Recent Advances in Extremophilic Microbiota: Microbiology and Biotechnology

A special issue of Microbiology Research (ISSN 2036-7481).

Deadline for manuscript submissions: closed (29 February 2024) | Viewed by 2645

Special Issue Editors


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Guest Editor
Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
Interests: endophytes; mycorrhizae; taxonomy of fungi; applied mycology; microbial biotechnology; food science & technology; secondary metabolites; enzymes in pharmaceutical industry; microbial biodterioration; microbial physiology and climate change
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Guest Editor
Department of Biological Sciences-Microbiology Section, Faculty of Science, Jeddah University, Jeddah 21959, Saudi Arabia
Interests: filamentous fungi; biocontrol; antibiotic sensitivity

Special Issue Information

Dear Colleagues,

Extremophiles are a class of organisms that flourish in harsh environmental conditions which most living forms find difficult to endure, such as high or low temperatures, pH levels, salinities, and pressure. The majority of the earth's crust, however, is exposed to harsh environmental conditions, with temperatures that can range from −89 °C in the Antarctic and Arctic to 400 °C at the bottom of the deep sea. Therefore, it is not unexpected that extremophiles have evolved and created effective coping mechanisms to survive at the most readily available pH, temperature, pressure, and other life-sustaining conditions. Extremophiles comprise animals, plants, insects, fungi, and bacteria. However, in this SI, we will deal exclusively with bacteria and fungi, with special attention paid to their applications in biotechnology.

We encourage distinguished authors and research experts to submit original research and review articles that target the relevant topics.

These include, but are not limited to:

1—Molecular Mechanisms of Extremophilic Industrially Important Enzymes.

2—Microbial Life Under Stress: Biochemical, Genomic, Transcriptomic, Proteomic, Bioinformatics, Evolutionary Aspects and Biotechnological Applications.

3—Thermophilic microbial-derived compounds in Biotechnology,

4—Microbial Enzymes from Extreme Environments.

5—Growth and Metabolism of Extremophilic Microorganisms.

6—Alkaliphilic Microorganisms in Biotechnology.

7—Waste Biomass Degradation by Thermophiles.

8—Microbial Evolution of Extremophiles.

9—Extremophiles from Marine Environments: Underexplored Sources of Antitumor, Anti-Infective and other Active Biomolecules.

10—Novel Natural Products from Extremophiles.

11—Plastic Degradation by Extremophiles.

12—Biotechnology from desert microbial extremophiles.

14—Endolith, Extremophilic Organisms from Rock,

15—Communication mechanisms in extremophiles: Exploring their existence and industrial applications

Prof. Dr. Ahmed M. Abdel-Azeem
Prof. Dr. Awatif Abid Al-Judaibi
Guest Editors

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Published Papers (2 papers)

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17 pages, 1776 KiB  
Article
In Silico Identification of Sugarcane Genome-Encoded MicroRNAs Targeting Sugarcane Mosaic Virus
by Wang Wenzhi, Muhammad Aleem Ashraf, Hira Ghaffar, Zainab Ijaz, Waqar ul Zaman, Huda Mazhar, Maryam Zulfqar and Shuzhen Zhang
Microbiol. Res. 2024, 15(1), 273-289; https://doi.org/10.3390/microbiolres15010019 - 16 Feb 2024
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Abstract
Sugarcane mosaic virus (SCMV) (genus, Potyvirus; family, Potyviridae) is widespread, deleterious, and the most damaging pathogen of sugarcane (Saccharum officinarum L. and Saccharum spp.) that causes a substantial barrier to producing high sugarcane earnings. Sugarcane mosaic disease (SCMD) is caused [...] Read more.
Sugarcane mosaic virus (SCMV) (genus, Potyvirus; family, Potyviridae) is widespread, deleterious, and the most damaging pathogen of sugarcane (Saccharum officinarum L. and Saccharum spp.) that causes a substantial barrier to producing high sugarcane earnings. Sugarcane mosaic disease (SCMD) is caused by a single or compound infection of SCMV disseminated by several aphid vectors in a non-persistent manner. SCMV has flexuous filamentous particle of 700–750 nm long, which encapsidated in a positive-sense, single-stranded RNA molecule of 9575 nucleotides. RNA interference (RNAi)-mediated antiviral innate immunity is an evolutionarily conserved key biological process in eukaryotes and has evolved as an antiviral defense system to interfere with viral genomes for controlling infections in plants. The current study aims to analyze sugarcane (Saccharum officinarum L. and Saccharum spp.) locus-derived microRNAs (sof-miRNAs/ssp-miRNAs) with predicted potential for targeting the SCMV +ssRNA-encoded mRNAs, using a predictive approach that involves five algorithms. The ultimate goal of this research is to mobilize the in silico- predicted endogenous sof-miRNAs/ssp-miRNAs to experimentally trigger the catalytic RNAi pathway and generate sugarcane cultivars to evaluate the potential antiviral resistance surveillance ability and capacity for SCMV. Experimentally validated mature sugarcane (S. officinarum, 2n = 8X = 80) and (S. spp., 2n = 100–120) sof-miRNA/ssp-miRNA sequences (n = 28) were downloaded from the miRBase database and aligned with the SCMV genome (KY548506). Among the 28 targeted mature locus-derived sof-miRNAs/ssp-miRNAs evaluated, one sugarcane miRNA homolog, sof-miR159c, was identified to have a predicted miRNA binding site, at nucleotide position 3847 of the SCMV genome targeting CI ORF. To verify the accuracy of the target prediction accuracy and to determine whether the sugarcane sof-miRNA/ssp-miRNA could bind the predicted SCMV mRNA target(s), we constructed an integrated Circos plot. A genome-wide in silico-predicted miRNA-mediated target gene regulatory network was implicated to validate interactions necessary to warrant in vivo analysis. The current work provides valuable computational evidence for the generation of SCMV-resistant sugarcane cultivars. Full article
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19 pages, 2328 KiB  
Article
Genome-Wide Identification of Cotton MicroRNAs Predicted for Targeting Cotton Leaf Curl Kokhran Virus-Lucknow
by Muhammad Aleem Ashraf, Judith K. Brown, Muhammad Shahzad Iqbal and Naitong Yu
Microbiol. Res. 2024, 15(1), 1-19; https://doi.org/10.3390/microbiolres15010001 - 19 Dec 2023
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Abstract
Cotton leaf curl Kokhran virus (CLCuKoV) (genus, Begomovirus; family, Geminiviridae) is one of several plant virus pathogens of cotton (Gossypium hirsutum L.) that cause cotton leaf curl disease in Pakistan. Begomoviruses are transmitted by the whitefly Bemisia tabaci cryptic species [...] Read more.
Cotton leaf curl Kokhran virus (CLCuKoV) (genus, Begomovirus; family, Geminiviridae) is one of several plant virus pathogens of cotton (Gossypium hirsutum L.) that cause cotton leaf curl disease in Pakistan. Begomoviruses are transmitted by the whitefly Bemisia tabaci cryptic species group and cause economic losses in cotton and other crops worldwide. The CLCuKoV strain, referred to as CLCuKoV-Bur, emerged in the vicinity of Burewala, Pakistan, and was the primary causal virus associated with the second CLCuD epidemic in Pakistan. The monopartite ssDNA genome of (2.7 Kb) contains six open reading frames that encode four predicted proteins. RNA interference (RNAi)-mediated antiviral immunity is a sequence-specific biological process in plants and animals that has evolved to combat virus infection. The objective of this study was to design cotton locus-derived microRNA (ghr-miRNA) molecules to target strains of CLCuKoV, with CLCuKoV-Lu, as a typical CLCuD-begomovirus genome, predicted by four algorithms, miRanda, RNA22, psRNATarget, and RNA hybrid. Mature ghr-miRNA sequences (n = 80) from upland cotton (2n = 4x = 52) were selected from miRBase and aligned with available CLCuKoV-Lu genome sequences. Among the 80 cotton locus-derived ghr-miRNAs analyzed, ghr-miR2950 was identified as the most optimal, effective ghr-miRNA for targeting the CLCuKoV-Lu genome (nucleotide 82 onward), respectively, based on stringent criteria. The miRNA targeting relies on the base pairing of miRNA–mRNA targets. Conservation and potential base pairing of binding sites with the ghr-miR2950 were validated by multiple sequence alignment with all available CLCuKoV sequences. A regulatory interaction network was constructed to evaluate potential miRNA–mRNA interactions with the predicted targets. The efficacy of miRNA targeting of CLCuKoV was evaluated in silico by RNAi-mediated mRNA cleavage. This predicted targets for the development of CLCuD-resistant cotton plants. Full article
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