Temporal covariation of epibacterial community and surface metabolome in the Mediterranean seaweed holobiont Taonia atomaria

Progress and future directions for seaweed holobiont research

In the marine environment, seaweeds (i.e. marine macroalgae) provide a wide range of ecological services and economic benefits. Like land plants, seaweeds do not provide these services in isolation, rather they rely on their associated microbial communities, which together with the host form the seaweed holobiont. However, there is a poor understanding of the mechanisms shaping these complex seaweed-microbe interactions, and of the evolutionary processes underlying these interactions. Here, we identify the current research challenges and opportunities in the field of seaweed holobiont biology. We argue that identifying the key microbial partners, knowing how they are recruited, and understanding their specific function and their relevance across all seaweed life history stages are among the knowledge gaps that are particularly important to address, especially in the context of the environmental challenges threatening seaweeds. We further discuss future approaches to study seaweed holobionts, and how we can apply the holobiont concept to natural or engineered seaweed ecosystems.

Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides

BACKGROUND

Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity, and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome, and metaproteome analyses.

RESULTS

Prominent active 0.2-3 µm free-living clades comprised Aurantivirga, "Formosa", Cd. Prosiliicoccus, NS4, NS5, Amylibacter, Planktomarina, SAR11 Ia, SAR92, and SAR86, whereas BD1-7, Stappiaceae, Nitrincolaceae, Methylophagaceae, Sulfitobacter, NS9, Polaribacter, Lentimonas, CL500-3, Algibacter, and Glaciecola dominated 3-10 µm and > 10 µm particles. Particle-attached bacteria were more diverse and exhibited more dynamic adaptive shifts over time in terms of taxonomic composition and repertoires of encoded polysaccharide-targeting enzymes. In total, 305 species-level metagenome-assembled genomes were obtained, including 152 particle-attached bacteria, 100 of which were novel for the sampling site with 76 representing new species. Compared to free-living bacteria, they featured on average larger metagenome-assembled genomes with higher proportions of polysaccharide utilization loci. The latter were predicted to target a broader spectrum of polysaccharide substrates, ranging from readily soluble, simple structured storage polysaccharides (e.g., laminarin, α-glucans) to less soluble, complex structural, or secreted polysaccharides (e.g., xylans, cellulose, pectins). In particular, the potential to target poorly soluble or complex polysaccharides was more widespread among abundant and active particle-attached bacteria.

CONCLUSIONS

Particle-attached bacteria represented only 1% of all bloom-associated bacteria, yet our data suggest that many abundant active clades played a pivotal gatekeeping role in the solubilization and subsequent degradation of numerous important classes of algal glycans. The high diversity of polysaccharide niches among the most active particle-attached clades therefore is a determining factor for the proportion of algal polysaccharides that can be rapidly remineralized during generally short-lived phytoplankton bloom events. Video Abstract.

Seasonal dynamics of a glycan-degrading flavobacterial genus in a tidally mixed coastal temperate habitat

Coastal marine habitats constitute hotspots of primary productivity. In temperate regions, this is due both to massive phytoplankton blooms and dense colonisation by macroalgae that mostly store carbon as glycans, contributing substantially to local and global carbon sequestration. Because they control carbon and energy fluxes, algae-degrading microorganisms are crucial for coastal ecosystem functions. Environmental surveys revealed consistent seasonal dynamics of alga-associated bacterial assemblages, yet resolving what factors regulate the in situ abundance, growth rate and ecological functions of individual taxa remains a challenge. Here, we specifically investigated the seasonal dynamics of abundance and activity for a well-known alga-degrading marine flavobacterial genus in a tidally mixed coastal habitat of the Western English Channel. We show that members of the genus Zobellia are a stable, low-abundance component of healthy macroalgal microbiota and can also colonise particles in the water column. This genus undergoes recurring seasonal variations with higher abundances in winter, significantly associated to biotic and abiotic variables. Zobellia can become a dominant part of bacterial communities on decaying macroalgae, showing a strong activity and high estimated in situ growth rates. These results provide insights into the seasonal dynamics and environmental constraints driving natural populations of alga-degrading bacteria that influence coastal carbon cycling.

Metabolomics and Microbiomics Insights into Differential Surface Fouling of Three Macroalgal Species of Fucus (Fucales, Phaeophyceae) That Co-Exist in the German Baltic Sea

The brown algal genus Fucus provides essential ecosystem services crucial for marine environments. Macroalgae (seaweeds) release dissolved organic matter, hence, are under strong settlement pressure from micro- and macrofoulers. Seaweeds are able to control surface epibionts directly by releasing antimicrobial compounds onto their surfaces, and indirectly by recruiting beneficial microorganisms that produce antimicrobial/antifouling metabolites. In the Kiel Fjord, in the German Baltic Sea, three distinct Fucus species coexist: F. vesiculosus, F. serratus, and F. distichus subsp. evanescens. Despite sharing the same habitat, they show varying fouling levels; F. distichus subsp. evanescens is the least fouled, while F. vesiculosus is the most fouled. The present study explored the surface metabolomes and epiphytic microbiota of these three Fucus spp., aiming to uncover the factors that contribute to the differences in the fouling intensity on their surfaces. Towards this aim, algal surface metabolomes were analyzed using comparative untargeted LC-MS/MS-based metabolomics, to identify the marker metabolites influencing surface fouling. Their epiphytic microbial communities were also comparatively characterized using high-throughput amplicon sequencing, to pinpoint the differences in the surface microbiomes of the algae. Our results show that the surface of the least fouling species, F. distichus subsp. evanescens, is enriched with bioactive compounds, such as betaine lipids MGTA, 4-pyridoxic acid, and ulvaline, which are absent from the other species. Additionally, it exhibits a high abundance of the fungal genera Mucor and Alternaria, along with the bacterial genus Yoonia-Loktanella. These taxa are known for producing antimicrobial/antifouling compounds, suggesting their potential role in the observed fouling resistance on the surface of the F. distichus subsp. evanescens compared to F. serratus and F. vesiculosus. These findings provide valuable clues on the differential surface fouling intensity of Fucus spp., and their importance in marine chemical defense and fouling dynamics.

Transcriptome Analysis Reveals the Genes Involved in Oxidative Stress Responses of Scallop to PST-Producing Algae and a Candidate Biomarker for PST Monitoring

Paralytic shellfish toxins (PST) could be accumulated in bivalves and cause safety problems. To protect public health, bivalves are examined for PST contamination before entering the market, usually by high-performance liquid chromatography (HPLC) or LC-tandem mass spectrometry (LC-MS/MS) in the lab, which needs PST standards not all available and is time-consuming for large sample sizes. To detect PST toxicity in bivalves rapidly and sensitively, a biomarker gene is highly demanded, but the related study is very limited. In this study, we fed a commercially important bivalve, Patinopecten yessoensis, with the PST-producing dinoflagellate Alexandrium catenella. After 1, 3, and 5 days of exposure, both PST concentrations and toxicity levels in the digestive gland continuously increased. Transcriptome analysis revealed that the differentially expressed genes were significantly enriched in oxidation-reduction process, which included the cytochrome P450 genes (CYPs), type I iodothyronine deiodinase (IOD1s), peroxidasin (PXDN), and acyl-Coenzyme A oxidase 1 (ACOX1) at day 1 and a superoxide dismutase (SOD) at day 5, highlighting the crucial roles of these genes in response to oxidative stress induced by PST. Among the 33 continuously upregulated genes, five showed a significant correlation between gene expression and PST concentration, with the highest correlation present in PyC1QL4-1, the gene encoding Complement C1Q-like protein 4, C1QL4. In addition, the correlation between PyC1QL4-1 expression and PST toxicity was also the highest. Further analysis in another aquaculture scallop (Chlamys farreri) indicated that the expression of CfC1QL4-1, the homolog of PyC1QL4-1, also exhibited significant correlations with both PST toxicity and concentration. Our results reveal the gene expression responses of scallop digestive glands to PST-producing algae and indicate that the C1QL4-1 gene might be a potential biomarker for PST monitoring in scallops, which may provide a convenient way for the early warning and sensitive detection of PST contamination in the bivalves.

Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.

Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity

BACKGROUND

Identifying meaningful ecological associations between host and components of the microbiome is challenging. This is especially true for hosts such as marine macroalgae where the taxonomic composition of the microbiome is highly diverse and variable in space and time. Identifying core taxa is one way forward but there are many methods and thresholds in use. This study leverages a large dataset of microbial communities associated with the widespread brown macroalga, Fucus distichus, across sites and years on one island in British Columbia, Canada. We compare three different methodological approaches to identify core taxa at the amplicon sequence variant (ASV) level from this dataset: (1) frequency analysis of taxa on F. distichus performed over the whole dataset, (2) indicator species analysis (IndVal) over the whole dataset that identifies frequent taxa that are enriched on F. distichus in comparison to the local environment, and (3) a two-step IndVal method that identifies taxa that are consistently enriched on F. distichus across sites and time points. We then investigated a F. distichus time-series dataset to see if those core taxa are seasonally consistent on another remote island in British Columbia, Canada. We then evaluate host-specificity of the identified F. distichus core ASVs using comparative data from 32 other macroalgal species sampled at one of the sites.

RESULTS

We show that a handful of core ASVs are consistently identified by both frequency analysis and IndVal approaches with alternative definitions, although no ASVs were always present on F. distichus and IndVal identified a diverse array of F. distichus indicator taxa across sites on Calvert Island in multiple years. Frequency analysis captured a broader suit of taxa, while IndVal was better at identifying host-specific microbes. Finally, two-step IndVal identified hundreds of indicator ASVs for particular sites/timepoints but only 12 that were indicators in a majority (> 6 out of 11) of sites/timepoints. Ten of these ASVs were also indicators on Quadra Island, 250 km away. Many F. distichus-core ASVs are generally found on multiple macroalgal species, while a few ASVs are highly specific to F. distichus.

CONCLUSIONS

Different methodological approaches with variable set thresholds influence core identification, but a handful of core taxa are apparently identifiable as they are widespread and temporally associated with F. distichus and enriched in comparison to the environment. Moreover, we show that many of these core ASVs of F. distichus are found on multiple macroalgal hosts, indicating that most occupy a macroalgal generalist niche rather than forming highly specialized associations with F. distichus. Further studies should test whether macroalgal generalists or specialists are more likely to engage in biologically important exchanges with host.

Allelopathic Potential of Mangroves from the Red River Estuary against the Rice Weed Echinochloa crus-galli and Variation in Their Leaf Metabolome

Mangroves are the only forests located at the sea–land interface in tropical and subtropical regions. They are key elements of tropical coastal ecosystems, providing numerous ecosystem services. Among them is the production of specialized metabolites by mangroves and their potential use in agriculture to limit weed growth in cultures. We explored the in vitro allelopathic potential of eight mangrove species’ aqueous leaf extracts (Avicennia marina, Kandelia obovata, Bruguiera gymnorhiza, Sonneratia apetala, Sonneratia caseolaris, Aegiceras corniculatum, Lumnitzera racemosa and Rhizophora stylosa) on the germination and growth of Echinochloa crus-galli, a weed species associated with rice, Oryza sativa. Leaf methanolic extracts of mangrove species were also studied via UHPLC-ESI/qToF to compare their metabolite fingerprints. Our results highlight that A. corniculatum and S. apetala negatively affected E. crus-galli development with a stimulating effect or no effect on O. sativa. Phytochemical investigations of A. corniculatum allowed us to putatively annotate three flavonoids and two saponins. For S. apetala, three flavonoids, a tannin and two unusual sulfated ellagic acid derivatives were found. Some of these compounds are described for the first time in these species. Overall, A. corniculatum and S. apetala leaves are proposed as promising natural alternatives against E. crus-galli and should be further assessed under field conditions.

Synergistic effects of temperature and light affect the relationship between Taonia atomaria and its epibacterial community: a controlled conditions study

In the context of global warming, this study aimed to assess the effect of temperature and irradiance on the macroalgal Taonia atomaria holobiont dynamics. We developed an experimental set-up using aquaria supplied by natural seawater with three temperatures combined with three irradiances. The holobiont response was monitored over 14 days using a multi-omics approach coupling algal surface metabolomics and metabarcoding. Both temperature and irradiance appeared to shape the microbiota and the surface metabolome, but with a distinct temporality. Epibacterial community first changed according to temperature, and later in relation to irradiance, while the opposite occurred for the surface metabolome. An increased temperature revealed a decreasing richness of the epiphytic community together with an increase of several bacterial taxa. Irradiance changes appeared to quickly impact surface metabolites production linked with the algal host photosynthesis (e.g. mannitol, fucoxanthin, dimethylsulfoniopropionate), which was hypothesized to explain modifications of the structure of the epiphytic community. Algal host may also directly adapt its surface metabolome to changing temperature with time (e.g. lipids content) and also in response to changing microbiota (e.g. chemical defences). Finally, this study brought new insights highlighting complex direct and indirect responses of seaweeds and their associated microbiota under changing environments.

Integration of spatio-temporal variations of surface metabolomes and epibacterial communities highlights the importance of copper stress as a major factor shaping host-microbiota interactions within a Mediterranean seaweed holobiont

BACKGROUND

Although considered as holobionts, macroalgae and their surface microbiota share intimate interactions that are still poorly understood. Little is known on the effect of environmental parameters on the close relationships between the host and its surface-associated microbiota, and even more in a context of coastal pollutions. Therefore, the main objective of this study was to decipher the impact of local environmental parameters, especially trace metal concentrations, on an algal holobiont dynamics using the Phaeophyta Taonia atomaria as a model. Through a multidisciplinary multi-omics approach combining metabarcoding and untargeted LC-MS-based metabolomics, the epibacterial communities and the surface metabolome of T. atomaria were monitored along a spatio-temporal gradient in the bay of Toulon (Northwestern Mediterranean coast) and its surrounding. Indeed, this geographical area displays a well-described trace metal gradient particularly relevant to investigate the effect of such pollutants on marine organisms.

RESULTS

Epibacterial communities of T. atomaria exhibited a high specificity whatever the five environmentally contrasted collecting sites investigated on the NW Mediterranean coast. By integrating metabarcoding and metabolomics analyses, the holobiont dynamics varied as a whole. During the occurrence period of T. atomaria, epibacterial densities and α-diversity increased while the relative proportion of core communities decreased. Pioneer bacterial colonizers constituted a large part of the specific and core taxa, and their decrease might be linked to biofilm maturation through time. Then, the temporal increase of the Roseobacter was proposed to result from the higher temperature conditions, but also the increased production of dimethylsulfoniopropionate (DMSP) at the algal surface which could constitute of the source of carbon and sulfur for the catabolism pathways of these taxa. Finally, as a major result of this study, copper concentration constituted a key factor shaping the holobiont system. Thus, the higher expression of carotenoids suggested an oxidative stress which might result from an adaptation of the algal surface metabolome to high copper levels. In turn, this change in the surface metabolome composition could result in the selection of particular epibacterial taxa.

CONCLUSION

We showed that associated epibacterial communities were highly specific to the algal host and that the holobiont dynamics varied as a whole. While temperature increase was confirmed to be one of the main parameters associated to Taonia dynamics, the originality of this study was highlighting copper-stress as a major driver of seaweed-epibacterial interactions. In a context of global change, this study brought new insights on the dynamics of a Mediterranean algal holobiont submitted to heavy anthropic pressures. Video abstract.

Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities

Kelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue, seawater and sediment were sampled during a 6-month in situ experiment simulating kelp detritus accumulation. Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession. Initially, dominant genera (Hellea, Litorimonas, Granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide-degraders such as Bacteroidia members which responded within 4 weeks. Acidimicrobiia, especially members of the Sva0996 marine group, colonized the degrading kelp biomass after 11 weeks. These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders. In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles. Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.

Infochemicals in terrestrial plants and seaweed holobionts: current and future trends

Since the holobiont concept came into the limelight ten years ago, we have become aware that responses of holobionts to climate change stressors may be driven by shifts in the microbiota. However, the complex interactions underlying holobiont responses across aquatic and terrestrial ecosystems remain largely unresolved. One of the key factors driving these responses is the infochemical-mediated communication in the holobiont. In order to come up with a holistic picture, in this Viewpoint we compare mechanisms and infochemicals in the rhizosphere of plants and the eco-chemosphere of seaweeds in response to climate change stressors and other environmental stressors, including drought, warming and nutrient stress. Furthermore, we discuss the inclusion of chemical ecology concepts that are of crucial importance in driving holobiont survival, adaptation and/or holobiont breakdown. Infochemicals can thus be regarded as a 'missing link' in our understanding of holobiont response to climate change and should be investigated while investigating the responses of plant and seaweed holobionts to climate change. This will set the basis for improving our understanding of holobiont responses to climate change stressors across terrestrial and aquatic ecosystems.

Integration of LC/MS-based molecular networking and classical phytochemical approach allows in-depth annotation of the metabolome of non-model organisms - The case study of the brown seaweed Taonia atomaria

Untargeted LC-MS based metabolomics is a useful approach in many research areas such as medicine, systems biology, environmental sciences or even ecology. In such an approach, annotation of metabolomes of non-model organisms remains a significant challenge. In this study, an analytical workflow combining a classical phytochemical approach, using the isolation and the full characterization of the chemical structure of natural products, together with the use of MS/MS-based molecular networking with various levels of restrictiveness was developed. This protocol was applied to the marine brown seaweed Taonia atomaria, a cosmopolitan algal species, and allowed to annotate more than 200 metabolites. First, the algal organic crude extracts were fractionated by flash-chromatography and the chemical structure of eight of the main chemical constituents of this alga were fully characterized by means of spectroscopic methods (1D and 2D NMR, HRMS). These compounds were further used as chemical standards. In a second step, the main fractions of the algal extracts were analyzed by UHPLC-MS/MS and the resulting data were uploaded to the Global Natural Products Social Molecular Networking platform (GNPS) to create several molecular networks (MNs). A first MN (MN-1) was built with restrictive parameters and allowed the creation of clusters composed by nodes with highly similar MS/MS spectra. Then, using database hits and chemical standards as "seed" nodes and/or similarity between MS/MS fragmentation pattern, the main clusters were easily annotated as common glycerolipids and phospholipids, much rare lipids -such as acylglycerylhydroxymethyl-N,N,N-trimethyl-ß-alanines or fulvellic acid derivatives- but also new glycerolipids bearing a terpene moiety. Lastly, the use of less and less constrained MNs allowed to further increase the number of annotated metabolites.

Chemically Mediated Microbial "Gardening" Capacity of a Seaweed Holobiont Is Dynamic

Terrestrial plants are known to “garden” the microbiota of their rhizosphere via released metabolites (that can attract beneficial microbes and deter pathogenic microbes). Such a “gardening” capacity is also known to be dynamic in plants. Although microbial “gardening” has been recently demonstrated for seaweeds, we do not know whether this capacity is a dynamic property in any aquatic flora like in terrestrial plants. Here, we tested the dynamic microbial “gardening” capacity of seaweeds using the model invasive red seaweed Agarophyton vermiculophyllum. Following an initial extraction of surface-associated metabolites (immediately after field collection), we conducted a long-term mesocosm experiment for 5 months to test the effect of two different salinities (low = 8.5 and medium = 16.5) on the microbial “gardening” capacity of the alga over time. We tested “gardening” capacity of A. vermiculophyllum originating from two different salinity levels (after 5 months treatments) in settlement assays against three disease causing pathogenic bacteria and seven protective bacteria. We also compared the capacity of the alga with field-collected samples. Abiotic factors like low salinity significantly increased the capacity of the alga to deter colonization by pathogenic bacteria while medium salinity significantly decreased the capacity of the alga over time when compared to field-collected samples. However, capacity to attract beneficial bacteria significantly decreased at both tested salinity levels when compared to field-collected samples. Dynamic microbial “gardening” capacity of a seaweed to attract beneficial bacteria and deter pathogenic bacteria is demonstrated for the first time. Such a dynamic capacity as found in the current study could also be applicable to other aquatic host–microbe interactions. Our results may provide an attractive direction of research towards manipulation of salinity and other abiotic factors leading to better defended A. vermiculophyllum towards pathogenic bacteria thereby enhancing sustained production of healthy A. vermiculophyllum in farms.

A Multi-Omics Analysis Suggests Links Between the Differentiated Surface Metabolome and Epiphytic Microbiota Along the Thallus of a Mediterranean Seaweed Holobiont

Marine macroalgae constitute an important living resource in marine ecosystems and complex ecological interactions occur at their surfaces with microbial communities. In this context, the present study aimed to investigate how the surface metabolome of the algal holobiont Taonia atomaria could drive epiphytic microbiota variations at the thallus scale. First, a clear discrimination was observed between algal surface, planktonic and rocky prokaryotic communities. These data strengthened the hypothesis of an active role of the algal host in the selection of epiphytic communities. Moreover, significant higher epibacterial density and α-diversity were found at the basal algal parts compared to the apical ones, suggesting a maturation gradient of the community along the thallus. In parallel, a multiplatform mass spectrometry-based metabolomics study, using molecular networking to annotate relevant metabolites, highlighted a clear chemical differentiation at the algal surface along the thallus with similar clustering as for microbial communities. In that respect, higher amounts of sesquiterpenes, phosphatidylcholines (PCs), and diacylglycerylhydroxymethyl-N,N,N-trimethyl-β-alanines (DGTAs) were observed at the apical regions while dimethylsulfoniopropionate (DMSP) and carotenoids were predominantly found at the basal parts of the thalli. A weighted UniFrac distance-based redundancy analysis linking the metabolomics and metabarcoding datasets indicated that these surface compounds, presumably of algal origin, may drive the zonal variability of the epibacterial communities. As only few studies were focused on microbiota and metabolome variation along a single algal thallus, these results improved our understanding about seaweed holobionts. Through this multi-omics approach at the thallus scale, we suggested a plausible scenario where the chemical production at the surface of T. atomaria, mainly induced by the algal physiology, could explain the specificity and the variations of the surface microbiota along the thallus.

Evaluation of a new primer combination to minimize plastid contamination in 16S rDNA metabarcoding analyses of alga-associated bacterial communities

Plant- and alga-associated bacterial communities are generally described via 16S rDNA metabarcoding using universal primers. As plastid genomes encode 16S rDNA related to cyanobacteria, these data sets frequently contain >90% plastidial sequences, and the bacterial diversity may be under-sampled. To overcome this limitation we evaluated in silico the taxonomic coverage for four primer combinations targeting the 16S rDNA V3-V4 region. They included a forward primer universal to Bacteria (S-D-Bact-0341-b-S-17) and four reverse primers designed to avoid plastid DNA amplification. The best primer combination (NOCHL) was compared to the universal primer set in the wet lab using a synthetic community and samples from three macroalgal species. The proportion of plastid sequences was reduced by 99%-100% with the NOCHL primers compared to the universal primers, irrespective of algal hosts, sample collection and extraction protocols. Additionally, the NOCHL primers yielded a higher richness while maintaining the community structure. As Planctomycetes, Verrucomicrobia and Cyanobacteria were underrepresented (70%-90%) compared to universal primers, combining the NOCHL set with taxon-specific primers may be useful for a complete description of the alga-associated bacterial diversity. The NOCHL primers represent an innovation to study algal holobionts without amplifying host plastid sequences and may further be applied to other photosynthetic hosts.

Salinity and Time Can Alter Epibacterial Communities of an Invasive Seaweed

The establishment of epibacterial communities is fundamental to seaweed health and fitness, in modulating ecological interactions and may also facilitate adaptation to new environments. Abiotic factors like salinity can determine bacterial abundance, growth and community composition. However, influence of salinity as a driver of epibacterial community composition (until species level) has not been investigated for seaweeds and especially under long time scales. We also do not know how abiotic stressors may influence the 'core' bacterial species of seaweeds. Following an initial (immediately after field collection) sampling of epibacterial community of an invasive red seaweed Agarophyton vermicullophylum, we conducted a long term mesocosm experiment for 5 months, to examine the influence of three different salinities (low, medium and high) at two different time points (3 months after start of experiment and 5 months, i.e., at the end of experiment) on the epibacterial community richness and composition of Agarophyton. Metagenomic sequencing showed that epibacterial communities changed significantly according to salinity and time points sampled. Epibacterial richness was significantly different between low and high salinities at both time points. Epibacterial richness also varied significantly between 3 months (after start of experiment) and 5 months (end of experiment) within low, medium and high salinity level. Irrespective of salinity levels and time points sampled 727 taxa consistently appeared in all Agarophyton samples hinting at the presence of core bacterial species on the surface of the alga. Our results indicate that both salinity and time can be major driving forces in structuring epibacterial communities of seaweeds with respect to richness and β-diversity. We highlight the necessity of conducting long term experiments allowing us to detect and understand epibacterial succession over time on seaweeds.

Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology

Brown algae are important primary producers and ecosystem engineers in the ocean, and Ectocarpus has been established as a laboratory model for this lineage. Like most multicellular organisms, Ectocarpus is associated with a community of microorganisms, a partnership frequently referred to as holobiont due to the tight interconnections between the components. Although genomic resources for the algal host are well established, its associated microbiome is poorly characterized from a genomic point of view, limiting the possibilities of using these types of data to study host-microbe interactions. To address this gap in knowledge, we present the annotated draft genome sequences of seventy-two cultivable Ectocarpus-associated bacteria. A screening of gene clusters related to the production of secondary metabolites revealed terpene, bacteriocin, NRPS, PKS-t3, siderophore, PKS-t1, and homoserine lactone clusters to be abundant among the sequenced genomes. These compounds may be used by the bacteria to communicate with the host and other microbes. Moreover, detoxification and provision of vitamin B pathways have been observed in most sequenced genomes, highlighting potential contributions of the bacterial metabolism toward host fitness and survival. The genomes sequenced in this study form a valuable resource for comparative genomic analyses and evolutionary surveys of alga-associated bacteria. They help establish Ectocarpus as a model for brown algal holobionts and will enable the research community to produce testable hypotheses about the molecular interactions within this complex system.