Journal of Microbiology

Volume 56(7); July 2018

Review

[MINIREVIEW] Interdependence between iron acquisition and biofilm formation in Pseudomonas aeruginosa: Donghoon Kang , Natalia V. Kirienko; J. Microbiol. 2018;56(7):449-457. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-8114-3

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Abstract: Bacterial biofilms remain a persistent threat to human healthcare due to their role in the development of antimicrobial resistance. To combat multi-drug resistant pathogens, it is crucial to enhance our understanding of not only the regulation of biofilm formation, but also its contribution to bacterial virulence. Iron acquisition lies at the crux of these two subjects. In this review, we discuss the role of iron acquisition in biofilm formation and how hosts impede this mechanism to defend against pathogens. We also discuss recent findings that suggest that biofilm formation can also have the reciprocal effect, influencing siderophore production and iron sequestration.

Journal Articles

Taxonomic description and draft genome of Pseudomonas sediminis sp. nov., isolated from the rhizospheric sediment of Phragmites karka: Pratiksha Behera , Madhusmita Mahapatra , Arman Seuylemezian , Parag Vaishampayan , V. Venkata Ramana , Neetha Joseph , Amaraja Joshi , Yogesh Shouche , Mrutyunjay Suar , Ajit K. Pattnaik , Gurdeep Rastogi; J. Microbiol. 2018;56(7):458-466. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-7549-x

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Abstract: The taxonomic position of a Gram-stain-negative, rod-shaped bacterial strain, designated PI11T , isolated from the rhizospheric sediment of Phragmites karka was characterized using a polyphasic approach. Strain PI11T could grow optimally at 1.0% NaCl concentration with pH 7.0 at 30°C and was positive for oxidase and catalase but negative for hydrolysis of starch, casein, and esculin ferric citrate. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain PI11T belonged to the genus Pseudomonas sharing the highest sequence similarities with Pseudomonas indoloxydans JCM 14246T (99.72%), followed by, Pseudomonas oleovorans subsp. oleovorans DSM 1045T (99.29%), Pseudomonas toyotomiensis JCM 15604T (99.15%), Pseudomonas chengduensis DSM 26382T (99.08%), Pseudomonas oleovorans subsp. lubricantis DSM 21016T (99.08%), and Pseudomonas alcaliphila JCM 10630T (99.01%). Experimental DNA-DNA relatedness between strain PI11T and P. indoloxydans JCM 14246T was 49.4%. The draft genome of strain PI11T consisted of 4,884,839 bp. Average nucleotide identity between the genome of strain PI11T and other closely related type strains ranged between 77.25–90.74%. The polar lipid pattern comprised of phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major (> 10%) cellular fatty acids were C18:1 ω6c/ω7c, C16:1 ω6c/ω7c, and C16:0. The DNA G + C content of strain PI11T was 62.4 mol%. Based on the results of polyphasic analysis, strain PI11T was delineated from other closely related type strains. It is proposed that strain PI11T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas sediminis sp. nov. is proposed. The type strain is PI11T (= KCTC 42576T = DSMZ 100245T).

Flavihumibacter profundi sp. nov., isolated from eutrophic freshwater sediment: Ting-Ting Ren , Chun-Zhi Jin , Feng-Jie Jin , Taihua Li , Chang-Jin Kim , Hee-Mock Oh , Hyung-Gwan Lee , Long Jin; J. Microbiol. 2018;56(7):467-471. Published online June 28, 2018; DOI: https://doi.org/10.1007/s12275-018-7567-8

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Abstract: A Gram-stain-positive, aerobic, non-motile, non-spore-forming, and rod-shaped bacterium, designated strain CHu64- 6-1T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17-m in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies placed the new isolate in the class Sphingobacteriia, and the isolate is notably most closely related to Flavihumibacter sediminis CJ663T (98.1% similarity), Flavihumibacter solisilvae 3-3T (97.8%), Flavihumibacter petaseus T41T (97.5%), Flavihumibacter cheonanensis WS16T (97.4%), and Flavihumibacter stibioxidans YS-17T (97.2%). The cells of strain CHu64-6-1T formed yellow colonies on R2A agar and contained MK-7 as the only menaquinone, phosphatidylethanolamine, an unidentified phospholipid, and two unidentified aminolipids as the major polar lipids, and C15:0 iso, C17:0 iso 3-OH, C15:1 iso G, and C16:1 ω5c as the major fatty acids (> 5%). The DNA G + C content of the genome was determined to be 46.5 mol%. The DNA-DNA hybridization values of strain CHu64-6-1T with F. sediminis CJ663T, F. solisilvae 3-3T, F. petaseus T41T, F. cheonanensis WS16T, and F. stibioxidans YS-17T were 12.4–33.2%. Based on the combined genotypic and phenotypic data, we propose that strain CHu64-6-1T represents a novel species of the genus Flavihumibacter, for which the name Flavihumibacter profundi sp. nov. is proposed. The type strain is CHu64-6-1T (= KCTC 62290T = CCTCC AB 2018060T).

Bacillus ferrooxidans sp. nov., an iron(II)-oxidizing bacterium isolated from paddy soil: Guo-Wei Zhou , Xiao-Ru Yang , Jian-Qiang Su , Bang-Xiao Zheng , Yong-Guan Zhu; J. Microbiol. 2018;56(7):472-477. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-7543-3

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Abstract: An endospore-forming bacterium, designated YT-3T, was isolated from a paddy soil in Yingtan, Jiangxi, China. Cells of strain YT-3T were Gram-positive, rod-shaped, facultative anaerobic, catalase, and oxidase positive. The optimum growth temperature and pH were 30°C (ranged from 15 to 50°C) and 6.5–7.0 (ranged from 3 to 11), respectively. Analysis of the 16S rRNA gene sequence showed that strain YT-3T was affiliated to the genus Bacillus and displayed the highest similarity to that of Bacillus drentensis JCM 21707T (98.3%), followed by B. ginsengisoli JCM 17335T (97.8%) and B. fumarioli JCM 21708T (97.0%). The similarity of rpoB gene sequence between strain YT-3T and B. drentensis JCM 21707T, B. ginsengisoli JCM 17335T and B. fumarioli JCM 21708T was 80.4%, 81.5%, and 82.1%, respectively. The genomic DNA G + C content was 44.9 mol%. The predominant respiratory quinone was Menaquinone-7, and meso-diaminopimelic acid was present in the peptidoglycan layer of cell wall. The major fatty acids were C15:0 anteiso (36.2%), C14:0 iso (19.6%), C15:0 iso (17.4%), and C16:0 iso (9.8%). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and ammoniac phospholipids. The DNA-DNA hybridization values between isolate YT-3T and B. drentensis (JCM 21707T), B. ginsengisoli (JCM 17335T), and B. fumarioli (JCM 21708T) were 36.3%, 30.3%, and 25.3%, respectively. On the basis of physiological, genetic and biochemical data, strain YT-3T represented a novel species of the genus Bacillus, for which the name Bacillus ferrooxidans sp. nov was proposed. The type strain is YT-3T (= KCTC 33875T = CCTCC AB 2017049T).

Pedobacter aquicola sp. nov., isolated from freshwater: Yochan Joung , Hye-jin Jang , Miri Park , Jaeho Song , Jang-Cheon Cho; J. Microbiol. 2018;56(7):478-484. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-7499-3

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Abstract: A non-motile, pink-pigmented bacterial strain designated IMCC25679T, was isolated from freshwater Lake Chungju of Korea. Phylogenetic trees based on 16S rRNA gene sequences showed that the strain IMCC25679T formed a lineage within the genus Pedobacter. The strain IMCC25679T was closely related to Pedobacter daechungensis Dae 13T (96.4% sequence similarity), Pedobacter rivuli HME8457T (95.3%) and Pedobacter lentus DS-40T (94.3%). The major fatty acids of IMCC- 25679T were iso-C15:0, iso-C16:0 and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine (PE), an unidentified sphingolipid (SL), an unidentified aminolipid (AL) and three unidentified polar lipids (PL). The DNA G + C content of IMCC25679T was 32.2 mol%. Based on the evidence presented in this study, the strain IMCC25679T represents a novel species within the genus Pedobacter, with the proposed name Pedobacter aquicola, sp. nov. The type strain is IMCC25679T (= KACC 19486T = NBRC113131T).

Proposal of three novel species of soil bacteria, Variovorax ureilyticus, Variovorax rhizosphaerae, and Variovorax robiniae, in the family Comamonadaceae: Tuan Manh Nguyen , Ngoc Hoang Trinh , Jaisoo Kim; J. Microbiol. 2018;56(7):485-492. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-8025-3

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Abstract: Three novel bacterial strains (UCM-2T, UCM-G28T, and UCM-G35T) were obtained while isolating soil bacteria for the development of antibiotics. Cells of these strains were Gram-negative, non-spore forming, motile by means of a single flagellum, and rod shaped. In all strains, the predominant isoprenoid quinone was ubiquinone-8 (Q-8). Cells contained C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), and C17:0 cyclo as the major fatty acids, and C10:0 3-OH as the major hydroxy fatty acid. The polar lipid profiles of the three novel strains were dominated by diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The genomic DNA G + C contents of strains UCM-2T, UCM-G28T, and UCMG35T were 67.5, 65.9, and 66.4 mol%, respectively. Phylogenetic analyses based on 16S rRNA sequences showed that strain UCM-2T was most closely related to Variovorax soli NBRC 106424T, whereas strains UCM-G28T and UCM-G35T were most similar to Variovorax ginsengisoli Gsoil 3165T. Values indicating DNA-DNA hybridization between the novel isolates and closely related species in the genus Variovorax were lower than the 70% cut-off point. These phenotypic, chemotaxonomic, and phylogenetic data indicate that the three isolates should be classified as new members of the genus Variovorax, for which the names Variovorax ureilyticus sp. nov., Variovorax rhizosphaerae sp. nov., and Variovorax robiniae sp. nov. are proposed. The type strains are UCM-2T (= KACC 18899T = NBRC 112306T), UCMG28T (= KACC 18900T = NBRC 112307T), and UCM-G35T (= KACC 18901T = NBRC 112308T), respectively.

Halomonas tibetensis sp. nov., isolated from saline lakes on Tibetan Plateau: Hui-bin Lu , Peng Xing , Lei Zhai , Dorji Phurbu , Qian Tang , Qing-long Wu; J. Microbiol. 2018;56(7):493-499. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-8076-5

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Abstract: Strains pyc13T and ZGT13 were isolated from Lake Pengyan and Lake Zigetang on Tibetan Plateau, respectively. Both strains were Gram-negative, catalase- and oxidase-positive, aerobic, rod-shaped, nonmotile, and nonflagellated bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains pyc13T and ZGT13 belong to the genus Halomonas, with Halomonas alkalicola 56-L4-10aEnT as their closest neighbor, showing 97.4% 16S rRNA gene sequence similarity. The predominant respiratory quinone of both strains was Q-9, with Q-8 as a minor component. The major fatty acids of both strains were C18:1 ω6c/C18:1 ω7c, C16:1 ω6c/C16:1 ω7c, C16:0, and C12:0 3OH. The polar lipids of both strains consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, glycolipid, phospholipids of unknown structure containing glucosamine, and unidentified phospholipids. The DNA G + C content of pyc13T and ZGT13 were 62.6 and 63.4 mol%, respectively. The DNA-DNA hybridization values of strain pyc13T were 34, 41, 61, 35, and 35% with the reference strains H. alkalicola 56-L4-10aEnT, H. sediminicola CPS11T, H. mongoliensis Z-7009T, H. ventosae Al12T, and H. fontilapidosi 5CRT, respectively. Phenotypic, biochemical, genotypic, and DNA-DNA hybridization data showed that strains pyc13T and ZGT13 represent a new species within the genus Halomonas, for which the name H. tibetensis sp. nov. is proposed. The type strain is pyc13T (= CGMCC 1.15949T = KCTC 52660T).

Hymenobacter jeollabukensis sp. nov., isolated from soil: Leonid N. Ten , Young Eun Han , Kyeung Il Park , In-Kyu Kang , Jeung-Sul Han , Hee-Young Jung; J. Microbiol. 2018;56(7):500-506. Published online June 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8085-4

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Abstract: A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated 1-3-3-8T, was isolated from soil and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 1-3-3-8T belongs to the family Cytophagaceae of phylum Bacteroidetes and is most closely related to Hymenobacter paludis KBP-30T (96.8% similarity), Hymenobacter ocellatus Myx2105T (96.8%), Hymenobacter coalescens WW84T (95.6%), and Hymenobacter deserti ZLB-3T (95.4%). The G + C content of the genomic DNA of strain 1-3-3-8T was 63.6 mol%. The isolate contained C15:0 iso (28.4%), summed feature 4 (C17:1 anteiso B/C17:1 iso I; 18.9%), and C15:0 anteiso (17.6%) as major fatty acids, MK-7 as the predominant respiratory quinone, and sym-homospermidine as the predominant polyamine. The major polar lipids were phosphatidylethanolamine and an unidentified lipid. The phenotypic and chemotaxonomic data supported the affiliation of strain 1-3-3-8T with the genus Hymenobacter. The DNA-DNA relatedness between strain 1-3-3-8T and H. paludis KCTC 32237T and H. ocellatus DSM 11117T were 24.5 and 27.4% respectively, clearly showing that the isolate is not related to them at the species level. Overall, the novel strain could be differentiated from its phylogenetic neighbors on the basis of several phenotypic, genotypic, and chemotaxonomic features. Therefore, strain 1-3-3-8T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter jeollabukensis sp. nov. has been proposed. The type strain is 1-3-3-8T (= KCTC 52741T = JCM 32192T).

Temporal and spatial impact of Spartina alterniflora invasion on methanogens community in Chongming Island, China: Xue Ping Chen , Jing Sun , Yi Wang , Heng Yang Zhang , Chi Quan He , Xiao Yan Liu , Nai Shun Bu , Xi-En Long; J. Microbiol. 2018;56(7):507-515. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-8062-y

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Abstract: Methane production by methanogens in wetland is recognized as a significant contributor to global warming. Spartina alterniflora (S. alterniflora), which is an invasion plant in China’s wetland, was reported to have enormous effects on methane production. But studies on shifts in the methanogen community in response to S. alterniflora invasion at temporal and spatial scales in the initial invasion years are rare. Sediments derived from the invasive species S. alterniflora and the native species Phragmites australis (P. australis) in pairwise sites and an invasion chronosequence patch (4 years) were analyzed to investigate the abundance and community structure of methanogens using quantitative real-time PCR (qPCR) and Denaturing gradient gel electrophoresis (DGGE) cloning of the methyl-coenzyme M reductase A (mcrA) gene. For the pairwise sites, the abundance of methanogens in S. alterniflora soils was lower than that of P. australis soils. For the chronosequence patch, the abundance and diversity of methanogens was highest in the soil subjected to two years invasion, in which we detected some rare groups including Methanocellales and Methanococcales. These results indicated a priming effect at the initial invasion stages of S. alterniflora for microorganisms in the soil, which was also supported by the diverse root exudates. The shifts of methanogen communities after S. alterniflora invasion were due to changes in pH, salinity and sulfate. The results indicate that root exudates from S. alterniflora have a priming effect on methanogens in the initial years after invasion, and the predominate methylotrophic groups (Methanosarcinales) may adapt to the availability of diverse substrates and reflects the potential for high methane production after invasion by S. alterniflora.

Antifungal activity of 3-acetylbenzamide produced by actinomycete WA23-4-4 from the intestinal tract of Periplaneta americana: Xia Fang , Juan Shen , Jie Wang , Zhi-li Chen , Pei-bin lin , Zhi-yu Chen , Lin-yan Liu , Huan-xiong Zeng , Xiao-bao Jin; J. Microbiol. 2018;56(7):516-523. Published online June 28, 2018; DOI: https://doi.org/10.1007/s12275-018-7510-z

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Abstract: Actinomycetes are well-known for producing numerous bioactive secondary metabolites. In this study, primary screening by antifungal activity assay found one actinomycete strain WA23-4-4 isolated from the intestinal tract of Periplaneta americana that exhibited broad spectrum antifungal activity. 16S rDNA gene analysis of strain WA23-4-4 revealed close similarity to Streptomyces nogalater (AB045886) with 86.6% sequence similarity. Strain WA23-4-4 was considered as a novel Streptomyces and the 16s rDNA sequence has been submitted to GenBank (accession no. KX291006). The maximum antifungal activity of WA23-4-4 was achieved when culture conditions were optimized to pH 8.0, with 12% inoculum concentration and 210 ml ISP2 medium, which remained stable between the 5th and the 9th day. 3-Acetyl benzoyl amide was isolated by ethyl acetate extraction of WA23- 4-4 fermentation broth, and its molecular formula was determined as C9H9NO2 based on MS, IR, 1H, and 13C NMR analyses. The compound showed significant antifungal activity against Candida albicans ATCC 10231 (MIC: 31.25 μg/ml) and Aspergillus niger ATCC 16404 (MIC: 31.25 μg/ml). However, the compound had higher MIC values against Trichophyton rubrum ATCC 60836 (MIC: 500 μg/ml) and Aspergillus fumigatus ATCC 96918 (MIC: 1,000 μg/ml). SEM analysis showed damage to the cell membrane of Candida albicans ATCC 10231 and to the mycelium of Aspergillus niger ATCC 16404 after being treatment with 3-acetyl benzoyl amide. In conclusion, this is the first time that 3-acetyl benzoyl amide has been identified from an actinomycete and this compound exhibited antifungal activity against Candida albicans ATCC 10231 and Aspergillus niger ATCC 16404.

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