Journal of Microbiology

Journal Articles

Description of Fervidibacillus gen. nov. with Two Species, Fervidibacillus albus sp. nov., and Fervidibacillus halotolerans sp. nov., Isolated from Tidal Flat Sediments and Emendation of Misclassificed Taxa in the Genus Caldibacillus: Sung&# , Mi&# , Hyun&# , Kae Kyoung Kwon; J. Microbiol. 2023;61(2):175-187. Published online February 17, 2023; DOI: https://doi.org/10.1007/s12275-023-00022-y

62 View
0 Download
3 Web of Science
3 Crossref

Two Gram-stain-positive, motile, endospore-forming, facultatively anaerobic strains, designated MEBiC13591T and MEBiC13594T, were isolated from tidal flat sediment of the Incheon City on the west coast of Korea. Growth of both novel strains was observed at pH 5–9 (optimum, pH 7–7.5), and in 0–8% NaCl (optimum, 2% for MEBiC13591T and 3% for MEBiC13594T). Strains MEBiC13591T and MEBiC13594T grew optimally at 50 °C, (37.5–56.1 °C) and 44 °C (20.7–50.7 °C), respectively. The main cellular fatty acids of strain MEBiC13591T were iso-C15: 0, anteiso-C15: 0, iso-C16: 0, iso-C17: 0 and anteiso-C17: 0, while those for strain MEBiC13594T were C14: 0, iso-C14: 0, iso-C15: 0, anteiso-C15: 0 and C16: 0. In both taxa, the major isoprenoid was MK-7. The genomic DNA G + C contents were 34.1 and 37.0 mol% for MEBiC13591T and MEBiC13594T, respectively. A 16S rRNA gene sequence analysis revealed that the novel strains showed high similarity with members of the genera Aeribacillus (95.0%) and Caldibacillus (93.5–94.5%); however, showed lower than 90% with Caldibacillus debilis TfT. Phylogenetic and Phylogenomic analysis revealed that two novel strains comprised distinct phyletic line with members formerly assigned to Caldibacillus. Based on genomic indices, such as AAI and ANI, members formerly affiliated with Caldibacillus and Bacillus as well as the novel strains should be classified into five independent genera. Based on the phenotypic, genomic and biochemical data, strains MEBiC13591T and MEBiC13594T represent two novel species in the novel genus, for which the names Fervidibacillus albus gen. nov., sp. nov. ( MEBiC13591T [= KCCM 43317T = KCTC 43181T = JCM 33662T = MCCC 1K04565T]), and Fervidibacillus halotolerans sp. nov. ( MEBiC13594T [= KCTC 43182T = JCM 34001T]) are proposed. Three additional genera Caldifermentibacillus, Palidibacillus, and Perspicuibacillus are also proposed by reclassification of the several species with valid names that formerly affiliated with the genera Caldibacillus.

Citations

Citations to this article as recorded by

An update on novel taxa and revised taxonomic status of bacteria isolated from domestic companion and agricultural animals described in 2023
Sara D. Lawhon, Claire R. Burbick, Trinity Krueger, Elena Ruiz-Reyes, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.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
Validation List no. 213. 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

Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra: Hye Min Kim , Min Jin Lee , Ji Young Jung , Chung Yeon Hwang , Mincheol Kim , Hee-Myong Ro , Jongsik Chun , Yoo Kyung Lee; J. Microbiol. 2016;54(11):713-723. Published online October 29, 2016; DOI: https://doi.org/10.1007/s12275-016-6294-2

61 View
0 Download
55 Crossref

Abstract

The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.

Citations

Citations to this article as recorded by

Arctic tundra soil depth, more than seasonality, determines active layer bacterial community variation down to the permafrost transition
Casper T. Christiansen, Katja Engel, Michael Hall, Josh D. Neufeld, Virginia K. Walker, Paul Grogan
Soil Biology and Biochemistry.2025; 200: 109624. CrossRef
Lanthanum and cerium added to soil influence microbial carbon and nitrogen cycling genes
Alin Song, Zhiyuan Si, Duanyang Xu, Buqing Wei, Enzhao Wang, Fayao Chong, Fenliang Fan
Journal of Environmental Management.2025; 373: 123509. CrossRef
Comparative genomic analyses of aerobic planctomycetes isolated from the deep sea and the ocean surface
Lise Øvreås, Nicolai Kallscheuer, Rita Calisto, Nicola Bordin, Julia E. Storesund, Christian Jogler, Damien Devos, Olga Lage
Antonie van Leeuwenhoek.2025;[Epub] CrossRef
Responses of soil greenhouse gas emissions to soil mesofauna invasions and its driving mechanisms in the alpine tundra: A microcosm study
Yujuan Kang, Haitao Wu, Qiang Guan, Zhongsheng Zhang
Science of The Total Environment.2024; 908: 168255. CrossRef
Flood risk assessment in arid and semi-arid regions using Multi-criteria approaches and remote sensing in a data-scarce region
Mohamed Adou Sidi Almouctar, Yiping Wu, Shantao An, Xiaowei Yin, Caiqing Qin, Fubo Zhao, Linjing Qiu
Journal of Hydrology: Regional Studies.2024; 54: 101862. CrossRef
The microbiome structure and shifts in surface and subsurface soil horizon of Haplic Luvisol under different crops cultivation
Agata Gryta, Anna Piotrowska-Długosz, Jacek Długosz, Magdalena Frąc
Applied Soil Ecology.2024; 202: 105557. CrossRef
Dynamic responses of soil microbial communities to seasonal freeze-thaw cycles in a temperate agroecosystem
Fangbo Deng, Hongtu Xie, Tiantian Zheng, Yali Yang, Xuelian Bao, Hongbo He, Xudong Zhang, Chao Liang
Science of The Total Environment.2024; 950: 175228. CrossRef
Isolation of biocrust cyanobacteria and evaluation of Cu, Pb, and Zn immobilisation potential for soil restoration and sustainable agriculture
Carlotta Pagli, Sonia Chamizo, Giada Migliore, Lorenza Rugnini, Giovanni De Giudici, Roberto Braglia, Antonella Canini, Yolanda Cantón
Science of The Total Environment.2024; 946: 174020. CrossRef
Impact of floods and landslides on rhizosphere bacterial communities: a high-throughput 16S rRNA gene sequencing study
Haseena Abdulkader, Kulkarni Surendra Gopal, Sandeep Sasidharan
Environmental Science and Pollution Research.2024;[Epub] CrossRef
Microbiome structure variation and soybean’s defense responses during flooding stress and elevated CO2
Lauryn Coffman, Hector D. Mejia, Yelinska Alicea, Raneem Mustafa, Waqar Ahmad, Kerri Crawford, Abdul Latif Khan
Frontiers in Plant Science.2024;[Epub] CrossRef
Comparative analysis of prokaryotic microbiomes in high-altitude active layer soils: insights from Ladakh and global analogues using In-Silico approaches
Ahmad Ali, Tatiana A. Vishnivetskaya, Archana Chauhan
Brazilian Journal of Microbiology.2024; 55(3): 2437. CrossRef
Vertical and temporal variations in activity, abundance, and composition of nitrite-driven anaerobic methanotrophs in a paddy field
Caiyu Geng, Lidong Shen, Bingjie Ren, Hechen Huang, Jinghao Jin, Wangting Yang, Evgenios Agathokleous, Jiaqi Liu, Yuling Yang, Yanan Bai, Yuzhi Song
Applied Soil Ecology.2024; 197: 105342. CrossRef
Vertical fungal community distribution patterns along a stratified soil profile in subalpine Larix principis-rupprechtii plantations on China's Luya mountain
Xiaojun Qi, Xiaoxia Liang, Baofeng Chai, Tong Jia
Fungal Biology.2024; 128(8): 2285. CrossRef
Seasonal variation in near-surface seasonally thawed active layer and permafrost soil microbial communities
Christopher C M Baker, Amanda J Barker, Thomas A Douglas, Stacey J Doherty, Robyn A Barbato
Environmental Research Letters.2023; 18(5): 055001. CrossRef
Bacterial community diversity and underlying assembly patterns along vertical soil profiles in wetland and meadow habitats on the Zoige Plateau, China
Hao-Cai Wang, Jin-Feng Qi, De-Rong Xiao, Yi Wang, Wei-Yu Shi, Hang Wang
Soil Biology and Biochemistry.2023; 184: 109076. CrossRef
Understory ferns promote the restoration of soil microbial diversity and function in previously degraded lands
Yuming Lu, Maokui Lyu, Xiaoling Xiong, Cui Deng, Yongmeng Jiang, Min Zeng, Jinsheng Xie
Science of The Total Environment.2023; 870: 161934. CrossRef
Seasonal dynamics of microbial communities in rhizosphere and bulk soils of two temperate forests
Tianle Xu, Yawen Shen, Zongju Ding, Biao Zhu
Rhizosphere.2023; 25: 100673. CrossRef
Molecular Ecological Network Structure and Potential Function of the Bacterial Community in the Soil Profile under Indigenous Tree Plantations in Subtropical China
Lin Qin, Yufeng Wang, Angang Ming, Shouhong Xi, Zhirou Xiao, Jinqian Teng, Ling Tan
Forests.2023; 14(4): 803. CrossRef
Changes in soil stoichiometry, soil organic carbon mineralization and bacterial community assembly processes across soil profiles
Guozhen Gao, Guilong Li, Ming Liu, Pengfa Li, Jia Liu, Shiyu Ma, Daming Li, Evangelos Petropoulos, Meng Wu, Zhongpei Li
Science of The Total Environment.2023; 903: 166408. CrossRef
The Unusual Dominance of the Yeast Genus Glaciozyma in the Deeper Layer in an Antarctic Permafrost Core (Adélie Cove, Northern Victoria Land) Is Driven by Elemental Composition
Ciro Sannino, Luigimaria Borruso, Ambra Mezzasoma, Benedetta Turchetti, Stefano Ponti, Pietro Buzzini, Tanja Mimmo, Mauro Guglielmin
Journal of Fungi.2023; 9(4): 435. CrossRef
Responses of dissolved organic carbon to freeze–thaw cycles associated with the changes in microbial activity and soil structure
You Jin Kim, Jinhyun Kim, Ji Young Jung
The Cryosphere.2023; 17(7): 3101. CrossRef
The ecological response and distribution characteristics of microorganisms and polycyclic aromatic hydrocarbons in a retired coal gas plant post-thermal remediation site
Zhenhua Zhao, Barry Mody Oury, Liling Xia, Zhirui Qin, Xiangyu Pan, Jichan Qian, Fangzhou Luo, Yong Wu, Luqi Liu, Wei Wang
Science of The Total Environment.2023; 857: 159314. CrossRef
The vertical distribution and control factor of microbial biomass and bacterial community at macroecological scales
Libing He, Xiangyang Sun, Suyan Li, Wenzhi Zhou, Zhe Chen, Xueting Bai
Science of The Total Environment.2023; 869: 161754. CrossRef
Distribution of microbial communities in seasonally frozen soil layers on the Tibetan Plateau and the driving environmental factors
Xiaojie Wang, Zhiqiang Yu, Guofeng Shen, Hefa Cheng, Shu Tao
Environmental Science and Pollution Research.2023; 30(1): 1919. CrossRef
From Surface to Subsurface: Diversity, Composition, and Abundance of Sessile and Endolithic Bacterial, Archaeal, and Eukaryotic Communities in Sand, Clay and Rock Substrates in the Laurentians (Quebec, Canada)
Julia Meyer, Sheri Zakhary, Marie Larocque, Cassandre S. Lazar
Microorganisms.2022; 10(1): 129. CrossRef
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
Temporal Variations Rather than Long-Term Warming Control Extracellular Enzyme Activities and Microbial Community Structures in the High Arctic Soil
Jeongeun Yun, Ji Young Jung, Min Jung Kwon, Juyoung Seo, Sungjin Nam, Yoo Kyung Lee, Hojeong Kang
Microbial Ecology.2022; 84(1): 168. CrossRef
Vertical and temporal variations of soil bacterial and archaeal communities in wheat-soybean rotation agroecosystem
Mika Yokota, Yupeng Guan, Yi Fan, Ximei Zhang, Wei Yang
PeerJ.2022; 10: e12868. CrossRef
Distribution characteristics and factors influencing microbial communities in the core soils of a seawater intrusion area in Longkou City, China
Shilei Sang, Heng Dai, Bill X. Hu, Zhenyu Huang, Yujiao Liu, Lijia Xu
Hydrogeology Journal.2022; 30(6): 1833. CrossRef
Summer thaw duration is a strong predictor of the soil microbiome and its response to permafrost thaw in arctic tundra
Karl J. Romanowicz, George W. Kling
Environmental Microbiology.2022; 24(12): 6220. CrossRef
Microbial communities in the diagnostic horizons of agricultural Isohumosols in northeast China reflect their soil classification
Zhuxiu Liu, Haidong Gu, Qin Yao, Feng Jiao, Junjie Liu, Jian Jin, Xiaobing Liu, Guanghua Wang
CATENA.2022; 216: 106430. CrossRef
Vertical distribution patterns and drivers of soil bacterial communities across the continuous permafrost region of northeastern China
Baihui Ren, Yuanman Hu, Rencang Bu
Ecological Processes.2022;[Epub] CrossRef
Spatial Variation of Microbial Community Structure and Its Driving Environmental Factors in Two Forest Types in Permafrost Region of Greater Xing′an Mountains
Dandan Song, Yuanquan Cui, Dalong Ma, Xin Li, Lin Liu
Sustainability.2022; 14(15): 9284. CrossRef
Differences in microbial diversity and environmental factors in ploughing-treated tobacco soil
Yuzhen Zhang, Guodong Bo, Minchong Shen, Guoming Shen, Jianming Yang, Shanyu Dong, Zhaohe Shu, Zhaobao Wang
Frontiers in Microbiology.2022;[Epub] CrossRef
The relationships of present vegetation, bacteria, and soil properties with soil organic matter characteristics in moist acidic tundra in Alaska
Sungjin Nam, Josu G. Alday, Mincheol Kim, Hyemin Kim, Yongkang Kim, Taesung Park, Hyoun Soo Lim, Bang Yong Lee, Yoo Kyung Lee, Ji Young Jung
Science of The Total Environment.2021; 772: 145386. CrossRef
Characteristics of microbial community composition and its relationship with carbon, nitrogen and sulfur in sediments
Wenfei Liao, Di Tong, Zhongwu Li, Xiaodong Nie, Yaojun Liu, Fengwei Ran, Shanshan Liao
Science of The Total Environment.2021; 795: 148848. CrossRef
Impact of River Channel Lateral Migration on Microbial Communities across a Discontinuous Permafrost Floodplain
Madison M. Douglas, Usha F. Lingappa, Michael P. Lamb, Joel C. Rowland, A. Joshua West, Gen Li, Preston C. Kemeny, Austin J. Chadwick, Anastasia Piliouras, Jon Schwenk, Woodward W. Fischer, Isaac Cann
Applied and Environmental Microbiology.2021;[Epub] CrossRef
Rainfall Alters Permafrost Soil Redox Conditions, but Meta-Omics Show Divergent Microbial Community Responses by Tundra Type in the Arctic
Karl J. Romanowicz, Byron C. Crump, George W. Kling
Soil Systems.2021; 5(1): 17. CrossRef
Soil bacterial communities vary more by season than with over two decades of experimental warming in Arctic tussock tundra
Grace Pold, Joshua P. Schimel, Seeta A. Sistla
Elementa: Science of the Anthropocene.2021;[Epub] CrossRef
Changes in microbial biomass, community composition and diversity, and functioning with soil depth in two alpine ecosystems on the Tibetan plateau
Tianle Xu, Xiao Chen, Yanhui Hou, Biao Zhu
Plant and Soil.2021; 459(1-2): 137. CrossRef
Nanoscale zerovalent iron, carbon nanotubes and biochar facilitated the phytoremediation of cadmium contaminated sediments by changing cadmium fractions, sediments properties and bacterial community structure
Xiaomin Gong, Danlian Huang, Yunguo Liu, Dongsheng Zou, Xi Hu, Lu Zhou, Zhibin Wu, Yang Yang, Zhihua Xiao
Ecotoxicology and Environmental Safety.2021; 208: 111510. CrossRef
Abiotic factors affecting the bacterial and fungal diversity of permafrost in a rock glacier in the Stelvio Pass (Italian Central Alps)
Ciro Sannino, Luigimaria Borruso, Ambra Mezzasoma, Dario Battistel, Stefano Ponti, Benedetta Turchetti, Pietro Buzzini, Mauro Guglielmin
Applied Soil Ecology.2021; 166: 104079. CrossRef
Organic Carbon Mineralization and Bacterial Community of Active Layer Soils Response to Short-Term Warming in the Great Hing’an Mountains of Northeast China
Xingfeng Dong, Chao Liu, Dalong Ma, Yufei Wu, Haoran Man, Xiangwen Wu, Miao Li, Shuying Zang
Frontiers in Microbiology.2021;[Epub] CrossRef
The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa (United States)
Jingjie Hao, Yen Ning Chai, Lucas Dantas Lopes, Raziel A. Ordóñez, Emily E. Wright, Sotirios Archontoulis, Daniel P. Schachtman, Jeremy D. Semrau
Applied and Environmental Microbiology.2021;[Epub] CrossRef
Microbial community structure in the river sediments from upstream of Guanting Reservoir: Potential impacts of reclaimed water recharge
En Xie, Xiaohui Zhao, Kun Li, Panwei Zhang, Xiuhua Zhou, Xiao Zhao
Science of The Total Environment.2021; 766: 142609. CrossRef
Substrate quality and not dominant plant community determines the vertical distribution and C assimilation of enchytraeids in peatlands
María Jesús Iglesias Briones, Noela Carrera, Jinhua Huang, Maria Esther Barreal, Rüdiger Maria Schmelz, Mark H. Garnett, Hefin Jones
Functional Ecology.2020; 34(6): 1280. CrossRef
Spatial Distribution of Toxic Metal(loid)s and Microbial Community Analysis in Soil Vertical Profile at an Abandoned Nonferrous Metal Smelting Site
Jiejie Yang, Siqi Wang, Ziwen Guo, Yan Deng, Menglong Xu, Siyuan Zhang, Huaqun Yin, Yili Liang, Hongwei Liu, Bo Miao, Delong Meng, Xueduan Liu, Luhua Jiang
International Journal of Environmental Research and Public Health.2020; 17(19): 7101. CrossRef
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
Journal of Microbiology.2019; 57(5): 325. CrossRef
Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores
Binu Mani Tripathi, Mincheol Kim, Yongwon Kim, Eunji Byun, Ji-Woong Yang, Jinho Ahn, Yoo Kyung Lee
Scientific Reports.2018;[Epub] CrossRef
Microbial diversity and biogeography in Arctic soils
Lucie A. Malard, David A. Pearce
Environmental Microbiology Reports.2018; 10(6): 611. CrossRef
Development of Shallow-Depth Soil Temperature Estimation Model Based on Thermal Response in Permafrost Area
Keunbo Park, Heekwon Yang, Bang Yong Lee, Dongwook Kim
Applied Sciences.2018; 8(10): 1886. CrossRef
Vertical profiles of microbial communities in perfluoroalkyl substance-contaminated soils
Yixiang Bao, Bingxin Li, Shuguang Xie, Jun Huang
Annals of Microbiology.2018; 68(6): 399. CrossRef
On the maverick Planctomycetes
Sandra Wiegand, Mareike Jogler, Christian Jogler
FEMS Microbiology Reviews.2018; 42(6): 739. CrossRef
Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates
Oliver Müller, Toke Bang‐Andreasen, Richard Allen White, Bo Elberling, Neslihan Taş, Timothy Kneafsey, Janet K. Jansson, Lise Øvreås
Environmental Microbiology.2018; 20(12): 4328. CrossRef
Soil Phospholipid Fatty Acid Biomarkers and β‐Glucosidase Activities after Long‐Term Manure and Fertilizer N Applications
Newton Z. Lupwayi, Derrick A. Kanashiro, Andrea H. Eastman, Xiying Hao
Soil Science Society of America Journal.2018; 82(2): 343. CrossRef

Research Support, Non-U.S. Gov't

Cupriavidus and Burkholderia Species Associated with Agricultural Plants that Grow in Alkaline Soils: Paulina Estrada-de los Santos , Nora Belinda Vacaseydel-Aceves , Lourdes Martínez-Aguilar , María Antonia Cruz-Hernández , Alberto Mendoza-Herrera , Jesús Caballero-Mellado; J. Microbiol. 2011;49(6):867-876. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1127-9

37 View
0 Download
29 Scopus

Abstract: The presence of Burkholderia, Cupriavidus, and Ralstonia species in northeastern Mexico was investigated. An analysis of the root surrounding soil from different agricultural plants led to the isolation of Burkholderia and Cupriavidus species but no Ralstonia strains. Most Cupriavidus species were unknown and grouped into two clusters according to ARDRA profiles. The 16S rRNA sequence analysis showed that the Cupriavidus isolates were highly related among them and with different Cupriavidus species with validated names. However, SDS-PAGE profiles were distinct among the different ARDRA profiles and to other Cupriavidus species examined, suggesting new species in the genus. This shows that Cupriavidus is more widely associated with plants than previously appreciated. The BCC isolate was 99% similar to B. cenocepacia by recA sequence analysis. Additionally, most Cupriavidus strains from the two largest groups grew on media containing up to 0.1 mg/ml of copper, 10.0 mg/ml arsenic and 1.0 mg/ml zinc. Burkholderia strains grew on media containing up to 10.0 mg/ml zinc, 5.0 mg/ml arsenic and 0.1 mg/ml copper.

First
Prev
Page of 1
Next
Last

Search