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International audience; A novel anaerobic methylotrophic halophilic methanogen strain SLHTYRO T was isolated from a deep hypersaline anoxic basin called "Tyro" located in the Eastern Mediterranean Sea. Cells of SLHTYRO T were motile cocci. The strain SLHTYRO T grew between 12 and 37 °C (optimum 30 °C), at pH between 6.5 and 8.2 (optimum pH 7.5) and salinity from 45 to 240 g L −1 NaCl (optimum 135 g L −1). Strain SLHTYRO T was methylotrophic methanogen able to use methylated compounds (trimethylamine, dimethylamine, monomethylamine and methanol). Strain SLHTYRO T was able to grow at in situ hydrostatic pressure and temperature conditions (35 MPa, 14 °C). Phylogenetic analysis based on 16S rRNA gene and mcrA gene sequences indicated that strain SLHTYRO T was affiliated to genus Methanohalophilus within the order Methanosarcinales. It shared >99.16% of the 16S rRNA gene sequence similarity with strains of other Methanohalophilus species. Based on ANIb, AAI and dDDH measurements, and the physiological properties of the novel isolate, we propose that strain SLHTYRO T should be classified as a representative of a novel species, for which the name Methanohalophilus profundi sp. nov. is proposed; the type strain is SLHTYRO T (=DSM 108854 = JCM 32768 = UBOCC-M-3308).

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International audience; Bitter rot is one of the prevalent diseases of apple (Malus pumila Mill.) worldwide. The disease affects the fruit preharvest in orchards and/or postharvest in storage, resulting in considerable economic losses. Until recently the reported causal agents in Europe belong to the Colletotrichum acutatum species complex (Baroncelli et al. 2014; Nodet et al. 2016); however, species belonging to C. gloeosporioides species complex were reported in the United States (Munir et al. 2016), South America (Velho et al. 2018), Korea (Park et al. 2018), and recently in Belgium (Grammen et al. 2019). In September 2017, bitter rot symptoms were observed on apple fruit (cultivars Joya Cripps Red, Granny Smith, and Pink Lady) in four orchards in the region of Occitanie in France. The rot began as circular brown spots, 1 to 2 mm in diameter, which enlarged rapidly. Sixteen isolates were obtained from symptomatic apples by culturing pieces of necrotic tissue on potato dextrose agar. Cultures showed light-gray, cottony mycelium that became darker with age, with the reverse color being brownish and becoming black with age. Conidia were produced in small orange masses and were mainly cylindrical, with rounded ends. For all isolates, the production of perithecia was observed in culture, and asci and ascospores were observed under the microscope. The width and length of 50 conidia were examined and ranged from 3.1 to 4 µm (average 3.5 µm) and from 8 to 13 µm (average 10.5 µm), respectively. Based on these morphological characteristics, those isolates correspond to teleomorph of species belonging to C. gloeosporioides species complex (Weir et al. 2012). Total genomic DNA was extracted from the 16 isolates, and the internal transcribed spacer region of rDNA was amplified using the universal primers ITS4 and ITS5 and then sequenced. For all isolates, the resulting sequences were 100% identical to C. fructicola sequences obtained by a BLAST search in GenBank. Three other loci (partial GAPDH, TUB2, and ApMat genes) were amplified and sequenced to further characterize two isolates (UBOCC-A-118064 and UBOCC-A-118065; GenBank accession nos. MK114103 to MK114110, respectively). Multilocus phylogenetic analysis carried out with the obtained and reference sequences (Da Lio et al. 2018) revealed that the isolates clustered within C. fructicola, as suggested by the BLAST results; this is also consistent with their initial identification as C. gloeosporioides. To confirm Koch’s postulates, for the two characterized isolates, 10 ‘Golden Delicious’ apples were surface sterilized and then wound inoculated with 20 μl of a conidial suspension (105 conidia/ml). After 10 days of incubation at 20°C, symptoms identical to those initially observed developed around the inoculation point, whereas controls inoculated with water remained symptomless. Fungal thalli reisolated from the lesions were morphologically similar to the original isolate. To our knowledge, this is the first report in Europe of C. fructicola causing bitter rot on apple. According to Munir et al. (2016), C. fructicola was reported to be more aggressive than species belonging to the C. acutatum species complex such as C. fioriniae previously identified in France (Nodet et al. 2016); moreover, this species is associated with Glomerella leaf spot, an emerging leaf disease never described in Europe (Velho et al. 2018). All those points encourage the development of species-specific management strategies for this pathogen in European countries.

A novel, strictly anaerobic, methylotrophic marine methanogen, strain SLH33T, was isolated from deep sediment samples covered by an orange microbial mat collected from the Napoli Mud Volcano. Cells of strain SLH33T were Gram-stain-negative, motile, irregular cocci that occurred singly. Cells utilized trimethylamine, dimethylamine, monomethylamine, methanol, betaine, N,N-dimethylethanolamine and choline (N,N,N-trimethylethanolamine) as substrates for growth and methanogenesis. The optimal growth temperature was 30 °C; maximum growth rate was obtained at pH 7.0 in the presence of 0.5 M Na+. The DNA G+C content of strain SLH33T was 43.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain SLH33T within the genus Methanococcoides . The novel isolate was related most closely to Methanococcoides methylutens TMA-10T (98.8 % 16S rRNA gene sequence similarity) but distantly related to Methanococcoides burtonii DSM 6242T (97.6 %) and Methanococcoides alaskense AK-5T (97.6 %). DNA–DNA hybridization studies indicated that strain SLH33T represents a novel species, given that it shared less than 16 % DNA–DNA relatedness with Methanococcoides methylutens TMA-10T. The name Methanococcoides vulcani sp. nov. is proposed for this novel species, with strain SLH33T ( = DSM 26966T = JCM 19278T) as the type strain. An emended description of the genus Methanococcoides is also proposed.

International audience; A novel strictly anaerobic thermophilic heterotrophic bacterium, strain SLHLJ1(T), was isolated from a Pacific hydrothermal sediment. Cells were Gram-negative coccobacilli (approximately 1.0 × 0.6 μm) with a toga. It grew at temperatures between 33 and 78 °C (optimum 70 °C). Elemental sulphur and L-cystine stimulated its growth. It contained C16:0, C16:1 ω11c, C18:0 and C18:1 ω9c as major fatty acids (>5%), 3 phospholipids and 2 glycolipids as polar lipids. Its DNA G+C content was 43.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain SLHLJ1(T) within the family Thermotogaceae. The novel isolate was most closely related to Kosmotoga arenicorallina (97.93 % 16S rRNA gene sequence similarity), K. olearia (92.43%) and K. shengliensis (92.17 %). On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons with its closest relatives, we propose its assignment to a novel species of the genus Kosmotoga. The name Kosmotoga pacifica sp. nov. is proposed with strain SLHLJ1(T) (=DSM 26965(T) = JCM 19180(T) = UBOCC 3254(T)) as the type species.