Biology subjects

Ser-Giacomi, E.

Publications and source records attributed to Ser-Giacomi, E..

4 recordsLinked to original sources

bioRxiv2026

Invariant scaling of the Species Abundance Distribution in observed and simulated marine plankton communities

Marine plankton are functionally diverse and span over five orders of magnitude in diameter, with important consequences for marine biogeochemical cycles. Marine ecosystem simulations are beginning to resolve this diversity; however, major uncertainties persist regarding the structure and function of planktonic ecosystems. Here we diagnosed plankton Species Abundance Distributions (SADs) in large-scale surveys and in a global, mechanistic plankton community simulation. The fitted slopes of the SADs vary by less than 10% across latitude, season, and biome in both observations and the simulation. Fitting parametric SADs further reveals spatial structure in the shape and functional form of the SAD aligned with established biogeographic provinces. Together, these results demonstrate a largely invariant structure of marine plankton communities that persists despite strong environmental gradients and taxonomic turnover. These findings suggest that the emergent shape and scaling of plankton SADs reflect fundamental constraints on community assembly and provide a compact quantitative diagnostic for planktonic ecosystem structure.

ecology↗

bioRxiv2025

Planetary-scale marine community modeling predicts metabolic synergy and viral impacts

The oceans buffer against climate change via biogeochemical cycles underpinned by microbial metabolic activities. While planetary-scale surveys provide baseline microbiome data, inferring metabolic and biogeochemical impacts remains challenging. Genome-scale modeling has addressed analogous issues at the cellular level, highlighting key metabolic reactions contingent upon specific environmental conditions. Here we adapt this mechanistic modeling framework towards analyzing global ocean microbial communities to reveal metabolic processes predicted to maintain ecosystem functioning. To achieve this, we developed a genome-scale superorganism metabolic model for each TARA Ocean metagenome or metatranscriptome (i.e., limited to reactions known from heterotrophic prokaryotes and viruses), and evaluated these models to establish a community-wide metabolic phenotype for each sample. To validate, we showed that even with reaction-mappable genes only ([~]1/4 of the total genes), model composition revealed metabolism-inferred ecological zones that matched taxonomy-inferred zones. Model inferred metabolic phenotypes revealed reaction cooperation associated with microbial metabolism and organism diversity. These phenotypes also suggest elevated ecological roles for viruses as model predictions suggest they genomically target community-critical metabolic reactions that underpin metabolic phenotype stability, and also demonstrate that, as metabolites are better understood, immediate estimates could be made for where viruses remineralize versus sink carbon. While this new constraints-based, agile, and mechanistic modeling framework is highly upgradable, it already begins to convert molecular-scale environmental omics data to ecological and even planetary-scale biogeochemical features that will better bring microbes and their viruses into Earth system and climate models.

systems biology↗

bioRxiv2019

Fine-scale fronts as hotspots of fish aggregation in the open ocean

Oceanic Lagrangian Coherent Structures have been shown to deeply influence the distribution of primary producers and, at the other extreme of the trophic chain, top predators. However, the relationship between these structures and intermediate trophic levels is much more obscure. In this paper we address this knowledge gap by comparing acoustic measurements of mesopelagic fish concentrations to satellite-derived fine-scale Lagrangian Coherent Structures in the open ocean. The results demonstrate unambiguously that higher fish concentrations are significantly associated with stronger Lagrangian Coherent Structures, and we observe that these features represent a limiting condition for high fish concentrations. A model, specifically built for mid trophic levels with realistic parameters, provides a possible mechanism of fish aggregation, and is coherent with the observations. These results may help to integrate intermediate trophic levels in trophic models, which can ultimately support management and conservation policies.

biophysics↗

bioRxiv2018

Ubiquitous abundance distribution of non-dominant plankton across the world’s ocean

Species Abundance Distributions (SADs) bear the imprint of ecological processes that shape biological communities, and are therefore used to discriminate among different scenarios of community assembly. Even though empirical distributions appear to follow a handful of qualitative laws, it is still unclear if and how quantitative variation in SADs reflects peculiar features of the communities and their environmental context. Here, we use the extensive dataset generated by the Tara Oceans expedition for marine microbial eukaryotes (protists) and an adaptive algorithm to explore how SADs vary across plankton communities in the global ocean. We show that the decay in abundance of non-dominant OTUs, comprising over 99% of local richness, is commonly governed by a power-law. The power-law exponent varies by less than 10% across locations and shows no biogeographical signature, but is weakly modulated by cell size. Our findings suggest that large-scale ubiquitous ecological processes govern the assembly of non-dominant plankton throughout the global ocean.

ecology↗