Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.4
4.1
Journals
Microorganisms
Special Issues
Genomics Approaches in Microbial Ecology
share announcement

Genomics Approaches in Microbial Ecology

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

Deadline for manuscript submissions: 31 May 2025 | Viewed by 8079

Special Issue Editors

Dr. Hugo César Ramírez-Saad

E-Mail Website
Guest Editor
Departamento Sistemas Biológicos, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico
Interests: microbial ecology; cactus rhizosphere; PGPR, bacterial diversity
Prof. Dr. César Hernández-Rodríguez

E-Mail Website
Guest Editor
Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas—IPN, Mexico City 11350, Mexico
Interests: maize microbiome;mine tailings bacterial diversity; molecular evolution

Special Issue Information

Dear Colleagues,

Microorganisms and their interactions are vital in biogeochemical and nutrient cycling, supporting all forms of life in this sense. In recent years the study of microbial communities, properly in the field of microbial ecology, has been nourished by novel approaches, namely genomics, metagenomics, epigenomics, proteomics, metabolomics, etc. They provide new insights into microbiomes’ structure and function, signaling metabolites' involvement, and the fate of specific microbial populations, among other topics, of the comprehensive set of microbial interactions occurring in natural, artificial, or man-influenced ecosystems.

This Special Issue is intended to harbor research papers on any topic of microbial ecology that have been carried out using mainly an omic methodological approach. Review papers within this profile are also welcome; please send an intention letter on the selected topic. The Special Issue is open, but not restricted to, the following topics:

  • Plant–microbiome interactions;
  • Microbial communities in extreme or nearly extreme environments;
  • Insect microbiome and ecology;
  • Microbial diversity in pristine and contaminated environments;
  • Aquatic and soil microbial diversity and ecology;
  • Microbial interactions in the rumen;
  • Human GIT microbiota.

Dr. Hugo César Ramírez-Saad
Prof. Dr. César Hernández-Rodríguez
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • soil microorganisms
  • microbes associated with plants
  • microbes associated with animals
  • microbial ecology
  • omics approaches
  • microbiomes
  • microbial communities
  • microbial symbioses
  • bacteria
  • archaea
  • fungi
  • algae
  • protists
  • viruses

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

23 pages, 5278 KiB  
Article
Comparative Genomics and Biosynthetic Cluster Analysis of Antifungal Secondary Metabolites of Three Strains of Streptomyces albidoflavus Isolated from Rhizospheric Soils
by Adilene Gonzalez-Silva, Magali San Juan-Mendo, Gustavo Delgado-Prudencio, Juan Alfredo Hernández-García, Violeta Larios-Serrato, César Aguilar, Lourdes Villa-Tanaca and César Hernández-Rodríguez
Microorganisms 2024, 12(12), 2637; https://doi.org/10.3390/microorganisms12122637 - 19 Dec 2024
Viewed by 979
Abstract
Streptomyces is a genus of Gram-positive bacteria with high GC content. It remains attractive for studying and discovering new antibiotics, antifungals, and chemotherapeutics. Streptomyces genomes can contain more than 30 cryptic and expressed biosynthetic gene clusters (BGC) encoding secondary metabolites. In this study, [...] Read more.
Streptomyces is a genus of Gram-positive bacteria with high GC content. It remains attractive for studying and discovering new antibiotics, antifungals, and chemotherapeutics. Streptomyces genomes can contain more than 30 cryptic and expressed biosynthetic gene clusters (BGC) encoding secondary metabolites. In this study, three Streptomyces strains isolated from jungle rhizospheric soil exhibited supernatants that can inhibit sensitive and fluconazole-resistant Candida spp. The genomes of the strains Streptomyces sp. A1, J25, J29 ori2 were sequenced, assembled de novo, and analyzed. The genome assemblies revealed that the size of the genomes was 6.9 Mb, with linear topology and 73.5% GC. A phylogenomic approach identified the strains with high similitudes between 98.5 and 98.7% with Streptomyces albidoflavus SM254 and R-53649 strains, respectively. Pangenomic analysis of eight genomes of S. albidoflavus strains deposited in the Genomes database recognized 4707 core protein orthogroups and 745 abundant accessory and exclusive protein orthogroups, suggesting an open pangenome in this species. The antiSMASH software detected candicidin and surugamide BGC-encoding polyene and octapeptide antifungal secondary metabolites in other S. albidoflavus. CORASON software was used to compare the synteny, and the abundance of genes harbored in the clusters was used. In conclusion, although the three strains belong to the same species, each possesses a distinct genome, as evidenced by the different phenotypes, including antifungal and extracellular enzymatic activities. Full article
(This article belongs to the Special Issue Genomics Approaches in Microbial Ecology)
►▼ Show Figures

Figure 1

17 pages, 1934 KiB  
Article
Verrucomicrobia of the Family Chthoniobacteraceae Participate in Xylan Degradation in Boreal Peat Soils
by Andrey L. Rakitin, Irina S. Kulichevskaya, Alexey V. Beletsky, Andrey V. Mardanov, Svetlana N. Dedysh and Nikolai V. Ravin
Microorganisms 2024, 12(11), 2271; https://doi.org/10.3390/microorganisms12112271 - 8 Nov 2024
Cited by 1 | Viewed by 949
Abstract
The phylum Verrucomicrobiota is one of the main groups of soil prokaryotes, which remains poorly represented by cultivated organisms. The major recognized role of Verrucomicrobiota in soils is the degradation of plant-derived organic matter. These bacteria are particularly abundant in peatlands, where xylan-type [...] Read more.
The phylum Verrucomicrobiota is one of the main groups of soil prokaryotes, which remains poorly represented by cultivated organisms. The major recognized role of Verrucomicrobiota in soils is the degradation of plant-derived organic matter. These bacteria are particularly abundant in peatlands, where xylan-type hemicelluloses represent one of the most actively decomposed peat constituents. The aim of this work was to characterize the microorganisms capable of hydrolyzing xylan under the anoxic conditions typical of peatland soils. The laboratory incubation of peat samples with xylan resulted in the pronounced enrichment of several phylotypes affiliated with the Verrucomicrobiota, Firmicutes, and Alphaproteobacteria. Sequencing of the metagenome of the enrichment culture allowed us to recover high-quality metagenome-assembled genomes (MAGs) assigned to the genera Caproiciproducens, Clostridium, Bacillus (Firmicutes), and Rhizomicrobium (Alphaproteobacteria), Cellulomonas (Actinobacteriota) and the uncultured genus-level lineage of the family Chthoniobacteraceae (Verrucomicrobiota). The latter bacterium, designated “Candidatus Chthoniomicrobium xylanophilum” SH-KS-3, dominated in the metagenome and its MAG was assembled as a complete closed chromosome. An analysis of the SH-KS-3 genome revealed potential endo-1,4-beta-xylanases, as well as xylan beta-1,4-xylosidases and other enzymes involved in xylan utilization. A genome analysis revealed the absence of aerobic respiration and predicted chemoheterotrophic metabolism with the capacity to utilize various carbohydrates, including cellulose, and to perform fermentation or nitrate reduction. An analysis of other MAGs suggested that Clostridium and Rhizomicrobium could play the role of primary xylan degraders while other community members probably took advantage of the availability of xylo-oligosaccharides and xylose or utilized low molecular weight organics. Full article
(This article belongs to the Special Issue Genomics Approaches in Microbial Ecology)
►▼ Show Figures

Figure 1

14 pages, 2067 KiB  
Article
Genotypic and Phenotypic Characterization of Pseudomonas atacamensis EMP42 a PGPR Strain Obtained from the Rhizosphere of Echinocactus platyacanthus (Sweet Barrel)
by Leilani Itzel Salinas-Virgen, María Eugenia de la Torre-Hernández, José Félix Aguirre-Garrido, Francisco Martínez-Abarca and Hugo César Ramírez-Saad
Microorganisms 2024, 12(8), 1512; https://doi.org/10.3390/microorganisms12081512 - 24 Jul 2024
Viewed by 1407
Abstract
Plant growth-promoting rhizobacteria (PGPR) are a group of bacteria that associate with the rhizosphere of plants; one of the most abundant bacterial genera in this ecological niche is Pseudomonas, which is constantly expanding due to the emergence of new species such as [...] Read more.
Plant growth-promoting rhizobacteria (PGPR) are a group of bacteria that associate with the rhizosphere of plants; one of the most abundant bacterial genera in this ecological niche is Pseudomonas, which is constantly expanding due to the emergence of new species such as Pseudomonas atacamensis, whose discovery in 2019 has led to the characterization of several strains from different environments but taxonomically related. The objective of this work was to phenotypically and molecularly characterize P. atacamensis strain EMP42, isolated from the rhizosphere of Echinocactus platyacanthus. The strain EMP42 is able to use different substrates and reduce oxidative stress in plants. It is capable of improving growth parameters such as the number of inflorescences and the height of the aerial body of Arabidopsis thaliana, as well as the germination and seedling survival of the cacti Echinocactus platyacanthus and Astrophytum capricorne. The genetic structure of P. atacamensis EMP42 consists of a closed chromosome of 6.14 Mbp, and 61.1% GC content. It has 5572 genes, including those associated with PGPR activities, such as the trpABCDE, SAP, phoABPRU and acsABC genes, among others, and three ncRNA loci, nine regulatory regions, five complete rRNA operons and three CRISPR-Cas loci, showing phylogenomic similarities with the reference strain P. atacamensis B21-026. Therefore, this study contributes to the understanding of genomic diversity within P. atacamensis and, particularly, highlights the potential application of strain EMP42 as a PGPR. Full article
(This article belongs to the Special Issue Genomics Approaches in Microbial Ecology)
►▼ Show Figures

Figure 1

8 pages, 1990 KiB  
Communication
Evaluation of a Multilocus Variable-Number Tandem-Repeat Analysis Scheme for Typing Ochrobactrum anthropi
by Yihan Wu, Liping Wang, Xiachun Hui and Guozhong Tian
Microorganisms 2024, 12(6), 1211; https://doi.org/10.3390/microorganisms12061211 - 16 Jun 2024
Viewed by 942
Abstract
Ochrobactrum anthropi (O. anthropi) is found in water, soil, plants and animals. Even though it has low virulence, it has increasingly been found to cause a number of infectious diseases in people with low immunity. The identification of O. anthropi mainly [...] Read more.
Ochrobactrum anthropi (O. anthropi) is found in water, soil, plants and animals. Even though it has low virulence, it has increasingly been found to cause a number of infectious diseases in people with low immunity. The identification of O. anthropi mainly uses biochemical methods, such as the API 20NE or Vitek-2. The typing studies of O. anthropi have mainly utilized PFGE, rep-PCR, AFLP, 16s rDNA sequencing, RecA-PCR RFLP, and MALDI-TOF MS. This study aims to evaluate the polymorphisms of variable-number tandem-repeats (VNTRs) within genomic DNA of O. anthropi strains. The tandem repeats (TRs) in genomic DNA are discovered using Tandem Repeat Finder software (version 4.09). Twelve different VNTRs are designated and assigned to the nomenclature. The primers for PCR of 12 loci are designed. The PCR product size is converted to the number of tandem repeats in every locus. The relatedness of 65 O. anthropi strains from geographically different countries are analyzed by means of 12-variable-number tandem-repeat analysis(MLVA-12). A total of 51 different genotypes are found in 65 O. anthropi strains. These strains, which were collected from the same environmental samples, hospitals, and countries, are clustered within the same or closely genotypes. The MLVA-12 assay has a good discriminatory power for species determination, typing of O. anthropi, and inferring the origin of bacteria. Full article
(This article belongs to the Special Issue Genomics Approaches in Microbial Ecology)
►▼ Show Figures

Figure 1

18 pages, 5660 KiB  
Article
Deconstructing the Dimensions of Mycobiome Fingerprints in Luohandu Cave, Guilin, Southern China
by Bai-Ying Man, Xing Xiang, Xiao-Yu Cheng, Hong-Mei Wang, Chun-Tian Su, Qi-Bo Huang, Yang Luo, Chao Zhang, Gang Cheng, Yu-Yang Ni and Xing-Hua Shao
Microorganisms 2024, 12(1), 211; https://doi.org/10.3390/microorganisms12010211 - 20 Jan 2024
Viewed by 1337
Abstract
Subterranean karst caves are windows into the terrestrial subsurface to deconstruct the dimensions of mycobiome fingerprints. However, impeded by the constraints of remote locations, the inaccessibility of specimens and technical limitations, the mycobiome of subterranean karst caves has remained largely unknown. Weathered rock [...] Read more.
Subterranean karst caves are windows into the terrestrial subsurface to deconstruct the dimensions of mycobiome fingerprints. However, impeded by the constraints of remote locations, the inaccessibility of specimens and technical limitations, the mycobiome of subterranean karst caves has remained largely unknown. Weathered rock and sediment samples were collected from Luohandu cave (Guilin, Southern China) and subjected to Illumina Hiseq sequencing of ITS1 genes. A total of 267 known genera and 90 known orders in 15 phyla were revealed in the mycobiomes. Ascomycota dominated all samples, followed by Basidiomycota and Mortierellomycota. The sediments possessed the relatively highest alpha diversity and were significantly different from weathered rocks according to the diversity indices and richness metrics. Fifteen families and eight genera with significant differences were detected in the sediment samples. The Ca/Mg ratio appeared to significantly affect the structure of the mycobiome communities. Ascomycota appeared to exert a controlling influence on the mycobiome co-occurrence network of the sediments, while Ascomycota and Basidiomycota were found to be the main phyla in the mycobiome co-occurrence network of weathered rocks. Our results provide a more comprehensive dimension to the mycobiome fingerprints of Luohandu cave and a new window into the mycobiome communities and the ecology of subterranean karst cave ecosystems. Full article
(This article belongs to the Special Issue Genomics Approaches in Microbial Ecology)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop