A comparison of prokaryote communities inhabiting sponges, bacterial mats, sediment and seawater in Southeast Asian coral reefs

Convergent photophysiology and prokaryotic assemblage structure in epilithic cyanobacterial tufts and algal turf communities

As global change spurs shifts in benthic community composition on coral reefs globally, a better understanding of the defining taxonomic and functional features that differentiate proliferating benthic taxa is needed to predict functional trajectories of reef degradation better. This is especially critical for algal groups, which feature dramatically on changing reefs. Limited attention has been given to characterizing the features that differentiate tufting epilithic cyanobacterial communities from ubiquitous turf algal assemblages. Here, we integrated an in situ assessment of photosynthetic yield with metabarcoding and shotgun metagenomic sequencing to explore photophysiology and prokaryotic assemblage structure within epilithic tufting benthic cyanobacterial communities and epilithic algal turf communities. Significant differences were not detected in the average quantum yield. However, variability in yield was significantly higher in cyanobacterial tufts. Neither prokaryotic assemblage diversity nor structure significantly differed between these functional groups. The sampled cyanobacterial tufts, predominantly built by Okeania sp., were co-dominated by members of the Proteobacteria, Firmicutes, and Bacteroidota, as were turf algal communities. Few detected ASVs were significantly differentially abundant between functional groups and consisted exclusively of taxa belonging to the phyla Proteobacteria and Firmicutes. Assessment of the distribution of recovered cyanobacterial amplicons demonstrated that alongside sample-specific cyanobacterial diversification, the dominant cyanobacterial members were conserved across tufting cyanobacterial and turf algal communities. Overall, these data suggest a convergence in taxonomic identity and mean photosynthetic potential between tufting epilithic cyanobacterial communities and algal turf communities, with numerous implications for consumer-resource dynamics on future reefs and trajectories of reef functional ecology.

A Study of Sponge Symbionts from Different Light Habitats

The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.

Microbiome composition of the marine sponge Cliona varians at the Neotropical Southern Caribbean Sea displays a predominant core of Rhizobiales and Nitrosopumilaceae

AIMS

This work aims to characterize the microbial diversity of the encrusting sponge Cliona varians, a pore-forming and coral reef bioeroding marine sponge of emerging spread related to ocean acidification.

METHODS AND RESULTS

We analyzed the microbiome composition by 16S V4 amplicon next-generation sequencing in a community of the bioeroding coral-reef encrusting/excavating marine sponge Cliona varians thriving at the Southern Caribbean Sea. 87.21% and 6.76% of the sequences retrieved were assigned to the domain Bacteria and Archaea. The most predominant operational taxonomic units were classified as members of the order Rhizobiales and family Nitrosopumilaceae, representing members of not yet characterized genera. Features found strictly conserved in the strain/genomic representatives reported in those microbial taxa are nitrogen fixation and transformation.

CONCLUSION

Our results suggest, in accordance with recent results, that these microbiome members and associated functions could be contributing to the biological fitness of the sponge to be able to colonize and bioerode in environments with low access and scarce availability of nitrogen source.

SIGNIFICANCE AND IMPACT OF STUDY

Coral reefs bioresources such as sponge holobionts are intriguing and complex ecosystems units. This study contributes to the knowledge of how C. varians microbiota is composed or shaped, which is crucial to understand its ecological functions.

The 'classic stromatolite' Cryptozoön is a keratose sponge-microbial consortium

Animal evolution transformed microbial mat development. Canonically inferred negative effects include grazing, disturbance and competition for space. In contrast, ancient examples of cooperation between microbial mats and invertebrates have rarely been reported. Late Cambrian (~485 million years) Cryptozoön is widely regarded as the first stromatolite to have received a taxonomic name and has been compared with present-day examples at Shark Bay, Australia. Here, we show that Cryptozoön is an interlayered consortium of keratose ('horny') sponge and microbial carbonate in roughly equal proportions. Cryptozoön's well-defined layering reflects repeated alternation of sponge and microbial mat. Its distinctive lateral growth is due to the ability of keratosans to colonize steep and overhanging surfaces. Contrary to the perception of Phanerozoic stromatolites as anachronistic survivors in a eukaryotic world, Cryptozoön suggests mutualistic behaviour in which sponges and microbial mats cooperated to gain support, stability and relief, while sharing substrates, bacteria and metabolites. Keratosan-microbial consortia may have been mistaken for stromatolites throughout the record of the past 500 million years, and possibly longer.

Population structure and microbial community diversity of two common tetillid sponges in a tropical reef lagoon

Sponges are predicted to dominate future reef ecosystems influenced by anthropogenic stressors and global climate change. The ecological success of sponges is attributed to their complex physiology, which is in part due to the diversity of their associated prokaryotic microbiome. However, the lack of information on the microbial community of many sponge species makes it difficult to gauge their interactions and functional contributions to the ecosystem. Here, we investigated the population dynamics and microbial community composition of two tetillid sponges identified as Cinachyrella sp. and Paratetilla sp., which are common on coral bommies in a reef lagoon in Bolinao, northwestern Philippines. The sponges ranged in size from 2.75 ± 2.11 to 6.33 ± 3.98 cm (mean ± standard deviation) and were found at an average density of 1.57 ± 0.79 to 4.46 ± 3.60 individuals per sq. m. on the bommies. The tetillid sponge population structure remained stable over the course of four years of monitoring. Prokaryotic communities associated with the sponges were distinct but had overlapping functions based on PICRUSt2 predictions. This convergence of functions may reflect enrichment of metabolic processes that are crucial for the survival of the tetillid sponges under prevailing conditions in the reef lagoon. Differentially enriched functions related to carbon, sulfur, fatty acid, and amino acid metabolism, cellular defense, and stress response, may influence the interactions of tetillid sponges with other biota on the bommies.