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Environmental Adaptability and Roles in Ammonia Oxidation of Aerobic Ammonia-Oxidizing Microorganisms in the Surface Sediments of East China Sea: Wenhui Li, Yu Zhen, Yuhong Yang, Daling Wang, Hui He; J. Microbiol. 2024;62(10):845-858. Published online August 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00166-5

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This study investigated the community characteristics and environmental influencing factors of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the surface sediments of the East China Sea. The research found no consistent pattern in the richness and diversity of AOA and AOB with respect to the distance from the shore, indicating a complex interplay of factors. The expression levels of AOA amoA gene and AOB amoA gene in the surface sediments of the East China Sea ranged from 4.49 × 10² to 2.17 × 10⁶ copies per gram of sediment and from 6.6 × 10¹ to 7.65 × 10⁴ copies per gram of sediment, respectively. Salinity (31.77 to 34.53 PSU) and nitrate concentration (1.51 to 10.12 μmol/L) were identified as key environmental factors significantly affecting the AOA community, while salinity and temperature (13.71 to 19.50 °C) were crucial for the AOB community. The study also found that AOA, dominated by the Nitrosopumilaceae family, exhibited higher gene expression levels than AOB, suggesting a more significant role in ammonia oxidation. The expression of AOB was sensitive to multiple environmental factors, indicating a responsive role in nitrogen cycles and ecosystem health. The findings contribute to a better understanding of the biogeochemical processes and ecological roles of ammonia-oxidizing microorganisms in marine sediments.

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Metabolism diversification of ammonia-oxidizing archaea and bacteria under different precipitation gradients and land legacies
Soumyadev Sarkar, Anna Kazarina, Paige M. Hansen, Kaitlyn Ward, Christopher Hargreaves, Nicholas Reese, Qinghong Ran, Willow Kessler, Ligia F.T. de Souza, Terry D. Loecke, Marcos V.M. Sarto, Charles W. Rice, Lydia H. Zeglin, Benjamin A. Sikes, Sonny T.M.
Applied Soil Ecology.2025; 206: 105831. CrossRef
Genetic and transcriptional profiles of ammonia oxidizing communities in Bohai sediments: abundance, activity, and environmental correlations
Yining Jiang, Xue Lou, Mingyang Wang, Minggang Zheng, Zhiyao Wang, Hui Chen
Frontiers in Microbiology.2025;[Epub] CrossRef

Cultivation of Diverse Novel Marine Bacteria from Deep Ocean Sediment Using Spent Culture Supernatant of Ca. Bathyarchaeia Enrichment: Sidra Erum Ishaq, Tariq Ahmad, Lewen Liang, Ruize Xie, Tiantian Yu, Yinzhao Wang, Fengping Wang; J. Microbiol. 2024;62(8):611-625. Published online July 10, 2024; DOI: https://doi.org/10.1007/s12275-024-00145-w

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Most microorganisms resist pure cultivation under conventional laboratory conditions. One of the primary issues for this un-culturability is the absence of biologically produced growth-promoting factors in traditionally defined growth media. However, whether cultivating microbes by providing spent culture supernatant of pivotal microbes in the growth medium can be an effective approach to overcome this limitation is still an under-explored area of research. Here, we used the spent culture medium (SCM) method to isolate previously uncultivated marine bacteria and compared the efficiency of this method with the traditional cultivation (TC) method. In the SCM method, Ca. Bathyarchaeia-enriched supernatant (10%) was used along with recalcitrant organic substrates such as lignin, humic acid, and organic carbon mixture. Ca. Bathyarchaeia, a ubiquitous class of archaea, have the capacity to produce metabolites, making their spent culture supernatant a key source to recover new bacterial stains. Both cultivation methods resulted in the recovery of bacterial species from the phyla Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota. However, our SCM approach also led to the recovery of species from rarely cultivated groups, such as Planctomycetota, Deinococcota, and Balneolota. In terms of the isolation of new taxa, the SCM method resulted in the cultivation of 80 potential new strains, including one at the family, 16 at the genus, and 63 at the species level, with a novelty ratio of ~ 35% (80/219). In contrast, the TC method allowed the isolation of ~ 10% (19/171) novel strains at species level only. These findings suggest that the SCM approach improved the cultivation of novel and diverse bacteria.

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Engineering the phycosphere: fundamental concepts and tools for the bottom-up design of microalgal-bacterial consortia
Austin Semple, Jagroop Pandhal
Applied Phycology.2025; 6(1): 21. CrossRef
Darkness to Discovery: A Comprehensive Mini-Review on Culturable and Non-Culturable Microbial Diversity from Deep Sea
Abhay B. Fulke, Nilkanth Sharma, Jayshree Nadekar
Microbial Ecology.2025;[Epub] CrossRef
The bacterial community of the freshwater bryozoan Cristatella Mucedo and its secondary metabolites production potential
Inmaculada Tocino-Márquez, Martin Zehl, Joana Séneca, Petra Pjevac, Manuel Felkl, Christian F. W. Becker, Alexander Loy, Thomas Rattei, Andrew N. Ostrovsky, Sergey B. Zotchev
Scientific Reports.2025;[Epub] CrossRef
Uncertainty Analysis of Biogas Generation and Gas Hydrate Accumulations in the Baiyun Sag, South China Sea
Pibo Su, Jinqiang Liang, Huai Cheng, Yaoyao Lv, Wei Zhang, Zuofei Zhu
Microorganisms.2024; 13(1): 5. CrossRef

Description of Deefgea piscis sp. nov., and Deefgea tanakiae sp. nov., isolated from the gut of Korean indigenous fish: Do-Hun Gim , So-Yeon Lee , Jeong Eun Han , Jae-Yun Lee , Seo Min Kang , Jin-Woo Bae; J. Microbiol. 2022;60(11):1061-1069. Published online September 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2250-5

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Three novel strains, (D17T, D13, and D25T) isolated from the gut of the Korean dark sleeper (Odontobutis platycephala), Kumgang fat minnow (Rhynchocypris kumgangensis), and the Korean oily bitterling (Tanakia koreensis) were identified as two novel species. Strains D17T and D13 showed the highest similarities in 16S rRNA gene and complete genome sequences to Deefgea rivuli WB 3.4-79T (98.0% and 97.9%, respectively, of 16S rRNA gene sequence similarity, 77.8% and 77.7%, respectively, of orthologous average nucleotide identity, Ortho- ANI, and 21.9% and 21.9%, respectively, of digital DNA-DNA hybridization, dDDH). Strain D17T showed the highest similarities in 16S rRNA gene and complete genome sequences to D13 (99.9% of 16S rRNA gene sequence similarity, 91.8% of OrthoANI, and 45.1% of dDDH); therefore, strains D17T and D13 were assigned as the same species. Strain D25T showed the highest similarities in 16S rRNA gene and complete genome sequences to D. chitinilytica Nsw-4T (98.2% of 16S rRNA gene sequence similarity, 82.4% of OrthoANI, and 25.1% of dDDH). Strains D17T and D13 were Gram-stain-negative, facultative anaerobes, rod-shaped, non-motile, and non-flagellated. Strain D25T was Gram-stain-negative, facultative anaerobe, rodshaped, and motile by a single polar flagellum. These strains had C16:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) as the major cellular fatty acids and possessed Q-8 as a major respiratory ubiquinone. All three strains contained phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. Based on polyphasic taxonomic data, strains D17T, D13, and D25T represent two novel species of the genus Deefgea. We propose the name Deefgea piscis sp. nov. for strains D17T (= KCTC 82958T = JCM 34941T) and D13 (= KCTC 92368), and Deefgea tanakiae sp. nov. for strain D25T (= KCTC 82959T = JCM 34942T).

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Systematic Literature Review Identifying Core Genera in the Gut Microbiome of Rainbow Trout (Oncorhynchus mykiss) and Species‐level Microbial Community Analysis Using Long‐Read Amplicon Sequencing
Mio Takeuchi, Kazuhiro Sugahara
Aquaculture, Fish and Fisheries.2025;[Epub] CrossRef
Interplay between antipredator behavior, parasitism, and gut microbiome in wild stickleback populations
Javier Edo Varg, Jaelle C. Brealey, David Benhaïm, Rafael Losada-Germain, Janette W. Boughman
npj Biofilms and Microbiomes.2025;[Epub] CrossRef
Fecal metagenomic and metabolomic analyses reveal non-invasive biomarkers of Flavobacterium psychrophilum infection in ayu ( Plecoglossus altivelis )
Mio Takeuchi, Erina Fujiwara-Nagata, Kyohei Kuroda, Kenji Sakata, Takashi Narihiro, Jun Kikuchi, Katherine McMahon
mSphere.2024;[Epub] CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
PLOS ONE.2023; 18(12): e0289072. CrossRef

Review

Transmissibility and pathogenicity of SARS-CoV-2 variants in animal models: Young-Il Kim , Mark Anthony B. Casel , Young Ki Choi; J. Microbiol. 2022;60(3):255-267. Published online March 2, 2022; DOI: https://doi.org/10.1007/s12275-022-2033-z

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As of February 2022, SARS-CoV-2 is still one of the most serious public health threats due to its high mortality rate and rapid spread of novel variants. Since the first outbreak in 2019, general understanding of SARS-CoV-2 has been improved through basic and clinical studies; however, knowledge gaps still exist in our understanding of the emerging novel SARSCoV- 2 variants, which impacts the corresponding development of vaccines and therapeutics. Especially, accumulation of mutations in SARS-CoV-2 and rapid spread in populations with previous immunity has resulted in selection of variants that evade the host immune response. This phenomenon threatens to render current SARS-CoV-2 vaccines ineffective for controlling the pandemic. Proper animal models are essential for detailed investigations into the viral etiology, transmission and pathogenesis mechanisms, as well as evaluation of the efficacy of vaccine candidates against recent SARS-CoV-2 variants. Further, the choice of animal model for each research topic is important for researchers to gain better knowledge of recent SARS-CoV-2 variants. Here, we review the advantages and limitations of each animal model, including mice, hamsters, ferrets, and non-human primates, to elucidate variant SARS-CoV-2 etiology and transmission and to evaluate therapeutic and vaccine efficacy.

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In vivo characterization of ACE2 expression in Sprague-Dawley rats and cultured primary brain pericytes highlights the utility of Rattus norvegicus in the study of COVID-19 brain pathophysiology
Eugene Park, Elaine Liu, Andrew J. Baker
Brain Research.2025; 1848: 149333. CrossRef
Utilizing non‐human primate models to combat recent COVID‐19/SARS‐CoV‐2 and viral infectious disease outbreaks
Taeho Kwon
Journal of Medical Primatology.2024;[Epub] CrossRef
Early detection of highly transmissible viral variants using phylogenomics
Michael R. May, Bruce Rannala
Science Advances.2024;[Epub] CrossRef
Animal Models, Zoonotic Reservoirs, and Cross-Species Transmission of Emerging Human-Infecting Coronaviruses
Yakhouba Kane, Gary Wong, George F. Gao
Annual Review of Animal Biosciences.2023; 11(1): 1. CrossRef
SARS-CoV-2 Aerosol and Intranasal Exposure Models in Ferrets
Elizabeth E. Zumbrun, Samantha E. Zak, Eric D. Lee, Philip A. Bowling, Sara I. Ruiz, Xiankun Zeng, Jeffrey W. Koehler, Korey L. Delp, Russel R. Bakken, Shannon S. Hentschel, Holly A. Bloomfield, Keersten M. Ricks, Tamara L. Clements, April M. Babka, John
Viruses.2023; 15(12): 2341. CrossRef
The Isolation and In Vitro Differentiation of Primary Fetal Baboon Tracheal Epithelial Cells for the Study of SARS-CoV-2 Host-Virus Interactions
Bharathiraja Subramaniyan, Sunam Gurung, Manish Bodas, Andrew R. Moore, Jason L. Larabee, Darlene Reuter, Constantin Georgescu, Jonathan D. Wren, Dean A. Myers, James F. Papin, Matthew S. Walters
Viruses.2023; 15(4): 862. CrossRef
Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
Two years of COVID-19 pandemic: where are we now?
Jinjong Myoung
Journal of Microbiology.2022; 60(3): 235. CrossRef
SARS CoV-2 (Delta Variant) Infection Kinetics and Immunopathogenesis in Domestic Cats
Miruthula Tamil Selvan, Sachithra Gunasekara, Ping Xiao, Kristen Griffin, Shannon R. Cowan, Sai Narayanan, Akhilesh Ramachandran, Darren E. Hagen, Jerry W. Ritchey, Jennifer M. Rudd, Craig A. Miller
Viruses.2022; 14(6): 1207. CrossRef

Journal Articles

Characterization of a cold-adapted debranching enzyme and its role in glycogen metabolism and virulence of Vibrio vulnificus MO6-24/O: Ah-Reum Han , Haeyoung Kim , Jong-Tae Park , Jung-Wan Kim; J. Microbiol. 2022;60(4):375-386. Published online February 14, 2022; DOI: https://doi.org/10.1007/s12275-022-1507-3

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Vibrio vulnificus MO6-24/O has three genes annotated as debranching enzymes or pullulanase genes. Among them, the gene encoded by VVMO6_03032 (vvde1) shares a higher similarity at the amino acid sequence level to the glycogen debranching enzymes, AmyX of Bacillus subtilis (40.5%) and GlgX of Escherichia coli (55.5%), than those encoded by the other two genes. The vvde1 gene encoded a protein with a molecular mass of 75.56 kDa and purified Vvde1 efficiently hydrolyzed glycogen and pullulan to shorter chains of maltodextrin and maltotriose (G3), respectively. However, it hydrolyzed amylopectin and soluble starch far less efficiently, and β-cyclodextrin (β-CD) only rarely. The optimal pH and temperature of Vvde1 was 6.5 and 25°C, respectively. Vvde1 was a cold-adapted debranching enzyme with more than 60% residual activity at 5°C. It could maintain stability for 2 days at 25°C and 1 day at 35°C, but it destabilized drastically at 40°C. The Vvde1 activity was inhibited considerably by Cu2+, Hg2+, and Zn2+, while it was slightly enhanced by Co2+, Ca2+, Ni2+, and Fe2+. The vvde1 knock-out mutant accumulated more glycogen than the wild-type in media supplemented with 1.0% maltodextrin; however, the side chain length distribution of glycogen was similar to that of the wild-type except G3, which was much more abundant in the mutant. Therefore, Vvde1 seemed to debranch glycogen with the degree of polymerization 3 (DP3) as the specific target branch length. Virulence of the pathogen against Caenorhabditis elegans was attenuated significantly by the vvde1 mutation. These results suggest that Vvde1 might be a unique glycogen debranching enzyme that is involved in both glycogen utilization and shaping of glycogen molecules, and contributes toward virulence of the pathogen.

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Characterization of glycogen-related glycoside hydrolase glgX and glgB from Klebsiella pneumoniae and their roles in biofilm formation and virulence
Xinyue Liu, Jialin Li, Ruibing Wu, Liping Bai
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Function of the mdxR gene encoding a novel regulator for carbohydrate metabolism and sporulation in Bacillus subtilis 168
Tianshi Wang, Jung-Wan Kim
Archives of Microbiology.2023;[Epub] CrossRef
Identification of a novel cyclomaltodextrinase annotated as a neopullulanase in the genome of Bacillus cereus
Bo-Ram Park, Davoodbasha MubarakAli, Jung-Wan Kim
Archives of Microbiology.2023;[Epub] CrossRef
Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
PLOS ONE.2023; 18(12): e0289072. CrossRef
Functional characterization of maltodextrin glucosidase for maltodextrin and glycogen metabolism in Vibrio vulnificus MO6-24/O
Hye-Young Kim, MubarakAli Davoodbasha, Jung-Wan Kim
Archives of Microbiology.2022;[Epub] CrossRef

Differences in seroprevalence between epicenter and non-epicenter areas of the COVID-19 outbreak in South Korea: Hye Won Jeong , Hyun-Ha Chang , Eun Ji Kim , Yu Kyung Kim , Se-Mi Kim , Eun-Ha Kim , Young-Il Kim , Mark Anthony B. Casel , Seong-Gyu Kim , Rare Rollon , Seung-Gyu Jang , Kwang-Min Yu , Hee-Sung Kim , Hee Sue Park , Su-Jin Park , Yong-Dae Kim , Eung-Gook Kim , Young Ki Choi; J. Microbiol. 2021;59(5):530-533. Published online April 28, 2021; DOI: https://doi.org/10.1007/s12275-021-1095-7

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To compare the standardized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence of high epicenter region with non-epicenter region, serological studies were performed with a total of 3,268 sera from Daegu City and 3,981 sera from Chungbuk Province. Indirect immunofluorescence assay (IFA) for SARS-CoV-2 IgG results showed a high seroprevalence rate in the Daegu City (epicenter) compared with a non-epicenter area (Chungbuk Province) (1.27% vs. 0.91%, P = 0.0358). It is noteworthy that the highest seroprevalence in Daegu City was found in elderly patients (70’s) whereas young adult patients (20’s) in Chungbuk Province showed the highest seroprevalence. Neutralizing antibody (NAb) titers were found in three samples from Daegu City (3/3, 268, 0.09%) while none of the samples from Chungbuk Province were NAb positive. These results demonstrated that even following the large outbreak, the seropositive rate of SARS-CoV-2 in the general population remained low in South Korea.

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Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
The Seroprevalence of SARS-CoV-2 in Children During Early COVID-19 Pandemic in Korea: A Nationwide, Population-Based Study
Jin Lee, Young June Choe, Dohsik Minn, Jong-Hyun Kim
Journal of Korean Medical Science.2022;[Epub] CrossRef

Paradesulfovibrio onnuriensis gen. nov., sp. nov., a chemolithoautotrophic sulfate-reducing bacterium isolated from the Onnuri vent field of the Indian Ocean and reclassification of Desulfovibrio senegalensis as Paradesulfovibrio senegalensis comb. nov.: Yun Jae Kim , Jhung-Ahn Yang , Jae Kyu Lim , Mi-Jeong Park , Sung-Hyun Yang , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee , Kae Kyoung Kwon; J. Microbiol. 2020;58(4):252-259. Published online February 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9376-0

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An anaerobic, rod-shaped, mesophilic, chemolithoautotrophic, sulfate-reducing bacterial strain IOR2T was isolated from a newly found deep-sea hydrothermal vent (OVF, Onnuri Vent Field) area in the central Indian Ocean ridge (11°24􍿁88􍿂􀁇 S 66°25􍿁42􍿂􀁇E, 2021 m water depth). The 16S rRNA gene sequence analysis revealed that the strain IOR2T was most closely related to Desulfovibrio senegalensis BLaC1T (96.7%). However, it showed low similarity with the members of the family Desulfovibrionaceae, such as Desulfovibrio tunisiensis RB22T (94.0%), D. brasiliensis LVform1T (93.9%), D. halophilus DSM 5663T (93.7%), and Pseudodesulfovibrio aespoeensis Aspo-2T (93.2%). The strain IOR2T could grow at 23– 42°C (optimum 37°C), pH 5.0–8.0 (optimum pH 7.0) and with 0.5–6.5% (optimum 3.0%) NaCl. The strain could use lactate, pyruvate, H2, and glycerol as electron donors and sulfate, thiosulfate, and sulfite as electron acceptors. The major fatty acids of the strain IOR2T were iso-C15:0, iso-C17:0, anteiso- C15:0, and summed feature 9 (C16:0 methyl/iso-C17:1ω9c). Both the strains IOR2T and BLaC1T could grow with CO2 and H2 as the sole sources of carbon and energy, respectively. Genomic evidence for the Wood-Ljungdahl pathway in both the strains reflects chemolithoautotrophic growth. The DNA G + C content of the strain IOR2T and BLaC1T was 58.1–60.5 mol%. Based on the results of the phylogenetic and physiologic studies, Paradesulfovibrio onnuriensis gen. nov., sp. nov. with the type strain IOR2T (= KCTC 15845T = MCCC 1K04559T) was proposed to be a member of the family Desulfovibrionaceae. We have also proposed the reclassification of D. senegalensis as Paradesulfovibrio senegalensis comb. nov.

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Sulfate-Reducing Bacteria Isolated from an Oil Field in Kazakhstan and a Description of Pseudodesulfovibrio karagichevae sp. nov.
Salimat K. Bidzhieva, Tatyana P. Tourova, Denis S. Grouzdev, Salima R. Samigullina, Diyana S. Sokolova, Andrey B. Poltaraus, Alexander N. Avtukh, Vera M. Tereshina, Andrey V. Mardanov, Nurlan S. Zhaparov, Tamara N. Nazina
Microorganisms.2024; 12(12): 2552. CrossRef
Sulfur fertilization integrated with soil redox conditions reduces Cd accumulation in rice through microbial induced Cd immobilization
Quan Zhang, Hai-Fei Chen, Dao-You Huang, Xiao-Bin Guo, Chao Xu, Han-Hua Zhu, Bo Li, Tong-Tong Liu, Ren-Wei Feng, Qi-Hong Zhu
Science of The Total Environment.2022; 824: 153868. CrossRef
Pseudodesulfovibrio sediminis sp. nov., a mesophilic and neutrophilic sulfate-reducing bacterium isolated from sediment of a brackish lake
Ayaka Takahashi, Hisaya Kojima, Miho Watanabe, Manabu Fukui
Archives of Microbiology.2022;[Epub] CrossRef
Diversity and biogenesis contribution of sulfate-reducing bacteria in arsenic-contaminated soils from realgar deposits
Xianbin Zhu, Liyuan Chen, Hongzhong Pan, Lei Wang, Xun Zhang, Dan Wang
Environmental Science and Pollution Research.2022; 29(21): 31110. CrossRef
A sulfate-reducing bacterial genus, Desulfosediminicola gen. nov., comprising two novel species cultivated from tidal-flat sediments
Jaeho Song, Juchan Hwang, Ilnam Kang, Jang-Cheon Cho
Scientific Reports.2021;[Epub] CrossRef
Desulfomarina profundi gen. nov., sp. nov., a novel mesophilic, hydrogen-oxidizing, sulphate-reducing chemolithoautotroph isolated from a deep-sea hydrothermal vent chimney
Yurina Hashimoto, Akihiro Tame, Shigeki Sawayama, Junichi Miyazaki, Ken Takai, Satoshi Nakagawa
International Journal of Systematic and Evolutionary Microbiology.2021;[Epub] CrossRef
Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment
Cynthia C. Gilmour, Ally Bullock Soren, Caitlin M. Gionfriddo, Mircea Podar, Judy D. Wall, Steven D. Brown, Joshua K. Michener, Maria Soledad Goñi Urriza, Dwayne A. Elias
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

Flavobacterium zhairuonensis sp. nov., a gliding bacterium isolated from marine sediment of the East China Sea: Sanjit Chandra Debnath , Ahmed Mohammed Abdo Miyah , Can Chen , Huan Sheng , Xue-Wei Xu , Yue-Hong Wu , Dao-Qiong Zheng , Jin-Zhong Xu , Ya-Nan Di , Pin-Mei Wang , Li Shen; J. Microbiol. 2019;57(12):1065-1072. Published online September 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9194-4

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A yellow pigmented, Gram-stain-negative, aerobic bacterium designated A5.7T was studied to evaluate the taxonomic position following the modern polyphasic approach. The strain was isolated from sediments near Zhairuo Island, which is situated in the East China Sea. Cells were non-spore forming rods without flagella but showed motility by gliding. Growth was observed at 15–35°C (optimum 28°C), pH 6.0–9.0 (optimum pH 6.5) and 0–2% (w/v) NaCl (optimum 0–0.5%) in LB broth. The major respiratory quinone of A5.7T was menaquinone 6. The major polar lipid of A5.7T was phosphatidylethanolamine and the predominant fatty acids (> 5%) were iso-C15:0, iso-C17:0 3-OH, C15:1 ω6c, iso-C15:0 3-OH, iso-C15:1 G, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl). Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Flavobacterium and shares the highest sequence similarities with Flavobacterium sharifuzzamanii A7.6T (98.5%), Flavobacterium tistrianum GB 56.1T (98.3%), Flavobacterium nitrogenifigens NXU-44T (97.8%), Flavobacterium anhuiense D3T (97.6%), Flavobacterium ginsenosidimutans THG 01T (97.6%), and Flavobacterium foetidum CJ42T (97.6%). Digital DNA-DNA hybridization and average nucleotide identity values between the strain and its closest phylogenetic neighbors showed the ranges from 19.6 to 34.1% and 73.7 to 87.9%, respectively. Therefore, based on polyphasic characteristics, strain A5.7T represents a novel species of the genus Flavobacterium for which the name Flavobacterium zhairuonensis sp. nov. is proposed. The type strain is A5.7T (= KCTC 62406T = MCCC 1K03494T).

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Three novel species of the genus Flavobacterium, Flavobacterium odoriferum sp. nov., Flavobacterium fragile sp. nov. and Flavobacterium luminosum sp. nov., isolated from activated sludge
Qi Ran, Xinran Du, Lin Han, Jingjing Wang, Yue-zhong Li
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum s
Hyunyoung Jo, Miri S. Park, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(5): 495. CrossRef
Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead)
Seomin Kang, Jae-Yun Lee, Jeong Eun Han, Yun-Seok Jeong, Do-Hun Gim, Jin-Woo Bae
Journal of Microbiology.2022; 60(9): 890. CrossRef
Flavobacterium litorale sp. nov., isolated from red alga
Neak Muhammad, Ho Le Han, Yong-Jae Lee, Jaeho Ko, Tra T. H. Nguyen, Song-Gun Kim
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Flavobacterium salilacus sp. nov., isolated from surface water of a hypersaline lake, and descriptions of Flavobacterium salilacus subsp. altitudinum subsp. nov. and Flavobacterium salilacus subsp. salilacus subsp. nov.
Sanjit Chandra Debnath, Can Chen, Ishrat Khan, Wen-Jie Wang, Dao-Qiong Zheng, Jin-Zhong Xu, Pin-Mei Wang
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4250. 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
Flavobacterium phycosphaerae sp. nov. isolated from the phycosphere of Microcystis aeruginosa
Minkyung Kim, Byoung-Hee Lee, Ki-Eun Lee, Woojun Park
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

Isolation and characterization of a novel piezotolerant bacterium Lysinibacillus yapensis sp. nov., from deep-sea sediment of the Yap Trench, Pacific Ocean: Libo Yu , Xixiang Tang , Shiping Wei , Yinkun Qiu , Xiashutong Xu , Guangxin Xu , Qilin Wang , Qian Yang; J. Microbiol. 2019;57(7):562-568. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8709-3

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A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated YLB-03T, with peritrichous flagella was isolated from deep-sea sediment of the Yap Trench at a depth of 4435 m. The bacterium was found to be catalase-positive but oxidase-negative. Growth of this bacterium was observed at 15–50°C (optimum 37°C), pH 5–10.5 (optimum 7), 0–5% NaCl (optimum 1%, w/v) and 0.1–50 MPa (optimum 0.1 MPa). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YLB-03T was a member of the genus Lysinibacillus. Strain YLB-03T was closely related to Lysinibacillus sinduriensis BLB-1T and Lysinibacillus chungkukjangi 2RL3-2T (98.4%), Lysinibacillus halotolerans LAM- 612T (98.0%), Lysinibacillus telephonicus KT735049T (97.5%), Lysinibacillus endophyticus C9T (97.5%), Lysinibacillus composti NCCP-36T and Lysinibacillus massiliensis 4400831T (97.3%). The ANI and the GGDC DNA-DNA hybridization estimate values between strain YLB-03T and closely related type strains were 73.7–76.3% and 34.7–38.7%, respectively. The principal fatty acids were anteiso-C15:0 and iso-C15:0. The G+C content of the chromosomal DNA was 39.6 mol%. The respiratory quinone was determined to be MK-7. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α) and the cell-wall sugars were glucose and xylose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The combined genotypic and phenotypic data showed that strain YLB-03T represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus yapensis sp. nov. is proposed, with the type strain YLB-03T (= MCCC 1A12698T = JCM 32871T).

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Bacteroides sedimenti sp. nov., isolated from a chloroethenesdechlorinating consortium enriched from river sediment: Mohamed Ismaeil , Naoko Yoshida , Arata Katayama; J. Microbiol. 2018;56(9):619-627. Published online August 23, 2018; DOI: https://doi.org/10.1007/s12275-018-8187-z

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A Gram-negative, anaerobic, non-motile, non-spore-forming bacterial strain, designated YN3PY1T, was isolated from a chloroethene-dechlorinating consortium originally enriched from river sediment. The strain enhanced the dechlorination of cis-dichloroethene to ethene by Dehalococcoides, especially at the early stages of cultivation. Strain YN3PY1T was the first isolate of the genus Bacteroides, obtained from animal- independent environments, and its 16S rRNA gene had the highest sequence similarity (97.1%) with Bacteroides luti JCM 19020T in the ‘Coprosuis’ clade of the genus Bacteroides. Strain YN3PY1T formed a phylogenetic cluster with other phylotypes detected from sediments and paddy soil, and the cluster was affiliated with a linage of so-called free-living Bacteroides detected from animal-independent environments, suggesting specific adaptations to sediment-like environments. The strain showed typical phenotypes of Bacteroides, i.e., polysaccharolytic anaerobe having anteiso-C15:0 as the most abundant fatty acid and MK-11 as one of the major respiratory quinones. Additionally, the strain uniquely transforms glucose to lactate and malate, has MK-12 as another major respiratory quinone, and grows at comparatively low temperatures, i.e. 10–40°C, with an optimum at 28°C. Based on the presented data, strain YN3PY1T (= KCTC 15656T = NBRC 113168T) can be proposed as a novel species of the genus Bacteroides and named as Bacteroides sedimenti sp. nov.

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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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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).

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Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments: Shiling Zheng , Bingchen Wang , Fanghua Liu , Oumei Wang; J. Microbiol. 2017;55(11):862-870. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7104-1

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Minerals that contain ferric iron, such as amorphous Fe(III) oxides (A), can inhibit methanogenesis by competitively accepting electrons. In contrast, ferric iron reduced products, such as magnetite (M), can function as electrical conductors to stimulate methanogenesis, however, the processes and effects of magnetite production and transformation in the methanogenic consortia are not yet known. Here we compare the effects on methanogenesis of amorphous Fe (III) oxides (A) and magnetite (M) with ethanol as the electron donor. RNAbased terminal restriction fragment length polymorphism with a clone library was used to analyse both bacterial and archaeal communities. Iron (III)-reducing bacteria including Geobacteraceae and methanogens such as Methanosarcina were enriched in iron oxide-supplemented enrichment cultures for two generations with ethanol as the electron donor. The enrichment cultures with A and non-Fe (N) dominated by the active bacteria belong to Veillonellaceae, and archaea belong to Methanoregulaceae and Methanobacteriaceae, Methanosarcinaceae (Methanosarcina mazei), respectively. While the enrichment cultures with M, dominated by the archaea belong to Methanosarcinaceae (Methanosarcina barkeri). The
results
also showed that methanogenesis was accelerated in the transferred cultures with ethanol as the electron donor during magnetite production from A reduction. Powder X-ray diffraction analysis indicated that magnetite was generated from microbial reduction of A and M was transformed into siderite and vivianite with ethanol as the electron donor. Our data showed the processes and effects of magnetite production and transformation in the methanogenic consortia, suggesting that significantly different effects of iron minerals on microbial methanogenesis in the iron-rich coastal riverine environment were present.

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Cyclobacterium sediminis sp. nov. isolated from a sea cucumber aquaculture farm and emended description of the genus Cyclobacterium: Seyeon Shin , Hyung-Yeel Kahng; J. Microbiol. 2017;55(2):90-95. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6484-6

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An aerobic, Gram-negative bacterium, designated strain SD70T, was isolated from sea cucumber aquaculture farm sediment in Taean, Korea, and its taxonomic status was established by undertaking a polyphasic study. Cells of strain SD70T were non-motile, catalase-, and oxidase-positive, nonspore- forming, and horseshoe-shaped. Optimal growth was observed under 25–30°C, pH 7.0–8.0, and 3.0–5.0% (w/v) NaCl conditions. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain SD70T fell within an evolutionary group comprising species of the genus Cyclobacterium. Strain SD70T shared 92.1–98.5% 16S rRNA sequence similarity values with the type strains of species of the genus Cyclobacterium. Relatively low levels of DNA-DNA relatedness were found between strain SD70T and C. marinum DSM 745T (40.2%) and C. amurskyense KMM 6143T (15.8%). The predominant cellular fatty acids were iso-C15:0 (32.1%), and anteiso-C15:0 (9.1%). Menaquinone MK-7 was the only respiratory quinone. The G+C content of the genomic DNA was 36 mol%. The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and seven unidentified lipids. On the basis of phenotypic and genotypic data, strain SD70T represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium sediminis sp. nov. is proposed. An emended description of the genus Cyclobacterium is also provided.

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International Journal of Systematic and Evolutionary Microbiology .2017; 67(7): 2081. CrossRef

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Abyssisolibacter fermentans gen. nov. sp. nov., isolated from deep sub-seafloor sediment: Wonduck Kim , Jung-Hyun Lee , Kae Kyoung Kwon; J. Microbiol. 2016;54(5):347-352. Published online April 20, 2016; DOI: https://doi.org/10.1007/s12275-016-6048-1

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A Gram-staining-negative, thin rod-shaped, anaerobic bacterium designated MCWD3T was isolated from sediment of the deep sea in Ulleung Basin, East Sea, Korea. The ranges of temperature, pH and NaCl for growth of this strain were 15– 40°C (optimum 29°C), 5.0–10.0 (optimum pH 6.5), and 1–5%, respectively. The major fatty acids were iso-C15:0 (30%) and iso-C15:0 dimethyl acetal (17%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminophospholipids, phospholipids, and aminolipids. The fermentation product from yeast extract was acetate. Phylogenetic analysis based on 16S rRNA genes indicated that the isolate was related to Sporosalibacterium faouarense (92.8% sequence identity), Clostridiisalibacter paucivorans (92.6%), and Brassicibacter mesophilus (92.4%). However, the isolate was differentiated from these genera by both physiological and chemotaxonomical properties. On the basis of a polyphasic taxonomic analysis, we propose that MCWD3T represents a novel taxon with the name Abyssisolibacter fermentans gen. nov. sp. nov.

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Dethiothermospora halolimnae gen. nov., sp. nov., a novel moderately halophilic, thermotolerant, bacterium isolated from a brine lake
Luke A. Fisher, Saloni R. Dangre, Arthur Odenheimer, Nirav Patel, Peter T. Doran, Jeff S. Bowman, Britney E. Schmidt, Douglas H. Bartlett
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
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Sung-Hyun Yang, Mi-Jeong Park, Hyun-Myung Oh, Kae Kyoung Kwon
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Neak Muhammad, Tra T.H. Nguyen, Yong-Jae Lee, Jaeho Ko, Forbes Avila, Song-Gun Kim
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Guangping Liu, Yongping Jin, Youduo Peng, Buyan Wan, Kun Xie
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Teddy Namirimu, Jihyun Yu, Jhung-Ahn Yang, Sung-Hyun Yang, Yun Jae Kim, Kae Kyoung Kwon
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Anaerosacchariphilus polymeriproducens gen. nov., sp. nov., an anaerobic bacterium isolated from a salt field
Wonduck Kim, Sung-Hyun Yang, Mi-Jeong Park, Jihye Oh, Jung-Hyun Lee, Kae Kyoung Kwon
International Journal of Systematic and Evolutionary Microbiology .2019; 69(7): 1934. CrossRef
Isolation and characterization of anaerobic microbes from marine environments in Korea
Wonduck Kim, Jung-Hyun Lee, Kae Kyoung Kwon
The Korean Journal of Microbiology.2016; 52(2): 183. CrossRef

Aliisedimentitalea scapharcae gen. nov., sp. nov., isolated from ark shell Scapharca broughtonii: Young-Ok Kim , Sooyeon Park , Bo-Hye Nam , Dong-Gyun Kim , Sung-Min Won , Ji-Min Park , Jung-Hoon Yoon; J. Microbiol. 2015;53(8):495-502. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5075-7

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A Gram-negative, aerobic, non-spore-forming, motile and ovoid or rod-shaped bacterial strain, designated MA2-16T, was isolated from ark shell (Scapharca broughtonii) collected from the South Sea, South Korea. Strain MA2-16T was found to grow optimally at 30캜, at pH 7.0?.0 and in the presence of 2.0% (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain MA2-16T clustered with the type strain of Sedimentitalea nanhaiensis. The novel strain exhibited a 16S rRNA gene sequence similarity value of 97.1% to the type strain of S. nanhaiensis. In the neighbour- joining phylogenetic tree based on gyrB sequences, strain MA2-16T formed an evolutionary lineage independent of those of other taxa. Strain MA2-16T contained Q-10 as the predominant ubiquinone and C18:1 ?c and 11-methyl C18:1 ?c as the major fatty acids. The major polar lipids of strain MA2-16T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA2- 16T was 57.7 mol% and its DNA-DNA relatedness values with the type strains of S. nanhaiensis and some phylogenetically related species of the genera Leisingera and Phaeobacter were 13?4%. On the basis of the data presented, strain MA2-16T is considered to represent a novel genus and novel species within the family Rhodobacteraceae, for which the name Aliisedimentitalea scapharcae gen. nov., sp. nov. is proposed. The type strain is MA2-16T (=KCTC 42119T =CECT 8598T).

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Genomic profiling of biosynthetic potentials of medicinal secondary metabolites for ‘Aliisedimentitalea scapharcae’ KCTC 42119T, isolated from ark shell
Jin-Cheng Rong, Lin-Lin Cui, Na Li, Mao-Li Yi, Bo-Tao Huang, Qi Zhao
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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
Journal of Microbiology.2017; 55(6): 421. CrossRef
Litorisediminivivens gilvus gen. nov., sp. nov., isolated from a tidal flat
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International Journal of Systematic and Evolutionary Microbiology.2016; 66(11): 4681. CrossRef

Microbial Communities in Semi-consolidated Carbonate Sediments of the Southwest Indian Ridge: Jiwei Li , Xiaotong Peng , Huaiyang Zhou , Jiangtao Li , Zhilei Sun , Shun Chen; J. Microbiol. 2014;52(2):111-119. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3133-1

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Abstract PDF

White semi-consolidated carbonate sediments attached to black ferromanganese oxide films were collected approximately 50 km west of a newly discovered hydrothermal field near the Southwest Indian Ridge (SWIR). The biodiversity of the prokaryotic communities within the field was examined using clone library-based culture-independent analysis of the exterior black oxides and the interior white carbonates. Subsequent 16S rRNA gene analysis suggested that Gammaproteobacteria, Acidobacteria, and Thaumarchaeota members dominated the bacterial and archaeal clone libraries. To further characterize the metabolic processes within the microbial community, analyses of the amoA (coding the alpha subunit of the ammonia monooxygenase for Archaea) and aprA (coding the alpha subunit of the dissimilatory adenosine-5'-phosphosulfate reductase for the sulfate-reducing and sulfur-oxidizing prokaryotes) functional genes were conducted. The functional gene analysis results suggested that Thaumarchaeota and Alphaproteobacteria members were the potential players that participated in N and S cycles in this marine carbonate sedimentary environment. This paper is the first to describe the microbial communities and their potential metabolic pathways within the semi-consolidated carbonate sediments of the SWIR.

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Bacterial Diversity and Composition of an Alkaline Uranium Mine Tailings-Water Interface: Nurul H. Khan , Viorica F. Bondici , Prabhakara G. Medihala , John R. Lawrence , Gideon M. Wolfaardt , Jeff Warner , Darren R. Korber; J. Microbiol. 2013;51(5):558-569. Published online September 14, 2013; DOI: https://doi.org/10.1007/s12275-013-3075-z

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Abstract PDF

The microbial diversity and biogeochemical potential associated with a northern Saskatchewan uranium mine watertailings interface was examined using culture-dependent and -independent techniques. Morphologically-distinct colonies from uranium mine water-tailings and a reference lake (MC) obtained using selective and non-selective media were selected for 16S rRNA gene sequencing and identification, revealing that culturable organisms from the uranium tailings interface were dominated by Firmicutes and Betaproteobacteria; whereas, MC organisms mainly consisted of Bacteroidetes and Gammaproteobacteria. Ion Torrent (IT) 16S rRNA metagenomic analysis carried out on extracted DNA from tailings and MC interfaces demonstrated the dominance of Firmicutes in both of the systems. Overall, the tailings-water interface environment harbored a distinct bacterial community relative to the MC, reflective of the ambient conditions (i.e., total dissolved solids, pH, salinity, conductivity, heavy metals) dominating the uranium tailings system. Significant correlations among the physicochemical data and the major bacterial groups present in the tailings and MC were also observed. Presence of sulfate reducing bacteria demonstrated by culture-dependent analyses and the dominance of Desulfosporosinus spp. indicated by Ion Torrent analyses within the tailings-water interface suggests the existence of anaerobic microenvironments along with the potential for reductive metabolic processes.

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Exploring functional microbiota for uranium sequestration in Zoige uranium mine soil
Xiang Wang, Li Zhao, Xu Zhang, Yanxia Wei, Aixia Lu, Jian Zhou, Guiqiang He, Philips O Akinwole, Xugang Dang
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Martina Kracmarova-Farren, Jakub Papik, Ondrej Uhlik, John Freeman, Andrea Foster, Mary-Cathrine Leewis, Courtney Creamer
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Concurrent reductive decontamination of chromium (VI) and uranium (VI) in groundwater by Fe(0)-based autotrophic bioprocess
Jianping Lu, Rongyue Geng, Han Zhang, Zhen Yu, Tao Chen, Baogang Zhang
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Viorica F. Bondici, George D. W. Swerhone, James J. Dynes, John R. Lawrence, Gideon M. Wolfaardt, Jeff Warner, Darren R. Korber
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Biogeochemical activity of microbial biofilms in the water column overlying uranium mine tailings
V.F. Bondici, N.H. Khan, G.D.W. Swerhone, J.J. Dynes, J.R. Lawrence, E. Yergeau, G.M. Wolfaardt, J. Warner, D.R. Korber
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Paenibacillus marinisediminis sp. nov., a Bacterium Isolated from Marine Sediment: Hae-Won Lee , Seong Woon Roh , Kyung June Yim , Na-Ri Shin , Jina Lee , Tae Woong Whon , Joon Yong Kim , Dong-Wook Hyun , Daekyung Kim , Jin-Woo Bae; J. Microbiol. 2013;51(3):312-317. Published online June 28, 2013; DOI: https://doi.org/10.1007/s12275-013-3198-2

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Abstract PDF: A Gram-negative, nonmotile, endospore-forming, rod-shaped bacterial strain LHW35T, which belonged to the genus Paenibacillus, was isolated from marine sediment collected from the south coast of the Republic of Korea. A phylogenetic analysis of 16S rRNA gene sequences indicated that strain LHW35T was most closely related to Paenibacillus taiwanensis G-soil-2-3T (97.2% similarity). The optimal growth conditions for strain LHW35T were 37°C, pH 6.0, and 0% (w/v) NaCl. The main isoprenoid quinone was menaquinone-7 (MK-7) and the major polyamine was spermidine. The diamino acid present in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acids were anteiso-C15:0 and C16:0. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, unidentified aminohospholipids, unidentified phospholipids, and unidentified polar lipids. A DNA-DNA hybridization experiment using the type strain of P. taiwanensis indicated <40% relatedness. The DNA G+C content was 45.0 mol%. Based on these phylogenetic, genomic, and phenotypic analyses, strain LHW35T should be classified as a novel species within the genus Paenibacillus, for which the name Paenibacillus marinisediminis sp. nov. is proposed. The type strain is LHW35T (=KACC 16317T =JCM 17886T).

Metagenomic Assessment of a Sulfur-Oxidizing Enrichment Culture Derived from Marine Sediment: Man-Young Jung , VinhHoa Pham , Soo-Je Park , So-Jeong Kim , Jong-Chan Chae , Yul Roh , Sung-Keun Rhee; J. Microbiol. 2010;48(6):739-747. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0257-9

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Abstract PDF

The biological oxidation of reduced sulfur compounds is a critically important process in global sulfur biogeochemistry. In this study, we enriched from marine sediments under denitrifying conditions, chemolithotrophic sulfur oxidizers that could oxidize a variety of reduced sulfur compounds: thiosulfate, tetrathionate, sulfide, and polysulfide. Two major phylotypes of 16S rRNA gene (>99% identity in each phylotype) were detected in this enrichment culture. In order to characterize sulfide oxidation, we sequenced and characterized one fosmid clone (43.6 kb) containing the group I sulfide-quinone reductase (sqr) gene. Interestingly, four putative rhodanese genes were found in this clone. Furthermore, comparative alignment with the closest genome of Thiomicrospira crunogena XCL2 revealed that three homologous genes were located within the vicinity of the sqr gene. Fosmid clones harboring carbon fixation (cbbL and cbbM) and denitrification (narG) genes were screened, and the phylogeny of the functional genes was analyzed. Along with the comparison between the sqr-containing fosmid clones and the relevant gamma-proteobacteria, our phylogenetic study based on the 16S rRNA gene and carbon fixation genes suggest the prevalence of chemolithotrophic gamma-proteobacteria in the denitrifying cultures. The findings of this study imply that a combination of cultivation and metagenomic approaches might provide us with a glimpse into the characteristics of sulfur oxidizers in marine sediments.

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Yihang Wang, Feiyu Xia, Shunan Jia, Yang Yang, Xiumei Zhang
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Bacterial Diversity in the Sediment from Polymetallic Nodule Fields of the Clarion-Clipperton Fracture Zone: Chun-Sheng Wang , Li Liao , Hong-Xiang Xu , Xue-Wei Xu , Min Wu , Li-Zhong Zhu; J. Microbiol. 2010;48(5):573-585. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0151-5

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Abstract PDF

The Clarion-Clipperton Fracture Zone (CCFZ) is located in the northeastern equatorial Pacific and contains abundant polymetallic nodules. To investigate its bacterial diversity, four libraries of 16S rRNA genes were constructed from sediments of four stations in different areas of the CCFZ. In total, 313 clones sequenced from the 4 libraries were assigned into 14 phylogenetic groups and 1 group of 28 unclassified bacteria. High bacterial diversity was predicted by the rarefaction analysis. The most dominant group overall was Proteobacteria, but there was variation in each library: Gammaproteobacteria was the most dominant group in two libraries, E2005-01 and ES0502, while Alphaproteobacteria and Deltaproteobacteria were the most dominant groups in libraries EP2005-03 and WS0505, respectively. Seven groups, including Alphaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Betaproteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes, were common to all four libraries. The remaining minor groups were distributed in libraries with different patterns. Most clones sequenced in this study were clustered with uncultured bacteria obtained from the environment, such as the ocean crust and marine sediment, but only distantly related to isolates. Bacteria involved in the cycling of metals, sulfur and nitrogen were detected, and their relationship with their habitat was discussed. This study sheds light on the bacterial communities associated with polymetallic nodules in the CCFZ and provides primary data on the bacterial diversity of this area.

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Deep-Sea Nodules and Co-rich Mn Crusts
G. P. Glasby, Jun Li, Zhilei Sun
Marine Georesources & Geotechnology.2015; 33(1): 72. CrossRef
Hydrocarbon-related microbial processes in the deep sediments of the Eastern Mediterranean Levantine Basin
Maxim Rubin-Blum, Gilad Antler, Alexandra V. Turchyn, Rami Tsadok, Beverly N. Goodman-Tchernov, Eli Shemesh, James A. Austin, Dwight F. Coleman, Yizhaq Makovsky, Orit Sivan, Dan Tchernov
FEMS Microbiology Ecology.2014; 87(3): 780. CrossRef
A comparison of microbial communities in deep-sea polymetallic nodules and the surrounding sediments in the Pacific Ocean
Yue-Hong Wu, Li Liao, Chun-Sheng Wang, Wei-Lin Ma, Fan-Xu Meng, Min Wu, Xue-Wei Xu
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Microbial diversity in deep-sea sediment from the cobalt-rich crust deposit region in the Pacific Ocean
Li Liao, Xue-Wei Xu, Xia-Wei Jiang, Chun-Sheng Wang, Dong-Sheng Zhang, Jian-Yu Ni, Min Wu
FEMS Microbiology Ecology.2011; 78(3): 565. CrossRef

Microbial Community Response to a Simulated Hydrocarbon Spill in Mangrove Sediments: Rodrigo Gouvêa Taketani , Natália Oliveira Franco , Alexandre Soares Rosado , Jan Dirk van Elsas; J. Microbiol. 2010;48(1):7-15. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0147-1

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Abstract PDF: In this study, we examined the hypothesis that the microbial communities in mangrove sediments with different chemical and historical characteristics respond differently to the disturbance of a hydrocarbon spill. Two different mangrove sediments were sampled, one close to an oil refinery that had suffered a recent oil spill and another that had not been in contact with oil. Based on the sampled sediment, two sets of mesocosms were built, and oil was added to one of them. They were subjected to mimicked mangrove conditions and monitored for 75 days. Archaeal and bacterial communities were evaluated through PCRDGGE. Both communities showed the emergence of small numbers of novel bands in response to oil pollution. 16S rRNA gene clone libraries were constructed from both mesocosms before the addition of oil and at day 75 after oil addition. LIBSHUFF analysis showed that both mangrove-based mesocosms contained similar communities at the start of the experiment and that they were different from the initial one, as well as from each other, after 75 days. These results hint at a role of environmental history that is not obvious from community diversity indicators, but is apparent from the response to the applied stress.

Journal Article

Monitoring Nutrient Impact on Bacterial Community Composition during Bioremediation of Anoxic PAH-Contaminated Sediment: Myungsu Kim , Seung Seob Bae , Mijin Seol , Jung-Hyun Lee , Young-Sook Oh; J. Microbiol. 2008;46(6):615-623. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0097-z

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Marine harbor sediments are frequently polluted with significant amount of polycyclic aromatic hydrocarbons (PAHs) some of which are naturally toxic, recalcitrant, mutagenic, and carcinogenic. To stimulate biodegradation of PAHs in PAH-contaminated sediments collected from near Gwangyang Bay, Korea, lactate was chosen as a supplementary carbonaceous substrate. Sediment packed into 600 ml air-tight jar was either under no treatment condition or lactate amended condition (1%, w/v). Microbial community composition was monitored by bacteria-specific and archaea-specific PCR-terminal restriction fragment length polymorphism (T-RFLP), in addition to measuring the residual PAH concentration. Results showed that lactate amendment enhanced biodegradation rate of PAHs in the sediment by 4 to 8 times, and caused a significant shift in archaebacterial community in terms of structure and diversity with time. Phylogenetic analysis of 23 archaeal clones with distinctive RFLP patterns among 288 archaeal clones indicated that majority of the archaeal members were closest to unculturable environmental rDNA clones from hydrocarbon-contaminated and/or methanogenesis-bearing sediments. Lactate amendment led to the enrichment of some clones that were most closely related to PAH-degrading Methanosarcina species. These results suggest a possible contribution of methanogenic community to PAH degradation and give us more insights on how to effectively remediate PAH-contaminated sediments.

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Effects of electron acceptors and donors on anaerobic biodegradation of PAHs in marine sediments
Qingguo Chen, Zhenzhen Li, Yu Chen, Mei Liu, Qiao Yang, Baikang Zhu, Jun Mu, Lijuan Feng, Zhi Chen
Marine Pollution Bulletin.2024; 199: 115925. CrossRef
Electrical current generation from a continuous flow macrophyte biocathode sediment microbial fuel cell (mSMFC) during the degradation of pollutants in urban river sediment
Felix Tetteh Kabutey, Jing Ding, Qingliang Zhao, Philip Antwi, Frank Koblah Quashie
Environmental Science and Pollution Research.2020; 27(28): 35364. CrossRef
Application of in situ Solid-Phase Microextraction on Mediterranean Sponges for Untargeted Exometabolome Screening and Environmental Monitoring
Barbara Bojko, Bora Onat, Ezel Boyaci, Eleftheria Psillakis, Thanos Dailianis, Janusz Pawliszyn
Frontiers in Marine Science.2019;[Epub] CrossRef
Effect of carbonyl cyanide m-chlorophenylhydrazone (CCCP) on microbial activity and polycyclic aromatic hydrocarbons (PAH) degradation in contaminated river sediments
G. Patricia Johnston, Z. Kalik, C. G. Johnston
Environmental Earth Sciences.2016;[Epub] CrossRef
Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil
Przemyslaw Sawulski, Nicholas Clipson, Evelyn Doyle
Biodegradation.2014; 25(6): 835. CrossRef
Anthracene biodegradation under nitrate-reducing condition and associated microbial community changes
Ying Wang, Rui Wan, Shuying Zhang, Shuguang Xie
Biotechnology and Bioprocess Engineering.2012; 17(2): 371. CrossRef
Molecular characterization of phenanthrene-degrading methanogenic communities in leachate-contaminated aquifer sediment
S. Y. Zhang, Q. F. Wang, S. G. Xie
International Journal of Environmental Science and Technology.2012; 9(4): 705. CrossRef
Increment in Anaerobic Hydrocarbon Degradation Activity of Halic Bay Sediments via Nutrient Amendment
Mustafa Kolukirik, Orhan Ince, Bahar K. Ince
Microbial Ecology.2011; 61(4): 871. CrossRef
Revealing archaeal diversity patterns and methane fluxes in Admiralty Bay, King George Island, and their association to Brazilian Antarctic Station activities
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Deep Sea Research Part II: Topical Studies in Oceanography.2011; 58(1-2): 128. CrossRef
Bioremediation of marine sediments contaminated by hydrocarbons: Experimental analysis and kinetic modeling
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Journal of Hazardous Materials.2010; 182(1-3): 403. CrossRef

Research Support, Non-U.S. Gov'ts

Microeukaryotic Diversity in Marine Environments, an Analysis of Surface Layer Sediments from the East Sea: Soo-Je Park , Byoung-Joon Park , Vinh Hoa Pham , Dae-No Yoon , Si-Kwan Kim , Sung-Keun Rhee; J. Microbiol. 2008;46(3):244-249. Published online July 5, 2008; DOI: https://doi.org/10.1007/s12275-007-0237-x

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Abstract PDF

Molecular techniques, based on clone library of 18S rRNA gene, were employed to ascertain the diversity of microeukaryotic organisms in sediments from the East Sea. A total of 261 clones were recovered from surface sediments. Most of the clone sequences (90%) were affiliated with protists, dominated by Ciliates (18%) and Dinoflagellates (19%) of Alveolates, phototrophic Stramenopiles (11%), and Cercozoa (20%). Many of the clones were related to uncultivated eukaryotes clones retrieved from anoxic environments with several highly divergent 18S rRNA gene sequences. However, no clones were related to cultivated obligate anaerobic protists. Protistan communities between subsurface layers of 1 and 9 cm shared 23% of total phylotypes which comprised 64% of total clones retrieved. Analysis of diversity indices and rarefaction curve showed that the protistan community within the 1 cm layer exhibited higher diversity than the 9 cm layer. Our results imply that diverse protists remain to be uncovered within marine benthic environments.

Citations

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Structural and electrical behaviours of PEDOT:PSS thin films in presence of negatively charged gold and silver nanoparticles: A green synthesis approach
Suman Sarkar, Ashim Chandra Bhowal, Raghuram Kandimalla, Sarathi Kundu
Synthetic Metals.2021; 279: 116848. CrossRef
Horizontal and vertical small-scale patterns of protist communities at the Atlantic deep-sea floor
Manon Hohlfeld, Alexandra Schoenle, Hartmut Arndt
Deep Sea Research Part I: Oceanographic Research Papers.2021; 171: 103515. CrossRef
Evidence from the resurrected family Polyrhabdinidae Kamm, 1922 (Apicomplexa: Gregarinomorpha) supports the epimerite, an attachment organelle, as a major eugregarine innovation
Gita G. Paskerova, Tatiana S. Miroliubova, Andrea Valigurová, Jan Janouškovec, Magdaléna Kováčiková, Andrei Diakin, Yuliya Ya. Sokolova, Kirill V. Mikhailov, Vladimir V. Aleoshin, Timur G. Simdyanov
PeerJ.2021; 9: e11912. CrossRef
Metabarcoding assessment of prokaryotic and eukaryotic taxa in sediments from Stellwagen Bank National Marine Sanctuary
Jennifer M. Polinski, John P. Bucci, Mark Gasser, Andrea G. Bodnar
Scientific Reports.2019;[Epub] CrossRef
Molecular diversity and biogeography of benthic ciliates in the Bohai Sea and Yellow Sea
Guihao Li, Lei Su, Qianqian Zhang, Xiaoli Zhang, Jun Gong
Acta Oceanologica Sinica.2019; 38(2): 78. CrossRef
Protistan community composition in anoxic sediments from three salinity-disparate Japanese lakes
Takafumi Kataoka, Ryuji Kondo
Estuarine, Coastal and Shelf Science.2019; 224: 34. CrossRef
Metabarcoding successfully tracks temporal changes in eukaryotic communities in coastal sediments
I S Salonen, P-M Chronopoulou, E Leskinen, K A Koho
FEMS Microbiology Ecology.2019;[Epub] CrossRef
Genetic Diversity of Benthic Microbial Eukaryotes in Response to Spatial Heterogeneity of Sediment Geochemistry in a Mangrove Ecosystem
Ping Zhu, Yaping Wang, Tiantian Shi, Guoqiang Huang, Jun Gong
Estuaries and Coasts.2018; 41(3): 751. CrossRef
Micro-eukaryotic plankton diversity in an intensive aquaculture system for production of Scophthalmus maximus and Solea senegalensis
C.M. Boaventura, F.J.R.C. Coelho, P.T. Martins, A.C.C. Pires, L.N. Duarte, A.P.T. Uetanabaro, D.F.R. Cleary, N.C.M. Gomes
Aquaculture.2018; 490: 321. CrossRef
A comparison of DNA extraction methods for biodiversity studies of eukaryotes in marine sediments
K Lekang, EM Thompson, C Troedsson
Aquatic Microbial Ecology.2015; 75(1): 15. CrossRef
Diversity and Distributional Patterns of Ciliates in Guaymas Basin Hydrothermal Vent Sediments
Kathryn J. Coyne, Peter D. Countway, Conrad A. Pilditch, Charles K. Lee, David A. Caron, Stephen C. Cary
Journal of Eukaryotic Microbiology.2013; 60(5): 433. CrossRef
Marine Protistan Diversity
David A. Caron, Peter D. Countway, Adriane C. Jones, Diane Y. Kim, Astrid Schnetzer
Annual Review of Marine Science.2012; 4(1): 467. CrossRef
Molecular Monitoring of Eukaryotic Plankton Diversity at Mulgeum and Eulsukdo in the Lower Reaches of the Nakdong River
Jee Eun Lee, Sang-Rae Lee, Seok-Hyun Youn, Sang Ok Chung, Jin Ae Lee, Ik Kyo Chung
The Sea.2012; 17(3): 160. CrossRef
Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing
Man Kit Cheung, Chun Hang Au, Ka Hou Chu, Hoi Shan Kwan, Chong Kim Wong
The ISME Journal.2010; 4(8): 1053. CrossRef
An SSU rDNA barcoding approach to the diversity of marine interstitial cercozoans, including descriptions of four novel genera and nine novel species
Chitchai Chantangsi, Brian S. Leander
International Journal of Systematic and Evolutionary Microbiology .2010; 60(8): 1962. CrossRef
Cultivation of Autotrophic Ammonia-Oxidizing Archaea from Marine Sediments in Coculture with Sulfur-Oxidizing Bacteria
Byoung-Joon Park, Soo-Je Park, Dae-No Yoon, Stefan Schouten, Jaap S. Sinninghe Damsté, Sung-Keun Rhee
Applied and Environmental Microbiology.2010; 76(22): 7575. CrossRef

Characterization of the Depth-Related Changes in the Microbial Communities in Lake Hovsgol Sediment by 16S rRNA Gene-Based Approaches: Young-Do Nam , Youlboong Sung , Ho-Won Chang , Seong Woon Roh , Kyoung-Ho Kim , Sung-Keun Rhee , Jung-Chan Kim , Joo-Yong Kim , Jung-Hoon Yoon , Jin-Woo Bae; J. Microbiol. 2008;46(2):125-136. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0189-1

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Abstract PDF: The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it represents a record of the environmental changes that took place between the Holocene (the present age) and Pleistocene (the last ice age; 12,000 14C years before present day). Here, we investigated how the current microbial <br>communities change as the depth increases by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes of the microbial communities. The microbial diversity, as estimated by the Shannon index, decreased as the depth increased. In particular, significant changes in archaeal diversity were observed in the middle depth (at 39~42 cm depth of total 60 cm depth) that marks the border between the Holocene and Pleistocene. Phylotype belonging to Beta- and Gamma-Proteobacteria were the predominant bacteria and most of these persisted throughout the depth examined. However, as the depth increased, some bacteria <br>(some genera belonging to Beta-Proteobacteria, Nitrospira, and OP8-9) were not detectable while others (some genera belonging to Alpha-, Beta-, Gamma-Proteobacteria) newly deteced by DGGE. Crenarchaea were the predominant archaea and only one phylotype belonging to Euryarchaea was found. Both the <br>archaeal and bacterial profiles revealed by the DGGE band patterns could be grouped into four and three subsets, respectively, subsets that were largely divided by the border between the Holocene and Pleistocene. Thus, the diversity of the current microbial communities in Lake Hovsgol sediments decreases with increasing <br>depth. These changes probably relate to the environmental conditions in the sediments, which were shaped by the paleoclimatic events taking place between the Holocene and Pleistocene.

The Diversity of Multi-drug Resistance Profiles in Tetracycline-Resistant Vibrio Species Isolated from Coastal Sediments and Seawater: Farzana Ashrafi Neela , Lisa Nonaka , Satoru Suzuki; J. Microbiol. 2007;45(1):64-68.; DOI: https://doi.org/2489 [pii]

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Abstract PDF: In this study we examined the multi-drug resistance profiles of the tetracycline (TC) resistant genus Vibrio to determine its susceptibility to two β-lactams, ampicillin (ABPC), and mecillinam (MPC), as well as to macrolide, erythromycin (EM). The results showed various patterns of resistance among strains that were isolated from very close geographical areas during the same year, suggesting diverse patterns of drug resistance in environmental bacteria from this area. In addition, the cross-resistance patterns suggested that the resistance determinants among Vibrio spp. are acquired differently within the sediment and seawater environments.

Enhancing the Intrinsic Bioremediation of PAH-Contaminated Anoxic Estuarine Sediments with Biostimulating Agents: Quang-Dung Bach , Sang-Jin Kim , Sung-Chan Choi , Young-Sook Oh; J. Microbiol. 2005;43(4):319-324.; DOI: https://doi.org/2259 [pii]

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Abstract PDF: Estuarine sediments are frequently polluted with hydrocarbons from fuel spills and industrial wastes. Polycyclic aromatic hydrocarbons (PAHs) are components of these contaminants that tend to accumulate in the sediment due to their low aqueous solubility, low volatility, and high affinity for particulate matter. The toxic, recalcitrant, mutagenic, and carcinogenic nature of these compounds may require aggressive treatment to remediate polluted sites effectively. In petroleum-contaminated sediments near a petrochemical industry in Gwangyang Bay, Korea, in situ PAH concentrations ranged from 10 to 2,900 ug/kg dry sediment. To enhance the biodegradation rate of PAHs under anaerobic conditions, sediment samples were amended with biostimulating agents alone or in combination: nitrogen and phosphorus in the form of slow-release fertilizer (SRF), lactate, yeast extract (YE), and Tween 80. When added to the sediment individually, all tested agents enhanced the degradation of PAHs, including naphthalene, acenaphthene, anthracene, fluorene, phenanthrene, fluoranthene, pyrene, chrysene, and benzo[a]pyrene. Moreover, the combination of SRF, Tween 80, and lactate increased the PAH degradation rate 1.2-8.2 times above that of untreated sediment (0.01-10 ug PAH/kg dry sediment/day). Our results indicated that in situ contaminant PAHs in anoxic sediment, including high molecular weight PAHs, were degraded biologically and that the addition of stimulators increased the biodegradation potential of the intrinsic microbial populations. Our results will contribute to the development of new strategies for in situ treatment of PAH-contaminated anoxic sediments.

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 PDF: 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.

Arthrobacter soli sp. nov., a Novel Bacterium Isolated from Wastewater Reservoir Sediment: Seong Woon Roh , Youlboong Sung , Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Jung-Hoon Yoon , Che Ok Jeon , Hee-Mock Oh , Jin-Woo Bae; J. Microbiol. 2008;46(1):40-44.; DOI: https://doi.org/10.1007/s12275-007-0239-8

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A novel Gram-positive bacterium, designated SYB2T, was isolated from wastewater reservoir sediment, and a polyphasic taxonomic study was conducted based on its morphological, physiological, and biochemical features, as well as the analysis of its 16S rRNA gene sequence. During the phylogenetic analysis of the strain SYB2T, results of a 16S rRNA gene sequence analysis placed this bacterium in the genus Arthrobacter within the family Micrococcaceae. SYB2T and Arthrobacter protophormiae ATCC 19271T, the most closely related species, both exhibited a 16S rRNA gene sequence similarity of 98.99%. The genomic DNA G+C content of the novel strain was found to be 62.0 mol%. The predominant fatty acid composition was anteiso-C15:0, anteiso-C17:0, iso-C16:0, and iso-C15:0. Analysis of 16S rRNA gene sequences and DNA-DNA relatedness, as well as physiological and biochemical tests, showed genotypic and phenotypic differences between strain SYB2T and other Arthrobacter species. The type strain of the novel species was identified as SYB2T (= KCTC 19291T= DSM 19449T).

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Pseudoruegeria aestuarii sp. nov., of the family Rhodobacteraceae, isolated from a tidal flat
In-Tae Cha, Inhye Park, Hae-Won Lee, Hyunjin Lee, Jung-Min Park, Seong Woon Roh, Hak-Jong Choi, Young-Do Nam, Yoo Kyung Lee, Myung-Ji Seo
International Journal of Systematic and Evolutionary Microbiology.2016; 66(8): 3125. CrossRef
Vulcanisaeta thermophila sp. nov., a hyperthermophilic and acidophilic crenarchaeon isolated from solfataric soil
Kyung June Yim, In-Tae Cha, Jin-Kyu Rhee, Hye Seon Song, Dong-Wook Hyun, Hae-Won Lee, Daekyung Kim, Kil-Nam Kim, Young-Do Nam, Myung-Ji Seo, Jin-Woo Bae, Seong Woon Roh
International Journal of Systematic and Evolutionary Microbiology.2015; 65(Pt_1): 201. CrossRef
Halolamina rubra sp. nov., a haloarchaeon isolated from non-purified solar salt
In-Tae Cha, Kyung June Yim, Hye Seon Song, Hae-Won Lee, Dong-Wook Hyun, Kil-Nam Kim, Jong-Soon Choi, Daekyung Kim, Sung-Jae Lee, Myung-Ji Seo, Hak-Jong Choi, Jin-Woo Bae, Sung-Keun Rhee, Seong Woon Roh, Young-Do Nam
Antonie van Leeuwenhoek.2014; 105(5): 907. CrossRef
Citrimicrobium luteum gen. nov., sp. nov., aerobic anoxygenic phototrophic bacterium isolated from the gut of a sea cucumber Stichopus japonicus
Hong-Joo Jung, In-Tae Cha, Kyung June Yim, Hye Seon Song, Kichul Cho, Daekyung Kim, Hae-Won Lee, Jae Kook Lee, Myung-Ji Seo, Seong Woon Roh, Sung-Jae Lee
Journal of Microbiology.2014; 52(10): 819. CrossRef
Halobellus rufus sp. nov., an extremely halophilic archaeon isolated from non-purified solar salt
In-Tae Cha, Kyung June Yim, Hye Seon Song, Hae-Won Lee, Dong-Wook Hyun, Kil-Nam Kim, Myung-Ji Seo, Daekyung Kim, Jong-Soon Choi, Sung-Jae Lee, Jin-Woo Bae, Sung-Keun Rhee, Hak-Jong Choi, Jin-Kyu Rhee, Young-Do Nam, Seong Woon Roh
Antonie van Leeuwenhoek.2014; 105(5): 925. CrossRef
Isolation and Characterization of vB_ArS-ArV2 – First Arthrobacter sp. Infecting Bacteriophage with Completely Sequenced Genome
Eugenijus Šimoliūnas, Laura Kaliniene, Miroslav Stasilo, Lidija Truncaitė, Aurelija Zajančkauskaitė, Juozas Staniulis, Juozas Nainys, Algirdas Kaupinis, Mindaugas Valius, Rolandas Meškys, Adam Driks
PLoS ONE.2014; 9(10): e111230. CrossRef
Halorubrum halophilum sp. nov., an extremely halophilic archaeon isolated from a salt-fermented seafood
Kyung June Yim, In-Tae Cha, Hae-Won Lee, Hye Seon Song, Kil-Nam Kim, Sung-Jae Lee, Young-Do Nam, Dong-Wook Hyun, Jin-Woo Bae, Sung-Keun Rhee, Myung-Ji Seo, Jong-Soon Choi, Hak-Jong Choi, Seong Woon Roh, Daekyung Kim
Antonie van Leeuwenhoek.2014; 105(3): 603. CrossRef
Halococcus sediminicola sp. nov., an extremely halophilic archaeon isolated from a marine sediment
Kyung June Yim, In-Tae Cha, Tae Woong Whon, Hae-Won Lee, Hye Seon Song, Kil-Nam Kim, Young-Do Nam, Sung-Jae Lee, Jin-Woo Bae, Sung-Keun Rhee, Jong-Soon Choi, Myung-Ji Seo, Seong Woon Roh, Daekyung Kim
Antonie van Leeuwenhoek.2014; 105(1): 73. CrossRef
Halapricum salinum gen. nov., sp. nov., an extremely halophilic archaeon isolated from non-purified solar salt
Hye Seon Song, In-Tae Cha, Kyung June Yim, Hae-Won Lee, Dong-Wook Hyun, Sung-Jae Lee, Sung-Keun Rhee, Kil-Nam Kim, Daekyung Kim, Jong-Soon Choi, Myung-Ji Seo, Hak-Jong Choi, Jin-Woo Bae, Jin-Kyu Rhee, Young-Do Nam, Seong Woon Roh
Antonie van Leeuwenhoek.2014; 105(5): 979. CrossRef
Draft Genome Sequence of Arthrobacter crystallopoietes Strain BAB-32, Revealing Genes for Bioremediation
M. N. Joshi, A. S. Pandit, A. Sharma, R. V. Pandya, S. M. Desai, A. K. Saxena, S. B. Bagatharia
Genome Announcements.2013;[Epub] CrossRef
Lactobacillus kimchiensis sp. nov., isolated from a fermented food
Jandi Kim, Joon Yong Kim, Min-Soo Kim, Seong Woon Roh, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_4): 1355. CrossRef
Paenibacillus marinisediminis sp. nov., a bacterium isolated from marine sediment
Hae-Won Lee, Seong Woon Roh, Kyung June Yim, Na-Ri Shin, Jina Lee, Tae Woong Whon, Joon Yong Kim, Dong-Wook Hyun, Daekyung Kim, Jin-Woo Bae
Journal of Microbiology.2013; 51(3): 312. CrossRef
Gillisia marina sp. nov., from seashore sand, and emended description of the genus Gillisia
Seong Woon Roh, Myunglip Lee, Hae-Won Lee, Kyung June Yim, Soo Yeon Heo, Kil-Nam Kim, Changmann Yoon, Young-Do Nam, Joon Yong Kim, Dong-Wook Hyun, Jin-Woo Bae, Joon Bum Jeong, Heewan Kang, Daekyung Kim
International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_10): 3640. CrossRef
Rhodopirellula rosea sp. nov., a novel bacterium isolated from an ark clam Scapharca broughtonii
Seong Woon Roh, Hae-Won Lee, Kyung June Yim, Na-Ri Shin, Jina Lee, Tae Woong Whon, Na-Lae Lim, Daekyung Kim, Jin-Woo Bae
Journal of Microbiology.2013; 51(3): 301. CrossRef
Paenibacillus oceanisediminis sp. nov. isolated from marine sediment
Jina Lee, Na-Ri Shin, Mi-Ja Jung, Seong Woon Roh, Min-Soo Kim, Jung-Sook Lee, Keun Chul Lee, Young-Ok Kim, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_2): 428. CrossRef
Ferrimonas pelagia sp. nov., isolated from seawater
Kyung June Yim, Myunglip Lee, Hae-Won Lee, Kil-Nam Kim, Hye-Mi Yang, Mi-Ju Kim, Dong-Wook Hyun, Jin-Woo Bae, Young-Do Nam, Changmann Yoon, Moo-Sang Kim, Seong Woon Roh, Daekyung Kim
International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_9): 3175. CrossRef
Kistimonas scapharcae sp. nov., isolated from a dead ark clam (Scapharca broughtonii), and emended description of the genus Kistimonas
Jina Lee, Na-Ri Shin, Hae-Won Lee, Seong Woon Roh, Min-Soo Kim, Young-Ok Kim, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2012; 62(Pt_12): 2865. CrossRef
Tropicimonas sediminicola sp. nov., isolated from marine sediment
Na-Ri Shin, Seong Woon Roh, Min-Soo Kim, Bora Yun, Tae Woong Whon, Young-Ok Kim, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2012; 62(Pt_10): 2424. CrossRef
Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food
Jandi Kim, Mi-Ja Jung, Seong Woon Roh, Young-Do Nam, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2011; 61(12): 2851. CrossRef
Microbacterium mitrae sp. nov., isolated from salted turban shell
Yun-Ji Kim, Seong Woon Roh, Mi-Ja Jung, Min-Soo Kim, Eun-Jin Park, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2011; 61(2): 399. CrossRef
Dietzia alimentaria sp. nov., isolated from a traditional Korean food
Jandi Kim, Seong Woon Roh, Jung-Hye Choi, Mi-Ja Jung, Young-Do Nam, Min-Soo Kim, Eun-Jin Park, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2011; 61(9): 2254. CrossRef
Arthrobacter livingstonensis sp. nov. and Arthrobacter cryotolerans sp. nov., salt-tolerant and psychrotolerant species from Antarctic soil
Lars Ganzert, Felizitas Bajerski, Kai Mangelsdorf, André Lipski, Dirk Wagner
International Journal of Systematic and Evolutionary Microbiology .2011; 61(4): 979. CrossRef
Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing
Seong Woon Roh, Kyoung-Ho Kim, Young-Do Nam, Ho-Won Chang, Eun-Jin Park, Jin-Woo Bae
The ISME Journal.2010; 4(1): 1. CrossRef
Kocuria koreensis sp. nov., isolated from fermented seafood
Eun-Jin Park, Seong Woon Roh, Min-Soo Kim, Mi-Ja Jung, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2010; 60(1): 140. CrossRef
Arthrobacter antarcticus sp. nov., isolated from an Antarctic marine sediment
Pavan Kumar Pindi, Ruth Manorama, Zareena Begum, S. Shivaji
International Journal of Systematic and Evolutionary Microbiology.2010; 60(10): 2263. CrossRef
Oceanobacillus kimchii sp. nov. Isolated from a traditional Korean fermented food
Tae Woong Whon, Mi-Ja Jung, Seong Woon Roh, Young-Do Nam, Eun-Jin Park, Kee-Sun Shin, Jin-Woo Bae
The Journal of Microbiology.2010; 48(6): 862. CrossRef
Kocuria atrinae sp. nov., isolated from traditional Korean fermented seafood
Eun-Jin Park, Min-Soo Kim, Seong Woon Roh, Mi-Ja Jung, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2010; 60(4): 914. CrossRef
Haladaptatus cibarius sp. nov., an extremely halophilic archaeon from seafood, and emended description of the genus Haladaptatus
Seong Woon Roh, Myung-Lip Lee, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology.2010; 60(5): 1187. CrossRef
Agromyces atrinae sp. nov., isolated from fermented seafood
Eun-Jin Park, Min-Soo Kim, Mi-Ja Jung, Seong Woon Roh, Ho-Won Chang, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2010; 60(5): 1056. CrossRef
Arthrobacter halodurans sp. nov., a new halotolerant bacterium isolated from sea water
Yi-Guang Chen, Shu-Kun Tang, Yu-Qin Zhang, Zhao-Yang Li, Lang-Bo Yi, Yong-Xia Wang, Wen-Jun Li, Xiao-Long Cui
Antonie van Leeuwenhoek.2009; 96(1): 63. CrossRef
Paracoccus aestuarii sp. nov., isolated from tidal flat sediment
S. W. Roh, Y.-D. Nam, H.-W. Chang, K.-H. Kim, M.-S. Kim, K.-S. Shin, J.-H. Yoon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(4): 790. CrossRef
Haloterrigena jeotgali sp. nov., an extremely halophilic archaeon from salt-fermented food
S. W. Roh, Y.-D. Nam, H.-W. Chang, K.-H. Kim, Y. Sung, M.-S. Kim, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(9): 2359. CrossRef
Nocardioides basaltis sp. nov., isolated from black beach sand
K.-H. Kim, S. W. Roh, H.-W. Chang, Y.-D. Nam, J.-H. Yoon, C. O. Jeon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(1): 42. CrossRef
Alishewanella aestuarii sp. nov., isolated from tidal flat sediment, and emended description of the genus Alishewanella
S. W. Roh, Y.-D. Nam, H.-W. Chang, K.-H. Kim, M.-S. Kim, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(2): 421. CrossRef
Sphingomonas aestuarii sp. nov., isolated from tidal flat sediment
S. W. Roh, K.-H. Kim, Y.-D. Nam, H.-W. Chang, M.-S. Kim, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(6): 1359. CrossRef
Halorubrum cibi sp. nov., an extremely halophilic archaeon from salt-fermented seafood
Seong Woon Roh, Jin-Woo Bae
The Journal of Microbiology.2009; 47(2): 162. CrossRef
Nitratireductor basaltis sp. nov., isolated from black beach sand
K.-H. Kim, S. W. Roh, H.-W. Chang, Y.-D. Nam, J.-H. Yoon, C. O. Jeon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(1): 135. CrossRef
Phylogenetic Characterization of Two Novel Commensal Bacteria Involved with Innate Immune Homeostasis inDrosophila melanogaster
Seong Woon Roh, Young-Do Nam, Ho-Won Chang, Kyoung-Ho Kim, Min-Soo Kim, Ji-Hwan Ryu, Sung-Hee Kim, Won-Jae Lee, Jin-Woo Bae
Applied and Environmental Microbiology.2008; 74(20): 6171. CrossRef
Marinobacter goseongensis sp. nov., from seawater
S. W. Roh, Z.-X. Quan, Y.-D. Nam, H.-W. Chang, K.-H. Kim, S.-K. Rhee, H.-M. Oh, C. O. Jeon, J.-H. Yoon, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2008; 58(12): 2866. CrossRef
Genomics of biological wastewater treatment
Roland J. Siezen, Marco Galardini
Microbial Biotechnology.2008; 1(5): 333. CrossRef
List of new names and new combinations previously effectively, but not validly, published

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2008; 58(9): 1993. CrossRef
Luteimonas aestuarii sp. nov., isolated from tidal flat sediment
Seong Woon Roh, Kyoung-Ho Kim, Young-Do Nam, Ho-Won Chang, Min-Soo Kim, Jung-Hoon Yoon, Hee-Mock Oh, Jin-Woo Bae
The Journal of Microbiology.2008; 46(5): 525. CrossRef
Marinomonas basaltis sp. nov., a marine bacterium isolated from black sand
H.-W. Chang, S. W. Roh, K.-H. Kim, Y.-D. Nam, J.-H. Yoon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2008; 58(12): 2743. CrossRef
Aliihoeflea aestuarii gen. nov., sp. nov., a novel bacterium isolated from tidal flat sediment
Seong Woon Roh, Kyoung-Ho Kim, Young-Do Nam, Ho-Won Chang, Min-Soo Kim, Kee-Sun Shin, Jung-Hoon Yoon, Hee-Mock Oh, Jin-Woo Bae
The Journal of Microbiology.2008; 46(5): 594. CrossRef

Distribution and activity of sulfate-reducing bacteria in lake soyang sediments: Jin, Ho Yong , Lee, Dong Hun , Zo, Young Gun , Kang Chan Su , Kim Sang Jong; J. Microbiol. 1996;34(2):131-136.

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Abstract PDF: In order to known the extend of contribution to the degradation of organic materials and nutrient recycling by sulfate-reducing bacteria (SRB) and methane-producing bacteria (MPB) in sediment, the distribution and activity of these two groups of microorganisms were studied montly in 1994 at two sites, one littoral (Sanggulri) and the other profundal (DAM), in Lake Soyang. In the seasonal distribution of two microorganisms, SRB were 1.07 × 10^3 - 2.42 × 10^5 cells/g-dry weight at Sanggulri, 2.40 × 10^5 - 1.29 × 10^6 at Dam and MPB were 0.52 × 10^3 cells/g-dry weight at Sangguri and 1.44 × 10^3 - 6.89 × 10^3 at Dam. In these results, the density of SRB in Lake Soyang is much higher than other lakes. These high values might be due to higher sulfate concentration, 0.69-4.05 mM, than normal freshwater, 0.01-1.2 mM. And a good correlation of SRB and chlorophyll a concentration implied that the important environmental factor on distribution of SRB might be the concentration of available organic matter. In a comparison of sulfate-reducing rate and methane producing rate in 1995, the activity of SRB for the degradation of organic matter was higher than MPB by factor of 359. Conclusively SRB superior to MPB in the distribution and activity are more important anaerobic bacteria in Lake Soyang sediments.

Effect of Moisture Content on Reductive Dechlorination of Polychlorinated Biphenyls and Population Dynamics of Dechlorinating Microorganisms: O-Seob Kwon , Young Eui Kim , Jong Gyu Park; J. Microbiol. 2001;39(3):195-201.

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Abstract PDF: The effect of moisture content on the reductive dechlorination of polychlorinated biphenyls and population dynamics of dechlorinating microorganisms was investigated in sediments spiked with Aroclor 1248. In sediment slurry with an overlying water layer, dechlorination ensued after a 4-week lag period and reduced the average number of chlorines per biphenyl from 3.91 to 3.15 after 48 weeks. In the sediments of reduced moisture content, however, dechlorination occurred after a lag period of 12 weeks and decreased the average number of chlorines per biphenyl to only 3.62, and the dechlorination rate was also slower. When the population size of dechlorinators, methanogens, and sulfate-reducing bacteria was determined by the most probable number techniques, however, no difference was found between the slurry and the low-moisture sediments, except for methanogens. The growth of dechlorinating populations coincided with the end of the lag period and they then increased by 3 orders of magnitude in two conditions. Specific growth rate of dechlorinators showed little difference between the slurry and the low-moisture sediments; however, growth yield was high in the sediments of reduced moisture content. The reduction of sediment moisture decreased the dechlorination rate and extent of PCBs but did not inhibit the growth of PCB dechlorinators.

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