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Microbial Adaptation and Tolerance to Environmental Stresses

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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 March 2022) | Viewed by 16512

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Special Issue Editor

Dr. Siqing Liu

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Guest Editor

National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL, USA
Interests: gram-positive bacteria; microbial fermentation; renewable biofuels and bioproducts; novel antibacterial agents; ethanol and butanol tolerance; lignocellulosic substrate utilization

Special Issue Information

Dear Colleagues,

Climate change has impacted every aspect of human lives as well as other living organisms on earth. We all know that the silent majority of microorganisms play significant roles in human health and the health of animals, plants, and other living things. We need to examine how microbes deal with environmental stresses in order to protect human health, food safety, and agriculture productivity. The impact of climate change to pathogenic microbes might be underestimated. More studies are essential to address the challenges microbes face. Understanding how microbes respond and adapt to environmental conditions will ultimately benefit the health of our planet and us.

In this Special Issue, we invite you to send contributions concerning microbial responses to environmental challenges involving 1) natural physical environmental factors such as temperature, air pollution, salt tolerance, osmotic stress, and increased accumulation of antibiotics and changes of pH in their environments, 2) fermentative bioreactor conditions such as increased production of biofuels and bioproducts in bioreactors, inhibitor tolerance, high substrate loading, microbial contamination and the dealing of various control strategies to reduce contaminations. Topics of other stress-related responses such as competitions and interactions within a microbial community are welcome.

Dr. Siqing Liu
Guest Editor

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

stress induced gene expression
ethanol tolerance
butanol tolerance
substrate inhibition
antibiotic resistance
inhibitor tolerance
osmotic stress

Published Papers (7 papers)

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Research

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21 pages, 6126 KiB

Open AccessArticle

Use of Flavin-Related Cellular Autofluorescence to Monitor Processes in Microbial Biotechnology

by Lucie Müllerová, Kateřina Marková, Stanislav Obruča and Filip Mravec

Microorganisms 2022, 10(6), 1179; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10061179 - 08 Jun 2022

Cited by 5 | Viewed by 2270

Abstract

Cellular autofluorescence is usually considered to be a negative phenomenon because it can affect the sensitivity of fluorescence microscopic or flow cytometric assays by interfering with the signal of various fluorescent probes. Nevertheless, in our work, we adopted a different approach, and green autofluorescence induced by flavins was used as a tool to monitor fermentation employing the bacterium Cupriavidus necator. The autofluorescence was used to distinguish microbial cells from abiotic particles in flow cytometry assays, and it was also used for the determination of viability or metabolic characteristics of the microbial cells. The analyses using two complementary techniques, namely fluorescence microscopy and flow cytometry, are simple and do not require labor sample preparation. Flavins and their autofluorescence can also be used in a combination with other fluorophores when the need for multi-parametrical analyses arises, but it is wise to use dyes that do not emit a green light in order to not interfere with flavins’ emission band (500–550 nm). Full article

(This article belongs to the Special Issue Microbial Adaptation and Tolerance to Environmental Stresses)

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9 pages, 642 KiB

Open AccessCommunication

Deep Subsurface Hypersaline Environment as a Source of Novel Species of Halophilic Sulfur-Oxidizing Bacteria

by Lea Nosalova, Maria Piknova, Katarina Bonova and Peter Pristas

Microorganisms 2022, 10(5), 995; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10050995 - 09 May 2022

Cited by 6 | Viewed by 1805

Abstract

The sulfur cycle participates significantly in life evolution. Some facultatively autotrophic microorganisms are able to thrive in extreme environments with limited nutrient availability where they specialize in obtaining energy by oxidation of reduced sulfur compounds. In our experiments focused on the characterization of halophilic bacteria from a former salt mine in Solivar (Presov, Slovakia), a high diversity of cultivable bacteria was observed. Based on ARDRA (Amplified Ribosomal DNA Restriction Analysis), at least six groups of strains were identified with four of them showing similarity levels of 16S rRNA gene sequences lower than 98.5% when compared against the GenBank rRNA/ITS database. Heterotrophic sulfur oxidizers represented ~34% of strains and were dominated by Halomonas and Marinobacter genera. Autotrophic sulfur oxidizers represented ~66% and were dominated by Guyparkeria and Hydrogenovibrio genera. Overall, our results indicate that the spatially isolated hypersaline deep subsurface habitat in Solivar harbors novel and diverse extremophilic sulfur-oxidizing bacteria. Full article

(This article belongs to the Special Issue Microbial Adaptation and Tolerance to Environmental Stresses)

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10 pages, 1506 KiB

Open AccessArticle

Short-Term Exposure to Thermophilic Temperatures Facilitates CO Uptake by Thermophiles Maintained under Predominantly Mesophilic Conditions

by Caitlin K. Wilson and Gary M. King

Microorganisms 2022, 10(3), 656; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030656 - 18 Mar 2022

Cited by 3 | Viewed by 1811

Abstract

Three phylogenetically and phenotypically distinct CO-oxidizing thermophiles (Alicyclobacillus macrosporangiidus CPP55 (Firmicutes), Meiothermus ruber PS4 (Deinococcus-Thermus) and Thermogemmatispora carboxidovorans PM5^T (Chloroflexi)) and one CO-oxidizing mesophile (Paraburkholderia paradisi WA^T (Betaproteobacteria)) isolated from volcanic soils were used to assess growth responses and CO uptake rates during incubations with constant temperatures (25 °C and 55 °C) and during multi-day incubations with a temperature regime that cycled between 20 °C and 55 °C on a diurnal basis (alternating mesophilic and thermophilic temperatures, AMTT). The results were used to test a conjecture that some thermophiles can survive in mesothermal habitats that experience occasional thermophilic temperatures. Meiothermus ruber PS4, which does not form spores, was able to grow and oxidize CO under all conditions, while the spore-forming Alicyclobacillus macrosporangiidus CPP55 grew and oxidized CO during the AMTT regime and at 55 °C, but was not active at 25 °C. Thermogemmatispora carboxidovorans PM5^T, also a spore former, only grew at 55 °C but oxidized CO during AMTT and 55 °C incubations. In contrast, the non-sporing mesophile, Paraburkholderia paradisi WA^T, was only able to grow and oxidize CO at 25 °C; growth and CO uptake ceased during the AMTT incubations after exposure to the initial round of thermophilic temperatures. Collectively, these results suggest that temporary, periodic exposure to permissive growth temperatures could help maintain populations of thermophiles in mesothermal habitats after deposition from the atmosphere or other sources. Full article

(This article belongs to the Special Issue Microbial Adaptation and Tolerance to Environmental Stresses)

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13 pages, 3507 KiB

Open AccessArticle

YgfY Contributes to Stress Tolerance in Shewanella oneidensis Neither as an Antitoxin Nor as a Flavinylation Factor of Succinate Dehydrogenase

by Ming-Xing Zhang, Kai-Li Zheng, Ai-Guo Tang, Xiao-Xia Hu, Xin-Xin Guo, Chao Wu and Yuan-Yuan Cheng

Microorganisms 2021, 9(11), 2316; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112316 - 09 Nov 2021

Cited by 3 | Viewed by 2101

Abstract

YgfY(SdhE/CptB) is highly conserved while has controversial functions in bacteria. It works as an antitoxin and composes a type IV toxin–antitoxin system with YgfX(CptA) typically in Escherichia coli, while functions as an flavinylation factor of succinate dehydrogenase and fumarate reductase typically in Serratia sp. In this study, we report the contribution of YgfY in Shewanella oneidensis MR-1 to tolerance of low temperature and nitrite. YgfY deficiency causes several growth defects of S. oneidensis MR-1 at low temperature, while YgfX do not cause a growth defect or morphological change of S. oneidensis MR1-1 and E. coli. YgfY do not interact with FtsZ and MreB nor with YgfX examined by bacterial two-hybrid assay. YgfY effect on growth under low temperature is not attributed to succinate dehydrogenase (SDH) because a mutant without SDH grows comparably with the wild-type strain in the presence of succinate. The ygfY mutant shows impaired tolerance to nitrite. Transcription of nitrite reductase and most ribosome proteins is significantly decreased in the ygfY mutant, which is consistent with the phenotypes detected above. Effects of YgfY on growth and nitrite tolerance are closely related to the RGXXE motif in YgfY. In summary, this study demonstrates pleiotropic impacts of YgfY in S. oneidensis MR-1, and sheds a light on the physiological versatility of YgfY in bacteria. Full article

(This article belongs to the Special Issue Microbial Adaptation and Tolerance to Environmental Stresses)

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15 pages, 23251 KiB

Open AccessArticle

Characterization of Inducible HSP70 Genes in an Antarctic Yeast, Glaciozyma antarctica PI12, in Response to Thermal Stress

by Nur Athirah Yusof, Jennifer Charles, Wan Nur Shuhaida Wan Mahadi, Abdul Munir Abdul Murad and Nor Muhammad Mahadi

Microorganisms 2021, 9(10), 2069; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9102069 - 30 Sep 2021

Cited by 3 | Viewed by 1929

Abstract

The induction of highly conserved heat shock protein 70 (HSP70) is often related to a cellular response due to harmful stress or adverse life conditions. In this study, we determined the expression of Hsp70 genes in the Antarctic yeast, Glaciozyma antarctica, under different several thermal treatments for several exposure periods. The main aims of the present study were (1) to determine if stress-induced Hsp70 could be used to monitor the exposure of the yeast species G. antarctica to various types of thermal stress; (2) to analyze the structures of the G. antarctica HSP70 proteins using comparative modeling; and (3) to evaluate the relationship between the function and structure of HSP70 in G. antarctica. In this study, we managed to amplify and clone 2 Hsp70 genes from G. antarctica named GaHsp70-1 and GaHsp70-2. The cells of G. antarctica expressed significantly inducible Hsp70 genes after the heat and cold shock treatments. Interestingly, GaHsp70-1 showed 2–6-fold higher expression than GaHsp70-2 after the heat and cold exposure. ATP hydrolysis analysis on both G. antarctica HSP70s proved that these psychrophilic chaperones can perform activities in a wide range of temperatures, such as at 37, 25, 15, and 4 °C. The 3D structures of both HSP70s revealed several interesting findings, such as the substitution of a β-sheet to loop in the N-terminal ATPase binding domain and some modest residue substitutions, which gave the proteins the flexibility to function at low temperatures and retain their functional activity at ambient temperatures. In conclusion, both analyzed HSP70s played important roles in the physiological adaptation of G. antarctica. Full article

(This article belongs to the Special Issue Microbial Adaptation and Tolerance to Environmental Stresses)

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23 pages, 23617 KiB

Open AccessArticle

Different Responses of Bacterial and Archaeal Communities in River Sediments to Water Diversion and Seasonal Changes

by Jiali Lv, Yangdan Niu, Ruiqiang Yuan and Shiqin Wang

Microorganisms 2021, 9(4), 782; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040782 - 08 Apr 2021

Cited by 12 | Viewed by 2596

Abstract

In recent years, different responses of archaea and bacteria to environmental changes have attracted increasing scientific interest. In the mid-latitude region, Fen River receives water transferred from the Yellow River, electrical conductivity (EC), concentrations of Cl⁻ and Na⁺ in water, total phosphorus (TP), and Olsen phosphorus (OP) in sediments were significantly affected by water transfer. Meanwhile, temperature and oxidation-reduction potential (ORP) of water showed significant seasonal variations. Based on 16S rRNA high-throughput sequencing technology, the composition of bacteria and archaea in sediments was determined in winter and summer, respectively. Results showed that the dominance of bacterial core flora decreased and that of archaeal core flora increased after water diversion. The abundance and diversity of bacterial communities in river sediments were more sensitive to anthropogenic and naturally induced environmental changes than that of archaeal communities. Bacterial communities showed greater resistance than archaeal communities under long-term external disturbances, such as seasonal changes, because of rich species composition and complex community structure. Archaea were more stable than bacteria, especially under short-term drastic environmental disturbances, such as water transfer, due to their insensitivity to environmental changes. These results have important implications for understanding the responses of bacterial and archaeal communities to environmental changes in river ecosystems affected by water diversion. Full article

(This article belongs to the Special Issue Microbial Adaptation and Tolerance to Environmental Stresses)

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Review

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17 pages, 1378 KiB

Open AccessReview

Gram-Negative Bacterial Envelope Homeostasis under Oxidative and Nitrosative Stress

by Thibault Chautrand, Djouhar Souak, Sylvie Chevalier and Cécile Duclairoir-Poc

Microorganisms 2022, 10(5), 924; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10050924 - 28 Apr 2022

Cited by 12 | Viewed by 2503

Abstract

Bacteria are frequently exposed to endogenous and exogenous reactive oxygen and nitrogen species which can damage various biomolecules such as DNA, lipids, and proteins. High concentrations of these molecules can induce oxidative and nitrosative stresses in the cell. Reactive oxygen and nitrogen species are notably used as a tool by prokaryotes and eukaryotes to eradicate concurrent species or to protect themselves against pathogens. The main example is mammalian macrophages that liberate high quantities of reactive species to kill internalized bacterial pathogens. As a result, resistance to these stresses is determinant for the survival of bacteria, both in the environment and in a host. The first bacterial component in contact with exogenous molecules is the envelope. In Gram-negative bacteria, this envelope is composed of two membranes and a layer of peptidoglycan lodged between them. Several mechanisms protecting against oxidative and nitrosative stresses are present in the envelope, highlighting the importance for the cell to deal with reactive species in this compartment. This review aims to provide a comprehensive view of the challenges posed by oxidative and nitrosative stresses to the Gram-negative bacterial envelope and the mechanisms put in place in this compartment to prevent and repair the damages they can cause. Full article

(This article belongs to the Special Issue Microbial Adaptation and Tolerance to Environmental Stresses)

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