Recent Trends in Bacterial Diversity and Evolution

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Phylogeny and Evolution".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 9772

Special Issue Editor


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Guest Editor
Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México. Ciudad Universitaria, Apdo. Postal 70228, CDMX C. P. 04510, México
Interests: pseudomonas aeruginosa molecular genetics; bacterial evolution; biosurfactants.

Special Issue Information

Dear Colleagues,

The genetic diversity and metabolic versatility of bacteria is immense. These organisms have a central role in geochemical cycles, are crucial for the functioning of all ecosystems, form part of plants and animals’ microbiomes and are causing agents of important infection diseases. All these aspects of bacterial biology are the focus of research and exciting results are arising.  

Bacterial genomes have characteristics not present in other organisms because they are mosaics that contain genes with different phylogenetic origin that are inherited by horizontal gene transfer. Because of this mosaicism, even strains belonging to the same bacterial species share only a fraction of their genomic information, which causes a serious theoretical and operational problem for bacterial taxonomy. Thus, bacterial evolution is a field with an intense theoretical debate which impacts other areas such as synthetic biology and the study of essential genes.

The high frequency of horizontal gene transfer among bacteria is the main cause of the high frequency of antibiotic resistant bacteria causing infection diseases. This problem is so important that it has been postulated that, in a few years, the increase in mortality caused by bacterial infections will reach levels seen in the pre-antibiotic era. Thus, the study of bacterial diversity and evolution has theoretical and practical importance.

The aim of this special issue of Diversity is to provide a platform where researchers working in the different aspects of bacterial diversity and evolution with different approaches and bacterial models, can publish their recent results, which will enable various perspectives of this exciting and challenging field to be shared and discussed.

Dr. Gloria Soberón-Chávez
Guest Editor

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Keywords

  • bacterial genetic diversity
  • bacterial metabolic versatility
  • role of bacteria in geochemical cycles
  • bacterial genomic plasticity
  • theoretical frame of bacterial evolution
  • bacterial taxonomy and ecology
  • bacterial antibiotic resistance.
  • bacterial symbiosis and parasitism
  • horizontal gene transfer and bacterial evolution
  • microbiome

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Published Papers (3 papers)

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Research

19 pages, 4909 KiB  
Article
Genomic Diversity of Bradyrhizobium from the Tree Legumes Inga and Lysiloma (Caesalpinioideae-Mimosoid Clade)
by Diana Hernández-Oaxaca, Karen L. Claro-Mendoza, Marco A. Rogel, Mónica Rosenblueth, Jorge A. Velasco-Trejo, Enrique Alarcón-Gutiérrez, José Antonio García-Pérez, Julio Martínez-Romero, Euan K. James and Esperanza Martínez-Romero
Diversity 2022, 14(7), 518; https://doi.org/10.3390/d14070518 - 27 Jun 2022
Cited by 4 | Viewed by 2928
Abstract
We identified diverse bradyrhizobia having distinct ERIC-PCR genomic fingerprints from native American trees Inga vera and Lysiloma spp. In addition, two nodule isolates recovered from Lysiloma divaricatum seedlings inoculated with soil from the tropical house of a UK botanical garden were also identified [...] Read more.
We identified diverse bradyrhizobia having distinct ERIC-PCR genomic fingerprints from native American trees Inga vera and Lysiloma spp. In addition, two nodule isolates recovered from Lysiloma divaricatum seedlings inoculated with soil from the tropical house of a UK botanical garden were also identified as Bradyrhizobium. Genomes were obtained (with sizes around 9 Mb each) from nine Inga and Lysiloma bradyrhizobial isolates; plasmids were detected in two of the Inga strains analyzed. Average Nucleotide Identity of whole genomes revealed five novel Bradyrhizobium genomospecies from Mexican trees, while the UK isolates were identified as Bradyrhizobium cajani and Bradyrhizobium brasilense. Inga vera and Lysiloma isolates, despite their genetic distances and different hosts, shared a common set of nod genes that suggested that I. vera and Lysiloma bradyrhizobia produce fucosylated, methylated and carbamylated lipochitooligosaccharides. Uptake hydrogenase hup, hyp and secretion system genes were found in some of the isolates. Lysiloma strains were found to be ineffective on I. vera. Some of the isolates may be used as plant inoculants. Full article
(This article belongs to the Special Issue Recent Trends in Bacterial Diversity and Evolution)
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23 pages, 4509 KiB  
Article
Survival and Genome Diversity of Vibrio parahaemolyticus Isolated from Edible Aquatic Animals
by Dingxiang Xu, Xu Peng, Lu Xie and Lanming Chen
Diversity 2022, 14(5), 350; https://doi.org/10.3390/d14050350 - 29 Apr 2022
Cited by 12 | Viewed by 3151
Abstract
Vibrio parahaemolyticus can cause acute gastroenteritis, wound infection, and septicemia in humans. The waterborne bacterium is frequently isolated from aquatic products worldwide. Nevertheless, little information in genome evolution of V. parahaemolyticus isolated from aquatic animals is yet available. Here we overcome this limitation [...] Read more.
Vibrio parahaemolyticus can cause acute gastroenteritis, wound infection, and septicemia in humans. The waterborne bacterium is frequently isolated from aquatic products worldwide. Nevertheless, little information in genome evolution of V. parahaemolyticus isolated from aquatic animals is yet available. Here we overcome this limitation by specifying six V. parahaemolyticus isolates recovered from edible shellfish, fish, and crustacean. Most isolates with multiple resistance phenotypes grew optimally at 3% NaCl and pH 8.5. Draft genome sequences of the six V. parahaemolyticus isolates (4,937,042 bp to 5,067,778 bp) were determined using the Illumina Hiseq × 10 sequencing platform. Comparative genomic analyses revealed 4622 to 4791 predicted protein-encoding genes, of which 1064 to 1107 were of unknown function. Various mobile genetic elements (MGEs) were identified in the V. parahaemolyticus genomes, including genome islands (n = 5 to 9), prophage gene clusters (n = 0 to 2), integrons (n = 1 to 11), and insertion sequences (n = 0 to 3). A number of antibiotic-resistant (n = 17 to 20), virulence-associated (n = 77 to 79), and strain-specific (n = 131 to 287) genes were also identified, indicating possible horizontal gene transfer via the MGEs and considerable genome variation in the V. parahaemolyticus isolates. Altogether, the results of this study fill prior gaps in our knowledge of the genome evolution of V. parahaemolyticus, as isolated from edible aquatic animals. Full article
(This article belongs to the Special Issue Recent Trends in Bacterial Diversity and Evolution)
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18 pages, 1542 KiB  
Article
Tracking the Origins of Pseudomonas aeruginosa Phylogroups by Diversity and Evolutionary Analysis of Important Pathogenic Marker Genes
by Sara E. Quiroz-Morales, Selene García-Reyes, Gabriel Yaxal Ponce-Soto, Luis Servín-González and Gloria Soberón-Chávez
Diversity 2022, 14(5), 345; https://doi.org/10.3390/d14050345 - 28 Apr 2022
Cited by 6 | Viewed by 3079
Abstract
Pseudomonas aeruginosa is a widespread environmental bacterium and an opportunistic pathogen that represents a health hazard due to its production of virulence factors and its high antibiotic resistance. The genome of most of the strains belonging to this bacterial species is highly conserved, [...] Read more.
Pseudomonas aeruginosa is a widespread environmental bacterium and an opportunistic pathogen that represents a health hazard due to its production of virulence factors and its high antibiotic resistance. The genome of most of the strains belonging to this bacterial species is highly conserved, and genes coding for virulence-associated traits are part of the species core-genome. Recently, the existence of phylogroups has been documented based on the analysis of whole genome sequences of hundreds of isolates. These clades contain both clinical and environmental strains, which show no particular geographical distribution. The major phylogroups (clades 1 and 2) are characterized by the nearly mutually exclusive production of the virulence effectors secreted by the type three secretion system (T3SS) ExoS and ExoU, respectively. Clade 3 is the most genetically diverse and shares with clade 5, which is closely related to clades 1 and 2, the production of the pore-forming exolysin A, and the lack of T3SS, among other characteristics. Here we analyze the 4955 P. aeruginosa genomes deposited in the Pseudomonas Genome Database and present some hypotheses on the origins of four of the five phylogroups of this bacterial species. Full article
(This article belongs to the Special Issue Recent Trends in Bacterial Diversity and Evolution)
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