Pengzhenrongella phosphoraccumulans sp. nov., isolated from high Arctic glacial till, and emended description of the genus Pengzhenrongella.

A yellow pigmented, Gram-stain-positive, motile, facultatively anaerobic and irregular rod-shaped bacteria (strain M0-14T) was isolated from a till sample collected from the foreland of a high Arctic glacier near the settlement of Ny-Ålesund in the Svalbard Archipelago, Norway. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that M0-14T formed a lineage within the family Cellulomonadaceae, suborder Micrococcineae. M0-14T represented a novel member of the genus Pengzhenrongella and had highest 16S rRNA gene sequence similarity to Pengzhenrongella sicca LRZ-2T (97.3 %). Growth occurred at 4-25 °C (optimum 4-18 °C), at pH 6.0-9.0 (optimum pH 7.0), and in the presence of 0-5 % (w/v) NaCl. The predominant menaquinone was MK-9(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipids were phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylinositol, one undefined phospholipid and five undefined phosphoglycolipids. The cell-wall diamino acid was l-ornithine whereas rhamnose and mannose were the cell-wall sugars. Polyphosphate particles were found inside the cells of M0-14T. Polyphosphate kinase and polyphosphate-dependent glucokinase genes were detected during genomic sequencing of M0-14. In addition, the complete pstSCAB gene cluster and phnCDE synthesis genes, which are important for the uptake and transport of phosphorus in cells, were annotated in the genomic data. According to the genomic data, M0-14T has a metabolic pathway related to phosphorus accumulation. The DNA G+C content of the genomic DNA was 70.8 %. On the basis of its phylogenetic relationship, phenotypic properties and chemotaxonomic distinctiveness, strain M0-14T represents a novel species of the genus Pengzhenrongella, for which the name Pengzhenrongella phosphoraccumulans sp. nov. is proposed. The type strain is M0-14T (= CCTCC AB 2012967T = NRRL B-59105T).

Resveratrol modulates the inflammatory response in hPDLSCs via the NRF2/HO-1 and NF-κB pathways and promotes osteogenic differentiation.

OBJECTIVE: The purpose of this study was to investigate resveratrol's specific role as an anti-inflammatory and osteogenic differentiation of hPDLSCs in periodontitis and to reveal the mechanisms involved. BACKGROUND: Numerous studies have shown that inhibiting the inflammatory response of periodontal tissues and promoting the regeneration of alveolar bone are crucial treatments for periodontitis. Resveratrol has been found to have certain anti-inflammatory property. However, the anti-inflammatory mechanism and osteogenic effect of resveratrol in periodontitis are poorly understood. MATERIALS AND METHODS: We constructed an in vitro periodontitis model by LPS stimulation of hPDLSCs and performed WB, RT-qPCR, and immunofluorescence to analyze inflammatory factors and related pathways. In addition, we explored the osteogenic ability of resveratrol in in vitro models. RESULTS: In vitro, resveratrol ameliorated the inflammatory response associated with activation of the NF-κB pathway through activation of the NRF2/HO-1 pathway, characterized by inhibition of p65/p50 nuclear translocation and the proinflammatory cytokines interleukin-1ß levels. Resveratrol also has a positive effect on osteogenic differentiation. CONCLUSIONS: Observations suggest that resveratrol modulates the inflammatory response in hPDLSCs via the NRF2/HO-1 and NF-κB pathways and promotes osteogenic differentiation.

A Pseudomonas Lysogenic Bacteriophage Crossing the Antarctic and Arctic, Representing a New Genus of Autographiviridae.

Polar regions tend to support simple food webs, which are vulnerable to phage-induced gene transfer or microbial death. To further investigate phage-host interactions in polar regions and the potential linkage of phage communities between the two poles, we induced the release of a lysogenic phage, vB_PaeM-G11, from Pseudomonas sp. D3 isolated from the Antarctic, which formed clear phage plaques on the lawn of Pseudomonas sp. G11 isolated from the Arctic. From permafrost metagenomic data of the Arctic tundra, we found the genome with high-similarity to that of vB_PaeM-G11, demonstrating that vB_PaeM-G11 may have a distribution in both the Antarctic and Arctic. Phylogenetic analysis indicated that vB_PaeM-G11 is homologous to five uncultured viruses, and that they may represent a new genus in the Autographiviridae family, named Fildesvirus here. vB_PaeM-G11 was stable in a temperature range (4-40 °C) and pH (4-11), with latent and rise periods of about 40 and 10 min, respectively. This study is the first isolation and characterization study of a Pseudomonas phage distributed in both the Antarctic and Arctic, identifying its lysogenic host and lysis host, and thus provides essential information for further understanding the interaction between polar phages and their hosts and the ecological functions of phages in polar regions.

Spatial and temporal conversion of nitrogen using Arthrobacter sp. 24S4-2, a strain obtained from Antarctica.

According to average nucleotide identity (ANI) analysis of the complete genomes, strain 24S4-2 isolated from Antarctica is considered as a potential novel Arthrobacter species. Arthrobacter sp. 24S4-2 could grow and produce ammonium in nitrate or nitrite or even nitrogen free medium. Strain 24S4-2 was discovered to accumulate nitrate/nitrite and subsequently convert nitrate to nitrite intracellularly when incubated in a nitrate/nitrite medium. In nitrogen-free medium, strain 24S4-2 not only reduced the accumulated nitrite for growth, but also secreted ammonia to the extracellular under aerobic condition, which was thought to be linked to nitrite reductase genes nirB, nirD, and nasA by the transcriptome and RT-qPCR analysis. A membrane-like vesicle structure was detected in the cell of strain 24S4-2 by transmission electron microscopy, which was thought to be the site of intracellular nitrogen supply accumulation and conversion. This spatial and temporal conversion process of nitrogen source helps the strain maintain development in the absence of nitrogen supply or a harsh environment, which is part of its adaption strategy to the Antarctic environment. This process may also play an important ecological role, that other bacteria in the environment would benefit from its extracellular nitrogen source secretion and nitrite consumption characteristics.

Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovénbreen, Arctic.

A rod-shaped, Gram-stain-negative, non-motile and aerobic bacterium, designated Q8-18T, was isolated from soil of glacier foreland in Austre Lovénbreen, Arctic, and subjected to a polyphasic taxonomic study. Strain Q8-18T grew optimally at 20 °C, pH 5.0-8.0 and in the presence of 0-1.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q8-18T belonged to the family Sphingobacteriaceae. Strain Q8-18T showed the highest sequence similarity to Pedobacter mendelii CCM 8685T (96.8%), Pedobacter lithocola CCM 8691T (96.8%), Pedobacter roseus CL-GP80T (96.7%), Pedobacter changchengzhani E01020T (96.7%), Pedobacter alluvionis DSM 19624T (96.6%), Pedobacter jejuensis THG-DR3T (96.3%), Pedobacter ginsengiterrae DCY49T (95.9%) and Pedobacter jamesrossensis CCM 8689T (95.9%). A whole genome-level comparison of strain Q8-18T with P. roseus CL-GP80T, P. changchengzhani E01020T, P. alluvionis DSM 19624T and Pedobacter heparinus LMG 10339T revealed average nucleotide identity values of 77.0, 76.0, 77.0 and 70.4%, respectively. The only respiratory isoprenoid quinone was menaquinone-7. The polar lipid profile of strain Q8-18T was found to contain one phosphatidylethanolamine, eight unidentified aminolipids, one aminophospholipids and five unidentified lipids. The G+C content of the genomic DNA was determined to be 35.4 mol%. The main fatty acids were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0 and anteiso-C15 : 0. On the basis of the evidence presented in this study, a novel species of the genus Pedobacter, Pedobacter mucosus sp. nov., is proposed, with the type strain Q8-18T (=CCTCC AB 2020009T=KCTC 82636T).

Paraconexibacter antarcticus sp. nov., a novel actinobacterium isolated from Antarctic tundra soil.

A Gram-negative, non-motile, aerobic bacterium, named 02-257T, was isolated from Antarctic soil. The cells are surrounded by relatively thin capsules and were catalase-positive and oxidase-negative cocci. Growth of strain 02-257T was observed at 4-35 °C (optimum, 28-30 °C), pH 6.0-8.0 (optimum, pH 6.0) and with 0-1.5% NaCl (optimum, 0 %). Strain 02-257 showed the highest 16S rRNA gene sequence similarity to Paraconexibacter algicola Seoho-28T (95.06 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 02-257T is a member of a novel species belonging to the clade formed by members of the genus Paraconexibacter in the family Paraconexibacteraceae. The DNA G+C content was 72.9 mol%. Strain 02-257T contained C16 : 0-iso (23.0 %), C18  :  1 ω9c (13.8 %), C16 : 0 (12.5 %) and C17 : 1 ω9c-iso (10.8 %) as major cellular fatty acids and menaquinone MK-7(H4) was detected as the only isoprenoid quinone. Diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositole mannoside, phosphatidylinositole dimannoside, unidentified phosphoglycolipid, unidentified aminophospholipid, two unidentified phospholipids, three unidentified aminolipids and six unidentified lipids were the major polar lipids. meso-Diaminopimelic acids were the diagnostic diamino acids in the cell-wall peptidoglycan. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain 02-257T is considered to represent a novel species of the genus Paraconexibacter, for which the name Paraconexibacter antarcticus sp. nov. is proposed. The type strain is 02-257T (=CCTCC AB 2021030T=KCTC 49619T).

Identification and functional studies of microbial volatile organic compounds produced by Arctic flower yeasts.

Microbial volatile organic compounds (mVOCs) can serve as a communication channel among microorganisms, insects and plants, making them important in ecosystem. In order to understand the possible role of mVOCs in Arctic ecology, the microbes in Arctic flowers and their mVOCs and effects on plants were investigated. This study aims to isolate different yeast species from the flowers of five Arctic plant species and further to explore the function of mVOCs emitted by these microbes to plant. It was found that the composition and amount of mVOCs produced by the isolated yeasts were considerably affected by changes in incubation temperature. When the incubation temperature rose, the species of alcohols, aldehydes, esters, organic acids, and ketones increased, but substances specific to low temperature decreased or disappeared. When yeasts were co-cultured with Arabidopsis thaliana without any direct contact, mVOCs produced by the isolated yeasts inhibited the seed germination of A. thaliana at low temperatures; however, the mVOCs promoted the chlorophyll content, fresh weight, root weight and flowering rate of Arabidopsis plants. Although the overall growth-promoting effect of yeast mVOCs was higher at 20°C than at 10°C, the growth-promoting effect on roots, flowers and chlorophyll was highest at 10°C. When cultured at 10°C, the mVOCs produced by Cystofilobasidium capitatum A37, Cryptococcus sp. D41, and Sporidiobolus salmonicolor D27 had the highest growth-promoting effects on the root, flowering rate and chlorophyll content of Arabidopsis, respectively. In the co-culture system, some new mVOCs were detected, such as hendecane, tetradecane, and 1-hexanol that have been proven to promote plant growth. In addition, mVOCs of the isolated Arctic yeasts could inhibit the growth of several microorganisms, especially filamentous fungi. It was the first time to prove that mVOCs produced by the isolated yeasts had varying effects on plant growth at different incubating temperatures, providing a reference for the interactions between microorganisms and plants and their possible responses to climate change in the Arctic area. Moreover, the characteristics of promoting plant growth and inhibiting microbial growth by mVOCs of Arctic yeasts would lay a foundation for potential applications in the future.

Dyadobacter sandarakinus sp. nov., isolated from Arctic tundra soil, and emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus.

Strain Q3-56T, isolated from Arctic tundra soil, was found to be a Gram-stain-negative, yellow-pigmented, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain Q3-56T grew optimally at pH 7.0 and 28 °C. The strain could tolerate up to 1 % (w/v) NaCl with optimum growth in the absence of NaCl. The strain was not sensitive to oxacillin and ceftazidime. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q3-56T belonged to the genus Dyadobacter. Strain Q3-56T showed the highest sequence similarities to Dyadobacter luticola T17T (96.58 %), Dyadobacter ginsengisoli Gsoil 043T (96.50 %), Dyadobacter flavalbus NS28T (96.43 %) and Dyadobacter bucti QTA69T (96.43 %). The predominant respiratory isoprenoid quinone was identified as MK-7, The polar lipid profile of strain Q3-56T was found to contain one phosphatidylethanolamine, three unidentified aminolipids, three unidentified lipids and one unidentified phospholipid. The G+C content of the genomic DNA was determined to be 49.1 mol%. The main fatty acids were summed feature 3 (comprising C16 : 1 ω7c/C16 : 1 ω6c), iso-C15 : 0, C16 : 1 ω5c and iso-C16 : 1 3-OH. On the basis of the evidence presented in this study, a novel species of the genus Dyadobacter, Dyadobacter sandarakinus sp. nov., is proposed, with the type strain Q3-56T (=CCTCC AB 2019271T=KCTC 72739T). Emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus are also provided.

Plasmonic tunable Ag-coated gold nanorod arrays as reusable SERS substrates for multiplexed antibiotics detection.

Antibiotic contaminants in aqueous media pose a serious threat to human and ecological environments. Therefore, it is necessary to develop robust strategies to detect antibiotic residues. For this purpose, a self-assembly and in situ electrochemical reduction method is utilized to tailor silver nanoparticles (AgNPs)-coated GNRs (AgNPs/GNRs) large-scale vertical arrays. These AgNPs/GNRs arrays exhibit outstanding surface-enhanced Raman scattering (SERS) activities because of abundant Raman hot-spots among the adjacent AgNPs and GNRs, but also excellent stability and reproducibility due to the close-packed arrayed nanostructure. These remarkable features validate this arrayed substrate for high-sensitivity 4-aminothiophenol analysis with a detection limit of 0.35 pM and self-cleaning via electrochemical stripping of the adsorbed analytes and AgNPs from the GNRs arrays, therefore realizing renewable SERS applications. Moreover, the distinct SERS performance of AgNPs/GNRs arrays is verified via the analysis of multiplexed antibiotics at tens of picomolar level and no apparent changes of SERS activities are observed when recyclability is explored. The result demonstrates that the proposed AgNPs/GNRs arrays provide a novel strategy for avoiding conventional, disposable SERS substrates, as well as expanding SERS applications for simultaneous sensing and stripping of environmental contaminants.

Roseovarius arcticus sp. nov., a bacterium isolated from Arctic marine sediment.

An aerobic, Gram-stain-negative, motile, rod or long-rod-shaped bacterial isolate, strain MK6-18T, was isolated from a marine sediment sample from Kongsfjorden, Arctic. The bacterium grew optimally at 20 °C, pH 7.0 and in the presence of 1.0-2.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MK6-18T belonged to the genus Roseovarius. Its closest phylogenetic neighbour was Roseovarius nanhaiticus NH52JT showing 96.97 % 16S rRNA gene sequence similarity. The genome of strain MK6-18T is 4.2 Mb long in size with a G+C content of 59.5 mol%. The average nucleotide identity value between the genomes of strain MK6-18T and Roseovarius nanhaiticus NH52JT, was 78.0 %. Similar to other species of the genus Roseovarius, strain MK6-18T had ubiquinone 10 as the predominant ubiquinone and C12 : 0, C16 : 0, summed feature 3 (C16 : 1ω7c/ω6c) and summed feature 8 (C18 : 1ω7c/ω6c) as the major fatty acids. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine; one unidentified polar lipid, one unidentified aminolipid and one unidentified lipid were also detected. This is the first time that a member of the genus Roseovarius has been isolated from the Arctic, which may promote the study of the distribution characteristics and environmental adaptability of this genus. On the basis of the data provided here, strain MK6-18T should be classed as representing a novel species of the genus Roseovarius, for which the name Roseovarius arcticus sp. nov. is proposed. The type strain is MK6-18T (=CCTCC AB 2018219T=KCTC 72187T).

Acidovorax antarcticus sp. nov., isolated from a soil sample of Collins Glacier front, Antarctica.

A Gram-stain-negative, rod-shaped, and aerobic bacterium, strain 16-35-5T, was isolated from Collins Glacier front soil from the Fildes Peninsula, Antarctica. The bacterium grew optimally at 28 °C, pH 7.0 and in the presence of 0-4.0 % (w/v) NaCl. On the basis of the results of 16S rRNA gene sequence phylogenetic analyses, it was concluded that 16-35-5T represented a member of the genus Acidovorax and had the highest sequence similarities with Acidovorax anthurii CFBP 3232T (96.48 %). The genome of 16-35-5T is 4.2 Mb long with a DNA G+C content of 66.3 mol%. Average nucleotide identity (ANI) value between the genomes of 16-35-5T and Acidovorax wautersii DSM 27981T, was 85.29 %. Strain 16-35-5T had ubiquinone-8 (Q-8) as the respiratory ubiquinone. The polar lipids of 16-35-5T were consisted of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The main fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 25.2 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 12.9 %), C16 : 0 (35.2 %), and C17 : 0 cyclo (19.0 %). On the basis of the evidence presented in this study, 16-35-5T should be classified as representing a novel species of the genus Acidovorax, for which the name Acidovorax antarcticus sp. nov., is proposed, with the type strain 16-35-5T (=CCTCC AB 2019325T=KCTC 72915T).

Kaistella flava sp. nov., isolated from Antarctic tundra soil, and emended descriptions of Kaistella yonginensis, Kaistella jeonii, Kaistella antarctica and Kaistella chaponensis.

A rod-shaped, yellow-pigmented, Gram-stain-negative, non-motile and aerobic bacterium, designated 7-3AT, was isolated from soil from King George Island, maritime Antarctica, and subjected to a polyphasic taxonomic study. Growth occurred at 4-37 °C (optimum, 20°C) and at pH 5.0-9.0 (optimum, pH 7.0-8.0). Tolerance to NaCl was up to 4 % (w/v) with optimum growth in the absence of NaCl. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 7-3AT represented a member of the family Flavobacteriaceae. Strain 7-3AT showed the highest sequence similarities with Kaistella yonginensis HMD 1043T (96.65 %), Kaistella carnis NCTC 13525T (96.53 %), Kaistella chaponensis DSM 23145T (96.27 %), Kaistella antarctica LMG 24720T (96.13 %) and Kaistella jeonii DSM 17048T (96.06 %). A whole genome-level comparison of 7-3AT with K. jeonii DSM 17048T, K. antarctica LMG 24720T, K. chaponensis DSM 23145T, and Kaistella palustris DSM 21579T revealed average nucleotide identity (ANI) values of 79.03, 82.25, 78.12, and 74.42 %, respectively. The major respiratory isoprenoid quinone was identified as MK-6 and a few ubiquinones Q-10 were identified. In addition, flexirubin-type pigments were absent. The polar lipid profile of 7-3AT was found to contain one phosphatidylethanolamine, six unidentified aminolipids (AL) and two unidentified lipids (L). The G+C content of the genomic DNA was determined to be 34.54 mol%. The main fatty acids were iso-C15 : 0, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl), anteiso-C15 : 0, iso-C13 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). On the basis of the evidence presented in this study, a novel species of the genus Kaistella, Kaistella flava sp. nov., is proposed, with the type strain 7-3AT (=CCTCC AB 2016141T= KCTC 52492T). Emended descriptions of Kaistella yonginensis, Kaistella jeonii, Kaistella antarctica and Kaistella chaponensis are also given.

Gene expression responses to Riemerella anatipestifer infection in the liver of ducks.

Riemerella anatipestifer is one of the most economically important pathogens of farm ducks worldwide. The molecular mechanisms that underlie its pathogenesis, particularly the host response to R. anatipestifer infection, are poorly understood. The differentially expressed gene profile of duck livers at 24 h following R. anatipestifer infection was therefore investigated using suppression subtractive hybridizaton analysis. A total of 45 differentially expressed genes were identified, which primarily included genes for proteins involved in acute-phase response, inflammatory response, immune response, wound healing and iron homeostasis. For the expression level of 20 genes from those 45 analysed by quantitative reverse transcriptase-polymerase chain reaction at 8, 24 and 48 h post infection, significant differences were observed among the three time points of measurements. The result from this study revealed a gene expression profile of duck liver during R. anatipestifer infection, and those genes with a role in the immune response and wound healing deserving further investigation to elucidate their respective roles during infection.

Genome sequence of poultry pathogen Riemerella anatipestifer strain RA-YM.

Riemerella anatipestifer is a Gram-negative, rod-shaped bacterium associated with epizootic infections in poultry. R. anatipestifer strain RA-YM, belonging to the serotype 1 prevalent in China, is a clinically isolated strain with high-level virulence. Here, we report the first genome sequence of this species.