Mono-specific algal diets shape microbial networking in the gut of the sea urchin Tripneustes gratilla elatensis

Habitat specificity modulates the bacterial biogeographic patterns in the Southern Ocean

Conceptual biogeographic frameworks have proposed that the relative contribution of environmental and geographical factors on microbial distribution depends on several characteristics of the habitat (e.g. environmental heterogeneity, species diversity, and proportion of specialist/generalist taxa), all of them defining the degree of habitat specificity, but few experimental demonstrations exist. Here, we aimed to determine the effect of habitat specificity on bacterial biogeographic patterns and assembly processes in benthic coastal ecosystems of the Southern Ocean (Patagonia, Falkland/Malvinas, Kerguelen, South Georgia, and King George Islands), using 16S rRNA gene metabarcoding. The gradient of habitat specificity resulted from a 'natural experimental design' provided by the Abatus sea urchin model, from the sediment (least specific habitat) to the intestinal tissue (most specific habitat). The phylogenetic composition of the bacterial communities showed a clear differentiation by site, driven by a similar contribution of geographic and environmental distances. However, the strength of this biogeographic pattern decreased with increasing habitat specificity: sediment communities showed stronger geographic and environmental divergence compared to gut tissue. The proportion of stochastic and deterministic processes contributing to bacterial assembly varied according to the geographic scale and the habitat specificity level. For instance, an increased contribution of dispersal limitation was observed in gut tissue habitat. Our results underscore the importance of considering different habitats with contrasting levels of specificity to better understand bacterial biogeography and assembly processes over oceanographic scales.

Taxonomic Diversity, Predicted Metabolic Pathway, and Interaction Pattern of Bacterial Community in Sea Urchin Anthocidaris crassispina

Bacterial assemblages associated with sea urchin are critical to their physiology and ecology within marine ecosystems. In this study, we characterized the bacterial communities in wild sea urchin Anthocidaris crassispina captured in Daya Bay, South China Sea. A total of 363 amplicon sequence variants belonging to nine phyla and 141 genera were classified from intestine, body surface, and surrounding seawater samples. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacteria phyla found in this study. A network analysis of bacterial interspecies interactions revealed varying complexity, stability, connectivity, and relationship patterns across the samples, with the most intricate network observed in the surrounding seawater. Metagenomic predictions highlighted the distinct bacterial metabolic pathways, with significant differences between intestine and seawater samples. Notably, pathways associated with polysaccharide degradation, including chitin derivatives, starch, and CoM biosynthesis, were markedly abundant, underscoring the gut microbiota's key role in digesting algae. In addition, other metabolic pathways in intestine samples were linked to immune response regulation of sea urchins. Overall, this study provides a comprehensive overview of the bacterial community structure and potential functional roles in A. crassispina.

The green seaweed Ulva: tomorrow's "wheat of the sea" in foods, feeds, nutrition, and biomaterials

Ulva, a genus of green macroalgae commonly known as sea lettuce, has long been recognized for its nutritional benefits for food and feed. As the demand for sustainable food and feed sources continues to grow, so does the interest in alternative, plant-based protein sources. With its abundance along coastal waters and high protein content, Ulva spp. have emerged as promising candidates. While the use of Ulva in food and feed has its challenges, the utilization of Ulva in other industries, including in biomaterials, biostimulants, and biorefineries, has been growing. This review aims to provide a comprehensive overview of the current status, challenges and opportunities associated with using Ulva in food, feed, and beyond. Drawing on the expertise of leading researchers and industry professionals, it explores the latest knowledge on Ulva's nutritional value, processing methods, and potential benefits for human nutrition, aquaculture feeds, terrestrial feeds, biomaterials, biostimulants and biorefineries. In addition, it examines the economic feasibility of incorporating Ulva into aquafeed. Through its comprehensive and insightful analysis, including a critical review of the challenges and future research needs, this review will be a valuable resource for anyone interested in sustainable aquaculture and Ulva's role in food, feed, biomaterials, biostimulants and beyond.

Alterations in sea urchin (Mesocentrotus nudus) microbiota and their potential contributions to host according to barren severity

Sea urchins are biotic factors driving the decline of kelp forests in marine ecosystems. However, few studies have analyzed the microbiota of surviving sea urchins in barren regions with scarce diet resources. Here, we analyzed the microbiota in the pharynx and gut of the sea urchin Mesocentrotus nudus located along the coast of an expanding barren region in South Korea. The ecological adaptation of genera in sea urchins was predicted using the neutral assembly model. The pharynx and gut microbiota were different, and microbes in the surrounding habitats dispersed more to the pharynx than to the gut. The gut microbiota in sea urchins is altered by barren severity and plays different roles in host energy metabolism. These findings help to understand the microbiota in sea urchins according to urchin barren and its contribution to the survival of sea urchins in severe barren regions with limited macroalgae.

Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin

Dietary influence on the microbiome in algivorous sea urchins such as Tripneustes gratilla elatensis suggests a bacterial contribution to the digestion of fiber-rich seaweed. An ecological insight into the spatial arrangement in the gut bacterial community will improve our knowledge of host-microbe relations concerning the involved taxa, their metabolic repertoire, and the niches of activity. Toward this goal, we investigated the bacterial communities in the esophagus, stomach, and intestine of Ulva-fed sea urchins through 16S rRNA amplicon sequencing, followed by the prediction of their functional genes. We revealed communities with distinct features, especially those in the esophagus and intestine. The esophageal community was less diverse and was poor in food digestive or fermentation genes. In contrast, bacteria that can contribute to the digestion of the dietary Ulva were common in the stomach and intestine and consisted of genes for carbohydrate decomposition, fermentation, synthesis of short-chain fatty acids, and various ways of N and S metabolism. Bacteroidetes and Firmicutes were found as the main phyla in the gut and are presumably also necessary in food digestion. The abundant sulfate-reducing bacteria in the stomach and intestine from the genera Desulfotalea, Desulfitispora, and Defluviitalea may aid in removing the excess sulfate from the decomposition of the algal polysaccharides. Although these sea urchins were fed with Ulva, genes for the degradation of polysaccharides of other algae and plants were present in this sea urchin gut microbiome. We conclude that the succession of microbial communities along the gut obtained supports the hypothesis on bacterial contribution to food digestion. IMPORTANCE Alga grazing by the sea urchin Tripneustes gratilla elatensis is vital for nutrient recycling and constructing new reefs. This research was driven by the need to expand the knowledge of bacteria that may aid this host in alga digestion and their phylogeny, roles, and activity niches. We hypothesized alterations in the bacterial compositional structure along the gut and their association with the potential contribution to food digestion. The current spatial insight into the sea urchin's gut microbiome ecology is novel and reveals how distinct bacterial communities are when distant from each other in this organ. It points to keynote bacteria with genes that may aid the host in the digestion of the complex sulfated polysaccharides in dietary Ulva by removing the released sulfates and fermentation to provide energy. The gut bacteria's genomic arsenal may also help to gain energy from diets of other algae and plants.

Ecological insights into the resilience of marine plastisphere throughout a storm disturbance

Among numerous research about marine plastisphere, the community living on the surface of plastic debris, little attention was given to the ecological mechanisms governing prokaryotes compared to eukaryotes, and even less focused on their resilience in a changing climate with more storm prevalence. Our current research recruited an integrated approach involving community succession across temporal dimension, ecological mechanisms that govern the assembly, and resilience to environmental perturbations to highlight the ecology of different kingdoms in the plastisphere. Towards this goal, we examined the succession of the prokaryotic and eukaryotic communities on artificial plastic nets in a sidestream of seawater from the Gulf of Aqaba over 35 days. A robust local storm enabled investigation of the alterations before, during, and after this disturbance, aiming at the community's potential to recover. Data from 16S and 18S rRNA sequencing and microscopic analyses decrypted the plastisphere diversity, community assembly, and stochasticity, followed by further analyses of functional and co-occurrence networks for the prokaryotic group. Prokaryotic and eukaryotic communities underwent exact opposite ecological mechanisms. While determinism driven by a robust environmental selection dictated the prokaryotic community assembly, stochasticity prevailed when this condition was relaxed. Interestingly, resilience against disturbance was observed in prokaryotes but not in eukaryotes. The decrease in compositional, functional diversity and network complexity in the prokaryotic community was reversed, presumably due to the niche specification process and high dispersal. Niche specification following perturbation was evident in some bacteria by selected functions associated with plastic degradation, stress response, and antibiotic resistance. On the contrary, eukaryotes decreased in diversity and were dominated by the commonly found Chlorophyta towards the later successional period. Novel findings on the ecology of marine plastisphere during perturbation encourage the integration of this aspect into prediction research.

Carbohydrate-Active Enzymes of a Novel Halotolerant Alkalihalobacillus Species for Hydrolysis of Starch and Other Algal Polysaccharides

Halotolerant bacteria capable of starch hydrolysis by their amylases will benefit various industries, specifically since the hydrolytic activity of current industrial amylases is inhibited or even absent in salt-rich or alkaline environments. Seeking novel enzymes, we analyzed the entire genome content of a marine bacterium isolated from the gut of sea urchins to compare it against other bacterial genomes. Conditions underlying α-amylase activity were examined in vitro at various salinities (0 to 4%) and temperatures (25°C to 37°C). Genomic analyses revealed the isolated bacterium as a new species of Alkalihalobacillus. Comparative analysis of the contents of carbohydrate-active enzymes revealed various α-amylases, each with its respective carbohydrate-binding module for starch hydrolysis. Functional analysis identified the hydrolysis of starch and the maltooligosaccharides maltose and dextrin into d- and UDP-glucose. The fastest growth and α-amylase production occurred at 3% salinity at a temperature of 30°C. The Alkalihalobacillus sp. consists of exclusive contents of α-amylases and other enzymes that may be valuable in the hydrolysis of the algal polysaccharides cellulose and laminarin. IMPORTANCE Toward the discovery of novel carbohydrate-active enzymes that may be useful in the hydrolysis of starch, we examined a halotolerant bacterial isolate of Alkalihalobacillus sp. regarding its genomic content and conditions underlying the production of active α-amylases. The production of α-amylases was measured in bacterial cultures at relatively high temperature (37°C) and salinity (4%). The Alkalihalobacillus sp. revealed an exclusive content of amylases and other carbohydrate-active enzymes compared to other relevant bacteria. These enzymes may be valuable for the hydrolysis of algal polysaccharides. The enzymatic cascade of the Alkalihalobacillus sp. for starch metabolism allows polysaccharide degradation into monosugars while preventing the accumulation of intermediate inhibitors of maltose or dextrin.