Microbial Diversity, Metagenomics, and Bioinformatics

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Microbial Diversity and Culture Collections".

Deadline for manuscript submissions: closed (15 May 2021) | Viewed by 5638

Special Issue Editor

Dr. Ri-Qing Yu
E-Mail Website
Guest Editor
Department of Biology, Center for Environment, Biodiversity and Conservation, The University of Texas at Tyler, Tyler, TX 75799, USA
Interests: environmental microbiology; microbial metagenomics and bioinformatics

Special Issue Information

Dear Colleagues,

Microorganisms are involved in almost all processes in the biosphere, ranging from maintenance of health of human beings to that of ecological sustainability on the Earth, and contribute to the transformation of key elements of life such as carbon, nitrogen, oxygen, and sulfur in natural and environmentally modified ecosystems. Microorganisms keep close syntrophic relationships with humans and animals either as pathogens or probiotics, contribute to the fermentation processes and biotechnology industries, help to degrade organic contaminants and transform toxic metals, support plant growth and suppress plant diseases, and play a key role in the discovery of new pharmaceuticals and biofuels.

Through the application of next-generation sequencing and bioinformatics techniques with culture-independent approaches, microbial metagenomics could help us to investigate unbiased samples of all genes from diverse sampled communities and allow studying microbial diversity and functions directly in their natural environments. With the rapid advancement of high-throughput sequencing-based bioinformatics and metagenomics, exploration of novel diversity would greatly enhance our understanding of the genetic, metabolic, physiological, and other traits of microorganisms, thus facilitating the potential application and benefits in biomedical and biotechnological industries, environmental protection, agriculture, and other fields.

For this Special Issue of “Microbial Diversity, Metagenomics, and Bioinformatics”, we invite submissions that address microbial diversity and metagenomics in natural habitats and contamination-modified ecosystems, microbial interactions with animals and plants, biomedical and human pathogens, novel microbial biodegradation and synthesis pathways related with metagenomics studies, new microbial bioinformatics studies, and other related aspects mentioned above.

Dr. Ri-Qing Yu
Guest Editor

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. Diversity 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 2600 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

  • Microbial and genetic diversity
  • Genomic diversity and taxonomy
  • Microbial metagenomics
  • Novel microbial bioinformatics methods
  • Microbial genes and genomes in environmental contamination
  • Genes and metagenomics in biogeochemical cycling
  • Microbial interactions with plants and animals
  • Bioinformatics and metagenomics in medical microbiology
  • Novel microbial pathways derived from metagenomics

Published Papers (2 papers)

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Research

17 pages, 4747 KiB  
Article
Metagenomics Analysis Reveals the Microbial Communities, Antimicrobial Resistance Gene Diversity and Potential Pathogen Transmission Risk of Two Different Landfills in China
Diversity 2021, 13(6), 230; https://doi.org/10.3390/d13060230 - 24 May 2021
Cited by 9 | Viewed by 2045
Abstract
In this study, we used a metagenomic approach to analyze microbial communities, antibiotic resistance gene diversity, and human pathogenic bacterium composition in two typical landfills in China. Results showed that the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in the two landfills, and [...] Read more.
In this study, we used a metagenomic approach to analyze microbial communities, antibiotic resistance gene diversity, and human pathogenic bacterium composition in two typical landfills in China. Results showed that the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in the two landfills, and archaea and fungi were also detected. The genera Methanoculleus, Lysobacter, and Pseudomonas were predominantly present in all samples. sul2, sul1, tetX, and adeF were the four most abundant antibiotic resistance genes. Sixty-nine bacterial pathogens were identified from the two landfills, with Klebsiella pneumoniae, Bordetella pertussis, Pseudomonas aeruginosa, and Bacillus cereus as the major pathogenic microorganisms, indicating the existence of potential environmental risk in landfills. In addition, KEGG pathway analysis indicated the presence of antibiotic resistance genes typically associated with human antibiotic resistance bacterial strains. These results provide insights into the risk of pathogens in landfills, which is important for controlling the potential secondary transmission of pathogens and reducing workers’ health risk during landfill excavation. Full article
(This article belongs to the Special Issue Microbial Diversity, Metagenomics, and Bioinformatics)
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15 pages, 2512 KiB  
Article
Effects of Fertilization Methods on Chemical Properties, Enzyme Activity, and Fungal Community Structure of Black Soil in Northeast China
Diversity 2020, 12(12), 476; https://doi.org/10.3390/d12120476 - 14 Dec 2020
Cited by 4 | Viewed by 2868
Abstract
Understanding the influence of fertilizer on soil quality is vital to agricultural management, yet there are few studies, particularly in black soil. In this study, soils under various treatments, namely no fertilizer, bio-organic + humic acid, bio-organic + chemical, and chemical fertilizer, were [...] Read more.
Understanding the influence of fertilizer on soil quality is vital to agricultural management, yet there are few studies, particularly in black soil. In this study, soils under various treatments, namely no fertilizer, bio-organic + humic acid, bio-organic + chemical, and chemical fertilizer, were sampled to identify their major physiochemical properties, and to investigate the fungal community structure using environmental sequencing techniques. Physiochemical properties and fungal community structure were examined at four important stages of the maize life cycle: seedling, jointing, heading period, and maturity. We found that chemical fertilizer in the mature stage increased the soil available phosphorous (AP) content. Organic matter content was greatly affected by bio-organic + chemical fertilizer during the mature stage. Bio-organic + humic acid significantly increased soil phosphatase activity in maturing maize, whilst chemical fertilizers reduced invertase activity. Taken together, our results clearly illustrated that bio-organic + humic and chemical fertilization indirectly alter fungal community structure via changing soil properties (especially AP). Chemical fertilizer markedly heightened the AP content, thereby decreasing specific fungal taxa, particularly Guehomyces. OM was of positive connection with bio-organic + humic acid and Mortierella abundance, respectively, through RDA analysis, which are in agreement with our result that bio-organic + humic acid fertilization to some extent increased Mortierella abundance. Additionally, bio-organic + humic acid decreased the abundance of Fusarium and Humicola, suggesting that bio-organic + humic acid possibly could help control crop disease. These results help to inform our fundamental understanding of the interactions between fertilizers, soil properties, and fungal communities. Full article
(This article belongs to the Special Issue Microbial Diversity, Metagenomics, and Bioinformatics)
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