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Microorganisms
Special Issues
Microbial Taxonomy and Environmental Metagenomics: Diversity, Dynamics, and Functional Genes
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Microbial Taxonomy and Environmental Metagenomics: Diversity, Dynamics, and Functional Genes

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

Deadline for manuscript submissions: 28 February 2026 | Viewed by 304

Special Issue Editors

Dr. Cassius V. Stevani

E-Mail Website
Guest Editor
Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil
Interests: bioluminescence; biotechnology; chemiluminescence; fungi; microbiology
Special Issues, Collections and Topics in MDPI journals
Dr. Renato Sanches Freire

E-Mail Website
Guest Editor
Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil
Interests: quimica ambiental; sensores

Special Issue Information

Dear Colleagues, 

Environmental microbiology has entered a new era with the integration of conventional taxonomy and metagenomics. Classical approaches to microbial systematics remain essential for describing, naming, and organizing the vast diversity of archaea, bacteria, and fungi. At the same time, advances in high-throughput sequencing and bioinformatics now enable the reconstruction of metagenome-assembled genomes (MAGs) and the recovery of genetic information from uncultured microorganisms. These complementary strategies are reshaping our understanding of microbial evolution, ecology, and function. Metagenomics also allows us to go far beyond taxonomy. By directly accessing the collective genomes of microbial communities, researchers are uncovering the diversity and dynamics of microorganisms in soils, aquatic systems, extreme habitats, and engineered environments. Functional genes related to biogeochemical cycles, stress adaptation, antimicrobial resistance, secondary metabolism, and other traits of environmental and biotechnological interest are increasingly being revealed. This dual focus, on both microbial diversity and gene-level function, offers unprecedented insights into how microorganisms shape ecosystems and respond to global changes. The purpose of this Special Issue is to bring together original research and reviews on microbial taxonomy and diversity explored through both conventional and metagenomic approaches. We particularly welcome studies on the systematics of archaea, bacteria, and fungi; investigations into the structure and dynamics of microbial communities; and the discovery of functional genes of environmental importance. Methodological innovations and integrative studies that connect taxonomy, ecology, and function are also encouraged. By bridging classical taxonomy with metagenomic discoveries, this Special Issue aims to highlight the expanding frontiers of microbial diversity research.

Dr. Cassius V. Stevani
Dr. Renato Sanches Freire
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 250 words) can be sent to the Editorial Office for assessment.

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

  • environmental microbiology
  • metagenomics
  • microbial diversity

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Published Papers (1 paper)

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Research

20 pages, 7027 KB  
Article
Cluster of Dominant Species and Grazing Jointly Influence the Soil Nitrogen and Phosphorus Cycling in Alpine Grasslands
by Wei Xu, Na Li, Wenting Liu, Weidong Lv, Mengqi Li, Haiming Ji, Yuzhen Liu, Xiaoxia Yang and Quanmin Dong
Microorganisms 2025, 13(12), 2736; https://doi.org/10.3390/microorganisms13122736 - 30 Nov 2025
Viewed by 156
Abstract
This study systematically analyzes the multi-layered regulatory mechanisms of grazing on soil nitrogen and phosphorus cycling functions, based on the combined effects of different grazing strategies and plant community spatial patterns in alpine grasslands. A controlled mixed grazing experiment with moderate intensity was [...] Read more.
This study systematically analyzes the multi-layered regulatory mechanisms of grazing on soil nitrogen and phosphorus cycling functions, based on the combined effects of different grazing strategies and plant community spatial patterns in alpine grasslands. A controlled mixed grazing experiment with moderate intensity was conducted on a livestock system adaptive management platform in the region surrounding Qinghai Lake on the Qinghai–Tibet Plateau, China. The experimental treatments included yak-only grazing (YG), Tibetan sheep-only grazing (SG), mixed grazing of yak and Tibetan sheep (MG), and no grazing (CK). The study quantitatively assessed the soil microbial nitrogen and phosphorus cycling functional genes in the rhizosphere of dominant species, including the Carex alatauensis and Potentilla acaulis, under different grazing intensities. The aim was to explore the effects of grazing strategy and clusters of dominant species on soil nitrogen and phosphorus cycling and their regulatory mechanisms. The results of this study show that, in the nitrogen cycle, grazing led to a decrease in total nitrogen (TN) content and an increase in ammonium nitrogen content in the dominant species communities. The MG treatment significantly enhanced the abundance of key nitrogen metabolism genes, such as ureC and gs. In the phosphorus cycle, most grazing treatments increased total phosphorus content, but changes in available phosphorus were variable among plant clusters. The MG and SG treatments significantly increased the abundance of functional genes such as aphA, ugpB, and phnW. Compared to the relatively stable soil nitrogen and phosphorus content, the abundance of functional genes exhibited significantly higher variability across different grazing treatments. The clusters of Potentilla acaulis maintained nutrient stability by enhancing nitrogen assimilation and phosphorus uptake, while the clusters of Carex alatauensis promoted ammonium nitrogen accumulation through a conservative strategy. The results indicate that grazing influences nitrogen and phosphorus availability by altering nutrient input and disturbance modes, while plant clusters optimize cycling through differential regulation of microbial functional genes in the community. Both factors jointly regulate nitrogen and phosphorus cycling in Alpine Grassland soils. Mixed grazing exhibited significant advantages in promoting nitrogen retention, enhancing phosphorus activation, and improving plant-microbe interactions, reflecting a comprehensive facilitation of nutrient cycling stability in alpine grasslands. These findings provide important theoretical insights for nutrient cycling management and sustainable grazing practices in alpine grasslands. Full article
(This article belongs to the Special Issue Microbial Taxonomy and Environmental Metagenomics: Diversity, Dynamics, and Functional Genes)
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