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 July 2024 | Viewed by 1992

Special Issue Editors


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Guest Editor
Departamento Sistemas Biológicos, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico
Interests: microbial ecology; cactus rhizosphere; PGPR, bacterial diversity

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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

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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

  • 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

Published Papers (2 papers)

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Research

8 pages, 1990 KiB  
Communication
Evaluation of a Multilocus Variable-Number Tandem-Repeat Analysis Scheme for Ty** Ochrobactrum anthropi
by Yihan Wu, Li** Wang, **achun Hui and Guozhong Tian
Microorganisms 2024, 12(6), 1211; https://doi.org/10.3390/microorganisms12061211 - 16 Jun 2024
Viewed by 339
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 ty** 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, ty** of O. anthropi, and inferring the origin of bacteria. Full article
(This article belongs to the Special Issue Genomics Approaches in Microbial Ecology)
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18 pages, 5660 KiB  
Article
Deconstructing the Dimensions of Mycobiome Fingerprints in Luohandu Cave, Guilin, Southern China
by Bai-Ying Man, **ng **ang, **ao-Yu Cheng, Hong-Mei Wang, Chun-Tian Su, Qi-Bo Huang, Yang Luo, Chao Zhang, Gang Cheng, Yu-Yang Ni and **ng-Hua Shao
Microorganisms 2024, 12(1), 211; https://doi.org/10.3390/microorganisms12010211 - 20 Jan 2024
Viewed by 859
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)
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