Stress-responses of microbes in oil reservoir under high tetracycline exposure and their environmental risks.

As the groundwater ecosystem is connected with surface, antibiotics and antibiotic resistance genes (ARGs) in aquatic environments will gradually infiltrate into the deep environment, posing a potential threat to groundwater ecosystem. However, knowledge on the environmental risk of antibiotics and ARGs in groundwater ecosystem and their ecological process still remains unexplored. In this study, lab-scale oil reservoirs under high tetracycline stress were performed to evaluate the dynamics of microbial communities, ARGs and potential functions by using 16S rRNA gene sequencing and metagenomics analysis. Although the presence of antibiotics remarkably reduced the microbial abundance and diversity in a short term, but remain stable or even increased after a long-term incubation. Antibiotic stress caused a greater diversity and abundance of ARGs, and higher numbers of ARGs-related species with the capacity to transfer ARGs to other microbes through horizontal gene transfer. Thus, a much more frequent associations of microbial community at both node- and network-level and a selective pressure on enrichment of antibiotic resistant bacteria related to "anaerobic n-alkane degradation" and "methylotrophic methanogenesis" were observed. It is important to emphasize that high antibiotic stress could also prevent some microbes related to "Sulfate reduction", "Fe(II) oxidation", "Nitrate reduction", and "Xylene and Toluene degradation". This study provides an insight into the long-term stress-responses of microbial communities and functions in oil reservoir under tetracycline exposure, which may help to elucidate the effect of antibiotic stress on biogeochemical cycling with microbial involvement in groundwater ecosystem.

Algoriphagus algorifonticola sp. nov., a marine bacterium isolated from cold spring area of South China Sea.

A Gram-stain-negative, aerobic, non-motile, short-rod-shaped bacterium, designated strain hg1T, was isolated from marine sediment within the cold spring area of South China Sea and subjected to a polyphasic taxonomic investigation. Colonies were circular and 1.0-2.0 mm in diameter, coral in colour, convex and smooth after growth on marine agar at 28 °C for 3 days. Strain hg1T was found to grow at 4-40 °C (optimum, 35-37 °C), at pH 6.5-9.0 (optimum, pH 7.5) and with 0-8 % (w/v) NaCl (optimum, 1.5-2 %). Chemotaxonomic analysis showed the sole respiratory quinone was MK-7, and the principal fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and iso-C16 : 0. The major polar lipids are phosphatidylethanolamine, an unidentified phospholipid and five unidentified glycolipids. The DNA G+C content of strain hg1T was 39.6 mol% based on the genome sequence. The comparison of 16S rRNA gene sequence similarities showed that hg1T was closely related to Algoriphagus ornithinivorans DSM 15282T (98.6 % sequence similarity), Algoriphagus zhangzhouensis MCCC 1F01099T (97.9 %) and Algoriphagus vanfongensis DSM 17529T (97.2 %); it exhibited 97.0 % or less sequence similarity to the type strains of other species of the genus Algoriphagus with validly published names. Phylogenetic trees reconstructed with the neighbour-joining, maximum-parsimony and maximum-likelihood methods based on 16S rRNA gene sequences showed that strain hg1T constituted a separate branch with A. ornithinivorans, A. zhangzhouensis, A. vanfongensis in a clade of the genus Algoriphagus. OrthoANI values between strain hg1T and A. ornithinivorans, A. zhangzhouensis and A. vanfongensis were 94.3, 74.1, 73.2 %, respectively, and in silico DNA-DNA hybridization values were 56.2, 18.5 and 18.3 %, respectively. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain hg1T is clearly distinct from recognized species of genus Algoriphagus. On the basis of these features, we propose that strain hg1T (=MCCC 1K03570T=KCTC 72111T) represents a novel species of the genus Algoriphagus with the name Algoriphagus algorifonticola sp. nov.

Reclassification of Enterobacter sp. FY-07 as Kosakonia oryzendophytica FY-07 and Its Potential to Promote Plant Growth.

Precise classification of bacteria facilitates prediction of their ecological niche. The genus Enterobacter includes pathogens of plants and animals but also beneficial bacteria that may require reclassification. Here, we propose reclassification of Enterobacter FY-07 (FY-07), a strain that has many plant-growth-promoting traits and produces bacterial cellulose (BC), to the Kosakonia genera. To re-examine the taxonomic position of FY-07, a polyphasic approach including 16S rRNA gene sequence analysis, ATP synthase ß subunit (atpD) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, RNA polymerase ß subunit (rpoB) gene sequence analysis, determination of DNA G + C content, average nucleotide identity based on BLAST, in silico DNA-DNA hybridization and analysis of phenotypic features was applied. This polyphasic analysis suggested that Enterobacter sp. FY-07 should be reclassified as Kosakonia oryzendophytica FY-07. In addition, the potential of FY-07 to promote plant growth was also investigated by detecting related traits and the colonization of FY-07 in rice roots.

Pseudomonas lopnurensis sp. nov., an endophytic bacterium isolated from Populus euphratica at the ancient Ugan river.

A Gram-stain negative, aerobic, rod-shaped, motile by a single polar flagellum, non-spore-forming bacterium, designated strain AL-54T, was isolated from the storage liquid in the stems of Populus euphratica tree at the ancient Ugan River in Xinjiang, PR China. Isolated AL-54T grew optimally at pH 7.0 and temperature 35 °C in the presence of 3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence demonstrated that the isolate belonged to the genus Pseudomonas and was closely related to Pseudomonas songnenensis NEAU-ST5-5 T (97.6%), Pseudomonas zhaodongensis NEAU-ST5-21 T (97.5%), Pseudomonas alcaliphila AL15-21T (97.3%), Pseudomonas toyotomiensis HT-3T (97.3%), Pseudomonas oleovorans subsp. lubricantis RS1T (97.3%), Pseudomonas stutzeri ATCC 17588T (97.3%), Pseudomonas chengduensis CGMCC 2318T (97.2%), and Pseudomonas xanthomarina KMM 1447T (97.1%). Multilocus Sequences Analysis (MLSA) of strain AL-54T based on the three housekeeping genes, rpoB, rpoD and gyrB further confirmed the phylogenetic assignment of the isolates. The G+C content was 64.7 mol%. The DNA-DNA hybridization with P. songnenensis NEAU-ST5-5 T, P. zhaodongensis NEAU-ST5-21T, P. alcaliphila AL15-21T, P. toyotomiensis HT-3T, P. oleovorans subsp. lubricantis RS1T, P. stutzeri ATCC 17588T, P. chengduensis CGMCC 2318T and P. xanthomarina KMM 1447T revealed 44.0%, 44.7%, 60.1%, 48.7%, 49.1%, 60.1%, 58.9% and 60.2% relatedness respectively. The predominant quinone system is ubiquinone-9 (Q-9). The major components of the cellular fatty acids (>10%) were summed feature 8 (comprising C18:1 ω7c /C18:1 ω6c), summed feature 3 (comprising C16:1 ω7c /C16:1 ω6c) and C16:0. The detected major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and phosphatidylcholine (PC). On the basis of phenotypic data, chemotaxonomic and phylogenetic properties, strain AL-54T can consider as a novel species within the genus Pseudomonas, for which the name Pseudomonas lopnurensis sp. nov. is proposed. The type strain is AL-54T (= JCM 19136T = CCTCC AB 2013066T = NRRL B-59987T).

Description of Erythrobacter mangrovi sp. nov., an aerobic bacterium from rhizosphere soil of mangrove plant (Kandelia candel).

A novel Gram-stain negative, aerobic, non-motile, rod-shaped bacterium, designated as strain EB310T, was isolated from rhizosphere soil of mangrove plant Kandelia candel in Fugong village, Zhangzhou, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EB310T belonged to the genus Erythrobacter, clustering with Erythrobacter pelagi JCM 17468T, Erythrobacter lutimaris KCTC 42109T and Erythrobacter marisflavi KCTC 62896T, and showed the highest 16S rRNA gene sequence similarity of 97.5% to Erythrobacter pelagi JCM 17468T. The genomic average nucleotide identity and in silico DNA-DNA hybridization values between strain EB310T and the reference strains were 71.0-75.5% and 19.8-20.0%, respectively. Growth ranges of the isolate occurred at 10-45 °C (optimum 28-30 °C), pH 5.5-9.5 (optimum pH 7.5) and 0-9.0% NaCl concentrations (optimum 2.0%, w/v). The strain did not produce bacteriochlorophyll a and flexirubin, but produced carotenoids. The strain contained Q-10 as the predominant ubiquinone and summed feature 3 (C16:1 ω7c/C16:1 ω6c) and summed feature 8 (C18:1 ω6c/C18:1 ω7c) as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylcholine. Differential phenotypic characteristics, together with chemotaxonomic, phylogenetic and genomic distinctiveness, indicated that strain EB310T is distinguishable from other members of the genus Erythrobacter. On the basis of the data exhibited, strain EB310T is considered to represent a novel species of the genus Erythrobacter, for which the name Erythrobacter mangrovi sp. nov., is proposed. The type strain is EB310T (= KCTC 72109T = MCCC 1K03690T). The genomic DNA G + C content is 62.9 mol%.

Discovery of Three 22-Membered Macrolides by Deciphering the Streamlined Genome of Mangrove-Derived Streptomyces sp. HM190.

Strain HM190, a moderate halophile, was isolated from rhizosphere soil of the mangrove Kandelia obovata in Fugong village, China. The 16S ribosomal RNA (rRNA) gene sequence and the results of phylogenetic analysis revealed that strain HM190 belonged to the genus Streptomyces and had the highest sequence similarity of 99.79% to Streptomyces heilongjiangensis NEAU-W2T. The complete genome of strain HM190 comprised 7,762,826 bp in a linear chromosome with 71.97% G + C content. According to antiSMASH analysis, a total of 30 biosynthetic gene clusters (BGCs) were predicted to be involved in secondary metabolism, 12 of which were responsible for the production of polyketide- and non-ribosomal peptide-derived secondary metabolites. Gene cluster 5 was responsible for macrolide biosynthesis in a strain-specific 126,331-bp genomic island belonging to the left-arm region. Combined genomics-metabolomics analysis led to the discovery of three 22-membered macrolides (compounds 1-3). Their structures were elucidated by using spectroscopic techniques including high-resolution electrospray ionization mass spectroscopy (HRESIMS) and nuclear magnetic resonance (NMR). The absolute configurations of compounds 1-3 were determined by the X-ray single crystal diffraction and NMR data analysis. All three compounds displayed moderate cytotoxic activities toward tumor cell lines HepG2, A549, and HCT116.

Halomonas endophytica sp. nov., isolated from liquid in the stems of Populus euphratica.

A Gram-stain-negative, aerobic, motile and rod-shaped bacterium, designated MC28T, was isolated from storage liquid collected from the stems of Populus euphratica in the Xinjiang province of China. The growth range of NaCl concentration was 0.5-6.0 % (w/v), with an optimum at 3.0 % (w/v), the temperature range for growth was 10-45 °C, with an optimum at 40 °C, and the pH range for growth was 6.0-9.0, with an optimum around pH 8.5. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MC28T formed a distinct lineage in the clade of genus Halomonas and is closely related to Halomonas desiderata DSM 9502T (96.4 %), Halomonas heilongjiangensis DSM 26881T (96.2 %) and Halomonas urumqiensis JCM 30202T (95.2 %). The average nucleotide identity, average amino acid identity and in silico DNA-DNA hybridization values between strain MC28T and the references strains were 77.2-80.3, 65.8-76.8 and 21.6-25.6 %, respectively. Chemotaxonomic analysis indicated that the main respiratory quinones were Q-9 and Q-8, the predominant cellular fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω9c, C16 : 0 and C17 : 1ω9c, the major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannoside, an aminophospholipid, an unidentified phospholipid, an unidentified aminolipid and two unidentified lipids. Based on its phenotypic, chemotaxonomic and phylogenetic characteristics, strain MC28T is considered to represent a novel species, for which the name Halomonas endophytica sp. nov. is proposed. The type strain is MC28T (=KCTC 52999T=MCCC 1K03343T).

[Microbiological characteristics of a Lysinibacillus strain isolated from Populous euphratica].

OBJECTIVE: The aim of this study was to identify the microbiological characteristics of a Lysinibacillus strain isolated from storage liquid in the stems of Populus euphratica trees. METHODS: Bacterial morphology and cultivation characteristics were studied by conventional cultivation and dyeing method. Biochemical characteristics, fatty acid components, menaquinone, polar lipids, phylogenetic analyses of 16S rRNA, determination of (G + C) mol% content and DNA- DNA hybridization were studied by polyphasic taxonomic approach. RESULTS: Strain ML-64 is Gram-positive, endospore-forming and rod-shaped. Colonies are pale-yellow, circular and entire margin. Temperature range for growth is between 10 and 45 degrees C (optimum at 37 degrees C ). The pH range for growth is between 6. 0 and 9.0 (optimum at 7.0). NaCl concentration range for growth is between 0 and 6% (optimum 3% ). Cells were positive for lipid esterase, Arginine dihydrolase, urease and Voges-Proskauer test. No sugars were fermented in the API 50CH strips. L-Serine, Methyl Pyruvate, α-Keto-Butyric, Acetoacetic Acid were oxidized. Resistant to polymyxin b (30 µg), novobiocin (30 µg), peillin G (10 U). 16S rRNA gene sequence demonstrated that strain ML-64 was closely related to Lysinibacillus chungkukjangi 2RL3-2T (100%) , Lysinibacillus sinduriensis BLB-1T (99.1%). DNA-DNA relatedness were 82% and 50. 9% with Lysinibacillus chungkukjangi 2RL3-2T and Lysinibacillus massiliensis CIP108446T, respectively. The genomic DNA G + C content of strain ML-64 was 36. 8% (mol). Major fatty acids were iso-C,,, (55. 05% ) and anteiso-C15,0 (20. 70% ). The predominant menaquinone is MK-7. Based on the phenotypic phylogenetic and genotypic analyses, the strain ML-64 is concluded to represent a new mutant strain of the Lysinibacillus chungkukjangi species, GenBank accession number is KC609752. CONCLUSION: As an endophytic bacterium of Populus euphratica, genomic structure of the strain ML-64 was greatly differentiated from the closest strain L. chungkukjangi, and suitably adapted to the endophytic environment of Populus euphratica.