Tepidiphilus margaritifer gen. nov., sp. nov., isolated from a thermophilic aerobic digester

A moderately thermophilic bacterium is described, strain N2-214T, that was isolated from an enrichment culture, growing on caprolactone, obtained from a sample from a water-treatment sludge aerobic digester operating at temperatures around 60 °C. The organism was aerobic, Gram-negative, oxidase- and catalase-positive, with a polar flagellum, and capable of growth at temperatures as high as 61 °C. The major fatty acids of strain N2-214T were C16 : 0, C18 : 1 and cyclo-C19 : 0. The phylogenetic relationships of the strain, derived from 16S rRNA gene sequence comparisons, demonstrated it to be a member of the {beta}-subclass of the Proteobacteria. The highest 16S rDNA sequence similarity of isolate N2-214T was to Azoarcus buckelii (91·9 %), Thauera aromatica (92 %) and Hydrogenophilus thermoluteolus (92·7 %). On the basis of phylogenetic analyses and physiological and chemotaxonomic characteristics, it is proposed that isolate N2-214T (=DSM 15129T=LMG 21637T) represents a new genus and species, Tepidiphilus margaritifer gen. nov., sp. nov

Caenibacterium thermophilum gen. nov., sp. nov., isolated from a thermophilic aerobic digester of municipal sludge

A bacterial strain, N2-680T (=DSM 15264T=LMG 21760T), isolated from a thermophilic aerobic digester of municipal sludge, was characterized with respect to its morphology, physiology and taxonomy. Phenotypically, the isolate was a Gram-negative rod with a polar flagellum, catalase- and oxidase-positive, containing cytoplasmic inclusions of poly-b-hydroxybutyrate and had an optimal growth temperature of about 47 6C. Strain N2-680T was unable to reduce nitrate and could use organic acids, amino acids and carbohydrates as single carbon sources. Chemotaxonomic analysis revealed that ubiquinone 8 was the major respiratory quinone of this organism and that phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids. At 50 6C, the major components in fatty acid methyl ester analysis were C16 : 0 and cyclo-C17 : 0. The highest 16S rDNA sequence identity of isolate N2-680T was to Leptothrix mobilis and Ideonella dechloratans (95?7%) and to Rubrivivax gelatinosus and Aquabacterium commune (95?6 %). 16S rDNA sequence similarities to species of two related thermophilic genera, Caldimonas manganoxidans and Tepidimonas ignava, were lower (93?6 and 94?7 %). On the basis of phylogenetic analyses and physiological and chemotaxonomic characteristics, it is proposed that isolate N2-680T represents a new genus and species, for which the name Caenibacterium thermophilum gen. nov., sp. nov. is propose

Bacterial diversity and bioaugmentation in floodwater of a paddy field in the presence of the herbicide molinate

This work aimed at studying variations on the diversity and composition of the bacterial community of a rice paddy field floodwater, subjected to conventional management, namely by using the herbicide molinate. The promotion of the herbicide biodegradation either by the autochthonous microbiota or by a bioaugmentation process was also assessed. This study comprehended four sampling campaigns at key dates of the farming procedures (seeding, immediately and 6 days after application of the herbicide molinate, and after synthetic fertilization) and the subsequent physic-chemical and microbiological characterization (pH, DOC and molinate contents, total cells, cultivable bacteria and DGGE profiling) of the samples. Multivariate analysis of the DGGE profiles showed temporal variations in the bacterial community structure and the Shannon's index values indicated that the bacterial diversity reached its minimum at the molinate application day. The highest bacterial diversity coincided with the periods with undetectable concentrations of the herbicide, although microcosm assays suggested that other factors than molinate may have been responsible for the decrease of the bacterial diversity. The ability of autochthonous microorganisms to degrade molinate and the influence of the herbicide on the bacterial community composition were assessed in microcosm assays using floodwater collected at the same dates. Given molinate was not degraded by autochthonous microorganisms, and considering it represents an environmental contaminant, bioaugmentation microcosms were assayed aiming the assessment of the feasibility of a bioremediation process to clean contaminated floodwater. A molinate-mineralizing culture, previously isolated, promoted molinate removal, induced alterations in the autochthonous bacterial community structure and diversity, and was undetected after 7 days of incubation, suggesting the feasibility of the process.info:eu-repo/semantics/acceptedVersio

Bacterial diversity and antibiotic resistance in water habitats: searching the links with the human microbiome

Water is one of the most important bacterial habitats on Earth. As such, water represents also a major way of dissemination of bacteria between different environmental compartments. Human activities led to the creation of the so-called urban water cycle, comprising different sectors (waste, surface, drinking water), among which bacteria can hypothetically be exchanged. Therefore, bacteria can be mobilized between unclean water habitats (e.g. wastewater) and clean or pristine water environments (e.g. disinfected and spring drinking water) and eventually reach humans. In addition, bacteria can also transfer mobile genetic elements between different water types, other environments (e.g. soil) and humans. These processes may involve antibiotic resistant bacteria and antibiotic resistance genes. In this review, the hypothesis that some bacteria may share different water compartments and be also hosted by humans is discussed based on the comparison of the bacterial diversity in different types of water and with the human-associated microbiome. The role of such bacteria as potential disseminators of antibiotic resistance and the inference that currently only a small fraction of the clinically relevant antibiotic resistome may be known is discussed.info:eu-repo/semantics/publishedVersio

Alicycliphilus

Alicycliphilus (A.li.cy.cli'phi.lus. Gr. neut. n. aleiphar annointing oil; Gr. masc. n. kyklos circle or ring; Gr. masc. n. philos friend; N.L. masc. n. Alicyciphilus alicyclic compound liking, referring to the substrates used for the isolation of this organism). Proteobacteria / Betaproteobacteria / Burkholderiales / Comamonadaceae / Alicycliphilus. Short rods, 1–2 μm long and 0.6 μm wide. Motile. Gram‐negative. Nonsporulating. Facultative anaerobe. Nitrate is reduced to N2. Mesophilic, with optimal growth at 28–30°C and pH 7.2–7.4 under aerobic or anoxic conditions. Chemoorganotroph, with strictly respiratory metabolism. Degrade aromatic and alicyclic compounds. Catalase‐ and cytochrome c oxidase‐positive. The respiratory quinone is ubiquinone 8, and major fatty acids are C16:1 ω7c, C16:0, and C18:1 ω7c. Major polar lipids are hosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The type strain of the type species was isolated from a wastewater treatment plant, cultivated with cyclohexanol as sole carbon source and nitrate as electron acceptor. DNA G + C content (mol%): 66 (HPLC) or 67.9 (genome analysis, GenBank). Type species: Alicycliphilus denitrificans Mechichi et al. 2003VP.info:eu-repo/semantics/acceptedVersio

Hydrogenophilus

Hy.dro.ge.ni'phi.lus. Gr. neut. n. hydor water; Gr. v. genein to produce; N.L. neut. n. hydrogenum hydrogen (that which produces water); Gr. masc. adj. philos loving, friendly to; N.L. masc. n. Hydrogenophilus hydrogen lover.Proteobacteria / Betaproteobacteria / Hydrogenophilales / Hydrogenophilaceae / Hydrogenophilus Straight rods, 0.4–0.8 × 1.0–3.0 µm during exponential growth. Occur singly or in pairs (in Hydrogenophilus islandicus and Hydrogenophilus thermoluteolus). Motile or nonmotile. Gram‐negative. Nonsporulating. Aerobic or microaerobic, having a strictly respiratory type of metabolism, with oxygen or nitrate as the terminal electron acceptor. Colonies are yellow or grayish. Thermophilic; two species grow optimally at 50–55°C, and another at 63°C. Facultatively chemolithoautotrophic; can use H2 as an electron donor and CO2 as a carbon source. CO2 is fixed via the Calvin–Benson cycle. Acetate, pyruvate, dl‐lactate, and dl‐malate can be used as electron donors and carbon sources. Ammonium can be used as a nitrogen source. The major quinone system is ubiquinone 8. Isolated from hot springs and surrounding soil.DNA G + C content (mol%): 61–65. Type species: Hydrogenophilus thermoluteolus Hayashi, Ishida, Yokota, Kodama and Igarashi 1999, 785VP.info:eu-repo/semantics/acceptedVersio

Melaminivora

Melaminivora [Me.la.mi.ni.vo'ra. N.L. neut. n. melaminum melamine; L. v. voro to eat, to devour; N.L. fem. n. Melaminivora melamine eating]. Proteobacteria / Betaproteobacteria / Burkholderiales / Comamonadaceae / Melaminivora Rods 2.0–3.5‐μm long and 0.5–0.9‐μm wide. Motile by a single unipolar flagellum. Gram‐negative. Nonsporulating. Aerobe. Nitrate is reduced to nitrite. Mesophilic, with the ability to grow between 15 and 50°C, pH 6–9.5, and at NaCl concentrations up to 7%. Chemoorganotroph. Catalase‐ and cytochrome c oxidase‐positive. The respiratory quinone is ubiquinone 8. The major fatty acids are summed feature 3 (C16:1 ω7c/iso‐C15:0 2‐OH), C16:0, and C18:1 ω7c. C10:0 3‐OH is also present. Predominant polar lipids are phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. DNA G + C content (mol%): 69.5–69.6 (HPLC). Type species: Melaminivora alkalimesophila Wang et al. 2014bVP.info:eu-repo/semantics/acceptedVersio

Schlegelella

Schle.gel.el'la. L. fem. dim. ending ‐ella; N.L. fem. n. Schlegelella named in honor of H. G. Schlegel, a pioneer in PHA research. Proteobacteria / Betaproteobacteria / Burkholderiales / Comamonadaceae / SchlegelellaShort rods 0.8–2.8 μm long and 0.4–0.6 μm wide. Motile. Gram‐negative. Nonsporulating. Aerobe. Moderately thermophilic or mesophilic, with optimal growth occurring at 45–50°C or 30–37°C, respectively. Chemoorganotroph. Accumulates polyhydroxyalkanoates (PHA). Catalase and cytochrome c oxidase variable. The major fatty acids are C16:0 and cyclo‐C17:0 or C16:1 ω7c and/or C16:1 ω6c, depending on the species. The type species is Schlegelella thermodepolymerans. Schlegelella aquatica and Schlegelella brevitalea are two other species with validly published names. DNA G + C content (mol%): 69.2–70.0 (HPLC) or 67.5–70.3 (genome analysis, GenBank). Type species: Schlegelella thermodepolymerans Elbanna et al. 2003VP.info:eu-repo/semantics/acceptedVersio