Ulisse Cardini

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 counts and bulk 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 rbc L 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 Long-Term Ecological Research Mare Chiara site in the Gulf of Naples, Italy, alongside microscopy, chlorophyll, physicochemical, and carbon-fixation data. Diatom rbc L DNA tracked abundance across five orders of magnitude despite seasonal shifts in community composition. Combining molecular and optical data revealed increased cellular rbc L copies and chlorophyll in low-light winter populations, suggesting enhanced photosynthetic capacity despite lower abundance. Furthermore, rbc L RNA reflected total carbon fixation rates and identified populations with differing carbon fixation activity. These results support rapid, RPA-based rbc L quantification as a robust approach for biomolecular ocean observing. Graphical

Sponges commonly form associations within seagrass meadows, but their potential impact on seagrass productivity and nutrient cycles remains poorly understood. This study investigates the association between the demosponge Chondrilla nucula and the Mediterranean seagrass Posidonia oceanica in two sampling occasions during the plant growth (spring) and senescence (autumn) seasons at a small inlet near Naples, Italy, where the sponge grows conspicuously within the seagrass bed. We found a non-linear relationship between the benthic cover of the sponge and the seagrass, with higher C. nucula cover linked to intermediate P. oceanica cover, suggesting spatial dependence. Posidonia oceanica showed higher net primary production (NPP) in spring, while C. nucula was net heterotrophic in spring but exhibited near zero metabolic balance in autumn. NPP remained stable when the two organisms were associated, regardless of the season. Chondrilla nucula consistently contributed inorganic nutrients to the association in the form of phosphate, ammonium, and substantial nitrate, recycling nutrients that potentially benefited P. oceanica in its growth season. In return, the seagrass released dissolved organic carbon in spring, which is consistent with supporting sponge heterotrophic nutrition. These findings suggest reciprocal benefits in the interaction between C. nucula and P. oceanica , with nutrient exchange facilitating a facultative mutualism that potentially supports and stabilizes the productivity of the seagrass ecosystem.

Wildfires are becoming more frequent and severe under a warming and drying climate, with Mediterranean regions emerging as global hotspots of megafire activity whose impacts extend from upland catchments to coastal waters. Although the terrestrial effects of fire are well established, the mechanisms by which wildfire by products influence marine ecosystems remain poorly resolved. Here, we investigate whether and how a Mediterranean megafire (12,000 ha) altered post fire fluxes of nutrients, sediments properties, and combustion derived compounds, causing changes in coastal biogeochemistry and ecosystem responses across land–sea and depth gradients. Ash-derived runoff generated a transient pulse of macronutrients and organic matter (TP, TDN, DOC and Si), producing short lived increases in turbidity and chlorophyll a in coastal waters. Stable isotopes and C/N ratios in primary producers indicated enhanced nitrogen uptake from riverine inputs, with intertidal macroalgal forests—particularly Ericaria spp.—showing marked short-term recovery. In contrast, responses were minimal in seagrass Posidonia oceanica and geniculate coralline algae, and absent in both subtidal macroalgal communities and deep coralligenous habitats. Our results show that megafires can temporarily reconfigure land-sea nutrient fluxes generating short-lived increases in primary productivity in oligotrophic Mediterranean coasts. As wildfire activity intensifies under climate change, understanding land–sea connectivity will be essential for predicting cascading impacts on coastal ecosystem functioning.

Seaweeds harbor a rich diversity of bacteria, providing them with metabolic resources and a surface for attachment and biofilm development. The host’s unique environment potentially shapes the bacterial genomes and promotes adaptations for a symbiotic lifestyle. To investigate whether the genomes of seaweed-associated bacteria are genetically and metabolically distinct from their close free-living relatives in seawater, we compared both the seaweed-associated and free-living counterparts of 72 bacterial genera across 16 seaweed hosts using whole-genome sequences or high-quality metagenome-assembled genomes. While taxonomic affiliation strongly influenced genome characteristics such as GC content, gene number, and size, host association had a lower effect overall. A reduced genome size was suggested only in Nereocystis luetkeana -associated microbes, while only Ascophyllum nodosum -associated bacteria had an increased GC content. Metabolic adaptations were indicated from the genomes of seaweed-associated bacteria, including enriched pathways for B vitamin production, complex carbohydrate utilization, and amino acid biosynthesis. In particular, Flavobacteriia showed the most pronounced differences between host-associated and free-living strains. We further hypothesized that bacteria associated with seaweed might have evolved to complement their host’s metabolism and tested this inference by analyzing the genomes of both the seaweed Ectocarpus subulatus and its 28 bacterial associates but found no evidence for such complementarity. Our analyses of 72 paired bacterial genomes highlighted significant metabolic differences in seaweed-associated strains with implications for carbon, nitrogen, and sulfur cycling in the coastal ocean. IMPORTANCE: We hypothesized that the unique environment of seaweeds in coastal oceans shapes bacterial genomes and promotes a symbiotic lifestyle. We compared the genomes of bacteria isolated from seaweed with bacteria from the same genus found free-living in seawater. For genome features that included the number of genes, the size of the genome, and the GC content, taxonomy was of greater importance than bacterial lifestyle. When we compared metabolic abilities, we again found a strong effect of taxonomy in determining metabolism. Although several metabolic pathways differed between free-living and host-associated bacteria, this was especially prominent for Flavobacteriia in the phylum Bacteroidota . Notably, bacteria living on seaweeds had an increased occurrence of genes for B vitamin synthesis, complex carbohydrate use, and nitrogen uptake, indicating that bacterial genomes reflect both their evolutionary history and the current environment they inhabit.

In the Mediterranean Sea, the demosponge _Chondrilla nucula_ can occur in close association with the native seagrass _Posidonia oceanica_. _C. nucula_ harbors a diverse and abundant microbial community, including potential nitrifiers. Thus, the sponge may contribute to the nitrogen (N) demand of the seagrass holobiont. In this study, we investigated potential nitrification rates (PNR) and inorganic N fluxes within this association at a site where _C. nucula_ covered 18 ± 3 % of the seagrass meadow area, during plant growth (spring) and senescence (autumn). Using incubation experiments with 15N-labeled ammonium, we measured PNR and inorganic N of the seagrass-sponge association, and of sponge and seagrass independently, under light and dark conditions. We supplemented these experiments with 16s rRNA gene amplicon sequencing to characterize the microbial community of the sponge. PNR was exclusively measured when the sponge was present (alone or in association with the seagrass). PNR was highest in the dark and when _C. nucula_ was associated with the seagrass, ranging from 21 ± 7 to 267 ± 33 nmol N g DW-1 h-1 in spring and autumn, respectively. Sponge-mediated PNR can support 8% of the N demand of the _P. oceanica_ holobiont during growth and 47 % during senescence. We identified key nitrifying bacterial and archaeal groups as members of the sponge’s microbial community. While _C. nucula_ released inorganic N, potentially sustaining the seagrass, it benefitted from dissolved organic carbon released by _P. oceanica_. These results suggest that the interaction between _C. nucula_ and _P. oceanica_ is mutually beneficial, ultimately supporting and stabilizing the seagrass ecosystem.

A bstract: In the Mediterranean Sea, the demosponge Chondrilla nucula can occur in close association with the native seagrass Posidonia oceanica . C. nucula harbors a diverse and abundant microbial community, including potential nitrifiers. Thus, the sponge may contribute to the nitrogen (N) demand of the seagrass holobiont. In this study, we investigated potential nitrification rates (PNR) and inorganic N fluxes within this association at a site where C. nucula covered 18 ± 3 % of the seagrass meadow area, during plant growth (spring) and senescence (autumn). Using incubation experiments with ¹⁵ N-labeled ammonium, we measured PNR and inorganic N of the seagrass-sponge association, and of sponge and seagrass independently, under light and dark conditions. We supplemented these experiments with 16s rRNA gene amplicon sequencing to characterize the microbial community of the sponge. PNR was exclusively measured when the sponge was present (alone or in association with the seagrass). PNR was highest in the dark and when C. nucula was associated with the seagrass, ranging from 21 ± 7 to 267 ± 33 nmol N g DW ^-1 h ^-1 in spring and autumn, respectively. Sponge-mediated PNR can support 8% of the N demand of the P. oceanica holobiont during growth and 47 % during senescence. We identified key nitrifying bacterial and archaeal groups as members of the sponge’s microbial community. While C. nucula released inorganic N, potentially sustaining the seagrass, it benefitted from dissolved organic carbon released by P. oceanica . These results suggest that the interaction between C. nucula and P. oceanica is mutually beneficial, ultimately supporting and stabilizing the seagrass ecosystem.

Sponges commonly form associations within seagrass meadows, but their potential impact on seagrass productivity and nutrient cycles remains poorly understood. This study investigates the association between the demosponge Chondrilla nucula and the Mediterranean seagrass Posidonia oceanica in two sampling occasions during the plant growth (spring) and senescence (autumn) seasons at a small inlet near Naples, Italy, where the sponge grows conspicuously within the seagrass bed. We found a non-linear relationship between the benthic cover of the sponge and the seagrass, with higher C. nucula cover linked to intermediate P. oceanica cover, suggesting spatial dependence. P. oceanica showed higher net primary production (NPP) in spring, while C. nucula was net heterotrophic in spring but exhibited slightly positive NPP in autumn. NPP remained stable when the two organisms were associated, regardless of the season. C. nucula consistently contributed inorganic nutrients to the association in the form of phosphate, ammonium, and substantial nitrate, recycling nutrients that potentially benefited P. oceanica in its growth season. In return, the seagrass consistently provided dissolved organic carbon, which aided sponge nutrition in spring. These findings suggest reciprocal benefits in the interaction between C. nucula and P. oceanica , with nutrient exchange facilitating a facultative mutualism that potentially supports and stabilizes the productivity of the seagrass ecosystem. SIGNIFICANCE STATEMENT: This study provides a novel exploration of the reciprocal interactions between the demosponge Chondrilla nucula and the Mediterranean seagrass Posidonia oceanica , revealing a facultative mutualism mediated by nutrient exchange. Our findings show a non-linear spatial dependence between sponge and seagrass cover and demonstrate the sponge’s substantial contributions of inorganic nutrients (phosphate, ammonium and conspicuous nitrate) to the seagrass, particularly during its productive spring season. In return, P. oceanica supplies dissolved organic matter, aiding sponge nutrition. This study uniquely quantifies these reciprocal nutrient exchanges across the plant growth and senescence seasons, demonstrating how such interactions stabilize net primary production and support ecosystem functioning. These insights address a critical gap in understanding the role of sponge-seagrass associations in nutrient cycling, highlighting their significance for the resilience, productivity, and metabolic balance of coastal ecosystems under changing environmental conditions.

The NEREA (Naples Ecological REsearch for Augmented observatories) initiative aims to establish an augmented observatory in the Gulf of Naples (GoN), designed to advance the understanding of marine ecosystems through a holistic approach. Inspired by the Tara Oceans expedition and building on the scientific legacy of the MareChiara Long-Term Ecological Research (LTER-MC) site, NEREA integrates traditional physical, chemical, and biological measurements with state-of-the-art methodologies such as metabarcoding and metagenomics. Here we present the first 10 months of NEREA data, collected from April 2019 to January 2020, encompassing physico-chemical parameters, plankton biodiversity (e.g., microscopy and flow cytometry), prokaryotic and eukaryotic metabarcoding, a prokaryotic gene catalogue, and a collection of 3818 prokaryotic Metagenome-Assembled Genomes (MAGs). NEREA’s efforts produce a significant volume of multifaceted data, which enhances our understanding of marine ecosystems and promotes the development of scientific hypotheses and ideas.

Summary: In the marine environment, seaweeds (i.e. marine macroalgae) provide a wide range of ecological services and economic benefits. Like land plants, seaweeds do not provide these services in isolation, rather they rely on their associated microbial communities, which together with the host form the seaweed holobiont. However, there is a poor understanding of the mechanisms shaping these complex seaweed–microbe interactions, and of the evolutionary processes underlying these interactions. Here, we identify the current research challenges and opportunities in the field of seaweed holobiont biology. We argue that identifying the key microbial partners, knowing how they are recruited, and understanding their specific function and their relevance across all seaweed life history stages are among the knowledge gaps that are particularly important to address, especially in the context of the environmental challenges threatening seaweeds. We further discuss future approaches to study seaweed holobionts, and how we can apply the holobiont concept to natural or engineered seaweed ecosystems.

Seagrass meadows form highly productive and diverse ecosystems in coastal areas worldwide, where they are increasingly exposed to ocean acidification (OA). Efficient nitrogen (N) cycling and uptake are essential to maintain plant productivity, but the effects of OA on N transformations in these systems are poorly understood. Here we show that complete N cycling occurs on leaves of the Mediterranean seagrass Posidonia oceanica at a volcanic CO₂ vent near Ischia Island (Italy), with OA affecting both N gain and loss while the epiphytic microbial community structure remains largely unaffected. Daily leaf-associated N₂ fixation contributes to 35% of the plant’s N demand under ambient pH, while it contributes to 45% under OA. Nitrification potential is only detected under OA, and N-loss via N₂ production increases, although the balance remains decisively in favor of enhanced N gain. Our work highlights the role of the N-cycling microbiome in seagrass adaptation to OA, with key N transformations accelerating towards increased N gain.