Larval settlement of the common Australian sea urchin Heliocidaris erythrogramma in response to bacteria from the surface of coralline algae

Pseudoalteromonas simplex sp. nov. Isolated from the Skin of Bandtail Puffer Fish (Sphoeroides spengleri)

A novel bacterial isolate A520T (A520T = CBAS 737T = CAIM 1944T) was obtained from the skin of bandtail puffer fish Sphoeroides spengleri (Tetraodontidae Family), collected in Arraial do Cabo (Rio de Janeiro, Brazil). A520T is Gram-stain-negative, flagellated and aerobic bacteria. Optimum growth occurs at 25-30 °C in the presence of 3% NaCl. The genome sequence of the novel isolate consisted of 4.5 Mb (4082 coding genes and G+C content of 41.1%). The closest phylogenetic neighbor was Pseudoalteromonas shioyasakiensis JCM 18891T (97.9% 16S rRNA sequence similarity, 94.8% Average Amino Acid Identity, 93% Average Nucleotide Identity and 51.8% similarity in Genome-to-Genome-Distance). Several in silico phenotypic features are useful to differentiate A520T from its closest phylogenetic neighbors, including trehalose, D-mannose, cellobiose, pyrrolidonyl-beta-naphthylamide, starch hydrolysis, D-xylose, lactose, tartrate utilization, sucrose, citrate, glycerol, mucate and acetate utilization, malonate, glucose oxidizer, gas from glucose, nitrite to gas, L-rhamnose, ornithine decarboxylase, lysine decarboxylase and yellow pigment. The genome of the novel species contains 3 gene clusters (~ 66.81 Kbp in total) coding for different types of bioactive compounds that could indicate ecological roles pertaining to the bandtail puffer fish host. Based on genome-based taxonomic approach, strain A520T (A520T = CBAS 737T = CAIM 1944T) is proposed as a new species, Pseudoalteromonas simplex sp. nov.

How the Ecology of Calcified Red Macroalgae is Investigated under a Chemical Approach? A Systematic Review and Bibliometric Study

Characteristics such as calcareous morphology and life cycle are used to understand the ecology of calcified rhodophytes. However, there is limited information regarding their chemical profiles and biological activities. Therefore, a systematic review (PRISMA) was conducted to assess the influence of the chemistry of calcareous rhodophytes on ecological interactions in the marine environment. The keywords used were: ["Chemical AND [Ecology OR Interaction OR Response OR Defense OR Effect OR Cue OR Mediated OR Induce]"] AND ["Red Seaweed" OR "Red Macroalgae" OR Rhodophy?] AND [Calcified OR Calcareous] in Science Direct, Scielo, PUBMED, Springer, Web of Science, and Scopus. Only English articles within the proposed theme were considered. Due to the low number of articles, another search was conducted with three classes and 16 genera. Finally, 67 articles were considered valid. Their titles, abstracts, and keywords were analyzed using IRaMuTeQ through factorial, hierarchical and similarity classification. Most of the studies used macroalgae thallus to evaluate chemical mediation while few tested crude extracts. Some substances were noted as sesquiterpene (6-hydroxy-isololiolide), fatty acid (heptadeca5,8,11-triene) and dibromomethane. The articles were divided into four classes: Herbivory, Competition, Settlement/Metamorphosis, and Epiphytism. Crustose calcareous algae were associated with studies of Settlement/Metamorphosis, while calcified algae were linked to herbivory. Thus, the importance of chemistry in the ecology of these algae is evident,and additional studies are needed to identify the substances responsible for ecological interactions. This study collected essential information on calcified red algae, whose diversity appears to be highly vulnerable to the harmful impacts of ongoing climate change.

Antibiotics alter development and gene expression in the model cnidarian Nematostella vectensis

Background

Antibiotics are commonly used for controlling microbial growth in diseased organisms. However, antibiotic treatments during early developmental stages can have negative impacts on development and physiology that could offset the positive effects of reducing or eliminating pathogens. Similarly, antibiotics can shift the microbial community due to differential effectiveness on resistant and susceptible bacteria. Though antibiotic application does not typically result in mortality of marine invertebrates, little is known about the developmental and transcriptional effects. These sublethal effects could reduce the fitness of the host organism and lead to negative changes after removal of the antibiotics. Here, we quantify the impact of antibiotic treatment on development, gene expression, and the culturable bacterial community of a model cnidarian, Nematostella vectensis.

Methods

Ampicillin, streptomycin, rifampicin, and neomycin were compared individually at two concentrations, 50 and 200 µg mL-1, and in combination at 50 µg mL-1 each, to assess their impact on N. vectensis. First, we determined the impact antibiotics have on larval development. Next Amplicon 16S rDNA gene sequencing was used to compare the culturable bacteria that persist after antibiotic treatment to determine how these treatments may differentially select against the native microbiome. Lastly, we determined how acute (3-day) and chronic (8-day) antibiotic treatments impact gene expression of adult anemones.

Results

Under most exposures, the time of larval settlement extended as the concentration of antibiotics increased and had the longest delay of 3 days in the combination treatment. Culturable bacteria persisted through a majority of exposures where we identified 359 amplicon sequence variants (ASVs). The largest proportion of bacteria belonged to Gammaproteobacteria, and the most common ASVs were identified as Microbacterium and Vibrio. The acute antibiotic exposure resulted in differential expression of genes related to epigenetic mechanisms and neural processes, while constant application resulted in upregulation of chaperones and downregulation of mitochondrial genes when compared to controls. Gene Ontology analyses identified overall depletion of terms related to development and metabolism in both antibiotic treatments.

Discussion

Antibiotics resulted in a significant increase to settlement time of N. vectensis larvae. Culturable bacterial species after antibiotic treatments were taxonomically diverse. Additionally, the transcriptional effects of antibiotics, and after their removal result in significant differences in gene expression that may impact the physiology of the anemone, which may include removal of bacterial signaling on anemone gene expression. Our research suggests that impacts of antibiotics beyond the reduction of bacteria may be important to consider when they are applied to aquatic invertebrates including reef building corals.

Kelp and sea urchin settlement mediated by biotic interactions with benthic coralline algal species

Species interactions can influence key ecological processes that support community assembly and composition. For example, coralline algae encompass extensive diversity and may play a major role in regime shifts from kelp forests to urchin-dominated barrens through their role in inducing invertebrate larval metamorphosis and influencing kelp spore settlement. In a series of laboratory experiments, we tested the hypothesis that different coralline communities facilitate the maintenance of either ecosystem state by either promoting or inhibiting early recruitment of kelps or urchins. Coralline algae significantly increased red urchin metamorphosis compared with a control, while they had varying effects on kelp settlement. Urchin metamorphosis and density of juvenile canopy kelps did not differ significantly across coralline species abundant in both kelp forests and urchin barrens, suggesting that recruitment of urchin and canopy kelps does not depend on specific corallines. Non-calcified fleshy red algal crusts promoted the highest mean urchin metamorphosis percentage and showed some of the lowest canopy kelp settlement. In contrast, settlement of one subcanopy kelp species was reduced on crustose corallines, but elevated on articulated corallines, suggesting that articulated corallines, typically absent in urchin barrens, may need to recover before this subcanopy kelp could return. Coralline species differed in surface bacterial microbiome composition; however, urchin metamorphosis was not significantly different when microbiomes were removed with antibiotics. Our results clarify the role played by coralline algal species in kelp forest community assembly and could have important implications for kelp forest recovery.

The role of microbial biofilms in range shifts of marine habitat-forming organisms

Marine species, such as corals and kelp, are responding to climate change by altering their distributions. Microbial biofilms underpin key processes that affect the establishment, maintenance, and function of these dominant habitat-formers. Climate-mediated changes to microbial biofilms can therefore strongly influence species' range shifts. Here, we review emerging research on the interactions between benthic biofilms and habitat-formers and identify two key areas of interaction where climate change can impact this dynamic: (i) via direct effects on biofilm composition, and (ii) via impacts on the complex feedback loops which exist between the biofilm microbes and habitat-forming organisms. We propose that these key interactions will be fundamental in driving the speed and extent of tropicalisation of coastal ecosystems under climate change.

Characterization and genomic analysis of a novel Pseudoalteromonas phage PS_L5

Pseudoalteromonas is a widely distributed bacterial genus that is associated with marine algae. However, there is still limited knowledge about their bacteriophage. In this study, we reported the isolation of a novel lytic bacteriophage that infects Pseudoalteromonas marina. Transmission electron microscopy revealed that PS_L5 had an icosahedral head of 52.6 ± 2 nm and a non-contractile tail with length of 96.5 ± 2 nm. The genome sequence of this phage was 34, 257 bp and had a GC content of 40.75%. Furthermore, this genome contained 61 predicted open reading frames (ORFs), which involved in various functions such as phage structure, packaging, DNA metabolism, host lysis and other additional functions. Additionally, the phylogenetic analysis based on major capsid protein showed that the phage PS_L5 was closely related to five other Pseudoalteromonas phages, namely PHS3, PHS21, AL, SL25 and Pq0 which also possessed the non-contractile long tail. This study provided the fundamental insights into the evolutionary dynamics of Pseudoalteromonas phages and the interaction between phage and host.

Coral larval settlement induction using tissue-associated and exuded coralline algae metabolites and the identification of putative chemical cues

Reef-building crustose coralline algae (CCA) are known to facilitate the settlement and metamorphosis of scleractinian coral larvae. In recent decades, CCA coverage has fallen globally and degrading environmental conditions continue to reduce coral survivorship, spurring new restoration interventions to rebuild coral reef health. In this study, naturally produced chemical compounds (metabolites) were collected from two pantropical CCA genera to isolate and classify those that induce coral settlement. In experiments using four ecologically important Caribbean coral species, we demonstrate the applicability of extracted, CCA-derived metabolites to improve larval settlement success in coral breeding and restoration efforts. Tissue-associated CCA metabolites induced settlement of one coral species, Orbicella faveolata, while metabolites exuded by CCA (exometabolites) induced settlement of three species: Acropora palmata, Colpophyllia natans and Orbicella faveolata. In a follow-up experiment, CCA exometabolites fractionated and preserved using two different extraction resins induced the same level of larval settlement as the unfractionated positive control exometabolites. The fractionated CCA exometabolite pools were characterized using liquid chromatography tandem mass spectrometry, yielding 145 distinct molecular subnetworks that were statistically defined as CCA-derived and could be classified into 10 broad chemical classes. Identifying these compounds can reveal their natural prevalence in coral reef habitats and facilitate the development of new applications to enhance larval settlement and the survival of coral juveniles.

Induction of larval settlement in crown-of-thorns starfish is not mediated by conspecific cues

Population irruptions of crown-of-thorns starfish (COTS; Acanthaster spp.) remain a major cause of coral reef degradation throughout the Pacific and Indian Oceans and are inherently modulated by larval settlement and recruitment success. Gregarious larval settlement, as exhibited by many other ecologically important marine invertebrates, can catalyse population growth and replenishment. However, whether conspecific cues induce or influence the settlement of COTS larvae remains a critical information gap. This experimental study examined the induction of COTS settlement in response to a range of conspecific cues associated with early- and late-stage herbivorous juveniles, corallivorous juveniles and adults. Competent COTS larvae were generally not induced to settle by the presence of conspecifics or cues associated with conspecifics, while the settlement success of COTS in the presence of coralline algae was not inhibited or enhanced by adding conspecific conditioned seawater. Rather than being reinforced by gregarious settlement, the recruitment of COTS populations appears dependent on associative settlement cues (i.e., coralline algae and/or associated microbial communities) signalling suitable benthic habitat.

Microbial community structure and settlement induction capacity of marine biofilms developed under varied reef conditions

Coral larval settlement relies on biogenic cues such as those elicited by microbial biofilm communities, a crucial element of coral recruitment. Eutrophication can modify these biofilm-associated communities, but studies on how this affects coral larval settlement are limited. In this study, we developed biofilm communities on glass slides at four sites with increasing distance from a mariculture zone. Biofilms farthest from the mariculture area were more effective at inducing the settlement of Acropora tenuis larvae. These biofilms were characterized by a greater proportion of crustose coralline algae (CCA) and gammaproteobacterial taxa compared to biofilms from sites closer to the mariculture zone, which had a greater proportion of cyanobacteria and no CCA. These findings suggest that nutrient enrichment due to mariculture activities alters the composition of biofilm-associated microbiome at nearby reef sites and indirectly causes poor coral larval settlement.

Comparative Genomic Insights into Bacterial Induction of Larval Settlement and Metamorphosis in the Upside-Down Jellyfish Cassiopea

Bacteria are important mediators of the larval transition from pelagic to benthic environments for marine organisms. Bacteria can therefore dictate species distribution and success of an individual. Despite the importance of marine bacteria to animal ecology, the identity of inductive microbes for many invertebrates are unknown. Here, we report the first successful isolation of bacteria from natural substrates capable of inducing settlement and metamorphosis of the planula larvae stage of a true jellyfish, the upside-down jellyfish Cassiopea xamachana. Inductive bacteria belonged to multiple phyla, with various capacity to induce settlement and metamorphosis. The most inductive isolates belonged to the genus Pseudoalteromonas, a marine bacterium known to induce the pelago-benthic transition in other marine invertebrates. In sequencing the genome of the isolated Pseudoalteromonas and a semiinductive Vibrio, we found biosynthetic pathways previously implicated in larval settlement were absent in Cassiopea inducing taxa. We instead identified other candidate biosynthetic gene clusters involved in larval metamorphosis. These findings could provide hints to the ecological success of C. xamachana compared to sympatric congeneric species within mangrove environments and provide avenues to investigate the evolution of animal-microbe interactions. IMPORTANCE The pelagic to benthic transition for the larvae of many marine invertebrate species are thought to be triggered by microbial cues. The microbial species and exact cue that initiates this transition remains unknown for many animals. Here, we identify two bacterial species, a Pseudoalteromonas and a Vibrio, isolated from natural substrate that induce settlement and metamorphosis of the upside-down jellyfish Cassiopea xamachana. Genomic sequencing revealed both isolates lacked genes known to induce the life history transition in other marine invertebrates. Instead, we identified other gene clusters that may be important for jellyfish settlement and metamorphosis. This study is the first step to identifying the bacterial cue for C. xamachana, an ecologically important species to coastal ecosystems and an emerging model system. Understanding the bacterial cues provides insight into marine invertebrate ecology and evolution of animal-microbe interactions.

Two-Component System Response Regulator ompR Regulates Mussel Settlement through Exopolysaccharides

The outer membrane protein (OMP) is a kind of biofilm matrix component that widely exists in Gram-negative bacteria. However, the mechanism of OMP involved in the settlement of molluscs is still unclear. In this study, the mussel Mytilus coruscus was selected as a model to explore the function of ompR, a two-component system response regulator, on Pseudoalteromonas marina biofilm-forming capacity and the mussel settlement. The motility of the ΔompR strain was increased, the biofilm-forming capacity was decreased, and the inducing activity of the ΔompR biofilms in plantigrades decreased significantly (p < 0.05). The extracellular α-polysaccharide and β-polysaccharide of the ΔompR strain decreased by 57.27% and 62.63%, respectively. The inactivation of the ompR gene decreased the ompW gene expression and had no impact on envZ expression or c-di-GMP levels. Adding recombinant OmpW protein caused the recovery of biofilm-inducing activities, accompanied by the upregulation of exopolysaccharides. The findings deepen the understanding of the regulatory mechanism of bacterial two-component systems and the settlement of benthic animals.

Stage-Specific Transcriptomes of the Mussel Mytilus coruscus Reveals the Developmental Program for the Planktonic to Benthic Transition

Many marine invertebrate larvae undergo complex morphological and physiological changes during the planktonic-benthic transition (a.k.a. metamorphosis). In this study, transcriptome analysis of different developmental stages was used to uncover the molecular mechanisms underpinning larval settlement and metamorphosis of the mussel, Mytilus coruscus. Analysis of highly upregulated differentially expressed genes (DEGs) at the pediveliger stage revealed enrichment of immune-related genes. The results may indicate that larvae co-opt molecules of the immune system to sense and respond to external chemical cues and neuroendocrine signaling pathways forecast and trigger the response. The upregulation of adhesive protein genes linked to byssal thread secretion indicates the anchoring capacity required for larval settlement arises prior to metamorphosis. The results of gene expression support a role for the immune and neuroendocrine systems in mussel metamorphosis and provide the basis for future studies to disentangle gene networks and the biology of this important lifecycle transformation.

Chemically mediated rheotaxis of endangered tri-spine horseshoe crab: potential dispersing mechanism to vegetated nursery habitats along the coast

Background

An enhanced understanding of larval ecology is fundamental to improve the management of locally depleted horseshoe crab populations in Asia. Recent studies in the northern Beibu Gulf, China demonstrated that nesting sites of Asian horseshoe crabs are typically close to their nursery beaches with high-density juveniles distributed around mangrove, seagrass and other structured habitats.

Methods

A laboratory Y-maze chamber was used to test whether the dispersal of early-stage juvenile tri-spine horseshoe crab Tachypleus tridentatus is facilitated by chemical cues to approach suitable nursery habitats. The juvenile orientation to either side of the chamber containing controlled seawater or another with various vegetation cues, as well as their movement time, the largest distance and displacement were recorded.

Results

The juveniles preferred to orient toward seagrass Halophila beccarii cues when the concentration reached 0.5 g l^-1, but ceased at 2 g l^-1. The results can be interpreted as a shelter-seeking process to get closer to the preferred settlement habitats. However, the juveniles exhibited avoidance behaviors in the presence of mangrove Avicennia marina and invasive saltmarsh cordgrass Spartina alterniflora at 2 g l^-1. The juveniles also spent less time moving in the presence of the A. marina cue, as well as reduced displacement in water containing the S. alterniflora cue at 1 and 2 g l^-1. These results may explain the absence of juvenile T. tridentatus within densely vegetated areas, which have generally higher organic matter and hydrogen sulfide.

Conclusion

Early-stage juvenile T. tridentatus are capable of detecting and responding to habitat chemical cues, which can help guide them to high-quality settlement habitats. Preserving and restoring seagrass beds in the intertidal areas should be prioritized when formulating habitat conservation and management initiatives for the declining horseshoe crab populations.

Red, Gold and Green: Microbial Contribution of Rhodophyta and Other Algae to Green Turtle (Chelonia mydas) Gut Microbiome

The fitness of the endangered green sea turtle (Chelonia mydas) may be strongly affected by its gut microbiome, as microbes play important roles in host nutrition and health. This study aimed at establishing environmental microbial baselines that can be used to assess turtle health under altered future conditions. We characterized the microbiome associated with the gastrointestinal tract of green turtles from Guinea Bissau in different life stages and associated with their food items, using 16S rRNA metabarcoding. We found that the most abundant (% relative abundance) bacterial phyla across the gastrointestinal sections were Proteobacteria (68.1 ± 13.9% “amplicon sequence variants”, ASVs), Bacteroidetes (15.1 ± 10.1%) and Firmicutes (14.7 ± 21.7%). Additionally, we found the presence of two red algae bacterial indicator ASVs (the Alphaproteobacteria Brucella pinnipedialis with 75 ± 0% and a Gammaproteobacteria identified as methanotrophic endosymbiont of Bathymodiolus, with <1%) in cloacal compartments, along with six bacterial ASVs shared only between cloacal and local environmental red algae samples. We corroborate previous results demonstrating that green turtles fed on red algae (but, to a lower extent, also seagrass and brown algae), thus, acquiring microbial components that potentially aid them digest these food items. This study is a foundation for better understanding the microbial composition of sea turtle digestive tracts.

Coralline photosynthetic physiology across a steep light gradient

Coralline algae (CA) are globally distributed and fulfil many important roles within coastal ecosystems. In this study, photosynthetically active radiation (PAR) measured for 616 days at 2 and 10 m in a temperate subtidal kelp forest in southern New Zealand provided context to photosynthesis vs. irradiance relationships for, and pigment concentrations of, an articulated coralline alga, Arthrocardia sp. and a crustose coralline species assemblage within the Hapalidiales order. The maximum photosynthetic rate Pmax of the Arthrocardia sp. (20.38 ± 2.38 µmol O2. gDW-1 h-1) was significantly higher than the Pmax of crustose coralline spp. (3.72 ± 0.74 µmol O2. gDW-1 h-1) at the same 2 m stratum. Pigment concentration of Arthrocardia sp. was significantly higher than that of crustose coralline spp. at the same depth, while pigment concentration of crustose coralline spp. at 2 and 10 m were not significantly affected by depth. The photosynthetic characteristics of these coralline algae represent a shade acclimated organism with low saturation irradiance (all Ek < 100 µmol photons m-2 s-1). Despite sevenfold difference in average daily dose between 2 and 10 m there was no significant effect of depth on the photosynthetic performance of crustose coralline algae measured. The lack of evidence for acclimation to low light could be because periods of clear water provide enough light to maintain photosynthesis, lower energetic requirements of species found at depth or constraints on the synthesis of photosynthetic pigments at greater depth.

Signalling molecules inducing metamorphosis in marine organisms

Covering: findings from early 1980s until early 2022Microbial-derived cues of marine biofilms induce settlement and metamorphosis of marine organisms, a process responsible for the emergence of diverse flora and fauna in marine habitats. Although this phenomenon is known for more than 80 years, the research field has only recently gained much momentum. Here, we summarize the currently existing biochemical and microbial knowledge about microbial signalling molecules, con-specific signals, and synthetic compounds that induce or prevent recruitment, settlement, and metamorphosis in invertebrate larvae. We discuss the possible modes of action and conclude with perspectives for future research directions in the field of marine chemical ecology.

Transcriptome Dynamics of an Oyster Larval Response to a Conspecific Cue-Mediated Settlement Induction in the Pacific Oyster Crassostrea gigas

The molecular mechanisms underlying the conspecific cue-mediated larval settlement in Crassostrea gigas is not yet fully understood. In this study, we described and compared the transcriptomes of competent pediveligers (Pedi) and conspecific cue-induced postlarvae (PL). A total of 2383 candidate transcripts were identified: 740 upregulated and 1643 downregulated transcripts, after settlement. Gene Ontology analysis revealed active chitin binding, calcium ion binding, and extracellular region processes in both stages. Results showed that the differential expression trend of six candidate transcripts were consistent between the quantitative real-time PCR and transcriptome data. The differential transcript expression related to shell formation showed closely linked dynamics with a gene regulatory network that may involve the interplay of various hormone receptors, neurotransmitters, and neuropeptide receptors working together in a concerted way in the Pedi and PL stages. Our results highlight the transcriptome dynamics underlying the settlement of oysters on conspecific adult shells and demonstrate the potential use of this cue as an attractant for wild and hatchery-grown oyster larval attachment on artificial substrates. It also suggests the possible involvement of an ecdysone signal pathway that may be linked to a neuroendocrine-biomineralization crosstalk in C. gigas settlement.

Bacterial lipopolysaccharide induces settlement and metamorphosis in a marine larva

How larvae of the many phyla of marine invertebrates find places appropriate for settlement, metamorphosis, growth, and reproduction is an enduring question in marine science. Biofilm-induced metamorphosis has been observed in marine invertebrate larvae from nearly every major marine phylum. Despite the widespread nature of this phenomenon, the mechanism of induction remains poorly understood. The serpulid polychaete Hydroides elegans is a well established model for investigating bacteria-induced larval development. A broad range of biofilm bacterial species elicit larval metamorphosis in H. elegans via at least two mechanisms, including outer membrane vesicles (OMVs) and complexes of phage-tail bacteriocins. We investigated the interaction between larvae of H. elegans and the inductive bacterium Cellulophaga lytica, which produces an abundance of OMVs but not phage-tail bacteriocins. We asked whether the OMVs of C. lytica induce larval settlement due to cell membrane components or through delivery of specific cargo. Employing a biochemical structure–function approach with a strong ecological focus, the cells and OMVs produced by C. lytica were interrogated to determine the class of the inductive compounds. Here, we report that larvae of H. elegans are induced to metamorphose by lipopolysaccharide produced by C. lytica. The widespread prevalence of lipopolysaccharide and its associated taxonomic and structural variability suggest it may be a broadly employed cue for bacterially induced larval settlement of marine invertebrates.

Direct and latent effects of ocean acidification on the transition of a sea urchin from planktonic larva to benthic juvenile

Ongoing ocean acidification is expected to affect marine organisms and ecosystems. While sea urchins can tolerate a wide range of pH, this comes at a high energetic cost, and early life stages are particularly vulnerable. Information on how ocean acidification affects transitions between life-history stages is scarce. We evaluated the direct and indirect effects of pH (pH_T 8.0, 7.6 and 7.2) on the development and transition between life-history stages of the sea urchin Strongylocentrotusdroebachiensis, from fertilization to early juvenile. Continuous exposure to low pH negatively affected larval mortality and growth. At pH 7.2, formation of the rudiment (the primordial juvenile) was delayed by two days. Larvae raised at pH 8.0 and transferred to 7.2 after competency had mortality rates five to six times lower than those kept at 8.0, indicating that pH also has a direct effect on older, competent larvae. Latent effects were visible on the larvae raised at pH 7.6: they were more successful in settling (45% at day 40 post-fertilization) and metamorphosing (30%) than larvae raised at 8.0 (17 and 1% respectively). These direct and indirect effects of ocean acidification on settlement and metamorphosis have important implications for population survival.

Impact of different enzymes on biofilm formation and mussel settlement

Enzymes have been known to impact the biofilm forming capacity. However, how the enzymes mediate the biofilm formation and macrofouling remains little known. Here, we investigated the effects of the three kinds of proteases, four kinds of glycosidases and one kind of lipase on the detachment of biofilms of Shewanella marisflavi ECSMB14101, identified biofilm total proteins response to enzyme treatments, and then tested the effects of biofilms treated with enzymes on the settlement of the mussel Mytilus coruscus plantigrades. The results showed that the cell density of bacteria in biofilms formed at different initial bacterial density were noticeably reduced after treating with all tested enzymes, and Neutrase and α-Amylase exhibited best removing efficiency of > 90%. Bacterial total proteins in S. marisflavi biofilm noticeably reduced or disappeared after treated by Alcalase. For the settlements of the mussel M. coruscus plantigrades, inducing capacities of S. marisflavi biofilm were noticeably suppressed and downregulation was > 75% at the initial density of 5 × 10⁶ cells/cm². Thus, the tested enzymes could effectively remove the adhered bacterial cell, inhibit the biofilm formation and finally suppress the mussel settlement. Our findings extend novel knowledge to developing eco-friendly approach to control micro- and macro-fouling.

Major loss of coralline algal diversity in response to ocean acidification

Calcified coralline algae are ecologically important in rocky habitats in the marine photic zone worldwide and there is growing concern that ocean acidification will severely impact them. Laboratory studies of these algae in simulated ocean acidification conditions have revealed wide variability in growth, photosynthesis and calcification responses, making it difficult to assess their future biodiversity, abundance and contribution to ecosystem function. Here, we apply molecular systematic tools to assess the impact of natural gradients in seawater carbonate chemistry on the biodiversity of coralline algae in the Mediterranean and the NW Pacific, link this to their evolutionary history and evaluate their potential future biodiversity and abundance. We found a decrease in the taxonomic diversity of coralline algae with increasing acidification with more than half of the species lost in high pCO₂ conditions. Sporolithales is the oldest order (Lower Cretaceous) and diversified when ocean chemistry favoured low Mg calcite deposition; it is less diverse today and was the most sensitive to ocean acidification. Corallinales were also reduced in cover and diversity but several species survived at high pCO₂ ; it is the most recent order of coralline algae and originated when ocean chemistry favoured aragonite and high Mg calcite deposition. The sharp decline in cover and thickness of coralline algal carbonate deposits at high pCO₂ highlighted their lower fitness in response to ocean acidification. Reductions in CO₂ emissions are needed to limit the risk of losing coralline algal diversity.

Reduction of mussel metamorphosis by inactivation of the bacterial thioesterase gene via alteration of the fatty acid composition

The molecular mechanism underlying modulation of metamorphosis of the bivalve Mytilus coruscus by bacteria remains unclear. Here, the functional role of the thioesterase gene tesA of the bacterium Pseudoalteromonas marina in larval metamorphosis was examined. The aim was to determine whether inactivation of the tesA gene altered the biofilm-inducing capacity, bacterial cell motility, biopolymers, or the intracellular c-di-GMP levels. Complete inactivation of tesA increased the c-di-GMP content in P. marina, accompanied by a reduced fatty acid content, weaker motility, upregulation of bacterial aggregation, and biofilm formation. The metamorphosis rate of mussel larvae on ΔtesA biofilms was reduced by ∼ 80% compared with those settling on wild-type P. marina. Exogenous addition of a mixture of extracted fatty acids from P. marina into the ΔtesA biofilms promoted the biofilm-inducing capacity. This study suggests that the bacterial thioesterase gene tesA altered the fatty acid composition of ΔtesA P. marina biofilms (BF) through regulation of its c-di-GMP, subsequently impacting mussel metamorphosis.

Bacteria-Stimulated Metamorphosis: an Ocean of Insights from Investigating a Transient Host-Microbe Interaction

Recent research on host-microbe interactions has focused on intimate symbioses. Yet transient interactions, such as the stimulation of animal metamorphosis by bacteria, can have significant impacts on each partner. During these short-lived interactions, swimming animal larvae identify a desirable location on the seafloor and undergo metamorphosis into a juvenile based on the presence of specific bottom-dwelling bacteria. While this phenomenon is critical for seeding new animals to establish or maintain benthic ecosystems, there is an ocean of fundamental questions that remain unanswered. Here, I propose an updated model of how bacteria stimulate animal metamorphosis based on evidence that bacteria inject a stimulatory protein that prompts tubeworm metamorphosis. I consider what we hope to learn about stimulatory bacterial products, how animals recognize these products, and the consequences for both partners. Finally, I provide examples of how studying an enigmatic host-microbe interaction can serve as an engine for scientific discovery.

The Influence of Bacteria on Animal Metamorphosis

The swimming larvae of many marine animals identify a location on the seafloor to settle and undergo metamorphosis based on the presence of specific surface-bound bacteria. While bacteria-stimulated metamorphosis underpins processes such as the fouling of ship hulls, animal development in aquaculture, and the recruitment of new animals to coral reef ecosystems, little is known about the mechanisms governing this microbe-animal interaction. Here we review what is known and what we hope to learn about how bacteria and the factors they produce stimulate animal metamorphosis. With a few emerging model systems, including the tubeworm Hydroides elegans, corals, and the hydrozoan Hydractinia, we have begun to identify bacterial cues that stimulate animal metamorphosis and test hypotheses addressing their mechanisms of action. By understanding the mechanisms by which bacteria promote animal metamorphosis, we begin to illustrate how, and explore why, the developmental decision of metamorphosis relies on cues from environmental bacteria.

Bacteroidetes bacteria, important players in the marine sponge larval development process

Bacteroidetes bacteria are frequently found in association with sponges, but their roles in host development are poorly understood. In this study, thirteen bacterial species (12 genera) isolated from the sponge Tedania sp. revealed a common ability to significantly promote sponge larval settlement at rates 30.00-53.33% higher than controls (p < 0.05). Three effective strategies were adapted: (i) two strains formed biofilms enhancing the settlement rate to 56.67-63.33% within three days. (ii) Five strains secreted hydrosoluble molecules improving larval settlement, reaching 59.17%. (iii) Six species produced extracellular vesicles (EVs) that significantly improved settlement by up to 86.67% (p < 0.05). The EV fluorescence demonstrated that they migrated inside the sponge larvae from the planktonic to metamorphosis stage. Generally, marine sponges specifically enrich Bacteroidetes bacteria because of the important player in host development, establishing the basis for reciprocal adaptive co-evolution between the microbial community and animals, even including higher organisms.

Reduced seawater pH alters marine biofilms with impacts for marine polychaete larval settlement

Ocean acidification (OA) can negatively affect early-life stages of marine organisms, with the key processes of larval settlement and metamorphosis potentially vulnerable to reduced seawater pH. Settlement success depends strongly on suitable substrates and environmental cues, with marine biofilms as key settlement inducers for a range of marine invertebrate larvae. This study experimentally investigated (1) how seawater pH determines growth and community composition of marine biofilms, and (2) whether marine biofilms developed under different pH conditions can alter settlement success in the New Zealand serpulid polychaete Galeolaria hystrix. Biofilms were developed under six pH_(T) treatments (spanning from 7.0 to 8.1 [ambient]) in a flow-through system for up to 14 months. Biofilms of different ages (7, 10 and 14 months) were used to assay successful settlement of competent G. hystrix larvae reared under ambient conditions. Biofilm microbiomes were characterized through amplicon sequencing of the small subunit ribosomal rRNA gene (16S and 18S). Biofilm community composition was stable over time within each pH treatment and biofilm age did not affect larval settlement selectivity. Seawater pH treatment strongly influenced biofilm community composition, as well as subsequent settlement success when biofilms were presented to competent Galeolaria larvae. Exposure to biofilms incubated under OA-treatments caused a decrease in larval settlement of up to 40% compared to the ambient treatments. We observed a decrease in settlement on biofilms relative to ambient pH for slides incubated at pH 7.9 and 7.7. This trend was reversed at pH 7.4, resulting in high settlement, comparable to ambient biofilms. Settlement decreased on biofilms from pH 7.2, and no settlement was observed on biofilms from pH 7.0. For the first time, we show that long-term incubation of marine biofilms under a wide range of reduced seawater pH treatments can alter marine biofilms in such a way that settlement success in marine invertebrates can be compromised.

Deep-sea bacteria trigger settlement and metamorphosis of the mussel Mytilus coruscus larvae

Bacteria from coast seawaters are widely known to induce larval recruitment of many invertebrates. However, whether and how deep-sea bacteria, that play crucial roles in the ecological and biogeochemical cycles, promote larval recruitment remains little known. Here, the interaction between deep-sea bacterial biofilms (BFs) and Mytilus coruscus larvae was tested. All these nine deep-sea bacterial isolates triggered planktonic-sessile transition, and the highest percentage of post-larvae was observed in Virgibacillus sp. 1 BF. Except for Pseudomonas sp. 3, Pseudoalteromonas sp. 32 and Bacillus sp. 13, other BF cell  densities were significantly related to their corresponding inductive efficiency. The deep-sea Virgibacillus sp. 1 BFʼs cue that triggers planktonic-sessile transition was uncovered. Treating Virgibacillus sp. 1 BFs through physic-chemical approaches reduced inducing impact and cell survival. The conditioned water collaborated with formalin-fixed Virgibacillus sp. 1 BF hoisted planktonic-sessile transition efficiency in comparison to each one alone. Thus, two signals derived from deep-sea bacteria trigger planktonic-sessile transition in M. coruscus. This finding firstly demonstrates that deep-sea bacteria has good potential for application in the mussel seed production and provides novel insight to clarify the bacteria-mussel interaction.

An unusual microbiome characterises a spatially-aggressive crustose alga rapidly overgrowing shallow Caribbean reefs

Several species of crustose coralline algae (CCA) and their associated microbial biofilms play important roles in determining the settlement location of scleractinian corals on tropical reefs. In recent decades, peyssonnelid algal crusts (PAC) have become spatial dominants across large areas of shallow Caribbean reefs, where they appear to deter the recruitment of scleractinians. Our genetic investigations of PAC in St. John, US Virgin Islands, amplifying the large-subunit ribosomal RNA and psbA protein D1 marker genes, revealed them to be identical to Ramicrusta textilis previously reported overgrowing corals in Jamaica. Specimens of PAC sampled from the Honduras were likewise identical, confirming that this crustose alga inhabits the easternmost and westernmost regions of the Caribbean. We also analysed 16S rDNA tag amplicon libraries of the biofilms associated with PAC and sympatric CCA, which is favoured for coral settlement. Our results show that the microbial communities on PAC (vs. CCA) are characterized by significantly lower numbers of the epibiotic bacterial genus Pseudoalteromonas, which facilitates the recruitment and settlement of marine invertebrates. From these data, we infer that PAC are therefore unlikely to be attractive as settlement sites for coral larvae. Given the significant ecological change anticipated on these reefs due to increasing cover of PAC, there is an urgent need to further investigate competitive interactions between PAC and scleractinian corals, and elucidate the role of PAC and their associated microbiomes in accentuating phase shifts from coral to algae on tropical reefs.

Genetic examination of the marine bacterium Pseudoalteromonas luteoviolacea and effects of its metamorphosis-inducing factors

Pseudoalteromonas luteoviolacea is a globally distributed marine bacterium that stimulates the metamorphosis of marine animal larvae, an important bacteria-animal interaction that can promote the recruitment of animals to benthic ecosystems. Recently, different P. luteoviolacea isolates have been shown to produce two stimulatory factors that can induce tubeworm and coral metamorphosis; Metamorphosis-Associated Contractile structures (MACs) and tetrabromopyrrole (TBP) respectively. However, it remains unclear what proportion of P. luteoviolacea isolates possess the genes encoding MACs, and what phenotypic effect MACs and TBP have on other larval species. Here, we show that 9 of 19 sequenced P. luteoviolacea genomes genetically encode both MACs and TBP. While P. luteoviolacea biofilms producing MACs stimulate the metamorphosis of the tubeworm Hydroides elegans, TBP biosynthesis genes had no effect under the conditions tested. Although MACs are lethal to larvae of the cnidarian Hydractinia symbiologicarpus, P. luteoviolacea mutants unable to produce MACs are capable of stimulating metamorphosis. Our findings reveal a hidden complexity of interactions between a single bacterial species, the factors it produces and two species of larvae belonging to different phyla.

Factors structuring the macrobenthos community in tidal algal reefs

Tidal algal reefs are considered high biodiversity habitats but have received little attention. Macrobenthos communities were characterized in a gradient of habitat types on the tidal flats in northwestern Taiwan, including algal reefs (R), mixed algal reefs and gravel (RG), mixed sand and gravel (SG) and sand (S). Both hydrodynamic movement and surface rugosity were highest in R, followed by RG, SG, and S. The faster the movement and the higher the rugosity were, the higher the density and taxon richness of the macrobenthos community. The relatively slower movement and accumulated sand in S likely resulted in stress on organisms, which led to a lower density and taxon richness of the macrobenthos community. Our results suggest that the main factors structuring the macrobenthos community in the diverse habitat types were hydrodynamic movement and surface rugosity.

A Shallow Water Ferrous-Hulled Shipwreck Reveals a Distinct Microbial Community

Shipwrecks act as artificial reefs and provide a solid surface in aquatic systems for many different forms of life to attach to, especially microbial communities, making them a hotspot of biogeochemical cycling. Depending on the microbial community and surrounding environment, they may either contribute to the wreck’s preservation or deterioration. Even within a single wreck, preservation and deterioration processes may vary, suggesting that the microbial community may also vary. This study aimed to identify the differences through widespread sampling of the microbial communities associated with the Pappy Lane shipwreck (NC shipwreck site #PAS0001), a shallow water ferrous-hulled shipwreck in Pamlico Sound, North Carolina to determine if there are differences across the wreck as well as from its surrounding environment. Loose shipwreck debris, drilled shipcores, surrounding sediment, and seawater samples were collected from the Pappy Lane shipwreck to characterize the microbial communities on and around the shipwreck. Results indicated that the shipwreck samples were more similar to each other than the surrounding sediment and aquatic environments suggesting they have made a specialized niche associated with the shipwreck. There were differences between the microbial community across the shipwreck, including between visibly corroded and non-corroded shipwreck debris pieces. Relative abundance estimates for neutrophilic iron-oxidizing bacteria (FeOB), an organism that may contribute to deterioration through biocorrosion, revealed they are present across the shipwreck and at highest abundance on the samples containing visible corrosion products. Zetaproteobacteria, a known class of marine iron-oxidizers, were also found in higher abundance on shipwreck samples with visible corrosion. A novel Zetaproteobacteria strain, Mariprofundus ferrooxydans O1, was isolated from one of the shipwreck pieces and its genome analyzed to elucidate the functional potential of the organism. In addition to iron oxidation pathways, the isolate has the genomic potential to perform carbon fixation in both high and low oxygen environments, as well as perform nitrogen fixation, contributing to the overall biogeochemical cycling of nutrients and metals in the shipwreck ecosystem. By understanding the microbial communities associated with shallow water ferrous-hulled shipwrecks, better management strategies and preservation plans can be put into place to preserve these artificial reefs and non-renewable cultural resources.

Distinct Temporal Succession of Bacterial Communities in Early Marine Biofilms in a Portuguese Atlantic Port

Marine biofilms are known to influence the corrosion of metal surfaces in the marine environment. Despite some recent research, the succession of bacterial communities colonizing artificial surfaces remains uncharacterized in some temporal settings. More specifically, it is not fully known if bacterial colonizers of artificial surfaces are similar or distinct in the different seasons of the year. In particular the study of early biofilms, in which the bacterial cells communities first adhere to artificial surfaces, are crucial for the development of the subsequent biofilm communities. In this work, we used amplicon-based NGS (next-generation sequencing) and universal 16S rRNA bacterial primers to characterize the early biofilm bacterial communities growing on 316 L stainless steel surfaces in a Northern Portugal port. Sampling spanned 30-day periods in two distinct seasons (spring and winter). Biofilm communities growing in steel surfaces covered with an anti-corrosion paint and planktonic communities from the same location were also characterized. Our results demonstrated that distinct temporal patterns were observed in the sampled seasons. Specifically, a significantly higher abundance of Gammaproteobacteria and Mollicutes was found on the first days of biofilm growth in spring (day 1 to day 4) and a higher abundance of Alphaproteobacteria during the same days of biofilm growth in winter. In the last sampled day (day 30), the spring biofilms significantly shifted toward a dominance of photoautotrophic groups (mostly diatoms) and were also colonized by some macrofouling communities, something not observed during the winter sampling. Our results revealed that bacterial composition in the biofilms was particularly affected by the sampled day of the specific season, more so than the overall effect of the season or overall sampling day of both seasons. Additionally, the application of a non-fouling-release anti-corrosion paint in the steel plates resulted in a significantly lower diversity compared with plates without paint, but this was only observed during spring. We suggest that temporal succession of marine biofilm communities should be taken in consideration for future antifouling/anti-biofilm applications.

Sea urchin larvae show resilience to ocean acidification at the time of settlement and metamorphosis

Extensive research has shown that the early life stages of marine organisms are sensitive to ocean acidification (OA). Less is known, however, on whether larval settlement and metamorphosis may be affected, or by which mechanisms. These are key processes in the life cycle of most marine benthic organisms, since they mark the transition between the free swimming larval stage to benthic life. We investigated whether OA could affect the larval settlement success of the sea urchin Evechinus chloroticus, a key coastal species with ecological, economic and cultural importance in New Zealand. We performed four settlement experiments to test whether reduced seawater pH (ranging from 8.1 to 7.0, at an interval of ~0.2 pH units) alters larval settlement and metamorphosis success. Our results show that settlement success was not significantly reduced when the larvae were exposed to a range of reduced seawater pH treatments (8.1-7.0) at time of settlement (on direct effects). Similarly, when presented with crustose coralline algae (CCA) pre-conditioned in seawater pH of either pH 8.1 or 7.7 for 28 days, larval settlement success remained unaltered (on indirect effects). We conclude that competent larvae in this species are resilient to OA at time of settlement. Further research on a range of taxa that vary in settlement selectivity and behaviour is needed in order to fully understand the effects of OA on the life cycle of marine invertebrates and the consequences it might have for future coastal marine ecosystems.

Hawaiian Bobtail Squid Symbionts Inhibit Marine Bacteria via Production of Specialized Metabolites, Including New Bromoalterochromides BAC-D/D'

Animals that deposit eggs must protect their embryos from fouling and disease by microorganisms to ensure successful development. Although beneficial bacteria are hypothesized to contribute to egg defense in many organisms, the mechanisms of this protection are only recently being elucidated. Our previous studies of the Hawaiian bobtail squid focused on fungal inhibition by beneficial bacterial symbionts of a female reproductive gland and eggs. Herein, using genomic and chemical analyses, we demonstrate that symbiotic bacteria from this gland can also inhibit other marine bacteria in vitro. One bacterial strain in particular, Pseudoalteromonas sp. JC28, had broad-spectrum abilities to inhibit potential fouling bacteria, in part via production of novel bromoalterochromide metabolites, confirmed via genomic annotation of the associated biosynthetic gene cluster. Our results suggest that these bacterial metabolites may contribute to antimicrobial activity in this association and that such defensive symbioses are underutilized sources for discovering novel antimicrobial compounds.

The Hawaiian bobtail squid, Euprymna scolopes, has a symbiotic bacterial consortium in the accessory nidamental gland (ANG), a female reproductive organ that protects eggs against fouling microorganisms. To test the antibacterial activity of ANG community members, 19 bacterial isolates were screened for their ability to inhibit Gram-negative and Gram-positive bacteria, of which two strains were inhibitory. These two antibacterial isolates, Leisingera sp. ANG59 and Pseudoalteromonas sp. JC28, were subjected to further genomic characterization. Genomic analysis of Leisingera sp. ANG59 revealed a biosynthetic gene cluster encoding the antimicrobial compound indigoidine. The genome of Pseudoalteromonas sp. JC28 had a 14-gene cluster with >95% amino acid identity to a known bromoalterochromide (BAC) cluster. Chemical analysis confirmed production of known BACs, BAC-A/A′ (compounds 1a/1b), as well as two new derivatives, BAC-D/D′ (compounds 2a/2b). Extensive nuclear magnetic resonance (NMR) analyses allowed complete structural elucidation of compounds 2a/2b, and the absolute stereochemistry was unambiguously determined using an optimized Marfey’s method. The BACs were then investigated for in vitro antibacterial, antifungal, and nitric oxide (NO) inhibitory activity. Compounds 1a/1b were active against the marine bacteria Bacillus algicola and Vibrio fischeri, while compounds 2a/2b were active only against B. algicola. Compounds 1a/1b inhibited NO production via lipopolysaccharide (LPS)-induced inflammation in RAW264.7 macrophage cells and also inhibited the pathogenic fungus Fusarium keratoplasticum, which, coupled with their antibacterial activity, suggests that these polyketide-nonribosomal peptides may be used for squid egg defense against potential pathogens and/or fouling microorganisms. These results indicate that BACs may provide Pseudoalteromonas sp. JC28 an ecological niche, facilitating competition against nonsymbiotic microorganisms in the host’s environment.

IMPORTANCE Animals that deposit eggs must protect their embryos from fouling and disease by microorganisms to ensure successful development. Although beneficial bacteria are hypothesized to contribute to egg defense in many organisms, the mechanisms of this protection are only recently being elucidated. Our previous studies of the Hawaiian bobtail squid focused on fungal inhibition by beneficial bacterial symbionts of a female reproductive gland and eggs. Herein, using genomic and chemical analyses, we demonstrate that symbiotic bacteria from this gland can also inhibit other marine bacteria in vitro. One bacterial strain in particular, Pseudoalteromonas sp. JC28, had broad-spectrum abilities to inhibit potential fouling bacteria, in part via production of novel bromoalterochromide metabolites, confirmed via genomic annotation of the associated biosynthetic gene cluster. Our results suggest that these bacterial metabolites may contribute to antimicrobial activity in this association and that such defensive symbioses are underutilized sources for discovering novel antimicrobial compounds.

Ocean acidification affects microbial community and invertebrate settlement on biofilms

Increased atmospheric CO₂ is driving ocean acidification (OA), and potential changes in marine ecosystems. Research shows that both planktonic and benthic communities are affected, but how these changes are linked remains unresolved. Here we show experimentally that decreasing seawater pH (from pH 8.1 to 7.8 and 7.4) leads to reduced biofilm formation and lower primary producer biomass within biofilms. These changes occurred concurrently with a re-arrangement of the biofilm microbial communities. Changes suggest a potential shift from autotrophic to heterotrophic dominated biofilms in response to reduced pH. In a complimentary experiment, biofilms reared under reduced pH resulted in altered larval settlement for a model species (Galeolaria hystrix). These findings show that there is a potential cascade of impacts arising from OA effects on biofilms that may drive important community shifts through altered settlement patterns of benthic species.

The Flagellar Gene Regulates Biofilm Formation and Mussel Larval Settlement and Metamorphosis

Biofilms are critical components of most marine systems and provide biochemical cues that can significantly impact overall community composition. Although progress has been made in the bacteria–animal interaction, the molecular basis of modulation of settlement and metamorphosis in most marine animals by bacteria is poorly understood. Here, Pseudoalteromonas marina showing inducing activity on mussel settlement and metamorphosis was chosen as a model to clarify the mechanism that regulates the bacteria–mussel interaction. We constructed a flagellin synthetic protein gene fliP deletion mutant of P. marina and checked whether deficiency of fliP gene will impact inducing activity, motility, and extracellular polymeric substances of biofilms. Furthermore, we examined the effect of flagellar proteins extracted from bacteria on larval settlement and metamorphosis. The deletion of the fliP gene caused the loss of the flagella structure and motility of the ΔfliP strain. Deficiency of the fliP gene promoted the biofilm formation and changed biofilm matrix by reducing β-polysaccharides and increasing extracellular proteins and finally reduced biofilm-inducing activities. Flagellar protein extract promoted mussel metamorphosis, and ΔfliP biofilms combined with additional flagellar proteins induced similar settlement and metamorphosis rate compared to that of the wild-type strain. These findings provide novel insight on the molecular interactions between bacteria and mussels.

The Shewanella genus: ubiquitous organisms sustaining and preserving aquatic ecosystems

The Gram-negative Shewanella bacterial genus currently includes about 70 species of mostly aquatic γ­-proteobacteria, which were isolated around the globe in a multitude of environments such as surface freshwater and the deepest marine trenches. Their survival in such a wide range of ecological niches is due to their impressive physiological and respiratory versatility. Some strains are among the organisms with the highest number of respiratory systems, depending on a complex and rich metabolic network. Implicated in the recycling of organic and inorganic matter, they are important components of organism-rich oxic/anoxic interfaces, but they also belong to the microflora of a broad group of eukaryotes from metazoans to green algae. Examples of long-term biological interactions like mutualism or pathogeny have been described, although molecular determinants of such symbioses are still poorly understood. Some of these bacteria are key organisms for various biotechnological applications, especially the bioremediation of hydrocarbons and metallic pollutants. The natural ability of these prokaryotes to thrive and detoxify deleterious compounds explains their use in wastewater treatment, their use in energy generation by microbial fuel cells and their importance for resilience of aquatic ecosystems.

Species-Specific Differences in the Microbiomes and Organic Exudates of Crustose Coralline Algae Influence Bacterioplankton Communities

Crustose coralline algae (CCA) are critical members of the coral reef ecosystem, yet they remain poorly studied. Recent research on CCA has shown that only a few species play a significant role in the settlement of coral larvae through either the production of chemical settlement cues or the facilitation of specific microbial communities that are hypothesized to influence coral settlement. Thus, defining how DOM exudates differ between CCA species and the bacterioplankton communities these exudates facilitate is important for understanding the role of CCA in invertebrate settlement. We conducted single day exudation experiments on two species of CCA to compare tissue microbiome community structure, DOM production and the effect of DOM on the bacterioplankton community. We collected exudates from Hydrolithon reinboldii and Porolithon onkodes in both filter-sterilized seawater and unfiltered seawater from Kāne'ohe Bay, Hawai'i. Our results demonstrate that while both species exude equivalent quantities of dissolved organic carbon they differ in the composition of fluorescent DOM and fostered distinct microbial communities. P. onkodes exudates facilitate more microbial OTUs associated with coral disease, whereas H. reinboldii facilitated OTUs known to produce antimicrobial compounds. Our results highlight species-specific differences in the composition of fDOM exudates of CCA and the effect of those on microbial community structure.

High bacterial diversity in nearshore and oceanic biofilms and their influence on larval settlement by Hydroides elegans (Polychaeta)

Settlement of many benthic marine invertebrates is stimulated by bacterial biofilms, although it is not known if patterns of settlement reflect microbial communities that are specific to discrete habitats. Here, we characterized the taxonomic and functional gene diversity (16S rRNA gene amplicon and metagenomic sequencing analyses), as well as the specific bacterial abundances, in biofilms from diverse nearby and distant locations, both inshore and offshore, and tested them for their ability to induce settlement of the biofouling tubeworm Hydroides elegans, an inhabitant of bays and harbours around the world. We found that compositions of the bacterial biofilms were site specific, with the greatest differences between inshore and offshore sites. Further, biofilms were highly diverse in their taxonomic and functional compositions across inshore sites, while relatively low diversity was found at offshore sites. Hydroides elegans settled on all biofilms tested, with settlement strongly correlated with bacterial abundance. Bacterial density in biofilms was positively correlated with biofilm age. Our results suggest that the localized distribution of H. elegans is not determined by 'selection' to locations by specific bacteria, but it is more likely linked to the prevailing local ecology and oceanographic features that affect the development of dense biofilms and the occurrence of larvae.

Inducers of settlement and metamorphosis of the shrimp Hippolyte inermis Leach in Posidonia oceanica

Larvae of the caridean shrimp Hippolyte inermis persist in the plankton of the Mediterranean up to about one month. Since they need to reach appropriate coastal areas for their recruitment in seagrass meadows, we hypothesized that leaves of Posidonia oceanica or, alternatively, algae present in their epiphytic biofilms, might be physically recognised as target substrates and trigger larval metamorphosis and settlement. Chemical cues could improve the finding of suitable habitats for settlement. Thus, the effects of leaves of P. oceanica and biofilms of the diatom Cocconeis scutellum parva, seasonally abundant in the leaf epiphytic stratum, were investigated along with the effect of volatile organic compounds (VOCs) extracted from the epiphytic diatom. The physical induction with P. oceanica accelerated larval settlement, stimulating an earlier and faster metamorphosis of larvae. C. scutellum parva produced a weaker effect on settlement; however, diatom’s VOCs had evident influence and accelerated metamorphosis and settlement. We concluded that such chemical cues as the VOCs produced by epiphytic diatoms, reinforce the effect of physical cues for the identification of suitable settlement locations for this shrimp.

Marine biofilms: diversity of communities and of chemical cues

Surfaces immersed in seawater are rapidly colonized by various microorganisms, resulting in the formation of heterogenic marine biofilms. These communities are known to influence the settlement of algae spores and invertebrate larvae, triggering a succession of fouling events, with significant environmental and economic impacts. This review covers recent research regarding the differences in composition of biofilms isolated from different artificial surface types and the influence of environmental factors on their formation. One particular phenomenon - bacterial quorum sensing (QS) - allows bacteria to coordinate swarming, biofilm formation among other phenomena. Some other marine biofilm chemical cues are believed to modulate the settlement and the succession of macrofouling organisms, and they are also reviewed here. Finally, since the formation of a marine biofilm is considered to be an initial, QS-dependent step in the development of marine fouling events, QS inhibition is discussed on its potential as a tool for antibiofouling control in marine settings.

Metagenomic assessment of body surface bacterial communities of the sea urchin, Tripneustes gratilla

Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface bacterial communities associated with T. gratilla, using a 16S rDNA gene metagenomics approach, to provide insight into the bacterial agents associated with this aquaculture species, as well as with this balding disease. Bacterial samples were collected from non-lesioned healthy animals obtained from natural locations along the eastern coast of South Africa, as well as from different cultured cohorts: non-lesioned healthy-, lesioned diseased- and non-lesioned stressed animals. A total of 1,067,515 individual bacterial operational taxonomic units (OTUs) were identified, belonging to 133 family-, 123 genus- and 113 species level OTU groups. Alpha diversity analyses, based on Chao1, Shannon and Simpson indices, showed that there were no statistically significant differences (ANOVA; P > 0.05) between the respective cohorts, as all cohorts displayed a high degree of bacterial diversity. Similarly, beta diversity analyses (Non-metric multidimensional scaling) showed a large degree of overlapping OTUs across the four cohorts. Within each cohort, various OTUs commonly associated with marine environments were found, predominantly belonging to the families Vibrionaceae, Saprospiraceae, Flavobacteriaceae and Sphingomonadaceae. Differential abundance analysis (DESeq2) revealed that OTUs that are differentially abundant across cohorts were likely not responsible for this balding disease, suggesting that complex bacterial agents, rather than a specific pathogenic agent, are likely causing this disease. Furthermore, the putative metabolic functions assigned to the bacterial communities showed that heterotrophic bacteria appear to be responsible for tissue lysis of degrading animal matter. The results from this study, obtained through univariate and multivariate-based approaches, contributes to future management strategies of this emerging aquaculture species by providing insight into the bacterial communities associated with both natural and cultured environments.

Polyurethane, epoxy resin and polydimethylsiloxane altered biofilm formation and mussel settlement

In many environments, biofilms are a major mode and an emergent form of microbial life. Biofilms play crucial roles in biogeochemical cycling and invertebrate recruitment in marine environments. However, relatively little is known about how marine biofilms form on different substrata and about how these biofilms impact invertebrate recruitment. Here, we performed a comparative analysis of a 28-day-old biofilm community on non-coated (a control glass) and coated substrata (polyurethane (PU), epoxy resin (EP) and polydimethylsiloxane (PDMS)) and examined the settlement of Mytilus coruscus plantigrades on these biofilms. PU, EP and PDMS deterred the development of marine biofilms by reducing the biofilm biomass including the biofilm dry weight, cell density of the bacteria and diatoms and chlorophyll a concentrations. Further analysis of bacterial community revealed that EP altered the bacterial community composition compared with that on the glass substrata by reducing the relative abundance of Ruegeria (Alphaproteobacteria) and by increasing the relative abundance of Methylotenera (Betaproteobacteria) and Cyanobacteria in the biofilms. However, bacterial communities developed on PU and PDMS, as well as glass and PU, EP and PDMS did not exhibit differences from each other. The M. coruscus settlement rates on biofilms on PU, EP and PDMS were reduced by 20-41% compared with those on the glass after 28 days. Thus, the tested coatings impacted the development of marine biofilms by altering the biofilm biomass and/or the bacterial community composition. The mussel settlements decreased in the biofilms that formed on the coatings compared with those on non-coated glass.

The impact of the Deepwater Horizon blowout on historic shipwreck-associated sediment microbiomes in the northern Gulf of Mexico

More than 2,000 historic shipwrecks spanning 500 years of history, rest on the Gulf of Mexico seafloor. Shipwrecks serve as artificial reefs and hotspots of biodiversity by providing hard substrate, something rare in deep ocean regions. The Deepwater Horizon (DWH) spill discharged crude oil into the deep Gulf. Because of physical, biological, and chemical interactions, DWH oil was deposited on the seafloor, where historic shipwrecks are present. This study examined sediment microbiomes at seven historic shipwrecks. Steel-hulled, World War II-era shipwrecks and wooden-hulled, 19^th century shipwrecks within and outside of the surface oiled area and subsurface plume were examined. Analysis of 16S rRNA sequence libraries, sediment radiocarbon age data, sedimentation rates, and hydrocarbons revealed that the German U-boat U-166 and the wooden-hulled sailing vessel known as the Mardi Gras Wreck, both in the Mississippi Canyon leasing area, were exposed to deposited oil during a rapid sedimentation event. Impacts to shipwreck microbiomes included a significant increase in Piscirickettsiaceae-related sequences in surface sediments, and reduced biodiversity relative to unimpacted sites. This study is the first to address the impact of the spill on shipwreck-associated microbiomes, and to explore how shipwrecks themselves influence microbiome diversity in the deep sea.

Settlement performance of the Mediterranean reef-builders Dendropoma cristatum (Biondi 1859) in response to natural bacterial films

The gastropod Dendropoma cristatum is a biogenic engineer of the central Mediterranean, forming reefs along the lower rocky intertidal fringe with a remarkable ecological role. To understand whether reef-associated biofilm cultivable bacterial and biofilm ageing may trigger the settlement of the juvenile snails, a combination of laboratory techniques and field experiments was used. Reef-associated biofilm cultivable bacteria were isolated, and a settlement-choice experiment was performed in situ on artificial biofilms composed of i) a mixture of six biofilm-forming selected isolates, ii) all the cultivable bacteria, and iii) 13-, 23-, 32-day old biofilms formed under natural conditions. Overall, settlement rate significantly differed among biofilm treatments (p < 0.0001). A significant positive correlation between biofilm ageing and juvenile D. cristatum settlement was assessed (r = 0.69 (p < 0.001), whereas the biofilm bacterial composition (relatively to the cultivable fraction) did not show any effect on the vermetid's settlement rate.

Lessons from simple marine models on the bacterial regulation of eukaryotic development

Molecular cues from environmental bacteria influence important developmental decisions in diverse marine eukaryotes. Yet, relatively little is understood about the mechanisms underlying these interactions, in part because marine ecosystems are dynamic and complex. With the help of simple model systems, including the choanoflagellate Salpingoeca rosetta, we have begun to uncover the bacterial cues that shape eukaryotic development in the ocean. Here, we review how diverse bacterial cues-from lipids to macromolecules-regulate development in marine eukaryotes. It is becoming clear that there are networks of chemical information circulating in the ocean, with both eukaryotes and bacteria acting as nodes; one eukaryote can precisely respond to cues from several diverse environmental bacteria, and a single environmental bacterium can regulate the development of different eukaryotes.