Helmholtz Institute for Functional Marine Biodiversity

Compositional data (CoDa) are prevalent in environmental research. They represent parts of a whole, such as percentages, proportions, and relative or absolute abundances. They are arrays of positive data that convey relevant information in the ratios between their components. Standard statistical techniques developed for real random observations often yield spurious results and are therefore unsuitable for CoDa, which has unique geometric properties. CoDa analysis is now widely acknowledged across various research fields, ranging from geoscience to social science, with a recent surge in popularity in microbial genomics. However, its adoption remains limited in natural organic matter (NOM) research, despite NOM data from key analytical tools such as mass spectrometry, fluorescence spectroscopy, and nuclear magnetic resonance spectroscopy all being compositional. Given the structural similarity between NOM and high-throughput sequencing data, for which CoDa analysis has been successfully adopted, we argue that CoDa analysis should also be consistently integrated into NOM research to prevent analytical pitfalls and misleading inferences. A few pioneering studies have applied CoDa analysis to NOM data, and a wide array of useful open-source tools are already available. This paper discusses step-by-step the application of CoDa analysis to NOM research, using ultrahigh-resolution mass spectrometry data as an illustrative example. The goal of the study is to provide the community with an overview of CoDa analysis and guide them on how to use it in practice.

Abstract Hydropower dams regulate water flows for millions of downstream inhabitants worldwide, altering water availability. Under a changing climate, flow control is often framed technically and politically as being essential for reducing drought and flood risks. However, it can also disrupt ecological flows, impact livelihoods and erode environmental knowledge. We contribute to this debate by examining how ribereños —rural communities in Colombia characterized by their interdependence with rivers—experience fluctuating water levels. We focus on ‘dry events’, situations where decreases in the river's water levels hinder ribereños' livelihoods. Our case study, the Lower Sogamoso River (dammed in 2014 by Hidrosogamoso Dam), no longer follows a clear pattern of rising and falling waters, which previously allowed ribereños to prepare socially and economically for seasonal activities. Drawing on a relational perspective on rivers and infrastructures, we mobilize the notion of rhythms to account for the temporal dimensions of hydrosocial relations and sociotechnical infrastructures. Using an interdisciplinary combination of ethnographic research and statistical analysis of hydrological and electricity data, three distinct situations come into view: the regular dry season, hourly low water levels and the 2015–2016 El Niño. Our findings demonstrate how temporal operations of hydropower and associated pricing mechanisms transform the hydrosocial relations of riverine communities. Daily operations disrupt gradual seasonal streamflow patterns, hindering seasonal livelihoods, while pricing decisions generate disruptive events on an hourly scale. During the 2015–2016 drought, the energy company's water storage and price bidding strategy led to unprecedented water level variations. Synthesis and applications . Our interdisciplinary approach made it possible to connect the temporal experiences of communities with large electricity market fluctuations. We emphasize that dry events must be assessed not only based on climatic conditions or dam presence but also taking into account the intersection of temporal logics at multiple scales. We underscore the need to evaluate streamflow variations at both daily and hourly scales, which are often overlooked in research and policy yet are essential for riverine cultures across the globe. Read the free Plain Language Summary for this article on the Journal blog. Spanish translation: Read the free Plain Language Summary for this article on the Journal blog.

Abstract Counting the number of isomers of a chemical molecule is one of the formative problems of graph theory. However, recent progress has been slow, and the problem has largely been ignored in modern network science. Here we provide an introduction to the mathematics of counting network structures and then use it to derive results for two new classes of molecules. In contrast to previously studied examples, these classes take additional chemical complexity into account and thus require the use of multivariate generating functions. The results illustrate the elegance of counting theory, highlighting it as an important tool that should receive more attention in network science.

Biodiversity faces several global threats and communities are likely to show complex delayed responses. Accurately measuring these lags is critical to properly understand diversity dynamics. Here, we investigated these delays with minimal data availability and found critical mismatches between the temporal dynamics of taxonomic and functional diversity in Wadden Sea bird communities. By analysing 17 long‐term time series spanning an average of 30+ years, we quantified the net imbalance between colonisations and extinctions (NICE) to measure delays in taxonomic (tNICE) and functional (fNICE) diversity. Our approach used empirically measured (trophic and morphological) traits, and in parallel, traits inferred through diffusion maps, allowing to quantify species traits only based on their co‐occurrence patterns over time. First, we found that diffusion maps are a relevant tool to quantify species traits when trait data are scarce. Moreover, we found that, while initial colonisations outnumbered extinctions, the taxonomic balance shifted dramatically toward local species losses, deviating significantly from neutral expectations. Yet despite this concerning trend, functional diversity was stable. This stability likely stems from functional redundancy among declining species, temporarily preventing functional changes. However, despite current functional resilience, the on‐going loss of taxonomically distinct species threatens to erode unique functional roles, potentially triggering abrupt shifts and/or collapse in ecosystem functions. Most critically, our study show how seemingly stable functional diversity can mask accelerating taxonomic losses, highlighting the urgent need for multi‐faceted biodiversity monitoring. As global changes intensify, combining taxonomic and functional assessments through advanced analytical methods becomes essential for detecting early warning signals of ecosystem deterioration and implementing effective conservation strategies.

Carbon mobilization in hydrothermal sediments and advective transport of dissolved organic matter (DOM) to the ocean affect deep-sea ecosystems. However, the link between hydrothermal processes and DOM reactivity in organic-rich subsurface sediments, and the impact of DOM release on the marine carbon cycle remain poorly understood. The Guaymas Basin (Gulf of California), with its organic-rich sediments, hydrothermal vent sites, and magmatic sill intrusions is an ideal candidate for studying the hydrothermal influences on DOM biogeochemistry. We analyzed sediment and porewater samples from IODP Expedition 385 from down to ∼330 m below seafloor and used hot-water Soxhlet extractions as a first-order approximation for simulating hydrothermal DOM mobilization. We assessed the molecular composition of solid-phase extractable (SPE) DOM via ultrahigh-resolution mass spectrometry (FT-ICR-MS) and quantified dissolved organic sulfur, nitrogen, and phosphorus (DOS SPE , DON SPE , DOP SPE ). We identified several biogeochemical processes transforming DOM: active microbial transformations in the upper sediments were related to enhanced DOM oxygenation, and elevated DON SPE and DOP SPE concentrations. Highly aromatic, probably recalcitrant DOM, accumulated under anoxic conditions in intermediate depths. Here, DOS SPE concentrations were highest, probably due to abiotic sulfide incorporation into DOM. Hydrothermal alteration near magmatic sills reduced DOM molecular diversity and caused a significant shift in the chemical composition of deep subsurface sediments influenced by high temperatures. Our data indicated that hydrothermal sediments release DOM, including DOS SPE , DON SPE and DOP SPE , to the ocean. Hence, hydrothermal discharge may not only sustain local benthic ecosystems by providing bioavailable DOM but also likely influences the deep-sea carbon pool by introducing recalcitrant DOM.

ABSTRACT Harbor seals ( Phoca vitulina ) are one of the most important apex‐predators in the Wadden Sea. However, baseline information on their distribution and behavior is still sparse and geographically restricted. Passive acoustic monitoring (PAM) of their underwater sounds can provide information about their fine‐scaled distribution and habitat use. This study is the first to analyze underwater vocal behavior of harbor seals in the Wadden Sea, exploring temporal patterns and characteristics of vocalizations. Passive acoustic data from the Dutch Wadden Sea were collected east of Lauwersoog during the breeding season in July 2021 and south of the island of Vlieland in September 2022. We describe and document four acoustically distinct harbor seal call types based on spectro‐temporal call characteristics. Results showed a significantly higher vocal activity for two out of the four call types during the breeding season and clear differences in the dial distribution of calls. The results of this study provide a basis for PAM‐based monitoring of harbor seal activity and a potential fundament for AI‐based call detection algorithms. The increasing evidence for the importance of underwater sound for aquatic habitat quality and suitability emphasizes the need to acoustically map critical habitats and document the natural sounds of living organisms.

BackgroundAnthropogenic activities have led to a global rise in water temperatures, prompting increased interest in how warming affects infectious disease ecology. While most studies have focused on individual host-parasite systems, there is a gap in understanding the impact of warming on multi-host, multi-parasite assemblages in natural ecosystems. To address this gap, we investigated freshwater eukaryotic parasite communities in ten natural lakes near Konin, Poland: five artificially heated and five non-heated “control” lakes. Since 1958, the heated lakes have experienced a mean annual temperature increase of 2 °C due to hot water discharge from two adjacent power plants. We collected seasonal environmental DNA (eDNA) samples from surface waters over a two-year period and applied targeted metabarcoding to compare the richness and distribution of eukaryotic parasites across lake types with a focus on protists and fungi.ResultsUsing literature searches and sequence metadata from GenBank, we identified putative parasites which included Alveolates, Stramenopiles, basal Fungi and Ichthyosporeans as well as their associated hosts. Heated lakes harboured distinct parasite assemblages with higher richness of chytrids and aphelids, suggesting thermal preferences among certain freshwater microeukaryotic parasites. Other groups exhibited clear seasonal trends with richness of oomycetes peaking in spring and summer, and that of Cryptomycota in winter and autumn. A general linear model revealed a marginally positive correlation between chytrid parasite richness and richness of their green algal, diatom, and dinoflagellate hosts. Post-hoc analyses indicated that heated lakes exhibited greater seasonal variation in chytrid parasite richness and a stronger correlation between host and parasite richness than control lakes.ConclusionThese findings demonstrate that warming can induce strong shifts in the richness and assemblages of freshwater microeukaryotic parasites. Using chytrids as a focal group, we additionally demonstrate that warming may amplify seasonal variation in parasite richness and strengthen host-parasite richness relationships.

Abstract In the context of global change, marine organisms are subjected not only to gradual changes in abiotic parameters, but also to an increasing number of extreme events, such as heatwaves. However, we still know little about the influence of heatwaves on the structure of marine communities, and experimental studies are needed to test the impact of heatwaves alone and in combination with other environmental drivers. Here, we conducted a mesocosm experiment to assess the potential impact of heatwaves on plankton communities, which we did under ambient and future environmental conditions. To simulate future environmental conditions, we simultaneously manipulated temperature and pH based on IPCC predictions for 2100, and dissolved N : P ratios based on the conditions expected in European coastal zones. While we did not observe any effects of simulated heatwaves on phytoplankton abundances, we identified that future environmental conditions may favor smaller phytoplankton species and that additional heatwaves may especially favor small phytoflagellates and coccolithophores. We also observed that future environmental conditions may reduce the abundances and modify the species composition of bacterioplankton, microzooplankton, and mesozooplankton, and that heatwaves may exacerbate these effects. Using a unique approach to examine the potential impacts of heatwaves under current and future environmental conditions on a natural multi‐trophic marine plankton community, we show that the combination of multiple global change drivers has the potential to perturb the entire basis of marine food webs.

In adaptive dynamical networks, the dynamics of the nodes and the edges influence each other. We show that we can treat such systems as a closed feedback loop between edge and node dynamics. Using recent advances on the stability of feedback systems from control theory, we derive local, sufficient conditions for steady states of such systems to be linearly stable. These conditions are local in the sense that they are written entirely in terms of the (linearized) behavior of the edges and nodes. We apply these conditions to the Kuramoto model with inertia written in an adaptive form and the adaptive Kuramoto model. For the former, we recover a classic result, and for the latter, we show that our sufficient conditions match necessary conditions where the latter are available, thus completely settling the question of linear stability in this setting. The method we introduce can be readily applied to a vast class of systems. It enables straightforward evaluation of stability in highly heterogeneous systems.