Journal of Microbiology

Journal Articles

Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil: Abhilash Bhattacharjee, Anil Kumar Singh; J. Microbiol. 2024;62(7):511-523. Published online June 21, 2024; DOI: https://doi.org/10.1007/s12275-024-00129-w

127 View
0 Download
1 Web of Science

Abstract: Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing & analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.

The synergy effect of arbuscular mycorrhizal fungi symbiosis and exogenous calcium on bacterial community composition and growth performance of peanut (Arachis hypogaea L.) in saline alkali soil: Dunwei Ci , Zhaohui Tang , Hong Ding , Li Cui , Guanchu Zhang , Shangxia Li , Liangxiang Dai , Feifei Qin , Zhimeng Zhang , Jishun Yang , Yang Xu; J. Microbiol. 2021;59(1):51-63. Published online November 17, 2020; DOI: https://doi.org/10.1007/s12275-021-0317-3

51 View
0 Download
19 Web of Science
19 Crossref

Peanut (Arachis hypogaea. L) is an important oil seed crop. Both arbuscular mycorrhizal fungi (AMF) symbiosis and calcium (Ca2+) application can ameliorate the impact of saline soil on peanut production, and the rhizosphere bacterial communities are also closely correlated with peanut salt tolerance; however, whether AMF and Ca2+ can withstand high-salinity through or partially through modulating rhizosphere bacterial communities is unclear. Here, we used the rhizosphere bacterial DNA from saline alkali soil treated with AMF and Ca2+ alone or together to perform high-throughput sequencing of 16S rRNA genes. Taxonomic analysis revealed that AMF and Ca2+ treatment increased the abundance of Proteobacteria and Firmicutes at the phylum level. The nitrogenfixing bacterium Sphingomonas was the dominant genus in these soils at the genus level, and the soil invertase and urease activities were also increased after AMF and Ca2+ treatment, implying that AMF and Ca2+ effectively improved the living environment of plants under salt stress. Moreover, AMF combined with Ca2+ was better than AMF or Ca2+ alone at altering the bacterial structure and improving peanut growth in saline alkali soil. Together, AMF and Ca2+ applications are conducive to peanut salt adaption by regulating the bacterial community in saline alkali soil.

Citations

Citations to this article as recorded by

Arbuscular mycorrhizal fungi drive bacterial community assembly in halophyte Suaeda salsa
Fengwei Diao, Bingbing Jia, Junqing Luo, Shengli Ding, Tai Liu, Wei Guo
Microbiological Research.2024; 282: 127657. CrossRef
Functional Characterization of Core and Unique Calcite-Dissolving Bacteria Communities from Peanut Fields
Alan Peper, Carter J. Newton, Sheena Lim, Wendy Zheng, Timothy Brenneman, Li Yang
Phytopathology®.2024; 114(5): 1011. CrossRef
Bacterial community composition of Hungarian salt-affected soils under different land uses
Ravi Kumar Gangwar, András Táncsics, Marianna Makádi, Milán Farkas, Mátyás Cserháti, Erika Michéli, Márta Fuchs, Tamás Szegi
Biologia Futura.2024; 75(3): 339. CrossRef
Peanut production in saline-alkali land of Yellow River Delta: influence of spatiotemporal changes of meteorological conditions and soil properties
Feifei Qin, Zhihong Xin, Jianguo Wang, Jialei Zhang, Jishun Yang, Feng Guo, Zhaohui Tang, Dunwei Ci
BMC Plant Biology.2024;[Epub] CrossRef
Multi-year crop rotation and quicklime application promote stable peanut yield and high nutrient-use efficiency by regulating soil nutrient availability and bacterial/fungal community
Liyu Yang, Caibin Wang, Xinhua He, Haiyan Liang, Qi Wu, Xuewu Sun, Miao Liu, Pu Shen
Frontiers in Microbiology.2024;[Epub] CrossRef
Arbuscular Mycorrhizal Fungi Restored the Saline–Alkali Soil and Promoted the Growth of Peanut Roots
Dunwei Ci, Feifei Qin, Zhaohui Tang, Guanchu Zhang, Jialei Zhang, Tong Si, Jishun Yang, Yang Xu, Tianyi Yu, Manlin Xu, Kang He
Plants.2023; 12(19): 3426. CrossRef
Green manure increases peanut production by shaping the rhizosphere bacterial community and regulating soil metabolites under continuous peanut production systems
Yang Xu, Hong Ding, Guanchu Zhang, Zelun Li, Qing Guo, Hao Feng, Feifei Qin, Liangxiang Dai, Zhimeng Zhang
BMC Plant Biology.2023;[Epub] CrossRef
The multifaceted roles of Arbuscular Mycorrhizal Fungi in peanut responses to salt, drought, and cold stress
Yuexu Liu, Jinhao Lu, Li Cui, Zhaohui Tang, Dunwei Ci, Xiaoxia Zou, Xiaojun Zhang, Xiaona Yu, Yuefu Wang, Tong Si
BMC Plant Biology.2023;[Epub] CrossRef
Advances and future research in ecological stoichiometry under saline-alkali stress
Keyi Zhang, Lei Chang, Guanghui Li, Yuefen Li
Environmental Science and Pollution Research.2023; 30(3): 5475. CrossRef
Arbuscular mycorrhizal fungi increased peanut (Arachis hypogaea L.) yield by changing the rhizosphere microbial community structure in saline-alkali soil
Jia Kang, Wenlong Yang, Shangwu Liu, Ning Xuan, Yahui Shao, Yun Geng, Muhammad Afzal, Yingxin Zhang, Shousong Yue, Rubina Mushtaq, Gao Chen
Frontiers in Microbiology.2023;[Epub] 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
Effects of phosphogypsum on enzyme activity and microbial community in acid soil
Changan Li, Yonggang Dong, Yun Yi, Juan Tian, Chao Xuan, Yan Wang, Yuanbo Wen, Jianxin Cao
Scientific Reports.2023;[Epub] CrossRef
Microbial keystone taxa drive crop productivity through shifting aboveground-belowground mineral element flows
Jia Lin Wang, Kai Lou Liu, Xue Qiang Zhao, Gui-Feng Gao, Yong Hong Wu, Ren Fang Shen
Science of The Total Environment.2022; 811: 152342. CrossRef
Peanut and cotton intercropping increases productivity and economic returns through regulating plant nutrient accumulation and soil microbial communities
Wei Xie, Kai Zhang, Xiaoying Wang, Xiaoxia Zou, Xiaojun Zhang, Xiaona Yu, Yuefu Wang, Tong Si
BMC Plant Biology.2022;[Epub] CrossRef
Illumina MiSeq Sequencing Reveals Correlations among Fruit Ingredients, Environmental Factors, and AMF Communities in Three Lycium Barbarum Producing Regions of China
Kaili Chen, Gang Huang, Yuekun Li, Xinrui Zhang, Yonghui Lei, Yang Li, Jie Xiong, Yanfei Sun, Kristen M. DeAngelis
Microbiology Spectrum.2022;[Epub] CrossRef
Genome-Wide Identification of Auxin Response Factors in Peanut (Arachis hypogaea L.) and Functional Analysis in Root Morphology
Lu Luo, Qian Wan, Zipeng Yu, Kun Zhang, Xiurong Zhang, Suqing Zhu, Yongshan Wan, Zhaojun Ding, Fengzhen Liu
International Journal of Molecular Sciences.2022; 23(10): 5309. CrossRef
Impact of an arbuscular mycorrhizal fungal inoculum and exogenous methyl jasmonate on the performance of tall fescue under saline-alkali condition
Hui Liu, Huimin Tang, Xiaozhen Ni, Yajie Zhang, Yingchao Wang
Frontiers in Microbiology.2022;[Epub] CrossRef
The resistance of peanut to soil-borne pathogens improved by rhizosphere probiotics under calcium treatment
Wei Zhang, Bo-wen Zhang, Jie-fu Deng, Lin Li, Tu-yong Yi, Yan-yun Hong
BMC Microbiology.2021;[Epub] CrossRef
Arbuscular mycorrhizal fungi alleviate salinity stress in peanut: Evidence from pot‐grown and field experiments
Wenjie Qin, Hengyu Yan, Bingyin Zou, Runze Guo, Dunwei Ci, Zhaohui Tang, Xiaoxia Zou, Xiaojun Zhang, Xiaona Yu, Yuefu Wang, Tong Si
Food and Energy Security.2021;[Epub] CrossRef

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

Impact of cry1AC-Carrying Brassica rapa subsp. pekinensis on Leaf Bacterial Community: Young Tae Kim , Kang Seon Lee , Moon Jung Kim , Seung Bum Kim; J. Microbiol. 2009;47(1):33-39. Published online February 20, 2009; DOI: https://doi.org/10.1007/s12275-008-0254-4

37 View
0 Download
1 Scopus

Abstract: The effects of Chinese cabbage (Brassica rapa subsp. pekinensis) carrying cry1AC derived from Bacillus thuringiensis (Bt) on leaf bacterial community were examined by analyzing the horizontal transfer of transgene fragments from plants to bacteria. The effect of plant pathogenic bacteria on the gene transfer was also examined using Pseudomonas syringae pathovar. maculicola. The frequency of hygromycin-resistant bacteria did not alter in Bt leaves, though slight increase was observed in Pseudomonas-infected Bt leaves with no statistical significance. The analysis of bacterial community profiles using the denaturing gradient gel electrophoresis (DGGE) fingerprinting indicated that there were slight differences between Bt and control Chinese cabbage, and also that infected tissues were dominated by P. syringae pv. maculicola. However, the cultured bacterial pools were not found to contain any transgene fragments. Thus, no direct evidence of immediate gene transfer from plant to bacteria or acquisition of hygromycin resistance could be observed. Still, long-term monitoring on the possibility of gene transfer is necessary to correctly assess the environmental effects of the Bt crop on bacteria.

pVC, a Small Cryptic Plasmid from the Environmental Isolate of Vibrio cholerae MP-1: Ruifu Zhang , Yanling Wang , Pak Chow Leung , Ji-Dong Gu; J. Microbiol. 2007;45(3):193-198.; DOI: https://doi.org/2543 [pii]

37 View
0 Download

Abstract: A marine bacterium was isolated from Mai Po Nature Reserve of Hong Kong and identified as Vibrio cholerae MP-1. It contains a small plasmid designated as pVC of 3.8 kb. Four open reading frames (ORFs) are identified on the plasmid, but none of them shows homology to any known protein. Database search indicated that a 440 bp fragment is 96% identical to a fragment found in a small plasmid of another V. cholerae. Further experiments demonstrated that a 2.3 kb EcoRI fragment containing the complete ORF1, partial ORF4 and their intergenic region could self-replicate. Additional analyses revealed that sequence upstream of ORF1 showed the features characteristic of theta type replicons. Protein encoded by ORF1 has two characteristic motifs existed in most replication initiator proteins (Rep): the leucine zipper (LZ) motif located at the N-terminal region and the alpha helix-turn-alpha helix motif (HTH) located at the C-terminal end. The results suggest that pVC replicates via the theta type mechanism and is likely a novel type of theta replicon.

Source Environment Feature Related Phylogenetic Distribution Pattern of Anoxygenic Photosynthetic Bacteria as Revealed by pufM Analysis: Yonghui Zeng , Nianzhi Jiao; J. Microbiol. 2007;45(3):205-212.; DOI: https://doi.org/2541 [pii]

38 View
0 Download

Abstract: Anoxygenic photosynthesis, performed primarily by anoxygenic photosynthetic bacteria (APB), has been supposed to arise on Earth more than 3 billion years ago. The long established APB are distributed in almost every corner where light can reach. However, the relationship between APB phylogeny and source environments has been largely unexplored. Here we retrieved the pufM sequences and related source information of 89 pufM containing species from the public database. Phylogenetic analysis revealed that horizontal gene transfer (HGT) most likely occurred within 11 out of a total 21 pufM subgroups, not only among species within the same class but also among species of different phyla or subphyla. A clear source environment feature related phylogenetic distribution pattern was observed, with all species from oxic habitats and those from anoxic habitats clustering into independent subgroups, respectively. HGT among ancient APB and subsequent long term evolution and adaptation to separated niches may have contributed to the coupling of environment and pufM phylogeny.

Review

The Use of the Rare UUA Codon to Define "Expression Space" for Genes Involved in Secondary Metabolism, Development and Environmental Adaptation in Streptomyces: Keith F. Chater , Govind Chandra; J. Microbiol. 2008;46(1):1-11.; DOI: https://doi.org/10.1007/s12275-007-0233-1

36 View
0 Download
118 Scopus

Abstract: In Streptomyces coelicolor, bldA encodes the only tRNA for a rare leucine codon, UUA. This tRNA is unnecessary for growth, but is required for some aspects of secondary metabolism and morphological development, as revealed by the phenotypes of bldA mutants in diverse streptomycetes. This article is a comprehensive review of out understanding of this unusual situation. Based on information from four sequenced genomes it now appears that, typically, about 2~3% of genes in any one streptomycete contain a TTA codon, most having been acquired through species-specific horizontal gene transfer. Among the few widely conserved TTA-containing genes, mutations in just one, the pleiotropic regulatory gene adpA, give an obvious phenotype: such mutants are defective in aerial growth and sporulation, but vary in the extent of their impairment in secondary metabolism in different streptomycetes. The TTA codon in adpA is largely responsible for the morphological phenotype of a bldA mutant of S. coelicolor. AdpA-dependent targets include several genes involved in the integrated action of extracellular proteases that, at least in some species, are involved in the conversion of primary biomass into spores. The effects of bldA mutations on secondary metabolism are mostly attributable to the presence of TTA codons in pathway-specific genes, particularly in transcriptional activator genes. This is not confined to S. coelicolor-it is true for about half of all known antibiotic biosynthetic gene sets from streptomycetes. Combined microarray and proteomic analysis of liquid (and therefore non-sporulating) S. coelicolor bldA mutant cultures revealed effects of the mutation during rapid growth, during transition phase, and in stationary phase. Some of these effects may be secondary consequences of changes in the pattern of ppGpp accumulation. It is argued that the preferential accumulation of the bldA tRNA under conditions in which growth is significantly constrained has evolved to favour the expression of genes that confer adaptive benefits in intermittently encountered sub-optimal environments. The evolution of this system may have been a secondary consequence of the selective pressure exerted by bacteriophage attack. Some biotechnological implications of bldA phenomenology are considered.

First
Prev
Page of 1
Next
Last

Search