Search for: All records

Abstract BackgroundAs coral diseases become more prevalent and frequent, the need for new intervention strategies also increases to counteract the rapid spread of disease. Recent advances in coral disease mitigation have resulted in increased use of antibiotics on reefs, as their application may halt disease lesion progression. Although efficacious, consequences of deliberate microbiome manipulation resulting from antibiotic administration are less well-understood– especially in non-diseased corals that appear visually healthy. Therefore, to understand how apparently healthy corals are affected by antibiotics, we investigated how three individual antibiotics, and a mixture of the three, impact the microbiome structure and diversity of a disease-resistant Caribbean staghorn coral (Acropora cervicornis) genotype. Over a 96-hour, aquarium-based antibiotic exposure experiment, we collected and processed coral tissue and water samples for 16S rRNA gene analysis. ResultsWe found that antibiotic type and dose distinctively impact microbiome alpha diversity, beta diversity, and community composition. In experimental controls, microbiome composition was dominated by an unclassified bacterial taxon from the orderCampylobacterales, while each antibiotic treatment significantly reduced the relative abundance of this taxon. Those taxa that persisted following antibiotic treatment largely differed by antibiotic type and dose, thereby indicating that antibiotic treatment may result in varying potential for opportunist establishment. ConclusionTogether, these data suggest that antibiotics induce microbiome dysbiosis– hallmarked by the loss of a dominant bacterium and the increase in taxa associated with coral stress responses. Understanding the off-target consequences of antibiotic administration is critical not only for informed, long-term coral restoration practices, but also for highlighting the importance of responsible antibiotic dissemination into natural environments. 

Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host’s responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade. 

Abstract Nutrient availability drives community structure and ecosystem processes, especially in tropical lagoons that are typically oligotrophic but often receive allochthonous inputs from land. Terrestrially derived nutrients are introduced to tropical lagoons by surface runoff and submarine groundwater discharge, which are influenced by seasonal precipitation. However, terrigenous inputs presumably diminish along the onshore–offshore gradients within lagoons. We characterized nutrient availability in the lagoons of a tropical high island, Moorea, French Polynesia, using spatially distributed measurements of nitrogen content in the tissues of a widespread macroalga during the rainy season over 4 yr. We used synoptic water column sampling to identify associations among macroalgal nutrient content and the composition of inorganic macronutrients, dissolved organic matter, and microbial communities. We paired these data with quantifications of land use in nearby watersheds to uncover links between terrestrial factors, aquatic chemistry, and microbial communities. Algal N content was highest near shore and near large, human‐impacted watersheds, and lower at offshore sites. Sites with high algal N had water columns with high nitrite + nitrate, silicate, and increased humic organic matter (based on a fluorescence Humification Index), especially following rain. Microbial communities were differentiated among nearshore habitats and covaried with algal N and water chemistry, supporting the hypothesis that terrigenous nutrient enrichment shapes microbial dynamics in otherwise oligotrophic tropical lagoons. This study reveals that land–sea connections create nutrient subsidies that are important for lagoon biogeochemistry and microbiology, indicating that future changes in land use or precipitation will modify ecosystem processes in tropical lagoons.