Sponges present a core prokaryotic community stable across Tropical Western Atlantic

From Sea to Freshwater: Shared and Unique Microbial Traits in Sponge Associated Prokaryotic Communities

Despite their ecological significance and biotechnological potential, freshwater sponges remain relatively understudied compared to their marine counterparts. In special, the prokaryotic communities of species from isolated yet highly diverse ecosystems, such as the Amazon Rainforest, remain unknown, leaving an important part of the Porifera microbiome underexplored. Using high-throughput sequencing of the 16S rRNA gene, we unraveled the structure of the microbiota associated to the freshwater sponges Heteromeyenia cristalina and Metania reticulata for the first time. Their microbiome was compared with that of the haplosclerid marine sponges Amphimedon viridis and Haliclona melana; and the tetractinellid Cinachyrella alloclada. Our findings reveal not only a shared core microbiome between the freshwater and marine environments but also indicate functional redundancy in their communities, suggesting that certain microbial metabolic functions are conserved across diverse habitats. Comparisons between ecosystems also revealed that microbiomes of freshwater sponges can be richer and more diverse than those of marine species. Moreover, we compared the microbiome of adults and asexual reproduction structures (buds and gemmules) of sponges from both habitats, revealing a remarkable similarity between adults and their respective offsprings, indicating an important role of vertical transmission in this mode of reproduction. Our observations emphasize the dynamic interactions and the adaptability of the sponge-associated microbiota, providing insights into how these symbiotic associations were affected during the colonization of freshwater environments and shedding light into how symbiotic relationships are maintained throughout generations.

The diversity, composition, network characteristics and community assembly of intestinal microbiome in sea cucumber reflect the differences in habitats and aquaculture practices

The possible differentiation of microbiomes in various habitats and aquaculture practices has rarely been studied until now. Here, the microbiomes of five different culture systems for sea cucumber Apostichopus japonicus were compared, including outdoor pond, indoor workshop, net cage, suspension cage, marine ranching. Samples of intestinal contents from sea cucumber, surrounding water and sediment were collected from these culture systems. Significant differentiations in microbial diversity, composition, function were found in various culture systems. Microbial source-tracking analysis indicated that intestinal microbiomes of sea cucumber were more similar to sediment than to surrounding water. Totally, 23 shared core operational taxonomic units (OTUs) were identified in intestinal microbiome of sea cucumber in these systems, belong to following orders: Rhodobacterales (15), Rhizobiales (3), Flavobacteriales (2), Verrucomicrobiales (1), Campylobacterales (1), unclassified (1). Meanwhile, unique core OTUs in various systems tended to aggregate toward oligotrophic, potentially beneficial, or pathogenic bacteria. Microbial network characteristics in marine ranching and suspension cage systems were consistent with those in high-stress habitats, exhibiting lower diversity, complexity, modularity, dominated by positive interactions. Conversely, opposite trends were observed in indoor workshop, outdoor pond, net cage systems. Strong diffusion limitations on intestinal microbial community of sea cucumber, particularly in marine ranching system, were elucidated. Distinct characteristics of microbiome in various culture systems reflected differences in habitats and aquaculture practices. These findings provide new insights into impact of aquaculture systems on microbial community in aquatic animals, could contribute to healthy aquaculture practices for sea cucumber industry.

Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial

Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.

Unveiling the early life core microbiome of the sea cucumber Apostichopus japonicus and the unexpected abundance of the growth-promoting Sulfitobacter

BACKGROUND

Microbiome in early life has long-term effects on the host's immunological and physiological development and its disturbance is known to trigger various diseases in host Deuterostome animals. The sea cucumber Apostichopus japonicus is one of the most valuable marine Deuterostome invertebrates in Asia and a model animal in regeneration studies. To understand factors that impact on host development and holobiont maintenance, host-microbiome association has been actively studied in the last decade. However, we currently lack knowledge of early life core microbiome during its ontogenesis and how it benefits the host's growth.

RESULTS

We analyzed the microbial community in 28 sea cucumber samples from a laboratory breeding system, designed to replicate aquaculture environments, across six developmental stages (fertilized eggs to the juvenile stage) over a three years-period to examine the microbiomes' dynamics and stability. Microbiome shifts occurred during sea cucumber larval ontogenesis in every case. Application of the most sophisticated core microbiome extraction methodology, a hybrid approach with abundance-occupancy core microbiome analyses (top 75% of total reads and > 70% occupation) and core index calculation, first revealed early life core microbiome consisted of Alteromonadaceae and Rhodobacteraceae, as well as a stage core microbiome consisting of pioneer core microbe Pseudoalteromonadaceae in A. japonicus, suggesting a stepwise establishment of microbiome related to ontogenesis and feeding behavior in A. japonicus. More interestingly, four ASVs affiliated to Alteromonadaceae and Rhodobacteraceae were extracted as early life core microbiome. One of the ASV (ASV0007) was affiliated to the Sulfitobactor strain BL28 (Rhodobacteraceae), isolated from blastula larvae in the 2019 raring batch. Unexpectedly, a bioassay revealed the BL28 strain retains a host growth-promoting ability. Further meta-pangenomics approach revealed the BL28 genome reads were abundant in the metagenomic sequence pool, in particular, in that of post-gut development in early life stages of A. japonicus.

CONCLUSION

Repeated rearing efforts of A. japonicus using laboratory aquaculture replicating aquaculture environments and hybrid core microbiome extraction approach first revealed particular ASVs affiliated to Alteromonadaceae and Rhodobacteraceae as the A. japonicus early life core microbiome. Further bioassay revealed the growth promoting ability to the host sea cucumber in one of the core microbes, the Sulfitobactor strain BL28 identified as ASV0007. Genome reads of the BL28 were abundant in post-gut development of A. japonicus, which makes us consider effective probiotic uses of those core microbiome for sea cucumber resource production and conservation. The study also emphasizes the importance of the core microbiome in influencing early life stages in marine invertebrates. Understanding these dynamics could offer pathways to improve growth, immunity, and disease resistance in marine invertebrates.

Microbiome diversity from sponges biogeographically distributed between South America and Antarctica

Sponges from South America and Antarctica are evolutionarily closely related. Specific symbiont signatures that could differentiate these two geographic regions are unknown. This study aimed to investigate the microbiome diversity of sponges from South America and Antarctica. In total 71 sponge specimens were analyzed (Antarctica: N = 59, 13 different species; South America: N = 12, 6 different species). Illumina 16S rRNA sequences were generated (2.88 million sequences; 40K ± 29K/sample). The most abundant symbionts were heterotrophic (94.8 %) and belonged mainly to Proteobacteria and Bacteroidota. EC94 was the most abundant symbiont and dominated the microbiome of some species (70-87 %), comprising at least 10 phylogroups. Each of the EC94 phylogroups was specific to one genus or species of sponge. Furthermore, South America sponges had higher abundance of photosynthetic microorganisms (2.3 %) and sponges from Antarctica, the highest abundance of chemosynthetic (5.5 %). Sponge symbionts may contribute to the function of their hosts. The unique features from each of these two regions (e.g., light, temperature, and nutrients) possibly stimulate distinct microbiome diversity from sponges biogeographically distributed across continents.

Fluxes of the Amazon River plume nutrients and microbes into marine sponges

Sponges have co-evolved with microbes for over 400 myr. Previous studies have demonstrated that sponges can be classified according to the abundance of microbes in their tissues as Low Microbial Abundance (LMA) and High Microbial Abundance (HMA). While LMA sponges rely mainly on water column microbes, HMA appear to rely much more on symbiotic fermentative and autotrophic microbes maintained in their tissues. However, it is unclear if this pattern holds when comparing different species of tropical sponges under extreme nutrient conditions and sediment loads in the water column, such as the Great Amazon Reef System (GARS), which covers an area of ~56,000 km² off the Amazon River mouth. Sponges are the major GARS benthic components. However, these sponges' microbiome across the GARS is still unknown. Here, we investigated water quality, isotopic values (δ¹³C and δ¹⁵N), metagenomic and lipidomic profiles of sponges obtained from different sectors throughout the GARS. >180 million shotgun metagenomic reads were annotated, covering 22 sponge species. Isotopic and lipidomic analyses suggested LMA sponges rely on the Amazon River Plume for nutrition. HMA sponges (N = 15) had higher Roseiflexus and Nitrospira abundance, whereas LMA sponges (N = 7) had higher Prochlorococcus and Pelagibacter abundance. Functional data revealed that the LMA sponge microbiomes had greater number of sequences related to phages and prophages as well as electron transport and photophosphorylation which may be related to photosynthetic processes associated with the Prochlorococcus and Synechococcus found in the LMA. The higher phages abundance in LMA sponges could be related to these holobionts' reduced defense towards phage infection. Meanwhile, HMA sponge microbiomes had higher Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR abundance, which may be involved in defense against phage infection. This study sheds light on the nutrient fluxes and microbes from the Amazon River plume into the sponge holobionts.