Microbial Life in Extreme Environments

A topical collection in Microorganisms (ISSN 2076-2607). This collection belongs to the section "Environmental Microbiology".

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Collection Editor
Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
Interests: molecular ecology of extreme environments; acidophiles; halophiles; subsurface geomicrobiology; astrobiology
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

We are pleased to announce the launch of a new Topical Collection entitled "Microbial Life in Extreme Environments". This Topical Collection aims to provide new insights into any aspect related of extremophiles, from the microbial ecology of diverse extreme environments to the physiology and molecular biology of extremophiles from the three domains and from the fundamental to the applied aspects of extreme microorganisms. We hope that this collection will provide an important forum for the dissemination of highly relevant research findings as well as the sharing of innovative ideas within the field.

We look forward to receiving your contributions.

Dr. Ricardo Amils
Collection Editor

Manuscript Submission Information

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Published Papers (9 papers)

2024

Jump to: 2023, 2022, 2021

14 pages, 2872 KiB  
Article
Fungal Methane Production Under High Hydrostatic Pressure in Deep Subseafloor Sediments
by Mengshi Zhao, Dongxu Li, Jie Liu, Jiasong Fang and Changhong Liu
Microorganisms 2024, 12(11), 2160; https://doi.org/10.3390/microorganisms12112160 - 26 Oct 2024
Viewed by 371
Abstract
Fungi inhabiting deep subseafloor sediments have been shown to possess anaerobic methane (CH4) production capabilities under atmospheric conditions. However, their ability to produce CH4 under in situ conditions with high hydrostatic pressure (HHP) remains unclear. Here, Schizophyllum commune 20R-7-F01, isolated [...] Read more.
Fungi inhabiting deep subseafloor sediments have been shown to possess anaerobic methane (CH4) production capabilities under atmospheric conditions. However, their ability to produce CH4 under in situ conditions with high hydrostatic pressure (HHP) remains unclear. Here, Schizophyllum commune 20R-7-F01, isolated from ~2 km below the seafloor, was cultured in Seawater Medium (SM) in culture bottles fitted with sterile syringes for pressure equilibration. Subsequently, these culture bottles were transferred into 1 L stainless steel pressure vessels at 30 °C for 5 days to simulate in situ HHP and anaerobic environments. Our comprehensive analysis of bioactivity, biomass, and transcriptomics revealed that the S. commune not only survived but significantly enhanced CH4 production, reaching approximately 2.5 times higher levels under 35 MPa HHP compared to 0.1 MPa standard atmospheric pressure. Pathways associated with carbohydrate metabolism, methylation, hydrolase activity, cysteine and methionine metabolism, and oxidoreductase activity were notably activated under HHP. Specifically, key genes involved in fungal anaerobic CH4 synthesis, including methyltransferase mct1 and dehalogenase dh3, were upregulated 7.9- and 12.5-fold, respectively, under HHP. Enhanced CH4 production under HHP was primarily attributed to oxidative stress induced by pressure, supported by intracellular reactive oxygen species (ROS) levels and comparative treatments with cadmium chloride and hydrogen peroxide. These results may provide a strong theoretical basis and practical guidance for future studies on the contribution of fungi to global CH4 flux. Full article
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18 pages, 5054 KiB  
Article
Association of Acidotolerant Cyanobacteria to Microbial Mats below pH 1 in Acidic Mineral Precipitates in Río Tinto River in Spain
by Felipe Gómez, Nuria Rodríguez, José Antonio Rodríguez-Manfredi, Cristina Escudero, Ignacio Carrasco-Ropero, José M. Martínez, Marco Ferrari, Simone De Angelis, Alessandro Frigeri, Maite Fernández-Sampedro and Ricardo Amils
Microorganisms 2024, 12(4), 829; https://doi.org/10.3390/microorganisms12040829 - 19 Apr 2024
Viewed by 1103
Abstract
This report describes acidic microbial mats containing cyanobacteria that are strongly associated to precipitated minerals in the source area of Río Tinto. Río Tinto (Huelva, Southwestern Spain) is an extreme acidic environment where iron and sulfur cycles play a fundamental role in sustaining [...] Read more.
This report describes acidic microbial mats containing cyanobacteria that are strongly associated to precipitated minerals in the source area of Río Tinto. Río Tinto (Huelva, Southwestern Spain) is an extreme acidic environment where iron and sulfur cycles play a fundamental role in sustaining the extremely low pH and the high concentration of heavy metals, while maintaining a high level of microbial diversity. These multi-layered mineral deposits are stable all year round and are characterized by a succession of thick greenish-blue and brownish layers mainly composed of natrojarosite. The temperature and absorbance above and below the mineral precipitates were followed and stable conditions were detected inside the mineral precipitates. Different methodologies, scanning and transmission electron microscopy, immunological detection, fluorescence in situ hybridization, and metagenomic analysis were used to describe the biodiversity existing in these microbial mats, demonstrating, for the first time, the existence of acid-tolerant cyanobacteria in a hyperacidic environment of below pH 1. Up to 0.46% of the classified sequences belong to cyanobacterial microorganisms, and 1.47% of the aligned DNA reads belong to the Cyanobacteria clade. Full article
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2023

Jump to: 2024, 2022, 2021

15 pages, 5474 KiB  
Article
Shock-Impacts and Vibrational g-Forces Can Dislodge Bacillus spp. Spores from Spacecraft Surfaces
by Andrew C. Schuerger and Adriana V. Borrell
Microorganisms 2023, 11(10), 2421; https://doi.org/10.3390/microorganisms11102421 - 28 Sep 2023
Viewed by 1391
Abstract
Mars spacecraft encounter numerous g-loads that occur along the launch or landing vectors (called axial vectors) or along lateral off-axes vectors. The goal of this research was to determine if there was a threshold for dislodging spores under brute-force dynamic shock compressional [...] Read more.
Mars spacecraft encounter numerous g-loads that occur along the launch or landing vectors (called axial vectors) or along lateral off-axes vectors. The goal of this research was to determine if there was a threshold for dislodging spores under brute-force dynamic shock compressional impacts (i.e., henceforth called shock-impacts) or long-term vibrationally induced g-loads that might simulate spacecraft launches or landings profiles. Results indicated that spores of Bacillus subtilis 168 and B. atrophaeus ATCC 9372 were dislodged from ChemFilm-coated aluminum coupons during shock impact events of 60 g’s or higher. In contrast, the threshold for dislodging B. pumilus SAFR-032 spores was approx. 80 g’s. Vibrational g-loading was conducted at approx. 12–15 g’s (z-axis) and 77 Hz. All three Bacillus spp. exhibited very modest spore dislodgement at 1, 4, or 8 min of induced vibrational g-loads. However, the numbers of spores released depended on the Earth’s g-vector relative to the bacterial monolayers. When the experimental hardware was placed in an ‘Up’ orientation (defined as the spores sat on the upper surface of the coupons and the coupons pointed up and away from Earth’s g-vector), zero to only a few spores were dislodged. When the experimental hardware was inverted and the coupon surfaces were in a ‘Down’ orientation, the number of spores released increased by 20–30 times. Overall, the results of both assays suggest that spores on spacecraft surfaces will not likely be dislodged during nominal launch and landing scenarios, with the exception of jettisoned hardware (e.g., heat shields or backshells) during landing that might hit the Martian terrain at high g’s. However, off-nominal landings hitting the Martian surface at >60 g’s are likely to release low numbers of spores into the atmosphere and regolith. Full article
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12 pages, 1683 KiB  
Article
Long-Term Monitoring of Bioaerosols in an Environment without UV and Desiccation Stress, an Example from the Cave Postojnska Jama, Slovenia
by Janez Mulec, Sara Skok, Rok Tomazin, Jasmina Letić, Tadej Pliberšek, Sanja Stopinšek and Saša Simčič
Microorganisms 2023, 11(3), 809; https://doi.org/10.3390/microorganisms11030809 - 22 Mar 2023
Cited by 5 | Viewed by 1978
Abstract
A natural cave environment subject to regular human visitation was selected for aerobiological study to minimize the effects of severe temperature fluctuations, UV radiation, and desiccation stress on the aerobiome. The longer sampling period of bioaerosols, up to 22 months, was generally not [...] Read more.
A natural cave environment subject to regular human visitation was selected for aerobiological study to minimize the effects of severe temperature fluctuations, UV radiation, and desiccation stress on the aerobiome. The longer sampling period of bioaerosols, up to 22 months, was generally not associated with a proportionally incremental and cumulative increase of microbial biomass. The culture-independent biomass indicator ATP enabled quick and reliable determination of the total microbial biomass. Total airborne microbial biomass was influenced by human visitation to the cave, as confirmed by significantly higher concentrations being observed along tourist footpaths (p < 0.05). Airborne beta-glucans (BG) and lipopolysaccharide (LPS) are present in cave air, but their impact on the cave remains to be evaluated. Staphylococcus spp., as an indicator of human presence, was detected at all sites studied. Their long-term survival decrease is likely due to high relative humidity, low temperature, the material to which they adhere, and potentially natural elevated radon concentration. The most commonly recorded species were: S. saprophyticus, which was identified in 52% of the studied sites, S. equorum in 29%, and S. warneri in 24% of the studied sites. Only a few isolates were assigned to Risk group 2: S. aureus, S. epidermidis, S. haemolyticus, S. pasteuri, and S. saprophyticus. Full article
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2022

Jump to: 2024, 2023, 2021

12 pages, 1111 KiB  
Article
Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in Halobacterium salinarum
by Evelyn Ayumi Onga, Ricardo Z. N. Vêncio and Tie Koide
Microorganisms 2022, 10(12), 2442; https://doi.org/10.3390/microorganisms10122442 - 10 Dec 2022
Cited by 2 | Viewed by 2151
Abstract
Halobacterium salinarum NRC-1 is an extremophile that grows optimally at 4.3 M NaCl concentration. In spite of being an established model microorganism for the archaea domain, direct comparisons between its proteome and transcriptome during osmotic stress are still not available. Through RNA-seq-based transcriptomics, [...] Read more.
Halobacterium salinarum NRC-1 is an extremophile that grows optimally at 4.3 M NaCl concentration. In spite of being an established model microorganism for the archaea domain, direct comparisons between its proteome and transcriptome during osmotic stress are still not available. Through RNA-seq-based transcriptomics, we compared a low salt (2.6 M NaCl) stress condition with 4.3 M of NaCl and found 283 differentially expressed loci. The more commonly found classes of genes were: ABC-type transporters and transcription factors. Similarities, and most importantly, differences between our findings and previously published datasets in similar experimental conditions are discussed. We validated three important biological processes differentially expressed: gas vesicles production (due to down-regulation of gvpA1b, gvpC1b, gvpN1b, and gvpO1b); archaellum formation (due to down-regulation of arlI, arlB1, arlB2, and arlB3); and glycerol metabolism (due to up-regulation of glpA1, glpB, and glpC). Direct comparison between transcriptomics and proteomics showed 58% agreement between mRNA and protein level changes, pointing to post-transcriptional regulation candidates. From those genes, we highlight rpl15e, encoding for the 50S ribosomal protein L15e, for which we hypothesize an ionic strength-dependent conformational change that guides post-transcriptional processing of its mRNA and, thus, possible salt-dependent regulation of the translation machinery. Full article
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16 pages, 5648 KiB  
Article
Antarctic Salt-Cones: An Oasis of Microbial Life? The Example of Boulder Clay Glacier (Northern Victoria Land)
by Maurizio Azzaro, Maria Papale, Carmen Rizzo, Emanuele Forte, Davide Lenaz, Mauro Guglielmin and Angelina Lo Giudice
Microorganisms 2022, 10(9), 1753; https://doi.org/10.3390/microorganisms10091753 - 30 Aug 2022
Cited by 5 | Viewed by 2074
Abstract
The evaporation of a localized, highly saline water body of the Boulder Clay debris-covered glacier, in the Northern Victoria Land, probably generated the accumulation of mirabilite (Na2SO4 × 10H2O) and thenardite (Na2SO4) in a [...] Read more.
The evaporation of a localized, highly saline water body of the Boulder Clay debris-covered glacier, in the Northern Victoria Land, probably generated the accumulation of mirabilite (Na2SO4 × 10H2O) and thenardite (Na2SO4) in a glacier salt-cone. Such an extremely cold and salty environment resembles the conditions on Mars, so it can be considered a terrestrial analog. The study was aimed at gaining a first glimpse at the prokaryotic community associated with Antarctic mirabilite and thenardite minerals and also to find clues about the origin of the salts. For this purpose, samples were analyzed by a next generation approach to investigate the prokaryotic (Bacteria and Archaea) diversity. Phylogenetic analysis allowed the identification of Bacteroidota, Actinobacteriota, Firmicutes, and Gammaproteobacteria as the main bacterial lineages, in addition to Archaea in the phylum Halobacterota. The genera Arthrobacter, Rhodoglobus, Gillisia, Marinobacter and Psychrobacter were particularly abundant. Interestingly, several bacterial and archaeal sequences were related to halotolerant and halophilic genera, previously reported in a variety of marine environments and saline habitats, also in Antarctica. The analyzed salt community also included members that are believed to play a major role in the sulfur cycle. Full article
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19 pages, 1377 KiB  
Article
Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt
by Guillermo Mateos, Adrián Martínez Bonilla, Sofía de Francisco de Polanco, José M. Martínez, Cristina Escudero, Nuria Rodríguez, Irene Sánchez-Andrea and Ricardo Amils
Microorganisms 2022, 10(8), 1585; https://doi.org/10.3390/microorganisms10081585 - 6 Aug 2022
Cited by 7 | Viewed by 3153
Abstract
The Iberian Pyrite Belt (IPB) is one of the largest deposits of sulphidic minerals on Earth. Río Tinto raises from its core, presenting low a pH and high metal concentration. Several drilling cores were extracted from the IPB’s subsurface, and strain T2.3D-1.1 was [...] Read more.
The Iberian Pyrite Belt (IPB) is one of the largest deposits of sulphidic minerals on Earth. Río Tinto raises from its core, presenting low a pH and high metal concentration. Several drilling cores were extracted from the IPB’s subsurface, and strain T2.3D-1.1 was isolated from a core at 121.8 m depth. We aimed to characterize this subterranean microorganism, revealing its phylogenomic affiliation (Average Nucleotide Identity, digital DNA-DNA Hybridization) and inferring its physiology through genome annotation, backed with physiological experiments to explore its relationship with the Fe biogeochemical cycle. Results determined that the isolate belongs to the Shewanella putrefaciens (with ANI 99.25 with S. putrefaciens CN-32). Its genome harbours the necessary genes, including omcA mtrCAB, to perform the Extracellular Electron Transfer (EET) and reduce acceptors such as Fe3+, napAB to reduce NO3 to NO2, hydAB to produce H2 and genes sirA, phsABC and ttrABC to reduce SO32−, S2O32− and S4O62−, respectively. A full CRISPR-Cas 1F type system was found as well. S. putrefaciens T2.3D-1.1 can reduce Fe3+ and promote the oxidation of Fe2+ in the presence of NO3 under anaerobic conditions. Production of H2 has been observed under anaerobic conditions with lactate or pyruvate as the electron donor and fumarate as the electron acceptor. Besides Fe3+ and NO3, the isolate also grows with Dimethyl Sulfoxide and Trimethyl N-oxide, S4O62− and S2O32− as electron acceptors. It tolerates different concentrations of heavy metals such as 7.5 mM of Pb, 5 mM of Cr and Cu and 1 mM of Cd, Co, Ni and Zn. This array of traits suggests that S. putrefaciens T2.3D-1.1 could have an important role within the Iberian Pyrite Belt subsurface participating in the iron cycle, through the dissolution of iron minerals and therefore contributing to generate the extreme conditions detected in the Río Tinto basin. Full article
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18 pages, 3716 KiB  
Review
Into the Unknown: Microbial Communities in Caves, Their Role, and Potential Use
by Katarzyna Kosznik-Kwaśnicka, Piotr Golec, Weronika Jaroszewicz, Daria Lubomska and Lidia Piechowicz
Microorganisms 2022, 10(2), 222; https://doi.org/10.3390/microorganisms10020222 - 20 Jan 2022
Cited by 28 | Viewed by 5281
Abstract
Caves have been an item of amateur and professional exploration for many years. Research on the karst caves has revealed great diversity of bacteria, algae, and fungi living on stone walls and speleothems, in mud puddles or sediments. They have become the source [...] Read more.
Caves have been an item of amateur and professional exploration for many years. Research on the karst caves has revealed great diversity of bacteria, algae, and fungi living on stone walls and speleothems, in mud puddles or sediments. They have become the source of interest for various research groups including geologists, chemists, ecologists, or microbiologists. The adaptations of cave-dwelling organisms applied to their survival are complex and some of their properties show potential to be used in various areas of human life. Secondary metabolites produced by cave’s bacteria show strong antimicrobial, anti-inflammatory, or anticancer properties. Furthermore, bacteria that can induce mineral precipitation could be used in the construction industry and for neutralization of radioisotopes. In this review we focus on bacteria and algae present in cave ecosystems, their role in shaping such specific environment, and their biotechnological and medical potential. Full article
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2021

Jump to: 2024, 2023, 2022

19 pages, 5877 KiB  
Article
Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction
by Valentín Pérez-Hernández, Mario Hernández-Guzmán, Marco Luna-Guido, Yendi E. Navarro-Noya, Elda M. Romero-Tepal and Luc Dendooven
Microorganisms 2021, 9(6), 1297; https://doi.org/10.3390/microorganisms9061297 - 15 Jun 2021
Cited by 1 | Viewed by 2579
Abstract
We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m−1, 17.3 dS m−1, and 33.4 dS m−1) and pH (9.3, 10.4, and 10.3) amended with young maize plants and their neutral [...] Read more.
We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m−1, 17.3 dS m−1, and 33.4 dS m−1) and pH (9.3, 10.4, and 10.3) amended with young maize plants and their neutral detergent fibre (NDF) fraction and aerobically incubated in the laboratory for 14 days while the soil bacterial community structure was monitored by means of 454-pyrosequencing of their 16S rRNA marker gene. We identified specific bacterial groups that showed adaptability to soil salinity, i.e., Prauseria in soil amended with young maize plants and Marinobacter in soil amended with NDF. An increase in soil salinity (17.3 dS m−1, 33.4 dS m−1) showed more bacterial genera enriched than soil with low salinity (1.9 dS m−1). Functional prediction showed that members of Alfa-, Gamma-, and Deltaproteobacteria, which are known to adapt to extreme conditions, such as salinity and low nutrient soil content, were involved in the lignocellulose degradation, e.g., Marinimicrobium and Pseudomonas as cellulose degraders, and Halomonas and Methylobacterium as lignin degraders. This research showed that the taxonomic annotation and their functional prediction both highlighted keystone bacterial groups with the ability to degrade complex C-compounds, such as lignin and (hemi)cellulose, in the extreme saline-alkaline soil of the former Lake of Texcoco. Full article
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