Journal of Microbiology

Volume 57(5); May 2019

Review

MINIREVIEW] Dynamics of microbial communities and CO2 and CH4 fluxes in the tundra ecosystems of the changing Arctic: Min Jung Kwon , Ji Young Jung , Binu M. Tripathi , Mathias Göckede , Yoo Kyung Lee , Mincheol Kim; J. Microbiol. 2019;57(5):325-336. Published online January 16, 2019; DOI: https://doi.org/10.1007/s12275-019-8661-2

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Arctic tundra ecosystems are rapidly changing due to the amplified effects of global warming within the northern high latitudes. Warming has the potential to increase the thawing of the permafrost and to change the landscape and its geochemical characteristics, as well as terrestrial biota. It is important to investigate microbial processes and community structures, since soil microorganisms play a significant role in decomposing soil organic carbon in the Arctic tundra. In addition, the feedback from tundra ecosystems to climate change, including the emission of greenhouse gases into the atmosphere, is substantially dependent on the compositional and functional changes in the soil microbiome. This article reviews the current state of knowledge of the soil microbiome and the two most abundant greenhouse gas (CO2 and CH4) emissions, and summarizes permafrost thaw-induced changes in the Arctic tundra. Furthermore, we discuss future directions in microbial ecological research coupled with its link to CO2 and CH4 emissions.

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Arctic tundra soil depth, more than seasonality, determines active layer bacterial community variation down to the permafrost transition
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Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils
Tatiana Demina, Heli Marttila, Igor S. Pessi, Minna K. Männistö, Bas E. Dutilh, Simon Roux, Jenni Hultman
Microbiome.2025;[Epub] CrossRef
Methane emission hotspots in a boreal forest-fen mosaic potentially linked to deep taliks
Mary Farina, William Christian, Nicholas Hasson, Timothy McDermott, Scott Powell, Roland Hatzenpichler, Hailey Webb, Gage LaRue, Kyoko Okano, Eric A Sproles, Jennifer D Watts
Environmental Research Letters.2025; 20(10): 104029. CrossRef
The effect of temperature on the activity of microorganisms in the area of the Bureiskiy Landslide
L. М. Kondratyeva, D. V. Andreeva, Z. N. Litvinenko, E. M. Golubeva
Biologiâ vnutrennih vod.2024; 17(5): 713. CrossRef
Effect of Temperature on the Activity of Microorganisms in the Area of the Bureiskiy Landslide
L. M. Kondratyeva, D. V. Andreeva, Z. N. Litvinenko, E. M. Golubeva
Inland Water Biology.2024; 17(5): 733. CrossRef
Effects of nitrogen and phosphorus additions on CH4 flux in wet meadow of Qinghai-Tibet Plateau
Jiangqi Wu, Yanhua Lu, Haiyan Wang, Guang Li
Science of The Total Environment.2023; 887: 163448. CrossRef
Root exclusion methods for partitioning of soil respiration: Review and methodological considerations
Mei-Yee CHIN, Sharon Yu Ling LAU, Frazer MIDOT, Mui Sie JEE, Mei Lieng LO, Faustina E. SANGOK, Lulie MELLING
Pedosphere.2023; 33(5): 683. CrossRef
Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies
Mark Dopson, Carolina González-Rosales, David S. Holmes, Nadia Mykytczuk
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Distinct Growth Responses of Tundra Soil Bacteria to Short-Term and Long-Term Warming
Jeffrey R. Propster, Egbert Schwartz, Michaela Hayer, Samantha Miller, Victoria Monsaint-Queeney, Benjamin J. Koch, Ember M. Morrissey, Michelle C. Mack, Bruce A. Hungate, John R. Spear
Applied and Environmental Microbiology.2023;[Epub] CrossRef
Effect of Low Temperature and Municipal Wastewater Organic Loading on Anaerobic Granule Reactor Performance
Anissa Sukma Safitri, Krista Michelle Michelle Kaster, Roald Kommedal
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Microbiogeochemical Traits to Identify Nitrogen Hotspots in Permafrost Regions
Claudia Fiencke, Maija E. Marushchak, Tina Sanders, Rica Wegner, Christian Beer
Nitrogen.2022; 3(3): 458. CrossRef
Response of vegetation and carbon fluxes to brown lemming herbivory in northern Alaska
Jessica Plein, Rulon W. Clark, Kyle A. Arndt, Walter C. Oechel, Douglas Stow, Donatella Zona
Biogeosciences.2022; 19(11): 2779. CrossRef
Changes in the microbial community structure triggered by permafrost peat thawing
V A Nikitkin, L G Kolesnichenko, E G Nikitkina, A V Pivovarova, E Kostenko, I V Lushchaeva
IOP Conference Series: Earth and Environmental Science.2021; 928(1): 012008. CrossRef
Impacts of Permafrost Degradation on Carbon Stocks and Emissions under a Warming Climate: A Review
Huijun Jin, Qiang Ma
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The Cold Region Critical Zone in Transition: Responses to Climate Warming and Land Use Change
Kunfu Pi, Magdalena Bieroza, Anatoli Brouchkov, Weitao Chen, Louis J.P. Dufour, Konstantin B. Gongalsky, Anke M. Herrmann, Eveline J. Krab, Catherine Landesman, Anniet M. Laverman, Natalia Mazei, Yuri Mazei, Mats G. Öquist, Matthias Peichl, Sergey Pozdnia
Annual Review of Environment and Resources.2021; 46(1): 111. CrossRef
Impacts of climate-induced permafrost degradation on vegetation: A review
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Advances in Climate Change Research.2021; 12(1): 29. CrossRef
WETMETH 1.0: a new wetland methane model for implementation in Earth system models
Claude-Michel Nzotungicimpaye, Kirsten Zickfeld, Andrew H. MacDougall, Joe R. Melton, Claire C. Treat, Michael Eby, Lance F. W. Lesack
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Operational Analysis and Medium-Term Forecasting of the Greenhouse Gas Generation Intensity in the Cryolithozone
Andrey V. Timofeev, Viktor Y. Piirainen, Vladimir Y. Bazhin, Aleksander B. Titov
Atmosphere.2021; 12(11): 1466. CrossRef
The Effect of Nitrogen Content on Archaeal Diversity in an Arctic Lake Region
Jinjiang Lv, Feng Liu, Wenbing Han, Yu Wang, Qian Zhu, Jiaye Zang, Shuang Wang, Botao Zhang, Nengfei Wang
Microorganisms.2019; 7(11): 543. CrossRef
Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska
Binu M. Tripathi, Hye Min Kim1, Ji Young Jung, Sungjin Nam, Hyeon Tae Ju, Mincheol Kim, Yoo Kyung Lee
Frontiers in Microbiology.2019;[Epub] CrossRef

Journal Articles

Edaphovirga cremea gen. nov., sp. nov., isolated from the rhizospheric soil of Codonopsis clematidea: Jin-Yan Xue , Meng-Yue Zhang , Yu Zhang , Juan Cheng , Li-Cheng Liu , Ying-Ying Wu , Tian-Yuan Zhang , Yi-Xuan Zhang; J. Microbiol. 2019;57(5):337-342. Published online February 26, 2019; DOI: https://doi.org/10.1007/s12275-019-8408-0

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A Gram-negative, facultatively anaerobic, non-motile, nonspore- forming, coccoid or rod-shaped and creamy-pigmented bacterium, designated SYP-B2100T, was isolated from the rhizospheric soil of Codonopsis clematidea in the Xinjiang Uygur Autonomous Region, China. The optimal growth occurred at 28°C, pH 5.0, in the absence of NaCl. The cells tested positive in catalase and methyl red tests but negative in oxidase, urease, gelatinase, milk coagulation, and peptonisation, H2S production, nitrate reduction, and Voges-Proskauer tests. The major isoprenoid quinone was ubiquinone-8 (Q-8). The major cellular fatty acids were C16:0 and summed feature 8. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The 16S rRNA gene sequence of strain SYP-B2100T was the most similar to that of Rahnella inusitata DSM 30078T (96.9%) within the family Enterobacteriaceae. The genomic DNA G+C content of strain SYP-B2100T was 50.3 mol%. The combined data from the phylogenetic, morphological, physiological, biochemical, and chemotaxonomic analyses presented in this study support the conclusion that strain SYP-B2100T represents a novel species of a new genus, for which the name Edaphovirga cremea gen. nov., sp. nov. is proposed; the type strain is SYPB2100T (= CGMCC 1.5857T = DSM 105170T = KCTC 62024T).

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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

Flavobacterium aquariorum sp. nov., isolated from freshwater of the North Han River: Yochan Joung , Hye-Jin Jang , Jaeho Song , Jang-Cheon Cho; J. Microbiol. 2019;57(5):343-349. Published online February 5, 2019; DOI: https://doi.org/10.1007/s12275-019-8436-9

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A non-motile, yellow-pigmented bacterial strain, designated IMCC34762T, was isolated from a freshwater sample collected from Lake Cheongpyeong in Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC- 34762T formed a lineage within the genus Flavobacterium and was most closely related to F. pectinovorum DSM 6368T (98.3% sequence similarity), followed by F. piscis CCUG 60099T (98.3%), F. branchiicola 59B-3-09T (98.2%), and F. saccharophilum DSM 1811T (98.2%). The average nucleotide identity and the genome-to-genome distance between strain IMCC34762T and the closely related strains were 61–62% and 26–27%, respectively, indicating that IMCC34762T is a novel species of the genus Flavobacterium. The major fatty acids (> 5%) of strain IMCC34762T were summed feature 3 (C16:1 ω6c and/or C16:1 ω7c, 17.3%), iso-C15:0 (15.0%), iso-C15:0 G (9.0%), C15:0 ω6c (7.4%), iso-C15:0 (7.4%), and iso-C16:0 (5.3%). The major respiratory quinone and polyamine were MK-6 and sym-homospermidine, respectively. The major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid, and an unidentified lipid. The DNA G+C content of strain IMCC34762T was 34.4 mol%. Based on the taxonomic data presented in this study, strain IMCC34762T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium aquariorum, sp. nov. is proposed. The type strain is IMCC34762T (= KACC 19725T = NBRC 113425T).

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Flavobacterium algoriphilum sp. nov., Flavobacterium arabinosi sp. nov., Flavobacterium cryoconiti sp. nov., Flavobacterium galactosi sp. nov., Flavobacterium melibiosi sp. nov., and Flavobacterium algoris sp. nov., six novel cold-adapted bacteria isolate
Lei-Lei Yang, Yu-Hua Xin, Qing Liu
BMC Microbiology.2025;[Epub] CrossRef
Flavobacterium anseongense sp. nov. and Flavobacterium wongokense sp. nov., isolated from freshwater and freshwater soil in South Korea
Jung-Hun Jo, Soon-Youl Lee, Se-Yoon Chun, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Unveiling the hidden threat: heavy metal accumulation in crops and soil microbial dynamics in a teaching experimental farmland
Xue Gu, Xuegang Yu, Qing Li, Yanjun Mao, Zhiwei Zhou, Huan Hu, Rui Huang, Jiayu Zhou, Yuanyi Sun, Yancheng Li, Aijiang Yang
Plant and Soil.2025;[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 erciyesense sp. nov., a putative non-pathogenic fish symbiont
Izzet Burcin Saticioglu
Archives of Microbiology.2021; 203(9): 5783. CrossRef
Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout
Muhammed Duman, Hilal Ay, Soner Altun, Nevzat Sahin, Izzet Burcin Saticioglu
International Journal of Systematic and Evolutionary Microbiology.2021;[Epub] CrossRef
Flavobacterium turcicum sp. nov. and Flavobacterium kayseriense sp. nov. isolated from farmed rainbow trout in Turkey
Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Muhammed Duman, Nevzat Sahin
Systematic and Applied Microbiology.2021; 44(2): 126186. CrossRef
Flavobacterium bernardetii sp. nov., a possible emerging pathogen of farmed rainbow trout (Oncorhynchus mykiss) in cold water
Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Nevzat Sahin, Muhammed Duman
Aquaculture.2021; 540: 736717. 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(7): 4043. CrossRef
Rhodoferax lacus sp. nov., isolated from a large freshwater lake
Miri Park, Jaeho Song, Gi Gyun Nam, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology .2019; 69(10): 3135. CrossRef

Acinetobacter chinensis, a novel Acinetobacter species, carrying blaNDM-1, recovered from hospital sewage: Yiyi Hu , Yu Feng , Jiayuan Qin , Xiaoxia Zhang , Zhiyong Zong; J. Microbiol. 2019;57(5):350-355. Published online February 26, 2019; DOI: https://doi.org/10.1007/s12275-019-8485-0

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Two strains of the genus Acinetobacter, named WCHAc- 010005 and WCHAc010052, were isolated from hospital sewage at West China Hospital in Chengdu, China. The two strains were found to be resistant to carbapenems due to the presence of carbapenemase gene blaNDM-1. Based on the comparative analysis of the rpoB sequence, the two strains formed a strongly supported and internally coherent cluster (intracluster identity of 98.7%), which was clearly separated from all known Acinetobacter species (≤ 83.4%). The two strains also formed a tight and distinct cluster based on the genuswide comparison of whole-cell mass fingerprints generated by MALDI-TOF mass spectrometry. In addition, the combination of their ability to assimilate malonate but not benzoate, and the inability to grow at 37°C could distinguish the two strains from all known Acinetobacter species. The two strains were subjected to whole genome sequencing using both short-read Illumina HiSeq2500 platform and the longread MinION sequencer. The average nucleotide identity and in silico DNA-DNA hybridization value between the genomes of WCHAc010005 and WCHAc010052 was 96.69% and 74.3% respectively, whereas those between the two genomes and the known Acinetobacter species were < 80% and < 30%, respectively. Therefore, the two strains represent a novel species of the genus Acinetobacter, for which the name Acinetobacter chinensis sp. nov. is proposed, and the type strain is WCHAc- 010005T (= GDMCC 1.1232T = KCTC 62813T).

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Evolution of RND efflux pumps in the development of a successful pathogen
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Lingtong Tang, Wei Shen, Zhikun Zhang, Jingping Zhang, Guangxi Wang, Li Xiang, Junping She, Xiaoyan Hu, Guoyuan Zou, Baoli Zhu, Yingshun Zhou
Infection and Drug Resistance.2020; Volume 13: 855. 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 .2019; 69(9): 2627. CrossRef

Mucibacter soli gen. nov., sp. nov., a new member of the family Chitinophagaceae producing mucin: Min-Kyeong Kim , Sewook Park , Tae-Su Kim , Yochan Joung , Ji-Hye Han , Seung Bum Kim; J. Microbiol. 2019;57(5):356-361. Published online February 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8512-1

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A Gram-stain-negative, mucus-forming, motile by gliding, non-spore-forming and short rod-shaped bacterial strain designated R1-15T was isolated from soil and its taxonomic position was evaluated using a polyphasic approach. Strain R1-15T grew at 15–37°C (optimum, 30°C), at pH 6–7 (optimum, pH 6) and in the presence of 0–1% (w/v) NaCl (optimum, 0%) on 0.1X TSA. On the basis of 16S rRNA gene sequence similarity, the novel strain was assigned to the family Chitinophagaceae of the phylum Bacteroidetes, and its closest related taxa were species of the genera Taibaiella (88.76– 90.02% sequence similarity), Lacibacter (89.24–90.00%), Chitinophaga (88.61–89.76%), and Terrimonas (89.04%). Flexirubin- type pigments were produced. The only isoprenoid quinone was MK-7, and the major polar lipid was phosphatidylethanolamine. Based on whole genome comparisons between the strain R1-15T and the type strains of relatives, the orthologous average nucleotide identity values were 66.9– 67.0%. The DNA G+C content of strain R1-15T was 43.8 mol%. The combination of phylogenetic, chemotaxonomic and phenotypic data clearly supported separation of strain R1-15T from related taxa, and thus the name Mucibacter soli gen. nov., sp. nov. is proposed. The type strain is R1-15T (= KCTC 62274T = JCM 31190T).

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Simplicispira sedimenti sp. nov., isolated from a sediment of drainage ditch in winery
Xing Chen, Yuan-Dong Li, Xiu-Ming Liu, Li Gao, Xing-Kui Zhou, Li-Min Dong, Gang Du, Neeli Habib, Wen-Jun Li, Yan-Qing Duan
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Dyella sedimenti sp. nov., Isolated from the Sediment of a Winery
Li Gao, Yuan-Dong Li, Xing-Kui Zhou, Xiu-Ming Liu, Hui-Tian Li, Wen-Jun Li, Yan-Qing Duan
Current Microbiology.2022;[Epub] CrossRef
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Journal of Environmental Chemical Engineering.2022; 10(1): 106934. CrossRef
Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil
Su Gwon Roh, Chan Lee, Min-Kyeong Kim, Hye-Jeong Kang, Yeong Seok Kim, Min Ji Kim, Adeel Malik, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2020; 70(4): 2682. CrossRef
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Yeong Seok Kim, Su Gwon Roh, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2020; 70(3): 2079. CrossRef
List of new names and new combinations previously effectively, but not validly, published
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International Journal of Systematic and Evolutionary Microbiology .2020; 70(1): 1. CrossRef

Microbial transformation of Se oxyanions in cultures of Delftia lacustris grown under aerobic conditions: Shrutika L. Wadgaonkar , Yarlagadda V. Nancharaiah , Claus Jacob , Giovanni Esposito , Piet N. L. Lens; J. Microbiol. 2019;57(5):362-371. Published online March 21, 2019; DOI: https://doi.org/10.1007/s12275-019-8427-x

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Delftia lacustris is reported for the first time as a selenate and selenite reducing bacterium, capable of tolerating and growing in the presence of ≥ 100 mM selenate and 25 mM selenite. The selenate reduction profiles of D. lacustris were investigated by varying selenate concentration, inoculum size, concentration and source of organic electron donor in minimal salt medium. Interestingly, the bacterium was able to reduce both selenate and selenite under aerobic conditions. Although considerable removal of selenate was observed at all concentrations investigated, D. lacustris was able to completely reduce 0.1 mM selenate within 96 h using lactate as the carbon source. Around 62.2% unaccounted selenium (unidentified organo-selenium compounds), 10.9% elemental selenium and 26.9% selenite were determined in the medium after complete reduction of selenate. Studies of the enzymatic activity of the cell fractions show that the selenite/selenate reducing enzymes were intracellular and independent of NADPH availability. D. lacustris shows an unique metabolism of selenium oxyanions to form elemental selenium and possibly also selenium ester compounds, thus a potential candidate for the remediation of selenium-contaminated wastewaters in aerobic environments. This novel finding will advance the field of bioremediation of selenium-contaminated sites and selenium bio-recovery and the production of potentially beneficial organic and inorganic reactive selenium species.

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Elham Lashani, Hamid Moghimi, Raymond J Turner, Mohammad Ali Amoozegar
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Dong-Wook Hyun, Hojun Sung, Pil Soo Kim, Ji-Hyun Yun, Jin-Woo Bae
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The Journal of Organic Chemistry.2021; 86(1): 980. CrossRef
Reduction of selenite to elemental Se(0) with simultaneous degradation of phenol by co-cultures of Phanerochaete chrysosporium and Delftia lacustris
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Journal of Microbiology.2019; 57(9): 738. CrossRef

Identification and characterization of a marine-derived chitinolytic fungus, Acremonium sp. YS2-2: Dawoon Chung , Kyunghwa Baek , Seung Seob Bae , Jaejoon Jung; J. Microbiol. 2019;57(5):372-380. Published online February 26, 2019; DOI: https://doi.org/10.1007/s12275-019-8469-0

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Chitin is the most abundant biopolymer in marine environments. To facilitate its utilization, our laboratory screened marine-derived fungal strains for chitinolytic activity. One chitinolytic strain isolated from seawater, designated YS2-2, was identified as Acremonium species based on morphological and phylogenetic analyses. Acremonium species are cosmopolitan fungi commonly isolated from both terrestrial and marine environments, but their chitinolytic activity is largely unknown. The extracellular crude enzyme of YS2-2 exhibited optimum chitinolytic activity at pH 6.0–7.6, 23–45°C, and 1.5% (w/v) NaCl. Degenerate PCR revealed the partial cDNA sequence of a putative chitinase gene, chiA, in YS2-2. The expression of chiA was dramatically induced in response to 1% (w/v) colloidal chitin compared to levels under starvation, chitin powder, and glucose conditions. Moreover, the chiA transcript levels were positively correlated with chitinolytic activities under various colloidal chitin concentrations, suggesting that ChiA mediates chitinolytic activity in this strain. Our results provide a basis for additional studies of marinederived chitinolytic fungi aimed at improving industrial applications.

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Intestinibaculum porci gen. nov., sp. nov., a new member of the family Erysipelotrichaceae isolated from the small intestine of a swine: Ji-Sun Kim , Hanna Choe , Yu-Ri Lee , Kyung Mo Kim , Doo-Sang Park; J. Microbiol. 2019;57(5):381-387. Published online February 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8631-8

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A strictly anaerobic, Gram-stain-positive, catalase-negative, non-motile, rod-shaped bacterium, designated SG0102T, was isolated from the small intestine of a swine. Optimal growth occurred at 37°C and pH 7.0. Furthermore, growth was observed in the presence of up to 3% (w/v) NaCl but not at salinity levels higher than 4%. The comparative analysis of 16S rRNA gene sequences showed that strain SG0102T was most closely related to Kandleria vitulina DSM 20405T (93.3%), followed by Catenibacterium mitsuokai KCTC 5053T (91.1%), Sharpea azabuensis KCTC 15217T (91.0%), and Eggerthia catenaformis DSM 5348T (89.6%). The average nucleotide identity values between strain SG0102T and related species, K. vitulina DSM 20405T, C. mitsuokai KCTC 5053T, S. azabuensis KCTC 15217T, and E. catenaformis DSM 5348T, were 71.0, 69.3, 70.0, and 69.2%, respectively. The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SG0102T belonged to the family Erysipelotrichaceae in the class Erysipelotrichia. The DNA G+C content of the strain SG0102T was 39.5 mol%. The major cellular fatty acids (> 10%) of strain SG0102T were C16:0, C16:0 dimethyl acetal, and C18:2 ω9/12c. The cell wall peptidoglycan of strain SG0102T contained the meso-diaminopimelic acid. The strain SG0102T produced lactic acid as a major end product of fermentation. These distinct phenotypic and phylogenetic properties suggest that strain SG0102T represents a novel species in a novel genus of the family Erysipelotrichaceae, for which the name Intestinibaculum porci gen. nov. sp. nov. is proposed. The type strain is SG0102T (= KCTC 15725T = NBRC 113396T).

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Growth and differentiation properties of pikromycin-producing Streptomyces venezuelae ATCC15439: Ji-Eun Kim , Joon-Sun Choi , Jung-Hye Roe; J. Microbiol. 2019;57(5):388-395. Published online February 5, 2019; DOI: https://doi.org/10.1007/s12275-019-8539-3

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Streptomycetes naturally produce a variety of secondary metabolites, in the process of physiological differentiation. Streptomyces venezuelae differentiates into spores in liquid media, serving as a good model system for differentiation and a host for exogenous gene expression. Here, we report the growth and differentiation properties of S. venezuelae ATCC- 15439 in liquid medium, which produces pikromycin, along with genome-wide gene expression profile. Comparison of growth properties on two media (SPA, MYM) revealed that the stationary phase cell viability rapidly decreased in SPA. Submerged spores showed partial resistance to lysozyme and heat, similar to what has been observed for better-characterized S. venezuelae ATCC10712, a chloramphenicol producer. TEM revealed that the differentiated cells in the submerged culture showed larger cell size, thinner cell wall than the aerial spores. We analyzed transcriptome profiles of cells grown in liquid MYM at various growth phases. During transition and/or stationary phases, many differentiationrelated genes were well expressed as judged by RNA level, except some genes forming hydrophobic coats in aerial mycelium. Since submerged spores showed thin cell wall and partial resistance to stresses, we examined cellular expression of MreB protein, an actin-like protein known to be required for spore wall synthesis in Streptomycetes. In contrast to aerial spores where MreB was localized in septa and spore cell wall, submerged spores showed no detectable signal. Therefore, even though the mreB transcripts are abundant in liquid medium, its protein level and/or its interaction with spore wall synthetic complex appear impaired, causing thinner- walled and less sturdy spores in liquid culture.

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Biocontrol activity of volatile organic compounds from Streptomyces alboflavus TD-1 against Aspergillus flavus growth and aflatoxin production: Mingguan Yang , Laifeng Lu , Jing Pang , Yiling Hu , Qingbin Guo , Zhenjing Li , Shufen Wu , Huanhuan Liu , Changlu Wang; J. Microbiol. 2019;57(5):396-404. Published online May 6, 2019; DOI: https://doi.org/10.1007/s12275-019-8517-9

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Aspergillus flavus is a saprophytic fungus that contaminates crops with carcinogenic aflatoxin. In the present work, the antifungal effects of volatile organic compounds (VOCs) from Streptomyces alboflavus TD-1 against A. flavus were investigated. VOCs from 8-day-old wheat bran culture of S. alboflavus TD-1 displayed strong inhibitory effects against mycelial growth, sporulation, and conidial germination of A. flavus. Severely misshapen conidia and hyphae of A. flavus were observed by scanning electron microscopy after exposure to VOCs for 6 and 12 h, respectively. Rhodamine 123 staining of mitochondria indicated that mitochondria may be a legitimate antifungal target of the VOCs from S. alboflavus TD-1. Furthermore, the VOCs effectively inhibited aflatoxin B1 production by downregulating genes involved in aflatoxin biosynthesis. Dimethyl trisulfide and benzenamine may play important roles in the suppression of A. flavus growth and production of aflatoxin. The results indicate that VOCs from S. alboflavus TD-1 have tremendous potential to be developed as a useful bio-pesticide for controlling A. flavus.

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Harnessing microbial volatiles to replace pesticides and fertilizers
Gareth Thomas, David Withall, Michael Birkett
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Inhibitory Effects of Eurotium cristatum on Growth and Aflatoxin B1 Biosynthesis in Aspergillus flavus
Qiannan Zhao, Yue Qiu, Xin Wang, Yuanyuan Gu, Yuzhu Zhao, Yidi Wang, Tianli Yue, Yahong Yuan
Frontiers in Microbiology.2020;[Epub] CrossRef
Effect of chlorogenic acid on controlling kiwifruit postharvest decay caused by Diaporthe sp.
Danfeng Zhang, Wanling Bi, Kai Kai, Yingwang Ye, Jia Liu
LWT.2020; 132: 109805. CrossRef
Genome Mining Revealed a High Biosynthetic Potential for Antifungal Streptomyces sp. S-2 Isolated from Black Soot
Piotr Siupka, Artur Piński, Dagmara Babicka, Zofia Piotrowska-Seget
International Journal of Molecular Sciences.2020; 21(7): 2558. CrossRef
Functional Application of Sulfur-Containing Spice Compounds
Jinxin Xie, Benjian Liao, Ri-Yuan Tang
Journal of Agricultural and Food Chemistry.2020; 68(45): 12505. CrossRef
Efficacy of volatile compounds from Streptomyces philanthi RL‐1‐178 as a biofumigant for controlling growth and aflatoxin production of the two aflatoxin‐producing fungi on stored soybean seeds
S. Boukaew, P. Prasertsan
Journal of Applied Microbiology.2020; 129(3): 652. CrossRef
Microenvironmental Interplay Predominated by Beneficial Aspergillus Abates Fungal Pathogen Incidence in Paddy Environment
Xiaoyan Fan, Haruna Matsumoto, Yue Wang, Yang Hu, Yufei Liu, Hongda Fang, Bartosz Nitkiewicz, Sharon Yu Ling Lau, Qiangwei Wang, Hua Fang, Mengcen Wang
Environmental Science & Technology.2019; 53(22): 13042. CrossRef

Expansion of antibacterial spectrum of xanthorrhizol against Gram-negatives in combination with PMBN and food-grade antimicrobials: Man Su Kim , Ha-Rim Kim , Haebom Kim , Soo-Keun Choi , Chang-Hwan Kim , Jae-Kwan Hwang , Seung-Hwan Park; J. Microbiol. 2019;57(5):405-412. Published online February 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8511-2

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Xanthorrhizol (XTZ), isolated from Curcuma xanthorrhiza, has potent antifungal and antibacterial activity. It shows very strong activity against Gram-positive bacteria, such as Streptococcus mutans and Staphylococcus aureus, but is generally not active against Gram-negative bacteria. In this study, we explored the possibility of using a combination strategy for expanding the antimicrobial spectrum of XTZ against Gram-negative bacteria. To take advantage of XTZ being a food-grade material, 10 food-grade or generally recognized as safe (GRAS) antimicrobial compounds with low toxicities were selected for combination therapy. In addition, polymyxin B nonapeptide (PMBN), which is less toxic than polymyxin B, was also selected as an outer membrane permeabilizer. The antibacterial activity of various double or triple combinations with or without XTZ were assayed in vitro against four Gram-negative bacterial species (Escherichia coli, Salmonella enterica serovar Typhi, Salmonella enterica serovar Typhimurium, and Vibrio cholerae), with synergistic combinations exhibiting clear activity subjected to further screening. The combinations with the greatest synergism were XTZ + PMBN + nisin, XTZ + PMBN + carvacrol, and XTZ + PMBN + thymol. These combinations also showed potent antimicrobial activity against Shigella spp., Yersinia enterocolitica, and Acinetobacter baumannii. In time-kill assays, the three combinations achieved complete killing of E. coli within 2 h, and S. Typhi and V. cholera within 15 min. This is the first report on expanding the activity spectrum of XTZ against Gram-negative bacteria through combination with PMBN and food-grade or GRAS substances, with the resulting findings being particularly useful for increasing the industrial and medical applications of XTZ.

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The efficacy of the food-grade antimicrobial xanthorrhizol against Staphylococcus aureus is associated with McsL channel expression
Elena A. Mordukhova, Jongwan Kim, Haiyan Jin, Kyoung Tai No, Jae-Gu Pan
Frontiers in Microbiology.2024;[Epub] CrossRef
Bacillus velezensis HY19 as a sustainable preservative in post-harvest citrus (Citrus reticulata Blanco L.) fruit management
Suping Li, Jingyu Hu, Shiqi Ning, Wei Li, Ru Jiang, Jianguo Huang, Yong Li
Food Control.2024; 155: 110068. CrossRef
Antimicrobial and Antiproliferative Effects of Zingiberaceae Oils: A Natural Solution for Oral Health
Muhammad Amirul Amil, Syarifah Nur Syed Abdul Rahman, Lee Fah Yap, Fathilah Abdul Razak, Marina Mohd Bakri, Lamis S. O. Salem, Xiu Yi Lim, Nur Athirah Reduan, Kae Shin Sim
Chemistry & Biodiversity.2024;[Epub] CrossRef
Synergy between Human Peptide LL-37 and Polymyxin B against Planktonic and Biofilm Cells of Escherichia coli and Pseudomonas aeruginosa
Kylen E. Ridyard, Mariam Elsawy, Destina Mattrasingh, Darien Klein, Janine Strehmel, Carole Beaulieu, Alex Wong, Joerg Overhage
Antibiotics.2023; 12(2): 389. CrossRef
Ethnobotany and the Role of Plant Natural Products in Antibiotic Drug Discovery
Gina Porras, François Chassagne, James T. Lyles, Lewis Marquez, Micah Dettweiler, Akram M. Salam, Tharanga Samarakoon, Sarah Shabih, Darya Raschid Farrokhi, Cassandra L. Quave
Chemical Reviews.2021; 121(6): 3495. CrossRef

Genome analysis of Rubritalea profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean: Jaeho Song , Ilnam Kang , Yochan Joung , Susumu Yoshizawa , Ryo Kaneko , Kenshiro Oshima , Masahira Hattori , Koji Hamasaki , Soochan Kim , Kangseok Lee , Jang-Cheon Cho; J. Microbiol. 2019;57(5):413-422. Published online February 26, 2019; DOI: https://doi.org/10.1007/s12275-019-8712-8

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Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC- 165T, a psychrophilic bacterium of the phylum Verrucomicrobia, was isolated from a depth of 2,000 m in the northwestern Pacific Ocean. In this study, the genome sequence of R. profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, is reported with description of the genome properties and comparison to surface-borne Rubritalea genomes. The draft genome consisted of four contigs with an entire size of 4,167,407 bp and G+C content of 47.5%. The SAORIC-165T genome was predicted to have 3,844 proteincoding genes and 45 non-coding RNA genes. The genome contained a repertoire of metabolic pathways, including the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, assimilatory sulfate reduction, and biosynthesis of nicotinate/nicotinamide, pantothenate/ coenzyme A, folate, and lycopene. The comparative genomic analyses with two surface-derived Rubritalea genomes showed that the SAORIC-165T genome was enriched in genes involved in transposition of mobile elements, signal transduction, and carbohydrate metabolism, some of which might be related to bacterial enhancement of ecological fitness in the deep-sea environment. Amplicon sequencing of 16S rRNA genes from the water column revealed that R. profundi-related phylotypes were relatively abundant at 2,000 m and preferred a particle-associated life style in the deep sea. These findings suggest that R. profundi represents a genetically unique and ecologically relevant verrucomicrobial group well adapted to the deep-sea environment.

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Cultivation of deep-sea bacteria from the Northwest Pacific Ocean and characterization of Limnobacter profundi sp. nov., a phenol-degrading bacterium
Mirae Kim, Jaeho Song, Seung Yeol Shin, Kazuhiro Kogure, Ilnam Kang, Jang-Cheon Cho
Frontiers in Marine Science.2024;[Epub] CrossRef
Profiling Branchial Bacteria of Atlantic Salmon (Salmo salar L.) Following Exposure to Antimicrobial Agents
Joel Slinger, James W. Wynne, Mark B. Adams
Frontiers in Animal Science.2021;[Epub] CrossRef

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