Journal of Microbiology

Journal Articles

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

Comparative genomics analysis of Pediococcus acidilactici species: Zhenzhen Li , Qi Song , Mingming Wang , Junli Ren , Songling Liu , Shancen Zhao; J. Microbiol. 2021;59(6):573-583. Published online May 15, 2021; DOI: https://doi.org/10.1007/s12275-021-0618-6

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Abstract

Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.

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Pediococcus acidilactici Y01 reduces HFD-induced obesity via altering gut microbiota and metabolomic profiles and modulating adipose tissue macrophage M1/M2 polarization
Yujing Wang, Yu Xue, Huan Xu, Qian Zhu, Kaili Qin, Zhonglei He, Aixiang Huang, Min Mu, Xinrong Tao
Food & Function.2025;[Epub] CrossRef
Draft genome sequence of Pediococcus acidilactici 3G3 isolated from Philippine fermented pork
Zachary B. Lara, Mia Beatriz C. Amoranto, Francisco B. Elegado, Leslie Michelle M. Dalmacio, Marilen Parungao Balolong, Catherine Putonti
Microbiology Resource Announcements.2024;[Epub] CrossRef
The Potential of Pediococcus acidilactici Cell-Free Supernatant as a Preservative in Food Packaging Materials
Katherine Kho, Adinda Darwanti Kadar, Mario Donald Bani, Ihsan Tria Pramanda, Leon Martin, Matthew Chrisdianto, Ferren Pratama, Putu Virgina Partha Devanthi
Foods.2024; 13(5): 644. CrossRef
The complete genome sequences of the two novel probiotics were isolated from the human gut microbiota: Pediococcus acidilactici WNYM01 and Pediococcus acidilactici WNYM02, vitamin B9, and B2-producers
Wagiha S. Elkalla, Yasser M. Ragab, Mohamed A. Ramadan, Nahla M. Mansour
Egyptian Pharmaceutical Journal.2024; 23(4): 702. CrossRef
Effects of Pediococcus acidilactici and Rhizopus Oryzae on protein degradation and flavor formation in fermented mutton sausages
Zihan Li, Wei Su, Yingchun Mu, Qi Qi, Li Jiang
LWT.2024; 213: 117075. CrossRef
Putative Probiotic Ligilactobacillus salivarius Strains Isolated from the Intestines of Meat-Type Pigeon Squabs
Shaoqi Tian, Yinhong Jiang, Qiannan Han, Chuang Meng, Feng Ji, Bin Zhou, Manhong Ye
Probiotics and Antimicrobial Proteins.2024;[Epub] CrossRef
Effect of ginsenoside fermented by Pediococcus acidilactici XM-06 on preventing diarrhea in mice via regulating intestinal barrier function and gut microbiota
Wen-Man Xu, Qi Liu, Si-Yao Fan, Zi-Xin Wang, Shi-Rui Lu, Jie Liu, Hong-Jie Piao, Wenxiu Ji, Wei-Wei Dong
Journal of Functional Foods.2024; 123: 106594. CrossRef
Population and functional genomics of lactic acid bacteria, an important group of food microorganism: Current knowledge, challenges, and perspectives
Weicheng Li, Qiong Wu, Lai‐yu Kwok, Heping Zhang, Renyou Gan, Zhihong Sun
Food Frontiers.2024; 5(1): 3. CrossRef
CRISPR-Cas systems of lactic acid bacteria and applications in food science
Yanhua Cui, Xiaojun Qu
Biotechnology Advances.2024; 71: 108323. CrossRef
Analyzing the genetic diversity and biotechnological potential of Leuconostoc pseudomesenteroides by comparative genomics
Ismail Gumustop, Fatih Ortakci
Frontiers in Microbiology.2023;[Epub] CrossRef
Recent developments in horizontal gene transfer with the adaptive innovation of fermented foods
Ruhong Wang, Junrui Wu, Nan Jiang, Hao Lin, Feiyu An, Chen Wu, Xiqing Yue, Haisu Shi, Rina Wu
Critical Reviews in Food Science and Nutrition.2023; 63(5): 569. CrossRef
Changes in Lacto-Fermented Agaricus bisporus (White and Brown Varieties) Mushroom Characteristics, including Biogenic Amine and Volatile Compound Formation
Elena Bartkiene, Paulina Zarovaite, Vytaute Starkute, Ernestas Mockus, Egle Zokaityte, Gintare Zokaityte, João Miguel Rocha, Romas Ruibys, Dovile Klupsaite
Foods.2023; 12(13): 2441. CrossRef
Lactiplantibacillus paraplantarum BPF2 and Pediococcus acidilactici ST6, Two Bacteriocinogenic Isolated Strains from Andalusian Spontaneous Fermented Sausages
José García-López, Claudia Teso-Pérez, Antonio Martín-Platero, Juan Peralta-Sánchez, Juristo Fonollá-Joya, Manuel Martínez-Bueno, Alberto Baños
Foods.2023; 12(13): 2445. CrossRef
Exploring the impact of initial moisture content on microbial community and flavor generation in Xiaoqu baijiu fermentation
Huan Wang, Chunhong Sun, Shengzhi Yang, Yulei Ruan, Linjie Lyu, Xuewu Guo, Xiaole Wu, Yefu Chen
Food Chemistry: X.2023; 20: 100981. CrossRef
Screening and Constructing a Library of Promoter-5′-UTR Complexes with Gradient Strength in Pediococcus acidilactici
Yize Jia, Chao Huang, Yin Mao, Shenghu Zhou, Yu Deng
ACS Synthetic Biology.2023; 12(6): 1794. CrossRef
Novel pathways in bacteriocin synthesis by lactic acid bacteria with special reference to ethnic fermented foods
Basista Rabina Sharma, Prakash M. Halami, Jyoti Prakash Tamang
Food Science and Biotechnology.2022; 31(1): 1. CrossRef
Genomic analysis and in vivo efficacy of Pediococcus acidilactici as a potential probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections
Hassan M. Al-Emran, Jannatul Ferdouse Moon, Md. Liton Miah, Nigar Sultana Meghla, Rine Christopher Reuben, Mohammad Jashim Uddin, Habiba Ibnat, Shovon Lal Sarkar, Pravas Chandra Roy, M. Shaminur Rahman, A. S. M. Rubayet Ul Alam, Ovinu Kibria Islam, Iqbal
Scientific Reports.2022;[Epub] CrossRef
Production of Antibacterial Agents and Genomic Characteristics of Probiotics Strains for the Foodborne Pathogen Control
Su Jin Kim, Jin Song Shin, Han Sol Park, Ji Seop Song, Ki Won Lee, Woo-Suk Bang, Tae Jin Cho
Current Topic in Lactic Acid Bacteria and Probiotics.2022; 8(1): 1. CrossRef

Effects of mycosubtilin homolog algicides from a marine bacterium, Bacillus sp. SY-1, against the harmful algal bloom species Cochlodinium polykrikoides: Seong-Yun Jeong , Hong-Joo Son; J. Microbiol. 2021;59(4):389-400. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1086-8

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Abstract

The marine bacterium, Bacillus sp. SY-1, produced algicidal compounds that are notably active against the bloom-forming alga Cochlodinium polykrikoides. We isolated three algicidal compounds and identified these as mycosubtilins with molecular weights of 1056, 1070, and 1084 (designated MS 1056, 1070, and 1084, respectively), based on amino acid analyses and 1H, 13C, and two-dimensional nuclear magnetic resonance spectroscopy, including 1H-15N heteronuclear multiple bond correlation analysis. MS 1056 contains a β- amino acid residue with an alkyl side chain of C15, which has not previously been seen in known mycosubtilin families. MS 1056, 1070, and 1084 showed algicidal activities against C. polykrikoides with 6-h LC50 values of 2.3 ± 0.4, 0.8 ± 0.2, and 0.6 ± 0.1 μg/ml, respectively. These compounds also showed significant algicidal activities against other harmful algal bloom species. In contrast, MS 1084 showed no significant growth inhibitory effects against other organisms, including bacteria and microalgae, although does inhibit the growth of some fungi and yeasts. These observations imply that the algicidal bacterium Bacillus sp. SY-1 and its algicidal compounds could play an important role in regulating the onset and development of harmful algal blooms in natural environments.

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Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms
Wonjae Kim, Yerim Park, Jaejoon Jung, Che Ok Jeon, Masanori Toyofuku, Jiyoung Lee, Woojun Park
Journal of Microbiology.2024; 62(3): 249. CrossRef
A Bacillus subtilis strain with efficient algaecide of Microcystis aeruginosa and degradation of microcystins
Yuanyuan Chen, Fei Xiong, Ying Zhu, Dongdong Zhai, Hongyan Liu, Lin Zhang, Ming Xia
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Dinoflagellate–Bacteria Interactions: Physiology, Ecology, and Evolution
Xiaohong Yang, Zijian Liu, Yanwen Zhang, Xinguo Shi, Zhen Wu
Biology.2024; 13(8): 579. CrossRef
Transcriptomics‐guided identification of an algicidal protease of the marine bacterium Kordia algicida OT‐1
Kristy S. Syhapanha, David A. Russo, Yun Deng, Nils Meyer, Remington X. Poulin, Georg Pohnert
MicrobiologyOpen.2023;[Epub] CrossRef
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Environmental Pollution.2023; 330: 121812. CrossRef
Algicidal Potential of the Endosymbiont Bacterial Consortium of the Seagrasses Enhalus acoroides and Thalassia hemprichii
G I Setiabudi, I N D Prasetia, K L Antara, G S br. Sitepu, J M Amelia, M D K Maharani
IOP Conference Series: Earth and Environmental Science.2023; 1224(1): 012039. CrossRef
Algicidal substances of Brevibacillus laterosporus and their effect on red tide organisms
Shanshan Liu, Zhiming Yu, Zaixing Wu, Xihua Cao, Ruihong Cheng, Xiuxian Song
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Algicidal activity of a novel bacterium, Qipengyuania sp. 3-20A1M, against harmful Margalefidinium polykrikoides: Effects of its active compound
So-Ra Ko, Ve Van Le, Ankita Srivastava, Mingyeong Kang, Hee-Mock Oh, Chi-Yong Ahn
Marine Pollution Bulletin.2023; 186: 114397. CrossRef
Review of Harmful Algal Blooms (HABs) Causing Marine Fish Kills: Toxicity and Mitigation
Jae-Wook Oh, Suraj Shiv Charan Pushparaj, Manikandan Muthu, Judy Gopal
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Algicidal Bacteria: A Review of Current Knowledge and Applications to Control Harmful Algal Blooms
Kathryn J. Coyne, Yanfei Wang, Gretchen Johnson
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Fen Liu, Shunni Zhu, Lei Qin, Pingzhong Feng, Jin Xu, Weizheng Zhou, Zhongming Wang
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Review

The functional study of human proteins using humanized yeast: Seho Kim , Juhee Park , Taekyung Kim , Jung-Shin Lee; J. Microbiol. 2020;58(5):343-349. Published online April 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0136-y

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Abstract

The functional and optimal expression of genes is crucial for survival of all living organisms. Numerous experiments and efforts have been performed to reveal the mechanisms required for the functional and optimal expression of human genes. The yeast Saccharomyces cerevisiae has evolved independently of humans for billions of years. Nevertheless, S. cerevisiae has many conserved genes and expression mechanisms that are similar to those in humans. Yeast is the most commonly used model organism for studying the function and expression mechanisms of human genes because it has a relatively simple genome structure, which is easy to manipulate. Many previous studies have focused on understanding the functions and mechanisms of human proteins using orthologous genes and biological systems of yeast. In this review, we mainly introduce two recent studies that replaced human genes and nucleosomes with those of yeast. Here, we suggest that, although yeast is a relatively small eukaryotic cell, its humanization is useful for the direct study of human proteins. In addition, yeast can be used as a model organism in a broader range of studies, including drug screening.

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Erta Zykaj, Chelsea Abboud, Paria Asadi, Simane Warsame, Hashem Almousa, Miroslav P. Milev, Brittany M. Greco, Marcos López-Sánchez, Drago Bratkovic, Aashiq H. Kachroo, Luis Alberto Pérez-Jurado, Michael Sacher
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Humanization reveals pervasive incompatibility of yeast and human kinetochore components
Guðjón Ólafsson, Max A B Haase, Jef D Boeke, G Brown
G3: Genes, Genomes, Genetics.2023;[Epub] CrossRef
Effects of Non-Thermal Plasma on Yeast Saccharomyces cerevisiae
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Research Support, Non-U.S. Gov'ts

Communities of ammonia oxidizers at different stages of Spartina alterniflora invasion in salt marshes of Yangtze River estuary: Fei Xia , Jemaneh Zeleke , Qiang Sheng , Ji-Hua Wu , Zhe-Xue Quan; J. Microbiol. 2015;53(5):311-320. Published online May 3, 2015; DOI: https://doi.org/10.1007/s12275-015-4660-0

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Abstract

Spartina alterniflora, an aggressive invasive plant species at the estuarine wetlands of China’s coasts, has become a major threat to the natural ecosystems. To understand its potential influence on nitrification processes, the community structures and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated using 454-pyrosequencing and quantitative real-time PCR (qPCR) in S. alterniflora invading salt marsh sediments at the Yangtze River estuary in Chongming island, Shanghai, China. Copy numbers of archaeal and bacterial ammonia monooxygenase subunit A (amoA) genes did not show accordant shifts with S. alterniflora invasion in the two sampling sites. However, the copy numbers of archaeal amoA gene were higher in summer than in spring. Phylogenetic analysis indicated that more than 90% of the archaeal and 92% of the bacterial amoA gene sequences were closely related to marine group I.1a and the clusters 13 and 15 in Nitrosospira lineage, respectively. The effect of different seasons (spring and summer) was important for the abundance variation of AOA, while different stages of S. alterniflora invasion did not show significant effect for both AOA and AOB. Variation of AOA community was significantly related to total carbon (TC) and sulfate concentration (P < 0.05), whereas the AOB community was significantly related to sulfate concentration, total nitrogen (TN), TC and pH (P < 0.05). In conclusion, the abundance and diversity of ammonia oxidizing microbial communities were not strongly affected by S. alterniflora invasion.

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Chromolaena odorata affects soil nitrogen transformations and competition in tropical coral islands by altering soil ammonia oxidizing microbes
Chengzhi Yuan, Jia Gao, Luping Huang, Shuguang Jian
Science of The Total Environment.2024; 950: 175196. CrossRef
Grazing disturbance significantly decreased soil organic carbon contents of alpine grasslands on the Tibetan Plateau
Hua Yang, Yonggang Zhang, Wei Li, Qingmin Xu, Huakun Zhou, Yangong Du
Frontiers in Environmental Science.2023;[Epub] CrossRef
Climatic effect from oyster reef restoration in Spartina alterniflora invaded intertidal mudflat: From the perspective of CH4 and N2O production
Wenjing Fu, Xiaoke Pang, Yifan Zhao, Chenglong Han, Yufei Liu, Xue Yu, Jianfeng Feng, Jing Fang, Bo Zhang, Xueqiang Lu
Estuarine, Coastal and Shelf Science.2023; 291: 108437. CrossRef
A comparative study of coastal wetland soil bacterial and fungal colonies following Spartina alterniflora invasion
Zhiyong Zhu, Chengfeng Yu, Min Xu
Ecological Indicators.2023; 156: 111207. CrossRef
Effects of Spartina alterniflora Invasion on Soil Microbial Community Structure and Ecological Functions
Minmin Cao, Lina Cui, Huimin Sun, Xiaomian Zhang, Xiang Zheng, Jiang Jiang
Microorganisms.2021; 9(1): 138. CrossRef
Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary
Fei Xia, Qiu-Yue Jiang, Ting Zhu, Bin Zou, Huan Liu, Zhe-Xue Quan
Science of The Total Environment.2021; 793: 148470. CrossRef
Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants
Dan-Qi Wang, Chen-Hao Zhou, Ming Nie, Ji-Dong Gu, Zhe-Xue Quan
Science of The Total Environment.2021; 768: 144993. CrossRef
Identifying Microbial Distribution Drivers of Archaeal Community in Sediments from a Black-Odorous Urban River—A Case Study of the Zhang River Basin
Chao Shen, Jiaqi Zhao, Guangwu Xie, Yulai Wang, Qiang Chen, Yu Yao
Water.2021; 13(11): 1545. CrossRef
Shifts of soil microbial community composition along a short-term invasion chronosequence of Spartina alterniflora in a Chinese estuary
Guangliang Zhang, Junhong Bai, Jia Jia, Wei Wang, Xin Wang, Qingqing Zhao, Qiongqiong Lu
Science of The Total Environment.2019; 657: 222. CrossRef
Spartina alterniflora invasion alters soil bacterial communities and enhances soil N2O emissions by stimulating soil denitrification in mangrove wetland
Gui-Feng Gao, Peng-Fei Li, Jia-Xin Zhong, Zhi-Jun Shen, Juan Chen, Yun-Tao Li, Alain Isabwe, Xue-Yi Zhu, Qian-Su Ding, Shan Zhang, Chang-Hao Gao, Hai-Lei Zheng
Science of The Total Environment.2019; 653: 231. CrossRef
Distribution of comammox and canonical ammonia‐oxidizing bacteria in tidal flat sediments of the Yangtze River estuary at different depths over four seasons
Q. Jiang, F. Xia, T. Zhu, D. Wang, Z. Quan
Journal of Applied Microbiology.2019; 127(2): 533. CrossRef
Significant alterations in soil fungal communities along a chronosequence of Spartina alterniflora invasion in a Chinese Yellow Sea coastal wetland
Wen Yang, Di Zhang, Xinwen Cai, Lu Xia, Yiqi Luo, Xiaoli Cheng, Shuqing An
Science of The Total Environment.2019; 693: 133548. CrossRef
Different Height Forms of Spartina alterniflora Might Select Their Own Rhizospheric Bacterial Communities in Southern Coast of China
Li’an Lin, Wenwen Liu, Manping Zhang, Xiaolan Lin, Yihui Zhang, Yun Tian
Microbial Ecology.2019; 77(1): 124. CrossRef
Seasonal and vertical variations in the characteristics of the nitrogen-related functional genes in sediments from urban eutrophic lakes
Xingjia Yin, Lijuan Chen, Danqing Tang, Yu Zhang, Guanglong Liu, Yumei Hua, Xiaoqiong Wan, Wenbing Zhou, Jianwei Zhao, Duanwei Zhu
Applied Soil Ecology.2019; 143: 80. CrossRef
Nitrifying activity and ammonia-oxidizing microorganisms in a constructed wetland treating polluted surface water
Bingxin Li, Yuyin Yang, Jianfei Chen, Zhen Wu, Yong Liu, Shuguang Xie
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Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China
Hui He, Yu Zhen, Tiezhu Mi, Lulu Fu, Zhigang Yu
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Temporal and spatial impact of Spartina alterniflora invasion on methanogens community in Chongming Island, China
Xue Ping Chen, Jing Sun, Yi Wang, Heng Yang Zhang, Chi Quan He, Xiao Yan Liu, Nai Shun Bu, Xi-En Long
Journal of Microbiology.2018; 56(7): 507. CrossRef
pH drives ammonia oxidizing bacteria rather than archaea thereby stimulate nitrification under Ageratina adenophora colonization
Haifeng Xiao, Douglas A. Schaefer, Xiaodong Yang
Soil Biology and Biochemistry.2017; 114: 12. CrossRef
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David Rodriguez, Trina M. Guerra, Michael R.J. Forstner, Dittmar Hahn
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Spatial Distribution of Microbial Communities Associated with Dune Landform in the Gurbantunggut Desert, China: Ruyin Liu , Ke Li , Hongxun Zhang , Junge Zhu , DevRaj Joshi; J. Microbiol. 2014;52(11):898-907. Published online October 31, 2014; DOI: https://doi.org/10.1007/s12275-014-4075-3

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Abstract

The microbial community compositions and potential ammonia oxidation in the topsoil at different positions of sand dune (stoss slope, crest, lee slope, and interdune) from the Gurbantunggut Desert, the largest semi-fixed desert in China, were investigated using several molecular methods. Actinobacteria and Proteobacteria (especially Alphaproteobacteria) were commonly the dominant taxa across all soil samples. Bacterial communities were similar in soils collected from the stoss slopes and interdunes (HC-BSCs, biological soil crusts with a high abundance of cyanobacteria), containing more abundant cyanobacterial populations (16.9–24.5%) than those (0.2–0.7% of Cyanobacteria) in the crests and lee slopes (LC-BSCs, biological soil crusts with a low abundance of cyanobacteria). The Cyanobacteria were mainly composed of Microcoleus spp., and quantitative PCR analysis revealed that 16S rRNA gene copy numbers of Cyanobacteria (especially genus Microcoleus) were at least two orders of magnitude higher in HC-BSCs than in LC-BSCs. Heterotrophic Geodermatophilus spp. frequently occurred in HC-BSCs (2.5–8.0%), whereas genera Arthrobacter, Bacillus, and Segetibacter were significantly abundant in LC-BSC communities. By comparison, the desert archaeal communities were less complex, and were dominated by Nitrososphaera spp. The amoA gene abundance of ammonia-oxidizing archaea (AOA) was higher than that of ammonia-oxidizing bacteria (AOB) in all soil samples, particularly in the interdunal soils (106–108 archaeal amoA gene copies per gram dry soil), indicating that AOA possibly dominate the ammonia oxidation at the interdunes.

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Review

Minireview] The History of Aerobic Ammonia Oxidizers: from the First Discoveries to Today: Maria Monteiro , Joana Séneca , Catarina Magalhães; J. Microbiol. 2014;52(7):537-547. Published online June 28, 2014; DOI: https://doi.org/10.1007/s12275-014-4114-0

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Abstract

Nitrification, the oxidation of ammonia to nitrite and nitrate, has long been considered a central biological process in the global nitrogen cycle, with its first description dated 133 years ago. Until 2005, bacteria were considered the only organisms capable of nitrification. However, the recent discovery of a chemoautotrophic ammonia-oxidizing archaeon, Nitrosopumilusmaritimus, changed our concept of the range of organisms involved in nitrification, highlighting the importance of ammonia-oxidizing archaea (AOA) as potential players in global biogeochemical nitrogen transformations. The uniqueness of these archaea justified the creation of a novel archaeal phylum, Thaumarchaeota. These recent discoveries increased the global scientific interest within the microbial ecology society and have triggered an analysis of the importance of bacterial vs archaeal ammonia oxidation in a wide range of natural ecosystems. In thismini review we provide a chronological perspective of the current knowledge on the ammonia oxidation pathway of nitrification, based on the main physiological, ecological and genomic discoveries.

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

Lactobacillus paracasei subsp. paracasei LC01 Positively Modulates Intestinal Microflora in Healthy Young Adults: Hao Zhang , Jing Sun , Xianting Liu , Chuan Hong , Yuanbo Zhu , Aiping Liu , Siqi Li , Huiyuan Guo , Fazheng Ren; J. Microbiol. 2013;51(6):777-782. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3279-2

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Abstract

Lactobacillus paracasei subsp. paracasei LC01 (LC01) can tolerate intestinal stresses and has antioxidant activity. To evaluate the effect of the bacterium on human intestinal microflora, a randomized, double-blind, placebo-controlled human trial was carried out. Fifty-two healthy adult volunteers were randomized equally to two groups. One group consumed 12% (wt/vol) skimmed milk supplemented with 1010 CFU of LC01 each day for the 4-week treatment period, and then consumed placebo in the next treatment period, separated by a 2-week washout. The other group followed the reverse order. Group-specific real-time PCR and biochemical analyses was used to determine the intestinal bacterial composition of fecal samples collected at the end of every period, and the concentration of short-chain fatty acids and ammonia. A significant inhibition in fecal Escherichia coli and increase in Lactobacillus, Bifidobacterium, and Roseburia intestinalis were observed after consumption of LC01. Acetic acid and butyric acid were significantly higher in the probiotic stage and fecal ammonia was significantly lower. The results indicated a modulation effect of LC01 on the intestinal microflora of young adults, suggesting a beneficial effect on bowel health. LC01 may have potential value as a probiotic.

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Seasonal Changes in Nitrogen-Cycle Gene Abundances and in Bacterial Communities in Acidic Forest Soils: Jaejoon Jung , Jinki Yeom , Jiwon Han , Jisun Kim , Woojun Park; J. Microbiol. 2012;50(3):365-373. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1465-2

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Abstract: The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change.

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Abstract: Corynebacterium ammoniagenes N424 was metabolically modified to isolate overproducers of deoxycytidine. Inosine auxotrophy (ino-) was initially introduced to prevent the flow of PRPP (phosphoribosyl pyrophosphate) into the purine biosynthetic pathway by random mutagenesis using N-methyl-N'-nitro-N-nitrosoguanidine. Following that, mutants possessing hydroxyurea resistance (HUr) were isolated to increase the activity of ribonucleoside diphosphate reductase, which catalyzes the reduction of ribonucleoside diphosphate to deoxyribonucleoside diphosphate. Then, in order to block the flow of dCTP into the TMP biosynthetic pathway via dUTP, thymine auxotrophy (thy-) was introduced into the mutant IH30 with ino- and HUr. The resulting mutant IM7, possessing the characteristics of ino-, HUr, and thy-, was deficient in dCTP deaminase and produced significantly higher amounts of deoxycytidine (81.3 mg/L) compared to its mother strain IH30 (6.2 mg/L). Deoxycytidine productivity was further enhanced by isolating the mutant IU19, which was resistant to 5-fluorouracil, an inhibitor of carbamoyl phosphate synthase. This enzyme catalyzed the synthesis of carbamoyl phosphate from glutamine, HCO3 -, and ATP. 5-Fluorouracil also inhibited aspartate transcarbamoylase, catalyzeing the condensation of carbamoyl phosphate and aspartate. Finally, 5-fluorocytosine resistance (FCr) was introduced into the mutant strain IU19 to relieve the repression caused by accumulation of pyrimidine nucleosides. The mutant strain IC14-C6 possessing all the five characteristics described above produced 226.3 mg/L of deoxycytidine, which was at least 2,000 fold higher compared to the wild type, and accumulated only a negligible amount of other pyrimidines under shake flask fermentation.

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