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Genes
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Genomics of Microbial Diversity, Evolution and Function
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Genomics of Microbial Diversity, Evolution and Function

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 August 2024) | Viewed by 8762

Special Issue Editor

Dr. Qiang Li

E-Mail Website
Guest Editor
Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
Interests: genomics; genetics; microbial diversity; molecular biology

Special Issue Information

Dear Colleagues,

Microorganisms are found in every corner of the Earth, possessing good ecological adaptability and environmental tolerance. At present, microorganisms are playing an increasingly important role in industries, agriculture, medicine, food, the environment, and other fields. With the rapid development of culturable and non-culturable technologies, humans have been able to gradually recognize the microbial populations we previously overlooked, and have promoted the development and application of new microbial resources. The diverse genetic resources of microorganisms are also constantly being explored and utilized using current genetic and molecular biology technologies. This Special Issue focuses on the use of genomics or genetics to reveal microbial diversity and evolution, and further explore microbial functions and their application potential. Review and research papers focusing on the current challenges, new insights, latest discoveries, latest progress, and future prospects in the field of microbial genomics are all welcome.

Dr. Qiang Li
Guest Editor

Manuscript Submission Information

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Keywords

  • computational genomics
  • genetics
  • bioinformatics
  • gene
  • molecular biology
  • microbial diversity
  • evolution

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Published Papers (5 papers)

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Research

17 pages, 2838 KiB  
Article
Assembly Mechanism of Rhizosphere Fungi in Plant Restoration in Lead Zinc Mining Areas
by Yue Deng, Wenqi Xiao, Zhuang Xiong, Ajia Sha, Yingyong Luo, Xiaodie Chen and Qiang Li
Genes 2024, 15(11), 1398; https://doi.org/10.3390/genes15111398 - 30 Oct 2024
Viewed by 258
Abstract
Background: So far, the assembly and response mechanism of soil fungi in the ecological restoration process of lead zinc mines is still unclear. Methods: In this study, we selected three plants for the ecological restoration of abandoned lead zinc mining areas and explored [...] Read more.
Background: So far, the assembly and response mechanism of soil fungi in the ecological restoration process of lead zinc mines is still unclear. Methods: In this study, we selected three plants for the ecological restoration of abandoned lead zinc mining areas and explored the community assembly mechanism by which soil fungi assist plants in adapting to the environment during the ecological restoration process. Results: The results revealed that the mining of lead zinc mines led to a significant decrease in soil fungal diversity, whereas the planting of three plants significantly increased the diversity of rhizosphere fungi. Mining activities significantly reduced the abundance of soil Fusarium, Macroventuria, Cladosporium, and Solicocozyma and increased the abundance of soil Helvella. After three ecologically restored plants were planted, the abundances of Fusarium and Cladosporium increased significantly, whereas the abundance of Helvella decreased significantly. In addition, Capronia was significantly enriched in the rhizosphere soils of three plant species in the mining area. β diversity and fungal guild analysis revealed that mining activities had a great impact on fungal communities and guilds. The ecological restoration of plants changed the guilds of rhizosphere fungi, making them closer to those of the control sample. In addition, the endophyte guild was significantly enriched in the rhizosphere soil of three ecologically restored plants, increasing their adaptability. Conclusions: The results provide a reference for screening lead zinc mine bioremediation strains and developing fungal plant joint remediation strategies. Full article
(This article belongs to the Special Issue Genomics of Microbial Diversity, Evolution and Function)
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15 pages, 3605 KiB  
Article
Diversity, Distribution and Structural Prediction of the Pathogenic Bacterial Effectors EspN and EspS
by Zhan Li, Yuru Hu, Yuan Song, Deyu Li, Xiaolan Yang, Liangyan Zhang, Tao Li and Hui Wang
Genes 2024, 15(10), 1250; https://doi.org/10.3390/genes15101250 - 26 Sep 2024
Viewed by 654
Abstract
Background: Many Gram-negative enterobacteria translocate virulence proteins (effectors) into intestinal epithelial cells using a type III secretion system (T3SS) to subvert the activity of various cell functions possess. Many T3SS effectors have been extensively characterized, but there are still some effector proteins whose [...] Read more.
Background: Many Gram-negative enterobacteria translocate virulence proteins (effectors) into intestinal epithelial cells using a type III secretion system (T3SS) to subvert the activity of various cell functions possess. Many T3SS effectors have been extensively characterized, but there are still some effector proteins whose functional information is completely unknown. Methods: In this study, two predicted effectors of unknown function, EspN and EspS (Escherichia coli secreted protein N and S), were selected for analysis of translocation, distribution and structure prediction. Results: The TEM1 (β-lactamase) translocation assay was performed, which showed that EspN and EspS are translocated into host cells in a T3SS-dependent manner during bacterial infection. A phylogenetic tree analysis revealed that homologs of EspN and EspS are widely distributed in pathogenic bacteria. Multiple sequence alignment revealed that EspN and its homologs share a conserved C-terminal region (673–1133 a.a.). Furthermore, the structure of EspN (673–1133 a.a.) was also predicted and well-defined, which showed that it has three subdomains connected by a loop region. EspS and its homologs share a sequence-conserved C-terminal (146–291 a.a.). The predicted structure of EspS (146–291 a.a.) is composed of a β-sheet consisting of four β-strands and several short helices, which has a TM score of 0.5014 with the structure of the Vibrio cholerae RTX cysteine protease domain (PDBID: 3eeb). Conclusions: These results suggest that EspN and EspS may represent two important classes of T3SS effectors associated with pathogen virulence, and our findings provide important clues to understanding the potential functions of EspN and EspS. Full article
(This article belongs to the Special Issue Genomics of Microbial Diversity, Evolution and Function)
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24 pages, 6666 KiB  
Article
Impact of Vanadium–Titanium–Magnetite Mining Activities on Endophytic Bacterial Communities and Functions in the Root Systems of Local Plants
by Zhuang Xiong, Yunfeng Zhang, Xiaodie Chen, Ajia Sha, Wenqi Xiao, Yingyong Luo, Lianxin Peng, Liang Zou and Qiang Li
Genes 2024, 15(5), 526; https://doi.org/10.3390/genes15050526 - 23 Apr 2024
Cited by 5 | Viewed by 1042
Abstract
This study utilized 16S rRNA high-throughput sequencing technology to analyze the community structure and function of endophytic bacteria within the roots of three plant species in the vanadium–titanium–magnetite (VTM) mining area. The findings indicated that mining activities of VTM led to a notable [...] Read more.
This study utilized 16S rRNA high-throughput sequencing technology to analyze the community structure and function of endophytic bacteria within the roots of three plant species in the vanadium–titanium–magnetite (VTM) mining area. The findings indicated that mining activities of VTM led to a notable decrease in both the biodiversity and abundance of endophytic bacteria within the root systems of Eleusine indica and Carex (p < 0.05). Significant reductions were observed in the populations of Nocardioides, concurrently with substantial increments in the populations of Pseudomonas (p < 0.05), indicating that Pseudomonas has a strong adaptability to this environmental stress. In addition, β diversity analysis revealed divergence in the endophytic bacterial communities within the roots of E. indica and Carex from the VTM mining area, which had diverged to adapt to the environmental stress caused by mining activity. Functional enrichment analysis revealed that VTM mining led to an increase in polymyxin resistance, nicotinate degradation I, and glucose degradation (oxidative) (p < 0.05). Interestingly, we found that VTM mining did not notably alter the endophytic bacterial communities or functions in the root systems of Dodonaea viscosa, indicating that this plant can adapt well to environmental stress. This study represents the primary investigation into the influence of VTM mining activities on endophytic bacterial communities and the functions of nearby plant roots, providing further insight into the impact of VTM mining activities on the ecological environment. Full article
(This article belongs to the Special Issue Genomics of Microbial Diversity, Evolution and Function)
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12 pages, 4506 KiB  
Article
Diversity, Distribution, and Chromosomal Rearrangements of TRIP1 Repeat Sequences in Escherichia coli
by Zhan Li, Xiong Liu, Nianzhi Ning, Tao Li and Hui Wang
Genes 2024, 15(2), 236; https://doi.org/10.3390/genes15020236 - 13 Feb 2024
Viewed by 4619
Abstract
The bacterial genome contains numerous repeated sequences that greatly affect its genomic plasticity. The Escherichia coli K-12 genome contains three copies of the TRIP1 repeat sequence (TRIP1a, TRIP1b, and TRIP1c). However, the diversity, distribution, and role of the TRIP1 repeat sequence in the [...] Read more.
The bacterial genome contains numerous repeated sequences that greatly affect its genomic plasticity. The Escherichia coli K-12 genome contains three copies of the TRIP1 repeat sequence (TRIP1a, TRIP1b, and TRIP1c). However, the diversity, distribution, and role of the TRIP1 repeat sequence in the E. coli genome are still unclear. In this study, after screening 6725 E. coli genomes, the TRIP1 repeat was found in the majority of E. coli strains (96%: 6454/6725). The copy number and direction of the TRIP1 repeat sequence varied in each genome. Overall, 2449 genomes (36%: 2449/6725) had three copies of TRIP1 (TRIP1a, TRIP1b, and TRIP1c), which is the same as E. coli K-12. Five types of TRIP1 repeats, including two new types (TRIP1d and TRIP1e), are identified in E. coli genomes, located in 4703, 3529, 5741, 1565, and 232 genomes, respectively. Each type of TRIP1 repeat is localized to a specific locus on the chromosome. TRIP1 repeats can cause intra-chromosomal rearrangements. A total of 156 rearrangement events were identified, of which 88% (137/156) were between TRIP1a and TRIP1c. These findings have important implications for future research on TRIP1 repeats. Full article
(This article belongs to the Special Issue Genomics of Microbial Diversity, Evolution and Function)
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14 pages, 4639 KiB  
Article
Exploring the Application Potential of Aquaculture Sewage Treatment of Pseudomonas chengduensis Strain WD211 Based on Its Complete Genome
by Huanlong Peng, Hangtao Wu, Wenjie Gu, Yusheng Lu, Hongjie Qin, Yi You, Donglai Zhou, Dan Wang, Lili Sun, Changmin Zhou and Yanling Zheng
Genes 2023, 14(12), 2107; https://doi.org/10.3390/genes14122107 - 21 Nov 2023
Viewed by 1451
Abstract
Pseudomonas chengduensis is a new species of Pseudomonas discovered in 2014, and currently, there is a scarcity of research on this bacterium. The P. chengduensis strain WD211 was isolated from a fish pond. This study investigated the purification capability and environmental adaptability [...] Read more.
Pseudomonas chengduensis is a new species of Pseudomonas discovered in 2014, and currently, there is a scarcity of research on this bacterium. The P. chengduensis strain WD211 was isolated from a fish pond. This study investigated the purification capability and environmental adaptability of strain WD211 in wastewater and described the basic features and functional genes of its complete genome. According to the results, the sewage treated with strain WD211 showed a decrease in concentration of 18.12% in total nitrogen, 89.39% in NH4+, 62.16% in NO3−, 79.97% in total phosphorus, and 71.41% in COD after 24 h. Strain WD211 is able to survive in a pH range of 6–11. It shows resistance to 7% sodium chloride and different types of antibiotics. Genomic analysis showed that strain WD211 may remove nitrogen and phosphorus through the metabolic pathway of nitrogen assimilation and phosphorus accumulation, and that it can promote organic decomposition through oxygenase. Strain WD211 possesses genes for producing betaine, trehalose, and sodium ion transport, which provide it with salt tolerance. It also has genes for antibiotic efflux and multiple oxidases, which give it antibiotic resistance. This study contributes to the understanding of the sewage treatment ability and potential applications of P. chengduensis. Full article
(This article belongs to the Special Issue Genomics of Microbial Diversity, Evolution and Function)
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