Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes

Multi-omics analysis of the correlation between surface microbiome and metabolome in Saccharina latissima (Laminariales, Phaeophyceae)

The microbiome of Saccharina latissima, an important brown macroalgal species in Europe, significantly influences its health, fitness, and pathogen resistance. Yet, comprehensive studies on the diversity and function of microbial communities (bacteria, eukaryotes, and fungi) associated with this species are lacking. Using metabarcoding, we investigated the epimicrobiota of S. latissima and correlated microbial diversity with metabolomic patterns (liquid chromatography coupled to tandem mass spectrometry). Specific epibacterial and eukaryotic communities inhabit the S. latissima surface, alongside a core microbiota, while fungal communities show lower and more heterogeneous diversity. Metabolomic analysis revealed a large diversity of mass features, including putatively annotated fatty acids, amino derivatives, amino acids, and naphthofurans. Multiple-factor analysis linked microbial diversity with surface metabolome variations, driven mainly by fungi and bacteria. Two taxa groups were identified: one associated with bacterial consortia and the other with fungal consortia, each correlated with specific metabolites. This study demonstrated a core bacterial and eukaryotic microbiota associated with a core metabolome and highlighted interindividual variations. Annotating the surface metabolome using Natural Products databases suggested numerous metabolites potentially involved in interspecies chemical interactions. Our findings establish a link between microbial community structure and function, identifying two microbial consortia potentially involved in the chemical defense of S. latissima.

Structural characteristics and intestinal flora metabolism mediated immunoregulatory effects of Lactarius deliciosus polysaccharide

Lactarius deliciosus, a widely appreciated mushroom with delightful tastes and texture, has exhibited immunomodulatory activity in vitro, while the effects on intestinal flora metabolisms in vivo are ambiguous. In this study, a L. deliciosus polysaccharide (LDP) was extracted and purified, and the structural characteristics were evaluated, as well as the immunological enhancement on tumor-bearing mice through regulating intestinal flora metabolisms. Results showed that LDP was a heteropolysaccharide (average molecular weight of 1.44 × 107 Da) with a backbone of α-(1 → 6)-Manp and branches of α-(1 → 6)-Galp, α-(1 → 3)-Fucp, α-(1 → 6)-Glcp, α-(1 → 4)-Glcp. Animal experiments indicated that LDP could significantly protect immune organs of tumor-beraing mice and suppress solid tumors growth with inhibitory rate of 51.61 % (high-dose, 100 mg/kg), and improve the intestinal lactobacillus contents, promote adenine mediated zeatin biosynthesis, then competitively antagonize A2A receptor and enhance the activities of CD4+ T cells and CD8+ T cells, finally effectively facilitate the apoptosis and elimination of tumor cells. These results would provide powerful data supports for the further antitumor mechanisms development and practical applications of L. deliciosus polysaccharide in food and drug industries.

Importance of quorum sensing crosstalk in the brown alga Saccharina latissima epimicrobiome

Brown macroalgae are colonized by diverse microorganisms influencing the physiology of their host. However, cell-cell interactions within the surface microbiome (epimicrobiome) are largely unexplored, despite the significance of specific chemical mediators in maintaining host-microbiome homeostasis. In this study, by combining liquid chromatography coupled to mass spectrometry (LC-MS) analysis and bioassays, we demonstrated that the widely diverse fungal epimicrobiota of the brown alga Saccharina latissima can affect quorum sensing (QS), a type of cell-cell interaction, as well as bacterial biofilm formation. We also showed the ability of the bacterial epimicrobiota to form and inhibit biofilm growth, as well as to activate or inhibit QS pathways. Overall, we demonstrate that QS and anti-QS compounds produced by the epimicrobiota are key metabolites in these brown algal epimicrobiota communities and highlight the importance of exploring this epimicrobiome for the discovery of new bioactive compounds, including potentially anti-QS molecules with antifouling properties.

The sugar kelp Saccharina latissima I: recent advances in a changing climate

BACKGROUND

The sugar kelp Saccharina latissima is a Laminariales species widely distributed in the Northern Hemisphere. Its physiology and ecology have been studied since the 1960s, given its ecological relevance on western temperate coasts. However, research interest has been rising recently, driven mainly by reports of negative impacts of anthropogenically induced environmental change and by the increased commercial interest in cultivating the species, with several industrial applications for the resulting biomass.

SCOPE

We used a variety of sources published between 2009 to May 2023 (but including some earlier literature where required), to provide a comprehensive review of the ecology, physiology, biochemical and molecular biology of S. latissima. In so doing we aimed to better understand the species' response to stressors in natural communities, but also inform the sustainable cultivation of the species.

CONCLUSION

Due to its wide distribution, S. latissima has developed a variety of physiological and biochemical mechanisms to adjust to environmental changes, including adjustments in photosynthetic parameters, modulation of osmolytes and antioxidants, reprogramming of gene expression and epigenetic modifications, among others summarized in this review. This is particularly important because massive changes in the abundance and distribution of S. latissima have already been observed. Namely, presence and abundance of S. latissima has significantly decreased at the rear edges on both sides of the Atlantic, and increased in abundance at the polar regions. These changes were mainly caused by climate change and will therefore be increasingly evident in the future. Recent developments in genomics, transcriptomics and epigenomics have clarified the existence of genetic differentiation along its distributional range with implications in the fitness at some locations. The complex biotic and abiotic interactions unraveled here demonstrated the cascading effects the disappearance of a kelp forest can have in a marine ecosystem. We show how S. latissima is an excellent model to study acclimation and adaptation to environmental variability and how to predict future distribution and persistence under climate change.

The effects of Lactobacillus reuteri microcapsules on radiation-induced brain injury by regulating the gut microenvironment

A radiation-induced brain injury (RIBI) is a major adverse event following radiotherapy of malignant tumors. RIBI would affect cognitive function, leading to a series of complications and even death. However, the pathogenesis of RIBI is still unclear, and it still lacks specific therapeutic drugs. The gut-brain bidirectional communication may be mediated by various microbiota and metabolites in the gastrointestinal tract. Probiotics are closely related to physiological health. The theory of the gut-brain axis provides us with a new idea to improve the gut microenvironment by supplementing probiotics against RIBI. Here, Lactobacillus reuteri microcapsules (LMCs) were prepared, which were predominantly irregular spheres with a rough surface under a scanning electron microscope and a narrow size distribution ranging from 20 to 700 μm. The transmission electron microscopy images showed that the structure of microcapsules containing Lactobacillus reuteri (L. reuteri) was a core and shell structure. The survival of L. reuteri in microcapsules was significantly more than that of free L. reuteri in the simulated stomach environment of pH 1.2. 16S rDNA sequencing showed that LMCs observably increased the relative abundance of Lactobacillus in RIBI mice. More importantly, compared with the RIBI model mice, the behavior of RIBI mice treated with LMCs was significantly improved. In addition, LMCs greatly alleviated the pathological damage of the hippocampus and intestines in the mice after irradiation and reduced the level of TNF-α and IL-6 in vivo. Generally, LMCs are a promising oral preparation, which provide new ideas and methods for the treatment of RIBI.

The Saccharina latissima microbiome: Effects of region, season, and physiology

Introduction

Saccharina latissima is a canopy-forming species of brown algae and, as such, is considered an ecosystem engineer. Several populations of this alga are exploited worldwide, and a decrease in the abundance of S. latissima at its southern distributional range limits has been observed. Despite its economic and ecological interest, only a few data are available on the composition of microbiota associated with S. latissima and its role in algal physiologyn.

Methods

We studied the whole bacterial community composition associated with S. latissima samples from three locations (Brittany, Helgoland, and Skagerrak) by 16S metabarcoding analyses at different scales: algal blade part, regions, season (at one site), and algal physiologic state.

Results and Discussion

We have shown that the difference in bacterial composition is driven by factors of decreasing importance: (i) the algal tissues (apex/meristem), (ii) the geographical area, (iii) the seasons (at the Roscoff site), and (iv) the algal host's condition (healthy vs. symptoms). Overall, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia dominated the general bacterial communities. Almost all individuals hosted bacteria of the genus Granulosicoccus, accounting for 12% of the total sequences, and eight additional core genera were identified. Our results also highlight a microbial signature characteristic for algae in poor health independent of the disease symptoms. Thus, our study provides a comprehensive overview of the S. latissima microbiome, forming a basis for understanding holobiont functioning.

DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes

DNA extraction and preservation bias is a recurring topic in DNA sequencing-based microbial ecology. The different methodologies can lead to distinct outcomes, which has been demonstrated especially in studies investigating prokaryotic community composition. Eukaryotic microbes are ubiquitous, diverse, and increasingly a subject of investigation in addition to bacteria and archaea. However, little is known about how the choice of DNA preservation and extraction methodology impacts perceived eukaryotic community composition. In this study, we compared the effect of two DNA preservation methods and six DNA extraction methods on the community profiles of both eukaryotes and prokaryotes in phototrophic biofilms on seagrass (Zostera marina) leaves from the Baltic Sea. We found that, whereas both DNA preservation and extraction method caused significant bias in perceived community composition for both eukaryotes and prokaryotes, extraction bias was more pronounced for eukaryotes than for prokaryotes. In particular, soft-bodied and hard-shelled eukaryotes like nematodes and diatoms, respectively, were differentially abundant depending on the extraction method. We conclude that careful consideration of DNA preservation and extraction methodology is crucial to achieving representative community profiles of eukaryotes in marine biofilms and likely all other habitats containing diverse eukaryotic microbial communities.