in polar and high-alpine environments. However, the direct contribution of algal pigmentation to snow reflectance has remained difficult to quantify because field observations cannot disentangle the effects of pigmentation from variation in biomass, species composition, and snow physical properties. Here, we characterized the optical effects of pigmentation using hyperspectral spectroradiometry to compare green, orange, and red cyst-like cells of a snow-derived Haematococcus isolate while controlling for developmental stage and cell abundance. Cysts became more red with increasing astaxanthin concentrations while chlorophyll-a concentrations remained relatively constant. Relative to green cysts, mean reflectance decreased by approximately 30% in orange cysts and 40% in red cysts. Integrated reflectance across the visible spectrum (350-800 nm) was negatively correlated with astaxanthin concentration. These results provide direct experimental evidence that algal pigmentation alone substantially reduces reflectance after controlling for cell abundance and developmental stage, and indicate that differences in snow physical properties may partly obscure this effect under natural field conditions. Our findings identify astaxanthin accumulation as an intrinsic driver of biological snow darkening and suggest that algal pigmentation, which may vary with species identity and physiological state, should be considered alongside biomass when predicting the radiative effects of snow algal blooms.

Microalgal fitness in nature is shaped by interactions within a diverse microbial community, yet most experimental studies have examined algal-bacterial interactions in pairwise systems. It is well established that bacteria can exhibit growth promoting or inhibiting effects on co-existing algae. Comparatively little information is available about how additional partners can alter the outcome of diatom-bacteria interactions. In the present study, we screened the pairwise interaction of the marine diatom Skeletonema marinoi with ten different bacteria. This screening identified Marinobacter adhaerens as a growth promoting and Vibrio cyclitrophicus HSW24 as growth inhibiting partner. Growth inhibition of V. cyclitrophicus was associated with cell lysis, chain fragmentation and altered pigmentation whereas M. adhaerens supported increased chlorophyll a fluorescence, uniform pigmentation, intact chains and healthy cell morphology. In a tripartite community containing both bacteria and the alga, M. adhaerens protected S. marinoi from the inhibitory effect of V. cyclitrophicus in a density dependent manner. Comparative metabolomics revealed distinct metabolic profiles between the pairwise and tripartite interactions. This allowed to identify metabolites that were up-regulated in the tripartite community and therefore candidates for the observed protection. Among these, kynurenic acid and N-acetyltyramine were identified in bioassays as protective molecules, thus clearly highlighting the importance of secondary metabolites in this interaction. The present findings demonstrate that a third bacterial partner can alter the outcome of an antagonistic algal-bacterial interaction by means of chemical mediators. This work has implications for our understanding of microbial community functioning that cannot only be derived from the investigation of pairwise interactions.

New maritime regulations restricting high-sulfur fuels have led to the transition to new low sulfur fuel oils (LFSOs). We do not know how LSFOs will behave in marine environments and how they will respond to available remediation strategies, presenting an environmental risk. The risk will be even higher in the remote high Arctic, especially along the Northwest Passage (NWP), for which an increase in shipping traffic is expected by the end of the century. In this study, we evaluated the long-term (one year) biodegradation potential of the native microbial community of NWP beach sediment using in situ mesocosm experiments with two different types of LSFOs: a marine gas oil (Marine diesel) and an ultra-low sulfur fuel oil (ULSFO). We observed that the lighter Marine diesel was biodegraded better (72.0%) than the heavier ULSFO (32.5%). We described composition of the microbial community of the mesocosms using 16S rRNA gene amplicon sequencing and observed a decrease in microbial diversity for the fuel-treated samples compared to the untreated controls. Despite the decrease in overall diversity, we observed significantly higher abundances of known hydrocarbon degrading microbes (e.g., Oleispira, Altererythrobacter, Gilvibacter, Pseudohongiella) in the fuel mesocosms. Our study showed the potential to implement biodegradation as a remediation strategy under the cold and oligotrophic environmental conditions present throughout the NWP. However, we also observed that microbes on their own cannot degrade the entirety of the removed fuel and other types of remediation will need to be considered to complement the natural biodegradation observed here.

The Southern Ocean harbors diverse marine microbial communities shaped by both local oceanographic conditions and dispersal limitations. However, this knowledge is mainly based on coastal Antarctic sites, whereas circumpolar Antarctic open sea and subantarctic ecosystems remain poorly explored. Here, we characterize marine microbial communities (using 16S rDNA high-throughput sequencing) and marine oceanographic data across two regions: the Subantarctic, involving two localities (the Magellan Strait and the Beagle Channel), and Antarctic open sea, involving two localities (Eastern Indian and Central South Pacific). We found extensive differences across regions and localities, characterized by distinct taxonomic patterns, alpha diversity, microbial composition, and enriched taxa profiles. Despite these differences, Clade Ia, Amylibacter, NS5 marine group, and NS2b marine group exhibited high prevalence across regions. Oceanographic parameters had variable relationships with microbial alpha diversity across regions: Sea surface temperature and salinity had a negative and positive correlation, respectively, in the Magellan Strait during 2024. In the Antarctic region, dissolved oxygen displayed a negative correlation in the Indian Ocean during 2024, whereas salinity displayed a more variable relationship in the Indian Ocean: positively correlated during 2024, while negatively correlated during 2025. Collectively, our results highlight a strong microbiological biogeographic structure in the Southern Ocean, both across broad scales (between Subantarctic and Antarctic regions) and within regions. Furthermore, our results show dynamic relationships between oceanographic variables and marine microbial diversity across Antarctic and Subantarctic regions.

Replication is central to most experimental and sampling designs, increasing inferential power and capturing fine-scale data heterogeneity. However, its importance remains poorly evaluated in some ecological and evolutionary settings. This is the case of metabarcoding studies using DNA recovered from sedimentary archives, in which biological signals may integrate ecological information through depositional and burial processes, and are often inferred from a single sediment core per site. Here, we evaluated the effect of different types of replication using sedimentary DNA (sedaDNA) metabarcoding data from two genetic markers (mitochondrial COI and nuclear 18S), under a nested sampling design. The design included three intertidal sites, three spatially separated sediment cores per site (biological replicates), two sediment depth horizons per core, and eight PCR (technical) replicates per sediment sample. Variance partitioning showed that site identity and sediment age group together explained >70% of the variation in beta diversity, indicating that among-site spatial variation and stratigraphic variation were the dominant drivers of community composition. In contrast, variation among different cores within sites was small and non-significant (<5%). Among PCR replicates from the same sediment sample, richness varied substantially, whereas Shannon diversity was more consistent. Despite this variability, differences in community composition among technical replicates remained smaller than among biological replicates and site identity, indicating limited influence on broader ecological patterns. Community composition was highly similar among replicate cores within sites, consistent with stratigraphic coherence. These results indicate limited within-site heterogeneity and suggest that, under stratigraphically coherent conditions, increasing biological replication may yield limited additional information, whereas enhancing technical replication and stratigraphic resolution can improve ecological inference from sedaDNA metabarcoding datasets.

Bottom trawls have been used for centuries, yet studies of their impact on marine ecosystems have largely been restricted to recent decades. Here, we reconstruct fishing effort for the international trawler fleets in the North Sea from the age of sail to early steam trawling, by synthesising historical data describing vessel numbers and specifications, gear dimensions, fishing grounds, and operational characteristics. The trawler fleet increased from ca 800 sailing vessels in the 1820s to ca 3500 at the peak in sail trawling in the 1880s. Subsequently, steam trawling fleets emerged, increasing to almost 2000 vessels in the 1910s, while sailing fleets declined. Trawling grounds, covering ca 7% of the North Sea in 1820s, expanded from coastal to offshore grounds, reaching ca 25% in the 1880s, and 46% in the 1910s after the transition to steam trawling. Using a hydro- and aerodynamic approach to model the wind conditions required for sail trawling, we show that about 55% to 80% of the time at sea was suitable for trawling, providing a new quantitative basis for estimating historical fishing effort. The surface area swept by the trawl per year increased from 35,000 km2 in 1820s to 225,000 km2 in 1880s and 500,000 km2 in 1910s, corresponding to ca 60% of present levels. The trawling intensity (swept area ratio) varied between 0.9-1.7 year-1 in the era of sail, increasing to ca 2.0 in the 1910s. The trawling footprint (unique area trawled) increased to 160,000 km2, about half the present level.

Nitrogen availability is a key factor shaping microbial metabolism, ecological adaptation, and nitrogen cycling in aquatic environments. Members of the genus Vibrio are ubiquitous heterotrophic bacteria in marine and aquaculture ecosystems, yet their responses to different inorganic nitrogen sources remain poorly understood. Here, we systematically compared the growth characteristics, nitrogen transformation capacity, and molecular responses of Vibrio harveyi and Vibrio parahaemolyticus under ammonium (NH4+), nitrate (NO3-), and nitrite (NO2-) conditions using physiological assays, comparative genomic analysis, and transcriptomic profiling. V. harveyi exhibited broader nitrogen utilization capacity and was able to grow under all three nitrogen conditions, whereas V. parahaemolyticus showed a strong preference for NH4+ and limited growth under NO3- and NO2- conditions. Moreover, V. harveyi displayed rapid population expansion accompanied by reduced long-term viability, while V. parahaemolyticus maintained greater population stability. Both species showed NO3- accumulation during growth despite lacking canonical nitrification genes under NH4+ condition, suggesting the potential involvement of non-canonical heterotrophic nitrification processes. Transcriptomic analysis revealed nitrogen source-dependent metabolic specialization in V. harveyi. NH4+ availability promoted motility-associated responses and metabolic overflow, whereas NO3- induced iron acquisition-related pathways and NO2- activated assimilatory nitrite reduction coupled with oxidative stress adaptation. These findings demonstrate that inorganic nitrogen availability drives divergent metabolic and adaptive strategies in Vibrio, providing new insights into their nitrogen metabolic potential and ecological roles in aquatic environments. ImportanceThis study demonstrates that V. harveyi and V. parahaemolyticus exhibit distinct inorganic nitrogen utilization strategies, with V. harveyi displaying broader nitrogen utilization capacity. Transcriptomic and metabolomic analyses revealed that different nitrogen sources drive distinct metabolic and environmental adaptation responses in V. harveyi, including enhanced motility-associated functions and metabolic overflow responses under NH4+ condition, increased iron acquisition pathways under NO3- condition, and activation of assimilatory nitrite reduction coupled with oxidative stress adaptation under NO2- condition. Furthermore, significant nitrate accumulation was observed in both Vibrio strains during ammonium cultivation despite the absence of canonical nitrification genes, suggesting unexplored nitrogen transformation potential in vibrios. This study expands our understanding of how inorganic nitrogen availability shapes microbial adaptation strategies and ecological functions in aquatic environments.

After introduction, many non-native marine species are dispersed planktonically. Secondary spread within the non-native range has been shown to prevent the establishment of the introduced species if the advection of larvae prevents sufficient return of larvae to maintain the population in the face of competition with native species. However, those studies have largely neglected the effects of spatial variation in alongshore larval transport. We examine the introduction of a novel species with planktonic dispersal into a more realistic coastal environment which includes spatial variation in larval transport estimated from the Mercator Ocean 1/12th degree global circulation model. The introduction may either be from a distant habitat, or through range expansion. We find that there are locations in the global coastal ocean where introduced species are more likely to persist because of spatial variation of coastal currents. These include regions where alongshore larval transport diverges, such as estuaries. The location where a non-native species is introduced may not be where it flourishes - it cannot be assumed that the region where invading species are first noticed to be abundant is the region where it was introduced. We extend closed-population theory to open coastal systems to estimate persistence as a function of local circulation, habitat extent, and the competitive advantage of the introduced species. Software is provided which allows the estimations of regions where introduced species are more likely to persist and flourish as a function of larval depth behavior, planktonic duration and release timing.

Squid abundance has been reported to increase globally between 1970 and 2010. This increase has been hypothesized to result from two primary factors: the loss of top predators due to overfishing and rising ocean temperatures. The decline in apex predators may lead to the expansion of squid populations either through reduced predation pressure or diminished competition with juvenile predators. Concurrently, increased temperatures could enhance the somatic growth rates of squid, thereby accelerating their population growth. However, empirically disentangling the impacts of predator loss and temperature on squid biomass remains challenging, especially in a food-web context. In this study, we used a size- and trait-based model of upper trophic levels that resolves the ecosystem structure -- biomass and trophic interactions of fish and squid -- for varying depth, temperature, and secondary production, to investigate two hypotheses of the historical expansion of squid, i.e., the effects of predator depletion from fishing and rising temperatures on squid biomass. Our model reveals that intensified fishing of squid predators -- specifically large demersal fish in shelf systems and large pelagic fish in open oceans -- leads to a slight increase in squid biomass. Conversely, elevated temperatures are associated with a decline in squid biomass. This temperature-driven reduction in biomass is attributed to an increased metabolism of squids beyond the available food supply. If historic overfishing on large marine predators continues to be curtailed, we expect a corresponding reduction in global squid biomass and fisheries potential, which could be further exacerbated by rising temperatures.

Temperature plays a central role in marine phytoplankton biogeographical dynamics, physiology and gene expression. Nonetheless, the transcriptional regulatory mechanisms controlling temperature acclimation in marine phytoplankton are yet to be characterized. Ostreococcus tauri was chosen as a model species for green marine phytoplankton due to its cellular and genomic simplicity, as well as its evolutionary position within the green lineage. In this study, epigenomic and transcriptomic data were integrated to characterize changes induced by temperature in the trimethylation of histone 3 at lysines 27 and 4 (H3K27me3 and H3K4me3) epigenetic marks established by the Polycomb (PcG) and Trithorax group (TrxG) complexes, respectively. H3K27me3 was found to be a repressive mark responding to temperature, showing predominantly significant increased levels at high temperatures. While H3K4me3 was associated with active transcription, presenting less evident variations in cultures acclimated to different temperatures. H3K27me3 was found only marginally associated with transposable elements, being mostly involved in the repression of specific biological processes, such as gene expression control by transcription factors, meiosis, motors proteins and cytoskeletal structures. No significant conservation was found between the H3K27me3 gene targets in the model plant Arabidopsis thaliana and Ostreococcus tauri. Nonetheless, transcriptions factors belonging to the MADS-box, WRKY and AP2 families were consistently repressed by H3K27me3 in both species, unveiling that, although the specific downstream targets of this epigenetic mark have diversified during evolution, its role in modulating higher order regulatory nodes remains evolutionary conserved.