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Microorganisms
Special Issues
Microbial Genetics and Evolution
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Microbial Genetics and Evolution

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 31037

Special Issue Editors

Prof. Dr. Renato Fani

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Guest Editor
Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
Interests: antibiotic resistance; bacterial genetics; endophytes; environmental microbiology; gene and genome evolution; molecular evolution
Special Issues, Collections and Topics in MDPI journals
Dr. Alessio Mengoni

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Guest Editor
Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
Interests: rhizospheric and endophytic microbiomes; microbial evolution; bacterial genetics and ecology
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Dr. Sara Del Duca

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Guest Editor
Department of Biology, University of Florence, 50019 Sesto Fiorentino, Florence, Italy
Interests: microbial genetics; gene evolution; histidine biosynthesis; bacterial communities
Special Issues, Collections and Topics in MDPI journals
Dr. Alberto Vassallo

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Guest Editor
Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
Interests: secondary metabolite production improvement; biotech applications; food safety; Streptomyces
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microorganisms have been thriving on Earth for billions of years and their environments have undergone fundamental changes over this time: thus, they have evolved extraordinary capacities to adapt to environmental and evolutionary challenges. Clues as to how they started and traveled along this evolutionary road are conserved in their genomes; the current structure and organization of genes and genomes have been increasingly characterized thanks to modern and efficient molecular techniques, making possible a better understanding of the mechanisms at the basis of their evolution, expansion, and shaping. From the appearance of complex networks of biochemical reactions and cell physiological processes to the emergence of new antibiotic resistances, from the coevolution with hosts and reciprocal adaptation to the development of complex mechanisms of gene expression, and from the methylation of genomes to the discovery of novel genetic engineering tools, microorganisms are extraordinary models to study evolution in action and its genetic basis. The diversity observed in the microbial world allows the comprehension of the processes behind genetic diversity; viruses, bacteria, archaea, and yeasts are the subjects of laboratory studies and in silico analyses, aiming to investigate the evolution of their genomes and the link between genotypes and phenotypes.

This Special Issue of Microorganisms aims to expand the current state of the art regarding microbial genetics and evolution. Research, review, and opinion articles concerning the current challenges of evolutionary-oriented microbial genetics fit the topic of this Special Issue perfectly.

Prof. Dr. Renato Fani
Prof. Dr. Alessio Mengoni
Dr. Sara Del Duca
Dr. Alberto Vassallo
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cellular adaptation
  • genome evolution
  • molecular mechanisms
  • genetic engineering
  • directed-evolution experiments
  • bioinformatics

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Published Papers (9 papers)

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Editorial

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3 pages, 196 KiB  
Editorial
Microbial Genetics and Evolution
by Sara Del Duca, Alberto Vassallo, Alessio Mengoni and Renato Fani
Microorganisms 2022, 10(7), 1274; https://doi.org/10.3390/microorganisms10071274 - 23 Jun 2022
Cited by 2 | Viewed by 2889
Abstract
Although proto-evolutionary ideas date back to the time of the ancient Greeks, the idea that organisms evolve was not considered a basic element of scientific knowledge until Charles Darwin published his “On the Origin of Species” in 1859 [...] Full article
(This article belongs to the Special Issue Microbial Genetics and Evolution)

Research

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19 pages, 2593 KiB  
Article
Effect of Non-Lethal Selection on Spontaneous Revertants of Frameshift Mutations: The Escherichia coli hisF Case
by Sara Del Duca, Anna Maria Puglia, Vito Calderone, Marco Bazzicalupo and Renato Fani
Microorganisms 2022, 10(4), 692; https://doi.org/10.3390/microorganisms10040692 - 23 Mar 2022
Cited by 4 | Viewed by 2505
Abstract
Microorganisms possess the potential to adapt to fluctuations in environmental parameters, and their evolution is driven by the continuous generation of mutations. The reversion of auxotrophic mutations has been widely studied; however, little is known about the reversion of frameshift mutations resulting in [...] Read more.
Microorganisms possess the potential to adapt to fluctuations in environmental parameters, and their evolution is driven by the continuous generation of mutations. The reversion of auxotrophic mutations has been widely studied; however, little is known about the reversion of frameshift mutations resulting in amino acid auxotrophy and on the structure and functioning of the protein encoded by the revertant mutated gene. The aims of this work were to analyze the appearance of reverse mutations over time and under different selective pressures and to investigate revertant enzymes’ three-dimensional structures and their correlation with a different growth ability. Escherichia coli FB182 strain, carrying the hisF892 single nucleotide deletion resulting in histidine auxotrophy, was subjected to different selective pressures, and revertant mutants were isolated and characterized. The obtained results allowed us to identify different indels of different lengths located in different positions in the hisF gene, and relations with the incubation time and the selective pressure applied were observed. Moreover, the structure of the different mutant proteins was consistent with the respective revertant ability to grow in absence of histidine, highlighting a correlation between the mutations and the catalytic activity of the mutated HisF enzyme. Full article
(This article belongs to the Special Issue Microbial Genetics and Evolution)
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20 pages, 3367 KiB  
Article
Organelle Engineering in Yeast: Enhanced Production of Protopanaxadiol through Manipulation of Peroxisome Proliferation in Saccharomyces cerevisiae
by Bo Hyun Choi, Hyun Joon Kang, Sun Chang Kim and Pyung Cheon Lee
Microorganisms 2022, 10(3), 650; https://doi.org/10.3390/microorganisms10030650 - 18 Mar 2022
Cited by 22 | Viewed by 3853
Abstract
Isoprenoids, which are natural compounds with diverse structures, possess several biological activities that are beneficial to humans. A major consideration in isoprenoid production in microbial hosts is that the accumulation of biosynthesized isoprenoid within intracellular membranes may impede balanced cell growth, which may [...] Read more.
Isoprenoids, which are natural compounds with diverse structures, possess several biological activities that are beneficial to humans. A major consideration in isoprenoid production in microbial hosts is that the accumulation of biosynthesized isoprenoid within intracellular membranes may impede balanced cell growth, which may consequently reduce the desired yield of the target isoprenoid. As a strategy to overcome this suggested limitation, we selected peroxisome membranes as depots for the additional storage of biosynthesized isoprenoids to facilitate increased isoprenoid production in Saccharomyces cerevisiae. To maximize the peroxisome membrane storage capacity of S.cerevisiae, the copy number and size of peroxisomes were increased through genetic engineering of the expression of three peroxisome biogenesis-related peroxins (Pex11p, Pex34p, and Atg36p). The genetically enlarged and high copied peroxisomes in S.cerevisiae were stably maintained under a bioreactor fermentation condition. The peroxisome-engineered S.cerevisiae strains were then utilized as host strains for metabolic engineering of heterologous protopanaxadiol pathway. The yields of protopanaxadiol from the engineered peroxisome strains were ca 78% higher than those of the parent strain, which strongly supports the rationale for harnessing the storage capacity of the peroxisome membrane to accommodate the biosynthesized compounds. Consequently, this study presents in-depth knowledge on peroxisome biogenesis engineering in S.cerevisiae and could serve as basic information for improvement in ginsenosides production and as a potential platform to be utilized for other isoprenoids. Full article
(This article belongs to the Special Issue Microbial Genetics and Evolution)
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16 pages, 2370 KiB  
Article
The Azurin Coding Gene: Origin and Phylogenetic Distribution
by Leandro Gammuto, Carolina Chiellini, Marta Iozzo, Renato Fani and Giulio Petroni
Microorganisms 2022, 10(1), 9; https://doi.org/10.3390/microorganisms10010009 - 22 Dec 2021
Cited by 5 | Viewed by 2844
Abstract
Azurin is a bacterial-derived cupredoxin, which is mainly involved in electron transport reactions. Interest in azurin protein has risen in recent years due to its anticancer activity and its possible applications in anticancer therapies. Nevertheless, the attention of the scientific community only focused [...] Read more.
Azurin is a bacterial-derived cupredoxin, which is mainly involved in electron transport reactions. Interest in azurin protein has risen in recent years due to its anticancer activity and its possible applications in anticancer therapies. Nevertheless, the attention of the scientific community only focused on the azurin protein found in Pseudomonas aeruginosa (Proteobacteria, Gammaproteobacteria). In this work, we performed the first comprehensive screening of all the bacterial genomes available in online repositories to assess azurin distribution in the three domains of life. The Azurin coding gene was not detected in the domains Archaea and Eucarya, whereas it was detected in phyla other than Proteobacteria, such as Bacteroidetes, Verrucomicrobia and Chloroflexi, and a phylogenetic analysis of the retrieved sequences was performed. Observed patchy distribution and phylogenetic data suggest that once it appeared in the bacterial domain, the azurin coding gene was lost in several bacterial phyla and/or anciently horizontally transferred between different phyla, even though a vertical inheritance appeared to be the major force driving the transmission of this gene. Interestingly, a shared conserved domain has been found among azurin members of all the investigated phyla. This domain is already known in P. aeruginosa as p28 domain and its importance for azurin anticancer activity has been widely explored. These findings may open a new and intriguing perspective in deciphering the azurin anticancer mechanisms and to develop new tools for treating cancer diseases. Full article
(This article belongs to the Special Issue Microbial Genetics and Evolution)
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8 pages, 1904 KiB  
Communication
Codh/Acs-Deficient Methanogens Are Prevalent in Anaerobic Digesters
by Misa Nagoya, Atsushi Kouzuma and Kazuya Watanabe
Microorganisms 2021, 9(11), 2248; https://doi.org/10.3390/microorganisms9112248 - 28 Oct 2021
Cited by 6 | Viewed by 2457
Abstract
Methanogens are archaea that grow by producing methane as a catabolic end product and thrive in diverse anaerobic habitats, including soil, sediments, oil reservoirs, digestive tracts, and anaerobic digesters. Methanogens have typically been classified into three types—namely, hydrogenotrophic, acetoclastic, and methylotrophic methanogens. In [...] Read more.
Methanogens are archaea that grow by producing methane as a catabolic end product and thrive in diverse anaerobic habitats, including soil, sediments, oil reservoirs, digestive tracts, and anaerobic digesters. Methanogens have typically been classified into three types—namely, hydrogenotrophic, acetoclastic, and methylotrophic methanogens. In addition, studies have found methanogens that require both hydrogen/CO2 and organics, such as acetate, for growth. Genomic analyses have shown that these methanogens lack genes for carbon monoxide dehydrogenase/acetyl-CoA synthase (Codh/Acs), one of the oldest enzymes that catalyzes the central step in the Wood–Ljungdahl pathway. Since these methanogens have been found dominant in such habitats as digestive tracts and anaerobic digesters, it is suggested that the loss of Codh/Acs confers ecological advantages on methanogens in these habitats. Comparisons in genomes of methanogens suggest the possibility that these methanogens have emerged recently in anaerobic digesters and are currently under the process of prevalence. We propose that an understanding of the genetic and ecological processes associated with the emergence and prevalence of these methanogens in anaerobic digesters would offer novel evolutionary insights into microbial ecology. Full article
(This article belongs to the Special Issue Microbial Genetics and Evolution)
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22 pages, 27077 KiB  
Article
Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing
by Valerio Vitali, Rebecca Rothering and Francesco Catania
Microorganisms 2021, 9(9), 1979; https://doi.org/10.3390/microorganisms9091979 - 17 Sep 2021
Cited by 5 | Viewed by 2853
Abstract
Amitosis is a widespread form of unbalanced nuclear division whose biomedical and evolutionary significance remain unclear. Traditionally, insights into the genetics of amitosis have been gleaned by assessing the rate of phenotypic assortment. Though powerful, this experimental approach relies on the availability of [...] Read more.
Amitosis is a widespread form of unbalanced nuclear division whose biomedical and evolutionary significance remain unclear. Traditionally, insights into the genetics of amitosis have been gleaned by assessing the rate of phenotypic assortment. Though powerful, this experimental approach relies on the availability of phenotypic markers. Leveraging Paramecium tetraurelia, a unicellular eukaryote with nuclear dualism and a highly polyploid somatic nucleus, we probe the limits of single-cell whole-genome sequencing to study the consequences of amitosis. To this end, we first evaluate the suitability of single-cell sequencing to study the AT-rich genome of P. tetraurelia, focusing on common sources of genome representation bias. We then asked: can alternative rearrangements of a given locus eventually assort after a number of amitotic divisions? To address this question, we track somatic assortment of developmentally acquired Internal Eliminated Sequences (IESs) up to 50 amitotic divisions post self-fertilization. To further strengthen our observations, we contrast empirical estimates of IES retention levels with in silico predictions obtained through mathematical modeling. In agreement with theoretical expectations, our empirical findings are consistent with a mild increase in variation of IES retention levels across successive amitotic divisions of the macronucleus. The modest levels of somatic assortment in P. tetraurelia suggest that IESs retention levels are largely sculpted at the time of macronuclear development, and remain fairly stable during vegetative growth. In forgoing the requirement for phenotypic assortment, our approach can be applied to a wide variety of amitotic species and could facilitate the identification of environmental and genetic factors affecting amitosis. Full article
(This article belongs to the Special Issue Microbial Genetics and Evolution)
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17 pages, 1862 KiB  
Article
The Histidine Biosynthetic Genes in the Superphylum Bacteroidota-Rhodothermota-Balneolota-Chlorobiota: Insights into the Evolution of Gene Structure and Organization
by Sara Del Duca, Christopher Riccardi, Alberto Vassallo, Giulia Fontana, Lara Mitia Castronovo, Sofia Chioccioli and Renato Fani
Microorganisms 2021, 9(7), 1439; https://doi.org/10.3390/microorganisms9071439 - 3 Jul 2021
Cited by 5 | Viewed by 3451
Abstract
One of the most studied metabolic routes is the biosynthesis of histidine, especially in enterobacteria where a single compact operon composed of eight adjacent genes encodes the complete set of biosynthetic enzymes. It is still not clear how his genes were organized in [...] Read more.
One of the most studied metabolic routes is the biosynthesis of histidine, especially in enterobacteria where a single compact operon composed of eight adjacent genes encodes the complete set of biosynthetic enzymes. It is still not clear how his genes were organized in the genome of the last universal common ancestor community. The aim of this work was to analyze the structure, organization, phylogenetic distribution, and degree of horizontal gene transfer (HGT) of his genes in the Bacteroidota-Rhodothermota-Balneolota-Chlorobiota superphylum, a group of phylogenetically close bacteria with different surviving strategies. The analysis of the large variety of his gene structures and organizations revealed different scenarios with genes organized in more or less compact—heterogeneous or homogeneous—operons, in suboperons, or in regulons. The organization of his genes in the extant members of the superphylum suggests that in the common ancestor of this group, genes were scattered throughout the chromosome and that different forces have driven the assembly of his genes in compact operons. Gene fusion events and/or paralog formation, HGT of single genes or entire operons between strains of the same or different taxonomic groups, and other molecular rearrangements shaped the his gene structure in this superphylum. Full article
(This article belongs to the Special Issue Microbial Genetics and Evolution)
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22 pages, 4529 KiB  
Article
Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter
by Irene Artuso, Paolo Turrini, Mattia Pirolo, Gabriele Andrea Lugli, Marco Ventura and Paolo Visca
Microorganisms 2021, 9(6), 1332; https://doi.org/10.3390/microorganisms9061332 - 19 Jun 2021
Cited by 10 | Viewed by 3623
Abstract
Bacteria belonging to the genus Aminobacter are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of A. anthyllidis LMG 26462T and [...] Read more.
Bacteria belonging to the genus Aminobacter are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of A. anthyllidis LMG 26462T and the presence of unclassified Aminobacter strains. Here, we determined the genome sequence of A. anthyllidis LMG 26462T and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus Aminobacter. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified Aminobacter strains belong to valid Aminobacter species or are putative new species. Since some members of the genus Aminobacter can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all Aminobacter species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all Aminobacter species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only A. anthyllidis LMG 26462T contains a symbiosis island implicated in nodulation and nitrogen fixation. Full article
(This article belongs to the Special Issue Microbial Genetics and Evolution)
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17 pages, 2047 KiB  
Article
Characterization and Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Pandemic and Non-Pandemic Vibrio parahaemolyticus Isolates from Seafood Sources
by Nawaporn Jingjit, Sutima Preeprem, Komwit Surachat and Pimonsri Mittraparp-arthorn
Microorganisms 2021, 9(6), 1220; https://doi.org/10.3390/microorganisms9061220 - 4 Jun 2021
Cited by 10 | Viewed by 3094
Abstract
Vibrio parahaemolyticus is one of the significant seafood-borne pathogens causing gastroenteritis in humans. Clustered regularly interspaced short palindromic repeats (CRISPR) are commonly detected in the genomes of V. parahaemolyticus and the polymorphism of CRISPR patterns has been applied as a genetic marker for [...] Read more.
Vibrio parahaemolyticus is one of the significant seafood-borne pathogens causing gastroenteritis in humans. Clustered regularly interspaced short palindromic repeats (CRISPR) are commonly detected in the genomes of V. parahaemolyticus and the polymorphism of CRISPR patterns has been applied as a genetic marker for tracking its evolution. In this work, a total of 15 pandemic and 36 non-pandemic V. parahaemolyticus isolates obtained from seafood between 2000 and 2012 were characterized based on hemolytic activity, antimicrobial susceptibility, and CRISPR elements. The results showed that 15/17 of the V. parahaemolyticus seafood isolates carrying the thermostable direct hemolysin gene (tdh+) were Kanagawa phenomenon (KP) positive. The Multiple Antibiotic Resistance (MAR) index ranged between 0.1 and 0.4, and 45% of the isolates have an MAR index ≥ 0.2. A total of 19 isolates were positive for CRISPR detection, including all tdh+ trh− isolates, two of tdh− trh+, and each of tdh+ trh+ and tdh− trh−. Four spacer types (Sp1 to Sp4) were identified, and CRISPR-positive isolates had at least one type of spacer homolog to the region of Vibrio alginolyticus megaplasmid. It is of interest that a specific CRISPR profile and spacer sequence type was observed with correlations to the hemolysin genotype (tdh/trh). Thus, these provide essential data on the exposure of foreign genetic elements and indicate shared ancestry within different genotypes of V. parahaemolyticus isolates. Full article
(This article belongs to the Special Issue Microbial Genetics and Evolution)
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