Aims The aim of this study was to identify the origin of faecal pollution impacting the Elorn estuary (Brittany, France) by applying microbial source tracking (MST) markers in both oysters and estuarine waters. Methods and Results The MST markers used were as follows: (i) human-, ruminant- and pig-associated Bacteroidales markers by real-time PCR and (ii) human genogroup II and animal genogroup I of F-specific RNA bacteriophages (FRNAPH) by culture/genotyping and by direct real-time reverse-transcriptase PCR. The higher occurrence of the human genogroup II of F-specific RNA bacteriophages using a culture/genotyping method, and human-associated Bacteroidales marker by real-time PCR, allowed the identification of human faecal contamination as the predominant source of contamination in oysters (total of 18 oyster batches tested) and waters (total of 24 water samples tested). The importance of using the intravalvular liquids instead of digestive tissues, when applying host-associated Bacteroidales markers in oysters, was also revealed. Conclusions This study has shown that the application of a MST toolbox of diverse bacterial and viral methods can provide multiple lines of evidence to identify the predominant source of faecal contamination in shellfish from an estuarine environment. Significance and Impact of the Study Application of this MST toolbox is a useful approach to understand the origin of faecal contamination in shellfish harvesting areas in an estuarine setting.

Two novel strains, HW T2.11^T and HW T5.17^T, were isolated from decaying wood (forest of Champenoux, France). Study of the 16S rRNA sequence similarity indicated that the novel strains belong to the genus Acidisoma. The sequence similarity of the 16S rRNA gene of HW T2.11^T with the corresponding sequences of A. tundrae and A. sibiricum was 97.30% and 97.25%, while for HW T5.17^T it was 96.85% and 97.14%, respectively. The DNA G+C contents of the strains were 62.32–62.50%. Cells were Gram-negative coccobacilli that had intracellular storage granules (poly-3-hydroxybutyrate (P3HB)) that confer resistance to environmental stress conditions. They were mesophilic and acidophilic organisms growing at 8–25 °C, at a pH of 2.0–6.5, and were capable of using a wide range of organic compounds and complex biopolymers such as starch, fucoidan, laminarin, pectin and cellulose, the latter two being involved in wood composition. The major cellular fatty acid was cyclo C_19:0ω8c and the major quinone was Q-10. Overall, genome relatedness indices between genomes of strains HW T2.11^T and HW T5.17^T (Orthologous Average Nucleotide Identity (OrthoANI) value = 83.73% and digital DNA-DNA hybridization score = 27.5%) confirmed that they belonged to two different species. Genetic predictions indicate that the cyclopropane fatty acid (CFA) pathway is present, conferring acid-resistance properties to the cells. The two novel strains might possess a class IV polyhydroxyalcanoate (PHA) synthase operon involved in the P3HB production pathway. Overall, the polyphasic taxonomic analysis shows that these two novel strains are adapted to harsh environments such as decaying wood where the organic matter is difficult to access, and can contribute to the degradation of dead wood. These strains represent novel species of the genus Acidisoma, for which the names Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov. are proposed. The type strains of Acidisoma silvae and Acidisomacellulosilytica are, respectively, HW T2.11^T (DSM 111006^T; UBOCC-M-3364^T) and HW T5.17^T (DSM 111007^T; UBOCC-M-3365^T).

A novel bacterial strain, HK31-G^T, was isolated from a subsurface geothermal aquifer (Hellisheidi, SW-Iceland) and was characterized using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA gene along with phylogenomic position indicated that the novel strain belongs to the genus Phenylobacterium. Cells are motile Gram-negative thin rods. Physiological characterization showed that strain HK31-G^T is a mesophilic bacterium able to grow from 10 to 30 °C, at pH values between 6 and 8 and at NaCl concentrations between 0 and 0.5 %. Optimal growth was observed without sodium chloride at 25 °C and pH 6. Strain HK31-G^T is chemoorganoheterotroph and its major saturated fatty acids are C_18:1ω7c, C_16:1ω6c and C_16:0, the predominant quinone is Q-10 and the major polar lipid is phosphatidylglycerol. The new strain also possesses the capacity to use ferrous iron (Fe(II)) as the sole energy source and can also be considered as a chemolithoautotrophic microorganism. The overall genome of strain HK31-G^T was estimated to be 4.46 Mbp in size with a DNA G + C content of 67.95 %. Genes involved in iron metabolism were identified, but no genes typically involved in Fe(II)-oxidation were found. According to the overall genome relatedness indices (OGRI) values, six MAGs from groundwater have been assigned to the same species as the new strain HK31-G^T. Furthermore, OGRI values between the genome of strain HK31-G^T and the genomes of its closest relatives are below the species delineation threshold. Therefore, given the polyphasic approach used, strain HK31-G^T represents a novel species of the genus Phenylobacterium, for which the name Phenylobacterium ferrooxidans sp. nov. is proposed. The type strain is HK31-G^T (DSM 116432^T = UBOCC-M-3429^T = LMG 33376^T).

A novel bacterial strain, designated BS-T2-15^T, isolated from forest soil in close proximity to decaying oak wood, was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences as well as phylogenomic analyses based on coding sequences of 340 concatenated core proteins indicated that strain BS-T2-15^T forms a distinct and robust lineage in the Rubrivivax–Roseateles –Leptothrix–Azohydromonas –Aquincola–Ideonella branch of the order Burkholderiales . The amino acid identity and the percentage of conserved proteins between the genome of strain BS-T2-15^T and genomes of closely related type strains ranged from 64.27 to 66.57% and from 40.89 to 49.27 %, respectively, providing genomic evidence that strain BS-T2-15^T represents a new genus. Its cells are Gram-stain-negative, aerobic, motile by a polar flagellum, rod-shaped and form incrusted white to ivory colonies. Optimal growth is observed at 20–22 °C, pH 6 and 0% NaCl. The predominant fatty acids of strain BS-T2-15^T are C_16 : 1 ω7c, C_16 : 0 and C_14 : 0 2-OH. Its polar lipid profile consists of a mixture of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol and its main respiratory quinone is ubiquinone 8. The estimated size of its genome is 6.28 Mb with a DNA G+C content of 69.56 mol%. Therefore, on the basis of phenotypic and genotypic properties, the new strain BS-T2-15^T represents a novel genus and species for which the name Scleromatobacter humisilvae gen. nov., sp. nov., is proposed. The type strain is BS-T2-15^T (DSM 113115^T=UBOCC-M-3373^T).

A novel bacterial strain, designated HK31-P ^T , was isolated from a deep subsurface geothermal aquifer in southwestern Iceland. Phylogenetic analyses, based on 16S rRNA gene sequences, revealed that the strain was affiliated to the genus Phreatobacter . Cells of the strain were Gram-negative, rod-shaped, motile by means of a polar flagellum and granule-containing. Colonies were small, circular, convex, smooth and white in colour. Growth under chemoorganoheterotrophic and aerobic conditions was observed at the following ranges: 20–35 °C (optimum, 30–35 °C), pH 7–9 (optimum, 8) and 0–0.5% salinity (optimum, 0%). The strain was also capable of growing under chemolithoautotrophic and (micro)aerobic conditions with Fe(II) as an electron donor. The major respiratory quinone identified was ubiquinone Q-10 (97.0%), and the predominant fatty acid was C _18:1  ω 7c. The dominant polar lipids consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid, along with several unidentified glycolipids, phospholipids and lipids. The G+C content of the genomic DNA of strain HK31-P ^T was 67.66 mol%, and its complete genome was 4.34 Mbp in size. The values of the digital DNA–DNA hybridization and average nucleotide identity indices between strain HK31-P ^T and the type species of the genus Phreatobacter ranged, respectively, from 21.30 to 27% and from 78.25 to 86.32%. These values are well below the accepted species delineation thresholds, thereby clearly indicating that strain HK31-P ^T represents a distinct genomic species within the genus Phreatobacter , strongly supporting that the former represents a new species belonging to the genus Phreatobacter . Therefore, based on this polyphasic approach, strain HK31-P ^T represents a new species within the genus Phreatobacter , for which the name Phreatobacter aquiterrae sp. nov. is proposed. The type strain is HK31-P ^T (DSM 116433 ^T =UBOCC-M-3430 ^T ).