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Microorganisms
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Microbial Diversity in Extreme Environments 2.0
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Microbial Diversity in Extreme Environments 2.0

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 6660

Special Issue Editors

Dr. Edgardo Rubén Donati

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Guest Editor
CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), Buenos Aires, Argentina
Interests: biomining; bioremediation; extremophiles; acid mine drainage; biotechnology in general
Special Issues, Collections and Topics in MDPI journals
Dr. María Sofía Urbieta

E-Mail Website
Guest Editor
CINDEFI (CCT La Plata-CONICET, Facultad de Ciencias Exactas—UNLP), Universidad Nacional de La Plata (UNLP), Buenos Aires B8508, Argentina
Interests: environmental microbiology; extremophilic microorganisms; biomining; bioremediation of heavy metals
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Extreme environments, characterized by physicochemical conditions beyond those considered normal for human life, have proven to be the habitat of fascinating microbial communities. The examination of microbial diversity in these environments, including deserts, hot springs, glaciers and even sites impacted by anthropogenic activities, has allowed not only a detailed understanding of the biogeochemistry of these places, but also the detection and eventual isolation of numerous new microbial species. Next-generation sequencing technologies have triggered a drastic change in biodiversity studies, providing better and much more detailed answers to the questions on structure and dynamics of microbial communities in each environment, but they have also opened new doors for the investigation of possible biotechnological applications from microorganisms, consortia and even biomolecules obtained from these extremophilic communities.

In this context, this second version of the successful Special Issue of Microorganisms “Microbial Diversity in Extreme Environments” invites you to send contributions concerning any aspect related to the microbial diversity found in extreme environments, be they natural or of anthropogenic origin, as well as the potential applications of the bacteria, archaea, or eukaryotes that inhabit them. The topics covered in this Special Issue include taxonomic diversity assessment, biogeochemical interrelationships, the temporal/spatial evolution of microbial communities exposed to changes in their environment, and the potential biotechnological applications of extremophiles obtained from extreme environments.

Dr. Edgardo Rubén Donati
Dr. María Sofía Urbieta
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 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • extremophiles
  • microbial ecology
  • metagenomics
  • microbial applications
  • geomicrobiology

Related Special Issue

Published Papers (6 papers)

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Research

15 pages, 1940 KiB  
Article
Analysis of Culturable Bacterial Diversity of Pangong Tso Lake via a 16S rRNA Tag Sequencing Approach
by Pooja Yadav, Joyasree Das, Shiva S. Sundharam and Srinivasan Krishnamurthi
Microorganisms 2024, 12(2), 397; https://doi.org/10.3390/microorganisms12020397 - 17 Feb 2024
Viewed by 941
Abstract
The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing [...] Read more.
The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments 2.0)
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21 pages, 5431 KiB  
Article
The First Description of the Microbial Diversity in the Amarillo River (La Rioja, Argentina), a Natural Extreme Environment Where the Whole Microbial Community Paints the Landscape Yellow
by Cecilia Elena Bernardelli, Deborah Colman, Edgardo Ruben Donati and María Sofía Urbieta
Microorganisms 2024, 12(2), 235; https://doi.org/10.3390/microorganisms12020235 - 23 Jan 2024
Viewed by 724
Abstract
The Amarillo River in Famatina, La Rioja, Argentina, is a natural acidic river with distinctive yellow-ochreous iron precipitates along its course. While mining activities have occurred in the area, the river’s natural acidity is influenced by environmental factors beyond mineralogy, where microbial species [...] Read more.
The Amarillo River in Famatina, La Rioja, Argentina, is a natural acidic river with distinctive yellow-ochreous iron precipitates along its course. While mining activities have occurred in the area, the river’s natural acidity is influenced by environmental factors beyond mineralogy, where microbial species have a crucial role. Although iron-oxidising bacteria have been identified, a comprehensive analysis of the entire microbial community in this extreme environment has not yet been conducted. In this study, we employ high-throughput sequencing to explore the bacterial and fungal diversity in the Amarillo River and Cueva de Pérez terraces, considered prehistoric analogues of the current river basin. Fe(II)-enrichment cultures mimicking different environmental conditions of the river were also analysed to better understand the roles of prokaryotes and fungi in iron oxidation processes. Additionally, we investigate the ecological relationships between bacteria and fungi using co-occurrence and network analysis. Our findings reveal a diverse bacterial community in the river and terraces, including uncultured species affiliated with Acidimicrobiia, part of an uncharacterised universal microbial acidic diversity. Acidophiles such as Acidithiobacillus ferrivorans, the main iron oxidiser of the system, and Acidiphilium, which is unable to catalyse Fe(II) oxidation but has a great metabolic flexibility,, are part of the core of the microbial community, showing significant involvement in intraspecies interactions. Alicyclobacillus, which is the main Fe(II) oxidiser in the enrichment culture at 30 °C and is detected all over the system, highlights its flexibility towards the iron cycle. The prevalence of key microorganisms in both rivers and terraces implies their enduring contribution to the iron cycle as well as in shaping the iconic yellow landscape of the Amarillo River. In conclusion, this study enhances our understanding of microbial involvement in iron mineral precipitation, emphasising the collaborative efforts of bacteria and fungi as fundamental geological agents in the Amarillo River. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments 2.0)
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14 pages, 1853 KiB  
Article
Changes in Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria along a Glacier Retreating Chronosequence in the Tianshan Mountains, China
by Xiukun Wu, Wei Zhang, Guangxiu Liu, Tuo Chen and Zhongqin Li
Microorganisms 2023, 11(12), 2871; https://doi.org/10.3390/microorganisms11122871 - 27 Nov 2023
Viewed by 679
Abstract
Glaciers retreating due to global warming create important new habitats, particularly suitable for studying ecosystem development where nitrogen is a limiting factor. Nitrogen availability mainly results from microbial decomposition and transformation processes, including nitrification. AOA and AOB perform the first and rate-limiting step [...] Read more.
Glaciers retreating due to global warming create important new habitats, particularly suitable for studying ecosystem development where nitrogen is a limiting factor. Nitrogen availability mainly results from microbial decomposition and transformation processes, including nitrification. AOA and AOB perform the first and rate-limiting step of nitrification. Investigating the abundance and diversity of AOA and AOB is essential for understanding early ecosystem development. The dynamics of AOA and AOB community structure along a soil chronosequence in Tianshan No. 1 Glacier foreland were analyzed using qPCR and clone library methods. The results consistently showed low quantities of both AOA and AOB throughout the chronosequence. Initially, the copy numbers of AOB were higher than those of AOA, but they decreased in later stages. The AOB community was dominated by “Nitrosospira cluster ME”, while the AOA community was dominated by “the soil and sediment 1”. Both communities were potentially connected to supra- and subglacial microbial communities during early stages. Correlation analysis revealed a significant positive correlation between the ratios of AOA and AOB with soil ammonium and total nitrogen levels. These results suggest that variations in abundance and diversity of AOA and AOB along the chronosequences were influenced by ammonium availability during glacier retreat. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments 2.0)
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23 pages, 3769 KiB  
Article
Bioprospecting of Actinobacterial Diversity and Antibacterial Secondary Metabolites from the Sediments of Four Saline Lakes on the Northern Tibetan Plateau
by Shao-Wei Liu, Xiao-Xu Zhai, Di Liu, Yu-Yu Liu, Li-Ying Sui, Ke-Ke Luo, Qin Yang, Fei-Na Li, Arina A. Nikandrova, Arina N. Imamutdinova, Dmitrii A. Lukianov, Ilya A. Osterman, Petr V. Sergiev, Ben-Yin Zhang, De-Jun Zhang, Chun-Mei Xue and Cheng-Hang Sun
Microorganisms 2023, 11(10), 2475; https://doi.org/10.3390/microorganisms11102475 - 01 Oct 2023
Viewed by 1755
Abstract
The Tibetan Plateau, known as the “Roof of the World” and “The Third Pole”, harbors numerous saline lakes primarily distributed in the Northern Tibetan Plateau. However, the challenging conditions of high altitude, low oxygen level, and harsh climate have limited investigations into the [...] Read more.
The Tibetan Plateau, known as the “Roof of the World” and “The Third Pole”, harbors numerous saline lakes primarily distributed in the Northern Tibetan Plateau. However, the challenging conditions of high altitude, low oxygen level, and harsh climate have limited investigations into the actinobacteria from these saline lakes. This study focuses on investigating the biodiversity and bioactive secondary metabolites of cultivable actinobacteria isolated from the sediments of four saline lakes on the Northern Tibetan Plateau. A total of 255 actinobacterial strains affiliated with 21 genera in 12 families of 7 orders were recovered by using the pure culture technique and 16S rRNA gene phylogenetic analysis. To facilitate a high-throughput bioactivity evaluation, 192 isolates underwent OSMAC cultivation in a miniaturized 24-well microbioreactor system (MATRIX cultivation). The antibacterial activity of crude extracts was then evaluated in a 96-well plate antibacterial assay. Forty-six strains demonstrated antagonistic effects against at least one tested pathogen, and their underlying antibacterial mechanisms were further investigated through a dual-fluorescent reporter assay (pDualrep2). Two Streptomyces strains (378 and 549) that produce compounds triggering DNA damage were prioritized for subsequent chemical investigations. Metabolomics profiling involving HPLC-UV/vis, UPLC-QTOF-MS/MS, and molecular networking identified three types of bioactive metabolites belonging to the aromatic polyketide family, i.e., cosmomycin, kidamycin, and hedamycin. In-depth analysis of the metabolomic data unveiled some potentially novel anthracycline compounds. A genome mining study based on the whole-genome sequences of strains 378 and 549 identified gene clusters potentially responsible for cosmomycin and kidamycin biosynthesis. This work highlights the effectiveness of combining metabolomic and genomic approaches to rapidly identify bioactive chemicals within microbial extracts. The saline lakes on the Northern Tibetan Plateau present prospective sources for discovering novel actinobacteria and biologically active compounds. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments 2.0)
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14 pages, 3885 KiB  
Article
Novel Insights on the Bacterial and Archaeal Diversity of the Panarea Shallow-Water Hydrothermal Vent Field
by Erika Arcadi, Emanuela Buschi, Eugenio Rastelli, Michael Tangherlini, Pasquale De Luca, Valentina Esposito, Rosario Calogero, Franco Andaloro, Teresa Romeo and Roberto Danovaro
Microorganisms 2023, 11(10), 2464; https://doi.org/10.3390/microorganisms11102464 - 30 Sep 2023
Viewed by 867
Abstract
Current knowledge of the microbial diversity of shallow-water hydrothermal vents is still limited. Recent evidence suggests that these peculiar and heterogeneous systems might host highly diversified microbial assemblages with novel or poorly characterized lineages. In the present work, we used 16S rRNA gene [...] Read more.
Current knowledge of the microbial diversity of shallow-water hydrothermal vents is still limited. Recent evidence suggests that these peculiar and heterogeneous systems might host highly diversified microbial assemblages with novel or poorly characterized lineages. In the present work, we used 16S rRNA gene metabarcoding to provide novel insights into the diversity of the bacterial and archaeal assemblages in seawater and sediments of three shallow-water hydrothermal systems of Panarea Island (Tyrrhenian Sea). The three areas were characterized by hot, cold, or intermediate temperatures and related venting activities. Microbial biodiversity in seawater largely differed from the benthic one, both in α-diversity (i.e., richness of amplicon sequence variants—ASVs) and in prokaryotic assemblage composition. Furthermore, at the class level, the pelagic prokaryotic assemblages were very similar among sites, whereas the benthic microbial assemblages differed markedly, reflecting the distinct features of the hydrothermal activities at the three sites we investigated. Our results show that ongoing high-temperature emissions can influence prokaryotic α-diversity at the seafloor, increasing turnover (β-)diversity, and that the intermediate-temperature-venting spot that experienced a violent gas explosion 20 years ago now displays the highest benthic prokaryotic diversity. Overall, our results suggest that hydrothermal vent dynamics around Panarea Island can contribute to an increase in the local heterogeneity of physical–chemical conditions, especially at the seafloor, in turn boosting the overall microbial (γ-)diversity of this peculiar hydrothermal system. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments 2.0)
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17 pages, 5970 KiB  
Article
Different Responses of Bacteria and Archaea to Environmental Variables in Brines of the Mahai Potash Mine, Qinghai-Tibet Plateau
by Linglu Xie, Shan Yu, Xindi Lu, Siwei Liu, Yukai Tang and Hailong Lu
Microorganisms 2023, 11(8), 2002; https://doi.org/10.3390/microorganisms11082002 - 03 Aug 2023
Cited by 1 | Viewed by 1031
Abstract
Salt mines feature both autochthonous and allochthonous microbial communities introduced by industrialization. It is important to generate the information on the diversity of the microbial communities present in the salt mines and how they are shaped by the environment representing ecological diversification. Brine [...] Read more.
Salt mines feature both autochthonous and allochthonous microbial communities introduced by industrialization. It is important to generate the information on the diversity of the microbial communities present in the salt mines and how they are shaped by the environment representing ecological diversification. Brine from Mahai potash mine (Qianghai, China), an extreme hypersaline environment, is used to produce potash salts for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. In this study, using high-throughput 16S rRNA gene amplicon sequencing and estimation of physicochemical variables, we examined brine samples collected from locations with the gradient of industrial activity intensity and discrete hydrochemical compositions in the Mahai potash mine. Our findings revealed a highly diverse bacterial community, mainly composed of Pseudomonadota in the hypersaline brines from the industrial area, whereas in the natural brine collected from the upstream Mahai salt lake, most of the 16S rRNA gene reads were assigned to Bacteroidota. Halobacteria and halophilic methanogens dominated archaeal populations. Furthermore, we discovered that in the Mahai potash mining area, bacterial communities tended to respond to anthropogenic influences. In contrast, archaeal diversity and compositions were primarily shaped by the chemical properties of the hypersaline brines. Conspicuously, distinct methanogenic communities were discovered in sets of samples with varying ionic compositions, indicating their strong sensitivity to the brine hydrochemical alterations. Our findings provide the first taxonomic snapshot of microbial communities from the Mahai potash mine and reveal the different responses of bacteria and archaea to environmental variations in this high-altitude aquatic ecosystem. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments 2.0)
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