Publications by authors named "Chiu-Chung Young"

191 Publications

Description of sp. nov., harboring antibiotic- and toxic compound-resistace genes, isolated from poultry manure.

Int J Syst Evol Microbiol 2021 Jul;71(7)

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-YST696, harbouring antibiotic- and toxic compound-resistace genes, isolated from poultry manure in Taiwan. Cells of CC-YST696 were short rods, motile with polar flagella, catalase- and oxidase-positive. Optimal growth occurred at 30 °С, pH 9 and with 1 % NaCl. The results of phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by CC-YST696 associated with (97.9 % sequence identity), (97.3 %) and (97.2 %), and with lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 72.8-80.0 % (=17) compared within the type strains of species of of the genus . CC-YST696 contained C, C, Cω7 11-methyl and Cω6/ Cω7 as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, three unidentified glycolipids, two unidentified phospholipids and three unidentified lipids. The DNA G+C content was 62.2 mol% and the predominant quinone was ubiquinone Q-10. On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-YST696 is proposed to represent a novel species of the genus , for which the name sp. nov. (type strain CC-YST696=BCRC 81284=JCM 34167) is proposed.
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http://dx.doi.org/10.1099/ijsem.0.004901DOI Listing
July 2021

Flavobacterium difficile sp. nov., isolated from a freshwater waterfall.

Arch Microbiol 2021 Sep 16;203(7):4449-4459. Epub 2021 Jun 16.

Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan.

A bacterial strain designated KDG-16 is isolated from a freshwater waterfall in Taiwan and characterized to determine its taxonomic affiliation. Cells of strain KDG-16 are Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and form light yellow colonies. Optimal growth occurs at 20-25 °C, pH 6-7, and with 0% NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set reveal that strain KDG-16 is affiliated with species in the genus Flavobacterium. Analysis of 16S rRNA gene sequences shows that strain KDG-16 shares the highest similarity with Flavobacterium terrigena DSM 17934 (97.7%). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain KDG-16 and the closely related Flavobacterium species are below the cut-off values of 95-96, 90 and 70%, respectively, used for species demarcation. Strain KDG-16 contains iso-C, iso-C G and iso-C 3-OH as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, one uncharacterized aminophospholipid, one uncharacterized phospholipid, two uncharacterized aminolipids and two uncharacterized lipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. Genomic DNA G + C content of strain KDG-16 is 31.6%. Based on the polyphasic taxonomic data obtained, strain KDG-16 is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium difficile sp. nov. is proposed. The type strain is KDG-16 (= BCRC 81194 = LMG 31332).
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http://dx.doi.org/10.1007/s00203-021-02440-1DOI Listing
September 2021

Agricultural management practices influence the soil enzyme activity and bacterial community structure in tea plantations.

Bot Stud 2021 May 18;62(1). Epub 2021 May 18.

Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung, 40227, Taiwan.

Background: The soil quality and health of the tea plantations are dependent on agriculture management practices, and long-term chemical fertilizer use is implicated in soil decline. Hence, several sustainable practices are used to improve and maintain the soil quality. Here, in this study, changes in soil properties, enzymatic activity, and dysbiosis in bacterial community composition were compared using three agricultural management practices, namely conventional (CA), sustainable (SA), and transformational agriculture (TA) in the tea plantation during 2016 and 2017 period. Soil samples at two-months intervals were collected and analyzed.

Results: The results of the enzyme activities revealed that acid phosphatase, arylsulfatase, β-glucosidase, and urease activities differed considerably among the soils representing the three management practices. Combining the redundancy and multiple regression analysis, the change in the arylsulfatase activity was explained by soil pH as a significant predictor in the SA soils. The soil bacterial community was predominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Bacteroidetes in the soil throughout the sampling period. Higher Alpha diversity scores indicated increased bacterial abundance and diversity in the SA soils. A significant relationship between bacterial richness indices (SOBS, Chao and ACE) and soil pH, K and, P was observed in the SA soils. The diversity indices namely Shannon and Simpson also showed variations, suggesting the shift in the diversity of less abundant and more common species. Furthermore, the agricultural management practices, soil pH fluctuation, and the extractable elements had a greater influence on bacterial structure than that of temporal change.

Conclusions: Based on the cross-over analysis of the bacterial composition, enzymatic activity, and soil properties, the relationship between bacterial composition and biologically-driven ecological processes can be identified as indicators of sustainability for the tea plantation.
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http://dx.doi.org/10.1186/s40529-021-00314-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131499PMC
May 2021

Corrigendum: gen. nov., sp. nov., a novel bacterium of the family isolated from an agricultural soil, and emended description of the genus .

Int J Syst Evol Microbiol 2021 05;71(5)

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan, ROC.

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http://dx.doi.org/10.1099/ijsem.0.004802DOI Listing
May 2021

sp. nov. and sp. nov., isolated from freshwater habitats.

Int J Syst Evol Microbiol 2019 Jun 8;71(3). Epub 2021 Feb 8.

Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC.

This study presents taxonomic descriptions of strains CYK-4 and TWA-26 isolated from freshwater habitats in Taiwan. Both strains were Gram-stain-negative, strictly aerobic, motile by gliding and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that both strains belonged to the genus . Analysis of 16S rRNA gene sequences showed that strains CYK-4 and TWA-26 shared 92.7 % sequence similarity and were most closely related to W201E (95.6 %) and JC164 (96.7 %), respectively. Both strains shared common chemotaxonomic characteristics comprising MK-6 as the main isoprenoid quinone, iso-C and iso-C G as the predominant fatty acids, phosphatidylethanolamine as the principal polar lipid, and homospermidine as the major polyamine. The DNA G+C contents of strains CYK-4 and TWA-26 were 41.5 and 31.8 mol%, respectively. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. On the basis of phenotypic and genotypic properties and phylogenetic inference, both strains should be classified as novel species within the genus , for which the names sp. nov. (type strain CYK-4=BCRC 81192=LMG 31330) and sp. nov. (type strain TWA-26=BCRC 81200=LMG 31333) are proposed.
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http://dx.doi.org/10.1099/ijsem.0.004682DOI Listing
June 2019

Volatile 1-octanol of tea (Camellia sinensis L.) fuels cell division and indole-3-acetic acid production in phylloplane isolate Pseudomonas sp. NEEL19.

Sci Rep 2021 Feb 2;11(1):2788. Epub 2021 Feb 2.

Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 40227, Taiwan, ROC.

Tea leaves possess numerous volatile organic compounds (VOC) that contribute to tea's characteristic aroma. Some components of tea VOC were known to exhibit antimicrobial activity; however, their impact on bacteria remains elusive. Here, we showed that the VOC of fresh aqueous tea leaf extract, recovered through hydrodistillation, promoted cell division and tryptophan-dependent indole-3-acetic acid (IAA) production in Pseudomonas sp. NEEL19, a solvent-tolerant isolate of the tea phylloplane. 1-octanol was identified as one of the responsible volatiles stimulating cell division, metabolic change, swimming motility, putative pili/nanowire formation and IAA production, through gas chromatography-mass spectrometry, microscopy and partition petri dish culture analyses. The bacterial metabolic responses including IAA production increased under 1-octanol vapor in a dose-dependent manner, whereas direct-contact in liquid culture failed to elicit such response. Thus, volatile 1-octanol emitting from tea leaves is a potential modulator of cell division, colonization and phytohormone production in NEEL19, possibly influencing the tea aroma.
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http://dx.doi.org/10.1038/s41598-021-82442-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7854675PMC
February 2021

sp. nov., isolated from a maize field.

Int J Syst Evol Microbiol 2021 Feb;71(2)

Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT486, isolated from soil sampled in a maize field in Taiwan. Cells of strain CC-CFT486 were short rods, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 8 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT486 associated with (97.0 % sequence identity), (97.0 %), (96.8 %) and (96.8 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 70.6-77.8 % (=11) compared within the type strains of the genus . Strain CC-CFT486 contained C, C, C 8c and C 9c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified aminophospholipids and three unknown phospholipids. The cell wall peptidoglycan of strains CC-CFT486 contained ll-diaminopimelic acid (ll-DAP) and the major polyamine was spermidine. The DNA G+C content was 70.6 mol% and the predominant quinone was menaquinone 9 (MK-9). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-CFT486 is proposed to represent a novel species, for which the name sp. nov. (type strain CC-CFT486=BCRC 81217=JCM 33499).
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http://dx.doi.org/10.1099/ijsem.0.004616DOI Listing
February 2021

sp. nov., isolated from maize field, and emended description of Nakamura 2004.

Int J Syst Evol Microbiol 2020 Nov;70(11):5725-5733

Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT480, isolated from soil sampled in a maize field in Taiwan, ROC. Cells of strain CC-CFT480 were rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 8 and 3 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT480 associated with (97.2 % sequence identity), (95.7 %), (95.4 %) and (95.2 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-CFT480 and were 74.2 and 20.1 %, respectively. Strain CC-CFT480 contained iso-C, C c alcohol and iso-C 10 as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown aminophospholipids, one uncharacterized aminophospholipid and two unknown phospholipids. The major polyamine was spermidine. The DNA G+C content was 34.8 mol% and the predominant quinone was menaquinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT480 is proposed to represent a novel species, for which the name sp. nov. (type strain CC-CFT480=BCRC 81216=JCM 33498).
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http://dx.doi.org/10.1099/ijsem.0.004470DOI Listing
November 2020

sp. nov., isolated from an abandoned construction timber.

Int J Syst Evol Microbiol 2020 Jun;70(6):3731-3739

Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC.

A bacterial strain CC-CTC003 was isolated from a synthetic wooden board. Cells of strain CC-CTC003 were Gram-stain-negative, rod-shaped, motile by gliding and formed yellow colonies. Optimal growth occurred at 25 °C, pH 7 and in the presence of 1 % NaCl. The phylogenetic analyses based on 16S rRNA genes revealed that strain CC-CTC003 belonged to the genus and was most closely related to (95.3 % sequence identity), (94.9 % sequence identity), (94.8 %) and (94.7 %) and had less than 94.7 % sequence similarity to other members of the genus. Average nucleotide identity (ANI) values between strain CC-CTC003 and the type strains of other closely related species were 70.1-74.1 %. The digital DNA-DNA hybridization (dDDH) with was 19.4 %. Strain CC-CTC003 contained C, -C, -C 3-OH, -C 3-OH, summed feature 3 (C 6c / C 7c) and summed feature 9 (C 10-methyl / -C 9c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, two aminolipids and one unidentified glycolipid. The major polyamine was -homospermidine and contained MK-6 as major isoprenoid quinone. The DNA G+C content of the genomic DNA was 39.2 mol%. On the basis of the phylogenetic inference and phenotypic data, strain CC-CTC003 should be classified as a novel species, for which the name sp. nov. is proposed. The type strain is CC-CTC003 (=BCRC 81146=JCM 32838).
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http://dx.doi.org/10.1099/ijsem.0.004227DOI Listing
June 2020

Description of Azoarcus nasutitermitis sp. nov. and Azoarcus rhizosphaerae sp. nov., two nitrogen-fixing species isolated from termite nest and rhizosphere of Ficus religiosa.

Antonie Van Leeuwenhoek 2020 Jul 28;113(7):933-946. Epub 2020 Mar 28.

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xingda Rd, Taichung, 40227, Taiwan.

A polyphasic taxonomic approach was used to characterise two presumably novel bacteria, designated strains CC-YHH838 and CC-YHH848 isolated from termite nest and rhizosphere of Ficus religiosa, respectively. These two nitrogen-fixing strains were observed to be Gram-staining-negative, aerobic rod, and colonies were yellowish in color. Growth of strains was observed at 20-37 °C, pH 7-8, and in the presence of 1-2% NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-YHH838 and CC-YHH848 associated with Thauera hydrothermalis (97.1% sequence identity), and formed a separate branch with Azoarcus indigens (95.4%), Aromatoleum aromaticum (96.2%), and lower sequence similarity to other species. The calculation of OrthoANI values pointed out strains CC-YHH838 and CC-YHH848 gave 78.9% and 79.8% compared to Thauera hydrothermalis, respectively. The major fatty acids (> 5%) were C, C cyclo, C 3-OH, Cω7c/Cω6c and Cω7c/Cω6c. The polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminophospholipid and phospholipids; the predominant polyamines were putrescine and spermidine. The predominant respiratory system was ubiquinone (Q-8) and the DNA G + C contents were 61.4 ± 0.1 mol% and 60.2 ± 1.3 mol%, respectively. Based on the phylogenetic and polyphasic comparisons, strains CC-YHH838 and CC-YHH848 are proposed to represent two novel species within the genus Azoarcus in the family Rhodocyclaceae, for which the name Azoarcus nasutitermitis sp. nov. (type strain CC-YHH838 = BCRC 81059 = JCM 32001) and Azoarcus rhizosphaerae sp. nov. (type strain CC-YHH848 = BCRC 81060 = JCM 32002) were proposed.
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http://dx.doi.org/10.1007/s10482-020-01401-wDOI Listing
July 2020

sp. nov., isolated from a fermentation process.

Int J Syst Evol Microbiol 2020 Apr 11;70(4):2602-2610. Epub 2020 Mar 11.

Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC.

A novel Gram-stain-positive, aerobic, motile with peritrichous flagella, rod-shaped bacterium, designated CC-MHH1044, was isolated from a preserved vegetable sample. A polyphasic taxonomic approach was applied to the isolates in order to clarify its taxonomic position. Growth of the strain CC-MHH1044 occurred at 15-50 °C (optimum, 30 °C), pH 6.0-8.0 (optimum, pH 7.0) and with 0-2.0 % (w/v) NaCl (optimum, 1 %, w/v). The genome of strain CC-MHH1044 consisted of 8.5 Mb and the genomic DNA G+C content was 58.5 mol%. Comparison of the 16S rRNA gene sequences showed that CC-MHH1044 belonged to the genus and showed a close relationship with the type strains of (96.2 %) and (95.9 %), and lower sequence similarity to other species. Average nucleotide identity values calculated from whole-genome sequencing data proved that CC-MHH1044 represents a distinct species. The dominant cellular fatty acids (>5 %) included iso-C(7.4 %), iso-C (6.4 %), anteiso-C(40.3 %), C (6.6 %) and iso-C (27.0 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids, one unidentified phospholipid and glycolipid. The major polyamine was spermidine. The predominant isoprenoid quinone was menaqinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits, together with results of comparative 16S rRNA gene sequence, average nucleotide identity and digital DNA-DNA hybridization analyses, we conclude that strain CC-MHH1044 represents a novel member of the genus , for which the name sp. nov. is proposed. The type strain is CC-MHH1044 (=BCRC 81147=JCM 32834).
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http://dx.doi.org/10.1099/ijsem.0.004080DOI Listing
April 2020

Differential visible spectral influence on carbon metabolism in heterotrophic marine flavobacteria.

FEMS Microbiol Ecol 2020 03;96(3)

Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan.

The visible spectrum of solar radiation is known to stimulate photoheterotrophic bacterial carbon metabolism. However, its impact on 'strictly' heterotrophic bacteria remains less explored. Here, we show that heterotrophic flavobacteria exhibit enhanced uptake and mineralization of dissolved organic carbon with increasing wavelengths of visible light, without employing any 'known' light-harvesting mechanisms. RNA sequencing identified blue light as a major constraint in the extracellular enzymatic hydrolysis of polymeric carbohydrates and acquisition of sugars, despite acting as a stimulus for inorganic carbon sequestration. In contrast, green-red and continuous full-spectrum lights activated diverse hydrolytic enzymes and sugar transporters, but obstructed inorganic carbon fixation. This 'metabolic switching' was apparent through limited nutrient uptake, suppressed light-sensitivity, oxidative stress response and promotion of inorganic carbon sequestration pathways under blue light. The visible light impact on metabolism may be of significant ecological relevance as it appears to promote cell-mediated mineralization of organic carbon in 'green-colored' chlorophyll-rich copiotrophic coastal seawater and inorganic carbon sequestration in 'blue-colored' oligotrophic open ocean. Thus, a novel regulatory role played by light on heterotrophic metabolism and a hidden potential of flavobacteria to sense and respond differentially to monochromatic lights influencing marine carbon cycling were unraveled.
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http://dx.doi.org/10.1093/femsec/fiaa011DOI Listing
March 2020

Description of Gemmobacter aestuarii sp. nov., isolated from estuarine surface water and reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013.

Arch Microbiol 2020 Jul 16;202(5):1035-1042. Epub 2020 Jan 16.

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan.

A Gram-stain-negative, tyrosine-metabolizing, non-motile, strictly aerobic, non-spore-forming, rod-shaped marine bacterium, designated strain CC-PW-75, was isolated from the estuarine water off Pintung, Taiwan. Strain CC-PW-75 formed a distinct phyletic lineage associated with Gemmobacter species, sharing the highest 16S rRNA gene sequence similarity with G. megaterium CF17 and G. straminiformis CAM-8 (96.0% each) followed by G. aquatilis IFAM 1031 and G. nectariphilus AST4 (95.8% each). Analysis of the draft genome (3.76 Mbp) revealed the presence of genes encoding light-harvesting complexes, photosynthetic reaction centers and proteins involved in the metabolism of CO, CO, HCO and HS. However, bacteriochlorophyll a was not detected. Average nucleotide identity values between the genome sequence of CC-PW-75 and the related Gemmobacter species (n = 6) were estimated to be 72.8-76.3%. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid in major amounts, and phosphatidylmonomethylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified lipid in minor amounts. Cω7c and/or Cω6c, C and Cω7c 11-methyl were identified to be major fatty acids. The DNA G + C content was 66.2 mol% (draft genome sequence). Ubiquinone-10 (Q-10) was the sole respiratory quinone. Based on the polyphasic taxonomic evidence, CC-PW-75 is most likely a novel species of the genus Gemmobacter, affiliated to the family Rhodobacteraceae, for which the name Gemmobacter aestuarii sp. nov. is proposed. The type strain is CC-PW-75 (= JCM 19754 = BCRC 80759). Also, we propose the reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013 using the polyphasic data presented in this study.
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http://dx.doi.org/10.1007/s00203-020-01809-yDOI Listing
July 2020

Draft genome sequence reveals co-occurrence of multiple antimicrobial resistance and plant probiotic traits in rice root endophytic strain Burkholderia sp. LS-044 affiliated to Burkholderia cepacia complex.

J Glob Antimicrob Resist 2020 03 3;20:28-30. Epub 2019 Dec 3.

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan; Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402, Taiwan. Electronic address:

Objectives: Members of the Burkholderia cepacia complex (Bcc) have been isolated from various environmental and clinical samples and reportedly pose a threat to human health. Here we examine the draft genome sequence of Burkholderia sp. LS-044, an antibiotic-resistant endophytic strain affiliated to the Bcc (ST895) inhabiting rice (Oryza sativa ssp. japonica cv. Tainung 71) root.

Methods: Antimicrobial susceptibility of LS-044 was evaluated comparatively with other Burkholderia sp. (CC-Al74 and CC-3XP9) using commercial ATB PSE 5 test strips. The genome of LS-044 was sequenced using an Illumina MiSeq platform. Plant probiotic and antimicrobial resistance genes were screened by Rapid Annotation using Subsystem Technology (RAST), CARD 2017, NCBI and/or UniProt.

Results: Plant-associated members of Bcc (LS-044 and CC-Al74) exhibited greater resistance to the majority of antibiotics tested. The draft genome sequence of LS-044 contained 8.78 Mbp in 62 contigs having a G + C content of 66.5%, 8868 coding sequences and 75 RNAs. The genome harboured genes coding for LysR-type β-lactamase transcription regulator, classes A, C and D β-lactamases, several metal-dependent β-lactamases, antibiotic efflux proteins, and proteins conferring resistance to colistin, streptothricin, colicin and fluoroquinolones. Similarly, it also possessed genes for copper homeostasis, copper-cobalt-zinc-cadmium-chromium resistance and reduction of mercury. Genes involved in flagellar motility, hydrolysis of murein and chitin, production of siderophore and auxin, and metabolism of aromatic compounds were also found.

Conclusion: Genome sequence data revealed an interlinked occurrence of plant probiotic traits and antimicrobial resistance in the rice root endophyte LS-044.
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http://dx.doi.org/10.1016/j.jgar.2019.11.017DOI Listing
March 2020

sp. nov., isolated from a freshwater pond.

Int J Syst Evol Microbiol 2020 Feb;70(2):805-813

Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan ROC.

Strain ICH-3, isolated from a freshwater pond in Taiwan 9ROC), was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that ICH-3 is affiliated with the species in the genus . ICH-3 was most closely related to JA2 and NCIB 8290 with 97.5 and 97.4 % 16S rRNA gene sequence similarity. The average nucleotide identity and digital DNA-DNA hybridization identity between ICH-3 and the two closely related strains were 77.3 and 20.9-21.0 %, respectively, indicating that ICH-3 represents a novel species of the genus . Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed white colonies. Optimal growth occurred at 30 °C, pH 7.5-8.0 and with 0.5 % NaCl. The major fatty acids (>20 %) of ICH-3 were summed feature 3 (comprising Cω7 and/or Cω6) and C. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and two uncharacterized phospholipids. The major isoprenoid quinone was Q-8. The genomic DNA G+C content of ICH-3 was 70.3 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain ICH-3 should be classified as representing a novel species of the genus , for which the name sp. nov. is proposed. The type strain is ICH-3 (=BCRC 81155=LMG 30930=KCTC 62866).
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http://dx.doi.org/10.1099/ijsem.0.003829DOI Listing
February 2020

sp. nov., isolated from paddy soil, and reclassification of (Zhao . 2017) as comb. nov.

Int J Syst Evol Microbiol 2020 Jan;70(1):397-405

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic taxonomic approach was used to characterize a nitrogen-fixing bacterium, designated strain CC-HIH110, isolated from paddy soil in Taiwan. Cells of strain CC-HIH110 were Gram-stain-negative, rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 7 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-HIH110 associated with (98.4 % sequence identity), (97.8 %), (97.7 %) and (96.0 %), and lower sequence similarity to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-HIH110 and the type strains of other closely related species were 71.5-88.6 % and 19.6-35.5 %, respectively. Strain CC-HIH110 contained C 3-OH, C 3-OH/iso C I and C 7/C 6 as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, three unknown aminophospholipids, two unknown phospholipids and an unknown lipid. The major polyamine was homospermidine. The DNA G+C content was 55.0 mol% and the predominant quinone was ubiquinone (Q-10). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-HIH110 is proposed to represent a novel species, for which the name sp. nov. (type strain CC-HIH110=BCRC 80932=JCM 31228). In addition, is reclassified as (type strain N19=ACCC 19962=KCTC 52413) comb. nov.
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http://dx.doi.org/10.1099/ijsem.0.003770DOI Listing
January 2020

sp. nov., isolated from water sampled from a rice paddy field.

Int J Syst Evol Microbiol 2019 Dec;69(12):3843-3850

Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Nan-Tzu, Kaohsiung City 811, Taiwan ROC.

Strain TER-1 was isolated from water sampled from a rice paddy field in Taiwan. Cells were Gram-negative, aerobic, motile, rod-shaped and formed pink-coloured colonies. Optimal growth occurred at 25-30 °C, pH 6-7 and in the presence of 0.5 % NaCl. Strain TER-1 could grow on C1 compounds such as methanol, formic acid, methylamine and dimethylamine as sole carbon source, and carry methanol dehydrogenase gene, which supports its methylotrophic metabolism. The results of phylogenetic analyses based on the 16S rRNA gene sequence, methanol dehydrogenase gene sequence and coding sequences of 92 protein clusters indicated that strain TER-1 formed a phylogenetic lineage in the genus . Strain TER-1 was most closely related to AR24 with 96.8 % 16S rRNA gene sequence similarity. Strain TER-1 showed 77.1-82.8 % average nucleotide identity and 16.4-20.2 % digital DNA-DNA hybridization identity with the strains of other species. The major fatty acid of strain TER-1 was Cω7. The predominant hydroxy fatty acid was C 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and two uncharacterized lipids. The only isoprenoid quinone was Q-10. The genomic DNA G+C content of strain TER-1 was 71.9 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TER-1 should be classified in a novel species of the genus , for which the name sp. nov. is proposed. The type strain is TER-1 (=BCRC 81157=LMG 30931=KCTC 62864).
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http://dx.doi.org/10.1099/ijsem.0.003693DOI Listing
December 2019

Draft Genome Sequence of Manganese-Oxidizing Bacterium Massilia sp. Strain Mn16-1_5, Isolated from Serpentine Soil in Taitung, Taiwan.

Microbiol Resour Announc 2019 Aug 8;8(32). Epub 2019 Aug 8.

Department of Environmental Science and Engineering, National Pingtung University of Science and Technology, Pingtung, Taiwan

sp. strain Mn16-1_5 was isolated from serpentine soil. This strain is able to oxidize manganese and has the potential for bioremediation of chromium. Here, we present a 5.53-Mb draft genome sequence of this strain with a G+C content of 64.8% that might provide more information for species delineation and oxidase genes in this strain.
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http://dx.doi.org/10.1128/MRA.00694-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687930PMC
August 2019

Inhella crocodyli sp. nov., isolated from a crocodile pond.

Int J Syst Evol Microbiol 2019 Aug 3;69(8):2424-2430. Epub 2019 Jun 3.

Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC.

Strain CCP-18, isolated from a freshwater pond in Taiwan, was characterized by using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CCP-18 belongs to the genus Inhella and has the highest levels of sequence similarity with respect to Inhella inkyongensis IMCC1713 (98.9 %) and Inhella fonticola TNR-25 (98.0 %). Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed white-coloured colonies. Optimal growth occurred at 25 °C, pH 6 and in the absence of NaCl. The major fatty acids of strain CCP-18 were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids, an unidentified phospholipid, an unidentified aminolipid and an unidentified lipid. The predominant polyamine was putrescine. The major isoprenoid quinone was Q-8. The draft genome was approximately 3.76 Mb in size with a G+C content of 68.9 mol%. The DNA-DNA hybridization values for strain CCP-18with I.inkyongensis IMCC1713 and I.nhella fonticola TNR-25 were less than 40 %. Based on the phylogenetic and phenotypic data, strain CCP-18 should be classified within the genus Inhella as a representative of a novel species, named Inhella crocodyli sp. nov. The type strain is CCP-18 (=BCRC 81120=LMG 30595=KCTC 62511).
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http://dx.doi.org/10.1099/ijsem.0.003496DOI Listing
August 2019

Mesorhizobium composti sp. nov., isolated from compost.

Antonie Van Leeuwenhoek 2019 Sep 4;112(9):1387-1398. Epub 2019 May 4.

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xingda Rd, Taichung, 40227, Taiwan.

A polyphasic taxonomic approach was used to characterize a presumptively novel diazotrophic bacterium, designated strain CC-YTH430, isolated from a compost sample in Taiwan. Cells of strain CC-YTH430 were found to be Gram-stain negative, facultative anaerobic rods that formed yellow-colored colonies on nutrient agar. Cell growth occurred at 15-40 °C, pH 5.0-9.0 and in the presence of 0-2% NaCl. Strain CC-YTH430 resembled Mesorhizobium species while sharing high pair-wise 16S rRNA gene sequence similarities with Mesorhizobium silamurunense, Mesorhizobium thiogangeticum, Mesorhizobium plurifarium, Mesorhizobium tamadayense, Mesorhizobium amorphae (96.9% each), Mesorhizobium sediminum (96.8%), and Mesorhizobium soli (96.5%) and < 96.5% similarity to other species. Strain CC-YTH430 showed 78.8-79.7% average nucleotide identity compared to the type strains of M. amorphae, M. plurifarium, M. soli, M. tamadayense and M. wenxiniae. The N-fixing activity of strain CC-YTH430 was 0.2 nmol ethylene h at 30 °C. The respiratory system was ubiquinone 10 (Q-10) and the DNA G+C content was 62.0 ± 0.2 mol%. The major fatty acids (> 5%) were C, C cyclo, C cyclo ω8c, C 3OH/C iso I and Cω7c/Cω6c. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine and an unidentified aminolipid in major amounts. In addition, phosphatidylethanolamine, an unidentified lipid and several unidentified polar lipids were also found in moderate-to-trace amounts. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-YTH430 is proposed to represent a novel Mesorhizobium species, for which the name Mesorhizobium composti sp. nov. (type strain CC-YTH430 = BCRC 81024 = JCM 31762) is proposed.
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http://dx.doi.org/10.1007/s10482-019-01270-yDOI Listing
September 2019

Rheinheimera riviphila sp. nov., isolated from a freshwater stream.

Arch Microbiol 2019 Sep 20;201(7):919-926. Epub 2019 Apr 20.

Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd., Nan-Tzu, Kaohsiung, 811, Taiwan.

Strain KYPC3, isolated from a freshwater stream in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KYPC3 belonged to the genus Rheinheimera. Strain KYPC3 exhibited 16S rRNA gene sequence similarity values of 94.8-97.9% to the type strains of species of the genus Rheinheimera. Strain KYPC3 was most closely related to Rheinheimera chironomi K19414 with 16S rRNA gene sequence similarity of 97.9%. Cells of strain KYPC3 were Gram-stain negative, aerobic, motile by means of a single-polar flagellum, non-spore forming, coccoid or short rods surrounded by a thick capsule and forming off-white coloured colonies. Growth occurred at 15-30 °C (optimum, 20-25 °C), at pH 6-8 (optimum, pH 7) and with 0-0.5% NaCl (optimum, 0%). The major fatty acids (> 10%) of strain KYPC3 were C 3-OH, summed feature 3 (Cω7c and/or Cω6c) and C. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid and an uncharacterized lipid. The major isoprenoid quinone was Q-8. The draft genome was approximately 4.75 Mb in size with a G + C content of 49.8 mol%. The DNA-DNA relatedness of strain KYPC3 with respect to recognized species of the genus Rheinheimera was significantly less than 70%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KYPC3 should be classified as a novel species of the genus Rheinheimera, for which the name Rheinheimera riviphila sp. nov. is presented. The type strain is KYPC3 (= BCRC 81008 = LMG 29729 = KCTC 52440).
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http://dx.doi.org/10.1007/s00203-019-01657-5DOI Listing
September 2019

Evaluation of synthetic gene encoding α-galactosidase through metagenomic sequencing of paddy soil.

J Biosci Bioeng 2019 Sep 5;128(3):274-282. Epub 2019 Apr 5.

Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 40227, Taiwan; Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 40227, Taiwan. Electronic address:

Many genes of industrial relevance can be found in soil. In this study, metagenome sequencing of paddy soil was performed with 55.68 Gb sequences and 1,787,113 putative open reading frames (ORFs). The functional profiles and metabolic pathway of soil metagenomes were examined using Gene Ontology, Metagenomics RAST, and Kyoto Encyclopedia of Genes and Genomes. To verify the protein function and assembly of ORFs, a putative gene encoding α-galactosidase, namely GalR, which shares 65% identity with an unpublished glycoside hydrolase (GH) 27 family protein, was synthesized using its optimal codon for overexpression in Escherichia coli. GalR was successfully obtained and characterized. The optimal temperature and pH for GalR activity were 30°C and pH 9, respectively. Enzymatic activity indicated that GalR was alkaliphilic and different from acidophilic α-galactosidase in the GH 27 family. Furthermore, 50% of the relative activity of GalR can be attained for 1.7 and 0.7 h preincubation at 40°C and 50°C, respectively. Significant inhibition of GalR was observed in the presence of ethylenediaminetetraacetic acid (EDTA), MgCl, sodium dodecyl sulfate (SDS), and HO; however, it was resistant to 0.1% methanol and ethanol and was slightly activated with NaCl and KCl. The specific activity of GalR was achieved at 11.6 and 0.59 μmol/min/mg of protein using p-nitrophenyl-α-d-galactopyranoside and raffinose as substrates, respectively. Consequently, the metagenomic sequencing-based strategy can provide information for mining novel genes.
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http://dx.doi.org/10.1016/j.jbiosc.2019.03.006DOI Listing
September 2019

Stagnimonas aquatica gen. nov., sp. nov., a new member of the family Nevskiaceae isolated from a freshwater mesocosm.

Int J Syst Evol Microbiol 2019 Jun 25;69(6):1606-1612. Epub 2019 Mar 25.

2​Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC.

A novel bacterial strain, designated THS-13, isolated from a freshwater mesocosm in Taiwan, was characterized by taking a polyphasic taxonomic approach. Cells of strain THS-13 were Gram-stain-negative, aerobic, rod-shaped, motile by means of a single polar flagellum and formed translucent white coloured colonies. Growth occurred at 20-35 °C (optimum, 25 °C), at pH 5-8 (pH 6) and with 0-2 % NaCl (1 %). Phylogenetic analyses based on 16S rRNA gene and coding sequences of 92 protein clusters revealed that the strain belonged to the family Nevskiaceae in the class Gammaproteobacteria and represented an independent taxon separated from other genera. Strain THS-13 shared low level of 16S rRNA gene sequence similarity (less than 93.0 %) to members of other genera in the family Nevskiaceae and was most closely related to Nevskia aquatilis F2-63 (92.9 %). Strain THS-13 showed less than 73.4 % average nucleotide identity and less than 23.8 % digital DNA-DNA hybridization identity compared to the type strains of related genera within the family Nevskiaceae. The predominant fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C16 : 0. The major isoprenoid quinone was Q-8 and the DNA G+C content was 67.6 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid and an uncharacterized aminolipid. On the basis of the genotypic and phenotypic data, strain THS-13 represents a novel species of a new genus in the family Nevskiaceae, for which we propose the name Stagnimonas aquatica gen. nov., sp. nov. The type strain is THS-13 (=BCRC 81158=LMG 30925=KCTC 62868).
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http://dx.doi.org/10.1099/ijsem.0.003365DOI Listing
June 2019

Flavobacterium niveum sp. nov., isolated from a freshwater creek.

Int J Syst Evol Microbiol 2019 Jan 30;69(1):271-277. Epub 2018 Nov 30.

3​Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC.

Strain TAPW14 was isolated from a freshwater creek in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TAPW14 belonged to the genus Flavobacterium and was most closely related to Flavobacterium akiainvivens IK-1 (96.6 % sequence identity) and Flavobacterium hauense BX12 (96.0 %) and less than 96 % sequence similarity to other members of the genus. Cells of strain TAPW14 were Gram-negative, strictly aerobic, motile by gliding, rod-shaped and formed white colonies. Optimal growth occurred at 20 °C, pH 7 and in the presence of 0.5 % NaCl. Strain TAPW14 contained summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and C16 : 0 as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 46.0 mol%. On the basis of the phylogenetic inference and phenotypic data, strain TAPW14 should be classified as a novel species, for which the name Flavobacteriumniveum sp. nov. is proposed. The type strain is TAPW14 (=BCRC 81055=LMG 30057=KCTC 52808).
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http://dx.doi.org/10.1099/ijsem.0.003150DOI Listing
January 2019

Rheinheimera coerulea sp. nov., isolated from a freshwater creek, and emended description of genus Rheinheimera Brettar et al. 2002.

Int J Syst Evol Microbiol 2018 Jul 25;68(7):2340-2347. Epub 2018 May 25.

Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC.

A bacterial strain designated TAPG2 was isolated from a freshwater creek in Taiwan and characterized using the polyphasic taxonomic approach. Cells of TAPG2 were Gram-stain negative, aerobic, motile, non-spore forming, short rods surrounded by a thick capsules and forming cream to dark-green colonies. Growth occurred at 15-37 °C (optimum, 25-30 °C), at pH 6.5-8 (optimum, pH 7) and with 0-1 % NaCl (optimum, 0.5 %). The major fatty acids (>10 %) of TAPG2 were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid, an uncharacterized aminolipid and an uncharacterized lipid. The polyamine profile was composed of the major compound putrescine and moderate amounts of spermidine. The only isoprenoid quinone was Q-8. The DNA G+C content was 53.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that TAPG2 represented a member of the genus Rheinheimera and was most closely related to Rheinheimera aquatica GR5 and Rheinheimera texasensis A62-14B with 98.6 and 98.2 % 16S rRNA gene sequence identities, respectively. However, DNA-DNA hybridization values of TAPG2 with type strains of the species with validly published names were lower than 30 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that TAPG2 should be classified as representing a novel species of the genus Rheinheimera, for which the name Rheinheimera coerulea sp. nov. is presented. The type strain is TAPG2 (=BCRC 81054=LMG 30056=KCTC 52815).
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http://dx.doi.org/10.1099/ijsem.0.002838DOI Listing
July 2018

Paracoccus fontiphilus sp. nov., isolated from a freshwater spring.

Int J Syst Evol Microbiol 2018 Jun 3;68(6):2054-2060. Epub 2018 May 3.

Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC.

Strain MVW-1, isolated from a freshwater spring in Taiwan, was characterized by using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain MVW-1 belongs to the genus Paracoccus and has the highest levels of sequence similarity to Paracoccus caeni MJ17 (97.6 %), Paracoccus sediminis CMB17 (97.4 %), Paracoccus angustae E6 (97.3 %) and Paracoccus acridae SCU-M53 (97.1 %). Cells were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, non-motile, rod-shaped and formed light orange-coloured colonies. Optimal growth occurred at 20-25 °C, pH 6-7, and in the presence of 0-3 % NaCl. The major fatty acid of strain MVW-1 was C18 : 1ω7c. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, an unidentified glycolipid, an unidentified aminolipid and three unidentified phospholipids. The predominant polyamines were spermidine, putrescine and cadaverine. The only isoprenoid quinone was Q-10. The genomic DNA G+C content of strain MVW-1 was 63.4 mol%. Strain MVW-1 exhibited less than 35 % DNA-DNA relatedness to P. caeni MJ17, P. angustae E6, P. sediminis CMB17 and P. acridae SCU-M53. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain MVW-1 should be classified in a novel species of the genus Paracoccus, for which the name Paracoccus fontiphilus sp. nov. is proposed. The type strain is MVW-1 (=BCRC 80974=LMG 29554=KCTC 52239).
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http://dx.doi.org/10.1099/ijsem.0.002793DOI Listing
June 2018

Flavobacterium fluviatile sp. nov., isolated from a freshwater creek.

Int J Syst Evol Microbiol 2018 Apr 2;68(4):1244-1250. Epub 2018 Mar 2.

Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC.

A yellowish-pink-coloured bacterial strain, TAPY14, was isolated from a freshwater creek in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TAPY14 belonged to the genus Flavobacterium and showed the highest similarity (97.3 %) with respect to Flavobacterium reichenbachii WB 3.2-61, Flavobacterium ginsengisoli DCY54 and Flavobacterium defluvii EMB117 and less than 97 % with other members of the genus. Cells of strain TAPY14 were Gram-stain-negative, strictly aerobic, motile by gliding and rod-shaped. Optimal growth occurred at 20-30 °C, pH 6 and in the presence of 0.5 % NaCl. Strain TAPY14 contained iso-C15 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 38.1 mol%. The DNA-DNA hybridization values for strain TAPY14 with F. reichenbachii DSM 21791, F. ginsengisoli JCM 17336 and F. defluvii DSM 17963 were less than 30 %. On the basis of the phylogenetic inference and phenotypic data, strain TAPY14 should be classified as a novel species, for which the name Flavobacterium fluviatile sp. nov. is proposed. The type strain is TAPY14 (=BCRC 81012=LMG 29733=KCTC 52446).
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http://dx.doi.org/10.1099/ijsem.0.002659DOI Listing
April 2018

Complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1, a flavobacterium isolated from coastal surface seawater.

Mar Genomics 2018 Feb 29;37:21-25. Epub 2017 Nov 29.

Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan; Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan. Electronic address:

Here we present the complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1, a flavobacterium isolated from coastal surface seawater. A 3.3Mb genome revealed remarkable specialization of this bacterium particularly in the degradation of sulfated polysaccharides available as detritus or in dissolved phase. Besides utilizing high molecular weight organic biopolymers, this strain appears to accomplish assimilatory sulfate reduction, sulfide oxidation, and acquisition and inter-conversion of inorganic carbon. Genes encoding zeaxanthin and three different kinds of DNA photolyase/cryptochrome (senses blue light) were present, while genes that code for blue light sensing BLUF domain proteins and red/far-red light sensing phytochromes were absent. Furthermore, CC-SAMT-1 lacked the rhodopsin photosystem and all other genes that confer any other known forms of phototrophy. The genomic data revealed that CC-SAMT-1 is highly adapted to sulfur-rich coastal environments, where it most likely contributes to marine carbon and sulfur cycles by metabolizing sulfated polysaccharides as well as inorganic sulfur.
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http://dx.doi.org/10.1016/j.margen.2017.09.003DOI Listing
February 2018

Sphingomonas colocasiae sp. nov., isolated from taro (Colocasia esculanta).

Int J Syst Evol Microbiol 2018 Jan 8;68(1):133-140. Epub 2017 Nov 8.

Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic approach was used to characterize an aerobic, Gram-stain-negative, rod-shaped bacterium (designed as strain CC-MHH0539) isolated from the chopped tuber of taro (Colocasia esculanta) in Taiwan. Strain CC-MHH0539 was able to grow at 15-30 °C (optimum, 25 °C), at pH 6.0-9.0 (optimum, 7.0) and with 0-1 % (w/v) NaCl. Strain CC-MHH0539 showed highest 16S rRNA gene sequence similarity to Sphingomonas laterariae LNB2 (96.8 %), Sphingobium boeckii 469 (96.5 %), Sphingomonas faucium E62-3 (96.4 %) and Sphingosinicella vermicomposti YC7378 (96.2 %) and <96.1 % similarity to other sphingomonads. Strain CC-MHH0539 was found to cluster mainly with the clade that accommodated members of the genus Sphingomonas. The dominant cellular fatty acids were C16 : 0, C16 : 1ω5c, C14 : 0 2-OH, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two sphingoglycolipids and two unidentified phospholipids were detected in strain CC-MHH0539. The DNA G+C content was 69.5 mol%. The respiratory quinone system and predominant polyamine was ubiquinone 10 (Q-10) and sym-homospermidine, respectively, which is in line with Sphingomonas representatives. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits, strain CC-MHH0539 is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas colocasiae sp. nov. is proposed. The type strain is CC-MHH0539 (=BCRC 80933=JCM 31229).
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http://dx.doi.org/10.1099/ijsem.0.002471DOI Listing
January 2018

Castellaniella fermenti sp. nov., isolated from a fermented meal.

Int J Syst Evol Microbiol 2018 Jan 8;68(1):52-57. Epub 2017 Nov 8.

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic taxonomic approach was used to characterize a presumably novel bacterium, designated strain CC-YTH191, isolated from a fermented meal in Taiwan. Cells of strain CC-YTH191 were Gram-stain-negative aerobic rods, which grew at 15-40 °C (optimal 25-30 °C), pH 6.0-9.0 (optimal 7.0) and 1-2 % (w/v) NaCl (optimal 1 %). On the basis of 16S rRNA gene sequence analysis, strain CC-YTH191 appeared to belong to the genus Castellaniella, and was closely related to Castellaniella hirudinis (96.7 % similarity), Castellaniella ginsengisoli (96.7 %) and Castellaniella caeni (96.0 %), while with other related species it shared <96.0 % similarity. The major cellular fatty acids of the isolate were C16 : 0, C17 : 0cyclo, C14 : 0 3OH/C16 : 1iso I and C18 : 1ω7c/C18 : 1ω6c. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, three unidentified phospholipids, an unidentified aminolipid and an unidentified aminophospholpid. Putrescine was the predominant polyamine followed by spermidine. The DNA G+C content was 62.2 mol% and the predominant quinone system was ubiquinone 8 (Q-8). All these features confirmed the placement of the strain CC-YTH191 as a novel species within the genus Castellaniella, for which the name Castellaniella fermenti sp. nov. is proposed. The type strain is CC-YTH191 (=BCRC 81023=JCM 31755).
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http://dx.doi.org/10.1099/ijsem.0.002436DOI Listing
January 2018
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