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.

Alterocin, an Antibiofilm Protein Secreted by Pseudoalteromonas sp. Strain 3J6.

We sought to identify and study the antibiofilm protein secreted by the marine bacterium Pseudoalteromonas sp. strain 3J6. The latter is active against marine and terrestrial bacteria, including Pseudomonas aeruginosa clinical strains forming different biofilm types. Several amino acid sequences were obtained from the partially purified antibiofilm protein, named alterocin. The Pseudoalteromonas sp. 3J6 genome was sequenced, and a candidate alt gene was identified by comparing the genome-encoded proteins to the sequences from purified alterocin. Expressing the alt gene in another nonactive Pseudoalteromonas sp. strain, 3J3, demonstrated that it is responsible for the antibiofilm activity. Alterocin is a 139-residue protein that includes a predicted 20-residue signal sequence, which would be cleaved off upon export by the general secretion system. No sequence homology was found between alterocin and proteins of known functions. The alt gene is not part of an operon and adjacent genes do not seem related to alterocin production, immunity, or regulation, suggesting that these functions are not fulfilled by devoted proteins. During growth in liquid medium, the alt mRNA level peaked during the stationary phase. A single promoter was experimentally identified, and several inverted repeats could be binding sites for regulators. alt genes were found in about 30% of the Pseudoalteromonas genomes and in only a few instances of other marine bacteria of the Hahella and Paraglaciecola genera. Comparative genomics yielded the hypothesis that alt gene losses occurred within the Pseudoalteromonas genus. Overall, alterocin is a novel kind of antibiofilm protein of ecological and biotechnological interest.IMPORTANCE Biofilms are microbial communities that develop on solid surfaces or interfaces and are detrimental in a number of fields, including for example food industry, aquaculture, and medicine. In the latter, antibiotics are insufficient to clear biofilm infections, leading to chronic infections such as in the case of infection by Pseudomonas aeruginosa of the lungs of cystic fibrosis patients. Antibiofilm molecules are thus urgently needed to be used in conjunction with conventional antibiotics, as well as in other fields of application, especially if they are environmentally friendly molecules. Here, we describe alterocin, a novel antibiofilm protein secreted by a marine bacterium belonging to the Pseudoalteromonas genus, and its gene. Alterocin homologs were found in about 30% of Pseudoalteromonas strains, indicating that this new family of antibiofilm proteins likely plays an important albeit nonessential function in the biology of these bacteria. This study opens up the possibility of a variety of applications.

Degradation dynamics and processes associated with the accumulation of Laminaria hyperborea (Phaeophyceae) kelp fragments: an in situ experimental approach.

A high proportion of the kelp Laminaria hyperborea production is exported from kelp forests following seasonal storms or natural annual old blade loss. Transport of drifting kelp fragments can lead to temporary accumulations in benthic subtidal habitats. We investigated the degradation processes of L. hyperborea in a low subtidal sandy bottom ecosystem by setting up a 6-month cage experiment to simulate accumulations of kelp fragments on the seafloor. We monitored temporal changes in biomass, nutritional quality (C:N ratio), respiration, quantum efficiency of photosystem II (Fv /Fm ), bacterial colonization, and chemical defense concentrations. Biomass decomposition started after 2 weeks and followed a classic negative exponential pattern, leading to 50% degradation after 8 weeks. The degradation process seemed to reach a critical step after 11 weeks, with an increase in respiration rate and phlorotannin concentration in the tissues. These results likely reflect an increase in bacterial activity and a weakening of the kelp cell wall. After 25 weeks of degradation, only 16% of the initial biomass persisted, but the remaining large fragments looked intact. Furthermore, photosystems were still responding to light stimuli, indicating that photosynthesis persisted over time. Reproductive tissues appeared on some fragments after 20 weeks of degradation, showing a capacity to maintain the reproductive function. Our results indicate that L. hyperborea fragments degrade slowly. As they maintain major physiological functions (photosynthesis, reproduction, etc.) and accumulate on adjacent ecosystems, they may play a long-term ecological role in coastal ecosystem dynamics.

Polysaccharide utilisation loci of Bacteroidetes from two contrasting open ocean sites in the North Atlantic.

Marine Bacteroidetes have pronounced capabilities of degrading high molecular weight organic matter such as proteins and polysaccharides. Previously we reported on 76 Bacteroidetes-affiliated fosmids from the North Atlantic Ocean's boreal polar and oligotrophic subtropical provinces. Here, we report on the analysis of further 174 fosmids from the same libraries. The combined, re-assembled dataset (226 contigs; 8.8 Mbp) suggests that planktonic Bacteroidetes at the oligotrophic southern station use more peptides and bacterial and animal polysaccharides, whereas Bacteroidetes at the polar station (East-Greenland Current) use more algal and plant polysaccharides. The latter agrees with higher abundances of algae and terrigenous organic matter, including plant material, at the polar station. Results were corroborated by in-depth bioinformatic analysis of 14 polysaccharide utilisation loci from both stations, suggesting laminarin-specificity for four and specificity for sulfated xylans for two loci. In addition, one locus from the polar station supported use of non-sulfated xylans and mannans, possibly of plant origin. While peptides likely represent a prime source of carbon for Bacteroidetes in open oceans, our data suggest that as yet unstudied clades of these Bacteroidetes have a surprisingly broad capacity for polysaccharide degradation. In particular, laminarin-specific PULs seem widespread and thus must be regarded as globally important.

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing.

Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.

Ecological coherence of diversity patterns derived from classical fingerprinting and Next Generation Sequencing techniques.

Changes in richness and bacterial community structure obtained via 454 Massively Parallel Tag Sequencing (MPTS) and Automated Ribosomal Intergenic Analysis (ARISA) were systematically compared to determine whether and how the ecological knowledge obtained from both molecular techniques could be combined. We evaluated community changes over time and depth in marine coastal sands at different levels of taxonomic resolutions, sequence corrections and sequence abundances. Although richness over depth layers or sampling dates greatly varied [∼ 30% and 70-80% new operational taxonomic units (OTU) between two samples with ARISA and MPTS respectively], overall patterns of community variations were similar with both approaches. Alpha-diversity estimated by ARISA-derived OTU was most similar to that obtained from MPTS-derived OTU defined at the order level. Similar patterns of OTU replacement were also found with MPTS at the family level and with 20-25% rare types removed. Using ARISA or MPTS datasets with lower resolution, such as those containing only resident OTU, yielded a similar set of significant contextual variables explaining bacterial community changes. Hence, ARISA as a rapid and low-cost fingerprinting technique represents a valid starting point for more in-depth exploration of community composition when complemented by the detailed taxonomic description offered by MPTS.

Evaluation of sequential filtration and centrifugation to capture environmental DNA and survey microbial eukaryotic communities in aquatic environments.

Sequential membrane filtration of water samples is commonly used to monitor the diversity of aquatic microbial eukaryotes. This capture method is efficient to focus on specific taxonomic groups within a size fraction, but it is time-consuming. Centrifugation, often used to collect microorganisms from pure culture, could be seen as an alternative to capture microbial eukaryotic communities from environmental samples. Here, we compared the two capture methods to assess diversity and ecological patterns of eukaryotic communities in the Thau lagoon, France. Water samples were taken twice a month over a full year and sequential filtration targeting the picoplankton (0.2-3 µm) and larger organisms (>3 µm) was used in parallel to centrifugation. The microbial eukaryotic community in the samples was described using an environmental DNA approach targeting the V4 region of the 18S rRNA gene. The most abundant divisions in the filtration fractions and the centrifugation pellet were Dinoflagellata, Metazoa, Ochrophyta, Cryptophyta. Chlorophyta were dominant in the centrifugation pellet and the picoplankton fraction but not in the larger fraction. Diversity indices and structuring patterns of the community in the two size fractions and the centrifugation pellet were comparable. Twenty amplicon sequence variants were significantly differentially abundant between the two size fractions and the centrifugation pellet, and their temporal patterns of abundance in the two fractions combined were similar to those obtained with centrifugation. Overall, centrifugation led to similar ecological conclusions as the two filtrated fractions combined, thus making it an attractive time-efficient alternative to sequential filtration.

Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay.

Haptophytes are a key phylum of marine protists, including ~300 described morphospecies and 80 morphogenera. We used 454 pyrosequencing on large subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size-fractioned plankton samples collected in the Bay of Naples. One group-specific primer set targeting the LSU rDNA D1/D2 region was designed to amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two size fractions (0.8-3 or 3-20 µm) and two sampling depths [subsurface, at 1 m, or deep chlorophyll maximum (DCM) at 23 m]. 454 reads were identified using a database covering the entire Haptophyta diversity currently sequenced. Our data set revealed several hundreds of Haptophyte clusters. However, most of these clusters could not be linked to taxonomically known sequences: considering OTUs(97%) (clusters build at a sequence identity level of 97%) on our global data set, less than 1% of the reads clustered with sequences from cultures, and less than 12% clustered with reference sequences obtained previously from cloning and Sanger sequencing of environmental samples. Thus, we highlighted a large uncharacterized environmental genetic diversity, which clearly shows that currently cultivated species poorly reflect the actual diversity present in the natural environment. Haptophyte community appeared to be significantly structured according to the depth. The highest diversity and evenness were obtained in samples from the DCM, and samples from the large size fraction (3-20 µm) taken at the DCM shared a lower proportion of common OTUs(97%) with the other samples. Reads from the species Chrysoculter romboideus were notably found at the DCM, while they could be detected at the subsurface. The highest proportion of totally unknown OTUs(97%) was collected at the DCM in the smallest size fraction (0.8-3 µm). Overall, this study emphasized several technical and theoretical barriers inherent to the exploration of the large and largely unknown diversity of unicellular eukaryotes.

Two decades of describing the unseen majority of aquatic microbial diversity.

Aquatic environments harbour large and diverse microbial populations that ensure their functioning and sustainability. In the current context of global change, characterizing microbial diversity has become crucial, and new tools have been developed to overcome the methodological challenges posed by working with microbes in nature. The advent of Sanger sequencing and now next-generation sequencing technologies has enabled the resolution of microbial communities to an unprecedented degree of precision. However, to correctly interpret microbial diversity and its patterns this revolution must also consider conceptual and methodological matters. This review presents advances, gaps and caveats of these recent approaches when considering microorganisms in aquatic ecosystems. We also discuss potentials and limitations of the available methodologies, from water sampling to sequence analysis, and suggest alternative ways to incorporate results in a conceptual and methodological framework. Together, these methods will allow us to gain an unprecedented understanding of microbial diversity in aquatic ecosystems.

Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets.

High-throughput sequencing techniques are becoming attractive to molecular biologists and ecologists as they provide a time- and cost-effective way to explore diversity patterns in environmental samples at an unprecedented resolution. An issue common to many studies is the definition of what fractions of a data set should be considered as rare or dominant. Yet this question has neither been satisfactorily addressed, nor is the impact of such definition on data set structure and interpretation been fully evaluated. Here we propose a strategy, MultiCoLA (Multivariate Cutoff Level Analysis), to systematically assess the impact of various abundance or rarity cutoff levels on the resulting data set structure and on the consistency of the further ecological interpretation. We applied MultiCoLA to a 454 massively parallel tag sequencing data set of V6 ribosomal sequences from marine microbes in temperate coastal sands. Consistent ecological patterns were maintained after removing up to 35-40% rare sequences and similar patterns of beta diversity were observed after denoising the data set by using a preclustering algorithm of 454 flowgrams. This example validates the importance of exploring the impact of the definition of rarity in large community data sets. Future applications can be foreseen for data sets from different types of habitats, e.g. other marine environments, soil and human microbiota.

Ecosystem-specific microbiota and microbiome databases in the era of big data.

The rapid development of sequencing methods over the past decades has accelerated both the potential scope and depth of microbiota and microbiome studies. Recent developments in the field have been marked by an expansion away from purely categorical studies towards a greater investigation of community functionality. As in-depth genomic and environmental coverage is often distributed unequally across major taxa and ecosystems, it can be difficult to identify or substantiate relationships within microbial communities. Generic databases containing datasets from diverse ecosystems have opened a new era of data accessibility despite costs in terms of data quality and heterogeneity. This challenge is readily embodied in the integration of meta-omics data alongside habitat-specific standards which help contextualise datasets both in terms of sample processing and background within the ecosystem. A special case of large genomic repositories, ecosystem-specific databases (ES-DB's), have emerged to consolidate and better standardise sample processing and analysis protocols around individual ecosystems under study, allowing independent studies to produce comparable datasets. Here, we provide a comprehensive review of this emerging tool for microbial community analysis in relation to current trends in the field. We focus on the factors leading to the formation of ES-DB's, their comparison to traditional microbial databases, the potential for ES-DB integration with meta-omics platforms, as well as inherent limitations in the applicability of ES-DB's.

A High Rate Algal Pond Hosting a Dynamic Community of RNA Viruses.

Despite a surge of RNA virome sequencing in recent years, there are still many RNA viruses to uncover-as indicated by the relevance of viral dark matter to RNA virome studies (i.e., putative viruses that do not match to taxonomically identified viruses). This study explores a unique site, a high-rate algal pond (HRAP), for culturing industrially microalgae, to elucidate new RNA viruses. The importance of viral-host interactions in aquatic systems are well documented, and the ever-expanding microalgae industry is no exception. As the industry becomes a more important source of sustainable plastic manufacturing, a producer of cosmetic pigments and alternative protein sources, and a means of CO2 remediation in the face of climate change, studying microalgal viruses becomes a vital practice for proactive management of microalgae cultures at the industrial level. This study provides evidence of RNA microalgal viruses persisting in a CO2 remediation pilot project HRAP and uncovers the diversity of the RNA virosphere contained within it. Evidence shows that family Marnaviridae is cultured in the basin, alongside other potential microalgal infecting viruses (e.g., family Narnaviridae, family Totitiviridae, and family Yueviridae). Finally, we demonstrate that the RNA viral diversity of the HRAP is temporally dynamic across two successive culturing seasons.

Comparative analysis between protist communities from the deep-sea pelagic ecosystem and specific deep hydrothermal habitats.

Protist communities associated with deep seawater and bivalves from six hydrothermal sites in the Pacific Ocean were characterized by microscopy and molecular rRNA gene surveys (18S rRNA) and compared with planktonic communities from Pacific deep-pelagic seawater (from 500 to 3000 m in depth). Genetic libraries from larger size fractions (>3 µm) of deep-pelagic water were mainly dominated by Dinophyceae, whereas small size fractions (<3 µm) mainly revealed radiolarians and Syndiniales. In contrast, more specific opportunistic detritivores and grazers, mostly belonging to Stramenopiles and Cercozoa, were detected from water surrounding vent chimneys. Protist communities were different in the pallial cavity of the giant hydrothermal bivalves Bathymodiolus thermophilus and Calyptogena magnifica, dominated by Ciliophora (primarily belonging to Phyllopharyngea, Oligohymenophorea and Oligotrichea) and Cercozoa. Interestingly, protist communities retrieved from the pallial cavity liquid of hydrothermal bivalves were remarkably homogeneous along the Southern East Pacific Rise, in contrast to bivalves collected on the Mid-Atlantic Ridge hydrothermal vents and cold seeps from the Gulf of Mexico. Hence, complex protist communities seem to occur inside hydrothermal bivalves, and these metazoa may constitute a stable micro-niche for micro-eukaryotes, including grazers, detritivores, symbionts and potential parasites. From these communities, new lineages within the ciliates may emerge.

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.

The genome of Ectocarpus subulatus - A highly stress-tolerant brown alga.

Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.

Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9T to Adapt to Macroalgal Niches.

About half of seaweed biomass is composed of polysaccharides. Most of these complex polymers have a marked polyanionic character. For instance, the red algal cell wall is mainly composed of sulfated galactans, agars and carrageenans, while brown algae contain alginate and fucose-containing sulfated polysaccharides (FCSP) as cell wall polysaccharides. Some marine heterotrophic bacteria have developed abilities to grow on such macroalgal polysaccharides. This is the case of Pseudoalteromonas carrageenovora 9T (ATCC 43555T), a marine gammaproteobacterium isolated in 1955 and which was an early model organism for studying carrageenan catabolism. We present here the genomic analysis of P. carrageenovora. Its genome is composed of two chromosomes and of a large plasmid encompassing 109 protein-coding genes. P. carrageenovora possesses a diverse repertoire of carbohydrate-active enzymes (CAZymes), notably specific for the degradation of macroalgal polysaccharides (laminarin, alginate, FCSP, carrageenans). We confirm these predicted capacities by screening the growth of P. carrageenovora with a large collection of carbohydrates. Most of these CAZyme genes constitute clusters located either in the large chromosome or in the small one. Unexpectedly, all the carrageenan catabolism-related genes are found in the plasmid, suggesting that P. carrageenovora acquired its hallmark capacity for carrageenan degradation by horizontal gene transfer (HGT). Whereas P. carrageenovora is able to use lambda-carrageenan as a sole carbon source, genomic and physiological analyses demonstrate that its catabolic pathway for kappa- and iota-carrageenan is incomplete. This is due to the absence of the recently discovered 3,6-anhydro-D-galactosidase genes (GH127 and GH129 families). A genomic comparison with 52 Pseudoalteromonas strains confirms that carrageenan catabolism has been recently acquired only in a few species. Even though the loci for cellulose biosynthesis and alginate utilization are located on the chromosomes, they were also horizontally acquired. However, these HGTs occurred earlier in the evolution of the Pseudoalteromonas genus, the cellulose- and alginate-related loci being essentially present in one large, late-diverging clade (LDC). Altogether, the capacities to degrade cell wall polysaccharides from macroalgae are not ancestral in the Pseudoalteromonas genus. Such catabolism in P. carrageenovora resulted from a succession of HGTs, likely allowing an adaptation to the life on the macroalgal surface.

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.

The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms.

Tenacibaculum maritimum is a devastating bacterial pathogen of wild and farmed marine fish with a broad host range and a worldwide distribution. We report here the complete genome sequence of the T. maritimum type strain NCIMB 2154T. The genome consists of a 3,435,971-base pair circular chromosome with 2,866 predicted protein-coding genes. Genes encoding the biosynthesis of exopolysaccharides, the type IX secretion system, iron uptake systems, adhesins, hemolysins, proteases, and glycoside hydrolases were identified. They are likely involved in the virulence process including immune escape, invasion, colonization, destruction of host tissues, and nutrient scavenging. Among the predicted virulence factors, type IX secretion-mediated and cell-surface exposed proteins were identified including an atypical sialidase, a sphingomyelinase and a chondroitin AC lyase which activities were demonstrated in vitro.

Where less may be more: how the rare biosphere pulls ecosystems strings.

Rare species are increasingly recognized as crucial, yet vulnerable components of Earth's ecosystems. This is also true for microbial communities, which are typically composed of a high number of relatively rare species. Recent studies have demonstrated that rare species can have an over-proportional role in biogeochemical cycles and may be a hidden driver of microbiome function. In this review, we provide an ecological overview of the rare microbial biosphere, including causes of rarity and the impacts of rare species on ecosystem functioning. We discuss how rare species can have a preponderant role for local biodiversity and species turnover with rarity potentially bound to phylogenetically conserved features. Rare microbes may therefore be overlooked keystone species regulating the functioning of host-associated, terrestrial and aquatic environments. We conclude this review with recommendations to guide scientists interested in investigating this rapidly emerging research area.