Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment

Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster beds

Oyster reefs and beds provide crucial ecosystem services, including water filtration, coastal protection, and habitat provision for marine species. However, these habitats face significant threats from climate change and anthropogenic stressors. To address these challenges, numerous oyster restoration initiatives have been undertaken globally. Intertidal microbial communities, comprising diverse bacteria, archaea, and unicellular eukaryotes, drive key biogeochemical processes, but remain poorly understood in ecosystems targeted for oyster restoration. We investigated the microbiome associated with the Olympia oyster (Ostrea lurida), a key restoration target in the western USA, by characterizing microbial abundance and diversity in sediment, oyster-associated biofilm, and oysters at four sites in San Francisco Bay. Our findings revealed distinct microbial assemblages in oysters and sediment compared to biofilm. Diversity, measured by the Shannon index, was highest at Heron's Head (5.47), followed by Brickyard Park (5.35), Dunphy Park (5.17), and Point Pinole (4.85). Notably, microbes Ruminococcus, Streptococcus, Staphylococcus, Prevotella, Porphyromonas, Parvimonas, Neisseria, Lactococcus, Haemophilus, Fusobacterium, Dorea, Clostridium, Campylobacter, Bacteroides, and Akkermansia were positively associated with biofilm collected from hard surfaces where oysters were attached at most sites. Potential implications of these microbial associations for oyster growth, survival, and interactions with environmental factors remain largely unexplored. Future research is warranted on culturing specific microbes to assess their functions and investigating environmental and ecological drivers of microbial diversity to determine relationships indicative of oyster health and potential for enhancing oyster recruitment.

Pseudoalteromonas Strains as Biofilm Control Agents in Ostrea edulis Aquaculture: Reducing Biofilm Biovolume While Preserving Microbial Diversity

Biofilms in aquaculture tanks pose significant challenges, hindering cleaning processes and contributing to antibiotic resistance. This study investigated the effects of four Pseudoalteromonas strains on flat oyster (Ostrea edulis) rearing, with a specific focus on biofilm control and microbial communities. After confirming the safety of these strains for O. edulis, we monitored biofilm development and bacterial communities during a 4-month sexual maturation period. Biofilm biovolume was quantified using confocal laser scanning microscopy (CLSM), and bacterial community composition was analyzed via 16S rRNA gene metabarcoding of both biofilm and seawater samples. Our results revealed differences in bacterial community structure between biofilms and seawater. Furthermore, the presence of specific Pseudoalteromonas strains significantly impacted the composition of bacterial communities within the tanks. β-diversity analyses demonstrated that each strain exerted a unique influence on the bacterial community structure. Some Pseudoalteromonas strains effectively reduced biofilm biovolume without negatively impacting bacterial richness or diversity. These observations suggest that certain Pseudoalteromonas strains can effectively control biofilm formation while maintaining a diverse and potentially beneficial microbial community in O. edulis rearing tanks. The use of these strains as additives in aquaculture systems could offer several advantages, including reduced cleaning time and costs and a potential decrease in biocide usage.

Light and dark biofilm adaptation impacts larval settlement in diverse coral species

BACKGROUND

Recovery of degraded coral reefs is reliant upon the recruitment of coral larvae, yet the mechanisms behind coral larval settlement are not well understood, especially for non-acroporid species. Biofilms associated with reef substrates, such as coral rubble or crustose coralline algae, can induce coral larval settlement; however, the specific biochemical cues and the microorganisms that produce them remain largely unknown. Here, we assessed larval settlement responses in five non-acroporid broadcast-spawning coral species in the families Merulinidae, Lobophyllidae and Poritidae to biofilms developed in aquaria for either one or two months under light and dark treatments. Biofilms were characterised using 16S rRNA gene sequencing to identify the taxa associated with settlement induction and/or inhibition.

RESULTS

We show that light and biofilm age are critical factors in the development of settlement inducing biofilms, where different biofilm compositions impacted larval settlement behaviour. Further, we show that specific biofilm taxa were either positively or negatively correlated with coral settlement, indicating potential inducers or inhibitors. Although these taxa were generally specific to each coral species, we observed bacteria classified as Flavobacteriaceae, Rhodobacteraceae, Rhizobiaceae and Pirellulaceae to be consistently correlated with larval settlement across multiple coral species.

CONCLUSIONS

Our work identifies novel microbial groups that significantly influence coral larval settlement, which can be targeted for the discovery of settlement-inducing metabolites for implementation in reef restoration programs. Furthermore, our results reinforce that the biofilm community on coral reef substrates plays a crucial role in influencing coral larval recruitment, thereby impacting the recovery of coral reefs.

Ecosystem transplant from a healthy reef boosts coral health at a degraded reef

Organismal communities associated with coral reefs, particularly invertebrates and microbes, play crucial roles in ecosystem maintenance and coral health. Here, we characterized the organismal composition of a healthy, non-urbanized reef (Site A) and a degraded, urbanized reef (Site B) in the Gulf of Eilat/Aqaba, Red Sea to assess its impact on coral health and physiology. Biomimetically designed terracotta tiles were conditioned for 6 months at both sites, then reciprocally transplanted, and scleractinian coral species, Acropora eurystoma and Stylophora pistillata, were attached for an additional 6 months. After 12 months, tiles from Site A transplanted to Site B exhibited greater invertebrate richness and diversity than Site B's original tiles (via Cytochrome c. Oxidase subunit I metabarcoding). Key bacteria from the healthy reef were more prevalent on Site A tiles and on the tiles transplanted to Site B (via 16S rRNA gene sequencing). Corals originally from Site B attached to transplanted healthy tiles (Site A) showed higher photochemical capacity, increased endosymbionts, and reduced physiological stress, measured by total antioxidant capacity and an integrated biomarker response. Our findings demonstrate the successful transfer of organismal communities between reefs, highlighting the potential benefits of healthy reef-associated invertebrates and microbes on coral physiology and their implications for reef restoration strategies.

Comparative analysis of biofilm bacterial communities developed on different artificial reef materials

AIMS

Artificial reefs play a vital role in restoring and creating new habitats for marine species by providing suitable substrates, especially in areas where natural substrates have been degraded or lost due to declining water quality, destructive fishing practices, and coral diseases. Artificial reef restoration aimed at coral larval settlement is gaining prominence and initially depends on the development of biofilms on reef surfaces. In this study, we hypothesized that different artificial reef materials selectively influence the composition of biofilm bacterial communities, which in turn affected coral larval settlement and the overall success of coral rehabilitation efforts. To test this hypothesis, we evaluated the impact of six different reef-made materials (porcelain, granite, coral skeleton, calcium carbonate, shell cement, and cement) on the development of biofilm bacterial communities and their potential to support coral larval settlement.

METHODS AND RESULTS

The biofilm bacterial communities were developed on different artificial reef materials and studied using 16S rRNA gene amplicon sequencing and analysis. The bacterial species richness and evenness were significantly (P < 0.05) low in the seawater, while these values were high in the reef materials. At the phylum level, the biofilm bacterial composition of all materials and seawater was majorly composed of Pseudomonadota, Cyanobacteria, and Bacteroidetes; however, significantly (P < 0.05) low Bacteroidetes were found in the seawater. At the genus level, Thalassomonas, Glaciecola, Halomicronema, Lewinella, Hyphomonas, Thalassospira, Polaribacter, and Tenacibaculum were significantly (P < 0.05) low in the coral skeleton and seawater, compared to the other reef materials. The genera Pseudoaltermonas and Thalassomonas (considered potential inducers of coral larval settlement) were highly abundant in the shell-cement biofilm, while low values were found in the biofilm of the other materials.

CONCLUSION

The biofilm bacterial community composition can be selective for different substrate materials, such as shell cement exhibited higher abundances of bacteria known to facilitate coral larval settlement, highlighting their potential in enhancing restoration outcomes.

Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture

Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.

Biofilm-forming bacteria associated with corals secrete melanin with UV-absorption properties

Corals are colonized by a plethora of microorganisms, and their diversity plays a significant role in the health and resilience of corals when they face oxidative stress leading to bleaching. In the current study, we examined 238 bacteria isolated from five different coral species (Acropora hyacinthus, Pocillopora damicornis, Podabacea crustacea, Porites lobata, and Pavona venosa) collected from the coral reef ecosystems of Kavaratti, Lakshadweep Islands, India. We found that bacteria such as Psychrobacter sp., Halomonas sp., Kushneria sp., Staphylococcus sp., Bacillus sp., Brachybacterium sp., Citrobacter sp., and Salinicola sp. were commonly present in the corals. On the other hand, Qipengyuania sp., Faucicola sp., Marihabitans sp., Azomonas sp., Atlantibacter sp., Cedecea sp., Krasalinikoviella sp., and Aidingimonas sp. were not previously reported from the corals. Among the bacterial isolates, a significant number showed high levels of biofilm formation (118), UV absorption (119), and melanin production (127). Considering these properties, we have identified a combination of seven bacteria from the genera Halomonas sp., Psychrobacter sp., Krasalinikoviella sp., and Micrococcus sp. as a potential probiotic consortium for protecting corals from oxidative stress. Overall, this study provides valuable insights into the coral microbiome and opens up possibilities for microbiome-based interventions to protect these crucial ecosystems in the face of global environmental challenges.

Metagenomic evaluation of bacteria in drinking water using full-length 16S rRNA amplicons

Escherichia coli and total coliforms are important tools for identifying potential faecal contamination in drinking water. However, metagenomics offers a powerful approach for delving deeper into a bacterial community when E. coli or total coliforms are detected. Metagenomics can identify microbes native to water systems, track community changes and potential pathogens introduced by contamination events, and evaluate the effectiveness of treatment processes. Here, we demonstrate how the dual application of traditional monitoring practices and metagenomics can improve monitoring and surveillance for water resource management. The robustness of long-read metagenomics across replicates is demonstrated by the effect and interaction between manganese filters and bacterial communities, as well as the impact of chlorination after coliform detection. These examples reveal how metagenomics can identify the complex bacterial communities in the distribution system and the source waters used to supply drinking water treatment plants (DWTPs). The knowledge gained increases confidence in identified causes and mitigations of potential contamination events. By exploring bacterial communities, we can gain additional insights into the impact of faecal contamination events and treatment processes. This insight enables more precise remediation actions and enhances confidence in communicating health risks to drinking water operators and the public.

Negative parental and offspring environmental effects of macroalgae on coral recruitment are linked with alterations in the coral larval microbiome

The persistence of reef-building corals is threatened by macroalgal competitors leading to a major demographic bottleneck in coral recruitment. Whether parental effects exist under coral-algal competition and whether they influence offspring performance via microbiome alterations represent major gaps in our understanding of the mechanisms by which macroalgae may hinder coral recovery. We investigated the diversity, variability and composition of the microbiome of adults and larvae of the coral Pocillopora acuta and surrounding benthic substrate on algal-removed and algal-dominated bommies. We then assessed the relative influence of parental and offspring environmental effects on coral recruitment processes by reciprocally exposing coral larvae from two parental origins (algal-removed and algal-dominated bommies) to algal-removed and algal-dominated environmental conditions. Dense macroalgal assemblages impacted the microbiome composition of coral larvae. Larvae produced by parents from algal-dominated bommies were depleted in putative beneficial bacteria and enriched in opportunistic taxa. These larvae had a significantly lower survival compared to larvae from algal-removed bommies regardless of environmental conditions. In contrast, algal-induced parental and offspring environmental effects interacted to reduce the survival of coral recruits. Together our results demonstrate negative algal-induced parental and offspring environmental effects on coral recruitment that could be mediated by alterations in the offspring microbiome.

Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster reefs

Oyster reefs are invaluable ecosystems that provide a wide array of critical ecosystem services, including water filtration, coastal protection, and habitat provision for various marine species. However, these essential habitats face escalating threats from climate change and anthropogenic stressors. To combat these challenges, numerous oyster restoration initiatives have been undertaken, representing a global effort to preserve and restore these vital ecosystems. A significant, yet poorly understood, component of oyster reefs is the microbial communities. These communities account for a substantial proportion of marine reefs and are pivotal in driving key biogeochemical processes. Particularly, the environmental microbiome plays a crucial role in supporting the health and resilience of oyster populations. In our study, we sought to shed light on the microbiome within oyster reef ecosystems by characterizing the abundance, and diversity of microorganisms in the soil, biofilm, and oysters in 4 sites using a combinatorial approach to identify differentially abundant microbes by sample type and by sampling location. Our investigation revealed distinct microbial taxa in oysters, sediment and biofilm. The maximum Shannon Index indicated a slightly increased diversity in Heron's Head (5.47), followed by Brickyard park (5.35), Dunphy Park (5.17) and Point Pinole (4.85). This is likely to be driven by significantly higher oyster mortality observed at Point Pinole during routine monitoring and restoration efforts. Interestingly Ruminococcus, Streptococcus, Staphylococcus, Prevotella, Porphyromonas, Parvimonas, Neisseria, Lactococcus, Haemophilus, Fusobacterium, Dorea, Clostridium, Campylobacter, Bacteroides, and Akkermansia were positively associated with the biofilm. Yet we have limited understanding of their beneficial and/or detrimental implications to oyster growth and survival. By unraveling the intricate relationships in microbial composition across an oyster reef, our study contributes to advancing the knowledge needed to support effective oyster reef conservation and restoration efforts.

Homogenization of bacterial plastisphere community in soil: a continental-scale microcosm study

Microplastics alter niches of soil microbiota by providing trillions of artificial microhabitats, termed the "plastisphere." Because of the ever-increasing accumulation of microplastics in ecosystems, it is urgent to understand the ecology of microbes associated with the plastisphere. Here, we present a continental-scale study of the bacterial plastisphere on polyethylene microplastics compared with adjacent soil communities across 99 sites collected from across China through microcosm experiments. In comparison with the soil bacterial communities, we found that plastispheres had a greater proportion of Actinomycetota and Bacillota, but lower proportions of Pseudomonadota, Acidobacteriota, Gemmatimonadota, and Bacteroidota. The spatial dispersion and the dissimilarity among plastisphere communities were less variable than those among the soil bacterial communities, suggesting highly homogenized bacterial communities on microplastics. The relative importance of homogeneous selection in plastispheres was greater than that in soil samples, possibly because of the more uniform properties of polyethylene microplastics compared with the surrounding soil. Importantly, we found that the degree to which plastisphere and soil bacterial communities differed was negatively correlated with the soil pH and carbon content and positively related to the mean annual temperature of sampling sites. Our work provides a more comprehensive continental-scale perspective on the microbial communities that form in the plastisphere and highlights the potential impacts of microplastics on the maintenance of microbial biodiversity and ecosystem functioning.

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.

Epilithic Bacterial Assemblages on Subtidal Rocky Reefs: Variation Among Alternative Habitats at Ambient and Enhanced Nutrient Levels

Temperate rocky reefs often support mosaics of alternative habitats such as macroalgal forests, algal turfs and sea urchin barrens. Although the composition of epilithic microbial biofilms (EMBs) is recognized as a major determinant of macroalgal recruitment, their role in regulating the stability of alternative habitats on temperate rocky reefs remains unexplored. On shallow rocky reefs of the Island of Capraia (NW Mediterranean), we compared EMB structure among canopy stands formed by the fucoid Ericaria brachycarpa, algal turfs, and urchin barrens under ambient versus experimentally enhanced nutrient levels. The three habitats shared a core microbial community consisting of 21.6 and 25.3% of total ASVs under ambient and enhanced nutrient conditions, respectively. Although Gammaproteobacteria, Alphaproteobacteria and Flavobacteriia were the most abundant classes across habitats, multivariate analyses at the ASV level showed marked differences in EMB composition among habitats. Enhancing nutrient level had no significant effect on EMBs, although it increased their similarity between macroalgal canopy and turf habitats. At both ambient and enriched nutrient levels, ASVs mostly belonging to Proteobacteria and Bacteroidetes were more abundant in EMBs from macroalgal canopies than barrens. In contrast, ASVs belonging to the phylum of Proteobacteria and, in particular, to the families of Rhodobacteraceae and Flavobacteriaceae at ambient nutrient levels and of Rhodobacteraceae and Bacteriovoracaceae at enhanced nutrient levels were more abundant in turf than canopy habitats. Our results show that primary surfaces from alternative habitats that form mosaics on shallow rocky reefs in oligotrophic areas host distinct microbial communities that are, to some extent, resistant to moderate nutrient enhancement. Understanding the role of EMBs in generating reinforcing feedback under different nutrient loading regimes appears crucial to advance our understanding of the mechanisms underpinning the stability of habitats alternative to macroalgal forests as well as their role in regulating reverse shifts.

Microbial Interactions with Dissolved Organic Matter Are Central to Coral Reef Ecosystem Function and Resilience

To thrive in nutrient-poor waters, coral reefs must retain and recycle materials efficiently. This review centers microbial processes in facilitating the persistence and stability of coral reefs, specifically the role of these processes in transforming and recycling the dissolved organic matter (DOM) that acts as an invisible currency in reef production, nutrient exchange, and organismal interactions. The defining characteristics of coral reefs, including high productivity, balanced metabolism, high biodiversity, nutrient retention, and structural complexity, are inextricably linked to microbial processing of DOM. The composition of microbes and DOM in reefs is summarized, and the spatial and temporal dynamics of biogeochemical processes carried out by microorganisms in diverse reef habitats are explored in a variety of key reef processes, including decomposition, accretion, trophictransfer, and macronutrient recycling. Finally, we examine how widespread habitat degradation of reefs is altering these important microbe-DOM interactions, creating feedbacks that reduce reef resilience to global change.