The complex interactions between epiphytic bacteria and marine macroalgae are still poorly understood, with limited knowledge about their community structure, interactions, and functions. This study focuses on comparing epiphytic prokaryotes community structure between three seaweed phyla; Chlorophyta, Rhodophyta, and Heterokontophyta in an easternmost rocky intertidal site of the Mediterranean Sea. By taking a snapshot approach and simultaneously collecting seaweed samples from the same habitat, we minimize environmental variations that could affect epiphytic bacterial assembly, thereby emphasizing host specificity. Through 16S rRNA gene amplicon sequencing, we identified that the microbial community composition was more similar within the same seaweed phylum host compared to seaweed host from other phyla. Furthermore, exclusive Amplicon Sequence Variants (ASVs) were identified for each algal phyla despite sharing higher taxonomic classifications across the other phyla. Analysis of niche breadth indices uncovers distinctive affinities and potential specialization among seaweed host phyla, with 39% of all ASVs identified as phylum specialists and 13% as generalists. Using taxonomy function prediction, we observed that the taxonomic variability does not significantly impact functional redundancy, suggesting resilience to disturbance. The study concludes that epiphytic bacteria composition is connected to host taxonomy, possibly influenced by shared morphological and chemical traits among genetically related hosts, implying a potential coevolutionary relationship between specific bacteria and their host seaweeds.

Acute environmental changes cause stress during conventional deep-sea biological sampling without in situ fixation and affect gene expressions of samples collected. However, the degree of influence and underlying mechanisms are hardly investigated. Here, we conducted comparative transcriptomic analyses between in situ and onboard fixed gills and between in situ and onboard fixed mantles of deep-sea mussel Gigantidas haimaensis to assess the effects of incidental sampling stress. Results showed that transcription, translation, and energy metabolism were upregulated in onboard fixed gills and mantles, thereby mobilizing rapid gene expression to tackle the stress. Autophagy and phagocytosis that related to symbiotic interactions between the host and endosymbiont were downregulated in the onboard fixed gills. These findings demonstrated that symbiotic gill and nonsymbiotic mantle responded differently to sampling stress, and symbiosis in the gill was perturbed. Further comparative metatranscriptomic analysis between in situ and onboard fixed gills revealed that stress response genes, peptidoglycan biosynthesis, and methane fixation were upregulated in the onboard fixed endosymbiotic Gammaproteobacteria inside the gills, implying that energy metabolism of the endosymbiont was increased to cope with sampling stress. Furthermore, comparative analysis between the mussel G. haimaensis and the limpet Bathyacmaea lactea transcriptomes resultedidentified six transcription factor orthologs upregulated in both onboard fixed mussel mantles and limpets, including sharply increased early growth response protein 1 and Kruppel-like factor 5. They potentially play key roles in initiating the response of sampled deep-sea macrobenthos to sampling stress. Our results clearly show that in situ fixed biological samples are vital for studying deep-sea environmental adaptation.

Organisms are now seen as holobionts, consortia of several species that interact metabolically such that they sustain and scaffold each other\'s existence and propagation. Sympoiesis, the development of the symbiotic relationships that form holobionts, is critical for our understanding the origins and maintenance of biodiversity. Rather than being the read-out of a single genome, development has been found to be sympoietic, based on multigenomic interactions between zygote-derived cells and symbiotic microbes. These symbiotic and sympoietic interactions are predicated on the ability of cells from different kingdoms of life (e.g., bacteria and animals) to communicate with one another and to have their chemical signals interpreted in a manner that facilitates development. Sympoiesis, the creation of an entity by the interactions of other entities, is commonly seen in embryogenesis (e.g., the creation of lenses and retinas through the interaction of brain and epidermal compartments). In holobiont sympoiesis, interactions between partners of different domains of life interact to form organs and biofilms, wherein each of these domains acts as the environment for the other. If evolution is forged by changes in development, and if symbionts are routinely involved in our development, then changes in sympoiesis can constitute an important factor in evolution.

Food webs are typically defined as being macro-organism-based (e.g., plants, mammals, birds) or microbial (e.g., bacteria, fungi, viruses). However, these characterizations have limits. We propose a multilayered food web conceptual model where microbial food webs are nested within food webs composed of macro-organisms. Nesting occurs through host-microbe interactions, which influence the health and behavior of host macro-organisms, such that host microbiomes likely alter population dynamics of interacting macro-organisms and vice versa. Here, we explore the theoretical underpinnings of multilayered food webs and the implications of this new conceptual model on food web ecology. Our framework opens avenues for new empirical investigations into complex ecological networks and provides a new lens through which to view a network\'s response to ecosystem changes.

BACKGROUND: Population stratification based on interindividual variability in gut microbiota composition has revealed the existence of several ecotypes named enterotypes in humans and various animal species. Enterotypes are often associated with environmental factors including diet, but knowledge of the role of host genetics remains scarce. Moreover, enterotypes harbor functionalities likely associated with varying abilities and susceptibilities of their host. Previously, we showed that under controlled conditions, 60-day-old pig populations consistently split into two enterotypes with either Prevotella and Mitsuokella (PM enterotype) or Ruminococcus and Treponema (RT enterotype) as keystone taxa. Here, our aim was to rely on pig as a model to study the influence of host genetics to assemble enterotypes, and to provide clues on enterotype functional differences and their links with growth traits.
RESULTS: We established two pig lines contrasted for abundances of the genera pairs specifying each enterotype at 60 days of age and assessed them for fecal microbiota composition and growth throughout three consecutive generations. Response to selection across three generations revealed, per line, an increase in the prevalence of the selected enterotype and in the average relative abundances of directly and indirectly selected bacterial genera. The PM enterotype was found less diverse than the RT enterotype but more efficient for piglet growth during the post-weaning period. Shotgun metagenomics revealed differentially abundant bacterial species between the two enterotypes. By using the KEGG Orthology database, we show that functions related to starch degradation and polysaccharide metabolism are enriched in the PM enterotype, whereas functions related to general nucleoside transport and peptide/nickel transport are enriched in the RT enterotype. Our results also suggest that the PM and RT enterotypes might differ in the metabolism of valine, leucin, and isoleucine, favoring their biosynthesis and degradation, respectively.
CONCLUSIONS: We experimentally demonstrated that enterotypes are functional ecosystems that can be selected as a whole by exerting pressure on the host genetics. We also highlight that holobionts should be considered as units of selection in breeding programs. These results pave the way for a holistic use of host genetics, microbiota diversity, and enterotype functionalities to understand holobiont shaping and adaptation. Video Abstract.

The coral holobiont is underpinned by complex metabolic exchanges between different symbiotic partners, which are impacted by environmental stressors. The chemical diversity of the compounds produced by the holobiont is high and includes primary and secondary metabolites, as well as volatiles. However, metabolites and volatiles have only been characterised in isolation so far. Here, we applied a paired metabolomic-volatilomic approach to characterise holistically the chemical response of the holobiont under stress. Montipora mollis fragments were subjected to high-light stress (8-fold higher than the controls) for 30 min. Photosystem II (PSII) photochemical efficiency values were 7-fold higher in control versus treatment corals immediately following high-light exposure, but returned to pre-stress levels after 30 min of recovery. Under high-light stress, we identified an increase in carbohydrates (> 5-fold increase in arabinose and fructose) and saturated fatty acids (7-fold increase in myristic and oleic acid), together with a decrease in fatty acid derivatives in both metabolites and volatiles (e.g., 80% decrease in oleamide and nonanal), and other antioxidants (~ 85% decrease in sorbitol and galactitol). These changes suggest short-term light stress induces oxidative stress. Correlation analysis between volatiles and metabolites identified positive links between sorbitol, galactitol, six other metabolites and 11 volatiles, with four of these compounds previously identified as antioxidants. This suggests that these 19 compounds may be related and share similar functions. Taken together, our findings demonstrate how paired metabolomics-volatilomics may illuminate broader metabolic shifts occurring under stress and identify linkages between uncharacterised compounds to putatively determine their functions.

BACKGROUND: Sponge-associated bacteria play important roles in the physiology of their host, whose recruitment processes are crucial to maintain symbiotic associations. However, the acquisition of bacterial communities within freshwater sponges is still under explored. Spongilla lacustris is a model sponge widely distributed in European rivers and lakes, producing dormant cysts (named gemmules) for their asexual reproduction, before winter. Through an in vitro experiment, this study aims to describe the dynamics of bacterial communities and their transmission modes following the hatching of these gemmules.
RESULTS: An overall change of bacterial β-diversity was observed through the ontology of the juvenile sponges. These temporal differences were potentially linked, first to the osculum acquisition and the development of a canal system, and then, the increasing colonization of the Chlorella-like photosymbionts. Gemmules hatching with a sterilized surface were found to have a more dispersed and less diverse microbiome, revealing the importance of gemmule epibacteria for the whole holobiont stability. These epibacteria were suggested to be vertically transmitted from the maternal tissues to the gemmule surface. Vertical transmission through the incorporation of bacterial communities inside of the gemmule, was also found as a dominant transmission mode, especially with the nitrogen fixers Terasakiellaceae. Finally, we showed that almost no ASVs were shared between the free-living community and the juveniles, suggesting that horizontal recruitment is unlikely to happen during the first stages of development. However, the free-living bacteria filtered are probably used as a source of nutrients, allowing an enrichment of copiotrophic bacteria already present within its microbiome.
CONCLUSIONS: This study brings new insight for a better understanding of the microbiome acquisition during the first stages of freshwater sponge development. We showed the importance of epibacterial communities on gemmules for the whole holobiont stability, and demonstrated the near absence of recruitment of free-living bacteria during the first stages.

Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute to their adaptation to changing environmental conditions. However, yeast and bacterial microbiota have usually been studied separately; therefore, the interaction between bacterial and yeast communities in the gut of Drosophila melanogaster (D. melanogaster) is often overlooked. In this study, we investigate the correlation between bacterial and yeast communities in the gut of D. melanogaster. Methods: We studied the shifts in the joint microbiome of Drosophila melanogaster, encompassing both yeasts and bacteria, during adaptation to substrate with varying salt concentrations (0%, 2%, 4%, and 7%) using plating for both yeasts and bacteria and NGS-sequencing of variable 16S rRNA gene regions for bacteria. Results: The microbiome of flies and their substrates was gradually altered at moderate NaCl concentrations (2% and 4% compared with the 0% control) and completely transformed at high salt concentrations (7%). The relative abundance of Acetobacter, potentially beneficial to D. melanogaster, decreased as NaCl concentration increased, whereas the relative abundance of the more halotolerant lactobacilli first increased, peaking at 4% NaCl, and then declined dramatically at 7%. At this salinity level, potentially pathogenic bacteria of the genera Leuconostoc and Providencia were dominant. The yeast microbiome of D. melanogaster also undergoes significant changes with an increase in salt concentration in the substrate. The total yeast abundance undergoes nonlinear changes: it is lowest at 0% salt concentration and highest at 2%-4%. At a 7% concentration, the yeast abundance in flies and their substrate is lower than at 2%-4% but significantly higher than at 0%. Conclusions: The abundance and diversity of bacteria that are potentially beneficial to the flies decreased, while the proportion of potential pathogens, Leuconostoc and Providencia, increased with an increase in salt concentration in the substrate. In samples with a relatively high abundance and/or diversity of yeasts, the corresponding indicators for bacteria were often lowered, and vice versa. This may be due to the greater halotolerance of yeasts compared to bacteria and may also indicate antagonism between these groups of microorganisms.

Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals\' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.

The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.