Seagrass ecosystems have been declining, and restorations are conducted in many parts of the world to compensate for habitat loss and restore the ecosystem services seagrasses provide. Assessment of transplantation success requires the monitoring of the level of biodiversity between the donor and transplanted sites. In this study, we assessed a seagrass ecosystem after restoration in terms of the diversity of marine organisms using environmental DNA (eDNA) to compare four sites: (1) bare sand, (2) a natural meadow of Cymodocea serrulata, (3) a natural meadow of Halophila ovalis, and (4) a transplanted seagrass meadow. The results showed the presence of 3 domains, 34 phyla, 59 classes, 92 orders, 155 families, 156 genera, and 121 species. Proteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes were the dominant bacterial phyla. Among eukaryotes, Phragmoplastophyta/Charophyta (epiphytes), Ascomycota (fungi), Cnidaria (jelly fish), and Arthropoda (Crabs and bivalves) were the dominant phyla. Dugong tails and commercial species (sea cucumber, dog conch, and swimming crab) have been observed in both the natural and transplanted meadows. Relative abundance among the four sites was significantly different. There were no differences in species richness and evenness between the four sites and no differences in species richness and evenness between the natural meadows and the transplanted seagrass meadow. It is possible that transplanted seagrass meadow can be successfully restored and established and can provide habitat for fauna and microbes. Additionally, fauna are not limited in their capacity to move between the natural and transplanted habitats. This study provides an assessment of biodiversity of restored seagrass patches and a better understanding of a seagrass ecosystem after restoration. However, to assess seagrass ecosystem services after restoration and the success of restoration actions, long-term monitoring of marine organism diversity and additional assessments are needed.

Reef degradation and algae-farming fish alter the structures and compositions of coral-algal-microbial communities. We collected epilithic macroalgae in different reef conditions and damselfish territories. The microbial communities were characterized by subjecting the V3-V4 hypervariable region of the 16S rRNA gene to amplicon sequencing. Metagenomic analysis revealed 2 domains, 51 phyla, 112 orders, and 238 families and the dominance of Proteobacteria and Bacteroidota in both fair and degraded reefs inside and outside territories. Chloroflexi on the degraded reef was dominant and its proportion was almost two and a half times compared to the fair reef, whereas Cyanobacteria was low on the degraded reef. Bacteroidota was dominant on the fair reef, whereas Actinobacteriota was scarce on this reef. For the damselfish territories, Chloroflexi was dominant inside the territory, whereas Bacteroidetes were found outside the territory. Differences in the microbial species diversity and richness were not apparent between all sites; however, species evenness was higher on the degraded reef condition and lower outside the territory. Important potential pathogens of reef organisms, such as Vibrio, Photobacterium, and Phormidium, were found on the degraded reef areas inside the damselfish territory. The farming behaviors of damselfish influenced microbial communities by changing the epilithic algal matrix that harbors many microbial communities. This study provides useful information on microbial biota in coral reef habitats which is further applicable to reef conservation and coastal management.

Increased seawater temperatures and nutrient loading are stressors that affect coral reefs and their microbiomes. In this study, filamentous algae were collected and exposed to different temperatures and nutrient concentrations through a laboratory experiment. Microbial DNA was extracted and analyzed using amplicon sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. In total, 1 domain, 51 phyla, 131 classes, 335 orders, 549 families, and 1905 species were identified. Proteobacteria and Bacteroidota were the dominant taxa reported. Elevated seawater temperatures and nutrient enrichment impacted microbial communities associated with turf algae under laboratory culture. Bacterial species diversity and abundance differed under different temperature and nutrient conditions. Proteobacteria and Actinobacteria were abundant in lower-temperature conditions, while Desulfobacterota, Spirochaetota, and Firmicutes were abundant in higher-temperature conditions. Ruegeria was abundant in low-temperature conditions, whereas Vibrio abundance was low. Regarding nutrient conditions, Proteobacteria and Cyanobacteria were abundant under high-nutrient conditions, while Firmicutes and Desulfobacterota were abundant under ambient-nutrient conditions. The higher nutrient concentration increased the abundance of pathogenic bacteria, such as Vibrio and Photobacterium, while Pseudoalteromonas, which is beneficial for reefs, was present under ambient nutrient conditions. This study demonstrates that temperature and nutrient enrichment can shape microbial communities under laboratory conditions, providing an experimental setting for further studies of bacterial functions and metabolic processes in natural conditions under thermal and nutrient stresses.

Halimeda-dominated habitats are ecologically significant tropical benthic ecosystems whose structural complexity supports diverse marine organisms, particularly associated microbes. However, the characteristics and ecological roles of these bacterial communities and their connectivity within Halimeda-dominated habitats remain poorly understood. This study examined microbial diversity and composition across four microenvironments of a Halimeda meadow, namely, ambient seawater, sediment, Halimeda thalli, and Holothuria atra feces, using the V3–V4 region of the 16S rRNA gene. A total of 44 phyla, 733 genera, and 827 species were identified, with Proteobacteria, Cyanobacteria, Bacteroidota, Desulfobacterota, and Actinobacteriota dominating across all samples. Microbial diversity and composition differed significantly among microenvironments, with sediment showing the highest species diversity and seawater showing the lowest. Halimeda thalli were dominated by Alphaproteobacteria, particularly Phycisphaerae and Parcubacteria, associated with nutrient cycling on macroalgal surfaces. Sediment was enriched with Desulfobacteria, Actinobacteria, and Chloroflexi. Seawater was characterized by Synechococcus CC9902, a primary producer in tropical waters. H. atra feces were dominated by Bacteroidia and Bdellovibrionota, representing a distinct bacterial community shaped by both gut-associated taxa and microorganisms derived from ingested sediments. Only 6.95% of genera were shared across all microenvironments, and feces and sediment shared the highest overlap (47.28%), suggesting that H. atra acts as a biogeochemical bridge that repackages benthic organic matter without fundamentally altering its microbial identity. The low overlap between Halimeda and seawater, as well as between seawater and both sediment and sea cucumber feces, suggests strong habitat-specific bacterial community assembly, with algal-associated bacterial communities being distinct from pelagic communities and seawater communities differing from benthic and fecal communities.