Max Planck Institute for Marine Microbiology

Dinoflagellates and diatoms are key marine phytoplankton, with ecological roles strongly influenced by their associated phycosphere bacteria. However, the ecophysiological functions of these bacteria remain enigmatic as a result of insufficient taxonomic and genomic characterization. Here, by combining single-cell isolation with a custom statistical pipeline, we profiled resident bacterial communities associated with 108 diatom and 86 dinoflagellate strains, collected across temperate and tropical oceans worldwide. We examined genomic traits of key bacterial populations through whole-genome sequencing of representative isolates. Taxonomic compositions of dinoflagellate- and diatom-associated microbiota were distinct, highlighting host-specific differences. Each microbiota harboured characteristic genera with adaptive traits reflecting host metabolic profiles. Dinoflagellate-associated bacteria were enriched in genes responsible for motility and sulfur-compound use, whereas diatom-associated bacteria specialized in glycan use. We identified 'foundation' genera, defined as taxa with high occupancy and community-level impact in both phycosphere types (for example, Marivita and Marinobacter), sharing host-specific traits with characteristic bacteria while universally excelling in environmental response and resistance. Notably, foundation bacteria were enriched in Type VI secretion systems, emerging as a universal hallmark of phycosphere bacteria across global oceans. Overall, this study provides insights into the taxonomic and metabolic nature of phycosphere bacteria, highlighting the profound influences of interspecific interactions on marine ecological processes.

Abstract Permeable sands on continental shelves host microbial communities that drive organic carbon turnover, oxygen fluxes and nitrogen loss. Advective porewater flow associated with sedimentary bedforms maintains these rates and fluxes. Modeling and laboratory studies suggest that advective porewater flow is tightly coupled to bedform stability. However, the impacts of in situ bedform stability on biogeochemical fluxes in subtidal sands remain unconstrained. We deployed a benthic lander at six stations in the North Sea to measure in situ bedform geometries, oxygen fluxes and primary productivity accompanied with ex situ incubations, glycan extraction and microscopy. We observed bedform migration velocities ranging between 0 and 3.2 cm h −1 , which were only 9–16% of expected values from mechanistic models. Bedform stability may be enhanced by high interstitial colloidal and particulate algal glycans concentrations (2–52 mmol C L −1 ) that are a representative component of extracellular polymeric substances. Benthic primary productivity as a source of carbon was negligible (< 0.003 mmol C m −2 d −1 ). Pore space glycan accumulation was attributed to algal biomass filtered out of the overlying water column by advective flow through the permeable sediment. Benthic glycan concentrations correlated significantly with oxygen consumption rates per volume porewater (17–207 μ mol L −1 PW h −1 ), whereas sediment oxygen fluxes (6–17 mmol m −2 d −1 ) significantly correlated with modeled porewater velocities. Overall, the impact of glycans as a proxy for pelagically derived algal biomass was twofold: (1) they drove higher oxygen consumption rates in surface sediments and (2) contributed to stabilization of bedforms, which almost doubled oxygen fluxes into the sediment.

ABSTRACT The coupling between ocean and atmosphere across the strong seasonal gradients in the Arctic is poorly understood. Here, we explored the microbial and glycobiological connectivity between the sea surface microlayer (SML), the underlying seawater (ULW), snow, and aerosol particles in Kongsfjorden (Svalbard, 79°N) during autumn and spring. The marked overlap between marine and atmospheric microbiomes illustrates considerable sea-air transfer, linked to seasonally distinct environmental communities. For instance, Polaribacter and Formosa were aerosolized during the spring bloom, compared to Colwellia in autumn. Air-mass trajectories and microbial source tracking revealed a greater marine contribution in autumn, whereas spring aerosols were shaped by stronger winds and the cryosphere. Aerosol particles nonetheless contained numerous unique taxa, including Actinobacteria likely originating from terrestrial sources. Linking bacterial, microeukaryotic, carbohydrate, and meteorological dynamics established an overarching perspective across seasons and habitats, identifying four distinct ecosystem states. Genome-sequenced bacterial model isolates, representing key environmental populations, encode adaptive traits such as carotenoid and ectoine biosynthesis, supporting survival in the SML and atmospheric transfer. Comparison with time-series records from the nearby Fram Strait revealed that many aerosolized bacteria are consistent microbiome components; with implications for ecology and biogeochemistry across the wider Arctic.

In shallow-water hydrothermal vents, the dynamic interface between the discharged reduced hydrothermal fluids and the oxidized seawater allows the establishment of gradients capable of supporting diverse and complex microbial mats. Due to their shallow depths and proximity to land masses, shallow vents are heavily influenced by dynamic forcing, tidal fluctuations, and episodic events (e.g., storms, tides, etc.). Although several studies have investigated the microbial communities inhabiting shallow vents in the last decades, less is known about how microbial communities respond to episodic events and how the complex interplay of physical and chemical drivers shapes the establishment and structure of microbial biofilms in these systems. Here we present data combining the taxonomic and functional diversity of the white microbial mats commonly found in sulfide rich shallow-water hydrothermal vents in Paleochori Bay (Milos Island, Greece), using a combined approach of 16S rRNA transcript amplicon sequencing (from RNA) and shotgun metagenomic sequencing (from which 16S rRNA genes were retrieved). We show that the white microbial mats of Milos shallow-water hydrothermal vents are dominated by Epsilonproteobacteria, now classified as Campylobacterota, with metabolic functions associated with chemolithoautotrophic lifestyles and exposed to a diverse array of viral communities. Taxonomic names follow the classification available at the time of analysis (2012). We explore how dynamic forcing and storm events influence microbial community restructuring and turn-over, and provide evidence that dynamic interactions with the benthic boundary layer play a key role in controlling the spatial distribution of taxa. Overall, our results show diverse processes through which geodynamic events influence microbial taxonomic and functional diversity.

Anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) form syntrophic partnerships in marine sediments to consume greenhouse gas methane. While direct interspecies electron transport is proposed to enable ANME/SRB symbiosis, its electrochemical properties remain uncharacterized. Here, using sediment-free enrichment cultures, we measured the electron transport capabilities of marine consortia under physiological conditions. Diverse ANME/SRB consortia exhibited high dry conductance close to electrogenic biofilms. This conductance diminished upon exposure to heat or oxygen but was preserved following paraformaldehyde fixation, indicating a biomolecular origin for this electric charge transfer. Cyclic voltammetry revealed redox activity centered at 28±11, 94±6, and 24±7millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively. Generator-collector measurements further demonstrated that these redox components facilitate electron transport over micrometer-scale distances, sufficient to link archaeal and bacterial partners. Collectively, our results establish that marine ANME/SRB symbiosis uses redox conduction, consistent with multiheme cytochrome c, for direct interspecies electron transport.

Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed by a diverse community of prokaryotic and eukaryotic microbes. However, the diversity of the microbiome and the potential role of the different microbial taxa in some wastewater treatment plant setups is not fully understood. We aimed to investigate the presence and diversity of denitrifying bacteria of the candidate family Azoamicaceae that form obligate symbioses with protists in wastewater treatment plants. Our analyses showed that denitrifying endosymbionts belonging to the Ca. Azoamicus genus are present in 20-50% of wastewater treatment plants worldwide. Time-resolved amplicon data from four Danish wastewater treatment plants showed high temporal fluctuations in the abundance and composition of the denitrifying endosymbiont community. Fifteen high-quality metagenome-assembled genomes of denitrifying endosymbionts, four of which were circular, were recovered. Genome annotation showed that a newly described, globally widespread species, Ca. Azoamicus parvus, lacked a nitrous oxide reductase, suggesting that its denitrification pathway is incomplete. This observation further expands the diversity of metabolic potentials found in denitrifying endosymbionts and indicates that the contribution of microbial eukaryote holobionts to the wastewater ecosystem dynamics of nitrogen removal and greenhouse gas production may have been underestimated and needs further study.

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.

Glycans shape microbiomes in the ocean and the gut, driving key steps in the global carbon cycle and human health. Yet, our ability to track microbial glycan turnover across microbiomes remains limited, as identifying active degraders without prior genomic knowledge remains a key challenge. Here, we introduce an activity-based fluorescence resonance energy transfer (FRET) probe that enables direct visualization and quantification of glycan metabolism in complex microbial communities. As a proof of concept, we investigated α-mannan degradation, a prominent glycan in algal blooms. Using automated glycan assembly, we synthesized a mannan hexasaccharide bearing a fluorescein–rhodamine FRET pair. The probe was validated using a recombinantly expressed endo-α-mannanase (GH76) from Salegentibacter sp. Hel_I_6. It was shown to function in cell lysates, pure cultures, and complex microbiomes (via plate assays and microscopy). This probe enabled spatiotemporal visualization of in situ α-mannan turnover in a marine microbiome. Glycan FRET probes are versatile tools for tracking glycan degradation across biological scales, from single enzymes to microbiomes.