Benthic Diatom Blooms of Blue Haslea spp. in the Mediterranean Sea.

Blue Haslea species are marine benthic pennate diatoms able to synthesize a blue-green water-soluble pigment, like marennine produced by H. ostrearia Simonsen. New species of Haslea synthetizing blue pigments were recently described (H. karadagensis, H. nusantara, H. provincialis and H. silbo). Their marennine-like pigments have allelopathic, antioxidative, antiviral and antibacterial properties, which have been demonstrated in laboratory conditions. Marennine is also responsible for the greening of oysters, for example, in the Marennes Oléron area (France), a phenomenon that has economical and patrimonial values. While blue Haslea spp. blooms have been episodically observed in natural environments (e.g., France, Croatia, USA), their dynamics have only been investigated in oyster ponds. This work is the first description of blue Haslea spp. benthic blooms that develop in open environments on the periphyton, covering turf and some macroalgae-like Padina. Different sites were monitored in the Mediterranean Sea (Corsica, France and Croatia) and two different blue Haslea species involved in these blooms were identified: H. ostrearia and H. provincialis. A non-blue Haslea species was also occasionally encountered. The benthic blooms of blue Haslea followed the phytoplankton spring bloom and occurred in shallow calm waters, possibly indicating a prominent role of light to initiate the blooms. In the absence of very strong winds and water currents that can possibly disaggregate the blue biofilm, the end of blooms coincided with the warming of the upper water masses, which might be profitable for other microorganisms and ultimately lead to a shift in the biofilm community.

Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects.

SUMMARY: To support small and large-scale genome mining projects, we present Post-processing Analysis tooLbox for ANTIsmash Reports (Palantir), a dedicated software suite for handling and refining secondary metabolite biosynthetic gene cluster (BGC) data annotated with the popular antiSMASH pipeline. Palantir provides new functionalities building on NRPS/PKS predictions from antiSMASH, such as improved BGC annotation, module delineation and easy access to sub-sequences at different levels (cluster, gene, module and domain). Moreover, it can parse user-provided antiSMASH reports and reformat them for direct use or storage in a relational database. AVAILABILITY AND IMPLEMENTATION: Palantir is released both as a Perl API available on CPAN (https://metacpan.org/release/Bio-Palantir) and as a web application (http://palantir.uliege.be). As a practical use case, the web interface also features a database built from the mining of 1616 cyanobacterial genomes, of which 1488 were predicted to encode at least one BGC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Was the Last Bacterial Common Ancestor a Monoderm after All?

The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis (dcw) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection.

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

BACKGROUND: Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts). FINDINGS: This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenomic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. TECHNICAL DETAILS: Nextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility. TESTING: The toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria. CONCLUSION: The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales.

Distribution of macroalgae in the area of Calvi (Corsica).

BACKGROUND: Macroalgae play a structuring role in benthic ecosystems, which makes it very important to monitor their cover rates and study their community structures and changes in time. Such studies are usually led by autonomous divers and often do not generate sufficient data to provide enough material for strategically-sound conservation plans. This paper describes the dataset generated in the framework of the evaluation of the potential of a complementary data acquisition method: annotating videos transects obtained using an underwater Remotely Operated Vehicle (ROV).The focus was on Cystoseirabrachycarpa, together with the abundance of several other macroalgae species, which could be identified using the ROV images after validation through specimen identification. Furthermore, in order to allow future uses, such as monitoring the status of colonisation of the invasive algae Caulerpacylindracea, the ROV was sent to some deeper transects on sedimentary habitats (40 m) below the Posidonia meadows lower limits. NEW INFORMATION: The project, while providing some interesting insights on using a ROV as a tool to study marine biodiversity, generated a dataset for the distribution of 19 macroalgae on both standardised and new transects in the Bay of Calvi (Katz et al. 2021). The observed species of macroalgae included: Acetabulariaacetabulum, Amphiroarigida, Caulerpaprolifera, Caulerpacylindracea, Codiumbursa, Colpomeniasinuosa, Corallinales (order), Cystoseirabrachycarpa, Cystoseiracrinita, Cystoseiraspinosa, Cystoseirazosteroides, Dictyota (genus), Flabelliapetiolata, Halopteris (genus), Halopterisscoparia, Jania (genus), Osmundariavolubilis, Padina pavonica and Peyssonneliasquamaria.The videos also showed that the invasive algae Caulerpacylindracea has spread between 2016 and 2019 and that more focused studies should be held in the Bay to assess the actual reach and possible impacts of this invasion.Finally, our ROV video transects have also underlined the significant presence of particular benthic macroalgae communities over habitat zones described as "soft-bottom" on benthic habitat maps. Although the biomass per unit area of these communities is probably lower than for most coastal rocky bottoms, this widely-spread habitat type holds a contribution to primary production to be considered in coastal ecosystem models.

Harmful or harmless: Biological effects of marennine on marine organisms.

Marennine is a water-soluble blue-green pigment produced by the marine diatom Haslea ostrearia. The diatom and its pigment are well known from oyster farming areas as the source of the greening of oyster gills, a natural process increasing their market value in Western France. Blooms of blue Haslea are also present outside oyster ponds and hence marine organisms can be exposed, periodically and locally, to significant amounts of marennine in natural environments. Due to its demonstrated antibacterial activities against marine pathogenic bacteria (e.g. Vibrio) and possible prophylactic effects toward bivalve larvae, marennine is of special interest for the aquaculture industry, especially bivalve hatcheries. The present study aimed to provide new insights into the effects of marennine on a large spectrum of marine organisms belonging to different phyla, including species of aquaculture interest and organisms frequently employed in standardised ecotoxicological assays. Different active solutions containing marennine were tested: partially purified Extracellular Marennine (EMn), and concentrated solutions of marennine present in H. ostrearia culture supernatant; the Blue Water (BW) and a new process called Concentrated Supernatant (CS). Biological effects were meanwhile demonstrated in invertebrate species for the three marennine-based solutions at the highest concentrations tested (e.g., decrease of fertilization success, delay of embryonic developmental stages or larval mortality). Exposure to low concentrations did not impact larval survival or development and even tended to enhance larval physiological state. Furthermore, no effects of marennine were observed on the fish gill cell line tested. Marennine could be viewed as a Jekyll and Hyde molecule, which possibly affects the earliest stages of development of some organisms but with no direct impacts on adults. Our results emphasize the need to determine dosages that optimize beneficial effects and critical concentrations not to be exceeded before considering the use of marennine in bivalve or fish hatcheries.

Consensus assessment of the contamination level of publicly available cyanobacterial genomes.

Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.