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The development of a procedure for the one-pot synthesis of glycosyl benzoates directly from unprotected sugars in aqueous media using 2-chloro-1,3-dimethylimidazolium chloride (DMC), thiobenzoic acid, and triethylamine is reported. These glycosyl donors are excellent substrates for wild-type and mutant glycosidases. β-Glucosyl benzoate was hydrolysed by the GH1 β-glucosidase derived from Halothermothrix orenii ( Hor GH1). Subsequent use of this substrate in thioligase-mediated glycosylation of p -nitrothiophenol demonstrated their superiority as donors compared to their p -nitrophenol counterparts with excellent conversions. Using a series of arene nucleophiles, we also demonstrate good to excellent conversions (up to 94%) of β-glucosyl benzoate to the corresponding p -nitrophenyl- and thioglycosides.

In order to expand the toolbox of enzymes available for thioglycoside synthesis, we describe here the first example of an extremophilic glycosyl hydrolase from Halothermothrix orenii ( Hor GH1) engineered towards thioglycosynthase activity with a novel combination of mutations. Using the triple mutant, Hor GH1 M299R/E166A/E354G, a range of thioglycosides from glycosyl fluoride donors and aromatic thiols could be synthesised with exquisite stereoselectivity and good to excellent conversions (61-93%).

Contaminants deriving from human activities represent a constantly growing threat to our environment and have a direct impact on plant and animal health. To alleviate this ecological imbalance, biocatalysis offers a green and sustainable alternative to conventional chemical processes. Due to their broad specificity, laccases are enzymes possessing excellent potential for synthetic biotransformations in various fields as well as for the degradation of organic contaminants. Herein, we produced laccases in submerged cultures of P. ostreatus and T. versicolor in three different media. The fungi/medium combination leading to the highest enzymatic activity was malt extract (2%) + yeast extract (3%) + glucose (0.8%). Laccase production was further increased by supplementing this medium with different concentrations of Cu 2+ , which also provided a better understanding of the induction effect. Additionally, we disclose preliminary results on the interaction of laccases with mediators (ABTS and violuric acid - VA) for two main applications: lignin depolymerisation with guaiacylglycerol-β-guaiacyl ether (GBG) as lignin model and micropollutant degradation with Remazol Brilliant Blue (RBB) as enzymatic bioremediation model. Promising results were achieved using VA to increase depolymerization of GBG dimer and to enhance RBB decolorisation.

Nassellaria are marine protists belonging to the Radiolaria lineage (Rhizaria). Their skeleton, made of opaline silica, exhibit an excellent fossil record, extremely valuable in micro-paleontological studies for paleo-environmental reconstruction. Yet, to date very little is known about the extant diversity and ecology of Nassellaria in contemporary oceans, and most of it is inferred from their fossil record. Here we present an integrative classification of Nassellaria based on taxonomical marker genes (18S and 28S ribosomal DNA) and morphological characteristics obtained by optical and scanning electron microscopy imaging. Our phylogenetic analyses distinguished 11 main morpho-molecular clades relying essentially on the overall morphology of the skeleton and not on internal structures as previously considered. Using fossil calibrated molecular clock we estimated the origin of Nassellaria among radiolarians primitive forms in the Devonian (ca. 420 Ma), that gave rise to living nassellarian groups in the Triassic (ca. 250 Ma), during the biggest diversification event over their evolutionary history. This morpho-molecular framework provides both a new morphological classification easier to identify under light microscopy and the basis for future molecular ecology surveys. Altogether, it brings a new standpoint to improve our scarce understanding of the ecology and worldwide distribution of extant nassellarians., (Copyright © 2019 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Environmental diversity surveys are crucial for the bioassessment of anthropogenic impacts on marine ecosystems. Traditional benthic monitoring relying on morphotaxonomic inventories of macrofaunal communities is expensive, time-consuming and expertise-demanding. High-throughput sequencing of environmental DNA barcodes (metabarcoding) offers an alternative to describe biological communities. However, whether the metabarcoding approach meets the quality standards of benthic monitoring remains to be tested. Here, we compared morphological and eDNA/RNA-based inventories of metazoans from samples collected at 10 stations around a fish farm in Scotland, including near-cage and distant zones. For each of 5 replicate samples per station, we sequenced the V4 region of the 18S rRNA gene using the Illumina technology. After filtering, we obtained 841,766 metazoan sequences clustered in 163 Operational Taxonomic Units (OTUs). We assigned the OTUs by combining local BLAST searches with phylogenetic analyses. We calculated two commonly used indices: the Infaunal Trophic Index and the AZTI Marine Biotic Index. We found that the molecular data faithfully reflect the morphology-based indices and provides an equivalent assessment of the impact associated with fish farms activities. We advocate that future benthic monitoring should integrate metabarcoding as a rapid and accurate tool for the evaluation of the quality of marine benthic ecosystems.

Diatoms are widely used as bioindicators for the assessment of water quality in rivers and streams. Classically, the diatom biotic indices are based on the relative abundance of morphologically identified species weighted by their autoecological value. Obtaining such indices is time-consuming, costly, and requires excellent taxonomic expertise, which is not always available. Here we tested the possibility to overcome these limitations using a next-generation sequencing (NGS) approach to identify and quantify diatoms found in environmental DNA and RNA samples. We analyzed 27 river sites in the Geneva area (Switzerland), in order to compare the values of the Swiss Diatom Index (DI-CH) computed either by microscopic quantification of diatom species or directly from NGS data. Despite gaps in the reference database and variations in relative abundance of analyzed species, the diatom index shows a significant correlation between morphological and molecular data indicating similar biological quality status for the majority of sites. This proof-of-concept study demonstrates the potential of the NGS approach for identification and quantification of diatoms in environmental samples, opening new avenues toward the routine application of genetic tools for bioassessment and biomonitoring of aquatic ecosystems.

Collodaria are ubiquitous and abundant marine radiolarian (Rhizaria) protists. They occur as either large colonies or solitary specimens, and, unlike most radiolarians, some taxa lack silicified structures. Collodarians are known to play an important role in oceanic food webs as both active predators and hosts of symbiotic microalgae, yet very little is known about their diversity and evolution. Taxonomic delineation of collodarians is challenging and only a few species have been genetically characterized. Here we investigated collodarian diversity using phylogenetic analyses of both nuclear small (18S) and large (28S) subunits of the ribosomal DNA, including 124 new sequences from 75 collodarians sampled worldwide. The resulting molecular phylogeny was compared to morphology-based classification. Our analyses distinguished the monophyletic clade of skeleton-less and spicule-bearing Sphaerozoidae from the sister clades Collosphaeridae (skeleton-bearing) and Collophidiidae (skeleton-less), while the Thalassicollidae was not retrieved as a monophyletic clade. Detailed morphological examination with electron microscopy combined with molecular analyses revealed many discrepancies, such as a mix between solitary and colonial species, co-existence of skeleton-less and skeleton-bearing specimens within the Collosphaeridae, as well as complex intraspecific variability in silicified structures. Such observations challenge a morphology-based classification and highlight the pertinence of an integrative taxonomic approach to study collodarian diversity., (Copyright © 2015 Elsevier GmbH. All rights reserved.)