Marine Microbiology: Resources, Ecology, and Biogeochemistry

Coastal aquaculture systems are complex environments with multiple microbial interactions that affect fish health and productivity. High-throughput amplicon sequencing is a valuable tool for identifying such bacterial communities and investigating the relationship between bacterial diversity and sustainability in these systems. In the present study, the seasonal dynamics of marine bacterial communities were assessed, in terms of diversity and composition, in three marine aquaculture farms in the northern Ionian Sea (western Greece) and a distant control site unaffected by aquaculture activities, using 16S rRNA amplicon metabarcoding. Results revealed that Proteobacteria, Bacteroidota, Cyanobacteria, and Verrucomicrobiota were the dominant phyla in the bacterial communities. Alpha diversity was significantly lower in the aquaculture farms compared to the control site. Season was the major factor driving bacterial community fluctuations. Comparative analysis between seasons revealed the presence of differentially abundant amplicon sequence variants (ASVs) in all pairwise comparisons, with the majority of them belonging to the phyla Bacteroidota (families Flavobacteriaceae, Cryomorphaceae) and Proteobacteria (family Rhodobacteraceae). Our study provides the first detailed description of bacterial communities present in Greek coastal aquaculture farms using amplicon metabarcoding analysis and expands our understanding of the impact of seasonality and environmental variables on marine bacterial community diversity and composition. Full article

In the marine coastal environment, freshwater and seawater coalescing communities are facing a complex set of abiotic and biotic cross-influences. This study aimed at evaluating the respective influences of blending and prokaryotic dynamics on community structure. For that, the surface salinity gradient of a nutrient-rich estuary (Arno River, Mediterranean Sea, Italy) was sampled at regular salinity intervals. When considering the whole length of the estuary and community-scale beta diversity metrics, a relatively smooth transition from freshwater to the sea was observed. Abiotic variability associated with salinity was the predominant constraint on the community structure, and the distribution of most taxa reflected their blending. However, while most of the dissolved substances enriched in freshwater experienced progressive dilution with seawater, heterotrophic prokaryotes demonstrated an important growth at intermediate salinity, interpreted as a heterotrophic assimilation of freshwater inputs by a few opportunistic marine taxa. The distribution of a number of taxa was significantly affected by variations in heterotrophic prokaryotes abundance, suggesting a putative influence of competitive interactions at intermediate salinities. A succession of different bacterial winners was observed from upstream to downstream, as well as losers represented by freshwater copiotrophs accompanied by some marine oligotrophs. Hence, coalescence drove a localized but major functional response of heterotrophic bacteria at intermediate salinity, hidden behind a majority of passively mixed bacterial taxa. This work paves the way for a stronger consideration of the trophic requirements of bacterial taxa to better understand community assembly in estuaries. Full article

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. Full article

The role of microorganisms in coral health, disease, and nutrition has been demonstrated in various studies. Environmental factors including pH, temperature, and dissolved oxygen also play crucial roles in maintaining sustainable coral ecosystems. However, how geographical and environmental factors influence bacterial diversity and community composition is unclear. Here, bacterial communities associated with Acropora formosa coral were sampled from four different locations—Phu Quoc Islands (Vietnam), Nha Trang (Vietnam), Ujung Gelam (Indonesia), and Bourake (New Caledonia)—and compared using tagged 16S rRNA sequencing. We identified 24 bacterial phyla, 47 classes, 114 orders, and 495 genera from 18 samples. Overall, Proteobacteria (1039 distant amplicon sequence variants [ASVs]) and Firmicutes (589 ASVs) were predominant, while Verrucomicrobiota (75 ASVs) and Planctomycetota (46 ASVs) were minor taxa. Alpha diversity analyses revealed that the bacterial community associated with Acropora formosa from Ujung Gelam had the highest indexes (Observed and Chao1), while the figures for Bourake were the lowest. Non-metric multidimensional scaling analysis (NMDS) showed significant differences in bacterial communities among locations (ADONIS, p = 1 × 10⁻⁴). Temperature was strongly correlated with the distribution of bacterial communities in Bourake, whereas pH and dissolved oxygen were significantly correlated with the presence of coral-associated bacterial communities in Phu Quoc and Nha Trang. Across all samples, 28 potential biological markers and 95 core ASVs were found, revealing significant differences in coral-associated bacterial communities. Collectively, these findings provide a comprehensive understanding of bacterial communities living in coral reefs across different geographic sites, which could be useful springboards for further studies. Full article

Phage-based pathogen control (i.e., phage therapy) has received increasing scientific attention to reduce and prevent the emergence, transmission, and detrimental effects of antibiotic resistance. In the current study, multidrug-resistant Vibrio natriegens strain AbY-1805 was isolated and tentatively identified as a pathogen causing the death of juvenile Pacific abalones (Haliotis discus hannai Ino). In order to apply phage therapy, instead of antibiotics, to treat and control V. natriegens infections in marine aquaculture environments, a lytic phage, vB_VnaS-L3, was isolated. It could effectively infect V. natriegens AbY-1805 with a short latent period (40 min) and high burst size (~890 PFU/cell). Treatment with vB_VnaS-L3 significantly reduced the mortality of juvenile abalones and maintained abalone feeding capacity over a 40-day V. natriegens challenge experiment. Comparative genomic and phylogenetic analyses suggested that vB_VnaS-L3 was a novel marine Siphoviridae-family phage. Furthermore, vB_VnaS-L3 had a narrow host range, possibly specific to the pathogenic V. natriegens strains. It also exhibited viability at a wide range of pH, temperature, and salinity. The short latent period, large burst size, high host specificity, and broad environmental adaptation suggest that phage vB_VnaS-L3 could potentially be developed as an alternative antimicrobial for the control and prevention of marine animal infections caused by pathogenic V. natriegens. Full article

Very few studies have investigated marine microbial colonization in polar regions, but climate-changing scenarios stress the importance of these investigations to protect life in such extremely vulnerable ecosystems. In two different coastal sites of the Ross Sea (Road and Tethys Bays, Antarctica) exposed to different stressors, the microbial biofilm colonizing the surface of plastic (polyvinyl chloride, PVC, and polyethylene, PE) panels left submerged in two experiments at different timescales (“short-term”: 3 months, and “long-term”: 9 and 12 months) was studied. The abundance and metabolic enzymatic activities [leucine aminopeptidase (LAP), beta-glucosidase (GLU) and alkaline phosphatase (AP)] of the prokaryotes and the microalgal abundance and species composition were analyzed, in parallel with the main environmental parameters. The prokaryotic community showed higher abundance and metabolic activities on PVC than on PE as opposed to microalgae. A peak in the microfouling prokaryotic abundance and metabolic functions was frequently recorded after 3 months of immersion, corresponding to the late austral summer period. LAP and AP were the most active enzymes, suggesting that microbial metabolic profiles were modulated by labile organic substrates. Our results suggest that the composition and function of microbial biofilm could be considered as sentinels of natural or anthropic-related disturbances. Full article

Algicidal bacteria are important in the control of toxic dinoflagellate blooms, but studies on the environmental behavior of related algal toxins are still lacking. In this study, Bacillus subtilis S3 (S3) showed the highest algicidal activity against Alexandrium pacificum (Group IV) out of six Bacillus strains. When treated with 0.5% (v/v) S3 bacterial culture and sterile supernatant, the algicidal rates were 69.74% and 70.22% at 12 h, respectively, and algicidal substances secreted by S3 were considered the mechanism of algicidal effect. During the algicidal process, the rapid proliferation of Alteromonas sp. in the phycosphere of A. pacificum may have accelerated the algal death. Moreover, the algicidal development of S3 released large amounts of intracellular paralytic shellfish toxins (PSTs) into the water, as the extracellular PSTs increased by 187.88% and 231.47% at 12 h, compared with the treatment of bacterial culture and sterile supernatant at 0 h, respectively. Although the total amount of PSTs increased slightly, the total toxicity of the algal sample decreased as GTX1/4 was transformed by S3 into GTX2/3 and GTX5. These results more comprehensively reveal the complex relationship between algicidal bacteria and microalgae, providing a potential source of biological control for harmful algal blooms and toxins. Full article