Journal Articles
- Quorum Quenching Potential of Reyranella sp. Isolated from Riverside Soil and Description of Reyranella humidisoli sp. nov.
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Dong Hyeon Lee, Seung Bum Kim
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J. Microbiol. 2024;62(6):449-461. Published online May 30, 2024
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DOI: https://doi.org/10.1007/s12275-024-00131-2
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Abstract
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Quorum quenching refers to any mechanism that inhibits quorum sensing processes.
In this study, quorum quenching activity among bacteria inhabiting riverside soil was screened, and a novel Gram-stain-negative, rod shaped bacterial strain designated MMS21-HV4-11(T), which showed the highest level of quorum quenching activity, was isolated and subjected to further analysis. Strain MMS21-HV4-11(T) could be assigned to the genus Reyranella of Alphaproteobacteria based on the 16S rRNA gene sequence, as the strain shared 98.74% sequence similarity with Reyranella aquatilis seoho-37(T), and then 97.87% and 97.80% sequence similarity with Reyranella soli KIS14-15(T) and Reyranella massiliensis 521(T), respectively. The decomposed N-acyl homoserine lactone was restored at high concentrations under acidic conditions, implying that lactonase and other enzyme(s) are responsible for quorum quenching. The genome analysis indicated that strain MMS21-HV4-11(T) had two candidate genes for lactonase and one for acylase, and expected protein structures were confirmed. In the quorum sensing inhibition assay using a plant pathogen Pectobacterium carotovorum KACC 14888, development of soft rot was significantly inhibited by strain MMS21-HV4-11(T).
Besides, the swarming motility by Pseudomonas aeruginosa PA14 was significantly inhibited in the presence of strain MMS21-HV4-11(T). Since the isolate did not display direct antibacterial activity against either of these species, the inhibition was certainly due to quorum quenching activity. In an extended study with the type strains of all known species of Reyranella, all strains were capable of degrading N-acyl homoserine lactones (AHLs), thus showing quorum quenching potential at the genus level. This is the first study on the quorum quenching potential and enzymes responsible in Reyranella. In addition, MMS21-HV4-11(T) could be recognized as a new species through taxonomic characterization, for which the name Reyranella humidisoli sp. nov. is proposed (type strain = MMS21-HV4-11( T) = KCTC 82780( T) = LMG 32365(T)).
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- Study of N-acyl homoserine lactone (AHL) degradation potential of bacteria isolated from environmental samples and their impact on quorum sensing regulated biofilm formation of Pseudomonas aeruginosa
Anju Tomy, Rakesh Yasarla
Journal of Environmental Chemical Engineering.2025; 13(2): 115974. CrossRef - Research progress of bacterial quorum sensing systems in synthetic biology applications
Boyu Luo, Tuoyu Liu, Zhi Sun, Yue Teng
Chinese Science Bulletin.2024; 69(36): 5213. CrossRef - Validation List no. 220. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2024;[Epub] CrossRef
- Impact of tillage practices on soil bacterial diversity and composition under the tobacco-rice rotation in China
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Yanping Lei , Yongliang Xiao , Lifeng Li , Chaoqiang Jiang , Chaolong Zu , Tian Li , Hui Cao
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J. Microbiol. 2017;55(5):349-356. Published online March 1, 2017
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DOI: https://doi.org/10.1007/s12275-017-6242-9
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Abstract
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Tobacco-rice rotation is a common farming system in south China, and many tillage practices such as straw mulching, do-lomite dust, and quicklime application have been adopted to improve crop production. These agricultural management practices alter soil physical and chemical properties and affect microbial life environment and community composition. In this research, six tillage practices including no tobacco and rice straw mulching (CK), tobacco and rice straw mulching (TrSr), rice straw returning fire (TrSc), tobacco and rice straw mulching with dolomite dust (TSD), rice straw returning fire and quicklime (TSQ), and rice straw returning fire, quicklime and reduced fertilizer (TSQf) were conducted to detect changes in soil bacterial diversity and composition using Illumina se-quencing. The results showed that the total number of opera-tional taxonomic units (OTUs) from the six treatments was 2030, and the number of mutual OTUs among all samples was 550. The TrSc treatment had the highest diversity and richness, while TSQf had the lowest. Soil physio-chemical properties and microbial diversity can influence each other. Proteobacteria and Actinobacteria had the greatest propor-tion in all treatments. The abundance of Nitrospirae was the highest in the TrSc treatment. The TSQf treatment had the highest abundance of Firmicutes. The abundance of Nitrospira in the TrSc treatment was 2.29-fold over CK. Streptomyces affiliated with Firmicutes improved by 37.33% in TSQf com-pared to TSQ. TSQf treatment was considered to be the most important factor in determining the relative abundance at the genus level.
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Songtao Ge, Linzheng Lyu, Guochang Sun, Quanhong Shou, Lingniao Kong, Taoying Wei, Qingzhong Mao, Ruyi Sha, Jianwei Mao, Zhanming Li, Milan Vukic
Journal of Food Processing and Preservation.2024;[Epub] CrossRef - Different rotation years change the structure and diversity of microorganisms in the nitrogen cycle, affecting crop yield
Tingting Ma, Kun Yang, Lei Yang, Yi Zhu, Biqiong Jiang, Zhipeng Xiao, Kaifeng Shuai, Ming Fang, Jia Gong, Zhiming Gu, Penghua Xiang, Yongjun Liu, Juan Li
Applied Soil Ecology.2024; 193: 105123. CrossRef - The impact of combined application of biochar and fertilizer on the biochemical properties of soil in soybean fields
Mingcong Zhang, Wei Xie, Xingjie Zhong, Yuqing Wang, Siyan Li, Yanhong Zhou, Chen Wang
PeerJ.2024; 12: e18172. CrossRef - Legacy effects of preceding crops improve flue-cured tobacco productivity in southwest China by optimizing soil structure, nutrients, and microbial interactions
Ke Ren, Kaiyuan Gu, Wenfeng Song, Jiaen Su, Zhimei Yang, Yi Chen, Binbin Hu, Chenggang He, Longchang C. Wang, Congming M. Zou
Plant and Soil.2024; 504(1-2): 247. CrossRef - Rotation with other crops slow down the fungal process in tobacco-growing soil
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Scientific Reports.2024;[Epub] CrossRef - Microbial community change and quality improve via endophytic colonization of tobacco by Saccharomyces cerevisiae
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Cui Feng, Zhengwei Yi, Wei Qian, Huiying Liu, Xiaosan Jiang, Raffaella Balestrini
PLOS ONE.2023; 18(1): e0270944. CrossRef - Soil bacterial community composition in rice-turtle coculture systems with different planting years
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Applied Soil Ecology.2022; 172: 104362. CrossRef - Eleven-year mulching and tillage practices alter the soil quality and bacterial community composition in Northeast China
Qingjun Cao, Gang Li, Fentuan Yang, Fanli Kong, Zhengguo Cui, Xiaoli Jiang, Yang Lu, Enping Zhang
Archives of Agronomy and Soil Science.2022; 68(9): 1274. CrossRef - Alternation of soil bacterial and fungal communities by tomato–rice rotation in Hainan Island in Southeast of China
Xiang Ma, Minglun Du, Peng Liu, Yanqiong Tang, Hong Li, Qianhua Yuan, Yunze Ruan, Lei Meng, Jiachao Zhang, Min Lin, Zhu Liu
Archives of Microbiology.2021; 203(3): 913. CrossRef -
Effect of organic and conventional farming on soil bacterial diversity of pecan tree (
Carya illinoensis
K. Kosh) orchard across two phenological stages
L.E. Palma‐Cano, H.A. Piñon‐Castillo, S.H. Tarango‐Rivero, A. Carbon, J. Salas‐Leiva, L.N. Muñoz‐Castellanos, C. Cravo‐Laureau, R. Duran, E. Orrantia‐Borunda
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Methuselah Mang'erere Nyamwange, Ezekiel Mugendi Njeru, Monicah Mucheru-Muna
Frontiers in Sustainable Food Systems.2021;[Epub] CrossRef - Effect of straw application time on soil properties and microbial community in the Northeast China Plain
Liwei Wang, Cheng Wang, Fangyuan Feng, Zhengniu Wu, Hongkui Yan
Journal of Soils and Sediments.2021; 21(9): 3137. CrossRef - Exploring the Microbiome Analysis and Visualization Landscape
Jannes Peeters, Olivier Thas, Ziv Shkedy, Leyla Kodalci, Connie Musisi, Olajumoke Evangelina Owokotomo, Aleksandra Dyczko, Ibrahim Hamad, Jaco Vangronsveld, Markus Kleinewietfeld, Sofie Thijs, Jan Aerts
Frontiers in Bioinformatics.2021;[Epub] CrossRef - Soil Bacterial Diversity and Potential Functions Are Regulated by Long-Term Conservation Tillage and Straw Mulching
Chang Liu, Lingling Li, Junhong Xie, Jeffrey A. Coulter, Renzhi Zhang, Zhuzhu Luo, Liqun Cai, Linlin Wang, Subramaniam Gopalakrishnan
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Xiaoqin Yang, Yang Wang, Luying Sun, Xiaoning Qi, Fengbin Song, Xiancan Zhu
Agronomy.2020; 10(10): 1526. CrossRef - Fungal Composition and Diversity of the Tobacco Leaf Phyllosphere During Curing of Leaves
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Yadong Yang, Peixin Wang, Zhaohai Zeng
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Journal of Microbiology.2019; 57(5): 413. CrossRef - Effects of tillage managements and maize straw returning on soil microbiome using 16S rDNA sequencing
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Journal of Integrative Plant Biology.2019; 61(6): 765. CrossRef - Metagenomic insights into effects of wheat straw compost fertiliser application on microbial community composition and function in tobacco rhizosphere soil
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Scientific Reports.2019;[Epub] CrossRef - Soil microbial community and activity are affected by integrated agricultural practices in China
X. C. Zhu, L. Y. Sun, F. B. Song, S. Q. Liu, F. L. Liu, X. N. Li
European Journal of Soil Science.2018; 69(5): 924. CrossRef - Effects of straw return on bacterial communities in a wheat-maize rotation system in the North China Plain
Dali Yu, Zhiguo Wen, Xiumei Li, Xiaojun Song, Huijun Wu, Peilong Yang, Wen-Xiong Lin
PLOS ONE.2018; 13(6): e0198087. CrossRef - Changes in the Microbial Community Structure and Soil Chemical Properties of Vertisols Under Different Cropping Systems in Northern China
Xiuli Song, Bo Tao, Jing Guo, Jingjing Li, Guofeng Chen
Frontiers in Environmental Science.2018;[Epub] CrossRef
Research Support, Non-U.S. Gov'ts
- Effects of blue light on pigment biosynthesis of Monascus
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Di Chen , Chunmao Xue , Mianhua Chen , Shufen Wu , Zhenjing Li , Changlu Wang
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J. Microbiol. 2016;54(4):305-310. Published online April 1, 2016
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DOI: https://doi.org/10.1007/s12275-016-6011-1
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Abstract
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The influence of different illumination levels of blue light
on the growth and intracellular pigment yields of Monascus
strain M9 was investigated. Compared with darkness, constant
exposure to blue light of 100 lux reduced the yields of six
pigments, namely, rubropunctatamine (RUM), monascorubramine
(MOM), rubropunctatin (RUN), monascorubrin
(MON), monascin (MS), and ankaflavin (AK). However,
exposure to varying levels of blue light had different effects
on pigment production. Exposure to 100 lux of blue light
once for 30 min/day and to 100 lux of blue light once and
twice for 15 min/day could enhance RUM, MOM, MS, and
AK production and reduce RUN and MON compared with
non-exposure. Exposure to 100 lux twice for 30 min/day
and to 200 lux once for 45 min/day decreased the RUM,
MOM, MS, and AK yields and increased the RUN and MON.
Meanwhile, the expression levels of pigment biosynthetic
genes were analyzed by real-time quantitative PCR. Results
indicated that gene MpPKS5, mppR1, mppA, mppB, mmpC,
mppD , MpFasA, MpFasB, and mppF were positively correlated
with the yields of RUN and MON, whereas mppE and
mppR2 were associated with RUM, MOM, MS, and AK
production.
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- Effects of blue light on pigment and citrinin production in Monascus ruber M7 via MrcreD, encoding an arrestin-like protein
Xiaodi Wang, Jingyi Wei, Fufang Tang, Fusheng Chen
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Critical Reviews in Food Science and Nutrition.2024; 64(14): 4674. CrossRef -
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Lentinula edodes
Berk. Pegler) Using Blue LED Light and Activated Charcoal. Revealing Eritadenine’s Novel In Vitro Bioherbicidal Activity Against
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Di Chen, Mianhua Chen, Shufen Wu, Zhenjing Li, Hua Yang, Changlu Wang
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- Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica
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Ying-wu Shi , Kai Lou , Chun Li , Lei Wang , Zhen-yong Zhao , Shuai Zhao , Chang-yan Tian
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J. Microbiol. 2015;53(10):678-685. Published online October 2, 2015
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DOI: https://doi.org/10.1007/s12275-015-5080-x
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Abstract
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We used Illumina-based 16S rRNA V3 amplicon pyrosequencing
to investigate the community structure of soil bacteria
from the rhizosphere surrounding Salicornia europaea, and
endophytic bacteria living in Salicornia europaea plants and
Sueada aralocaspica seeds growing at the Fukang Desert
Ecosystem Observation and Experimental Station (FDEOES)
in Xinjiang Province, China, using an Illumina genome analyzer.
A total of 89.23 M effective sequences of the 16S rRNA
gene V3 region were obtained from the two halophyte species.
These sequences revealed a number of operational taxonomic
units (OTUs) in the halophytes. There were between
22–2,206 OTUs in the halophyte plant sample, at the 3%
cutoff level, and a sequencing depth of 30,000 sequences.
We identified 25 different phyla, 39 classes and 141 genera
from the resulting 134,435 sequences. The most dominant
phylum in all the samples was Proteobacteria (41.61%–99.26%;
average, 43.30%). The other large phyla were Firmicutes (0%–
7.19%; average, 1.15%), Bacteroidetes (0%–1.64%; average,
0.44%) and Actinobacteria (0%–0.46%; average, 0.24%). This
result
suggested that the diversity of bacteria is abundant in
the rhizosphere soil, while the diversity of bacteria was poor
within Salicornia europaea plant samples. To the extent of
our knowledge, this study is the first to characterize and
compare the endophytic bacteria found within different halophytic
plant species roots using PCR-based Illumina pyrosequencing
method
.
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- Microbial communities inhabiting oil-contaminated soils from two major oilfields in Northern China: Implications for active petroleum-degrading capacity
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Weimin Sun , Yiran Dong , Pin Gao , Meiyan Fu , Kaiwen Ta , Jiwei Li
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J. Microbiol. 2015;53(6):371-378. Published online May 30, 2015
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DOI: https://doi.org/10.1007/s12275-015-5023-6
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Abstract
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Although oilfields harbor a wide diversity of microorganisms
with various metabolic potentials, our current knowledge
about oil-degrading bacteria is limited because the vast majority
of oil-degrading bacteria remain uncultured. In the
present study, microbial communities in nine oil-contaminated
soils collected from Daqing and Changqing, two of the
largest oil fields in China, were characterized through highthroughput
sequencing of 16S rRNA genes. Bacteria related
to the phyla Proteobacteria and Actinobacteria were dominant
in four and three samples, respectively. At the genus level,
Alkanindiges, Arthrobacter, Pseudomonas, Mycobacterium,
and Rhodococcus were frequently detected in nine soil samples.
Many of the dominant genera were phylogenetically
related to the known oil-degrading species. The correlation
between physiochemical parameters within the microbial
communities was also investigated. Canonical correspondence
analysis revealed that soil moisture, nitrate, TOC, and pH
had an important impact in shaping the microbial communities
of the hydrocarbon-contaminated soil. This study provided
an in-depth analysis of microbial communities in oilcontaminated
soil and useful information for future bioremediation
of oil contamination.
-
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