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

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 15958

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Prof. Dr. María José Bonete

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Department of Agrochemistry and Biochemistry, Universitat d'Alacant, E-03080 Alicante, Spain
Interests: extremophiles; haloarchaea; nitrogen metabolism; stress response; bioremediation
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Dr. Mónica Camacho

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Department of Agrochemistry and Biochemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, E-03080 Alicante, Spain
Interests: genomics; proteomics; extremophiles; systems biology; protein expression and characterization; protein-protein interactions
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Dr. Julia Esclapez

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Department of Agrochemistry and Biochemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
Interests: archaea; molecular biology; stress response; proteins; small RNAs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent decades, extremophilic microorganisms have gained increasing attention in biotechnological applications and bioremediation processes due to their unique metabolic capabilities, the production of stable enzymes under extremely hostile conditions, and unique biomaterials and secondary metabolites. The diversity in extreme environments is usually low, but the few species that colonize them have become highly adapted as a result of their enormous variety of strategies. Interestingly, in most cases, they are obligate extremophiles since they do not have the ability to live in "normal" environments. The biological characteristics of extremophiles and the adaptation mechanisms developed for their molecular machinery may have great economic potential in many industrial processes, including environmental applications in food, agriculture and pharmaceuticals, among others.

In this Special Issue of Microorganisms, we welcome contributions (original articles as well as reviews) related to microorganism diversity in extremophilic environments, microbial community dynamics, metagenomics, physiological characterization of microorganisms, stress response, and molecular biology. We encourage researchers to send their work on recent advancements in extreme environments to this Special Issue.

Prof. Dr. María José Bonete
Dr. Mónica Camacho
Dr. Julia Esclapez
Guest Editors

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Keywords

extremophilic organisms
stress response
metagenomics
genomics
biotechnological applications
microbial physiology
microbial ecology
metabolisms
extreme environmental microbiome

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Published Papers (11 papers)

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Research

21 pages, 6419 KiB

Open AccessArticle

Exiguolysin, a Novel Thermolysin (M4) Peptidase from Exiguobacterium oxidotolerans

by Brendan F. Gilmore, Tracy A. White, Alessandro Busetti, Matthew I. McAteer, Christine A. Maggs and Thomas P. Thompson

Microorganisms 2024, 12(11), 2311; https://doi.org/10.3390/microorganisms12112311 - 14 Nov 2024

Viewed by 369

Abstract

This study details a comprehensive biochemical and structural characterization of exiguolysin, a novel thermolysin-like, caseinolytic peptidase secreted by a marine isolate of Exiguobacterium oxidotolerans strain BW26. Exiguolysin demonstrated optimal proteolytic activity at 37 °C and pH 3, retaining 85% activity at 50 °C, highlighting its potential stability under broad reaction conditions. SDS-PAGE and LC-MS analysis identified the enzyme as a 32 kDa M4-family metalloprotease. Exiguolysin activity was inhibited by 1,10-phenanthroline, confirming its dependence on metal ions for activity. Zymographic analysis and substrate specificity assays revealed selective hydrolysis of matrix metalloproteinase (MMP) substrates but no activity against elastase substrates. Analysis of the predicted gene sequence and structural predictions using AlphaFold identified the presence and position of HEXXH and Glu-Xaa-Xaa-Xaa-Asp motifs, crucial for zinc binding and catalytic activity, characteristic of ‘Glu-zincins’ and members of the M4 peptidase family. High-throughput screening of a 20 × 20 N-alpha mercaptoamide dipeptide inhibitor library against exiguolysin identified SH-CH₂-CO-Met-Tyr-NH₂ as the most potent inhibitor, with a Ki of 1.95 μM. Notably, exiguolysin selectively inhibited thrombin-induced PAR-1 activation in PC-3 cells, potentially indicating a potential mechanism of virulence in modulating PAR-1 signalling during infection by disarming PARs. This is the first detailed characterization of a peptidase of the M4 (thermolysin) family in the genus Exiguobacterium which may have industrial application potential and relevance as a putative virulence factor. Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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14 pages, 2027 KiB

Open AccessArticle

Long-Term Contaminant Exposure Alters Functional Potential and Species Composition of Soil Bacterial Communities in Gulf Coast Prairies

by Candice Y. Lumibao and Yue Liu

Microorganisms 2024, 12(7), 1460; https://doi.org/10.3390/microorganisms12071460 - 18 Jul 2024

Viewed by 641

Abstract

Environmental pollution is a persistent threat to coastal ecosystems worldwide, adversely affecting soil microbiota. Soil microbial communities perform critical functions in many coastal processes, yet they are increasingly subject to oil and heavy metal pollution. Here, we assessed how small-scale contamination by oil and heavy metal impacts the diversity and functional potential of native soil bacterial communities in the gulf coast prairie dunes of a barrier island in South Texas along the northern Gulf of Mexico. We analyzed the bacterial community structure and their predicted functional profiles according to contaminant history and examined linkages between species diversity and functional potential. Overall, contaminants altered bacterial community compositions without affecting richness, leading to strongly distinct bacterial communities that were accompanied by shifts in functional potential, i.e., changes in predicted metabolic pathways across oiled, metal, and uncontaminated environments. We also observed that exposure to different contaminants can either lead to strengthened or decoupled linkages between species diversity and functional potential. Taken together, these findings indicate that bacterial communities might recover their diversity levels after contaminant exposure, but with consequent shifts in community composition and function. Furthermore, the trajectory of bacterial communities can depend on the nature or type of disturbance. Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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23 pages, 5076 KiB

Open AccessArticle

Selective Isolation and Identification of Microorganisms with Dual Capabilities: Leather Biodegradation and Heavy Metal Resistance for Industrial Applications

by Manuela Bonilla-Espadas, Basilio Zafrilla, Irene Lifante-Martínez, Mónica Camacho, Elena Orgilés-Calpena, Francisca Arán-Aís, Marcelo Bertazzo and María-José Bonete

Microorganisms 2024, 12(5), 1029; https://doi.org/10.3390/microorganisms12051029 - 20 May 2024

Viewed by 1313

Abstract

Tanning, crucial for leather production, relies heavily on chromium yet poses risks due to chromium’s oxidative conversion, leading to significant wastewater and solid waste generation. Physico-chemical methods are typically used for heavy metal removal, but they have drawbacks, prompting interest in eco-friendly biological remediation techniques like biosorption, bioaccumulation, and biotransformation. The EU Directive (2018/850) mandates alternatives to landfilling or incineration for industrial textile waste management, highlighting the importance of environmentally conscious practices for leather products’ end-of-life management, with composting being the most researched and viable option. This study aimed to isolate microorganisms from tannery wastewater and identify those responsible for different types of tanned leather biodegradation. Bacterial shifts during leather biodegradation were observed using a leather biodegradation assay (ISO 20136) with tannery and municipal wastewater as the inoculum. Over 10,000 bacterial species were identified in all analysed samples, with 7 bacterial strains isolated from tannery wastewaters. Identification of bacterial genera like Acinetobacter, Brevundimonas, and Mycolicibacterium provides insights into potential microbial candidates for enhancing leather biodegradability, wastewater treatment, and heavy metal bioremediation in industrial applications. Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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13 pages, 1351 KiB

Open AccessArticle

Fodinisporobacter ferrooxydans gen. nov., sp. nov.—A Spore-Forming Ferrous-Oxidizing Bacterium Isolated from a Polymetallic Mine

by Zhen Jiang, Xiutong Li, Zonglin Liang, Zebao Tan, Nan Zhou, Ying Liu, Zhenghua Liu, Huaqun Yin, Kun Luo, Supawadee Ingsriswang, Shuangjiang Liu and Chengying Jiang

Microorganisms 2024, 12(5), 853; https://doi.org/10.3390/microorganisms12050853 - 25 Apr 2024

Cited by 1 | Viewed by 1047

Abstract

A novel acidophilic, aerobic bacterium strain, MYW30-H2^T, was isolated from a heap of polymetallic mine. Cells of strain MYW30-H2^T were Gram-stain-positive, endospore-forming, motile, and rod-shaped. Strain MYW30-H2^T grew at a temperature range of 30–45 °C (optimum 40 °C) and a pH range of 3.5–6.0 (optimum 4.0) in the presence of 0–0.5% (w/v) NaCl. Strain MYW30-H2^T could grow heterotrophically on yeast extract and glucose, and grow mixotrophically using ferrous iron as an electron donor with yeast extract. Menaquinone-7 (MK-7) was the sole respiratory quinone of the strain. Iso-C_15:0 and anteiso-C_15:0 were the major cellular fatty acids. The 16S rRNA gene sequence analysis showed that MYW30-H2^T was phylogenetically affiliated with the family Alicyclobacillaceae, and the sequence similarity with other Alicyclobacillaceae genera species was below 91.51%. The average amino acid identity value of the strain with its phylogenetically related species was 52.3–62.1%, which fell into the genus boundary range. The DNA G+C content of the strain was 44.2%. Based on physiological and phylogenetic analyses, strain MYW30-H2^T represents a novel species of a new genus of the family Alicyclobacillaceae, for which the name Fodinisporobacter ferrooxydans gen. nov., sp. nov. is proposed. The type strain is MYW30-H2^T (=CGMCC 1.17422^T = KCTC 43278^T). Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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12 pages, 6769 KiB

Open AccessCommunication

Metagenomic Analysis of Antarctic Ocean near the King Sejong Station Reveals the Diversity of Carotenoid Biosynthetic Genes

by Woo Yeon Cho and Pyung Cheon Lee

Microorganisms 2024, 12(2), 390; https://doi.org/10.3390/microorganisms12020390 - 15 Feb 2024

Cited by 1 | Viewed by 1256

Abstract

Carotenoids, biotechnologically significant pigments, play crucial biological roles in marine microorganisms. While various environments have been explored to understand the diversity of carotenoids and their biosynthesis, the Antarctic Ocean remains relatively under-investigated. This study conducted a metagenomic analysis of seawater from two depths (16 and 25 m) near the King Sejong Station in the Antarctic Ocean. The analysis revealed a rich genetic diversity underlying C40 (astaxanthin, myxol, okenone, spheroidene, and spirilloxanthin), C30 (diaponeurosporene, diapolycopene, and staphyloxanthin), and C50 (C.p. 450) carotenoid biosynthesis in marine microorganisms, with notable differential gene abundances between depth locations. Exploring carotenoid pathway genes offers the potential for discovering diverse carotenoid structures of biotechnological value and better understanding their roles in individual microorganisms and broader ecosystems. Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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16 pages, 3468 KiB

Open AccessArticle

The Great Gobi A Strictly Protected Area: Characterization of Soil Bacterial Communities from Four Oases

by Antonia Esposito, Sara Del Duca, Francesco Vitali, Gaia Bigiotti, Stefano Mocali, Giulia Semenzato, Alessio Papini, Giacomo Santini, Nadia Mucci, Anna Padula, Claudia Greco, Battogtokh Nasanbat, Gantulga Davaakhuu, Munkhtsetseg Bazarragchaa, Francesco Riga, Claudio Augugliaro, Lorenzo Cecchi, Renato Fani and Marco Zaccaroni

Microorganisms 2024, 12(2), 320; https://doi.org/10.3390/microorganisms12020320 - 3 Feb 2024

Cited by 1 | Viewed by 1703

Abstract

Understanding how microbial communities survive in extreme environmental pressure is critical for interpreting ecological patterns and microbial diversity. Great Gobi A Strictly Protected Area represents an intriguing model for studying the bacterial community since it is a protected and intact wild area of the Mongolian desert. In this work, the composition of a bacterial community of the soil from four oases was characterized by extracting total DNA and sequencing through the Illumina NovaSeq platform. In addition, the soil’s chemical and physical properties were determined, and their influence on shaping the microbial communities was evaluated. The results showed a high variability of bacterial composition among oases. Moreover, combining specific chemical and physical parameters significantly shapes the bacterial community among oases. Data obtained suggested that the oases were highly variable in physiochemical parameters and bacterial communities despite the similar extreme climate conditions. Moreover, core functional microbiome were constituted by aerobic chemoheterotrophy and chemoheterotrophy, mainly contributed by the most abundant bacteria, such as Actinobacteriota, Pseudomonadota, and Firmicutes. This result supposes a metabolic flexibility for sustaining life in deserts. Furthermore, as the inhabitants of the extreme regions are likely to produce new chemical compounds, isolation of key taxa is thus encouraged. Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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13 pages, 2628 KiB

Open AccessArticle

Diversity of Microbial Mats in the Makgadikgadi Salt Pans, Botswana

by Sevasti Filippidou, Alex Price, Charlotte Spencer-Jones, Anthony Scales, Michael C. Macey, Fulvio Franchi, Lesedi Lebogang, Barbara Cavalazzi, Susanne P. Schwenzer and Karen Olsson-Francis

Microorganisms 2024, 12(1), 147; https://doi.org/10.3390/microorganisms12010147 - 11 Jan 2024

Cited by 3 | Viewed by 1512

Abstract

The Makgadikgadi Salt Pans are the remnants of a mega paleo-lake system in the central Kalahari, Botswana. Today, the Makgadikgadi Basin is an arid to semi-arid area receiving water of meteoric origin during the short, wet season. Large microbial mats, which support primary production, are formed due to desiccation during the dry season. This study aimed to characterise the microbial diversity of the microbial mats and the underlying sediment. The focus was the Ntwetwe Pan, located west of the Makgadikgadi Basin. Metagenomic analyses demonstrated that the mats consisted of a high relative abundance of Cyanobacteriota (synonym Cyanobacteria) (20.50–41.47%), Pseudomonadota (synonym Proteobacteria) (15.71 to 32.18%), and Actinomycetota (synonym Actinobacteria) (8.53–32.56%). In the underlying sediments, Pseudomonadota, Actinomycetota, and Euryarchaeota represented over 70% of the community. Localised fluctuations in water content and pH did not significantly affect the microbial diversity of the sediment or the mats. Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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26 pages, 7202 KiB

Open AccessArticle

First Genome Sequence of the Microcolonial Black Fungus Saxispiralis lemnorum MUM 23.14: Insights into the Unique Genomic Traits of the Aeminiaceae Family

by Diana S. Paiva, Luís Fernandes, António Portugal and João Trovão

Microorganisms 2024, 12(1), 104; https://doi.org/10.3390/microorganisms12010104 - 4 Jan 2024

Cited by 1 | Viewed by 1564

Abstract

Saxispiralis lemnorum MUM 23.14 is an extremotolerant microcolonial black fungus, originally isolated from a biodeteriorated limestone artwork in Portugal. This recently introduced species belongs to the Aeminiaceae family, representing the second member of this monophyletic clade. This fungus exhibits a unique set of characteristics, including xerophily, cold tolerance, high UV radiation tolerance, and an exceptional ability to thrive in NaCl concentrations of up to 30% while also enduring pH levels ranging from 5 to 11. To gain insights into its genomic traits associated with stress resistance mechanisms, specialization, and their potential implications in stone biodeterioration, we conducted a comprehensive genome sequencing and analysis. This draft genome not only marks the first for the Saxispiralis genus but also the second for the Aeminiaceae family. Furthermore, we performed two comparative genomic analyses: one focusing on the closest relative within the Aeminiaceae family, Aeminium ludgeri, and another encompassing the genome of different extremotolerant black fungi. In this study, we successfully achieved high genome completeness for S. lemnorum and confirmed its close phylogenetic relationship to A. ludgeri. Our findings revealed traits contributing to its extremophilic nature and provided insights into potential mechanisms contributing to stone biodeterioration. Many traits are common to both Aeminiaceae species and are shared with other black fungi, while numerous unique traits may be attributed to species-specific characteristics. Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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17 pages, 2149 KiB

Open AccessArticle

Analysis of Microbial Diversity in South Shetland Islands and Antarctic Peninsula Soils Based on Illumina High-Throughput Sequencing and Cultivation-Dependent Techniques

by Siqi Cui, Jie Du, Lin Zhu, Di Xin, Yuhua Xin and Jianli Zhang

Microorganisms 2023, 11(10), 2517; https://doi.org/10.3390/microorganisms11102517 - 9 Oct 2023

Cited by 3 | Viewed by 1531

Abstract

To assess the diversity of bacterial taxa in Antarctic soils and obtain novel microbial resources, 15 samples from 3 sampling sites (DIS5, GWS7, FPS10) of South Shetland Islands and 2 sampling sites (APS18, CIS17) of Antarctic Peninsula were collected. High-throughput sequencing (HTS) of 16S rRNA genes within these samples was conducted on an Illumina Miseq platform. A total of 140,303 16S rRNA gene reads comprising 802 operational taxonomic units (OTUs) were obtained. After taxonomic classification, 25 phyla, 196 genera, and a high proportion of unidentified taxa were detected, among which seven phyla and 99 genera were firstly detected in Antarctica. The bacterial communities were dominated by Actinomycetota (40.40%), Pseudomonadota (17.14%), Bacteroidota (10.55%) and Chloroflexota (10.26%). Based on the HTS analyses, cultivation-dependent techniques were optimized to identify the cultivable members. A total of 30 different genera including 91 strains were obtained, the majority of which has previously been reported from Antarctica. However, for the genera Microterricola, Dyadobacter, Filibacter, Duganella, Ensifer, Antarcticirhabdus and Microvirga, this is the first report in Antarctica. In addition, seven strains represented novel taxa, two of which were psychropoilic and could be valuable resources for further research of cold-adaptability and their ecological significance in Antarctica. Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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16 pages, 5376 KiB

Open AccessArticle

Identification, Antioxidant Capacity, and Matrix Metallopeptidase 9 (MMP-9) In Silico Inhibition of Haloarchaeal Carotenoids from Natronococcus sp. and Halorubrum tebenquichense

by Mariana Delgado-Garcia, Osvaldo Gómez-Secundino, Jorge A. Rodríguez, Juan Carlos Mateos-Díaz, Marcelo Muller-Santos, Cristobal N. Aguilar and Rosa Maria Camacho-Ruiz

Microorganisms 2023, 11(9), 2344; https://doi.org/10.3390/microorganisms11092344 - 19 Sep 2023

Cited by 4 | Viewed by 1413

Abstract

Natural pigments from haloarchaea are of great interest; bacterioruberin is the major pigment, it shows higher antioxidant power when compared with β-carotene. However, characterization of bacterioruberin and its isomers along with its antioxidant and the matrix metallopeptidase 9 (MMP-9) inhibition activities in extracts from Natronoccoccus sp. TC6 and Halorubrum tebenquichense SU10 was not previously described, being the aim of this work. The carotenoids profile was performed by UV-Vis spectrophotometry, thin-layer chromatography, nuclear magnetic resonance spectroscopy, and high-resolution mass spectrometry (UPLC-ESI-MS/MS). Antioxidant capacity was determined for DPPH, ABTS, and FRAP. In addition, MMP-9 inhibition was studied using docking simulations. The carotenoid profile of studied strains was composed of bacterioruberin, some derivatives like mono, bis, and tris anhydrobacterioruberin, and also some bacterioruberin cis isomers. The carotenoid pools showed antioxidant capacity for DPPH > ABTS > FRAP; Natronococcus sp. TC6 carotenoid pool was better for ABTS and DPPH, while Halorubrum tebenquichense SU10 carotenoid pool was better for FRAP. Additionally, docking and molecular dynamics suggest that bacterioruberin inhibits MMP-9 through hydrophobic interactions near the catalytic site. Bacterioruberin shows the higher binding energy of −8.3 (kcal/mol). The carotenoids profile of both strains was elucidated, their antioxidant activity and singular participation of each carotenoid on MMP-9 in silico inhibition were evaluated. Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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17 pages, 9569 KiB

Open AccessArticle

Comprehensive Bioinformatics Analysis of the Biodiversity of Lsm Proteins in the Archaea Domain

by Gloria Payá, Vanesa Bautista, Mónica Camacho, Julia Esclapez and María-José Bonete

Microorganisms 2023, 11(5), 1196; https://doi.org/10.3390/microorganisms11051196 - 3 May 2023

Cited by 2 | Viewed by 2059

Abstract

The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq proteins. Sm and Lsm proteins are found in the Eukarya and Archaea domains, respectively, while Hfq proteins exist in the Bacteria domain. Even though Sm and Hfq proteins have been extensively studied, archaeal Lsm proteins still require further exploration. In this work, different bioinformatics tools are used to understand the diversity and distribution of 168 Lsm proteins in 109 archaeal species to increase the global understanding of these proteins. All 109 archaeal species analyzed encode one to three Lsm proteins in their genome. Lsm proteins can be classified into two groups based on molecular weight. Regarding the gene environment of lsm genes, many of these genes are located adjacent to transcriptional regulators of the Lrp/AsnC and MarR families, RNA-binding proteins, and ribosomal protein L37e. Notably, only proteins from species of the class Halobacteria conserved the internal and external residues of the RNA-binding site identified in Pyrococcus abyssi, despite belonging to different taxonomic orders. In most species, the Lsm genes show associations with 11 genes: rpl7ae, rpl37e, fusA, flpA, purF, rrp4, rrp41, hel308, rpoD, rpoH, and rpoN. We propose that most archaeal Lsm proteins are related to the RNA metabolism, and the larger Lsm proteins could perform different functions and/or act through other mechanisms of action. Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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