Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.7
3.6
Journals
Biology
Special Issues
Functions, Diversity and Molecular Ecology of Microbe in Extreme Environments
share announcement

Functions, Diversity and Molecular Ecology of Microbe in Extreme Environments

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (30 August 2023) | Viewed by 10331

Special Issue Editors

Dr. Gaosen Zhang

E-Mail Website1 Website2
Guest Editor
Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
Interests: microbial ecology and microbial resources in varied extreme environments, especially radiation-resistant microorganisms
Dr. Wasim Sajjad

E-Mail Website
Guest Editor
Department of Biological Sciences, Section Microbiology and Immunology, National University of Medical Sciences, Rawalpindi 46000, Pakistan
Interests: extremophiles; radio-resistant microbes; extremozymes; value added chemicals/compounds; secondary metabolites
Dr. Imran Khan

E-Mail Website
Guest Editor
Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
Interests: marine microbiology; microbial natural products; analytical chemistry; fermentation technology; metabolomics and proteomics

Special Issue Information

Dear Colleagues,

The revolutionary history in most of our planet is dominated by prokaryotes, continuously evolving and adapting themselves in extreme niches. Extremophiles in particular, those thriving under multiple extreme conditions such as high temperature, salt, acidity, pressure, radiation, and limiting nutrient conditions, represent key areas of research. Extremophiles do not only survive under such harsh environmental conditions but are also now considered among one of the superclass to cope with high-level radiations, microgravity, vaccum, and pressure in space.

In this issue, we invite submissions pertaining to how microbes respond to extreme environments at different ecological levels: from community to individuals. At the community level, extreme environments select the suitable microorganisms from the available seed pool and the stresses shape their populations. Stress gradient is very helpful for disentangling the mechanisms in microbial community assembly. At the individual level, indigenous microorganisms have evolved specific genetic capabilities to survive and sometimes thrive under harsh environmental conditions. To protect cells from extreme environmental stresses, they may produce bioactive products, including specific small organic molecules (extremolytes).

Recent advances in cultivation, DNA sequencing technologies, and -omics (metagenomics, metaproteomics, etc.) methods have greatly contributed to the rapid advancement of our understanding of microbial diversity, ecological function, and interactions with extreme environments. With this proposed research topic we aim to report on the recent advances in our understanding of how microbes live in extreme habitats, to unlock major scientific discoveries, and also to advance the field of extremophiles. We welcome contributions of original research articles, reviews, or opinions that are related to the proposed topic. Here, due to the particularity of indigenous microorganisms in extreme environments, we especially encourage submissions about studies with culture-dependent methods and microbial characteristics related to environmental stress.

Dr. Gaosen Zhang
Dr. Wasim Sajjad
Dr. Imran Khan 
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. Biology 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

  • extreme environment

  • microbial community
  • extremophiles
  • extremolytes
  • resistant mechanism
  • microbial ecology
  • biosignatures
  • microbe-environment interactions

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

15 pages, 2848 KiB  
Article
Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies
by Weronika Goraj, Anna Pytlak, Jarosław Grządziel, Anna Gałązka, Zofia Stępniewska and Anna Szafranek-Nakonieczna
Biology 2023, 12(11), 1420; https://doi.org/10.3390/biology12111420 - 11 Nov 2023
Viewed by 1060
Abstract
The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of [...] Read more.
The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH4 mL−1 day−1. Full article
(This article belongs to the Special Issue Functions, Diversity and Molecular Ecology of Microbe in Extreme Environments)
►▼ Show Figures

Figure 1

23 pages, 6618 KiB  
Article
Metagenomic and Culture-Based Analyses of Microbial Communities from Petroleum Reservoirs with High-Salinity Formation Water, and Their Biotechnological Potential
by Vitaly V. Kadnikov, Nikolai V. Ravin, Diyana S. Sokolova, Ekaterina M. Semenova, Salimat K. Bidzhieva, Alexey V. Beletsky, Alexey P. Ershov, Tamara L. Babich, Marat R. Khisametdinov, Andrey V. Mardanov and Tamara N. Nazina
Biology 2023, 12(10), 1300; https://doi.org/10.3390/biology12101300 - 2 Oct 2023
Cited by 2 | Viewed by 1542
Abstract
The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum [...] Read more.
The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum reservoirs, microbial community composition was studied for petroleum reservoirs with high-salinity formation water located in Tatarstan (Russia) using metagenomic and culture-based approaches. Bacteria of the phyla Desulfobacterota, Halanaerobiaeota, Sinergistota, Pseudomonadota, and Bacillota were revealed using 16S rRNA-based high-throughput sequencing in halophilic microbial communities. Sulfidogenic bacteria predominated in the studied oil fields. The 75 metagenome-assembled genomes (MAGs) of prokaryotes reconstructed from water samples were assigned to 16 bacterial phyla, including Desulfobacterota, Bacillota, Pseudomonadota, Thermotogota, Actinobacteriota, Spirochaetota, and Patescibacteria, and to archaea of the phylum Halobacteriota (genus Methanohalophilus). Results of metagenomic analyses were supported by the isolation of 20 pure cultures of the genera Desulfoplanes, Halanaerobium, Geotoga, Sphaerochaeta, Tangfeifania, and Bacillus. The isolated halophilic fermentative bacteria produced oil-displacing metabolites (lower fatty acids, alcohols, and gases) from sugar-containing and proteinaceous substrates, which testify their potential for MEOR. However, organic substrates stimulated the growth of sulfidogenic bacteria, in addition to fermenters. Methods for enhanced oil recovery should therefore be developed, combining the production of oil-displacing compounds with fermentative bacteria and the suppression of sulfidogenesis. Full article
(This article belongs to the Special Issue Functions, Diversity and Molecular Ecology of Microbe in Extreme Environments)
►▼ Show Figures

Graphical abstract

18 pages, 2652 KiB  
Article
Prokaryotic Life Associated with Coal-Fire Gas Vents Revealed by Metagenomics
by Vitaly V. Kadnikov, Andrey V. Mardanov, Alexey V. Beletsky, Olga V. Karnachuk and Nikolai V. Ravin
Biology 2023, 12(5), 723; https://doi.org/10.3390/biology12050723 - 15 May 2023
Cited by 1 | Viewed by 1493
Abstract
The natural combustion of underground coal seams leads to the formation of gas, which contains molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific thermal ecosystems are formed. Here, 16S rRNA gene profiling and shotgun [...] Read more.
The natural combustion of underground coal seams leads to the formation of gas, which contains molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific thermal ecosystems are formed. Here, 16S rRNA gene profiling and shotgun metagenome sequencing were employed to characterize the taxonomic diversity and genetic potential of prokaryotic communities of the near-surface ground layer near hot gas vents in an open quarry heated by a subsurface coal fire. The communities were dominated by only a few groups of spore-forming Firmicutes, namely the aerobic heterotroph Candidatus Carbobacillus altaicus, the aerobic chemolitoautotrophs Kyrpidia tusciae and Hydrogenibacillus schlegelii, and the anaerobic chemolithoautotroph Brockia lithotrophica. Genome analysis predicted that these species can obtain energy from the oxidation of hydrogen and/or carbon monoxide in coal gases. We assembled the first complete closed genome of a member of uncultured class-level division DTU015 in the phylum Firmicutes. This bacterium, ‘Candidatus Fermentithermobacillus carboniphilus’ Bu02, was predicted to be rod-shaped and capable of flagellar motility and sporulation. Genome analysis showed the absence of aerobic and anaerobic respiration and suggested chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, N-acetylglucosamine, and tricarboxylic acid cycle intermediates. Bu02 bacterium probably plays the role of a scavenger, performing the fermentation of organics formed by autotrophic Firmicutes supported by coal gases. A comparative genome analysis of the DTU015 division revealed that most of its members have a similar lifestyle. Full article
(This article belongs to the Special Issue Functions, Diversity and Molecular Ecology of Microbe in Extreme Environments)
►▼ Show Figures

Figure 1

24 pages, 20405 KiB  
Article
Rediscovery of Remarkably Rare Anaerobic Tentaculiferous Ciliate Genera Legendrea and Dactylochlamys (Ciliophora: Litostomatea)
by Ondřej Pomahač, Daniel Méndez-Sánchez, Kateřina Poláková, Michael Müller, Michel-Marie Solito, William A. Bourland and Ivan Čepička
Biology 2023, 12(5), 707; https://doi.org/10.3390/biology12050707 - 12 May 2023
Cited by 2 | Viewed by 2587
Abstract
Free-living anaerobic ciliates are of considerable interest from an ecological and an evolutionary standpoint. Extraordinary tentacle-bearing predatory lineages have evolved independently several times within the phylum Ciliophora, including two rarely encountered anaerobic litostomatean genera, Legendrea and Dactylochlamys. In this study, we significantly [...] Read more.
Free-living anaerobic ciliates are of considerable interest from an ecological and an evolutionary standpoint. Extraordinary tentacle-bearing predatory lineages have evolved independently several times within the phylum Ciliophora, including two rarely encountered anaerobic litostomatean genera, Legendrea and Dactylochlamys. In this study, we significantly extend the morphological and phylogenetic characterization of these two poorly known groups of predatory ciliates. We provide the first phylogenetic analysis of the monotypic genus Dactylochlamys and the three valid species of Legendrea based on the 18S rRNA gene and ITS-28S rRNA gene sequences. Prior to this study, neither group had been studied using silver impregnation methods. We provide the first protargol-stained material and also a unique video material including documentation, for the first time, of the hunting and feeding behavior of a Legendrea species. We briefly discuss the identity of methanogenic archaeal and bacterial endosymbionts of both genera based on 16S rRNA gene sequences, and the importance of citizen science for ciliatology from a historical and contemporary perspective. Full article
(This article belongs to the Special Issue Functions, Diversity and Molecular Ecology of Microbe in Extreme Environments)
►▼ Show Figures

Figure 1

Review

Jump to: Research

19 pages, 1532 KiB  
Review
Challenges and Approaches of Culturing the Unculturable Archaea
by Muhammad Rafiq, Noor Hassan, Maliha Rehman, Muhammad Hayat, Gullasht Nadeem, Farwa Hassan, Naveed Iqbal, Hazrat Ali, Sahib Zada, Yingqian Kang, Wasim Sajjad and Muhsin Jamal
Biology 2023, 12(12), 1499; https://doi.org/10.3390/biology12121499 - 7 Dec 2023
Cited by 3 | Viewed by 2851
Abstract
Since Carl Woese’s discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved [...] Read more.
Since Carl Woese’s discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices. Full article
(This article belongs to the Special Issue Functions, Diversity and Molecular Ecology of Microbe in Extreme Environments)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop