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Plant microbiomes are known to serve several important functions for their host, and it is therefore important to understand their composition as well as the factors that may influence these microbial communities. The microbiome of Thalassia testudinum has only recently been explored, and studies to-date have primarily focused on characterizing the microbiome of plants in a single region. Here, we present the first characterization of the composition of the microbial communities of T. testudinum across a wide geographical range spanning three distinct regions with varying physicochemical conditions. We collected samples of leaves, roots, sediment, and water from six sites throughout the Atlantic Ocean, Caribbean Sea, and the Gulf of Mexico. We then analyzed these samples using 16S rRNA amplicon sequencing. We found that site and region can influence the microbial communities of T. testudinum, while maintaining a plant-associated core microbiome. A comprehensive comparison of available microbial community data from T. testudinum studies determined a core microbiome composed of 14 ASVs that consisted mostly of the family Rhodobacteraceae. The most abundant genera in the microbial communities included organisms with possible plant-beneficial functions, like plant-growth promoting taxa, disease suppressing taxa, and nitrogen fixers.

Abstract Using the Mediterranean coral Balanophyllia europaea naturally growing along a pH gradient close to Panarea island (Italy) as a model, we explored the role of host-associated microbiomes in coral acclimatization to ocean acidification (OA). Coral samples were collected at three sites along the gradient, mimicking seawater conditions projected for 2100 under different IPCC (The Intergovernmental Panel on Climate Change) scenarios, and mucus, soft tissue and skeleton associated microbiomes were characterized by shotgun metagenomics. According to our findings, OA induced functional changes in the microbiomes genetic potential that could mitigate the sub-optimal environmental conditions at three levels: i. selection of bacteria genetically equipped with functions related to stress resistance; ii. shifts in microbial carbohydrate metabolism from energy production to maintenance of cell membranes and walls integrity; iii. gain of functions able to respond to variations in nitrogen needs at the holobiont level, such as genes devoted to organic nitrogen mobilization. We hence provided hypotheses about the functional role of the coral associated microbiome in favoring host acclimatation to OA, remarking on the importance of considering the crosstalk among all the components of the holobiont to unveil how and to what extent corals will maintain their functionality under forthcoming ocean conditions.

Against the accelerating pace of worldwide species extinction, reliable biodiversity assessments are critical, both as baselines and to track potential declines. DNA metabarcoding techniques allow for fast and comprehensive assessment of biodiversity in both terrestrial and marine habitats. However, these methods need to be adapted and standardised for each ecosystem in order to be effective. Seagrass meadows are among the most diverse marine habitats and are irreplaceable in terms of the ecosystem services they provide, yet metabarcoding has never been implemented for these systems. In this study, we developed and tested a protocol for metabarcoding the eukaryotic community of meadows of the iconic species, Posidonia oceanica L. (Delile). This seagrass is the main habitat-forming species in Mediterranean coastal waters and is known for its high diversity due to the structural complexity of its canopy and rhizome structures. This habitat is experiencing a range-wide retreat, and there is an urgent need for fast and efficient methods for its biomonitoring and detection of early changes. Our proposed method involves direct sampling of the community, collecting and processing the leaves and rhizome strata separately. To test the utility of the method in distinguishing between different meadow conditions, we sampled two distinct meadows that differ in their prevailing wind and surge conditions, and a nearby rocky reef for comparison. We then adapted a method and pipeline for COI metabarcoding using generalist primers that target the eukaryote diversity present. We detected a high diversity in the two meadows analysed (3,350 molecular operational taxonomic units, dominated by Metazoa and Archaeplastida) and a clear differentiation of the seagrass samples from those of the nearby rocky reefs. The leaves and rhizomes harboured clearly distinct assemblages, and differences were also detected between the two meadows sampled. This new tool has the potential to deliver big biodiversity data for seagrass habitats in a fast and efficient way, which is crucial for the implementation of protection and management measures for this key coastal habitat.

Climate change is impacting marine ecosystem community dynamics on a global scale. While many have assessed direct effects of climate change, indirect effects on marine ecosystems produced by biotic interactions remain poorly understood. For example, warming-induced range expansions and increased consumption rates of herbivores can lead to significant and unexpected changes in seagrass-dominated ecosystems. To better understand the threats tropicalization presents for the functioning of turtlegrass (Thalassia testudinum) meadows, we focused on the extensive turtlegrass beds of St. Joseph Bay, Florida in the northern Gulf of Mexico, a location with increasing numbers of tropically-associated green turtles. Our goals were to investigate experimentally how different grazing rates (natural and simulated),including high levels reflective of green turtle herbivory, coupled with nutrient supply, might alter turtlegrass structure and functioning in a higher latitude, subtropical turtlegrass meadow. We found that 4 months of varying levels of herbivory did not affect turtlegrass productivity, while 7 months of herbivory reduced percent cover, and 10 months reduced shoot density. Nutrient additions had few important effects. Ten months into the study, a massive recruitment of the herbivorous sea urchin (Lytechinus variegatus), whose densities reached 19 urchins/m2 completely overgrazed our study area and a large portion of the lush turtlegrass meadows of St. Joseph Bay. While local turtlegrass overgrazing had been previously noted at these urchin densities, a total loss of seagrass in such a large area has rarely ever been recorded. Overgrazing of the kind we observed, likely a result of both urchin and increasing green turtle grazing, can result in the loss of many key ecosystem services. As tropicalization continues, understanding how changes in biotic interactions, such as increased herbivory, affect higher latitude seagrass meadows will be necessary for their proper management and conservation.

Seagrasses worldwide provide key habitats for fish assemblages. Biogeographical disparities in ocean climate conditions and seasonal regimes are well-known drivers of the spatial and temporal variation in seagrass structure, with potential effects on associated fish assemblages. Whether taxonomically disparate fish assemblages support a similar range of ecological functions remains poorly tested in seagrass ecosystems. In this study, we examined variation in the abundance, diversity (from a taxonomic and functional perspective), and assemblage structure of fish community inhabiting nine meadows of the seagrass Cymodocea nodosa across three regions in the Mediterranean (Mallorca and Alicante) and the adjacent Atlantic (Gran Canaria), and identified which attributes typifying the structure of meadows, and large-scale variability in ocean climate, contributed most to explaining such ecological variation. Despite a similar total number of species between Mallorca and Gran Canaria, the latter region had more taxonomically and functionally diverse fish assemblages relative to the western Mediterranean regions, which translated into differences in multivariate assemblage structure. While variation in the abundance of the most conspicuous fish species was largely explained by variation in seagrass structural descriptors, most variation in diversity was accounted for by a descriptor of ocean climate (mean seasonal SST), operating at regional scales. Variation in fish assemblage structure was, to a lesser extent, also explained by local variability in seagrass structure. Beyond climatic drivers, our results suggest that lower temporal variability in the canopy structure of C. nodosa meadows in Gran Canaria provides a more consistent source of food and protection for associated fish assemblages, which likely enhances the more abundant and diverse fish assemblages there.

The fish Sarpa salpa (L.) is one of the main macroherbivores in the western Mediterranean. Through direct and indirect mechanisms, this herbivore can exert significant control on the structure and functional dynamics of seagrass beds and macroalgae. Past research has suggested nutritional quality of their diet influences S. salpa herbivory, with the fish feeding more intensively and exerting greater top down control on macrophytes with higher internal nutrient contents. However recent findings have questioned this notion and shown that herbivores do not preferentially feed on macrophytes with higher nutrient contents, but rather feed on a wide variety of them with no apparent selectivity. To contribute to this debate, we conducted a field fertilization experiment where we enriched leaves of the seagrass Posidonia oceanica, a staple diet for S. salpa, and examined the response by the herbivore. These responses included quantification of leaf consumption in fertilized and non-fertilized/control plots within the bed, and food choice assays where fertilized and non-fertilized/control leaves were simultaneously offered to the herbivore. Despite the duration of leaf exposure to herbivores (30 days) and abundant schools of S. salpa observed around the plots, leaf consumption was generally low in the plots examined. Consumption was not higher on fertilized than on non-fertilized leaves. Food choice experiments did not show strong evidence for selectivity of enriched leaves. These results add to a recent body of work reporting a broad generalist feeding behavior by S. salpa with no clear selectivity for seagrass with higher nutrient content. In concert, this and other studies suggest S. salpa is often generalist consumers not only dictated by diet nutrient content but by complex interactions between other traits of nutritional quality, habitat heterogeneity within their ample foraging area, and responses to predation risk.

Abstract Background The vaginal microbiota of healthy women consists of a wide variety of anaerobic and aerobic bacterial genera and species dominated by the genus Lactobacillus. The activity of lactobacilli helps to maintain the natural healthy balance of the vaginal microbiota. This role is particularly important during pregnancy because vaginal dismicrobism is one of the most important mechanisms for preterm birth and perinatal complications. In the present study, we characterized the impact of a dietary supplementation with the probiotic VSL#3, a mixture of Lactobacillus, Bifidobacterium and Streptococcus strains, on the vaginal microbiota and immunological profiles of healthy women during late pregnancy. Results An association between the oral intake of the probiotic VSL#3 and changes in the composition of the vaginal microbiota of pregnant women was revealed by PCR-DGGE population profiling. Despite no significant changes were found in the amounts of the principal vaginal bacterial populations in women administered with VSL#3, qPCR results suggested a potential role of the probiotic product in counteracting the decrease of Bifidobacterium and the increase of Atopobium, that occurred in control women during late pregnancy. The modulation of the vaginal microbiota was associated with significant changes in some vaginal cytokines. In particular, the decrease of the anti-inflammatory cytokines IL-4 and IL-10 was observed only in control women but not in women supplemented with VSL#3. In addition, the probiotic consumption induced the decrease of the pro-inflammatory chemokine Eotaxin, suggesting a potential anti-inflammatory effect on the vaginal immunity. Conclusion Dietary supplementation with the probiotic VSL#3 during the last trimester of pregnancy was associated to a modulation of the vaginal microbiota and cytokine secretion, with potential implications in preventing preterm birth. Trial registration ClinicalTrials.gov NCT01367470

Abstract Background Playing a strategic role in the host immune function, the intestinal microbiota has been recently hypothesized to be involved in the etiology of atopy. In order to investigate the gastrointestinal microbial ecology of atopic disease, here we performed a pilot comparative molecular analysis of the faecal microbiota in atopic children and healthy controls. Results Nineteen atopic children and 12 healthy controls aged 4–14 years were enrolled. Stools were collected and the faecal microbiota was characterized by means of the already developed phylogenetic microarray platform, HTF-Microbi.Array, and quantitative PCR. The intestinal microbiota of atopic children showed a significant depletion in members of the Clostridium cluster IV, Faecalibacterium prausnitzii, Akkermansia muciniphila and a corresponding increase of the relative abundance of Enterobacteriaceae. Conclusion Depleted in key immunomodulatory symbionts, the atopy-associated microbiota can represent an inflammogenic microbial consortium which can contribute to the severity of the disease. Our data open the way to the therapeutic manipulation of the intestinal microbiota in the treatment of atopy by means of pharmaceutical probiotics.

Abstract Background Affecting the core functional microbiome, peculiar high level taxonomic unbalances of the human intestinal microbiota have been recently associated with specific diseases, such as obesity, inflammatory bowel diseases, and intestinal inflammation. Results In order to specifically monitor microbiota unbalances that impact human physiology, here we develop and validate an original DNA-microarray (HTF-Microbi.Array) for the high taxonomic level fingerprint of the human intestinal microbiota. Based on the Ligase Detection Reaction-Universal Array (LDR-UA) approach, the HTF-Microbi.Array enables specific detection and approximate relative quantification of 16S rRNAs from 30 phylogenetically related groups of the human intestinal microbiota. The HTF-Microbi.Array was used in a pilot study of the faecal microbiota of eight young adults. Cluster analysis revealed the good reproducibility of the high level taxonomic microbiota fingerprint obtained for each of the subject. Conclusion The HTF-Microbi.Array is a fast and sensitive tool for the high taxonomic level fingerprint of the human intestinal microbiota in terms of presence/absence of the principal groups. Moreover, analysis of the relative fluorescence intensity for each probe pair of our LDR-UA platform can provide estimation of the relative abundance of the microbial target groups within each samples. Focusing the phylogenetic resolution at division, order and cluster levels, the HTF-Microbi.Array is blind with respect to the inter-individual variability at the species level.

Abstract Background The human gut harbors a diverse community of microorganisms which serve numerous important functions for the host wellbeing. Functional foods are commonly used to modulate the composition of the gut microbiota contributing to the maintenance of the host health or prevention of disease. In the present study, we characterized the impact of one month intake of a synbiotic food, containing fructooligosaccharides and the probiotic strains Lactobacillus helveticus Bar13 and Bifidobacterium longum Bar33, on the gut microbiota composition and metabolic profiles of 20 healthy subjects. Results The synbiotic food did not modify the overall structure of the gut microbiome, as indicated by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The ability of the probiotic L. helveticus and B. longum strains to pass through the gastrointestinal tract was hypothesized on the basis of real-time PCR data. In spite of a stable microbiota, the intake of the synbiotic food resulted in a shift of the fecal metabolic profiles, highlighted by the Gas Chromatography Mass Spectrometry Solid Phase Micro-Extraction (GC-MS/SPME) analysis. The extent of short chain fatty acids (SCFA), ketones, carbon disulfide and methyl acetate was significantly affected by the synbiotic food consumption. Furthermore, the Canonical discriminant Analysis of Principal coordinates (CAP) of GC-MS/SPME profiles allowed a separation of the stool samples recovered before and after the consumption of the functional food. Conclusion In this study we investigated the global impact of a dietary intervention on the gut ecology and metabolism in healthy humans. We demonstrated that the intake of a synbiotic food leads to a modulation of the gut metabolic activities with a maintenance of the gut biostructure. In particular, the significant increase of SCFA, ketones, carbon disulfide and methyl acetate following the feeding period suggests potential health promoting effects of the synbiotic food.

Abstract Background Lactic acid bacteria of the genus Lactobacillus and Bifidobacterium are one of the most important health promoting groups of the human intestinal microbiota. Their protective role within the gut consists in out competing invading pathogens for ecological niches and metabolic substrates. Among the features necessary to provide health benefits, commensal microorganisms must have the ability to adhere to human intestinal cells and consequently to colonize the gut. Studies on mechanisms mediating adhesion of lactobacilli to human intestinal cells showed that factors involved in the interaction vary mostly among different species and strains, mainly regarding interaction between bacterial adhesins and extracellular matrix or mucus proteins. We have investigated the adhesive properties of Lactobacillus plantarum, a member of the human microbiota of healthy individuals. Results We show the identification of a Lactobacillus plantarum LM3 cell surface protein (48 kDa), which specifically binds to human fibronectin (Fn), an extracellular matrix protein. By means of mass spectrometric analysis this protein was identified as the product of the L. plantarum enoA1 gene, coding the EnoA1 alfa-enolase. Surface localization of EnoA1 was proved by immune electron microscopy. In the mutant strain LM3-CC1, carrying the enoA1 null mutation, the 48 kDa adhesin was not anymore detectable neither by anti-enolase Western blot nor by Fn-overlay immunoblotting assay. Moreover, by an adhesion assay we show that LM3-CC1 cells bind to fibronectin-coated surfaces less efficiently than wild type cells, thus demonstrating the significance of the surface displaced EnoA1 protein for the L. plantarum LM3 adhesion to fibronectin. Conclusion Adhesion to host tissues represents a crucial early step in the colonization process of either pathogens or commensal bacteria. We demonstrated the involvement of the L. plantarum Eno A1 alfa-enolase in Fn-binding, by studying LM3 and LM3-CC1 surface proteins. Isolation of LM3-CC1 strain was possible for the presence of expressed enoA2 gene in the L. plantarum genome, giving the possibility, for the first time to our knowledge, to quantitatively compare adhesion of wild type and mutant strain, and to assess doubtless the role of L. plantarum Eno A1 as a fibronectin binding protein.

Hemp seed flour (Cannabis sativa) is a non-traditional matrix alternative to wheat for baked goods production. The aim of this study was to investigate the microbiota of two liquid sourdoughs (SLs) based on hemp or a wheat–hemp mixture, before and after spontaneous or piloted fermentation (Lactiplantibacillus plantarum ITM21B or Weissella cibaria C43-11 used as starters). Culture-dependent and -independent (high-throughput sequencing of bacterial phylogenetic V3-V4 regions of the 16S rRNA gene) methods, were used to evaluate the microbial community. The effect of fermentation on the content of bioactive molecules (polyphenols, organic acids, proteins, and amino acids) was also investigated. Results indicated that the microbial community of all SLs was mainly (99.7 ÷ 100%) composed of Firmicutes and Proteobacteria, and the latter was the unique phylum before fermentation in formulations produced exclusively with hemp flour. Two PCoA plots (Test adonis with pseudo-F ratio, p > 0.05) showed no significance difference between the microbial communities of the formulations. However, the relative abundance variation at the family level in the wheat–hemp-based mixture SLs showed a significant enrichment of the Lactobacillaceae family (Kruskal–Wallis test, p = 0.04). Moreover, results confirmed hemp seed flour as a suitable fermentation substrate to obtain microbial consortia allowing for an increase in organic acids, especially lactic acid (9.12 ± 1.22 and 7.45 ± 0.75 mmol/kg with Lpb. plantarum and W. cibaria, respectively), in both piloted fermentations, and in polyphenols by 21% and amino acids by 158% in SL fermented by the C43-11 strain. [ABSTRACT FROM AUTHOR]