Eudoraea adriatica gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae

This is an author manuscript that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology, copyright Society for General Microbiology, but has not been copy-edited, formatted or proofed. Cite this article as appearing in International Journal of Systematic and Evolutionary Microbiology. This version of the manuscript may not be duplicated or reproduced, other than for personal use or within the rule of 'Fair Use of Copyrighted Materials' (section 17, Title 17, US Code), without permission from the copyright owner, Society for General Microbiology. The Society for General Microbiology disclaims any responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final copy-edited, published article, which is the version of record, can be found at http://mic.sgmjournals.org, and is freely available without a subscription.International audienceA novel aerobic, non-motile, Gram-negative bacterium, designated AS06/20a(T), was isolated from coastal waters of the Adriatic Sea and subjected to polyphasic taxonomic analysis. Cells were rod-shaped and formed non-pigmented punctiform colonies on agar plates. The novel isolate grew heterotrophically on a variety of carbon compounds, including organic acids, carbohydrates, polyols, amino acids and complex organic substrates. Cells grew at 15-33 degrees C (optimum 30 degrees C), pH 6.5-8.5 (optimum pH 7.5-8.0) and between 2 and 6 % (w/v) NaCl (optimum 2 %). The dominant fatty acids (>5 %) detected in strain AS06/20a(T) were iso-C(15 : 1) G, iso-C(15 : 0), iso-C(15 : 0) 3-OH, iso-C(17 : 1)omega9c and iso-C(17 : 0) 3-OH. The major respiratory quinone was MK-6. The G+C content of the genomic DNA was 38.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain AS06/20a(T) fell within the family Flavobacteriaceae in the phylum Bacteroidetes. Comparative 16S rRNA gene sequence analysis indicated that strain AS06/20a(T) was most closely related to members of the genera Zeaxanthinibacter and Robiginitalea, sharing 92-93 % 16S rRNA gene sequence similarity with representatives of these genera. It is proposed, from the results of the polyphasic taxonomic analysis, that the strain should be placed in a new genus, Eudoraea gen. nov., with Eudoraea adriatica sp. nov. as the type species. The type strain is AS06/20a(T) (=DSM 19308(T)=CIP 109577(T)=OOB 358(T))

Skin microbiome and its interplay with the environment

Advances in sequencing, bioinformatics and analytics now allow the structure, function and interrelations of whole microbial communities to be studied in greater detail. Collaborative efforts and multidisciplinary studies, crossing the boundary between environmental and medical microbiology, have allowed specific environmental, animal and human microbiomes to be characterized. One of the main challenges for microbial ecology is to link the phylogenetic diversity of host-associated microbes to their functional roles within the community. Much remains to be learned on the way microbes colonize the skin of different living organisms and the way the skin microbiome reacts to the surrounding environment (air, water, etc.). In this review, we discuss examples of recent studies that have used modern technology to provide insights into microbial communities in water and on skin, such as those in natural resources (thermal spring water), large mammals (humpback whales) and humans (the skin microbiome). The results of these studies demonstrate how a greater understanding of the structure and functioning of microbiota, together with their interactions with the environment, may facilitate the discovery of new probiotics or postbiotics, provide indicators for the quality of the environment, and show how changes in lifestyle and living environment, such as urbanization, can impact on the skin microbiome and skin health and disease in humans

Hellea balneolensis gen. nov., sp. nov., a prosthecate alphaproteobacterium from the Mediterranean Sea

This is an author manuscript that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology, copyright Society for General Microbiology, but has not been copy-edited, formatted or proofed. Cite this article as appearing in International Journal of Systematic and Evolutionary Microbiology. This version of the manuscript may not be duplicated or reproduced, other than for personal use or within the rule of 'Fair Use of Copyrighted Materials' (section 17, Title 17, US Code), without permission from the copyright owner, Society for General Microbiology. The Society for General Microbiology disclaims any responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final copy-edited, published article, which is the version of record, can be found at http://mic.sgmjournals.org, and is freely available without a subscription.International audienceA novel aerobic, heterotrophic, prosthecate bacterium, designated 26III/A02/215(T), was isolated from surface water of the north-western Mediterranean Sea. Cells stained Gram-negative and were straight to slightly curved rods, forming red colonies on agar plates. The strain grew at 15-37 degrees C inclusive (optimum 30 degrees C) and grew optimally at seawater salinity. Growth was observed on organic acids, amino acids and complex organic substrates. The fatty acids (>5 %) detected in strain 26III/A02/215(T) were C(17 : 1)omega6c, C(18 : 1)omega7c and C(17 : 0). The lipid pattern indicated the presence of phosphatidylglycerol, glucuronopyranosyldiglyceride, monoglycosyldiglyceride, an unidentified glycolipid and three unidentified phospholipids. Phosphatidylethanolamine and diphosphatidylglycerol were absent. Ubiquinone Q-10 was the only respiratory lipoquinone. The G+C content of the genomic DNA was 46.8 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain 26III/A02/215(T) belonged to the Hyphomonas-Hirschia-Robiginitomaculum branch of the order Caulobacterales. This affiliation was consistent with the results of polar lipid analyses. Among this group, the novel isolate was most closely related to Robiginitomaculum antarcticum (93.9 % 16S rRNA gene sequence similarity to the type strain). On the basis of genotypic, chemotaxonomic and phenotypic distinctness, we propose a novel genus, Hellea gen. nov., with Hellea balneolensis sp. nov. as the type species. The type strain of Hellea balneolensis is 26III/A02/215(T) (=DSM 19091(T) =CIP 109500(T) =OOB 269(T))

Balneola alkaliphila sp. nov., a marine bacterium isolated from the Mediterranean Sea

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2008/publication-5292.pdfInternational audienceA novel aerobic, Gram-negative bacterium, designated strain CM41_14b(T), was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were non-motile, straight rods, 2.6 microm long and 0.7 microm wide and formed pale-orange colonies on marine agar medium. The G+C content of the genomic DNA was 39 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain within the genus Balneola (phylum Bacteroidetes). On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species for which the name Balneola alkaliphila sp. nov. is proposed. The type strain is CM41_14b(T) (=DSM 19538(T)=CIP 109603(T)=OOB 103(T))

Covid-19: where is the data?

The arrival of the COVID-19 pandemic has led many to argue that scholarly communication and publishing is undergoing a revolution, in terms of not only the wider opening of access to research, but also the data underlying it. In this post Julien Larrègue, Philippe Vincent-Lamarre, Frédéric Lebaron, and Vincent Larivière, discuss findings from their study of papers submitted to the preprint server medRxiv, which shows levels of open data to be stubbornly lo

Proteome analysis of the UVB-resistant marine bacterium Photobacterium angustum S14

The proteome of the marine bacterium Photobacterium angustum S14 was exposed to UVB and analyzed by the implementation of both the post-digest ICPL labeling method and 2D-DIGE technique using exponentially growing cells. A total of 40 and 23 proteins were quantified in all replicates using either the ICPL or 2D-DIGE methods, respectively. By combining both datasets from 8 biological replicates (4 biological replicates for each proteomics technique), 55 proteins were found to respond significantly to UVB radiation in P. angustum. A total of 8 UVB biomarkers of P. angustum were quantified in all replicates using both methods. Among them, the protein found to present the highest increase in abundance (almost a 3-fold change) was RecA, which is known to play a crucial role in the so-called recombinational repair process. We also observed a high number of antioxidants, transport proteins, metabolism-related proteins, transcription/translation regulators, chaperonins and proteases. We also discuss and compare the UVB response and global protein expression profiles obtained for two different marine bacteria with trophic lifestyles: the copiotroph P. angustum and oligotroph Sphingopyxis alaskensis

The space of cultural practices: from the construction of social space to the study of subgroups through specific class analysis.

Quels sont les déterminants sociaux des orientations culturelles et, en particulier, quel est l’effet de la position de classe sur les différences observées dans l’univers des pratiques culturelles? Le présent article revisite cette question désormais classique de sociologie de la culture et de sociologie de la stratification, à partir de données d’une enquête par questionnaire menée en France en 2003 (“Participation culturelle et sportive”). En mobilisant une démarche systémati-que d’analyse géométrique des données, il s’agit ici de discuter empiriquement l’importance de l’effet de l’appartenance de classe, telle qu’elle peut être saisie à partir de nomenclatures socio--professionnelles à différents niveaux d’agrégation. Une fois déterminé l’effet de l’appartenance de classe et évalué son importance selon divers critères, on étudie dans un second temps les variations sociales à l’intérieur de trois groupes sociaux particuliers, afin de montrer que l’on peut interpréter sociologiquement la diversité de pratiques culturelles au sein de différentes catégories sociales, voire à des niveaux encore plus fins.What are the social determinants of cultural orientations and, in particular, what is the effect of class position on the differences observed in the universe of cultural practices? This article revisits this classic question of the sociology of culture and the sociology of stratification, based on the data of a survey conducted in France in 2003 ("Cultural and sports participation"). Mobilizing a systematic approach based on geometric data analysis, the aim of this article is to discuss empirically the importance of class belonging effect, as it can be understood from socio-professional nomenclatures at different levels of aggregation. Once the effect of class belonging has been determined and its importance according to various criteriaassessed, the social variations within three social groups are examined, in order to show that it is possible to interpret sociologically the diversity of cultural practices within different social categories, possibly even in more refined levels.Quais são as determinantes sociais das orientações culturais e, em particular, qual é o efeito da po-sição de classe sobre as diferenças observadas no universo das práticas culturais? O presente artigo revisita essa questão doravante clássica da sociologia da cultura e da sociologia da estratificação, a partir dos dados de uma pesquisa por questionário, realizada na França em 2003 (“Participação cultural e esportiva”). Mobilizando uma abordagem sistemática de análise geométrica dos dados, trata-se aqui de discutir empiricamente a importância do efeito de pertencimento de classe, tal como pode ser apreendida a partir de nomenclaturas socioprofissionais em diferentes níveis de agregação. Uma vez determinado o efeito do pertencimento de classe e avaliada sua importância de acordo com diversos critérios, estudaremos, em seguida, as variações sociais no interior de três grupos sociais em particular, a fim de mostrar que é possível interpretar sociologicamente a diversidade de práticas culturais no seio de diferentes categorias sociais, eventualmente em níveis ainda mais finos

Thalassobaculum salexigens sp. nov., a new member of the family Rhodospirillaceae from the NW Mediterranean Sea, and emended description of the genus Thalassobaculum

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/00001/11201/7846.pdfInternational audienceA novel Gram-negative bacteria, named CZ41_10a(T), was isolated from coastal surface waters of the north-western Mediterranean Sea. Cells were motile, pleomorphic rods, 1.6 mum long and 0.7 mum wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 65 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the new isolate in the genus Thalassobaculum, a member of the family Rhodospirillaceae, class Alphaproteobacteria. Unlike Thalassobaculum litoreum CL-GR58(T), its closest relative, strain CZ41_10a(T) was unable to grow anaerobically and did not exhibit nitrate reductase activity. On the basis of DNA-DNA hybridization, fatty acid content and physiological and biochemical characteristics, this isolate represents a novel species for which the name Thalassobaculum salexigens sp. nov. is proposed. The type strain is CZ41_10a(T) (=DSM 19539(T)=CIP 109604(T)=MOLA [corrected] 84(T)). An emended description of the genus Thalassobaculum is also given

Proteogenomic analysis of Epibacterium mobile BBCC367, a relevant marine bacterium isolated from the South Pacific Ocean

Epibacterium mobile BBCC367 is a marine bacterium that is common in coastal areas. It belongs to the Roseobacter clade, a widespread group in pelagic marine ecosystems. Species of the Roseobacter clade are regularly used as models to understand the evolution and physiological adaptability of generalist bacteria. E. mobile BBCC367 comprises two chromosomes and two plasmids. We used gel-free shotgun proteomics to assess its protein expression under 16 different conditions, including stress factors such as elevated temperature, nutrient limitation, high metal concentration, and UVB exposure. Comparison of the different conditions allowed us not only to retrieve almost 70% of the predicted proteins, but also to define three main protein assemblages: 584 essential core proteins, 2,144 facultative accessory proteins and 355 specific unique proteins. While the core proteome mainly exhibited proteins involved in essential functions to sustain life such as DNA, amino acids, carbohydrates, cofactors, vitamins and lipids metabolisms, the accessory and unique proteomes revealed a more specific adaptation with the expression of stress-related proteins, such as DNA repair proteins (accessory proteome), transcription regulators and a significant predominance of transporters (unique proteome). Our study provides insights into how E. mobile BBCC367 adapts to environmental changes and copes with diverse stresses

Melitea salexigens gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea

International audienceA novel aerobic, Gram-negative bacterial strain, designated 5IX/A01/131 T , was isolated from waters in the coastal north-western Mediterranean Sea. The cells were motile, straight rods, 1.6 mm long and 0.5 mm wide, and formed cream colonies on marine 2216 agar. The G+C content of the genomic DNA was 57 mol %. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, strain 5IX/A01/ 131 T represents a novel genus and species, for which the name Melitea salexigens gen. nov., sp. nov. is proposed. The type strain of Melitea salexigens is 5IX/A01/131 T (=DSM 19753 T = CIP 109757 T = MOLA 225 T)