This study isolated a novel thermophilic CO-utilising bacterium, strain AZ2, from marine hydrothermal sediment collected on the island of São Miguel, Azores, Portugal, and proposed that strain AZ2T represents the type strain of a novel genus and species, named Thermobium azorense gen. nov.
Based on further phenotypic, genomic, and phylogenetic analysis, strain F2T represents a novel genus and species within the family Anaerovoracaceae with the proposed name Peptonella octanoica gen. sp.
Dinesh Kumar Nallasamy, B. Lindner, Christopher E. Lawson· bioRxiv· 0 citations
Two novel facultatively anaerobic thermophilic members of the genus Limisphaera (Verrucomicrobiota), strains 4302-coT and VF2T, were isolated from terrestrial hot springs of Geyser Valley (Kamchatka) and the Lake Baikal region, Russia. Cells were motile cocci, forming aggregates; strain 4302-coT grew optimally at a range of 60–65 °C and pH 7.4 and strain VF2T at 55 °C and pH 8.5. Both were chemoorganoheterotrophs utilizing mono-, di-, and polysaccharides, including cellulose, xylan, xanthan gum, arabinan, gluco-, and galactomannans. Both grew anaerobically by fermentation or by respiration with nitrite, nitrate, ferric citrate, or ferrihydrite; dissimilatory iron reduction is reported here for the first time within the phylum Verrucomicrobiota. Their genomes encoded more than 100 glycoside hydrolases and more than 15 polysaccharide lyases, indicating high hydrolytic potential. Additionally, the metabolic pathways of sugar catabolism, fermentation, and both aerobic and anaerobic respiration were reconstructed. A GH51 glycoside hydrolase of strain 4302-coT phylogenetically related to endoglucanases was heterologously expressed and shown to be active at 70 °C with unusually broad specificity, hydrolyzing both β-1,4 and β-1,3 linkages. Based on phylogenomic analysis and phenotypic features, the strains are assigned to two novel species, for which the names Limisphaera vallis sp. nov. and Limisphaera sibirica sp. nov. are proposed.
O. Podosokorskaya, T. Sokolova, K. Zayulina et al.· Life· 0 citations
Novel facultatively anaerobic moderately thermophilic bacteria, strains OK-6-MeT and OK-1-Me, were isolated from the hot springs of Karmadon (North Ossetia, Russian Federation). Gram-stain-negative, motile rods were present singly, in rosettes, and formed biofilms. Both strains grew optimally at 55 °C, pH 7.0 and did not require sodium chloride. They were chemoorganoheterotrophs, growing on mono-, di- and polysaccharides (cellulose, xylan, lichenan, xyloglucan, mannan, locust bean gum, pectin) as well as proteinaceous substrates (gelatin, casein). Growth under anaerobic conditions was observed both in the presence and absence of external electron acceptors (sulfur, thiosulfate, nitrite, arsenate, Fe-citrate, ferrihydrite). Major cellular fatty acids of both strains were iso-C15:0, anteiso-C15:0, and anteiso-C17:0. The size of the genomes were 3.3 and 3.2 Mb for strain OK-6-MeT and OK-1-Me, respectively. Genomic DNA G + C content was 37% for both strains. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, the strains represented a new species of the genus Melioribacter of family Melioribacteraceae within the class Ignavibacteria, for which the name Melioribacter sulfuriphilus sp. nov. is proposed, with type strain OK-6-MeT (= B-3972T = CGMCC 1.18264 T = BIM B-2154T = UQM 41932T). Analysis of OK-1 and OK-6 metagenomes revealed presence of various genes involved in carbon (CO2 fixation, carbohydrate hydrolysis, hydrocarbons degradation, fermentation), nitrogen (nitrate, nitrite, NO and N2O reduction) and sulfur cycles (sulfate reduction, sulfur or thiosulfate reduction, oxidation of sulfur compounds). MAGs OK-1-035 and OK-6-024 almost identical to genomes of strain OK-1-Me and OK-6-MeT presumably are integral part of these complex trophic chains.
O. Podosokorskaya, A. Merkel, A. Novikov et al.· Systematic and Applied Micro...· 0 citations
The genus Methylococcus is represented by obligately aerobic gram-negative cocci and diplococci, which utilize methane as a source of carbon and energy. These bacteria inhabit a wide spectrum of habitats with high methane availability. Vast majority of the currently characterized members of this genus are thermotolerant microorganisms with high sensitivity to NaCl. Here, we report description of the first halotolerant Methylococcus representative, strain Мс7T, which was isolated from a landfill cover soil. Cells of this strain (1.6 µm in size) were larger than those of earlier described Methylococcus species (~1 µm) and grew in the temperature range 28–53°C with the optimum at 40°C and рН 5.5–7.5 with the optimum at рН 6.5–7.0. The tolerance of strain Мс7T to NaCl (1.5%, wt/vol) exceeded that in other Methylococcus spp. This methanotroph demonstrated growth in the medium with the total salt content of up to 25 g L–1. The 16S rRNA gene sequence of strain Мс7T displayed highest similarity (98.56%) to that of M. geothermalis IM1T. The finished genome sequence of strain Мс7T was 4.0 Mbp in size and contained 2 rrn operons, about 3700 protein-encoding genes including 2 copies of gene clusters of particulate methane monooxygenase (MMO) and one gene cluster of soluble MMO. The G + C DNA content was 63.44%. The average nucleotide identity between the genome sequences of strain Мс7T and M. geothermalis IM1T was 88.56%. Based on the number of phenotypic and genotypic differences we propose to classify strain Мс7T (=VKM B-4034T) as representing a novel species of the genus Methylococcus, M. magnus.
R. Z. Suleimanov, O. V. Danilova, I. Y. Oshkin et al.· Microbiology· 0 citations
These findings provide a cultivated representative of the family Symbiobacteriaceae with physiological and metabolic responses to n-hexadecane, thereby providing a basis for further investigation of hydrocarbon metabolism.
Huilin Wen, Ge Liu, Chaomin Sun et al.· Microorganisms· 0 citations
Per- and polyfluoroalkyl substances (PFAS) such as GenX (HFPO-DA) are aerobically recalcitrant contaminants for which biological treatment options remain scarce; the best-characterized microbial degraders require strictly anaerobic conditions and external cofactors. We isolated Cladosporium halotolerans strain CsHGX-1 from activated sludge at a municipal wastewater treatment plant using GenX as the sole carbon source. Whole-genome sequencing (32.4 Mb; 11,201 genes) revealed a PFAS-degradation gene repertoire substantially expanded relative to congeneric Cladosporium species, including 26 dehalogenases (four type-II haloacid dehalogenases, HADs), 141 cytochrome P450s, and 558 esterases/hydrolases. Under aerobic conditions with GenX (50 mg L-1) as the sole carbon source, strain CsHGX-1 removed 47.6 ± 1.7% of GenX within 48 h, accompanied by fluoride release (0.079 ± 0.018 mM) that was absent in abiotic controls, confirming genuine C-F bond cleavage. Time-resolved RNA sequencing (0, 6, 24, 48 h; n = 6 biological replicates) revealed a phase-structured transcriptional program: oxidative genes, including cytochrome P450s, peaked first (6 h; up to 25.4-fold), hydroxylation and reactive-oxygen-species-management genes peaked next (24 h; up to 33.5-fold), and the three type-II HAD genes peaked last (48 h; up to 50.9-fold), coincident with fluoride accumulation. A parallel resazurin metabolic assay over 5 days confirmed sustained catabolic activity in GenX-exposed cultures relative to controls (1.37-1.52-fold; p ≤ 0.003). These findings identify strain CsHGX-1 as, to our knowledge, the first Ascomycete fungus for which genomic and transcriptomic evidence links oxidative activation to haloacid-dehalogenase-mediated defluorination of an aerobically recalcitrant PFAS, extending the known diversity of fungal PFAS degraders beyond Basidiomycota white-rot taxa. IMPORTANCE GenX is a PFAS “replacement” chemical that the U.S. Environmental Protection Agency added to its list of hazardous constituents in 2024, yet no aerobic biological treatment exists for it: every well-characterized microbial degrader requires oxygen-free conditions and added cofactors. We show that a fungus recovered from ordinary wastewater sludge breaks down GenX while using oxygen, the same conditions already used in conventional treatment plants, with no nutrient or reductant supplementation. Genome sequencing showed why this strain is unusual: it carries far more dehalogenase and cytochrome P450 genes than its close relatives. Time-course RNA sequencing showed these genes switch on in a defined order, oxidation first, then carbon-fluorine bond cleavage, matching the appearance of free fluoride in the culture. This links genome content to a functional outcome in an Ascomycete fungus, suggesting aerobic fungal defluorinators may already be present, unrecognized, in engineered wastewater systems.
Esaú De la Vega-Camarillo, Gayan Abeysinghe, S. Mathur et al.· bioRxiv· 0 citations
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