Microbiota Influences Morphology and Reproduction of the Brown Alga Ectocarpus sp

Epiphytic microbiome associated with intertidal seaweeds in the Mediterranean Sea: comparative analysis of bacterial communities across seaweed phyla

The complex interactions between epiphytic bacteria and marine macroalgae are still poorly understood, with limited knowledge about their community structure, interactions, and functions. This study focuses on comparing epiphytic prokaryotes community structure between three seaweed phyla; Chlorophyta, Rhodophyta, and Heterokontophyta in an easternmost rocky intertidal site of the Mediterranean Sea. By taking a snapshot approach and simultaneously collecting seaweed samples from the same habitat, we minimize environmental variations that could affect epiphytic bacterial assembly, thereby emphasizing host specificity. Through 16S rRNA gene amplicon sequencing, we identified that the microbial community composition was more similar within the same seaweed phylum host compared to seaweed host from other phyla. Furthermore, exclusive Amplicon Sequence Variants (ASVs) were identified for each algal phyla despite sharing higher taxonomic classifications across the other phyla. Analysis of niche breadth indices uncovers distinctive affinities and potential specialization among seaweed host phyla, with 39% of all ASVs identified as phylum specialists and 13% as generalists. Using taxonomy function prediction, we observed that the taxonomic variability does not significantly impact functional redundancy, suggesting resilience to disturbance. The study concludes that epiphytic bacteria composition is connected to host taxonomy, possibly influenced by shared morphological and chemical traits among genetically related hosts, implying a potential coevolutionary relationship between specific bacteria and their host seaweeds.

Exchange or Eliminate: The Secrets of Algal-Bacterial Relationships

Algae and bacteria have co-occurred and coevolved in common habitats for hundreds of millions of years, fostering specific associations and interactions such as mutualism or antagonism. These interactions are shaped through exchanges of primary and secondary metabolites provided by one of the partners. Metabolites, such as N-sources or vitamins, can be beneficial to the partner and they may be assimilated through chemotaxis towards the partner producing these metabolites. Other metabolites, especially many natural products synthesized by bacteria, can act as toxins and damage or kill the partner. For instance, the green microalga Chlamydomonas reinhardtii establishes a mutualistic partnership with a Methylobacterium, in stark contrast to its antagonistic relationship with the toxin producing Pseudomonas protegens. In other cases, as with a coccolithophore haptophyte alga and a Phaeobacter bacterium, the same alga and bacterium can even be subject to both processes, depending on the secreted bacterial and algal metabolites. Some bacteria also influence algal morphology by producing specific metabolites and micronutrients, as is observed in some macroalgae. This review focuses on algal-bacterial interactions with micro- and macroalgal models from marine, freshwater, and terrestrial environments and summarizes the advances in the field. It also highlights the effects of temperature on these interactions as it is presently known.

Maintaining beneficial alga-associated bacterial communities under heat stress: insights from controlled co-culture experiments using antibiotic-resistant bacterial strains

Brown algae, like many eukaryotes, possess diverse microbial communities. Ectocarpus-a model brown alga-relies on these communities for essential processes, such as growth development. Controlled laboratory systems are needed for functional studies of these algal-bacterial interactions. We selected bacterial strains based on their metabolic networks to provide optimal completion of the algal metabolism, rendered them resistant to two antibiotics, and inoculate them to establish controlled co-cultures with Ectocarpus under continuous antibiotic treatment. We then monitored the stability of the resulting associations under control conditions and heat stress using 16S metabarcoding. Antibiotics strongly reduced bacterial diversity both in terms of taxonomy and predicted metabolic functions. In the inoculated sample, 63%-69% of reads corresponded to the inoculated strains, and the communities remained stable during temperature stress. They also partially restored the predicted metabolic functions of the natural community. Overall, the development of antibiotic-resistant helper cultures offers a promising route to fully controlled laboratory experiments with algae and microbiota and thus represents an important step towards generating experimental evidence for specific host-microbe interactions in the systems studied. Further work will be required to achieve full control and progressively expand our repertoire of helper strains including those currently 'unculturable'.

Effects of Hyphomonas Strains on the Growth of Red Algae Pyropia Species by Attaching Specifically to Their Rhizoids

Bacteria and marine macroalgae form close associations, while various bacteria affect the morphogenesis and growth of macroalgae. Hyphomonas strains exhibit normal morphogenetic activity in protoplasts of the red alga Pyropia yezoensis (nori). However, the effects of the bacteria on the growth of Pyropia from protoplast cells to regenerated thalli remain unknown. Here, we assessed the growth of P. yezoensis and Pyropia tenera using combined cultures of three Hyphomonas strains (LNM10-16, SCM-2, and LNM-9) and three algal media (artificial seawater with vitamins, artificial seawater, and natural seawater) over 7 weeks. Third week after culture, the three Hyphomonas strains showed almost similar levels of normal growth activity for both Pyropia species. However, at 7 weeks, significant differences were observed among the three Hyphomonas strains in terms of length, length-to-width ratio, and normal morphology of Pyropia thalli. LNM10-16 significantly promoted the thalli length and length-to-width ratios of both Pyropia species in artificial seawater without vitamins and natural seawater, compared with the other two Hyphomonas strains. P. yezoensis cultured in artificial seawater with vitamins showed a much higher demand for LNM10-16 in development of the thalli length than P. tenera. These results may be explained by differences in the growth activities of Hyphomonas strains and the nutrient requirements of Pyropia species. Furthermore, the bacteria were more specifically attached to the rhizoid surfaces of both species. This study is the first to reveal that Hyphomonas strains affect the growth of Pyropia species by attaching to their rhizoids.

First report of Planomicrobium okeanokoites associated with Himantothallus grandifolius (Desmarestiales, Phaeophyta) from Southern Hemisphere

Gram-positive, aerobic, motile, rod-shaped, mesophilic epiphytic bacterium Planomicrobium okeanokoites was isolated from the surface of endemic species Himantothallus grandifolius in Larsemann Hills, Eastern Antarctica. The diversity of epiphytic bacterial communities living on marine algae remains primarily unexplored; virtually no reports from Antarctic seaweeds. The present study used morpho-molecular approaches for the macroalgae and epiphytic bacterium characterization. Phylogenetic analysis was performed using mitochondrial genome encoded COX1 gene; chloroplast genome encodes rbcL; nuclear genome encoded large subunit ribosomal RNA gene (LSU rRNA) for Himantothallus grandifolius and ribosomal encoded 16S rRNA for Planomicrobium okeanokoites. Morphological and molecular data revealed that the isolate is identified as Himantothallus grandifolius, which belongs to Family Desmarestiaceae of Order Desmarestiales in Class Phaeophyceae showing 99.8% similarity to the sequences of Himantothallus grandifolius, from King George Island, Antarctica (HE866853). The isolated bacterial strain was identified on the basis of chemotaxonomic, morpho-phylogenetic, and biochemical assays. A phylogenetic study based on 16S rRNA gene sequences revealed that the epiphytic bacterial strain SLA-357 was closest related to the Planomicrobium okeanokoites showing 98.7% sequence similarity. The study revealed the first report of this species from the Southern Hemisphere to date. Also, there has been no report regarding the association between the Planomicrobium okeanokoites and Himantothallus grandifolius; however, there are some reports on this bacterium isolated from sediments, soils, and lakes from Northern Hemisphere. This study may open a gateway for further research to know about the mode of interactions and how they affect the physiology and metabolism of each other.

A pathway to improve seaweed aquaculture through microbiota manipulation

Eukaryotic hosts are associated with microbial communities that are critical to their function. Microbiota manipulation using beneficial microorganisms, for example, in the form of animal probiotics or plant growth-promoting microorganisms (PGPMs), can enhance host performance and health. Recently, seaweed beneficial microorganisms (SBMs) have been identified that promote the growth and development and/or improve disease resistance of seaweeds. This knowledge coincides with global initiatives seeking to expand and intensify seaweed aquaculture. Here, we provide a pathway with the potential to improve commercial cultivation of seaweeds through microbiota manipulation, highlighting that seaweed restoration practices can also benefit from further understanding SBMs and their modes of action. The challenges and opportunities of different approaches to identify and apply SBMs to seaweed aquaculture are discussed.

Effects of anthropogenic stress on hosts and their microbiomes: Treated wastewater alters performance and gut microbiome of a key detritivore ( Asellus aquaticus )

Human activity is a major driver of ecological and evolutionary change in wild populations and can have diverse effects on eukaryotic organisms as well as on environmental and host-associated microbial communities. Although host-microbiome interactions can be a major determinant of host fitness, few studies consider the joint responses of hosts and their microbiomes to anthropogenic changes. In freshwater ecosystems, wastewater is a widespread anthropogenic stressor that represents a multifarious environmental perturbation. Here, we experimentally tested the impact of treated wastewater on a keystone host (the freshwater isopod Asellus aquaticus) and its gut microbiome. We used a semi-natural flume experiment, in combination with 16S rRNA amplicon sequencing, to assess how different concentrations (0%, 30%, and 80%) of nonfiltered wastewater (i.e. with chemical toxicants, nutrients, organic particles, and microbes) versus ultrafiltered wastewater (i.e. only dissolved pollutants and nutrients) affected host survival, growth, and food consumption as well as mid- and hindgut bacterial community composition and diversity. Our results show that while host survival was not affected by the treatments, host growth increased and host feeding rate decreased with nonfiltered wastewater - potentially indicating that A. aquaticus fed on organic matter and microbes available in nonfiltered wastewater. Furthermore, even though the midgut microbiome (diversity and composition) was not affected by any of our treatments, nonfiltered wastewater influenced bacterial composition (but not diversity) in the hindgut. Ultrafiltered wastewater, on the other hand, affected both community composition and bacterial diversity in the hindgut, an effect that in our system differed between sexes. While the functional consequences of microbiome changes and their sex specificity are yet to be tested, our results indicate that different components of multifactorial stressors (i.e. different constituents of wastewater) can affect hosts and their microbiome in distinct (even opposing) manners and have a substantial impact on eco-evolutionary responses to anthropogenic stressors.

Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation

Microbes can modify their hosts' stress tolerance, thus potentially enhancing their ecological range. An example of such interactions is Ectocarpus subulatus, one of the few freshwater-tolerant brown algae. This tolerance is partially due to its (un)cultivated microbiome. We investigated this phenomenon by modifying the microbiome of laboratory-grown E. subulatus using mild antibiotic treatments, which affected its ability to grow in low salinity. Low salinity acclimation of these algal-bacterial associations was then compared. Salinity significantly impacted bacterial and viral gene expression, albeit in different ways across algal-bacterial communities. In contrast, gene expression of the host and metabolite profiles were affected almost exclusively in the freshwater-intolerant algal-bacterial communities. We found no evidence of bacterial protein production that would directly improve algal stress tolerance. However, vitamin K synthesis is one possible bacterial service missing specifically in freshwater-intolerant cultures in low salinity. In this condition, we also observed a relative increase in bacterial transcriptomic activity and the induction of microbial genes involved in the biosynthesis of the autoinducer AI-1, a quorum-sensing regulator. This could have resulted in dysbiosis by causing a shift in bacterial behaviour in the intolerant algal-bacterial community. Together, these results provide two promising hypotheses to be examined by future targeted experiments. Although they apply only to the specific study system, they offer an example of how bacteria may impact their host's stress response.

The Influence of Host Specificity and Temperature on Bacterial Communities Associated with Sargassum (Phaeophyceae) Species

Host-related microbiota are critically important for the adaptation/acclimation of hosts to changing environments, but how environmental factors and host characteristics shape the microbial communities remains largely unknown. We investigated the effects of temperature on habitat-forming macroalgae and their associated bacterial communities. Three Sargassum species (S. horneri, S. fusiforme, and S. thunbergii) and seawater samples were sampled in Gouqi Island, China, and these macroalgal samples were incubated at different temperatures (10, 20, and 27°C) for 7 d. Bacterial communities were identified from the 16S rRNA gene V3-V4 regions. The algae-associated bacterial communities of the field samples were significantly different from seawater, implying host specificity. During laboratory incubation, decreased physiological status (photosynthetic rate and oxidative stress response) was detected for all the species at 10°C, especially with regard to S. horneri and S. fusiforme. For each host, associated bacterial communities at 20 and 27°C clustered closely, and these were separated from samples at 10°C based on constrained PCoA analyses. Permutational multivariate analysis of variance revealed that algae-associated bacterial communities were more affected by host species (23.3%) than by temperature (2.48%) during laboratory incubation. The changes in bacterial community composition may be influenced by algae metabolites, which should be tested in a future study. These results further contribute to our understanding of algal microbiome changes in response to environmental changes.

Auxin Regulates Apical Stem Cell Regeneration and Tip Growth in the Marine Red Alga Neopyropia yezoensis

The red alga Neopyropia yezoensis undergoes polarized elongation and asymmetrical cell division of the apical stem cell during tip growth in filamentous generations of its life cycle: the conchocelis and conchosporangium. Side branches are also produced via tip growth, a process involving the regeneration and asymmetrical division of the apical stem cell. Here, we demonstrate that auxin plays a crucial role in these processes by using the auxin antagonist 2-(1H-Indol-3-yl)-4-oxo-4-phenyl-butyric acid (PEO-IAA), which specifically blocks the activity of the auxin receptor TRANSPORT INHIBITOR RESPONSE1 (TIR1) in land plants. PEO-IAA repressed both the regeneration and polarized tip growth of the apical stem cell in single-celled conchocelis; this phenomenon was reversed by treatment with the auxin indole-3-acetic acid (IAA). In addition, tip growth of the conchosporangium was accelerated by IAA treatment but repressed by PEO-IAA treatment. These findings indicate that auxin regulates polarized tip cell growth and that an auxin receptor-like protein is present in N. yezoensis. The sensitivity to different 5-alkoxy-IAA analogs differs considerably between N. yezoensis and Arabidopsis thaliana. N. yezoensis lacks a gene encoding TIR1, indicating that its auxin receptor-like protein differs from the auxin receptor of terrestrial plants. These findings shed light on auxin-induced mechanisms and the regulation of tip growth in plants.

Bacterial Communities of Lab and Field Northern House Mosquitoes (Diptera: Culicidae) Throughout Diapause

Diapause is a hormonally driven response which is triggered by environmental cues that signal impending adverse conditions and prompts metabolic, developmental, and behavioral changes to allow survival until the return of favorable conditions. Microbial symbionts have been shown to influence the metabolism, development, and behavior of their host organisms, all of which are common diapause-associated characteristics. Surveys of bacterial components in relation to diapause have been examined in few systems, of which the species are usually inactive during dormancy, such as eggs or pupae. This is specifically intriguing as adult female diapause in Culex pipiens (Diptera: Culicidae) can last between 4 and 7 mo and females remain mobile within their hibernacula. Furthermore, it is unknown how microbiota changes associated with prolonged dormancy are different between the lab and field for insect systems. This study aims to characterize how the microbiota of C. pipiens changes throughout diapause under both field and lab settings when provided identical food and water resources. Based on these studies, C. pipiens microbiota shifts as diapause progresses and there are considerable differences between field and lab individuals even when provided the same carbohydrate and water sources. Specific bacterial communities have more association with different periods of diapause, field and lab rearing conditions, and nutritional reserve levels. These studies highlight that diapausing mosquito microbiota studies ideally should occur in field mesocosms and at multiple locations, to increase applicability to wild C. pipiens as prolonged exposure to artificial rearing conditions could impact metrics related to diapause-microbiome interactions. Additionally, these findings suggest that it would be worthwhile to establish if the microbiota shift during diapause impacts host physiology and whether this shift is critical to diapause success.

The microbiome of the habitat-forming brown alga Fucus vesiculosus (Phaeophyceae) has similar cross-Atlantic structure that reflects past and present drivers1

Latitudinal diversity gradients have provided many insights into species differentiation and community processes. In the well-studied intertidal zone, however, little is known about latitudinal diversity in microbiomes associated with habitat-forming hosts. We investigated microbiomes of Fucus vesiculosus because of deep understanding of this model system and its latitudinally large, cross-Atlantic range. Given multiple effects of photoperiod, we predicted that cross-Atlantic microbiomes of the Fucus microbiome would be similar at similar latitudes and correlate with environmental factors. We found that community structure and individual amplicon sequencing variants (ASVs) showed distinctive latitudinal distributions, but alpha diversity did not. Latitudinal differentiation was mostly driven by ASVs that were more abundant in cold temperate to subarctic (e.g., Granulosicoccus_t3260, Burkholderia/Caballeronia/Paraburkholderia_t8371) or warm temperate (Pleurocapsa_t10392) latitudes. Their latitudinal distributions correlated with different humidity, tidal heights, and air/sea temperatures, but rarely with irradiance or photoperiod. Many ASVs in potentially symbiotic genera displayed novel phylogenetic biodiversity with differential distributions among tissues and regions, including closely related ASVs with differing north-south distributions that correlated with Fucus phylogeography. An apparent southern range contraction of F. vesiculosus in the NW Atlantic on the North Carolina coast mimics that recently observed in the NE Atlantic. We suggest cross-Atlantic microbial structure of F. vesiculosus is related to a combination of past (glacial-cycle) and contemporary environmental drivers.

A mesocosm study on bacteria-kelp interactions: Importance of nitrogen availability and kelp genetics

Macroalgal holobiont studies involve understanding interactions between the host, its microbiota, and the environment. We analyzed the effect of bacteria-kelp interactions on phenotypic responses of two genetically distinct populations of giant kelp, Macrocystis pyrifera (north and south), exposed to different nitrogen (N) concentrations. In co-culture experiments with different N concentration treatments, we evaluated kelp growth responses and changes in three specific molecular markers associated with the N cycle, both in epiphytic bacteria (relative abundance of nrfA-gene: cytochrome c nitrite reductase) and macroalgae (expression of NR-gene: nitrate reductase; GluSyn-gene: glutamate synthase). Both kelp populations responded differently to N limitation, with M. pyrifera-south sporophytes having a lower specific growth rate (SGR) under N-limiting conditions than the northern population; M. pyrifera-north sporophytes showed no significant differences in SGR when exposed to low-N and high-N concentrations. This corresponded to a higher GluSyn-gene expression in the M. pyrifera-north sporophytes and the co-occurrence of specific nrfA bacterial taxa. These bacteria may increase ammonium availability under low-N concentrations, allowing M. pyrifera-north to optimize nutrient assimilation by increasing the expression of GluSyn. We conclude that bacteria-kelp interactions are important in enhancing kelp growth rates under low N availability, although this effect may be regulated by the genetic background of kelp populations.

Internal microbial zonation during the massive growth of marimo, a lake ball of Aegagropila linnaei in Lake Akan

Marimo (lake ball) is an uncommon ball-like aggregation of the green alga, Aegagropila linnaei. Although A. linnaei is distributed in fresh and brackish waters in the northern hemisphere, marimo colonies are found only in particular habitats. Here, we report the bacterial communities inside various sizes and aggregating structures of natural marimo collected from Lake Akan, Japan. We observed multi-layers composed of sediment particles only in the sizable radial-type marimo with >20 cm diameter and not in the tangled-type marimo. The deeper layers were enriched by Nitrospira, potential sulfur-oxidizing bacteria, and sulfate-reducing bacteria. Microorganisms of the multi-layers would form biofilms incorporating nearby sediment, which would function as microbial “seals” within large radial-type marimo. These findings provide clues to deciphering the growth of endangered marimo.

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The radial type of marimo (lake ball) can grow to over 20 cm in diameter

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The sizable radial-type marimo develops the internal multi-layers and hollow structure

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The layers provide different diverse microbiomes and structural strength

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The internal multi-layers support the massive growth of the radial-type marimo

Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines

Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases.

Bacterial Communities Show Algal Host (Fucus spp.)/Zone Differentiation Across the Stress Gradient of the Intertidal Zone

The intertidal zone often has varying levels of environmental stresses (desiccation, temperature, light) that result in highly stress-tolerant macrobiota occupying the upper zone while less tolerant species occupy the lower zone, but little comparative information is available for intertidal bacteria. Here we describe natural (unmanipulated) bacterial communities of three Fucus congeners (F. spiralis, high zone; F. vesiculosus, mid zone; F. distichus, low zone) as well as those of F. vesiculosus transplanted to the high zone (Dry and Watered treatments) and to the mid zone (Procedural Control) during summer in Maine (United States). We predicted that bacterial communities would be different among the differently zoned natural congeners, and that higher levels of desiccation stress in the high zone would cause bacterial communities of Dry transplants to become similar to F. spiralis, whereas relieving desiccation stress on Watered transplants would maintain the mid-zone F. vesiculosus bacterial community. Bacteria were identified as amplicon sequence variants (ASVs) after sequencing the V4 hypervariable region of the 16S rRNA gene. Microbiome composition and structure were significantly different between the differently zoned congeners at each tissue type (holdfasts, receptacles, vegetative tips). ASVs significantly associated with the mid-zone congener were frequently also present on the high-zone or low-zone congener, whereas overlap in ASVs between the high-zone and low-zone congeners was rare. Only 7 of 6,320 total ASVs were shared among tissues over all congeners and transplant treatments. Holdfast bacterial community composition of Dry transplants was not significantly different from that of F. spiralis, but Watered holdfast communities were significantly different from those of F. spiralis and not significantly different from those of procedural controls. Additional stressor(s) appeared important, because bacterial communities of Dry and Watered transplants were only marginally different from each other (p = 0.059). The relative abundance of Rhodobacteraceae associated with holdfasts generally correlated with environmental stress with highest abundance associated with F. spiralis and the two high-zone transplant treatments. These findings suggest that the abiotic stressors that shape distributional patterns of host species also affect their bacterial communities.

Ectocarpus: an evo-devo model for the brown algae

Ectocarpus is a genus of filamentous, marine brown algae. Brown algae belong to the stramenopiles, a large supergroup of organisms that are only distantly related to animals, land plants and fungi. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity. For many years, little information was available concerning the molecular mechanisms underlying multicellular development in the brown algae, but this situation has changed with the emergence of Ectocarpus as a model brown alga. Here we summarise some of the main questions that are being addressed and areas of study using Ectocarpus as a model organism and discuss how the genomic information, genetic tools and molecular approaches available for this organism are being employed to explore developmental questions in an evolutionary context.

Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host-microbial interactions

Systems modelled in the context of molecular and cellular biology are difficult to represent with a single calibrated numerical model. Flux optimisation hypotheses have shown tremendous promise to accurately predict bacterial metabolism but they require a precise understanding of metabolic reactions occurring in the considered species. Unfortunately, this information may not be available for more complex organisms or non-cultured microorganisms such as those evidenced in microbiomes with metagenomic techniques. In both cases, flux optimisation techniques may not be applicable to elucidate systems functioning. In this context, we describe how automatic reasoning allows relevant features of an unconventional biological system to be identified despite a lack of data. A particular focus is put on the use of Answer Set Programming, a logic programming paradigm with combinatorial optimisation functionalities. We describe its usage to over-approximate metabolic responses of biological systems and solve gap-filling problems. In this review, we compare steady-states and Boolean abstractions of metabolic models and illustrate their complementarity via applications to the metabolic analysis of macro-algae. Ongoing applications of this formalism explore the emerging field of systems ecology, notably elucidating interactions between a consortium of microbes and a host organism. As the first step in this field, we will illustrate how the reduction in microbiotas according to expected metabolic phenotypes can be addressed with gap-filling problems.

Revisiting Australian Ectocarpus subulatus (Phaeophyceae) From the Hopkins River: Distribution, Abiotic Environment, and Associated Microbiota

In 1995 a strain of Ectocarpus was isolated from Hopkins River Falls, Victoria, Australia, constituting one of few available freshwater or nearly freshwater brown algae, and the only one belonging to the genus Ectocarpus. It has since been used as a model to study acclimation and adaptation to low salinities and the role of its microbiota in these processes. To provide more background information on this model, we assessed if Ectocarpus was still present in the Hopkins river 22 years after the original finding, estimated its present distribution, described its abiotic environment, and determined its in situ microbial composition. We sampled for Ectocarpus at 15 sites along the Hopkins River as well as 10 neighboring sites and found individuals with ITS and cox1 sequences identical to the original isolate at three sites upstream of Hopkins River Falls. The salinity of the water at these sites ranged from 3.1 to 6.9, and it was rich in sulfate (1-5 mM). The diversity of bacteria associated with the algae in situ (1312 operational taxonomic units) was one order of magnitude higher than in previous studies of the original laboratory culture, and 95 alga-associated bacterial strains were isolated from algal filaments on site. In particular, species of Planctomycetes were abundant in situ but rare in laboratory cultures. Our results confirmed that Ectocarpus was still present in the Hopkins River, and the newly isolated algal and bacterial strains offer new possibilities to study the adaptation of Ectocarpus to low salinity and its interactions with its microbiome.

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.

Community characteristics and ecological roles of bacterial biofilms associated with various algal settlements on coastal reefs

Bacterial biofilms, which are a group of bacteria attaching to and ultimately forming communities on reefs, perform essential ecological functions in coastal ecosystems. Particularly, they may attract or repulse the settling down of opportunistic algae. However, this phenomenon and the interaction mechanism are not fully understood. This study investigated reefs from the Changdao coastal zone to determine the structures and functions of bacterial biofilms symbiosing with various algae using high-throughput sequencing analysis. The Shannon diversity index of microbiota with algal symbiosis reached 5.34, which was higher than that of microbiota wherein algae were absent (4.80). The beta diversity results for 11 samples revealed that there existed a separation between bacterial communities on reefs with and without attached algae, while communities with similar algae clustered together. The taxa mostly associated with algae-symbiotic microbiota are the Actinobacteria phylum, and the Flavobacteriia and Gammaproteobacteria classes. The Cyanobacteria phylum was not associated with algae-symbiotic microbiota. As revealed by functional analysis, the bacteria mostly involved in the metabolism of sulfur were represented by brown and red algae in the biofilm symbiosis. Bacteria related to the metabolism of certain trace elements were observed only in specific groups. Moreover, phototrophy-related bacteria were less abundant in samples coexisting with algae. This study established the link between bacterial biofilms and algal settlements on costal reefs, and revealed the possible holobiont relationship between them. This may provide new technical directions toward realizing algal cultivation and management during the construction of artificial reef ecosystems.

Scalable and exhaustive screening of metabolic functions carried out by microbial consortia

Motivation

The selection of species exhibiting metabolic behaviors of interest is a challenging step when switching from the investigation of a large microbiota to the study of functions effectiveness. Approaches based on a compartmentalized framework are not scalable. The output of scalable approaches based on a non-compartmentalized modeling may be so large that it has neither been explored nor handled so far.

Results

We present the Miscoto tool to facilitate the selection of a community optimizing a desired function in a microbiome by reporting several possibilities which can be then sorted according to biological criteria. Communities are exhaustively identified using logical programming and by combining the non-compartmentalized and the compartmentalized frameworks. The benchmarking of 4.9 million metabolic functions associated with the Human Microbiome Project, shows that Miscoto is suited to screen and classify metabolic producibility in terms of feasibility, functional redundancy and cooperation processes involved. As an illustration of a host-microbial system, screening the Recon 2.2 human metabolism highlights the role of different consortia within a family of 773 intestinal bacteria.

Availability and implementation

Miscoto source code, instructions for use and examples are available at: https://github.com/cfrioux/miscoto.

Bacterial-Fungal Interactions in the Kelp Endomicrobiota Drive Autoinducer-2 Quorum Sensing

Brown macroalgae are an essential component of temperate coastal ecosystems and a growing economic sector. They harbor diverse microbial communities that regulate algal development and health. This algal holobiont is dynamic and achieves equilibrium via a complex network of microbial and host interactions. We now report that bacterial and fungal endophytes associated with four brown algae (Ascophyllum nodosum, Pelvetia canaliculata, Laminaria digitata, and Saccharina latissima) produce metabolites that interfere with bacterial autoinducer-2 quorum sensing, a signaling system implicated in virulence and host colonization. Additionally, we performed co-culture experiments combined to a metabolomic approach and demonstrated that microbial interactions influence production of metabolites, including metabolites involved in quorum sensing. Collectively, the data highlight autoinducer-2 quorum sensing as a key metabolite in the complex network of interactions within the algal holobiont.

Chemically-Mediated Interactions Between Macroalgae, Their Fungal Endophytes, and Protistan Pathogens

Filamentous fungi asymptomatically colonize the inner tissues of macroalgae, yet their ecological roles remain largely underexplored. Here, we tested if metabolites produced by fungal endophytes might protect their host against a phylogenetically broad spectrum of protistan pathogens. Accordingly, the cultivable fungal endophytes of four brown algal species were isolated and identified based on LSU and SSU sequencing. The fungal metabolomes were tested for their ability to reduce the infection by protistan pathogens in the algal model Ectocarpus siliculosus. The most active metabolomes effective against the oomycetes Eurychasma dicksonii and Anisolpidium ectocarpii, and the phytomixid Maullinia ectocarpii were further characterized chemically. Several pyrenocines isolated from Phaeosphaeria sp. AN596H efficiently inhibited the infection by all abovementioned pathogens. Strikingly, these compounds also inhibited the infection of nori (Pyropia yezoensis) against its two most devastating oomycete pathogens, Olpidiopsis pyropiae, and Pythium porphyrae. We thus demonstrate that fungal endophytes associated with brown algae produce bioactive metabolites which might confer protection against pathogen infection. These results highlight the potential of metabolites to finely-tune the outcome of molecular interactions between algae, their endophytes, and protistan pathogens. This also provide proof-of-concept toward the applicability of such metabolites in marine aquaculture to control otherwise untreatable diseases.

Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore

BACKGROUND

Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade complex polysaccharides from land plants while in marine herbivores, the digestive microbiota is poorly characterized. Most of the latter are generalists and consume red, green, and brown macroalgae, three distinct lineages characterized by a specific composition in complex polysaccharides, which represent half of their biomass. Subsequently, each macroalga features a specific epiphytic microbiota, and the digestive microbiota of marine herbivores is expected to vary with a monospecific algal diet. We investigated the effect of four monospecific diets (Palmaria palmata, Ulva lactuca, Saccharina latissima, Laminaria digitata) on the composition and specificity of the digestive microbiota of a generalist marine herbivore, the abalone, farmed in a temperate coastal area over a year. The microbiota from the abalone digestive gland was sampled every 2 months and explored using metabarcoding.

RESULTS

Diversity and multivariate analyses showed that patterns of the microbiota were significantly linked to seasonal variations of contextual parameters but not directly to a specific algal diet. Three core genera: Psychrilyobacter, Mycoplasma, and Vibrio constantly dominated the microbiota in the abalone digestive gland. Additionally, a less abundant and diet-specific core microbiota featured genera representing aerobic primary degraders of algal polysaccharides.

CONCLUSIONS

This study highlights the establishment of a persistent core microbiota in the digestive gland of the abalone since its juvenile state and the presence of a less abundant and diet-specific core community. While composed of different microbial taxa compared to terrestrial herbivores, the digestive gland constitutes a particular niche in the abalone holobiont, where bacteria (i) may cooperate to degrade algal polysaccharides to products assimilable by the host or (ii) may have acquired these functions through gene transfer from the aerobic algal microbiota.

A Functional Perspective Analysis of Macroalgae and Epiphytic Bacterial Community Interaction

Macroalgae are photosynthetic, multicellular, sessile eukaryotic organisms that offer diverse habitats for the colonization of epiphytic bacteria, therefore establishing biological interactions of diverse complexity. This review focusses on the interactions between macroalgae and their Epiphytic Bacterial Community (EBC); the main aims are to ascertain whether (1) the epiphytic bacterial groups differ at the phylum and genus levels of the macroalgae; (2) the methodologies used so far to study these microorganisms are related in any way to eventual variations of the EBCs on macroalgae; and (3) the EBC of macroalgae has a functional means rather a simple taxonomic grouping. Results showed firstly the taxonomic grouping of macroalgae does not explain the composition and structure of the EBCs. Secondly, the methodology used is important for describing EBCs; and thirdly, multiple bacteria can have the same function and thus to describe the functionality of EBCs it is important to recognize host-specific and generalist bacteria. We recommend the incorporation of a complementary approach between the taxonomic composition and the functional composition analyzes of EBCs, as well as the use of methodological tools that allow analysis of interactions between the EBCs and their hosts, based on the "holobiont" concept.

Exploring the Cultivable Ectocarpus Microbiome

Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal–bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the rare biosphere and they may form the basis for the temporal changes in the Ectocarpus microbiome.

Furthering knowledge of seaweed growth and development to facilitate sustainable aquaculture

Macroalgae (seaweeds) are the subject of increasing interest for their potential as a source of valuable, sustainable biomass in the food, feed, chemical and pharmaceutical industries. Compared with microalgae, the pace of knowledge acquisition in seaweeds is slower despite the availability of whole-genome sequences and model organisms for the major seaweed groups. This is partly a consequence of specific hurdles related to the large size of these organisms and their slow growth. As a result, this basic scientific field is falling behind, despite the societal and economic importance of these organisms. Here, we argue that sustainable management of seaweed aquaculture requires fundamental understanding of the underlying biological mechanisms controlling macroalgal life cycles - from the production of germ cells to the growth and fertility of the adult organisms - using diverse approaches requiring a broad range of technological tools. This Viewpoint highlights several examples of basic research on macroalgal developmental biology that could enable the step-changes which are required to adequately meet the demands of the aquaculture sector.

Towards an understanding of spiral patterning in the Sargassum muticum shoot apex

In plants and parenchymatous brown algae the body arises through the activity of an apical meristem (a niche of cells or a single cell). The meristem produces lateral organs in specific patterns, referred to as phyllotaxis. In plants, two different control mechanisms have been proposed: one is position-dependent and relies on morphogen accumulation at future organ sites; the other is a lineage-based system which links phyllotaxis to the apical cell division pattern. Here we examine the apical patterning of the brown alga, Sargassum muticum, which exhibits spiral phyllotaxis (137.5° angle) and an unlinked apical cell division pattern. The Sargassum apex presents characteristics of a self-organising system, similar to plant meristems. In contrast to complex plant meristems, we were unable to correlate the plant morphogen auxin with bud positioning in Sargassum, nor could we predict cell wall softening at new bud sites. Our data suggests that in Sargassum muticum there is no connection between phyllotaxis and the apical cell division pattern indicating a position-dependent patterning mechanism may be in place. The underlying mechanisms behind the phyllotactic patterning appear to be distinct from those seen in plants.