Journal of Microbiology

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Gramella fulva sp. nov., isolated from a dry surface of tidal flat: Sae Hyun Hwang , Woon Mo Hwang , Keunsoo Kang , Tae-Young Ahn; J. Microbiol. 2019;57(1):23-29. Published online November 19, 2018; DOI: https://doi.org/10.1007/s12275-019-8370-x

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A novel Gram-stain-negative, aerobic, motile by means of gliding, and short rod-shaped bacterium, designated strain SH35T, was isolated from the dry surface of a tidal flat in Hwasung-si, South Korea. Growth occurred at 10–40°C (optimum 30°C), at pH 6.0–8.0 (optimum pH 7.0), in 1–12% NaCl (optimum 2%), and was inhibited in the absence of NaCl and Ca2+ ions. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SH35T belonged to the genus Gramella and was a member of the family Flavobacteriaceae with highest sequence similarity to Gramella flava JLT2011T (96.1%), followed by Gramella oceani CCAMSZ- TT (95.6%), and 93.0–94.9% to other recognized Gramella species. The major cellular fatty acids (> 5% of the total) of strain SH35T were iso-C15:0, Iso-C16:0, anteiso-C15:0, iso-C17:0 3-OH and summed feature 9 (C16:0 10-methyl and/or C17:1 iso ω9с). The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and nine unidentified polar lipids. The major respiratory quinone and the predominant polyamine were menaquinone-6 (MK-6) and symhomospermidine, respectively. The DNA G + C content was 40.5 mol% (39.7% based on total genome calculations). Based on phylogenetic analysis and physiological and biochemical characterization, strain SH35T represents a novel species of the genus Gramella, for which the name Gramella fulva sp. nov. is proposed. The type strain is SH35T (= KACC 19447T = JCM 32369T).

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Gramella oceanisediminis sp. nov., isolated from deep-sea sediment of the Indian Ocean
Lin Yang, Haolei Shi, Qian Li, Minggang Zheng, Qiliang Lai, Li Zheng
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Proposal of Christiangramia gen. nov., Neomelitea gen. nov. and Nicoliella gen. nov. as replacement names for the illegitimate prokaryotic generic names Gramella Nedashkovskaya et al. 2005, Melitea Urios et al. 2008 and Nicolia Oliphant et al. 2022, respe
Umakant Bhoopati Deshmukh, Aharon Oren
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Gramella sediminis sp. nov., isolated from a tidal flat of the Yellow Sea
Hui-Jing Niu, Kai-Shi Dong, Li Guan, Li-Ping Sun, Qin Wang, Yan-Jiao Zhang, Yi Li, Cheng-Qiang Xia, Cai-Xia Pei
International Journal of Systematic and Evolutionary Microbiology.2022;[Epub] CrossRef
Pyomelanin-Producing Brevundimonas vitisensis sp. nov., Isolated From Grape (Vitis vinifera L.)
Lingmin Jiang, Doeun Jeon, Jueun Kim, Chul Won Lee, Yuxin Peng, Jiyoon Seo, Ju Huck Lee, Jin Hyub Paik, Cha Young Kim, Jiyoung Lee
Frontiers in Microbiology.2021;[Epub] CrossRef
Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds
Lingmin Jiang, Chan Ju Lim, Song-Gun Kim, Jae Cheol Jeong, Cha Young Kim, Dae-Hyuk Kim, Suk Weon Kim, Jiyoung Lee
Journal of Microbiology.2020; 58(1): 24. CrossRef
Jejubacter calystegiae gen. nov., sp. nov., moderately halophilic, a new member of the family Enterobacteriaceae, isolated from beach morning glory
Lingmin Jiang, Dexin Wang, Jung-Sook Lee, Dae-Hyuk Kim, Jae Cheol Jeong, Cha Young Kim, Suk Weon Kim, Jiyoung Lee
Journal of Microbiology.2020; 58(5): 357. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(3): 1443. CrossRef
Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots
Lingmin Jiang, Myoung Hui Lee, Jae Cheol Jeong, Dae-Hyuk Kim, Cha Young Kim, Suk Weon Kim, Jiyoung Lee
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef
Peribacillus faecalis sp. nov., a moderately halophilic bacterium isolated from the faeces of a cow
Lingmin Jiang, Won Yong Jung, Zhun Li, Mi-Kyung Lee, Seung-Hwan Park, Se Won Kang, Jung-Sook Lee, Hyunjung Jung, Tai-Young Hur, Hyeun Bum Kim, Jae-Kyung Kim, Ju-Hoon Lee, Ju Huck Lee, Jiyoung Lee
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

Jindonia aestuariivivens gen. nov., sp. nov., isolated from a tidal flat on the south-western sea in Republic of Korea: Sooyeon Park , Sun Young Yoon , Min-Ji Ha , Jung-Hoon Yoon; J. Microbiol. 2017;55(6):421-427. Published online March 1, 2017; DOI: https://doi.org/10.1007/s12275-017-6621-2

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Abstract

A Gram-stain-negative, aerobic, non-flagellated, and coccoid, ovoid or rod-shaped bacterium, designated JDTF-65T, was isolated from a tidal flat on the south-western sea in Republic of Korea. Strain JDTF-65T grew optimally at 25°C, at pH 7.0– 8.0 and in the presence of 2.0% (w/v) NaCl. Strain JDTF-65T exhibited 16S rRNA gene sequence similarities of 97.1–97.6% to the type strains of ‘Aliisedimentitalea scapharcae’, Phaeo-bacter gallaeciensis, Phaeobacter inhibens, Leisingera aqui-marina, Tropicibacter litoreus, Sulfitobacter pseudonitzschiae, and Pseudoseohaeicola caenipelagi. Phylogenetic trees based on 16S rRNA gene sequences showed that strain JDTF-65T forms an independent lineage within the radiation enclosed by the family Rhodobacteraceae. Strain JDTF-65T contained Q-10 as the predominant ubiquinone and C18:1 ω7c as the major fatty acid. The major polar lipids of strain JDTF-65T were phosphatidylcholine, phosphatidylethanolamine, phos-phatidylglycerol, one unidentified aminolipid, and one un-identified lipid. The DNA G+C content of strain JDTF-65T was 56.8 mol% and its DNA-DNA relatedness values with the type strains of the phylogenetically related species were 13– 27%. Differential phenotypic properties revealed that strain JDTF-65T is separated from representatives of some phylo-genetically related taxa. On the basis of the data presented, strain JDTF-65T represents a new genus and species within the family Rhodobacteraceae, for which the name Jindonia aestuariivivens gen. nov., sp. nov. is proposed. The type strain of Jindonia aestuariivivens is JDTF-65T (=KCTC 52564T =NBRC 112534T).

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Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(6): 576. CrossRef
Kangsaoukella pontilimi gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from a tidal mudflat
Soon Dong Lee, Hanna Choe, Ji-Sun Kim, In Seop Kim
International Journal of Systematic and Evolutionary Microbiology .2020; 70(10): 5235. CrossRef
Kandeliimicrobium roseum gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from mangrove rhizosphere soil
Kai-Ling Wang, Zhi-Man Song, Cu-Huang Rong, Ling-Yun Hao, Qi-Liang Lai, Shuang-Fei Li, Ying Xu
International Journal of Systematic and Evolutionary Microbiology .2018; 68(7): 2158. CrossRef
Pseudopontivivens aestuariicola gen. nov., sp. nov., a Novel Bacterium of the Class Alphaproteobacteria Isolated from a Tidal Flat
Sooyeon Park, Jeehyun Choi, Ji-Min Park, Jung-Hoon Yoon
Current Microbiology.2018; 75(11): 1516. CrossRef

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Identification and Characterization of Metagenomic Fragments from Tidal Flat Sediment: Byung Kwon Kim , Yoon-Dong Park , Hyun-Myung Oh , Jongsik Chun; J. Microbiol. 2009;47(4):402-410. Published online September 9, 2009; DOI: https://doi.org/10.1007/s12275-009-0099-5

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Abstract: Phylogenetic surveys based on cultivation-independent methods have revealed that tidal flat sediments are environments with extensive microbial diversity. Since most of prokaryotes in nature cannot be easily cultivated under general laboratory conditions, our knowledge on prokaryotic dwellers in tidal flat sediment is mainly based on the analysis of metagenomes. Microbial community analysis based on the 16S rRNA gene and other phylogenetic markers has been widely used to provide important information on the role of microorganisms, but it is basically an indirect means, compared with direct sequencing of metagenomic DNAs. In this study, we applied a sequence-based metagenomic approach to characterize uncultivated prokaryotes from tidal flat sediment. Two large-insert genomic libraries based on fosmid were constructed from tidal flat metagenomic DNA. A survey based on end-sequencing of selected fosmid clones resulted in the identification of clones containing 274 bacterial and 16 archaeal homologs in which majority were of proteobacterial origins. Two fosmid clones containing large metagenomic DNAs were completely sequenced using the shot- gun method. Both DNA inserts contained more than 20 genes encoding putative proteins which implied their ecological roles in tidal flat sediment. Phylogenetic analyses of evolutionary conserved proteins indicate that these clones are not closely related to known prokaryotes whose genome sequence is known, and genes in tidal flat may be subjected to extensive lateral gene transfer, notably between domains Bacteria and Archaea. This is the first report demonstrating that direct sequencing of metagenomic gene library is useful in underpinning the genetic makeup and functional roles of prokaryotes in tidal flat sediments.

Rapid Phylogenetic Dissection of Prokaryotic Community Structure in Tidal Flat Using Pyrosequencing: Bong-Soo Kim , Byung Kwon Kim , Jae-Hak Lee , Myungjin Kim , Young Woon Lim , Jongsik Chun; J. Microbiol. 2008;46(4):357-363. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0071-9

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Abstract: Dissection of prokaryotic community structure is prerequisite to understand their ecological roles. Various methods are available for such a purpose which amplification and sequencing of 16S rRNA genes gained its popularity. However, conventional methods based on Sanger sequencing technique require cloning process prior to sequencing, and are expensive and labor-intensive. We investigated prokaryotic community structure in tidal flat sediments, Korea, using pyrosequencing and a subsequent automated bioinformatic pipeline for the rapid and accurate taxonomic assignment of each amplicon. The combination of pyrosequencing and bioinformatic analysis showed that bacterial and archaeal communities were more diverse than previously reported in clone library studies. Pyrosequencing analysis revealed 21 bacterial divisions and 37 candidate divisions. Proteobacteria was the most abundant division in the bacterial community, of which Gammaand Delta-Proteobacteria were the most abundant. Similarly, 4 archaeal divisions were found in tidal flat sediments. Euryarchaeota was the most abundant division in the archaeal sequences, which was further divided into 8 classes and 11 unclassified euryarchaeota groups. The system developed here provides a simple, in-depth and automated way of dissecting a prokaryotic community structure without extensive pretreatment such as cloning.

Thalassobius aestuarii sp. nov., Isolated from Tidal Flat Sediment: Hana Yi , Jongsik Chun; J. Microbiol. 2006;44(2):171-176.; DOI: https://doi.org/2368 [pii]

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Abstract: A strictly aerobic, non-motile, ovoid-shaped Alphaproteobacteria, designated strain JC2049T,was isolated from a tidal flat sediment sample. The results of 16S rRNA gene sequence analysis indicated that this isolate belonged to the genus Thalassobius, with a sequence similarity of 96.9-97.3% to other valid Thalassobius spp. The cells required 1-7% NaCl for growth (optimum 2%) and accumulated poly-β-hydroxybutyrate. Nitrite was reduced to nitrogen, but nitrate was not reduced to nitrite. No genetic potential for aerobic anoxygenic photosynthesis was detected. The primary isoprenoid quinone (Ubiquinone-10), predominant cellular fatty acids (C18:1ω7c, 11 methyl C18:1ω7c and C16:0) and DNA G+C content (61 mol%) were all consistent with the assignment of this isolate to the genus Thalassobius. Several phenotypic characteristics clearly distinguished our isolate from other Thalassobius species. The degree of genomic relatedness between strain JC2049T and other Thalassobius species was in a range of 20-43%. The polyphasic data presented in this study indicates that our isolate should be classified as a novel species within the genus Thalassobius. The name Thalassobius aestuarii sp. nov. is therefore proposed for this isolate; the type strain is JC2049T (= IMSNU 14011T = KCTC 12049T = DSM 15283T).

Archaeal Diversity in Tidal Flat Sediment as Revealed by 16S rDNA Analysis: Bong-Soo Kim , Huyn-Myung Oh , Hojeong Kang , Jongsik Chun; J. Microbiol. 2005;43(2):144-151.; DOI: https://doi.org/2170 [pii]

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Abstract: During the past ten years, Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages. More recently, the presence of novel archaeal phylogenetic lineages has been discovered in coastal marine environments, freshwater lakes, polar seas, and deep-sea hydrothermal vents. Therefore, we conducted an investigation into the archaeal community existing in tidal flat sediment collected from Ganghwa Island, Korea. Phylogenetic analysis of archaeal 16S rDNA amplified directly from tidal flat sediment DNA revealed the presence of two major lineages, belonging to the Crenarchaeota (53.9%) and Euryarchaeota (46.1%) phyla. A total of 102 clones were then sequenced and analyzed by comprehensive phylogenetic analysis. The sequences determined in our samples were found to be closely related to the sequences of clones which had been previously obtained from a variety of marine environments. Archaeal clones exhibited higher similarities (83.25 - 100%) to sequences from other environments in the public database than did those (75.22 - 98.46%) of previously reported bacterial clones obtained from tidal flat sediment. The results of our study suggest that the archaeal community in tidal flat sediment is remarkably diverse.

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